ARTICLE | doi:10.20944/preprints201909.0325.v1
Subject: Arts And Humanities, Philosophy Keywords: speciesism; intuition; evolutionary debunking arguments; experimental philosophy; species-egalitarianism; conservation; singer; williams; kagan; jacquet
Online: 29 September 2019 (06:07:31 CEST)
This article argues for five correctives to the current ethical debate about speciesism, and proposes normative, conceptual, methodological and experimental avenues to move this debate forward. Firstly, it clarifies the Principle of Equal Consideration of Interests and points out limitations of its scope. Secondly, it disambiguates between ‘favouritist’ and ‘species-relative’ views about moral treatment. Thirdly, it argues that not all moral intuitions about speciesism should be given equal weight. Fourthly, it emphasizes the importance of empirical research to corroborate statements about ‘folk speciesism’. Fifthly, it disambiguates between the moral significance of species and the moral status of their individual members. For each of these issues, it is shown that they have either been overlooked, or been given inapt treatment, in recent contributions to the debate. Building on the correctives, new directions are proposed for ethical inquiry into the moral relevance of species and species membership.
ARTICLE | doi:10.20944/preprints201710.0104.v1
Subject: Computer Science And Mathematics, Applied Mathematics Keywords: evolutionary dynamics; quantitative trait; Manhattan norm; Euclidean norm; Chebyshev norm; parasitism; exploitation; egalitarianism
Online: 16 October 2017 (07:35:46 CEST)
Various distance metrics and their induced norms are employed in the quantitative modeling of evolutionary dynamics. Minimization of these distance metrics when applied to evolutionary optimization are hypothesized to result in different outcomes. Here, we apply the different distance metrics to the evolutionary trait dynamics brought about by the interaction between two competing species infected by parasites (exploiters). We present deterministic cases showing the distinctive selection outcomes under the Manhattan, Euclidean and Chebyshev norms. Specifically, we show how they differ in the time of convergence to the desired optima (e.g., no disease), and in the egalitarian sharing of carrying capacity between the competing species. However, when randomness is introduced to the population dynamics of parasites and to the trait dynamics of the competing species, the distinctive characteristics of the outcomes under the three norms become indistinguishable. Our results provide theoretical cases when evolutionary dynamics using different distance metrics exhibit similar outcomes.
ARTICLE | doi:10.20944/preprints202311.1862.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Ex-situ conservation; exotic species; Gullele; invasive species; native species
Online: 29 November 2023 (11:05:04 CET)
Gullele Botanic Garden was established to preserve and safeguard indigenous, rare, endemic and endangered plant species that have economic significance. A study was conducted to identify and map non-native plant species that exist in various land use types, including natural vegetation, plantation, roadside, and garden edges. The research involved placing plots at different distances in each land use type and collecting vegetation data with geo-location information for exotic and invasive species. The data was analyzed using Sorensen's similarity index to measure the similarity between plant communities. Invasive species were identified using ArcGIS, and descriptive statistical methods were employed to analyze the remaining data. The recorded a total of 80 plant species belonging to 70 genera in 44 families in the garden, with Fabaceae and Asteraceae having the most species. Acacia decurrens, Acacia melanoxylon, Cuscuta campestris, Galinsoga parviflora, Nerium oleander, and Cyathula uncinulata are the most prevalent invasive or potentially invasive species among the species that have been documented. These species are spreading quickly and may displace native plant species if not properly managed. The study found that roadside and garden edge land use types had the most diverse exotic plants, with Acacia decurrens, Nerium oleander, Acacia melanoxylon, Agave species, Cyathula uncinulata, and Eucalyptus species being the most dominant exotic species in the garden. The total density of exotic species was 2.36 plants/m2. The study provides valuable information for managing and conserving both native and exotic plant species in the garden.
ARTICLE | doi:10.20944/preprints202310.1555.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: crayfish; Procambarus clarkii; alien species; invasive species; alien species adaptation; salinity tolerance
Online: 25 October 2023 (08:39:03 CEST)
Background: The red swamp crayfish Procambarus clarkii (Girard, 1852), native to the United States and northern Mexico, has been introduced in many countries worldwide. The species has a remarkable invasiveness, due to its high reproductive rate and to its ability to tolerate broad ranges of water parameters like salinity. Nevertheless, no consistent observations of P. clarkii have been reported in the marine environment until now. Methods: Through the observations of a personal acquaintance and of two volunteers who published photos of the species on Facebook marine biology and fishing groups, we collected data showing the presence of the crayfish within marine ecosystems. Results: P. clarkii has been spotted in three different localities, in two of which observations are recurrent. The species can live miles from the nearest freshwater stream, and can colonise the depths up to 20 meters. Conclusions: The multiple observations of P. clarkii collected in our study uncover a persistent presence of the species within some marine areas, rather than its mere sporadic occurrence. As resistance to increasing salinities is influenced by multiple genes, genetic admixture between genetically-differentiated individuals coming from distinct geographical origins could have brought together different salinity-resistance genes, leading to the formation of these resilient phenotypes.
ARTICLE | doi:10.20944/preprints201803.0083.v1
Subject: Environmental And Earth Sciences, Ecology Keywords: ladybeetles; guide for identification; aborigenous species; introduced species
Online: 12 March 2018 (06:54:21 CET)
Although ladybirds of European Russia and the Caucasus have been the subject of numerous ecological and faunistic investigations, there is an evident lack of appropriate identification key for them. All previous keys have been published in Russian. The most modern key was published more than 50 years ago and included only about 60 % of species. Guides for identification of Coccinellidae of other countries are not appropriate for European Russia, since do not include many species occurring in the regions. New, original key to subfamilies, genera, and species of ladybirds (Coccinellidae) of the European Russia and Russian Caucasus is presented. All native species recorded in the region and all alien species introduced to this region are included. Some species from the adjacent regions are added. In total, 110 species are keyed and illustrated with line drawings. Photographs of rare and endemic species are provided. Information on the distribution of species within the region under consideration is provided. Synonymy of Chilocorus kuwanae with Ch. renipustulatus is presented and discussed.
REVIEW | doi:10.20944/preprints202103.0212.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Cyanobacteria; Arthrospira; species concept; typus; species concept in prokaryotes
Online: 8 March 2021 (11:18:31 CET)
Cyanobacteria are prokaryotes whose taxonomy follows the same rules of a code (the International Botanical Nomenclature Code, IBNC) built for eukaryotic photosynthetic organisms. Hence, names of cyanobacteria follow the same rules and are assigned to biological entities (species) that should correspond to eukaryotic species. The main difficulty in the current situation is that the species concept in eukaryotes is based theoretically mainly on the biological species concept, that is centered on genetic exchange through sexual reproduction or lack of them. However, as shown, this difference is important from a theoretical point of view, but also in eukaryotes, the boundaries between different species are very rarely checked experimentally by direct observation of sexual barriers and hybridization events. The main concept for species delimitation is hence that related to morphology and, more recently and always in relation to morphology, DNA sequences. The introduction of distances obtained from matrixes of aligned sequences in the framework of a barcoding project provides a quantitative interpretation of species delimitation in relation to genetic distance that can be used both in eukaryotes and prokaryotes. However, the introduction of quantitative criteria needs the definition of distance thresholds to identify the boundaries between different species and, for doing that, it is necessary to test the distance thresholds in models of traditionally defined and recognized species. An alternative approach may be the comparison of the molecular distance (quantitative approach) to data about the capability of strains/species to exchange genetic information. Unfortunately data about this last question is still scarce. The adoption of molecular criteria to check species boundaries based on morphological characters has proved particularly challenging in cyanobacteria: a known example is provided. In conclusion, the only possible approach appears to be the association of molecular data to the increase of available data about the cell structure and the variation thereof in different physiological situations, particularly at the ultrastructural level. A further necessity is the check of the typus for a large number of cyanobacteria species, often based on old basionyms. In many of these cases the typus is often a drawing and more rarely a herbarium specimen or a microscope slide. In many cases an epitypification or a neotypification appears to be necessary.
ARTICLE | doi:10.20944/preprints202211.0024.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: carnivore species; western Michoacán; actual species distribution; prioritization; conservation areas
Online: 1 November 2022 (09:02:43 CET)
The present study contributes to bridging the gap on research related to the presence and distribution patterns of carnivore mammals in the western state of Michoacán, highlighting the importance and need to increase efforts aimed at the study and monitoring of wildlife present in this region. The distribution of carnivore in western Mexico was modeled through the application a two-scale approach: a large, modeled region, corresponding to the western part of the country, for which models were obtained that represent the distribution potential of the species, and, the second modeled study area that includes only the western portion of the state of Michoacán, in which models of the current distribution of the species for this region were proposed. A series of predictive models were generated on the current distribution of 11 species of carnivore species (Canis latrans, Urocyon cinereoargenteus, Herpailurus yagouaroundi, Leopardus pardalis, Leopardus wiedii, Puma concolor, Panthera onca, Conepatus leuconotus, Bassariscus astutus, Nasua narica, Procyon lotor), from which, prioritization exercises were carried out on important areas for the conservation of these species, as well as the comparison and analysis of the existing natural protected areas (NPA) in the study area. The different exercises for prioritizing areas for conservation yielded similar results and show the potential percentages of the landscape that can be subjected to protection and conservation programs.
ARTICLE | doi:10.20944/preprints202104.0746.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: abundance; diversity; indicator species; Riyadh, species richness, urbanization; Wadi Hanifa
Online: 28 April 2021 (10:42:11 CEST)
The dramatic increased rates of uncontrolled urbanization in various parts of the World have resulted in loss of native species and overall threats to biodiversity. Over the last few decades Saudi Arabia has witnessed a remarkably rapid population growth and unparalleled levels of urbanization, leading to threats to biodiversity. Ants were pitfall-trapped across an urban-rural gradient to evaluate ant assemblage responses to urbanization in Wadi Hanifa, Riyadh, Central Saudi Arabia. Fifteen sampling sites were selected along three different urbanization gradients, each traversing urban, suburban and rural zones. Within each site 10 traps were distributed and operated for 7 consecutive days, at 3-monthly intervals throughout one year. Vegetation, ground cover, and chemical and physical soil variables at sampling sites were analyzed concurrently. Ant abundance, species richness, evenness, and diversity indices of Shannon and Simpson were calculated for each site using PC-ORD to demonstrate diversity patterns along the urbanization gradients. Ant assemblages were assessed by detrended corresponding analysis (DCA), canonical correspondence analysis (CCA), and analysis of similarity (ANOSIM) using PC-ORD. Indicator species analysis was conducted to define representative species along the urbanization gradient. A total of 42 ant species were identified. The diversity parameters were consistent across the urbanization gradient. However, significant differences were observed in the ant assemblages between rural and urban, suburban and urban, but only marginal between rural and suburban. Eleven ant species were identified as indicator species (IV values between 50.7-80.7%). The ant assemblages were influenced by flora, ground cover, and soil variables.
ARTICLE | doi:10.20944/preprints202012.0502.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: invasive species; ecological niche models; species distribution models; vector surveillance
Online: 21 December 2020 (10:50:19 CET)
Aedes scapularis is a neotropical mosquito known to transmit pathogens of medical and veterinary importance. Its recent establishment in southeastern Florida has potential public health implications. We used an ecological niche modeling approach to predict the abiotic environmental suitability for Ae. scapularis across much of the Americas and Caribbean Islands. Georeferenced occurrence data obtained from the Global Biodiversity Inventory Facility and recent collection records of Ae. scapularis from southern Florida served as input for model calibration. Environmental layers included bioclimatic variables provided in 2000 to 2010 average Modern Era Retrospective-analysis for Research and Applications climatic (MERRAclim) data. Models were run in the software program Maxent. Isothermality values found often in costal environments contributed strongest to model performance. Model projections suggested areas predicted suitable for Ae. scapularis across portions of the Amazon Basin, the Yucatán Peninsula, the Florida Peninsula, and multiple Caribbean Islands. Additionally, model predictions suggested connectivity of highly suitable or relatively suitable environments spanning the United States Gulf Coast, which may facilitate geographic expansion of this species. At least sixteen Florida counties were predicted highly suitable for Ae. scapularis, suggesting vigilance is needed by vector control and public health agencies to recognize further spread of this vector.
REVIEW | doi:10.20944/preprints202311.0779.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Galapagos, One Health, Planetary Health, wildlife, conservation, endemic species, invasive species
Online: 13 November 2023 (10:35:35 CET)
The Galápagos archipelago is a vast reservoir of terrestrial and marine biodiversity and is particularly susceptible to human, animal, and environmental impacts. Climate change, globalization, and the blurring of human-domestic animal-wildlife interfaces are poised to bring new threats and challenges to the region. A One Health perspective that simultaneously considers human, animal, and environmental health is imperative in assessing and mitigating the challenges facing the Galápagos Islands. Many challenges facing biodiversity in the Galápagos Islands can ultimately be linked to anthropogenic factors. In Part I of this review, we reviewed the impacts of invasive species and identified infectious diseases of importance. In Part II of this review, we discuss the impacts of climate change and ocean acidification, and highlight the effects of several direct human activities, including tourism, overfishing, pollution, land use, and human-wildlife conflict. We also review the socioeconomic and political context of the Galápagos Islands, including current challenges in water and energy use, sanitation, and economic stability. We examine the importance of investment in local development for building resiliency and sustainability in the archipelago. Finally, we discuss the impact of the COVID-19 pandemic in the region. Throughout this two-part review, we build a cohesive picture of One Health in the Galápagos Islands by integrating past work, current needs, and emerging threats. We also consider overarching goals for conservation, ecosystem management, and socioeconomic sustainability that have been previously defined by both governmental and non-governmental stakeholders, and identify discrete, implementable, and interdisciplinary recommendations that will facilitate achievement of those goals.
REVIEW | doi:10.20944/preprints202311.0775.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Galapagos; one health; planetary health; wildlife; conservation; endemic species; invasive species
Online: 13 November 2023 (08:54:46 CET)
The Galápagos archipelago is a vast reservoir of terrestrial and marine biodiversity, owing in large part to its relatively recent volcanic genesis and colonization by humans. This unique ecological system is particularly susceptible to human, animal, and environmental impacts. Climate change, globalization, and the blurring of human-domestic animal-wildlife interfaces are poised to bring new threats and challenges to the region. A One Health perspective that simultaneously considers human, animal, and environmental health is imperative in assessing and mitigating the challenges facing the Galápagos Islands.In Part I of this review, we provide the historical context for biodiversity in the archipelago; discuss the role of invasive species in habitat destruction, fragmentation, and competition with endemic species; and summarize the established and emerging infectious disease threats. We also discuss the imperative to implement research, surveillance, and preventative measures to identify and manage future threats from a One Health perspective, with a specific emphasis on implications for wildlife health. In Part II, we outline the socioeconomic context of life in the Galápagos Islands, evaluate the current and predicted effects of climate change, and discuss direct anthropogenic factors affecting Galápagos biodiversity, such as tourism, fishing, pollution, and the illegal wildlife trade. We also examine the impact of the COVID-19 pandemic in the region. Throughout this two-part review, we build a cohesive picture of One Health in the Galápagos Islands by integrating past work, current needs, and emerging threats. We also consider overarching goals for conservation, ecosystem management, and socioeconomic sustainability that have been previously defined by both governmental and non-governmental stakeholders, and we identify discrete, implementable, and interdisciplinary recommendations that will facilitate achievement of those goals.
ARTICLE | doi:10.20944/preprints202308.1674.v3
Subject: Biology And Life Sciences, Insect Science Keywords: China; Sycanus; taxonomy; DNA barcoding; species delimitation; phylogeny; new species; biology
Online: 5 September 2023 (02:40:40 CEST)
Due to the variation of the body coloration and the similarity of the related species, there are still some unresolved problems and debates in the taxonomic study of the genus Sycanus in China. We conducted the inter-specific phylogenetic analyses and the species delimitation for Sycanus in China based on DNA barcoding dataset of the mitochondrial cytochrome c oxidase subunit I gene of 81 samples and partial 28S rDNA sequences of 34 samples. The result showed that all the samples were divided into twelve species by integrating the results of DNA barcoding and morphological comparison. In the present paper, the genus Sycanus in China was reviewed systematically, all species were described or re-described, keyed, illustrated and photographed, among them, Sycanus taiwanensis Zhao & Cai sp. nov., Sycanus flavicorius Li & Cai sp. nov. and Sycanus hainanensis Wang & Cai sp. nov. were described as new to science. The biological informations of Sycanus falleni Stål, 1863 and Sycanus croceus Hsiao, 1979 were briefly recorded.
REVIEW | doi:10.20944/preprints202307.1324.v2
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: karyotype diversity; genome stability; species richness; species eveneness; non-adaptive radiation
Online: 31 July 2023 (10:51:13 CEST)
A strong correlation between karyotype diversity and species richness in mammals was first reported over forty years ago: in mammalian phylogenetic clades, standard deviation of karyotype diversity (KD) closely corresponds to the standard deviation of species richness (SR). These initial studies, however, did not control for phylogenetic signal, raising the possibility that the correlation was due to phylogenetic relatedness among species in a clade. Accordingly, karyotype diversity trivially reflects species diversity simply as a passive consequence of adaptive radiations. A more recent study in mammals has controlled for phylogenetic signal and established the correlation as phylogenetically independent, suggesting that species diversity cannot, in itself, explain the observed corresponding karyotype diversity. The correlation is therefore remarkable because the mechanisms contributing to karyotype diversity are evolutionarily independent of the mechanisms contributing to species diversity. Recently, it was shown in salamanders that the two processes generating genetic diversity and species diversity are indeed independent and operate in parallel, suggesting a potential non-adaptive and non-causal relationship between the two fundamental variables involved in adaptive radiations. The following will examine the relationship between KD and SR in the context of Motoo Kimura’s theory of non-adaptive radiation.
