ARTICLE | doi:10.20944/preprints202101.0189.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Portunus trituberculatu; climate change; species distribution model; suitable habitat
Online: 11 January 2021 (12:33:19 CET)
Species have shown their habital variations in responding to climate change, especially during the spring and summer spawning seasons. The species distribution model (SDM) is considered the most favorable tool to study the potential effects of climate change on species distribution. Therefore, we developed the ensemble SDM to predict the changes in species distribution of Portunus trituberculatus among different seasons in 2050 and 2100 under the climate scenarios RCP4.5 and RCP8.5. The results of SDM indicate that the distribution of this species will move northward and have obviouse seasonal variations. Meanwhile, the suitable habitat for the species will be significantly reduced in summer, with loses rates ranging from 45.23% (RCP4.5) to 88.26% (RCP.8.5) by 2100s. Habitat reduction will mainly occur in the East China Sea and southern part of the Yellow Sea, while there will be a small increase in the northern Bohai Sea. These findings will be important to manage the ecosystem and fishery, provide an information forecast of this species in the future, and maintain species diversity if the seawater temperature rises.
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.
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.
ARTICLE | doi:10.20944/preprints202008.0424.v1
Subject: Environmental And Earth Sciences, Oceanography Keywords: seagrass; fuzzy inference system; modeling; species abundance; Mediterranean Sea
Online: 20 August 2020 (04:39:47 CEST)
A Mamdani-type fuzzy-logic model has been developed to link Mediterranean seagrass abundance to the prevailing environmental conditions. Big Databases, as UNEP-WCMC (seagrass abundance), CMEMS and EMODnet (oceanographic/environmental) and human-impact parameters were utilized for this expert system. Model structure and input parameters were tested according to their capacity to accurately predict seagrass families at specific locations. The optimum FIS comprised of four input variables: water depth, sea surface temperature and nitrates and bottom chlorophyll-a concentration, exhibiting fair accuracy (76%). Results illustrated that Posidoniaceae prefers cool (16-18oC) and low chlorophyll-a presence (< 0.2 mg/m3); Zosteraceae favors cool (16-18oC) and mesotrophic waters (Chl-a > 0.2 mg/m3), but also slightly warmer (18-19.5 oC) with lower Chl-a levels (< 0.2 mg/m3); Cymodoceaceae lives from warm, oligotrophic (19.5-21.0oC and Chl-a < 0.3 mg/m3) to moderately warm mesotrophic sites (18-21.3oC and 0.3 – 0.4 mg/m3 Chl-a). Finally, Hydrocharitaceae thrives in warm Mediterranaean waters (21-23oC) of low chlorophyll-a content (< 0.25 mg/m3). Climate change scenarios showed that Posidoniaceae and Zosteraceae tolerate bathymetric changes, Posidoniaceae and Zosteraceae are mostly affected by sea temperature rise, while Hydrocharitaceae exhibits tolerance in higher sea temperature rise. This FIS could be used by national and regional policy-makers and public authorities.
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/preprints202010.0467.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Climate Change; Ethiopia; Hagenia abyssinica; MaxEnt; Species Distribution Model
Online: 22 October 2020 (21:38:10 CEST)
Research Highlights: Hagenia abyssinica is geographically localized, poor regenerated and endangered species in Ethiopia. Ethiopia has been experiencing variability of rainfall and rise in temperature due to the climate change. This study has hypothesized that the suitable areas for the species will be narrowed by the year 2070. Background and Objective The prediction of species distribution models help to implement appropriate conservation actions. The aim of this research was to identify the current and likely future distribution range and suitable areas for the species, and to determine the presence of H. absyssinica in risk in a short-term future. Material and method: To this end, occurrence data, bioclim variables, soil, elevation, and land cover map of Ethiopia were used. MaxEnt was used to predict distribution. Climate change impacts on the distribution of the species was performed using bioclimatic variables of the future climate data, 2070 (average for 2061-2080) was obtained from IPPC5 (CMIP5) at 30 seconds (1km) spatial resolution. The climate data was projected from GCMs, downscaled and calibrated using rcp4.5. Results: Both current and likely future distribution models were excellent and significantly better than random performance. This study has computed 59987 km2 to be the low impact area for the species under current conditions and will remain habitat under future climates and 39025 km2 area has been identified as the possible high impact areas or declining habitat. The model has also determined that 1238724 km2 of the areas are unsuitable at present and for future climates. The current study found that 15751 km2 of the area will be modified as a new suitable area for H. abyssinica due to climate change. Conclusion: Species distribution modeling is essential for the implementation of conservation actions that are compatible with the inevitable changing climatic conditions of the country.