ARTICLE | doi:10.20944/preprints202301.0506.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Beetles; abundance; diversity; indicator species; Riyadh; species richness; urbanization; Wadi Hanifa
Online: 27 January 2023 (12:57:42 CET)
Urbanization affects all elements of the pre-urban environment, including soils, hydrology, vegetation, and microclimate. Recently, Saudi Arabia has experienced rapid urbanization and growth. Thus, the country's biodiversity has been threatened. In Riyadh, beetle assemblages were assessed along a rural-suburban-urban gradient. A total of 2,791 individuals from 94 species belonging to seven families were collected at 15 sites along three different gradients of urbanization in Wadi Hanifa. Tenebrionidae dominated abundance (60.1%) and richness (38%). Beetle abundance, evenness, and diversity were not different among habitats; however, species richness was higher in rural habitats. DCA and CCA analyses showed distinct differences among sites along gradients. Urbanization intensity, soil variables, and land cover were significantly correlated with DCA axis 1, while elevation and flora were significantly correlated with DCA axis 2. The most critical operating environmental variables in Wadi Hanifa were buildings, elevation, soil organic carbon, litter cover, and litter depth, as well as plants such as Launaea capitata, Lycium shawii, Alhagi graecorum, and Heliotropium currasavicum. Ten species in our study are associated with urban habitats, six with suburban habitats, and seven with rural habitats. Consequently, expanding urban areas may negatively affect the richness and composition of beetles and may result in the loss of some native species.
ARTICLE | doi:10.20944/preprints201911.0055.v1
Subject: Computer Science And Mathematics, Geometry And Topology Keywords: topology; fractal; renormalization; species
Online: 6 November 2019 (06:47:34 CET)
In previous studies, the authors utilized a single-dimensional operationalization of species density that implies induction of hierarchy and time with certain topologies. For further clarification of induced fractals including the relation to renormalization in physics, here a theoretical development is proposed based on a newly identified fact, namely that scaling parameters for magnetization exactly correspond to imaginary parts of Riemann zeta nontrivial zeros. An analogy to magnetization and accompanying Fake Monster Algebra is invoked to lend support to this theory, along with empirical species density data for a wild Dictyostelia community. A master torus and a Lagrangian/Hamiltonian are derived expressing fractal structures as a solution for diminishing divergent terms in renormalization.
ARTICLE | doi:10.20944/preprints201701.0044.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: Aflatoxins; Peanuts; Aspergillus species
Online: 9 January 2017 (09:40:46 CET)
Aflatoxin contaminates foods including peanuts. Aflatoxin is a carcinogenic toxin mainly produced bty Aspergillus flavus. Other Aspergillus species that rarely produce aflatoxins are A. nomius and A. niger. Aflatoxin is associated with liver failure, hepatocellular carcinoma (HCC) and death. Recent studies have shown that peanuts in Kenya are highly contaminated with aflatoxins but information gaps exist on the characterization of the Aspergillus species that produce aflatoxins in peanuts in Kenya. Therefore, this gap necessitated the determination of the Aspergillus species producing aflatoxins in peanuts from the main growing districts of Busia and Kisii Central districts. One hundred and two (102) peanuts samples were collected from farmers’ in each district Aspergillus species were isolated from the peanut samples by using the dilution plate technique on modified Rose Bengal agar. Phenotypical characterization of the identified Aspergillus section flavus isolates from the peanuts samples was determined using the procedure of Mellon and Cotty. This study identified five (5) Aspergillus species as contaminants in peanuts analyzed in this study. They were Aspergillus flavus L-strain, Aspergillus flavus S-strain, Aspergillus parasiticus, Aspergillus niger and Aspergillus tamari. Overall, the occurrence of Aspergillus flavus L- strain and A. flavus S- strain were significantly higher than other species identified (H = 15.55, df = 4, P = 0.004) in peanuts from the two districts. However, A. flavus S-strain was the most dominant species identified in the study with a mean occurrence of 45.1%. Aspergillus flavus L- strain was the most common isolate (58.8%) in peanuts from Busia district while A. flavus S- strain was the most common strain (60.2%) in peanuts from Kisii Central district. Overall, the occurrence of Aspergillus flavus L strain and A. flavus S strain were significantly higher than other species identified (H = 15.55, df = 4, P = 0.004) in peanuts from the two districts. However, A. flavus S-strain was the most dominant species (F=3.15, df =25, P=0.031) with an overall mean occurrence of 45.1%. The confirmation of occurrence of other species that produce toxins such as A. niger and A. tamarii which also produces cyclopiazonic acid suggests the need to screen peanuts for other carcinogenic mycotoxins.
ARTICLE | doi:10.20944/preprints202304.1062.v1
Subject: Environmental And Earth Sciences, Remote Sensing Keywords: LiDAR; Tree Segmentation; Tree Species Identification; Tree Species Identification; DBN; Forest Parameter
Online: 27 April 2023 (09:35:20 CEST)
The rapid development of LiDAR technology has promoted great changes in forest resource surveys. The airborne LiDAR point cloud can provide precise tree height and detailed vertical structure of the tree stands. Coordinating some representative ground sample plots, LiDAR can be used to estimate key forest resource indicators such as forest stock volume, diameter at breast height, and forest biomass at a large scale. By establishing relationship models between the forest parameters of sample plots and the calculated parameters of LiDAR, these developments may eventually expand the models to large-scale forest resource surveys of entire areas. In this study, eight sample plots in northeast China are used to verify and update the information using point cloud obtained by the LiDAR scanner riegl-vq-1560i. Firstly, the tree crowns are segmented using the profile-rotating algorithm, and dominant trees height are used to check and rectify the tree locations. Secondly, considering the correlation between forestry parameters and tree species, we establish models to distinguish between species using geometric characteristics of tree crowns. Thirdly, when the tree species is known, parameters such as height, crown width, diameter at breast height, biomass and stock volume can be extracted from trees. The prediction models of forestry parameters can also be verified, which can be extended to accurate large-scale forestry surveys based on LiDAR data. Finally, experiment results demonstrate that the F-score of the eight plots in the tree segmentation exceed 0.95, the accuracy of tree species correction exceeds 90%, and the R2 of tree height, east-west canopy width, north-south canopy width, diameter at breast height, above-ground biomass and stock volume are 0.893, 0.757, 0.694, 0.840, 0.896 and 0.891, respectively. The above results indicate that the LiDAR-based estimation of forestry parameters is practical and that these forestry parameter prediction models can be widely applied in forest resource monitoring.
ARTICLE | doi:10.20944/preprints202308.2064.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Fusarium species; Sarocladium species; rice; pathogenic variability; genetic diversity; mycotoxins; sub-Saharan Africa
Online: 31 August 2023 (03:52:29 CEST)
Sarocladium and Fusarium species are commonly identified as causal agents of rice sheath rot disease worldwide. However, limited knowledge exists about their genetic, pathogenic, and toxigenic diversity in sub-Saharan African (SSA) countries, where an increasing incidence of this disease has been observed. This study aimed at identifying, characterizing, as well as assessing the genetic, pathogenic, and toxigenic diversity of the pathogens associated with rice sheath rot disease in Mali, Nigeria, and Rwanda. In this study seventy fungal isolates were obtained from rice plants displaying disease symptoms on research and farmer’s fields in Mali, Nigeria, and Rwanda. Thus, an extensive comparative analysis was conducted to assess their genetic, pathogenic, and toxigenic diversity. The Fusarium spp. were characterized using the translation elongation factor (EF-1α) region, while a concatenation of Internal Transcribed Spacer (ITS) and Actin-encoding regions were used to resolve Sarocladium species. Phylogenetic analysis revealed four Fusarium species complexes. The dominant complex in Nigeria was the Fusarium incarnatum-equiseti species complex (FIESC), comprising F. hainanense, F. sulawesiense, F. pernambucatum, and F. tanahbumbuense, while F. incarnatum was found in Rwanda. The Fusarium fujikuroi species complex (FFSC) was predominant in Rwanda and Mali, with species such as F. andiyazi, F. madaense, and F. casha in Rwanda, and F. annulatum and F. nygamai in Mali. F. marum was found in Nigeria. Furthermore, Fusarium oxysporum species complex (FOSC) members, F. callistephi and F. triseptatum, were found in Rwanda and Mali, respectively. Two isolates of F. acasiae-mearnsii, belonging to the Fusarium sambucinum species complex (FSAMSC) were obtained in Rwanda. Isolates of Sarocladium which were previously classified in three phylogenetic groups were resolved into three species which are: attenuatum, oryzae and sparsum. S. attenuatum was dominant in Rwanda, while S. oryzae and S. sparsum were found in Nigeria. Also, the susceptibility of FARO44, a rice cultivar released by Africa Rice Centre (AfricaRice) was tested against isolates from the four Fusarium species complexes and the three Sarocladium species. All isolates evaluated could induce typical sheath rot symptoms albeit with varying disease development levels. In addition, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine variation in the in vitro mycotoxins of the Fusarium species. Regional differences were observed in the in vitro mycotoxins profiling. Out of the forty-six isolates tested, nineteen were able to produce one to four mycotoxins. Notably, very high zearalenone (ZEN) production was specific to the two F. hainanense isolates from Ibadan-Nigeria, while Fusarium nygamai isolates from Mali produced high amounts of fumonisins. To the best of our knowledge, it seems this study is the first to elucidate genetic, pathogenic, and toxigenic diversity of Fusarium species associated with the rice sheath rot disease complex in selected countries in SSA.
ARTICLE | doi:10.20944/preprints202307.0393.v1
Subject: Medicine And Pharmacology, Urology And Nephrology Keywords: oxidative stress; nitrosative stress; reactive oxygen species; reactive nitrogen species; oxidation–reduction potential
Online: 6 July 2023 (08:37:32 CEST)
Reactive oxygen species and reactive nitrogen species in semen are both essential for fertilization process; however, they become harmful at excessive levels, causing oxidative stress and nitrosative stress, respectively. Recently, oxidation–reduction potential (ORP) has been used as a marker for measuring oxidative stress, and this study investigated the possibility of comprehensively evaluating nitrosative stress. The correlation between standardized ORP (sORP) and 8-hydroxy-2′-deoxyguanosine (8-OHdG) and NOx per unit sperm was tested. Based on the previously reported cutoff value, samples were classified into oxidative stress-positive and negative groups. Thereafter, a receiver operating characteristic curve was drawn on 8-OHdG and NOx, and each optimal cutoff value was determined. Both standardized 8-OHdG and NOx significantly correlated with sORP. Although both correlated significantly with sORP in the oxidative stress group, no correlation was found in the nonoxidative stress group. The optimal standardized 8-OHdG level to determine oxidative stress status was 0.52 ng/106 spermatozoa, and the standardized NOx was 0.17 µM/106 spermatozoa/mL. The ORP is a simpler and quicker assay that can comprehensively assess oxidative and nitrosative stresses. Optimal cutoff values for both stresses were established in this study.
ARTICLE | doi:10.20944/preprints202011.0415.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Bamboo; indigenous species; Kenya; AGB
Online: 16 November 2020 (11:43:12 CET)
The Kenya Forestry Service permits rental of low-density national forest areas for use as common farmland, but public access to such areas is restricted to prevent deforestation against a background of rising demand for fuel wood. This study was conducted to clarify characteristics relating to the production of indigenous bamboo (a useful wood resource) by the approximately 23% of locals who work on common farmland in central Kenya’s Kamae forest management area, with estimation to determine above-ground biomass. The results showed that bamboo still represents 60% of such biomass, indicating sustainability in the industry.
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: tweedie; glm; species counts; butterfly
Online: 29 September 2019 (02:40:40 CEST)
Background: The diversity of butterflies relies on the accessibility of food plants and the quality of their habitat. Methods: The purpose of this study was to evaluate the diversity butterfly based on latent GLM in 3 different Habitat. At the same time, we perform the step construction of Tweedie Distribution both in species levels and individual level. Results: Our finding can be shown by accuracy AIC, AICc, and BIC. Conclusions: In modelling with latent glm tweedie it can conclude that the our model is suitable for use at the species or individual level.
REVIEW | doi:10.20944/preprints202309.0352.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Ectoparasite; Taxon cycle; relict; Great speciator; Invasive species; Supertramp; Endangered species; Conservation; Taxonomy; Phylogeny
Online: 6 September 2023 (03:30:42 CEST)
This overview of extant Siphonaptera lists 19 families with major hosts and general distribution, estimated numbers of genera, species, and subspecies, with a brief taxonomic and phylogenetic review. With around 10 new species described annually, global flea fauna has an estimated extant 249 genera, 2215 species, and 714 subspecies, mostly mammal parasites but 5% of species are on birds. Host specificity varies from euryxenous (i.e. infesting two or more host orders)(e.g. cat fleas, Ctenocephalides felis felis) to monoxenous (e.g. rabbit fleas, Spilopsyllus cuniculi) . The largest family is the paraphyletic Hystrichopsyllidae, making up a third of all flea species. The largest monophyletic family, Ceratophyllidae (rodent and bird fleas), comprise another 20%, and has dispersed to every continent including Antarctica. Fleas descend from scorpionflies (Mecoptera), possibly snow scorpionflies (Boreidae) or Nannochoristidae, and even giant fossils found from the Mesozoic could be Siphonaptera. Flea diversification shows evidence of taxon cycles: "Relict" families such as helmet fleas (Stephanocircidae) have a disjunct distribution reflecting the breakup of Gondwanaland, 70 million years ago. "Niche specialists" include nest fleas (Anomiopsyllus), bat fleas (Ischnopsyllidae), and burrowing fleas, the chigoes (Tungidae). By contrast, Ceratophyllidae fleas could be considered "great speciators". Cat fleas and several other synanthropic flea species are invasive "supertramps". Although those species are intensively studied, many flea species and their hosts require urgent surveys and conservation.
COMMUNICATION | doi:10.20944/preprints201905.0078.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: information entropy, information theoretics, macroecology, metabolic theory, scaling, species abundance distribution, species-area relationship
Online: 7 May 2019 (11:24:30 CEST)
The Maximum Entropy Theory of Ecology, or METE, is a theoretical framework of macroecology that makes a variety of realistic ecological predictions about how species richness, abundance of species, metabolic rate distributions, and spatial aggregation of species interrelate in a given region. In the METE framework, "ecological state variables" (representing total area, total species richness, total abundance, and total metabolic energy) describe macroecological properties of an ecosystem. METE incorporates these state variables into constraints on underlying probability distributions. The method of Lagrange multipliers and maximization of information entropy (MaxEnt) lead to predicted functional forms of distributions of interest. We demonstrate how information entropy is maximized for the general case of a distribution, which has empirical information that provides constraints on the overall predictions. We then show how METE’s two core functions are derived. These functions, called the "Spatial Structure Function" and the "Ecosystem Structure Function" are the core pieces of the theory, from which all the predictions of METE follow (including the Species Area Distribution, the Species Abundance Distribution, and various metabolic distributions). Primarily, we consider the discrete distributions predicted by METE.We also explore the parameter space defined by the METE’s state variables and Lagrange multipliers. We aim to provide a comprehensive resource for ecologists who want to understand the derivations and assumptions of basic mathematical structure of METE.
ARTICLE | doi:10.20944/preprints202305.1950.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: species distribution modeling; tuna species; climate change scenarios; potential suitability habitat; predictor variables; ensemble models
Online: 29 May 2023 (03:02:46 CEST)
The potential impacts of climate change on the distribution of tuna in Pacific Island Countries’ Exclusive Economic Zones have yet to be investigated rigorously, and so their persistence and abundance in these areas remain uncertain. Here, we estimate optimal fisheries areas for four tuna species; Albacore (Thunnus alalunga), Bigeye (Thunnus obesus), Skipjack (Katsuwonus pelamis), and Yellowfin (Thunnus albacares). We consider different climate change scenarios, RCP 2.6, RCP 4.5, RCP 6.0 and RCP 8.5, within a set of tuna catch records in the Exclusive Economic Zone of Tonga. Using environmental and CPUE datasets, species distribution modelling estimated and predicted these fisheries areas in the current and future climatic scenarios. Our projections indicate an expansion in area and a shift of productive areas to the southern part of this Exclusive Economic Zone of Tonga. This is an indication that future climatic scenarios might be suitable for the species under study however, changes in trophic layers, ocean currents and ocean chemistry might alter this finding. Information provided here will be relevant in planning future national actions towards proper management of these species.
ARTICLE | doi:10.20944/preprints202104.0400.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Integrated Species distribution models; Maximum likelihood; Point-counts; Presence-only data; Site-Occupancy; species abundance
Online: 15 April 2021 (08:09:25 CEST)
Species distribution models have become tools of great importance in ecology since the advanced knowledge of suitable habitat of species is needed in the process of the world's biodiversity conservation. Models that use presence-only data are of great interests and are widely used in ecology due to their easy access. However, these models do not estimate accurately the true spatial species distribution based solely on presence-only data since they do not account for biases induced by the sampling techniques used and imperfect detection. To address this gap, Hierarchical integrated models have been recently introduced. Through this study, we assessed the relative performance of these new SDMs models using simulated data. The performance of the models was tested by comparing the estimates of parameters of the distribution models they provide with parameters used to simulate the distribution of the virtual species. The best model was the one whose estimates were close to the true distribution parameters of the virtual species. Results showed that analyzing Presence-only data in conjunction with Point-counts data through the Dorazio's Hierarchical model produced estimates of the coecients of the species intensity models with high precision and less bias while the Koshkina integrated model showed poor performance. Site-occupancy data, being not informative of species abundance, did not allow reducing biases in Presence-only data. The Dorazio's Hierarchical model produced estimates with high precision even with low detection probability. We have also found that the species rarity tends to in ate the variability of the models' estimates making modelling abundant species to be more accurate than modelling less abundant species. Hence, to model the species distribution with high precision based on Presence-only data, additional Point-counts data are required to account for sampling bias and imperfect detection.
ARTICLE | doi:10.20944/preprints201910.0132.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: enemy release hypothesis; multitrophic interactions; Darwin’s naturalization hypothesis; competition; alien species; exotic species; mesocosm experiment
Online: 11 October 2019 (07:40:52 CEST)
1. Darwin’s naturalization hypothesis predicts that alien species closely related to native species are less likely to naturalize because of strong competition due to niche overlap. Closely related species are likely to attract similar herbivores and to release similar plant volatiles following herbivore attack, thus could attract the same predators. However, the importance of phylogenetic relatedness on the interaction between alien and native plants has never been tested in a multitrophic context. 2. In a mesocosm experiment we grew six alien target plant species alone and in competition with nine native plant species of varying phylogenetic relatedness. To test the effects of multitrophic interactions on the performance of alien target species, we used enclosure cages to expose plants to the presence and absence of herbivorous arthropods, predatory arthropods and nematodes. 3. Surprisingly, biomass and number of flowering structures increased with presence of competitors for some of the alien species, but overall there was no consistent competition effect. Similarly, we found that none of the multitrophic-interaction treatments affected survival, biomass or number of flowering structures of the alien species. 4. We conclude there was no significant relationship between performance measures of the alien species and their phylogenetic relatedness to the native competitors.
BRIEF REPORT | doi:10.20944/preprints202303.0002.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: NoxO1; Nox1; NoxA1; reactive oxygen species
Online: 1 March 2023 (02:27:40 CET)
Activity of the Nox1 centered NADPH oxidase complex depends on the activator NoxA1 and the organizer NoxO1. NoxO1 itself is not involved in electron transfer for superoxide formation. Instead, by creating proximity of all components in the right place NoxO1 enables a constitutive formation of reactive oxygen species by that complex. All subunits should form the complex in a 1:1:1 ratio. When analyzing different cell lines in this study, we found an unequal expression of the component on mRNA level with an excess of NoxO1. Even with plasmid-based overexpression of individual components of Nox1 centered NADPH oxidase complex results in different expression of their mRNA, with NoxO1 mRNA being best expressed. Despite an unchanged high level of NoxO1 mRNA over a wide range of transfected plasmid, protein expression is increased with accelerating plasmid concentrations. We thought to analyze the ability of NoxO1 to induce ROS formation, when present in different ratio to Nox1 and NoxA1. To this end, we used Hek293 cells with constitutive expression of Nox1 and NoxA1 transfected with increasing concentrations of NoxO1. Our results suggest that ROS formation by the Nox1 centered NADPH oxidase strongly depends on the level of NoxO1 and a surplus of NoxO1 further increases the activity of the complex.
ARTICLE | doi:10.20944/preprints202209.0424.v1
Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: Candida albicans; Lactobacillus species; biofilm; probiotics
Online: 27 September 2022 (12:34:41 CEST)
Antifungal agents are not always efficient in resolving vulvovaginal candidiasis (VVC), a common genital infection caused by overgrowth of Candida spp., including Candida albicans, or preventing recurrent infections. Although lactobacilli (which are dominant microorganisms constituting healthy human vaginal microbiota) are important barriers against VVC, the Lactobacillus metabolite concentration needed to suppress VVC is unknown. Therefore, we quantitatively evaluated Lactobacillus metabolite concentrations to determine their effect on Candida spp., including 27 vaginal strains of Lactobacillus crispatus, Lactobacillus jensenii, Lactobacillus gasseri, Lacticaseibacillus rhamnosus, and Limosilactobacillus vaginalis, with inhibitory abilities against biofilms of Candida clinical isolates. Lactobacillus culture supernatants suppressed viable bacteria by approximately 24%-92% relative to preformed Candida biofilms, but their suppression differed between strains, not species. Lactate production was necessary to suppress preformed biofilms and hyphal elongation of C. albicans, whereas hydrogen peroxide was not always essential. Both lactic acid and hydrogen peroxide were required to suppress Candida planktonic cell growth. Lactobacillus strains that significantly inhibited biofilm formation in culture supernatant also inhibited Candida adhesion to epithelial cells in an actual live bacterial adhesion competition test. Healthy human microflora and their metabolites may play important roles in the development of new antifungal agent against VVC caused by C. albicans.
ARTICLE | doi:10.20944/preprints202006.0367.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Fish; invertebrates; conservation; threatened species; exploitation
Online: 30 June 2020 (10:38:07 CEST)
Substantial resources are invested in conservation of marine biodiversity globally. Fishing is the primary threat to many marine species and is one we can manage. However, threatened marine species are legally caught in industrial fisheries. To determine the magnitude and extent of this problem, we analysed global fisheries catch and import data and found reported catch records of 91 globally threatened species, thirteen of which are traded internationally. Seventy-three species targeted in industrial fisheries account for 99% of threatened species catch volume and value. Our results are a conservative estimate of threatened species catch and trade because we only consider species-level data, excluding group records; for example, we omit ‘sharks and rays,’ which represents over 200 threatened species. Although most fishing countries are involved in catch or trade of threatened species, it is driven largely by European nations. On land and for charismatic marine animals (e.g., whales), industrial-scale harvest of species at risk of extinction is controversial and usually highly regulated. In contrast, fishing for endangered fish and invertebrates is widespread but poorly documented. Given the development of new fisheries monitoring technologies and the current push for stronger international mechanisms for biodiversity management, industrial fishing of threatened fish and invertebrates should no longer be neglected in conservation and sustainability commitments.
REVIEW | doi:10.20944/preprints202005.0410.v1
Subject: Biology And Life Sciences, Virology Keywords: coronavirus; prevention; species; symptom; virus origin
Online: 25 May 2020 (11:09:25 CEST)
There are many types of coronavirus on the bases of important hosts including human, rat, turkey, rabbit, etc. The virus looks like a crown or corona of the sun with its round projection, spike. Now a day, newly emerged coronavirus disease (COVID 19) was first detected at Wuhan, China in December 2019 and it became a public health emergency international concern. Although a couple of researches has been conducting, much secretes of the virus and disease is still not understood and not reached a common understanding yet. However, sharing basic information is crucial based on the existing published research articles and updated information. Therefore, this review aimed to draw attention to the COVID 19 pandemic facts, opportunities, and challenges based on up to date information on cases in Ethiopia. Accordingly, the coronavirus is a single-stranded, non-segmented RNA genome virus. Two third of the genome (5'end) consists of two genes that code nonstructural proteins and the other 2-7 genes (3' end) code structural proteins including spike, envelope, membrane, and nucleocapsid. The virus transmits from animal to human and suggested as it might be originated from a bat and/or seafood. Coronavirus transmit human to human by direct contact and droplets during coughing and sneezing and common symptoms like fever, dry cough, and tiredness, short breathing, etc. can be seen from the patient. So that stay at home and social distancing are the most practicing pre-prevention methods. The disease causes high economic loss, face to face education closure, community cultural practice, and mass gathering activities are prohibited. However, various charity associations and creativities found increase than before. To this end, peoples should accept and follow governmental advice and instructions to escape from the pandemic.
ARTICLE | doi:10.20944/preprints202004.0415.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: LiDAR: structural complexity; species richness; topography
Online: 23 April 2020 (14:59:15 CEST)
Questions: Elevation, biodiversity, and forest structure are commonly correlated, but their relationships near the positive extremes of biodiversity and elevation are unclear. We asked 1) How does forest structure vary with elevation in a high biodiversity, high topographic complexity region? 2) Does forest structure predict vascular plant biodiversity? 3) Is plant biodiversity more strongly related to elevation or to forest structure? Location: Great Smoky Mountains National Park, USAMethods: We used terrestrial LiDAR scanning (TLS) to characterize vegetation structure in 12 forest plots. We combined two new canopy structural complexity metrics with traditional TLS-derived forest structural metrics and vascular plant biodiversity data to investigate correlations among forest structure metrics, biodiversity, and elevation. Results: Forest structure varied widely across plots spanning the elevational range of GRSM. Our new measures of canopy density (Depth) and structural complexity (σDepth) were sensitive to structural variations and effectively summarized horizontal and vertical dimensions of structural complexity. Vascular plant biodiversity was negatively correlated with elevation, and more strongly positively correlated with vegetation structure variables. Conclusions: The strong correlations we observed between canopy structural complexity and biodiversity suggest that structural complexity metrics could be used to assay plant biodiversity over large areas in concert with airborne and spaceborne platforms.
ARTICLE | doi:10.20944/preprints202308.1852.v2
Subject: Environmental And Earth Sciences, Environmental Science Keywords: big leaf mahogany; distribution map; invasive species management; invasive alien plant species; Mt. Banahaw de Nagcarlan
Online: 30 August 2023 (04:59:39 CEST)
Invasive alien plant species (IAPS) pose one of the most significant threats to native biodiversity. Swietenia macrophylla, or big leaf mahogany, is among the most threatening invasive plants in the Philippines. This article aimed to formally document the presence of S. macrophylla along the edges of Mt. Banahaw de Nagcarlan, a protected area on Luzon Island, Philippines. The study also sought to identify the management strategies being implemented by various government institutions for addressing big leaf mahogany and other invasive plants. A total of 1591 individuals of S. macrophylla were documented in mixed land-use areas and roadsides. These were found to have been introduced by the Department of Environment and Natural Resources in 1991 as a reforestation species. Fortunately, no individuals were observed beyond the buffer zone towards the protected area. The identification of management strategies for big leaf mahogany and other IAPS revealed that there is no established approach specifically addressing the presence of S. macrophylla at the site. However, some institutions advocate for the conservation of native plants through tree planting activities and educational campaigns. Furthermore, no collaborative efforts were observed among stakeholders and institutions. The results of this study highlight the urgent need for managing the S. macrophylla population. Planning and enforcement of strategies require collaborative efforts among stakeholders to prevent its entry into the protected area and ensure the preservation of native biodiversity.
ARTICLE | doi:10.20944/preprints202308.0145.v1
Subject: Environmental And Earth Sciences, Ecology Keywords: definition; degrees of separation; objective; primary conservation; secondary conservation; tertiary conservation; native species; ecological replacement species
Online: 2 August 2023 (10:19:57 CEST)
The term “conservation,” as it relates to biodiversity in a Western context, has had a contested history and as conservation science and societal values have evolved, consensus over its precise meaning has remained elusive. The broad scope of contemporary definitions hampers effective communication during a period of environmental crisis and is troublesome for any derivative concept which aims to quantify the efforts of the conservation community. This presents an avoidable hindrance to the systematic planning of the conservation field. To remedy this situation, we provide an outcome separation framework that is based on the expected degree of separation of the action’s proximate outcome from its intended, ultimate outcome for native habitat and/or native or ecological replacement species. Framing a definition of conservation through this lens of outcome separation allows for conservation-related actions to be clearly categorized into one of three discrete tiers (primary, secondary, and tertiary) based on both the proximate outcome’s degree of separation from its intended, ultimate outcome and the conservation status of native habitat and/or native or ecological replacement species. A distillation of this tiered framework also provides a fully inclusive, succinct definition of biodiversity conservation that is resilient to future conceptual evolutions of the field.
REVIEW | doi:10.20944/preprints202202.0284.v1
Subject: Biology And Life Sciences, Aquatic Science Keywords: Recreational fisheries fishery management; introgressive hybridization; stocking; non-native species; allochthonous species; trout fishing; trout taxonomy
Online: 23 February 2022 (03:09:39 CET)
During the last 150 years, the trout-culture industry focused on enhancing trout populations by stocking, in response to the growing anglers’ demand and the habitat degradation associated to the rapid urbanization and hydropower development. The industrialized north of Italy, home to the Italian Alpine and subalpine trout populations, is the source of most of the revenues of the national trout-culture industry. Its rapid growth and the massive introduction of non-native interfertile trouts eroded the genetic diversity of native lineages, leading to harsh confrontations between scientists, institutions, and sportfishing associations. We review here the state of art of the taxonomy and distribution of the northern Italian native trouts, presenting both scientific results and historical documentation. We think the only native trouts in this region are Salmo marmoratus, widespread in this region, plus small and fragmented populations of S. ghigii, present only in the Southwestern Alps. We strongly recommend the interruption of stocking of domesticated interfertile non-native trouts in this area, and recommend the adoption of Evolutionary Significant Units for salmonid fishery management. We further propose future research directions for a sustainable approach to the conservation and ecosystem management of the fishery resources and inland waters of northern Italy.
REVIEW | doi:10.20944/preprints202202.0180.v2
Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: oxidative stress; nitrative stress; reactive oxygen species; reactive nitrogen species; nitric oxide inflammation; obesity; peroxynitrite; adipose tissue
Online: 30 September 2022 (11:10:38 CEST)
It is now well accepted that most chronic diseases have a common feature which is “low-grade” inflammation. Whether inflammation is causal or rather consequent to these diseases is still a matter of debate. A key factor of inflammation is considered to be “oxidative stress”, which is the result of an alteration of redox homeostasis which is critical for the regulation of physiological cell and organ metabolism and proliferation. The term “oxidative stress” is how-ever often used in an inappropriate manner as the primary target of the initial oxidative radical, superoxide ion, is nitric oxide which, being in large excess, acts as a “buffer”, yielding reactive nitrogen species. It is only once the superoxide fluxes exceed the nitric oxide fluxes that true “oxidative stress” occurs. Nitro-oxidative stress is a more appropriate term which takes into account the evolving generation of reactive nitrogen and oxygen species and their effects on cell and organ pathophysiology. The molecular bases of redox homeostasis and nitro-oxidative stress will be presented and discussed using obesity-linked inflammation as a path-ophysiological example.
CONCEPT PAPER | doi:10.20944/preprints202005.0321.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: trans-species O-glycosylation; trans-species functional bridge; phenotype-specific plasma glycosylation; glycosidic exclusion; ontogenetic Tn formation
Online: 12 January 2021 (12:33:29 CET)
The coevolution of species drives diversity in animals and plants and contributes to natural selection, whereas in host–parasite coevolution, a parasite may complete an incomplete evolutionary/developmental function by utilizing the host cell’s machinery. Analysis of related older data suggests that Plasmodium falciparum (P. falciparum), the pathogen of malaria tropica, cannot survive outside its human host because it is unable to perform the evolutionarily first protein glycosylation of serologically A-like, O-GalNAcα1-Ser/Thr-R, Tn antigen (“T nouvelle”) formation, owing to its inability for synthesizing the amino sugar N-acetyl-d-galactosamine (GalNAc). This parasite breaks the species barrier via hijacking the host's physiological A-like/Tn formation through abundantly expressing serine residues and creating hybrid A-like/Tn structures, which in the human blood group O(H) are attacked by the germline-encoded nonimmune polyreactive immunoglobulin M (IgM), exerting the highly anti-A/B/H-aggressive isoagglutinin activities. These activities physiologically undergo the ABO(H) blood group phenotype formation, occurring on the surfaces of red blood cells (RBC), epithelial and endothelial cells and on plasma proteins by identical glycosylation, performed by the ABO(H)-allelic glycotransferases, phenotypically downregulating the anti-A/B/H-reactive IgM (isoagglutinin) activities in the non-O blood groups. ABO(H) phenotype diversity, this way glycosidically linked and molecularly connected to humoral immunity, becomes exposed to the evolution.
ARTICLE | doi:10.20944/preprints202009.0536.v1
Subject: Chemistry And Materials Science, Physical Chemistry Keywords: 3,3’,5,5’-tetramethylbenzidine; reactive oxygen species (ROS); reactive nitrogen species (RNS); photoacoustic probes; optical sensors; singlet oxygen
Online: 23 September 2020 (04:17:34 CEST)
Photoacoustic imaging is attracting a great deal of interest owing to its distinct advantages over other imaging techniques such as fluorescence or magnetic resonance image. Availability of photoacoustic probes for reactive oxygen and nitrogen species (ROS/RNS) could shed light on a plethora of biological processes mediated by these key intermediates. Tetramethylbenzidine (TMB) is a non-toxic and non-mutagenic colorless dye that develops a distinctive blue color upon oxidation. In this work we have investigated the potential of TMB as photoacoustic probe for ROS/RNS. Our results indicate that TMB reacts with hypochlorite, hydrogen peroxide, singlet oxygen and nitrogen dioxide to produce the blue oxidation product, while ROS such as the superoxide radical anion, sodium peroxide, hydroxyl radical or peroxynitrite yield a colorless oxidation product. TMB does not penetrate Escherichia coli cytoplasm but is capable of detecting singlet oxygen generated in its outer membrane.
ARTICLE | doi:10.20944/preprints201611.0140.v1
Subject: Biology And Life Sciences, Forestry Keywords: understory species; allometric biomass equation; species-specific and multispecies; temperate coniferous and broadleaved mixed forest; northeastern China
Online: 28 November 2016 (04:41:35 CET)
Understory plants are important components of forest ecosystem productivity and diversity. Compared to biomass models of overstory canopy trees, few are available for understory saplings and shrubs and therefore their roles in estimation of forest carbon pools are often ignored. In this study, we harvested 24 understory species including 4 saplings, 9 tree-like shrubs and 11 typical shrubs in coniferous and broadleaved mixed forest in northeastern China and developed the best fit allometric equations of above- and below-ground and total biomass by species-specific or multispecies using morphological measurements of basal diameter, height and crown area as independent variables. The result showed that single basal diameter, height or crown area had good explanatory power for both species-specific and multispecies (p<0.001). The best-fit models included only basal diameter in sapling and tree-like shrubs, and combinations of crown area, height, and basal diameter in typical shrubs. The logarithmic model was most desired among the 4 model forms of linear, quadratic, multiple linear and logarithmic, for species-specific and multispecies. The models we developed should help the estimation of forest ecosystem carbon stocks, especially for belowground component, and provide tools for quantification of individual species biomass of understory plants.