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.
REVIEW | doi:10.20944/preprints201811.0517.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: distribution; species; wild chilli pepper; Capsicum annuum var. glabriusculum
Online: 21 November 2018 (06:45:41 CET)
Capsicum annuum var. glabriusculum, is a variety of wild chili pepper belonging to the family Solanaceae and is considered as the origin for all cultivated chili species of the world. This species is an important genetic resource for agriculture and food, is widely distributed in northeastern Mexico in altitudes from 0 – 1200 m.a.s.l. This species grows mainly at low altitudes and its upper limit reaches 1000m., it prefers temperatures above 18.3O C and its production and harvest may ocurr at two seasons, one during the beginning of the summer and the main one ocurring in the middle of the autumn in northeast México. It is estimated that the main production occurs in the state of Tamaulipas with 84 tons per year and is harvested from 23 municipalities. Concentration of capseicins and dihydrocapsaicine from wild populations may vary considerably from one location to another in the municipalities, ecotypes and diverse climatic conditions from this wide geographic zone. The high demands of wild chili as well as the variability on concentration of capseicins in fruits are considered as some of the main reasons why intensive cultivation of this species should be carried out in Northeastern Mexico.
ARTICLE | doi:10.20944/preprints202301.0253.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Selenium species; Maize plants; Se fractions; Rock-soil-plant interface; Selenium accumulation
Online: 13 January 2023 (10:55:32 CET)
Maize (Zea mays) is one of the most important staple food and primary source of livestock feed in the world. As the consumption of maize grown on the selenium-enriched soils of Naore Valley is one of the apparent causes of selenosis in the area, this work collected and analyzed total Se, Se fractions, and Se species distributions in maize plant samples, including grains, leaves, stalks, roots, rhizosphere soils, and the most representative parent rock materials from Naore Valley, Ziyang County, China. The Se distribution in soils markedly correlated with the weathered Se-enriched bedrocks, but most of the Se in the analyzed soils is enclosed as recalcitrant residual Se and organic-sulfide bound Se. In contrast, Se in rocks had a comparatively higher bioavailability and is bounded mainly to organic matter and sulfides minerals, with very few of the Se enclosed in the residual fraction. Maize plants might take a large amount of Se from the organic-sulfide bound Se fraction in the Se-rich soils, the weathered products from bedrocks or plant litters. Total Se concentrations in the collected samples were observed in descending order soil>leaf>root>grain>stalk. The predominant Se species detected in maize plants was SeMet. Se inorganic forms, mainly Se(VI), decreased from root to grain and were possibly assimilated into organic forms. Se (IV) was barely present. The natural increases in Se concentration affected mainly leaf and root dry-weight biomass as they are the organs that coped with the highest Se accumulation. This paper offers an insight into the uptake, accumulation, and distribution of Se forms in natural Se-rich maize crops and an opportunity for shifting Se-rich soils from menaces to valuable resources for growing Se-rich agricultural products.
ARTICLE | doi:10.20944/preprints202210.0020.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: The Fall Armyworm; Spodoptera frugiperda; invasive species; mapping distribution; DNA-barcoding
Online: 4 October 2022 (11:02:51 CEST)
Spodoptera frugiperda is an invasive pest that has spread in various parts of the world. These pests have the ability to spread and adapt highly to new habitats. Until now, it is not known with certainty the distribution of these invasive pests in Eastern Indonesia, especially Bali and Nusa Tenggara. This study aims to map the spatial distribution and genetic distribution of S. frugiperda which damages maize in the areas of Bali and Nusa Tenggara. This research was conducted using a survey method from May to September 2022 covering the islands of Bali, Lombok, Sumbawa, Sumba, Flores, and Timor. The results showed that S. frugiperda had spread evenly in Bali and Nusa Tenggara. The results of PCR amplification in the COI gene from 9 sample isolates from all research locations showed the similarity of DNA bands leading to the Spodoptera frugiperda species with a banding pattern length of 683 – 697. These results indicated that the distribution of genetic variants of corn caterpillars in Bali, NTB, and NTT was confirmed as S. frugiperda species. However, the isolated gene S. frugiferda, which was shown by the alignment results of the sequences from Lombok, was confirmed as a different strain from strains from Bali, Sumba, Sumbawa, Flores, and Timor. This incident can be seen from the difference in the protein base composition of S. frugiperda from Bali, Sumba, Sumbawa, Timor, and Flores. The results of phylogenetic analysis in this study confirmed 3 clusters of the genetic closeness of S. frugiperda. Cluster-1 comes from the results of the search for specimens of JB FAW and KB FAW from Bali, SB FAW and SB FAW Sorghum from Sumba, SW FAW from Sumbawa, KP FAW from Timor, and FL FAW from Flores. Cluster-2 is an isolate outside of our species. Cluster-3 comes from the search for LT and LS FAW specimens from Lombok. The genetic distance between cluster-1 and cluster-3 is quite far, which is 0.20 mu.
ARTICLE | doi:10.20944/preprints202305.0987.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: Maximum Entropy; species distribution model; ground validation; endemic; tree-frog; Protected Area; Biodiversity Hotspot
Online: 15 May 2023 (07:19:47 CEST)
Conservation of tropical endemic amphibians largely suffers from Wallacean shortfall, a gap to which predictive species distribution models have contributed significantly to bridge by delineating probable distribution and the underlying suitable habitat within their distributional range. However, rarely is a prediction model ground-truthed to evaluate their predictive performance. Here we present a species distribution modeling approach using maximum entropy algorithm corrected for smaller sample size, in guiding explorative surveys aimed at optimizing survey effort and discovering unrecorded populations of Zhangixalus suffry, a rhacophorid tree-frog endemic to the northeastern part of the Indian subcontinent along with the factors limiting their distribution. With only 16 established historical locality data to model for (after spatial thinning to reduce autocorrelation) and a set of environmental predictors (climatic, topographic, and landscape composition), our model prediction enabled the successful discovery of seven new population records from unreported landscapes, extending its southernmost distributional limit over a considerable distance. The final composite distribution model combining all the locality records (n=23) predicted similar core areas of suitable habitat consistent with the known geographic distribution of the species but showed poor representation under existing coverage of Protected Area (PA) network in the Region with only 7% representation of suitable habitat under protection. Habitat suitability of a site was significantly governed by factors related to precipitation (precipitation seasonality and precipitation of the warmest quarter) and topographic factors that can influence it (elevation and aspect). This corroborates with the known ecology of Rhacophorid frogs, especially concerning their seasonal explosive reproductive strategy and foam nest-building behavior.Through this study, we propose explorative surveys guided by species distribution models to expedite unknown population discovery of rare, tropical endemic amphibians and using such taxa as surrogates in identifying conservation priority zones that can be directly applied to reserve design and conservation and management planning.