ARTICLE | doi:10.20944/preprints202311.1291.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Antibiotic resistance; Dessie; Kombolcha; Prevalence; Salmonella species
Online: 21 November 2023 (10:45:42 CET)
Bacteria are the major pathogens affecting food safety and foods of animal origin are main vehicles of human illness since food animals are the main reservoirs for many food-borne pathogens. Moreover, emergence and spread of multidrug-resistant food-borne bacterial pathogens become a significant public health concern globally. A cross-sectional study was conducted from October 2019 to July 2021 to estimate the prevalence, identify associated factors, and determine antibiotic resistance pattern of Salmonella species from foods of bovine origin in Dessie and Kombolcha towns. A total of 384 samples were collected. Simple and systematic random sampling techniques were employed for sampling milking cows and carcasses among cattle slaughtered at abattoirs, respectively. Samples from milk tanks, milk products, and beef were also selected randomly. Salmonella species were isolated and identified according to recommended standard bacteriological protocols. All the detected Salmonella species isolates were screened for in vitro antimicrobial susceptibility using agar disc diffusion method against 12 antimicrobial disks. The collected raw data were analyzed using descriptive and inferential analysis techniques. The overall prevalence rate of Salmonella species was 7.0%. The highest prevalence rate of Salmonella species (16.7%) was obtained from milk tank samples but not detected in milk products. Multidrug resistance to three and more than three drugs was observed among all isolated Salmonella species. All Salmonella species isolates (100.0%) were found to be resistant to Erythromycin, Tetracycline, and Vancomycin. The majority of the isolates (96.3%) were also resistant to Doxycycline and Polymyxin B. On the other hand, all isolates (100.0%) were sensitive to Gentamicin and Ciprofloxacin. The detection of multidrug-resistant Salmonella species showed that foods of bovine origin produced in the study sites were not safe for consumption. Hence, preventive measures are required to reduce bacterial contamination, concurrently to improve the wholesomeness and safety of foods of bovine origin.
ARTICLE | doi:10.20944/preprints202307.1579.v1
Subject: Environmental And Earth Sciences, Ecology Keywords: species composition; tree diversity; regeneration; forest management
Online: 25 July 2023 (05:37:03 CEST)
Tropical forests provide habitats for diverse flora and fauna. In addition, they are essential in regulating the climate while at the same time millions of people depend on them for their livelihoods. As seen by rising political commitment and worldwide promises to reduce rates of deforestation and boost restoration of degraded forest ecosystems, forests are becoming more widely acknowledged for their role as a nature-based solution to many sustainable development concerns. Understanding tropical forest dynamics and their conservation have so become more important. This study analyzed, the forest stand structure, tree species composition, abundance and diversity and the regeneration status of Londiani Forest. Londiani Forest is divided into three blocks, namely Kedowa, Chebewor and Londiani and from each of these blocks belt transects 25 m wide and 1 km long were established 100 m from the edge of the forest to reduce edge effects. At every 200 m along the transect, 25 m × 25 m quadrats were set up in which, an inventory of all tree species was done. For tree species that could not be identified in the field, the local name was provided by para-taxonomists who participated in the data collection and the species name was later identified with the help of a taxonomist or a manual of woody tree species of Londiani Forest. The diameter at breast height (DBH) was measured at 1.3 m from the ground using a diameter tape. Tree height was measured using a Suunto angular clinometer. A nested quadrat 5 m x 5 m quadrat within the 25 m x 25 m quadrat was used to sample saplings while a 1 m x 1 m quadrat was used for sampling seedlings. Regeneration status was assessed using the number of seedlings and saplings. Stumps of trees cut were counted including identifying tree species from which the tree stump was derived. Data from the quadrats were entered into Microsoft Excel. Total stem density, species density, basal area, species basal area, relative density and species diversity were determined. A total of 1,308 individual trees belonging to 34 different species from 24 families were recorded. Kedowa had the highest (27) species richness followed by Chebewor (19) then Londiani (14). There was a statistically significant difference in species richness among the three forest blocks (p<0.05). There were no statistically significant differences in the mean DBH (F=0.560; p=0.729) and height class distribution (F= 0.821, p=.558) among the three forest blocks. There was a statistically significant difference in stem density (F=12.22; p=0.005) and woody species diversity (F=0.32; p=0.001) within the three forests blocks. There was no statistically significant difference in the basal area distribution within the three forest blocks p>0.005. The similarity index ranged from 0.34 to 0.47. In all the forest blocks, there was evidence of seedlings and saplings indicating that there was regeneration. Results clearly show that while the Londiani Forest shows variation in characteristics, there is clear evidence that it is regenerating.
ARTICLE | doi:10.20944/preprints202307.0712.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: avifauna; checklist; habitat variation; species diversity; Vavuniya
Online: 13 July 2023 (07:11:21 CEST)
Vavuniya District is located in the lowland dry zone district of the Northern Province of Sri Lanka, which is still unexplored with a natural forest cover of 1,238 km2. Literature relates to the avifaunal birds is still a gap in the Vavuniya, as there are already studies about the diversity of water avifaunal species. In addition to that, the habitat diversity within the study area was discussed using a prepared checklist and the community indices like the Shannon-Weiner index (H’), Simpson’s diversity index (D), Simpson’s evenness (E), and Species richness (R) across various habitat ecosystems: Woodland-Paddy land (H1); Woodland-Water catchment area (H2); Forest (H3); Grassland with inundated land ecosystem (H4); and Manage garden with Occasional trees (H5); of the Pampaimadu premise, University of Vavuniya. The study area is located 10 km from the center of Vavuniya along the A30 highway, with the dry-mixed evergreen forest as vegetation. The checklist resulted in the observation of 93 avifaunal species belonging to 47 families (including 9 endemics, and 5 nationally threatened species). Family Columbidae (Rock Pigeon: Columba livia (n=123)) is found (68%) to be observed with the highest frequency and evenly distributed across different habitats but the family Ardeidae is found extensively dominating in H5 (39%). H1 is with the highest H` (3.5) and D (0.96); while H3 has the highest R (2.52) and E (0.62). Many anthropogenic disturbances, such as habitat alterations, intentional wildfire, and road mortality are the key threats encountered by the avifaunal species in the study area.
ARTICLE | doi:10.20944/preprints202307.0256.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Ochthomantis; Mantidactylus; cryptic species; morphology; 16S; Madagascar
Online: 5 July 2023 (04:03:22 CEST)
The subgenus Ochthomantis is an obligate forest and stream-dwelling group of Mantellid frogs, endemic to Madagascar, with six species currently recognized. However, this group suffers from ongoing taxonomic confusion due to low numbers of examined specimens, and failure to con-sider morphological variation from development and sexual dimorphism. Here we examined the morphology of 637 adult sexed specimens, collected by us in the field, and from other Mu-seum collections. We also sequenced the 16S mtDNA gene for each lineage, to determine con-gruence between morphological and molecular data sets, and to help delimit species. Our results demonstrate that the subgenus Ochthomantis includes 11 valid species: five already recognized; M. catalai and M. poissoni that we resurrect from synonymy, and four new species which we de-scribe here. Because Mantidactylus majori groups with other Mantidactylus, we do not consider it a member of the subgenus Ochthomantis. All species have restricted distributions and elevational ranges in the humid forests of Madagascar. This study demonstrates the utility of studying cryp-tic species using both diagnostic morphological characters and molecular data. It is hoped that discovery of this new cryptic biodiversity will initiate conservation activities for those species with the most restricted distributions.
ARTICLE | doi:10.20944/preprints202306.0413.v3
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: PFAS; metabolism; transcriptomics; transcriptome; cross-species analysis
Online: 28 June 2023 (02:33:02 CEST)
In the recent decades, per- and polyfluoroalkyl substances (PFAS) have garnered widespread public attention due to their persistence in the environment and detrimental effects on the health of living organisms, spurring the generation of several transcriptome-centered investigations to understand the biological basis of their mechanism. In this study, we collected 2144 publicly available samples from 7 distinct animal species to examine the molecular responses to PFAS exposure and to determine if there are conserved responses. Our comparative transcriptional analysis revealed that exposure to PFAS is conserved across different tissues, molecules and species. We identified and reported several genes exhibiting consistent and evolutionarily conserved transcriptional response to PFAS, such as ESR1, HADHA and ID1, as well as several pathways including lipid metabolism, immune response and hormone pathways. This study provides the first evidence that distinct PFAS molecules induce comparable transcriptional changes and affect the same metabolic processes across inter-species borders. Our findings have significant implications for understanding the impact of PFAS exposure on living organisms and the environment. We believe that this study offers a novel perspective on the molecular responses to PFAS exposure and provides a foundation for future research into developing strategies for mitigating the detrimental effects of these substances in the ecosystem.
ARTICLE | doi:10.20944/preprints202306.1428.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Talpinae species; chromosome evolution; comparative chromosome painting
Online: 20 June 2023 (10:31:18 CEST)
In recent years, the number of mole species for which the species status has been confirmed using genetic methods has been continuously increasing. Unfortunately, cytogenetic analysis is not available for all species. Here, for the first time, a GTG-banded karyotype of the small-toothed mole from Vietnam, Euroscaptor parvidens, a representative of the eastern clade of the genus Euroscaptor, was described. Through comparative analysis of available Euroscaptor (E. parvidens, E. klossi, and E. malayana) and Oreoscaptor (O.mizura) karyotypes we find cytogenetic signatures. Zoo-FISH with sorted chromosomes of the Siberian mole Talpa altaica on chromosome sets of the small-toothed mole E. parvidens, the small Japanese mole M. imaizumii from the close genus Mogera and the Japanese shrew mole Urotrichus talpoides from the tribe Urotrichini made it possible to identify syntenic regions between species that diverged about 35 million years ago. The low rate of chromosomal changes within the species of the genus Talpa - T.altaica and T.europaea - and the high rate of karyotypic reshuffling within the Asian genera of the tribe were confirmed. The pericentric inversions on four pairs of autosomes are shared between the closely related genera Euroscaptor, Oreoscaptor, and Mogera, while many more apomorphic rearrangements have occurred in each lineage additionally. The highest rate of chromosomal changes was recorded in the lineage of the small-toothed mole.
ARTICLE | doi:10.20944/preprints202208.0525.v1
Subject: Biology And Life Sciences, Insect Science Keywords: new species; Biogeography; Mediterranean; Red List; Bioacoustics
Online: 30 August 2022 (14:38:12 CEST)
In late April 2022, during the hearing of the audio files from an unsupervised bioacoustic assessment of the shearwater populations (Aves, Procellariiformes) on the coast of Pantelleria island (Italy, Sicily), a cricket song of unknown attribution was heard. The first bioacoustic analyses, including FFT-based spectrograms and sound pressure envelopes, confirmed that it could not be attributed to the known sound of any Italian nor Mediterranean species of cricket. In the ensuing weeks, field research made on purpose in the original station and in further localities in the southern coast of Pantelleria provided photographs, living specimens and further audio records. As soon as the photos were shared among the authors, it became clear that the species belonged to the genus Acheta. Further bioacoustic analyses and morphological comparison with type specimens of Mediterranean and North-African congenerics in relevant collections and in the scientific literature were conducted: they confirmed that the findings could only be attributed to a still undescribed species, that escaped detection due to its impervious and unfrequented habitat. Acheta pantescus n. sp. is apparently restricted to the effusive coastal cliffs of the island of Pantelleria, a habitat whose scant extension and vulnerability require environmental protection actions such as the inclusion in a special Red List by the IUCN Italian Committee.
REVIEW | doi:10.20944/preprints202205.0289.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: mitochondria; reactive species; eustress; distress; bioenergetic; microbiota
Online: 23 May 2022 (09:41:06 CEST)
From oxidative eustress and distress, to bioenergetic metabolism, and cell death, the reactive species interactome (RSI) and mitochondria are two connected metabolisms that require further investigation improving redox medicine. The step before, finding new clues needs a comprehensive discussion of the two metabolisms, and their relationship. Here, the review focuses on the RSI-mitochondria axis, from mitochondrial roles to crosstalk between mitochondria and other organelles, and the major implication of the RSI in mitochondrial roles. Specifically, the review discussed the apoptosis-necroptosis-ferroptosis death traingle, mitochondrial protein quality control system, calcium homeostasis, and mitochondrial metabolome. Through mitochondrial diseases, and mitochondrial dysfunction associated with diseases, the RSI-mitochondria axis is proposed as a brand-new perspective, including with the involvement of bacterial microbiota, on redox signaling, and redox medicine.
ARTICLE | doi:10.20944/preprints202204.0021.v1
Subject: Environmental And Earth Sciences, Paleontology Keywords: Ophiuroidea; microfossils; fossil record; new species; Cenozoic
Online: 5 April 2022 (08:41:15 CEST)
The fossil record of the Ophiuroidea is still patchy, especially in the Cenozoic. Only four species have been described from the entire Oligocene, which is in stark contrast to the present-day diversity counting more than 2000 species. Here, we describe two new species of ophiuroid, Ophiura tankardi sp. nov. and Ophiodoris niersteinensis sp. nov., from the Lower Oligocene of the Mainz Basin. The species are based on microfossils extracted from the sieving residues of bulk sediment samples from a flush drill in Nierstein, Rhineland-Palatinate. The new species belong to extant genera and add to the poor Oligocene fossil record of the class. Based on present-day distributions, the occurrence of Ophiodoris suggests deep sublittoral to shallow bathyal palaeodepths for the Nierstein area of the Mainz Basin.
REVIEW | doi:10.20944/preprints202202.0014.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: drought stress; reactive oxygen species; climate change
Online: 1 February 2022 (12:53:40 CET)
Each year, the global population and agriculture suffer critical agricultural output losses as a result of severe drought devastation. Physiological drought occurs when plants are unable to extract water from the soil, even though it is available in the root zone. Apart from having a significant effect on plant physiology, drought stress has the effect of reducing crop yield. Drought stress influences plant metabolism both directly and indirectly. Drought stress alters the morpho-anatomical, physiological, and biochemical composition of plants, thereby decreasing transpiration water loss and increasing the efficiency with which plants use their water. Constant water loss through transpiration, combined with previously lost water, results in leaf water deficits. Nonetheless, drought stress has a wide variety of effects, ranging from lesions to confusion. Plant health is harmed when their ability to absorb water and nutrients, interact with their environment, and breathe is harmed. Apart from oxidative damage to plants, it may also result in cell death, which can occur under certain conditions when cells are exposed to their environment. Drought induces a plethora of physiological and molecular changes in plants, the majority of which assist them in adapting to the harsh environment. To mitigate drought's adverse effects, we must first gain a better understanding of how drought affects plant physiology. The purpose of this research is to better understand how drought affects plant development by examining the causes and effects of drought stress.
ARTICLE | doi:10.20944/preprints202011.0656.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: orchid books; database; species; documentations; policy; extinction
Online: 26 November 2020 (07:36:45 CET)
Orchids totalling close to 4000 species in Malaysia are one of the most diverse and most widespread family here had gained momentum in recognition among policy makers and guardians of the forest as one of the profiles that fit and can benefit plant conservation on a broad scale in recent years. Listed not only as conservation indicator but also as priority germplasm for sustainable floriculture industry in the country, a milestone that could safeguard wild orchids from verge of extinction in the natural habitat. Through our 30 years of studying orchids in the wild, we understand more about the distribution, rarity, threats and extinction of orchids than ever before, and we have the scientific tools to address many of the problems, yet many species face daily threats including habitat loss and unsustainable exploitation mainly via Internet trade. Prior to executing workable conservation plan, various research institutions working closely with Forestry Departments in Malaysia to first inventory and document the orchid species richness in the country. Selangor, Sarawak and Perlis Forestry Departments in collaboration with UPM have published seven orchid books that cover various habitat types. Selangor Forestry Department is leading on publishing biodiversity data in form of books for its various ecotourism’s sites and State Parks, and had published two books on orchids. Sarawak state has published one on the limestone orchids, and Perlis is the first to embark on the feat published one in 2010 and currently preparing a new book that includes other flagship wild flowers. Realizing the importance of documenting its biodiversity wealth, Malaysia has developed an information system that would be a one-stop retrieval point or repository for biodiversity facts and as a part of the commitments to CBD to facilitate reporting and the transfer of biological diversity and conservation-related information both nationally and internationally.
Subject: Biology And Life Sciences, Biophysics Keywords: microbiome; complex networks; species diversity; criticality; RSA; information flow; transitions
Online: 28 March 2019 (09:10:18 CET)
The human microbiome is an extremely complex ecosystem considering the amount of bacterial species, their interactions, and its variability over time. Here we untangle the complexity of the human microbiome for the Irritable Bowel Syndrome (IBS) that is the most prevalent functional gastrointestinal disorder in human populations. Based on a novel information theoretic network inference model we detect species interaction networks that are functionally and structurally different for healthy and unhealthy individuals. Healthy networks are characterized by a neutral symmetrical pattern of species interactions and scale-free topology versus random unhealthy networks. We detect an inverse scaling relationship between species total outgoing information flow, meaningful of node interactivity, and relative species abundance (RSA). The top ten interacting species are also the least relatively abundant for the healthy microbiome and the most detrimental. These findings support the idea about the diminishing role of network hubs and hubs should be defined considering the total outgoing information flow rather than the node degree. Macroecologically, the healthy microbiome is characterized by the highest total species diversity growth rate, the lowest species turnover, and the smallest variability of RSA for all species. This result challenges current views that posit a universal association between healthy states and the highest absolute species diversity in ecosystems. Additionally, we show how the transitory microbiome is unstable and microbiome criticality is not at the phase transition between healthy and unhealthy states. We stress out the importance of considering interacting pairs versus single node dynamics when characterizing the microbiome and of ranking these pairs in terms of their dynamics. Interactions (i.e. species collective behavior) shape transition from healthy to unhealthy states.\\ The macroecological characterization of the microbiome is useful for diagnostic purposes and disease etiognosis, while species-specific analyses can detect species that are more beneficial leading to personalized design of pre- and pro-biotic treatments and microbiome engineering.