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/preprints202305.0902.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: 2’-fucosyllactose, microglia polarization, anti-inflammation, reactive oxygen species, ischemic injury
Online: 12 May 2023 (08:11:06 CEST)
Cerebral ischemic stroke is one of the leading causes of death and disability worldwide. 2’-fucosyllactose (2’-FL), a human milk oligosaccharide, has anti-inflammatory effects and plays a protective role in arterial thrombosis, but its role in ischemic stroke remains unclear. This study aimed to investigate the neuroprotective effects of 2’-FL and its potential mechanisms in a mouse model of ischemic stroke. The administration of 2’-FL led to a reduction in the size of cerebral infarct and reactive oxygen species (ROS)-related products in the brain of MCAO mice. Further, 2’-FL promotes the recovery of neurological deficits and motor function in neurological scores and behavior tests. Biochemical studies showed that 2’-FL reduced upregulated IL-10 and downregu-lated TNF-α. Additionally,2’-FL enhanced M2-type microglial polar2’-FL upregulated IL-10 and downregulated TNF-α ization at 7 days after MCAO, with an increase in IL-4 levels and STAT6 activation at 3 days after MCAO. Our data showed that 2’-FL reduced the neurological symptoms of ischemic stroke and ROS accumulation in the brain through IL-4/STAT6-dependent M2-type mi-croglial polarization in MCAO mice. These results demonstrate that 2’-FL is a potentially effective therapeutic agent for ischemic stroke.
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/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/preprints202009.0286.v1
Subject: Computer Science And Mathematics, Applied Mathematics Keywords: strong solution; regularity of weak Solutions; a single-species ecosystem; Lyapunov function; Mountain Pass Lemma; unique existence
Online: 13 September 2020 (12:26:12 CEST)
In this paper, the authors employ Mountain Pass Lemma, the method of weak solution regularization and Lyapunov function method to derive the unique existence of globally exponential stable positive stationary solution of a single-species model with diffusion and delayed feedback. The obtained stability criterion illuminates that under some suitable conditions, a certain internal competition is conducive to the overall stability of the population, and a certain amount of family planning is conducive to the overall stability of the population. A numerical example and three tables show the effectiveness of the proposed methods.
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/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.
ARTICLE | doi:10.20944/preprints202101.0390.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: protein structure; relative solvent accessibility; secondary structure; phylogeny; models of sequence evolution; gene tree-species tree discordance; incomplete lineage sorting; Ctenophora; Porifera
Online: 19 January 2021 (16:46:25 CET)
Despite the long history of using protein sequences to infer the tree of life the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure; we test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of “strongly decisive” sites (alignment positions that support a specific tree topology) in a dataset comprising >1,500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology (ctenophores sister to other animals) regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments; buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies whereas solvent exposed and helix sites had unequal numbers of sites supporting the minority topologies. Given the plausible trees equal support for minority topologies is consistent with discordance among gene trees, making it possible the relatively slowly evolving buried (and sheet and coil) sites are giving an accurate picture of the true species tree as well as the amount of conflict among gene trees. Alternatively, the apparent support could reflect currently uncharacterized processes of molecular evolution. Regardless, it is clear that analyses of the deepest branches in the animal tree of life using sites in different structural environments are associated with a subtle data type effect that results in distinct phylogenetic signals.
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/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.
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/preprints202306.0413.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: PFAS; metabolism; transcriptomics; transcriptome; cross-species analysis
Online: 6 June 2023 (08:22:33 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 analyzed 2144 publicly available datasets from 7 distinct species to examine the molecular responses to PFAS exposure and 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 re-sponse to PFAS, such as ESR1, HADHA and ID1, as well as several pathways including lipid me-tabolism, 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 under-standing 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.
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.
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/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/preprints201807.0317.v3
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Boswellia serrata Roxb.; Curcuma longa L.; intestinal bowel diseases (IBD); Caco-2; PBMC; HMC-1.1; mast cells; cytokines; trans epithelial electrical resistance (TEER); reactive oxygen species (ROS)
Online: 8 November 2018 (04:53:46 CET)
Inflammatory bowel diseases, which consist of chronic inflammatory conditions of the colon and the small intestine, are considered a global disease of our modern society. Recently, the interest toward the use of herbal therapies for the management of inflammatory bowel diseases has increased because of their effectiveness and favorable safety profile, compared to conventional drugs. Boswellia serrata Roxb. and Curcuma longa L. are amongst the most promising herbal drugs, however, their clinical use in inflammatory bowel diseases is limited and little is known on their mechanism of action. The aim of this work was to investigate the effects of two phytochemically characterized extracts of B. serrata and C. longa in an in vitro model of intestinal inflammation. Their impact on cytokine release and reactive oxygen species production, as well as the maintenance of the intestinal barrier function and on intestinal mucosa immune cells infiltration, has been evaluated. The extracts showed a good protective effect on the intestinal epithelium at 1 µg/ml, with TEER values increasing by approximately 1.5 fold, compared to LPS-stimulated cells. C. longa showed an anti-inflammatory mechanism of action, reducing IL-8, TNF-α and IL-6 production by approximately 30%, 25% and 40%, respectively, compared to the inflammatory stimuli. B. serrata action was linked to its antioxidant effect, with ROS production being reduced by 25%, compared to H2O2-stimulated Caco-2 cells. C. longa and B. serrata resulted to be promising agents for the management of inflammatory bowel diseases by modulating in vitro parameters which have been identified in the clinical conditions.
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.
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.
REVIEW | doi:10.20944/preprints202107.0361.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: wound healing; oxidative stress; antioxidant dressing; reactive oxygen species.
Online: 15 July 2021 (13:32:15 CEST)
(1) Background: Reactive oxygen species (ROS) play a crucial role in the preparation of the normal wound healing response. Therefore, a correct balance between low or high levels of ROS is essential. Antioxidant dressings that regulate this balance is a target for new therapies. The purpose of this review is to identify the compounds with antioxidant properties that have been tested for wound healing and to summarize the available evidence on their effects. (2) Methods: A literature search was conducted and included any study that evaluated the effects or mechanisms of antioxidants in the healing process (in vitro, animal models, or human studies). (3) Results: Seven compounds with antioxidant activity were identified (Curcumin, N-acetyl cysteine, Chitosan, Gallic Acid, Edaravone, Crocin, Safranal, and Quercetin) and 46 studies reporting the effects on the healing process of these antioxidants compounds were included. (4) Conclusions: These results highlight that numerous novel investigations are being conducted to develop more efficient systems for wound healing activity. The application of antioxidants is useful against oxidative damage and accelerates wound healing. Designing biomaterials that can scavenge excess reactive oxygen species requires new technologies and further research, especially human studies.
SHORT NOTE | doi:10.20944/preprints202005.0023.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Invasive Alien Species; Guadeloupe; Geoplanidae; Platydemus manokwari; Citizen Science
Online: 2 May 2020 (16:44:46 CEST)
The land flatworm Platydemus manokwari (Platyhelminthes, Geoplanidae) is recorded for the first time from the island of Guadeloupe (French West Indies) in the Caribbean arc. Photographs and records were obtained from citizen science and ranged from the end of 2018 to 2020; specimens were deposited in the collections of the Muséum National d'Histoire Naturelle in Paris, France. This is the first record in Guadeloupe and the second for an island in the Caribbean, after Porto Rico.