REVIEW | doi:10.20944/preprints201807.0260.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: mitochondria; invertebrate; reactive oxygen species; oxidative phosphorylation
Online: 16 July 2018 (08:27:03 CEST)
Neurodegenerative diseases like Alzheimer’s disease (AD) are poised to become a global health crisis, and therefore understanding the mechanisms underlying the pathogenesis is critical for the development of therapeutic strategies. Mutations in genes encoding presenilin occur in most familial Alzheimer’s disease but the role of PSEN in AD is not fully understood. In this review, the potential modes of pathogenesis of AD are discussed, focusing on calcium homeostasis and mitochondrial function. Moreover, research using Caenorhabditis elegans to explore the effects of calcium dysregulation due to presenilin mutations on mitochondrial function, oxidative stress and neurodegeneration is explored.
ARTICLE | doi:10.20944/preprints201707.0063.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Sulfur reduced species; Biofilms; Chalcopyrite, Biooxidation; Hydrophobicity
Online: 21 July 2017 (17:31:25 CEST)
A bioelectrochemical study of charge transfer in the biofilm/chalcopyrite interface was performed to investigate the effect of surficial sulfur reduced species (SRS), as non-stochiometric compounds or polysulfides (Sn2-), and elemental sulfur (S0) on a biofilm structure during the earliest stages (1, 12 and 24 h) of chalcopyrite biooxidation by A. thiooxidans alone and adding Leptospirillum sp. The surface of massive chalcopyrite electrodes was exposed to the bacteria, which were analyzed electrochemically, spectroscopically, and microscopically. At the studied earlier times, charge transfer and significant differences in the biofilm structure were detected, depending on the presence of Leptospirillum sp. acting on A. thiooxidans biofilms. Such differences were a consequence of a continuous chalcopyrite pitting and promoting changes in biofilm hydropathy. A. thiooxidans modifies the reactive properties of SRS and favors an acidic dissolution, which shifts into ferric when Leptospirillum sp. is present. A. thiooxidans allows H+ and Fe3+ diffusion, and Leptospirillum sp. allows surpassing the charge transfer (reactivity) barrier between the mineral interface and the ions. The observed changes of hydropathy on the interface are associated to ions and electrons activity and transfer. Finally, a model of S0 biooxidation by A. thiooxidans alone or with Leptospirillum sp., is proposed.
ARTICLE | doi:10.20944/preprints202008.0036.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Arctic-alpine flora; Extinction due to climate change; Narrow endemism; Papaver alpinum aggr; Scree species; Species distribution modelling
Online: 2 August 2020 (15:06:03 CEST)
Glacial relicts, especially those with very narrow habitat requirements, are particularly affected by global warming and thus good models for studying the future biodiversity patterns of the Alps. We have used as a model taxon Papaver occidentale, a glacial relict endemic to the Western Prealps, belonging to the alpine poppy complex (P. alpinum aggr.). All known localities were visited, each population was georeferenced and the number of individuals was estimated. Species Distribution Modelling (SDM) was used to evaluate the present and future potential distribution range and habitat suitability, taking into account the specificity of its habitat (calcareous screes). According to our study, there are globally 19 natural populations of P. occidentale. The total number of individuals was estimated at 30756 (with 72% of all individuals in canton of Bern). The taxon is a highly specialized alpine plant growing preferentially between 1900 and 2100 m a.s.l. on north facing screes. Predictions for the end of the 21st century indicate that suitable area will significantly decrease, for both the entire studied area (0-30% remaining) and sites nearby current P. occidentale populations (0-17% remaining). Under the most severe scenario, the species risks complete extinction. The long-term in situ conservation of P. occidentale, and all other taxa of the P. alpinum complex, is unlikely to be achieved without slowing global climate change. More generally, our fine-scale study shows that local environmental buffering of large-scale climate change in high-mountain flora may be very limited in specialised taxa of such patchy environments as screes.
ARTICLE | doi:10.20944/preprints201803.0252.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Curculionidae; Cossoninae; Rhyncolini; Rhyncolina; taxonomy; new species; mature larva; morphology; host plant; Cape Verde; biogeography; microclimate; species competition
Online: 29 March 2018 (14:53:47 CEST)
The genus Aphanommata in the Old World is reviewed. Aphanommata kuscheli sp. nov. from São Nicolau and A. strakai sp. nov. from Fogo (both Cape Verde islands) are described. Aphanommata euphorbiarum (Wollaston, 1867) from Santo Antão in the Cape Verde islands is redescribed and its lectotype is designated. All three Aphanommata species from the Cape Verde islands as well as A. filum (Mulsant & Rey, 1859) from Old World are diagnosed, illustrated, and keyed. Mature larva of A. kuscheli sp. nov. is described, larval morphology is discussed and the current state of knowledge about immature stages of Cossoninae is summarized. Vertical and inter-insular distributional pattern of Cape Verde Aphanommata and Pselactus is reviewed and discussed.
CONCEPT PAPER | doi:10.20944/preprints202005.0097.v5
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2–human carbohydrate interaction; trans-species glycosylation; A-like/Tn structure; trans-species glycan bridge
Online: 13 November 2020 (09:42:18 CET)
While the angiotensin converting enzyme 2 (ACE2) protein is defined as the primary severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor, the viral serine molecule might be mobilized by the host's transmembrane protease serine subtype 2 (TMPRSS2) enzyme from the viral spike (S) protein and hijack the host’s N-acetyl-D-galactosamine (GalNAc) metabolism. The resulting hybrid, serologically A-like/Tn (T-nouvelle) structure potentially acts as a host–pathogen functional molecular bridge. In humans, this intermediate structure will hypothetically be replaced by ABO(H) blood group-specific, mucin-type structures, in the case of infection hybrid epitopes, implicating the phenotypically glycosidic accommodation of plasma proteins. The virus may, by mimicking the synthetic pathways of the ABO(H) blood groups, bind to the cell surfaces of the blood group O(H) by formation of a hybrid H-type antigen as the potential precursor of hybrid non-O blood groups, which does not affect the highly anti-glycan aggressive anti-A and anti-B isoagglutinin activities, exerted by the germline-encoded nonimmune immunoglobulin M (IgM). In the non-O blood groups, which have developed from the H-type antigen, these IgM activities are downregulated by phenotypic glycosylation, while adaptive immunoglobulins might arise in response to the hybrid A and B blood group structures, bonds between autologous carbohydrates and foreign peptides, suggesting the exertion of autoreactivity. The non-O blood groups thus become a preferred target for the virus, whereas blood group O(H) individuals, lacking the A/B phenotype-determining enzymes and binding the virus alone by hybrid H-type antigen formation, have the least molecular contact with the virus and maintain the critical anti-A and anti-B isoagglutinin activities, exerted by the ancestral IgM, which is considered the humoral spearhead of innate immunity.
ARTICLE | doi:10.20944/preprints202310.1511.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: feeding strategies; food webs; native species; trophic niche
Online: 24 October 2023 (09:39:44 CEST)
Background: Understanding the trophic ecology of threatened freshwater fishes is relevant to managing their conservation. The genus Orestias is endemic to the Andes region and shows great biogeographical interest in the Neotropics due to its adaptation to the high-altitude systems of the Andes as well as because several species are considered threatened. (2) Methods: Here, we synthesize the documented trophic interaction of Orestias spp. in freshwater ecosystems of the Andes region available in the literature and use available data to explore the trophic interaction of Orestias species via null models. (3) Results: Our findings showed that Orestias spp. consume a wide range of prey (i.e., mainly aquatic insects, crustaceans, and mollusks) that varied according to their habitats and feeding morphology. The null model revealed that species associations in diet were random because of the presence of many repeated species. Our results would reveal that some Orestias spp. may show an opportunistic feeding strategy that concurs with previous reports. Additionally, we highlight major information gaps associated with the trophic ecology of Orestias spp. and propose some direction for future studies. (4): Our study provides valuable in-formation on Orestias spp. trophic ecology, which may be useful for developing conservation strategies for native fish in the Neotropical region.
ARTICLE | doi:10.20944/preprints202308.1085.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Bt soybean; chemical control; defoliator species; sublethal effects
Online: 15 August 2023 (08:26:46 CEST)
An increase in Spodoptera species was reported in Bt soybean fields expressing Cry1Ac insecticidal proteins in Brazil, requiring additional management with chemical insecticides. Here, we evaluated the dose effects of flubendiamide and thiodicarb on Spodoptera cosmioides (Walker, 1858), Spodoptera eridania (Stoll, 1782), Spodoptera albula (Walker, 1857) and Spodoptera frugiperda (J. E. Smith, 1797) (Lepidoptera: Noctuidae) that survived on MON 87751 × MON 87708 × MON 87701 × MON 89788, expressing Cry1A.105, Cry2Ab2 and Cry1Ac; MON 87701 × MON 89788 soybean, expressing Cry1Ac; and non-Bt soybean. On unsprayed Cry1A.105/Cry2Ab2/Cry1Ac soybean, only S. frugiperda showed ~60% mortality after 10 d, whereas S. cosmioides, S. eridania and S. albula showed >81% mortality. Surviving larvae of all species on this Bt soybean showed >80% mortality when exposed to the field label dose of flubendiamide (70 mL/ha) or thiodicarb (400 g/ha) or at 50% of these doses. In contrast, all four species had <25% and <19% mortality on Cry1Ac and non-Bt soybean, respectively. Surviving S. cosmioides, S. eridania and S. albula on these soybean types presented >83% mortality post-exposure to both dose levels of flubendiamide and thiodicarb. Some S. frugiperda larvae surviving on Cry1Ac and non-Bt soybean sprayed with a 50% dose of either insecticide developed into adults. However, L1 larvae developing on Cry1Ac soybean leaves sprayed with flubendiamide and L2 larvae on this soybean sprayed with thiodicarb had a prolonged immature stage, and females lower fecundity, which are likely to impact its population growth on soybean.
REVIEW | doi:10.20944/preprints202305.1248.v1
Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: NAFLD; NASH; insulin resistance; reactive oxygen species; CEACAM1
Online: 17 May 2023 (12:34:09 CEST)
Nonalcoholic fatty liver disease (NAFLD) has become a widely studied subject due to its increasing prevalence and links to diseases such as type 2 diabetes and obesity. It has severe complications, including nonalcoholic steatohepatitis, cirrhosis, hepatocellular carcinoma, and portal hypertension that can lead to liver transplantation in some cases. To better prevent and treat this pathology, it is important to understand its underlying physiology. Here, we identify three main factors that play a crucial role in the physiopathology of NAFLD: oxidative stress, insulin resistance, and the key role of carcinoembryonic antigen related cell adhesion molecule 1 (CEACAM1). We discuss the pathophysiology linking these factors to NAFLD pathophysiology.
ARTICLE | doi:10.20944/preprints202305.0480.v1
Subject: Environmental And Earth Sciences, Oceanography Keywords: phytoplankton; Black Sea; biogeochemistry; species composition; diatoms; coccolithophores
Online: 8 May 2023 (08:47:26 CEST)
Biogeochemistry of waters is an essential regulator of phytoplankton dynamics, determining the level of species bloom and the change of dominants. The paper investigated the seasonal dynamics of phytoplankton and the nutrient concentration and their ratios in the NE Black Sea in 2017-2021. Two taxonomic groups, diatoms, and coccolithophores, determine seasonal dynamics and significantly contribute to the total phytoplankton biomass. Coccolithophores annually, except in 2020, formed bloom in early June. Large diatoms in summer annually, except in 2019, dominated with biomass exceeding 1000 mg m-3. During the bloom of these taxonomic groups, their contribution to the total phytoplankton biomass exceeded 90%. Each group has characteristic biogeochemical niches in the nitrogen and phosphorus concentrations coordinates. The regulation of the biogeochemistry of water is the position of the seasonal thermocline. With a high-lying and sharp gradient thermocline (the average for five years is 6.87 m), low nitrogen concentrations and a nitrogen-to-phosphorus ratio below the Redfield ratio are created in the upper mixed layer. These conditions are optimal for the dominance of coccolithophores. When the thermocline is deepened (the average for five years is 17.96 m), the phosphorus concentration decreases significantly and the ratio of nitrogen to phosphorus is significantly higher than the Redfield ratio, and these conditions lead to the dominance of large diatoms. The results of experimental studies with nitrogen and phosphorus additives in the natural phytoplankton population confirm the above statements. The addition of phosphorus leads to an increased role of coccolithophores in the total phytoplankton biomass, the addition of nitrogen alone contributes to the growth of large diatoms, and the combined addition of phosphorus and nitrogen in a ratio close to the Redfield ratio leads to the dominance of small diatoms.
ARTICLE | doi:10.20944/preprints202301.0214.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: community transformations; species loss; geospatial classification; Spartina patens
Online: 12 January 2023 (07:20:07 CET)
Salt marshes are globally important ecosystems, but many have been lost or transformed due to the impacts of global change. There have been attempts to broadly quantify salt marsh communities, especially the ubiquitous grasses which serve as foundation species such as Spartina alterniflora and Spartina patens, the latter of which is being lost due to sea level rise. However, few researchers have used high-resolution geospatial imagery to quantify fine-scale changes in the distribution of grasses or to track losses of S. patens. To address this issue, we utilized a simple and rapid method of classifying geospatial marsh imagery with cloud-based machine learning in Google Earth Engine (>92% accuracy for S. patens regardless of imagery age). Our methods allowed us to characterize full landscapes (two geospatially proximal areas, >7,000 ha each) of critical salt marshes on the New Jersey coast and to evaluate fine-scale (1-m) community transformations in response to global change with imagery from 2006 to 2019. Notably, one marsh experienced very little change while the other experienced an 81.17% (1,087 ha) loss of S. patens, illuminating disparate patterns of change for two geographically proximal ecosystems. Further exploration revealed an association in the loss of S. patens with increases in streamflow and total nitrogen content in the rivers that run through each marsh. These results signify the importance of broad-scale ecological studies that evaluate fine-scale community transformations and for management strategies that do not generalize across landscapes of an ecosystem-type.
ARTICLE | doi:10.20944/preprints202212.0428.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: soybean agroecosystem; Bradyrhizobium species; magnetic susceptibility; humic substances.
Online: 22 December 2022 (11:37:56 CET)
In this study, the influence of the environment on soil conditions, e.g. heavy metals and soil magnetic susceptibility, on the total number of bacteria and the species of Bradyrhizobium in the field cultivation of the soybean variety Lissabon, the seeds of which had been inoculated with HiStick®Soy, were evaluated. Field experiments were carried out with the random plot method on the Cambisol with a texture of silt loam. The experiment consisted of 24 objects in six combinations and four replications using sewage sludge and fly ash. In the soil samples, the total number of bacteria and the number of the species of Bradyrhizobium were determined using the culture-plate method. The total content of heavy metals (Cu, Zn, Cd, Ni, Pb, Cr, Hg, Fe) in the analyzed objects, compared to the limit values, allowed them to be classified as uncontaminated soils despite the application of sewage sludge and fly ash according to the experimental scheme, showed a significant difference between them. The study of the magnetic parameter χ indicated a significant differentiation between objects from 34.0 to 65.8 × 10-8m3kg-1. High correlation coefficients between χ and Fe (r = 0.789), Zn (r = 0.653), Cr (r = 0.617) and TOC (r = 0.949) indicated that the source of these elements was external organic matter. Biological tests (total content of bacteria and species of Bradyrhizobium) in different experimental variants indicated significant relationships between them and showed the resistance of the microbial community in the field cultivation of Lissabon soybean to heavy metal contamination from sewage sludge and fly ash.
ARTICLE | doi:10.20944/preprints202207.0157.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Methylococcaceae; methanotroph; Indian rice field; Methylmonas; novel species
Online: 11 July 2022 (09:56:06 CEST)
An aerobic methanotroph, strain Kb3T, was isolated from a rhizospheric soil sample collected from a tropical Indian rice field. The cells were motile, Gram-negative bacilli, formed pink colonies and pink turbid/pellicles in the liquid medium. Biochemical characteristics showed that strain Kb3T utilised only methane and methanol as its sole carbon and energy sources. The isolate's 16S rRNA gene sequence expressed 99.52% similarity to the recently described valid species Methylomonas fluvii EbB (Mmf), with 92% query cover. But examining the genome similarity between Kb3 and EbB, a DDH value of 44.20% [41.6 - 46.7%] and an Ortho-ANI value of 91.48 was observed that were below the current cut-off values for species differentiation. Also, the 16S rRNA gene phylogeny and the phylogenomic analysis branched the two species separately. The major fatty acid in Methylomonas sp. Kb3 was C14:0, followed by C16:1 ω5c. The genome sequence revealed the size of strain Kb3 is 5.1 Mb, with the G + C content of 51.8%. Strain Kb3T shared the closest relatedness with Methylomonas sp. LW13 reveals a 99.66% 16S rRNA gene similarity, an Ortho-ANI value of 97.9%, a DDH value of 87.3%, and a close branching in the phylogenomic tree Kb3 and LW13 together form a new species. The genomic and phylogenetic distinction between species Mmf and strain Kb3 supports Kb3T to be described as a novel species within the genus Methylomonas, with the proposed name, Methylomonas aquatica sp. nov. (Mma) and the type strain being Kb3T (=MCC 4012, =JCM 33634, =KCTC 72521).
ARTICLE | doi:10.20944/preprints202203.0225.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: chemotherapy; muscle atrophy; Doxorubicin; mitochondria; reactive oxygen species
Online: 16 March 2022 (08:22:57 CET)
Doxorubicin (Dox) is a commonly used chemotherapeutic that can adversely affect skeletal muscle, including causing muscle atrophy. Dox is known to induce an event known as mitochondrial permeability transition (MPT) in cardiac muscle and this plays an important role in Dox-mediated cardiac toxicity. Further to this, recent evidence identifies MPT as a mechanism of atrophy in skeletal muscle, suggesting that MPT may underlie some of the Dox-related toxicity in skeletal muscle. To test this hypothesis, we used cultured human primary myotubes, C2C12 myotubes, and single adult mouse flexor digitorum brevis (FDB) muscle fibers in experiments involving Dox treatment with or without inhibitors of MPT. Dox treatment of myotubes caused myonuclear translocation of the mitochondrial protein apoptosis inducing factor (AIF) and increased mitochondrial reactive oxygen species (mROS), consistent with the known consequences of MPT. Furthermore, Dox caused atrophy in C2C12 myotubes grown on patterned plates, human primary myotubes, and single muscle fibers from adult mice. Notably, Dox-induced atrophy could be prevented by a wide variety of agents that inhibit MPT, as well as by inhibiting mROS or Caspase 3. In conclusion, our results indicate that MPT plays an important role in driving Dox-mediated skeletal muscle atrophy.
ARTICLE | doi:10.20944/preprints202202.0117.v1
Subject: Biology And Life Sciences, Virology Keywords: Bunyavirales; Nairoviridae; Peribunyaviridae; Phenuiviridae; taxonomy; nomenclature; species demarcation
Online: 8 February 2022 (14:38:01 CET)
In recent years, the taxonomy of the families of Phenuiviridae, Nairoviridae, and Peribunyavidae in Bunyavirales was updated frequently, because many novel viruses in these families have been identified and the species demarcation criteria of these families have been changed. As per these criteria and sequence analysis, we found that the taxonomy of 19 species in these families should be revised. We presented six proposals for optimizing virus species taxonomy using the examples from these families. First, the species demarcation criteria for the same family (e.g., Peribunyavidae) should be unified. Second, the methods and parameters for the taxonomic calculation in the same order (e.g., Bunyavirales) should be unified. Third, virus species taxonomy should be based on phylogenetic relationships, rather than a cutoff value of sequence identities that is a self-contradictory demarcation criterion, although sequence identities aid virus taxonomy greatly. Fourth, virus species taxonomy should be based on the phylogenetic relationship of a key viral gene (e.g., the RdRp gene of Bunyavirales), which is important for the taxonomy of virus recombinants or reassortants. Fifth, a virus can be demarcated without a species before its biomedical significance has been revealed. Sixth, names of all viruses and virus species should be constituted exclusively with common characters (English letters and Arab numbers), to minimize difficulty in spelling and communication. These proposals are rational, flexible, and can accommodate all known viruses. They can also bridge the taxonomy history and the future demands due to their flexibility.
ARTICLE | doi:10.20944/preprints202201.0007.v1
Subject: Biology And Life Sciences, Forestry Keywords: allelopathy; biochar; invasive species; island ecosystems; Psidium cattleianum
Online: 4 January 2022 (12:37:04 CET)
Many tropical invasive species have allelopathic effects that contribute to their success in native plant communities. Pyrolyzed biomass (“biochar”) can sorb toxic compounds, including allelochemicals produced by invasive plants, potentially reducing their inhibitory effects on native species. Strawberry guava (Psidium cattleianum) is among the most important allelopathic invasive species in tropical islands and recognized as the most serious invasive species threat in the global biodiversity hotspot of Mauritius. We investigated the effects of additions of locally produced biochar on native tree species in a field experiment conducted in areas invaded by strawberry guava within Mauritius’ largest national park. Growth and survivorship of native tree species were monitored over 2 ½ years in plots subjected to four treatments: non-weeded, weeded, weeded + 25 t/ha biochar and weeded + 50 t/ha biochar. Native tree growth and survivorship were strongly suppressed by strawberry guava. Biochar treatments dramatically increased native tree performance, with more than a doubling in growth, and substantially increased native tree survivorship and species diversity, while suppressing strawberry guava regeneration, consistent with growth-promoting properties and sorption of allelochemicals. We conclude that biochars, including “sustainable biochars” produced from locally accessible biomass using low-tech pyrolysis systems, have considerable potential to counteract effects of allelopathic invaders and increase the capacity for native species regeneration in tropical island ecosystems.
REVIEW | doi:10.20944/preprints202007.0328.v3
Subject: Biology And Life Sciences, Other Keywords: Evolution; Speciation; Crossbreeding; Hybridization; Species spectrum; Polyploidization; Somatic cell hybridization; Mutation
Online: 3 March 2022 (10:25:51 CET)
Although Darwin‘s evolutionary mutation theory has been widely accepted, many endeavors have been tried to challenge it. With more and more observation of successful hybridization and hybrids, the sexual isolation between species has become vague. The mechanism of evolution has been expanded from the classical model of evolution to multiple routes of speciation. Furthermore, a fundamental crossbreeding theory has been raised and proved by two lines of evidences: paleopolyploidy and fan-shaped spectrum of species. Ancient genome duplications are widespread throughout eukaryotic lineages, particularly in plants. The genome polyploidization, especially in the somatic cell hybridization, can break through the sexual incompatibility between diploid counterparts to hybridize and produce new species. By comparing characteristics, all species in every taxon, both in the extinct fossil and extant organisms, can be arranged into fan-shaped spectrum according to their similarity: left primitive type-middle advanced type-right primitive type. The species are primitive at the two ends and advanced at the middle. The primitive two species always resemble two types of more primitive species that can be confirmed as their ancestors respectively, and the middle species is half similar to the two ancestors respectively. These suggest that the species in the spectrum come from two different ancestors by crossbreeding and gene combination. As a sum, advanced species originated from crossbreeding of two primitive ancestors, by major method of polyploidization, and proved by results of fan-shaped spectrum of species. Then, sex is the cause, force and opportunity for evolution.
ARTICLE | doi:10.20944/preprints202111.0212.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: oats; fusarium sambucinum species complex; deoxynivalenol; nivalenol; mycotoxin
Online: 11 November 2021 (13:05:00 CET)
Oats are a nutrient rich cereal used for animal feed and growing in human consumption. This cereal can be affected by Fusarium spp., causing the disease Fusarium Head Blight. This disease is caused mainly by species within the Fusarium graminearum species complex, and are also responsible for producing mycotoxins that are harmful to humans and animals. This study aimed to investigate fungal diversity in Brazilian oat samples, focusing on the Fusarium sambucinum species complex and the presence of type B trichothecenes (deoxynivalenol and its derivatives, and nivalenol) from two different regions; Paraná (PR) and Rio Grande do Sul (RS). The isolated fungi from oat grains were identified as species from the genera: Fusarium, Phoma and Alternaria. The majority of Fusarium isolates belonged to the Fusarium sambucinum species complex; identified as F. graminearum s.s., F. meridionale and F. poae. In the RS region, F. poae was the most frequent fungus, while FGSC was the most frequent in the PR region. The majority of F. graminearum s.s. isolates were of the 15-ADON genotype, while some 3-ADON genotypes were identified; however, F. meridionale and F. poae were all of the NIV genotype. Mycotoxin analysis revealed that 92% and 100% of the samples from PR and RS were contaminated with type B trichothecenes, respectively. The oats from PR were predominantly contaminated with DON, whereas NIV was predominant in oats from RS. Analysis showed that 24% of the samples were contaminated with DON at levels higher than Brazilian regulations. Co-contamination of DON, its derivatives and NIV was observed in 84% and 57.7% of the samples from PR and RS, respectively. The results provide new information on Fusarium contamination in Brazilian oats, highlighting the importance for further studies on mycotoxins.
ARTICLE | doi:10.20944/preprints202110.0367.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Bacteria; culturomics; genome; species; sp. nov.,; taxono-genomics
Online: 25 October 2021 (15:47:32 CEST)
Marseille-Q4369 is a strain that we isolated from human healthy skin and characterized by taxono-genomic approach. Marseille-Q4369 exhibited 99.80% 16S rRNA sequence similarity with Agrococcus pavilionensisT the phylogenetically closest bacterium with standing in nomenclature. Furthermore, digital DNA–DNA hybridization revealed a maximum identity similarity of only 52.4% and an OrthoANI parameter provided a value of 93.63% between the novel organism and Agrococcus pavilionensisT. Marseille-Q4369 was observed to be a yellowish-pigmented, Gram-positive, coccoïd, facultative aerobic bacterium, and belonging to the Microbacteriaceae family. The major fatty acids detected are 12-methyl-tetradecanoic acid (66%), 14-methyl-hexadecanoic acid (24%) followed by 13-methyl-tetradecanoic acid (5%). The genome size of strain Marseille-Q4369 was 2,737,735-bp long with a 72,27 % G+C content. Taken altogether, these results confirm the status of this strain as a new member of the Agrococcus genus for which the name of Agrococcus massiliensis is proposed (=CSUR-Q4369 = DSM112404).
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Quercus; oak, canopy; fogging; new species; inventory; Norway
Online: 8 June 2021 (13:16:34 CEST)
(1) We document the invertebrate fauna collected from 24 oak canopies in east and west Norway as a contribution to the Norwegian Biodiversity Information Centre’s “The Norwegian Taxonomy Initiative”. (2) A snap-shot inventory of the canopies was recorded by means of emitting a mist of synthetic pyrethroid into the canopies at night using a petrol-driven fogger, collecting the specimens in butterfly nets spread on the ground under the canopy. (3) Almost the entire catch of more than 6800 specimens was identified to 722 species. Out of 92 species new to the Norwegian fauna, 21 were new to science and additionally 15 were new to the Nordic fauna. Diptera alone constituted nearly half of the species represented with 61 new records (18 new species). Additionally, 24 Hymenoptera (one new species), six oribatid mites (two new species) and one Thysanoptera were new to the Norwegian fauna. (4) Our study emphasis the importance of oak tree as habitat both for a specific fauna and occasional visitors and it demonstrates that the canopy fogging technique is an efficient way to find the ‘hidden fauna’ of Norwegian forests. The low number of red listed species found reflects how poor the Norwegian insect fauna is still studied. Moreover, the implication of the IUCN red list criteria for new described or newly observed species is discussed.
ARTICLE | doi:10.20944/preprints202012.0679.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Antimicrobial resistance; Salmonella species; E.coli; Broiler chickens; Malaysia
Online: 28 December 2020 (10:49:17 CET)
Abstract:Salmonella species (spp) and Escherichia coli (E. coli) are the most common infectious pathogens in poultry. Antimicrobials were given either for the treatment or growth promoters that can increase the possibility of emergence of bacterial resistance towards antimicrobials. The aim of this study was to determine the prevalence of antimicrobial resistant (AMR) Salmonella spp and E. coli isolated from a sample of broiler farms in East Coast Malaysia from 2018-2019. A total of 384 cloacal swabs were collected from broilers farms in Kelantan, Terengganu, and Pahang. The bacteria were isolated and confirmed by bacteriological and serological methods. Following that, confirmed isolates were subjected to antimicrobial susceptibility test. Salmonella spp and E. coli were recovered from the cloacal swabs samples with the overall prevalence of 6.5% and 51.8% respectively. In Kelantan, Terengganu and Pahang, the prevalence of Salmonella spp were 7%, 6.5% and 5.8% respectively, while the prevalence for E. coli were 50%, 48.3% and 58% respectively. Salmonella spp and E. coli displayed resistance towards the following antimicrobials: erythromycin (100% for both pathogens), chloramphenicol (76.2%, 84.5%), tetracycline (62%, 94.6%), ampicillin (47.7%, 87%), sulfamethoxazole/trimethoprim (42.9%, 83.3%), ciprofloxacin (4.8%, 23.8%), nalidixic acid (9.6%, 60.7%), streptomycin (19%,66%), and kanamycin (28.6%,57%), cephalotin (0%, 11%), gentamicin (0%, 20.2%) respectively. No resistance were recorded towards colistin for both pathogens. Multidrug resistance (MDR) was recorded in 82% of Salmonella spp and 100% of E. coli. These findings demonstrate the high prevalence of MDR Salmonella spp. and E. coli in broiler farms in East coast Malaysia. This could be attributed to the excessive use of antimicrobial agents by the poultry farm owners. Enhanced control measures and a strong monitoring system should be urgently implemented to reduce the emergence of antimicrobial resistance that is harmful to public health.
ARTICLE | doi:10.20944/preprints202009.0480.v2
Subject: Engineering, Aerospace Engineering Keywords: invasive species; thermal imaging; habitat identification; deep learning
Online: 21 September 2020 (06:01:38 CEST)
Invasive species are significant threats to global agriculture and food security being the major causes of crop loss. An operative biosecurity policy requires full automation of detection and habitat identification of the potential pests and pathogens. Unmanned Aerial Vehicles (UAVs) mounted thermal imaging cameras can observe and detect pest animals and their habitats, and estimate their population size around the clock. However, their effectiveness becomes limited due to manual detection of cryptic species in hours of captured flight videos, failure in habitat disclosure and the requirement of expensive high-resolution cameras. Therefore, the cost and efficiency trade-off often restricts the use of these systems. In this paper, we present an invasive animal species detection system that uses cost-effectiveness of consumer-level cameras while harnessing the power of transfer learning and an optimised small object detection algorithm. Our proposed optimised object detection algorithm named Optimised YOLO (OYOLO) enhances YOLO (You Only Look Once) by improving its training and structure for remote detection of elusive targets. Our system, trained on the massive data collected from New South Wales and Western Australia, can detect invasive species (rabbits, Kangaroos and pigs) in real-time with a higher probability of detection (85–100 %), compared to the manual detection. This work will enhance the visual analysis of pest species while performing well on low, medium and high-resolution thermal imagery, and equally accessible to all stakeholders and end-users in Australia via a public cloud.
ARTICLE | doi:10.20944/preprints202001.0326.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: laminin; reactive oxygen species; congenital muscular dystrophy; therapy
Online: 27 January 2020 (09:34:14 CET)
Congenital muscular dystrophy with laminin α2 chain-deficiency (LAMA2-CMD) is a severe neuromuscular disorder without a cure. Using transcriptome and proteome profiling as well as functional assays, we previously demonstrated significant metabolic impairment in skeletal muscle from LAMA2-CMD patients and mouse models. Reactive oxygen species (ROS) increase when oxygen homeostasis is not maintained and here, we investigate whether oxidative stress indeed is involved in the pathogenesis of LAMA2-CMD. We also analyse the effects of two antioxidant molecules, N-acetyl-L-cysteine (NAC) and vitamin E, on disease progression in the dy2J/dy2J mouse model of LAMA2-CMD. We demonstrate increased ROS levels in LAMA2-CMD mouse and patient skeletal muscle. Furthermore, NAC treatment (150 mg/kg IP for 6 days/week during 3 weeks) led to muscle force loss prevention, reduced central nucleation and decreased the occurrence of apoptosis, inflammation, fibrosis and oxidative stress in LAMA2-CMD muscle. In addition, vitamin E (40 mg/kg oral gavage for 6 days/week during 2 weeks) improved morphological features and reduced inflammation and ROS levels in dy2J/dy2J skeletal muscle. We suggest that NAC and to some extent vitamin E might be potential future supportive treatments for LAMA2-CMD as they improve numerous pathological hallmarks of LAMA2-CMD.
ARTICLE | doi:10.20944/preprints201904.0329.v2
Subject: Biology And Life Sciences, Plant Sciences Keywords: Cistanthe; Chilean floristic region; species; specioids; taxonomy; nomenclature
Online: 6 May 2019 (09:37:06 CEST)
Cistanthe subspeciosa Hershk. (Cistanthe Spach sect. Cistanthe; Montiaceae) here is described as a herbaceous to suffruticose perennial from the vicinity of Copiapó, Chile. Its epithet is juxtaposed with its rank in order to highlight its subspecific aesthetic. In particular, the specioid is infrequent, locally restricted, and lacks unique diagnostic traits. Rather, it is diagnosed by a combination of traits characteristic of different Cistanthe species from the region, none of which can be identified as the referential species to which Cs. subspeciosa might be considered subspecific. The intersection between species nomenclature and species ontology thus is discussed. I hypothesize that Cs. subspeciosa is irrigated primarily by mountain runoff rather than localized precipitation, and that it might be both resistant to and dependent upon high substrate metal concentrations characteristic of the Copiapó region. The ornamental value of this and other Cistanthe species is discussed. Finally, additional historical details pertaining to Calandrinia spectabilis Otto & Dietr. and Cistanthe philhershkovitziana are provided.
ARTICLE | doi:10.20944/preprints201812.0151.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Peripatidae, conservation status, survival, urban populations, threatened species
Online: 12 December 2018 (14:07:09 CET)
ABSTRACT: Charismatic species, like the panda, play an important role in conservation, and velvet worms arguably are charismatic worms. Thanks to their extraordinary hunting mechanism, they have inspired from a female metal band in Japan, to origami worms in Russia and video game monsters in the USA. Objective: To assess their conservation status in Costa Rica. Methods: we located all collection records of the 29 known species from the Onychophora Database in the map of the Costa Rican Conservation Network. Results: We found that seven species are protected inside forest reserves, five in Protected Zones, four in Wildlife Refuges, two in National Parks and one, Principapillatus hitoyensis, in a strictly pristine Biological Reserve. The largest species in the world, Peripatus solorzanoi, occurs both inside a Forest Reserve and in protected private land. Protection inside Costa Rican nature areas is enforced year round by personnel that includes armed guards, and is supported by educational programs in surrounding communities. Twelve species have not been found in protected areas, but in Costa Rica, all biological species, named and unnamed, are protected by law and cannot be legally collected, or exported, without technically issued permits. Conclusion: Like in the only other country with similar information (New Zealand), the conservation of onychophorans seems to be of least concern for at least two thirds of the known species. Epiperipatus isthmicola, recently rediscovered after a century of absence in collections, can be considered Threatened because nearly all of its natural habitat has now been covered by a city.
ARTICLE | doi:10.20944/preprints201810.0587.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: CITES; chikanda; conservation; DNA barcoding; orchids; species delimitation
Online: 25 October 2018 (05:10:27 CEST)
In Zambia wild edible terrestrial orchids are used to produce a local delicacy called chikanda, which has become increasingly popular throughout the country. Commercialization puts orchid populations in Zambia and neighbouring countries at risk of overharvesting. Hitherto, no study has documented which orchid species are traded on local markets, as orchid tubers are difficult to identify morphologically. In this study, the core land-plant DNA barcoding markers rbcL and matK were used in combination with nrITS to determine which species were sold on Zambian markets. Eighty-two interviews were conducted to determine harvesting areas, as well as possible sustainability concerns. By using nrITS DNA barcoding, a total of 16 orchid species in six different genera could be identified. Both rbcL and matK proved suitable to identify the tubers up to genus- or family level. Disa robusta, Platycoryne crocea and Satyrium buchananii were identified most frequently and three previously undocumented species were encountered on the market. Few orchid species are currently listed on the global IUCN Red List. Local orchid populations and endemic species could be at risk of overharvesting due to the intensive and indiscriminate harvesting of chikanda orchids and we therefore encourage increased conservation assessment of terrestrial African orchids.