ARTICLE | doi:10.20944/preprints202002.0446.v1
Subject: Biology And Life Sciences, Forestry Keywords: Kafta-sheraro national park; woody species structure; regeneration status
Online: 28 February 2020 (16:24:09 CET)
The natural vegetation study was conducted in Kafta-sheraro national park (KSNP) North, Ethiopia to explore floristic composition, structure and regeneration of woody species in the home of African elephant. In the park, the above information is not well documented which is necessary for conservation. Data were collected From August to December 2018. The vegetation data were collected from 161 quadrats of size 20m×20m, 5mx5m for shrub ̸ tree, sapling and seedling respectively. Individual trees and shrubs DBH >=2.5cm and height >=2m were measured using Tape meter and Clinometer respectively. DBH, frequency, density, basal area, and IVI were used for vegetation structure. A total of 70 woody species 46 (65.7%) trees, 18 (25.7%) shrubs and 6 (8.6%) tree ̸ shrub) were identified. The total basal area and density of 79.3 m2 ha-1, and 466 ±12.8 (S.E.) individuals ha-1 were calculated for 64 woody species. Fabaceae was the most dominant family occupied 16 species (23.0%) followed by Combretaceae 8 species (11.4%). Acacia mellifera and Combretum hartmannianum were the most dominant and frequent species. Abnormal patterns of selected woody species were dominantly identified. Regenerating status all the woody plant species was categorized as “Fair” (18.75%), “Poor” (7.81 %) and “None” (73.44%). However, there is good initiation for conservation of the park; still the vegetation of the park was threatened by firewood collection, charcoal production, fire, intensive farming, mining and over grazing. Therefore, the study area as the habitat for the population of the African elephant; the KSNP should be recommended the highest conservation priority and studied the soil seed bank of species having poor regeneration condition.
COMMUNICATION | doi:10.20944/preprints202002.0240.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: species goal; post-2020; Global Biodiversity Framework; CBD; conservation
Online: 17 February 2020 (04:13:50 CET)
Urgent action is required to ‘bend the curve’ on biodiversity loss. However, the ‘species goal’ (Goal B) unveiled in the recently released Zero Draft of the Post-2020 Global Biodiversity Framework (GBF) is inadequate for mobilizing conservation actions to achieve the outcomes required to halt and reverse species declines. Here we examine the limitations of the goal as presented in the Zero Draft and propose a more ambitious goal for species. The conservation community must ensure that the species goal of the GBF captures what is actually needed from a species perspective for the Post-2020 Framework to achieve its 2030 mission “to put biodiversity on a path to recovery for the benefit of planet and people”, lest the mission be doomed from the start.
REVIEW | doi:10.20944/preprints202002.0119.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: predator-prey; insects; arthropods; entomology; herpetology; species interactions; predation
Online: 10 February 2020 (05:29:27 CET)
Arthropod predators preying on vertebrates is generally overlooked in ecological studies, as it is not typically observed in nature and generally considered a rare event. This is likely due to the cryptic nature of these predatory events, the relatively small size of arthropods, and the difficulty in collating published data which is scattered throughout the literature. Although arthropods are known to readily hunt and consume vertebrates, very little is known about these predatory events. In this study, a systematic literature review was conducted to provide a conceptual framework, identify global patterns, and create a searchable database of arthropod preying on vertebrates. This study represents the largest global assessment of arthropod predators and vertebrate prey with over a thousand recorded observations collated from over 80 countries across every continent except Antarctica, where no arthropod predator exists. Arthropod predators were represented by six classes (insects, arachnids, centipedes, and crustaceans: Malacostraca, Ostracoda, Hexanauplia) and over 80 families. Vertebrate prey were represented by five classes (birds, mammals, reptiles, amphibians, fish) and 160 families. The most common prey were frogs consisting of over a third of all observations. The most commonly preyed reptiles were nearly all lizards, half of mammal prey were bats, nearly a third of fish were Cypriniformes, and half of bird prey were passerines. Spiders represented over half of all predatory events found and were the main predator for all vertebrates except birds, which were preyed mostly upon praying mantises. However, prey varied between spider families. For insects, true bugs (Hemiptera) and beetles preyed mostly on amphibians while the aquatic Odonata larvae preyed on amphibians and fish. Decapod predators were observed preying equally between reptiles, birds, and amphibians; with centipedes preying mainly on reptiles and mammals. Predation was mostly recorded from the Americas and Australia, with countries and regions varying between predator and prey groups. This study demonstrates that arthropods are indeed an overlooked predator of vertebrates. Recognizing and quantifying these predator-prey interactions is vital for identifying patterns and the potential impact of these relationships on shaping vertebrate populations and communities. Understanding the possible threat of arthropod predators may be especially important to improve the success of conservation efforts by accounting for predators which may currently be overlooked.
ARTICLE | doi:10.20944/preprints202001.0173.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: wetlands; methanotrophs; India; tropical; novel species; Type Ib; Methylotetracoccus
Online: 16 January 2020 (11:51:52 CET)
We enriched and isolated a novel gammproteobacterial methanotroph; strain FWC3, from tropical freshwater wetland, near Nagaon beach, Alibag, India. FWC3 is a coccoid, flesh pink/peach pigmented, non-motile methanotroph and the cells are present in pairs and as tetracocci. The culture can grow on methane (20%) as well as on a wide range of methanol from concentrations (0.02%-5%). Based on the comparison of genome data, FAME analysis, morphological characters and biochemical characters, FWC3 belongs to the tentatively and newly but not validly described genus ‘Methylotetracoccus’ of which only a single species strain was described, Methylotetracoccus oryzae C50C1. The ANI index between FWC3 and C50C1 strains is 94%, and the DDH value is 55.7%, less than the cut-off values 96% and 70%, respectively. The genome size of FWC3 is smaller (3.4 Mbp) compared to that of C50C1 (4.8 Mbp). Additionally, the FAME profile of FWC3 shows differences in cell wall fatty acid profiles compared to Methylotetracoccus oryzae C50C1. Also, there are other differences on the morphological, physiological and genomic levels. We propose FWC3 to be a member of a novel species of the genus Methylotetracoccus, for which the name Methylotetracoccus aquaticus is proposed. Also, an amended description of the genus Methylotetracoccus gen. nov. is given here. FWC3 is available in two international culture collections with the accession numbers: MCC 4198 (Microbial Culture collection, India) and JCM 33786 (Japan Collection of Microorganisms, Japan).
ARTICLE | doi:10.20944/preprints201911.0303.v1
Subject: Chemistry And Materials Science, Biomaterials Keywords: chitin; Vespa velutina; Asian hornet; polymer; invasive species; insects
Online: 25 November 2019 (03:44:34 CET)
The isolation and characterization of chitin (CHI) obtained from Vespa velutina (CHIVV) is described. Moreover, a trapping procedure is presented to selectively catch the invasive species. The chitin contents of dry Vespa velutina was observed to be 11.7 %. The physicochemical properties of CHIVV was characterized by Fourier transform infrared spectroscopy (FTIR), solid-state NMR (ssNMR), elemental analysis (EA), scanning electron microscopy (SEM) and thermogravimetric analysis (TG). Obtained CHIVV is close to pure (43, 47% C, 6.94% H, and 6.85% N) and full acetylated with a value of 95.44%. Also, lifetime and kinetic parameters such as activation E and the frequency factor A using model-free and model-fitting methods, were determined. For CHIVV the solid state mechanism that follows the thermodegradation is of type F2 (Random nucleation around two nuclei). Vespa velutina chitin should not be used at temperatures above 60ºC, since its half-life would be only one year, and from an industrial point of view it would not be profitable. Based on certain factors such as the current and probable continued abundance of Vespa velutina and the quality of the product obtained, the invasive Asian hornet is a promising alternative source of chitin.
REVIEW | doi:10.20944/preprints201905.0238.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: gene flow; Oryza species, wild rice; GM crops; biosafety
Online: 20 May 2019 (10:09:42 CEST)
Several transgenic rice lines have been developed and are currently under field trials around the world. There are future plans for the commercial release of transgenic rice into the environment. Rice is an autogamous plant and therefore not perceived to be a very high candidate for pollen mediated gene flow to wild and weedy relatives. However, in a tropical environment like Ghana, where sexually compatible wild Oryza species which belongs to the AA genome are present within the ecology of cultivated rice, the possibility of gene flow to wild species cannot be overlooked. There is little evidence on gene flow and its consequences on the wild rice species should they acquire useful genes through gene flow. This review discusses the chances of cultivated to wild rice gene flow in Ghana and the biosafety considerations that should be put in place before the commercial release of genetically modified (GM) rice.