ARTICLE | doi:10.20944/preprints201807.0042.v1
Subject: Biology And Life Sciences, Forestry Keywords: species, edible, food bearing, diversity, neighborhoods, urban forest
Online: 3 July 2018 (12:10:53 CEST)
In Africa, 80% of households in urban areas are food insecure and is coupled with a dramatically changing urban food culture towards increased consumption of sugary and fatty foods. Consequently, incidences of obesity and undernourishment in many African cities are becoming escalating. Urban and peri-urban forestry emerges as a complementary measure to contribute towards elimination of urban hunger and improved nutritional security. However, there is scanty knowledge about the composition, diversity and socioeconomic contributions of urban food trees in African cities and this hinders policy discussions integrating urban forestry into the food security discourse. This paper examines the diversity and composition of the urban forest and food trees of Accra and sheds light on perceptions of urbanites regarding food tree cultivation and availability in the city. Using a mixed methods approach, about 105 respondents in six neighbourhoods of Accra were interviewed while over 200 100-m2 plots were surveyed across five land use types. Twenty-two out of the 70 woody species in Accra are edible. The food tree abundance in the city is about half of the total number of trees enumerated. The species richness and abundance of the edible trees and all trees in the city were significantly different among land use types (p<0.0001) and neighbourhood types (p<0.0001). The diversity of food bearing tree species was much higher in the poorer neighbourhoods than in the wealthier neighbourhoods. Respondents in wealthier neighbourhoods indicated that tree and fruit tree cover of the city was generally low and showed greater interests in cultivating fruit trees and expanding urban forest cover than poorer neighbourhoods. These findings demonstrate the need for urban food policy reforms that integrate urban grown tree foods in the urban food system/culture.
ARTICLE | doi:10.20944/preprints201805.0453.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Photodynamic inactivation, reactive oxygen species, chitosan, cell wall
Online: 30 May 2018 (16:19:51 CEST)
Photodynamic inactivation (PDI) combines the nontoxic photosensitizer (PS) and visible light to generate reactive oxygen species (ROS), which can cause oxidative damages in (on) microbial organisms. Previously, we have shown that chitosan can augment the bactericidal efficacy mediated by PDI against bacteria and Candida. In this study, we showed that the antimicrobial action of chitosan to augment PDI relates to the enlargement of cell surface destruction. The microbial cell surfaces exhibit severe irregular shapes after PDI in the presence of chitosan. Furthermore, increase in the concentrations or incubation time of chitosan significantly reduce the amounts of photosensitizers TBO required, indicating that chitosan could be a synergistic agent with PDI against human pathogens. A prolonged lag phase was found in PDI surviving microbial cells, in which chitosan can act to synergistically eradicate the cells. Once the impaired cells rebuild their cellular functions from PDI-induced damage, the increased cytotoxic effect of chitosan disappeared. Together, our results suggest that chitosan with an augmented bactericidal activity after PDI is to inhibit the rehabilitation of PDI surviving cells, leading to microbial death.
ARTICLE | doi:10.20944/preprints202311.1446.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Brassinosteroids; Orobanche cumana; Reactive oxygen species; Sunflower; Antioxidants defense
Online: 23 November 2023 (09:42:08 CET)
Broomrape (Orobanche cumana), root parasitic weed, negatively affects sunflower, thereby causing severe yield losses and required controls on O. cumana infestation. Brassinosteroids (BRs) plays key roles in plant growth and provides resilience to weed infection. This designed study evaluated the mechanisms by which BRs ameliorates O. cumana infection in sunflower (Helianthus annuus). The pretreatment of sunflower seeds with various concentrations of BRs (1, 10, and 100 nM) were applied with and without O. cumana infestation. Under O. cumana infection, a significant reduction in plant height (38.61%), fresh/dry biomass, photosynthesis and regulation in plant defense (POX, GST), BRs signaling (BAK1, BSK1 to BSK4) and synthesis (BRI1, BR6OX2) associated genes. Moreover, O. cumana elevated the levels of MDA, OH‒, H2O2 and O2•‒ in leaves/roots by 77%/112%, 62%/104%, 57%/98% and 55%/89.4% and caused ultrastructural damages in leaves/roots, suggesting the severe oxidative or cellular damages in sunflower. In response, plants activate activities of SOD and POD enzymes as well as reduced or oxidized glutathione, but unable to stimulate APX and CAT activities. Addition of BRs, especially at 10 nM notably lowered the production of oxidative stress, activated the enzymatic and non-enzymatic antioxidants. The downregulation in the reported genes by BRs attributed to the increased resilience of sunflower (via susceptible reaction). In nutshell, the pretreatment of BRs enhanced the sunflower resistance to O. cumana infection by improving the planta growth and biomass, photosynthesis, activating the antioxidant defense system, lowering the oxidative stress, cellular damages and modulating the expression of BR synthesis and signaling genes.
ARTICLE | doi:10.20944/preprints202311.1415.v1
Subject: Biology And Life Sciences, Aquatic Science Keywords: Plastic pollution; biodiversity; entanglement; ingestion; endangered species; digital media
Online: 22 November 2023 (12:18:25 CET)
Abandoned, lost, or otherwise discarded fishing gear (ALDFG) is a primary contributor to the entanglement of numerous marine species. Utilizing digital media platforms like Google, Facebook, and Instagram we conducted an assessment of the detrimental effects of ALDFG and plastic litter, on the biodiversity of Italy's marine ecosystem. Our investigation revealed that plastic litter has adverse consequences on various forms of marine life, including reptiles, mammals, birds, fish, crustaceans, and mollusks, along different Italian geographical sub-areas. Several records of interaction between plastic and endangered and vulnerable marine species have been described. Our reports even highlight the impact on marine turtles, mainly on Caretta caretta. This is the first report of entangled with fishing nets in Cetorhinus maximus, Oblada melanura, Serranus scriba, Homarus gammarus, Octopus vulgaris, and Phoenicopterus roseus. Furthermore, we identified that ghost nets have repercussions for endangered and vulnerable marine species. This update sheds light on the ongoing adverse effects of ghost nets on the Italian marine ecosystem, yet it is crucial to acknowledge that the true extent of the problem remains underestimated.
ARTICLE | doi:10.20944/preprints202311.0985.v1
Subject: Biology And Life Sciences, Forestry Keywords: Forest resilience; invasive species; impacts; silvopastoral systems; sustainable management
Online: 15 November 2023 (09:35:35 CET)
Forest management aims to preserve ecosystem integrity, maintaining resilience thresholds. For this, conservation and invasion patterns must be determined in managed landscapes. The objective was to identify proxies (landscape and environmental patterns) that allowed the plant species invasion and define thresholds of human impacts to improve management practices. We also want to identify indicator species for the different kinds of impacts and environments. 165 plots were measured in Nothofagus antarctica forests and associated open-lands (dry and wet grasslands) in Tierra del Fuego (Argentina). We found differences in the studied variables across landscape and among different uses and impact types. Human impacts influenced over land types, emphasizing the importance of managing intensities. Indicator plant species allowed to identify potential ecological thresholds related to human impacts and the establishment of species linked to ecological and economic degradation, e.g. Bolax gummifera and Azorella trifurcata were associated with high grazing pressure in grasslands and fire in forested areas, while Rumex acetosella and Achillea millefolium, typically associated with forested areas, were related to high harvesting pressure and fire impacts. These findings contribute to understanding the long-term effects of some impacts, and allow us to define variables of monitoring and indicator species for each impact type.
ARTICLE | doi:10.20944/preprints202311.0016.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: macrobenthos; species diversity; community structure; Cosmonaut Se; Environmental factors
Online: 1 November 2023 (04:33:02 CET)
The Cosmonaut Sea is an under-studied area and a “blank canvas” for macrobenthos research. Here, we report on the species diversity and community structure of macrobenthos collected using the tringle trawl on the 38th Chinese National Antarctic Research Expedition (CHINARE) in the Cosmonaut Sea, East Antarctica. A total of 11 tringle trawls were deployed at different depths across the shelf, slope and seamount of the Cosmonaut Sea. A total of 275 macrobenthic species were found from 207-1994 m. The species richness per station varied from 23 to 89. Echinoderms (100 species), arthropods (48 species) and mollusks (36 species) were the most dominant groups. Echinoderms and arthropods dominated in abundance at seamount stations, and echinoderms, arthropods and polychaetes dominated in abundance at slope stations, while bryozoans, corals, ascidians and sponges were abundant on the Cosmonaut Sea Shelf. Depth was the major driving force influencing the distribution of macrobenthos. The main components were two core communities. One was dominated by sessile suspension feeders and associated fauna. Variants of this community include sponges and bryozoans. The other core community was dominated by mobile deposit feeders, infauna and grazers–epifauna, which included arthropods and echinoderms. The results showed that the slope (40-50° E, 65-67° S) of the Cosmonaut Sea may be an important area with complex ecological processes. The results of this study contribute to the knowledge of species diversity and communities of macrobenthos in the Cosmonaut Sea and provide monitoring data for future ecosystem health assessments and better protection.
ARTICLE | doi:10.20944/preprints202309.1673.v1
Subject: Environmental And Earth Sciences, Ecology Keywords: tree organs; urban tree species; rainwater interception capacity; Shanghai
Online: 25 September 2023 (11:09:25 CEST)
The process of rainfall interception by tree organs is crucial in mitigating the impact of intense rainfall on urban drainage systems, particularly in the context of climate change. this study selected ten commonly found tree species in Shanghai. Main parts of trees, including leaves, branches, and bark, were collected to analyze their ability to intercept rainwater. The optimized Artificial Rainfall Simulation System (ARSS) was applied to simulate the rainfall. The time-changing process of rainwater interception in three organs was measured during a 180-minute rainfall event which under four different rainfall intensities (4, 8, 12, and 16 mm/h, respectively). Process models of rainwater interception in different organs were fitted with adsorption kinetic equations. The rainwater interception process of tree organs complied with the quasi 2nd-order adsorption kinetic equation. The rainwater interception capacity of leaves, branches, and bark of ten urban tree species ranged from 0.05 to 0.34 mm, 0.13 to 0.24 mm, and 0.29 to 1.22 mm, respectively. The rainwater interception capacity of three organs significantly differs (p<0.05). It reveals that bark exhibits the highest rainwater interception ability. Coniferous tree species have a greater ability to intercept rainwater than broad-leaved tree species. There are also differences in the rainwater interception ability of trees in urban and natural areas.
REVIEW | doi:10.20944/preprints202306.2234.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: atopic dermatitis; antioxidant agents; oxidative stress; reactive oxygen species
Online: 3 July 2023 (03:12:41 CEST)
Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by itching, impaired epidermal barrier function and unbalanced inflammatory response. The pathophysiology involves immune dysregulation, with a predominance of T-helper 2 cells. AD is triggered by many known and unknown factors, including oxidative stress. Reactive oxygen species (ROS) contribute to AD pathogenesis by causing cellular damage and inflammation. Moreover, increased oxidative stress in AD leads to hyperactivation of the MAP kinase pathway, extracellular signal-regulated kinase (ERK) and p38, with DNA damage and subsequent skin barrier dysfunction. This narrative review provides a comprehensive overview of the role of natural antioxidant compounds, highlighting their potential therapeutic value in AD management. They include vitamin D, vitamin E, pyridoxine (vitamin B6), Vitamin C, carotenoids and melatonin, in AD. Despite some studies have shown an association between vitamin D, vitamin E, vitamin C and carotenoids levels and AD course, conflicting results exist. Pyridoxine supplementation has shown mixed results, and melatonin has demonstrated antioxidant and anti-inflammatory properties in AD; in fact, melatonin treatment resulted in a decrease in symptoms in patients with AD, although no significant correlation with changes in sleep latency was reported. In addition, iron and zinc (Zn) supplementation can also improve AD symptoms. Further research is needed to elucidate the optimal use of these natural antioxidants in AD treatment
REVIEW | doi:10.20944/preprints202306.1706.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Antioxidant activity; autopolyploidy; legumes; salinity stress; reactive oxygen species.
Online: 25 June 2023 (03:41:56 CEST)
Salinity stress affect plant growth and development by causing osmotic stress, and nutrient imbalances through excess Na+, K+ and Cl- ion accumulations that induce toxic effects during germination, seedling development, vegetative growth, flowering, and fruit set. However, the effects of salt stress on such processes, especially in polyploidised leguminous plants remains unexplored and scantly reported compared to their diploid counterparts. This paper discusses the physiological and molecular response of legumes towards salinity stress based osmotic and ionic imbalances in plant cells. A multigenic response involving various compatible solutes, osmolytes, ROS, polyamines and antioxidant activity, together with genes encoding proteins involved in the signal transduction, regulation and response mechanisms to this stress were identified and discussed. This discussion reaffirms polyploidisation as the driving force in plant evolution and adaptation to environmental stress constraints such as drought, feverish temperatures, and in particular, salt stress. As a result, thorough physiological and molecular elucidation of the role of gene duplication through induced autopolyploidisation and possible mechanisms regulating salinity stress tolerance in grain legumes must be further studied.
ARTICLE | doi:10.20944/preprints202306.0212.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Cheiridiidae; False scorpions; Levant; Species List; Syarinidae; Taxonomy; Zoogeography
Online: 2 June 2023 (14:16:19 CEST)
The location of Israel at the junction of three continents leads to a unique faunal combination of Palearctic and Afrotropic zoogeographic origins. Following systematic revisions over the past sixty years and the discovery of new species, the only available key to the pseudoscorpions (Arachnida: Pseudoscorpiones) of Israel (Beier 1963) has become outdated. We provide here an up-to-date checklist of the pseudoscorpion species of Israel including distribution maps, and the first illustrated identification key of the Israeli fauna based on morphological characters. Prior to our study this fauna comprised twelve families, 26 genera and 52 morphospecies, including several “subspecies”. We increase this number and list 61 pseudoscorpion morphospecies that belong to 28 genera and fourteen families. Most species are Palearctic and Mediterranean, and only a few are Afrotropic. Two families new to Israel are reported here for the first time: Syarinidae and Cheiridiidae. Both families are cosmopolitan and have representatives in the Mediterranean region. The putative new species are presented here at a genus level and will be described separately elsewhere.
ARTICLE | doi:10.20944/preprints202306.0088.v1
Subject: Biology And Life Sciences, Virology Keywords: Canine; feline; chaphamaparvovirus; codon usage; phylogenetic; cross-species transmission
Online: 1 June 2023 (12:26:50 CEST)
Chaphamaparvovirus (ChPV) is an ancient virus that has been detected in a variety of hosts. In this study, based on the phylogenetic analysis and the adaptability of ChPV to multiple hosts, we evaluated the potential of feline (FeChPV) and canine ChPV (CaChPV) for cross-species transmis-sion. Phylogenetic analysis showed that FeChPV and CaChPV were closely related. Notably, two strains of ChPVs isolated from domestic cats and 2 from dogs clustered together with CaChPVs and FeChPVs, respectively, suggesting the stringent boundaries between canine and feline ChPV may be broken. Further analysis revealed that CaChPV and FeChPV were more adapted to dogs than to cats, strongly suggesting the possibility of unidirectional or bidirectional transmission be-tween dogs and cats. Mutation analysis identified several shared mutations in cross-species-transmissible strains that were not located within immune epitopes. Furthermore, the VP struc-tures of FeChPV and CaChPV exhibited a high degree of similarity across both cross-species-transmissible and non-cross-species-transmissible strains. However, definitive experimental evi-dence is lacking, and its capacity for cross-species transmission should be approached with cau-tion and elucidated in further studies.
ARTICLE | doi:10.20944/preprints202305.0238.v1
Subject: Environmental And Earth Sciences, Pollution Keywords: wastewater; river water; groundwater; migration species; bottom sediments; modeling
Online: 4 May 2023 (08:36:06 CEST)
The development of mineral deposits causes changes that are comparable to natural exogenous geological processes, and in local areas of intensive mining activity prevail over them. In this article, a diamond deposit is selected, developed by quarries of great depth, and a forecast is made of the impact of drainage water discharge on changes in the composition of surface water and bottom sediments during the entire period of development of the deposit. Modeling was per-formed according to various scenarios, taking into account changes in the total dissolved solids of groundwater from 0.5 to 21.7 g/kg H2O. Thermodynamic calculations were carried out using the HCh software package. The role of dissolved organic carbon in the migration of chemical elements and the effect of DOC on the precipitation of chemical elements from mixing solutions is given. It has been established that fulvic acid completely binds to Fe in the Fe(OH)2FA– complex in all types of natural waters and under all mixing scenarios. With humic acid, such a sharp competitive complex formation does not occur. It is distributed among the various elements more evenly. It was determined that the mass of precipitating iron in the presence of DOC decreases by 18-27%, and its precipitation in winter is more intense. In contrast to Fe, precipitation of Ca, Mg, and C from solution with DOC is higher in summer, and there are more of them in solution in winter. This study contributed to a better understanding of the behavior of heavy metals in surface waters and sediments under anthropogenic pressures in order to improve the sustainable management of water resources in the face of anthropogenic activities.
REVIEW | doi:10.20944/preprints202304.0367.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: species distribution modeling; machine learning; MaxEnt; bryophytes; climatic change
Online: 14 April 2023 (10:35:42 CEST)
Species distribution modeling (SDM) has come a long way since its inception. Starting as simple bioclimatic envelope models based on expert knowledge, species distribution models (SDMs) have evolved into complex and sophisticated models that incorporate multiple sources of data and machine learning algorithms. Today, SDMs play a crucial role in addressing pressing conservation and management issues, including the impacts of climate change on species ranges and the as-sessment of species vulnerability to extinction. In this article, we will embark on a journey through the history, present, and future of SDM, exploring its evolution from bioclimatic envelopes to machine learning. We will also provide practical tips on how to use SDMs effectively and discuss the exciting future developments in this field. Whether you are a seasoned SDM expert or new to this field, this article will provide valuable insights into the exciting world of SDM. By exploring the rich history and current state of the field, we hope to shed light on the tremendous potential of SDM for improving our understanding of the distribution of species in a changing world.
ARTICLE | doi:10.20944/preprints202304.0047.v1
Subject: Biology And Life Sciences, Parasitology Keywords: Invasive species; eosinophilic meningoencephalitis; cytochrome c oxidase subunit I
Online: 4 April 2023 (14:31:38 CEST)
The nematode Angiostrongylus cantonensis has been reported worldwide, however, some basic questions remain unanswered about the presence of A. cantonensis in Ecua-dor: 1) Was the invasion of A. cantonensis in Ecuador unique, or did it occur in different waves? 2) Was this invasion as recent as historical records suggest? 3) Did this inva-sion come from other regions of South America or elsewhere? To address these issues, we assessed the genetic diversity of MT-CO1 gene sequences from isolates obtained in eleven of Ecuador's 24 provinces. Our Bayesian inference phylogenetic tree recovered A. cantonensis as a well-supported monophyletic group. All eleven sequences from Ec-uador were identical and identified as AC17a. The haplotype AC17a, found in Ecuador and the USA, formed a cluster with AC17b (USA); AC13 (Thailand); and AC12a-b (Cambodia). It is notable that all the samples, obtained in different geographic and climatic regions of different Ecuadorian provinces, had no genetic difference between them. Despite the lack of genetic information on A. cantonensis in Latin America, ex-cept in Brazil, our finding differs from previous studies by its absence of genetic diver-sity in Ecuador. We concluded that the invasion of A. cantonensis in Ecuador may have occurred: 1) as a one-time event, 2) recently, and 3) from Asia via the USA. Further re-search should include samples from countries neighboring Ecuador to delve deeper in-to this.
ARTICLE | doi:10.20944/preprints202211.0490.v2
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Ticks; species distribution models; habitat suitability models; Illinois; climate
Online: 6 February 2023 (03:09:45 CET)
The greater U.S. Midwest is on the leading edge of tick and tick-borne disease (TBD) expansion, with tick and TBD encroachment into Illinois occurring from both the northern and the southern regions. To assess historical and future habitat suitability of four ticks of medical concern within the state, we fit individual and mean-weighted ensemble species distribution models for Ixodes scapularis, Amblyomma americanum, Dermacentor variabilis, and a newly invading species, Amblyomma maculatum using a variety of landscape and mean climate variables for the periods of 1970-2000, 2041-2060, and 2061-2080. Ensemble model projections for the historical climate were consistent with known distributions of each species but predicted the habitat suitability of A. maculatum to be much greater throughout Illinois than what known distributions demonstrate. Presence of forest and wetlands were the most important landcover classes predicting occurrence of all tick species. As the climate warmed, the expected distribution of all species became strongly responsive to precipitation and temperature variables, particularly precipitation of the warmest quarter and mean diurnal range, as well as proximity to forest cover and water sources. The suitable habitat all species was predicted to shrink in the 2050 climate scenario, and then increase more broadly statewide in the 2070 scenario, but at reduced likelihoods. Predicting where ticks may invade and concentrate as the climate changes will be important to anticipate, prevent, and treat TBD in Illinois.
ARTICLE | doi:10.20944/preprints202212.0379.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Permafrost, Subarctic, thermokarst lakes, zooplankton, species composition, trophic structure
Online: 21 December 2022 (03:30:38 CET)
Environmental physical and chemical factors controlling the abundance and biodiversity of zooplankton in permafrost-affected lakes are poorly known yet they determine the response of the ecosystems to on-going climate change and water warming. Here we assessed the current status of zooplankton communities of lake ecosystems in the North-West of the Bolshezemelskaya tundra (Nenets Autonomous district), and provide new information about the composition and structure of zooplankton. Results demonstrate that the structure of zooplankton communities is influenced by morphometric features of lakes and the degree of their overgrowth by macrophytes. According to the level of zooplankton development, most tundra lakes were of the oligotrophic type with an average biomass of up to 1 g/m3. The largest number of species was observed in zooplankton communities of small lakes with an area of up to 0.02 km2 and overgrown with macrophytes. The analysis of factors that influence the formation of the lakes zoocenosis demonstrated that the species composition and quantitative characteristics of zooplankton are chiefly controlled by pH and water mineralization. A comparison of the results obtained with the literature data on the lakes of this region collected 60 years ago confirms that the ecosystems of the studied lakes are in a stable state. Overall, these new insights will improve our knowledge of factors controlling the zooplankton spatial dynamics in unique but quite abundant thermokarst lakes of NE European Tundra, subjected to on-going climate warming.
REVIEW | doi:10.20944/preprints202208.0396.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: non-indigenous species; ballast water; Greek seas; Mediterranean Sea
Online: 23 August 2022 (05:28:17 CEST)
The Greek seas as a part of the Eastern Mediterranean Sea, have been considered as a hotspot for the entrance of non-indigenous species (NIS). Ballast water functions as a major pathway for the spread of NIS in new environments, posing significant threats to both the ecosystems and human health. Nine non-indigenous fish species, originating from the Red Sea, have been introduced to the Greek seas since 1925. Despite the implemented laws for limiting the spread of NIS and the subsequent impacts, current global environmental issues, such as climate change and micro-plastic pollution, could result in a rapid spread and establishment of NIS in hot-spot regions, including the Greek seas. A more systematic use of advanced tools for the systematic monitoring of all NIS in the Mediterranean Sea is necessary.
REVIEW | doi:10.20944/preprints202204.0117.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: cold stress; wheat; hormonal; reactive oxygen species; epigenetic regulation
Online: 13 April 2022 (07:35:35 CEST)
Cold stress is a major environmental factor affecting the growth, development, and productivity of various crop species. With the current trajectory of global climate change, low temperatures are becoming more frequent and can significantly decrease crop yield. Wheat (Triticum aestivum L.) is the first crop to be domesticated and is the most popular cereal crop in the world. Due to a lack of systematic research on cold response pathways and gene regulatory networks, the underlying molecular mechanisms of cold signal transduction in wheat are poorly understood. This study reviews recent progress in wheat, including the ICE-CBF-COR signaling pathway in cold stress and the effects of cold stress on hormonal pathways, reactive oxygen species (ROS), and epigenetic regulation. This review also highlights outstanding issues that are crucial for understanding the interactions between wheat and low-temperature conditions.
ARTICLE | doi:10.20944/preprints202204.0029.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Lacticaseibacillus species; probiotic potential; genetic traits; presence in genomes
Online: 6 April 2022 (04:54:20 CEST)
This study aimed to exploring the intra-species distribution of genetic characters that favor the persistence in the gastrointestinal tract (GIT) and host interaction of bacteria belonging to the species Lacticaseibacillus genus. These bacterial species comprise commercial probiotics with the widest use among consumers and strains naturally occurring in GIT and in fermented food. Since little is known on the distribution of genetic traits for adhesion capacity, polysaccharide production, biofilm formation, utilization of substrates critically important for survival in GIT, that influence probiotic characteristics, a list of genetic determinants involved in such functions was created by a search for specific genes involved in the above aspects in the genome the extensively characterized probiotic L. rhamnosus GG. The presence/absence and variability of each gene in other Lacticaseibacillus spp. genomes was assessed by alignment with the publicly available fully annotated genome sequences. Eighty-two gene loci were compared, and 49 of these were found to be absent in some genomes in a species or strain-specific mode. A set of genes was found to be conserved, indicating that all strains of the genus may exert some probiotic effects. Among the variable loci a taurine utilization operon and a α-L-fucosidase were examined for presence/absence in 26 strains isolated from infant feces by PCR based tests. Results were variable among the isolates, though their common origin indicated the capacity to survive in the intestinal niche. This study indicated that the capacity to exert probiotic actions of Lacticaseibacillus spp. depends on a conserved set of genes and is enhanced by variable genetic factors whose role is only in part elucidated. The selection of strains of the most promising probiotic candidates to be used in food is feasible by analyzing presence/absence of a set of variable traits.
ARTICLE | doi:10.20944/preprints202112.0354.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: whole genome sequencing; cancer predisposition; mucin; reactive oxygen species
Online: 22 December 2021 (11:44:20 CET)
Familial colorectal cancer (CRC) is only partially explained by known germline predisposing genes. We performed whole genome sequencing in 15 Polish families of many affected individuals, without mutations in known CRC predisposing genes. We focused on loss-of-function variants and functionally characterized them. We identified a frameshift variant in the CYBA gene (c.246delC) in one family and a splice site variant in the TRPM4 gene (c.25-1 G>T) in another family. While both variants were absent or extremely rare in gene variant databases, we identified four additional Polish familial CRC cases and two healthy elderly individuals with the CYBA variant (odds ratio 2.46, 95% confidence interval 0.48-12.69). Both variants led to a premature stop codon and to a truncated protein. Functional characterization of the variants showed that knockdown of CYBA or TRPM4 depressed generation of reactive oxygen species (ROS) in LS174T and HT-29 cell lines. Knockdown of TRPM4 resulted in decreased MUC2 protein production. CYBA encodes a component in the NADPH oxidase system which generates ROS and controls, e.g., bacterial colonization in the gut. Germline CYBA variants are associated with early onset inflammatory bowel disease, supported with experimental evidence on loss of intestinal mucus barrier function due to ROS deficiency. TRPM4 encodes a calcium-activated ion channel, which in a human colonic cancer cell line controls calcium-mediated secretion of MUC2, a major component of intestinal mucus barrier. We suggest that the gene defects in CYBA and TRPM4 mechanistically involve intestinal barrier integrity through ROS and mucus biology, which converges in chronic bowel inflammation.
ARTICLE | doi:10.20944/preprints202111.0113.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Body-size; Cerrado; Evolutionary history; Nymphalidae; Phylogeny; Species traits
Online: 5 November 2021 (10:35:29 CET)
Introduction: Body size is correlated with many aspects of an animal species' natural history, such as life span, abundance, dispersal capacity and diet breadth. However, contrasting trends have been reported for the relationship between body size and these ecological traits. Methods: Butterfly species from fruit-feeding guilds were used to investigate whether body size correlates with species abundances, dispersal, permanence, and diet breadth in a Neotropical savanna in Brazil (Cerrado). We used Blomberg’s K and Phylogenetic Generalized Least Squares models (PGLS) to measure phylogenetic signal strength in species traits, and to estimate size-dispersal-diet breadth associations while taking shared ancestry into account. Results: 539 individuals from 27 species were captured, and 190 individuals were recaptured, representing a 35% recapture rate. We found that body size negatively influenced butterfly abundance. In contrast, body size was positively associated with dispersal levels, distance traveled, number of traps visited, individual permanence, and diet breadth. These results indicate that larger butterflies have a greater proportion of dispersing individuals over longer distances, as they permanence were detected over longer periods than their smaller relatives. Moreover, larger butterflies are more generalized, based on the number of host plant families and genera they consume. Smaller butterflies demand fewer resources, which is reflected in their higher survival in small patches, and may explain their lower dispersal ability, and higher diet specialization. Nevertheless, lower dispersal ability, if not compensated by large population sizes, may threaten small-bodied species inhabiting environments with intense deforestation rates, such as the Cerrado. Conclusions: Body size positively influences dispersal and diet breadth in the fruit-feeding butterflies collected in this study.
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Amphipoda; invasive species; population genetics; miogenome; Ponto-Caspian; SNP
Online: 7 September 2021 (10:56:34 CEST)
The Ponto-Caspian region is the main donor of invasive amphipods to freshwater ecosystems, with at least 13 species successfully established in European inland waters. Dikerogammarus spp. and Pontogammarus robustoides are among the most successful, due to their strong invasive impact on local biota. However, genomic knowledge on these invaders is scarce, while phylogeography and population genetics have been based on short fragments of mitochondrial markers or nuclear mi-crosatellites. In this study, we provide: (i) reconstruction of four mitogenomes for four invasive gammarids; (ii) comparison between the structure of the newly obtained mitogenomes and to those from literature; (iii) SNP calling rates for individual D. villosus and D. haemobaphes from different invasion sites across Europe; and (iv) the first time-calibrated full mitogenome reconstruction of several Ponto-Caspian taxa. We have sequenced, assembled and annotated four mitogenomes, each from D. villosus, D. hae-mobaphes, D. bispinosus and Pontogammarus robustoides. We found that, in comparison to other gammarids, the mitogenomes of Ponto-Caspian species show a translocation between the tRNA-E and tRNA-R positions. Phylogenetic reconstruction using the mitogenomes identified that Ponto-Caspian gammarids form a well-supported group that originated in the Miocene. Our study supports paraphyly in the family Gammaridae. These mitogenomes serve as vital genetic resources for the development of new markers for PCR-based identification methods and demographic studies.
ARTICLE | doi:10.20944/preprints202108.0480.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Leptospira; bats; Colombia; leptospirosis; species; type; 16S ribosomal gene
Online: 25 August 2021 (09:54:58 CEST)
Leptospirosis is a globally distributed zoonotic disease caused by pathogenic bacteria of the genus Leptospira. This zoonotic disease affects humans, domestic, or wild animals. Colombia is considered an endemic country for leptospirosis; and Antioquia is the second department in Colombia with the highest number of reported leptospirosis cases. Currently, many studies report bats as reservoirs of Leptospira spp. but its prevalence in these mammals is unknown. In the present study we aimed to better understand the role of bats as reservoir hosts of Leptospira species and to evaluate the genetic diversity of circulating Leptospira species in Antioquia-Colombia. We captured 206 bats in the municipalities of Chigorodó (43 bats), Carepa (43 bats), Apartadó (39 bats), Turbo (40 bats), and Necoclí (41 bats) in the Urabá region (Antioquia-Colombia). Twenty bats were positive for Leptospira spp. infection (20/206 - 9,70%) and the species of infected bats were Carollia perspicillata, Dermatura rava, Glossophaga soricina, Molossus molossus, Artibeus planirostris, and Uroderma convexum. These species have different feeding strategies such as frugivorous, insectivores, and nectarivores. The infecting Leptospira species identified were Leptospira borgpetersenii (3/20 – 15%), Leptospira alexanderi (2/20 – 10%), Leptospira noguchii (6/20 – 30%), Leptospira interrogans (3/2 – 15%), and Leptospira kirschneri (6/20 – 30%). The results of this research show the importance of bats in the epidemiology, ecology and evolution of Leptospira in this host-pathogen association. This is the first step in deciphering the role played by bats in the epidemiology of human leptospirosis in the endemic region of Uraba (Antioquia-Colombia).
ARTICLE | doi:10.20944/preprints202108.0424.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: hydrazone; Candida species; antifungal agents; Candida albicans; Candida glabrata
Online: 23 August 2021 (10:29:47 CEST)
The treatment of benzylidenemalononitriles 3a-c with phenylhydrazines 4a-n in refluxing ethanol did not provide pyrazole derivatives but furnished hydrazones 1a-o. The structure of hydrazones was secured by X-Ray analysis. Newly synthesized hydrazones 1a-o were tested against 8 Candida spp. strains in a dose response assay to determine the minimum inhibitory concentration (MIC99). Five compounds 1c, 1d, 1i, 1k and 1l were identified as promising antifungal agents against Candida spp. (C. albicans SC5314, C. glabrata, C. tropicalis, C. parapsilosis and C. glabrata (R azoles)) with MIC99 values ranging from 16 to 32 µg/mL. To further evaluate the antifungal potential of the active compounds, they have been assayed against a mammalian cell line HEK293 to determine general cell toxicity and on NCI-60 cancer cell lines panel, demonstrating selectivity antifungal activity over cytotoxicity.
ARTICLE | doi:10.20944/preprints202108.0356.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Land-use change; forest conversion; species loss; fragmentation; deforestation
Online: 17 August 2021 (10:10:09 CEST)
Remote sensing/GIS techniques are a versatile tool for x-raying serial forest structural changes in retrospect. It would be impossible to evaluate past occurrences and changes in forest extents in past decades at Effan Forest Reserve without non-conventional means. Therefore, we adopted remote sensing technology using Landsat images to evaluate land-use change and degradation rates in the area with a view to ascertaining causal factors for possible minimization of forest degradation in Effan Forest Reserve. Land-use/land-cover changes were analyzed using USGS-Landsat TM and ETM images of 1987, 2002, 2014 and 2019. Field-data were collected using handheld GPS receiver and spatial statistical analyses were conducted using the ground control points (GCPs). For inventory data, a systematic sampling technique was adopted using ten 1.05 km-transects at 500 m intervals. A total of 50 sample plots of 50 × 50 m were used. All tree species with Dbh ≥10 cm were enumerated. Nineteen tree species in ten families were encountered with Vitellaria paradoxa as the most-frequently occurring species in the area. IUCN-listed endangered Pterocarpus erinaceus, hitherto abundant in the area, was rarely encountered during the survey, while Vitellaria paradoxa is gradually shrinking, going the relative abundance in the area. The result further showed that primary and secondary forests decreased considerably by 258.03 ha (46.72%) and 9.18 ha (3.63%), respectively, with a total forest loss of 50.3% in 32 years (8.4 hayr-1, 1.6% per annum). While forest plantation size doubled by 369.72 ha within the period. This is worrisome as the remaining fragmented forests appeared to be on the decline, except the riparian vegetation, due to inaccessibility to the riparian by loggers. It thus appeared that forest protection approaches were ineffective. Increased protection efforts could save this forest reserve, and the concerned authority should consider a focused-enrichment planting involving indigenous species for ecosystem-repair.