ARTICLE | doi:10.20944/preprints201904.0189.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: exotic species; native communities; biological invasion; dynamics of invasion
Online: 16 April 2019 (12:50:43 CEST)
The establishment and spread of exotic species is a contemporary major concern. Alien species may become invasive in their new habitat, leading to both/either environmental and/or economic impacts. I briefly reviewed the literature in the last decade about the relationship of exotic species and native communities. I identified that professionals usually approach the subject in two main points of view: (1) researchers tend to point out the impacts of alien species on entire communities, evaluating if the relationship is positive, negative or neutral; (2) they focus on the eco-evolutionary processes involved in the introductions, the dynamics of invasion, and individual study cases. When evaluating the response of introductions to entire communities, evidence seems to be ambiguous and may support positive, negative or neutral relationship, especially depending on the scale approached. The unique eco-evolutionary pathways of each introduction may be a great shortcoming in the searching for generalities. On the other hand, advances have been made in understanding the dynamics of invasion on different lineages through a more selective/individualized approach. I suggest that the dynamics of invasion might be studied through a perspective in which different eco-evolutionary processes, levels of organization (from gene to entire communities), the history of the organism(s) and time are taken into account. Individual cases might be compared in attempt to understand how the relationship exotic and native works and in the search for generalities.
COMMUNICATION | doi:10.20944/preprints201902.0249.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: climate change; tropicalization; species distribution; range expansion; North Atlantic
Online: 27 February 2019 (05:14:25 CET)
Climate change and the overall increase of seawater temperature is causing a poleward shift in species distribution, which includes a phenomenon described as tropicalization of temperate regions. This work aims at reporting the first records of four species off the southwestern Iberian Peninsula, namely oceanic puffer Lagocephalus lagocephalus Linnaeus, 1758, Madeira rockfish Scorpaena maderensis Valenciennes, 1833, ornate wrasse Thalassoma pavo Linnaeus, 1758, and bearded fireworm Hermodice carunculata Pallas, 1766. These last three species, along with other occurrences of aquatic fauna and flora along the Portuguese coast, reveal an ongoing process of poleward expansion of several species for which a comprehensive survey along the entire Iberian Peninsula is urgent. The putative origins of these subtropical and tropical species off continental Portugal are discussed, as well as the urgent need of public awareness due to potential health risks resulting from the toxicity of two of the four species reported in this paper.
ARTICLE | doi:10.20944/preprints201901.0143.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: acidity; alkalinity; antioxidant defense; methylglyoxal; phytotoxicity; reactive oxygen species
Online: 15 January 2019 (07:37:11 CET)
Soil pH, either low (acidity) or high (alkalinity) is one of the major constraints that affect many biochemical and biological processes within the cell. The present study was carried out to understand the oxidative damage and antioxidant defense in wheat (Triticum aestivum L. cv. BARI Gom-25) grown under different pH regimes. Eight-day-old seedlings were exposed to growing media with different pH levels (4.0, 5.5, 7.0 and 8.5). Seedlings grown in pH 4.0 and in pH 8.5 showed reductions in biomass, water, and chlorophyll contents; whereas plants grown at pH 7.0 (neutral) exhibited better performance. Extremely acidic (pH 4.0) and/or strongly alkaline (pH 8.5)-stress also increased oxidative damages in wheat by excess reactive oxygen species (ROS) generation and methylglyoxal (MG) production, which increased lipid peroxidation and disrupted the redox state. In contrary, the lowest oxidative damage was observed at neutral condition followed by strong acidic condition (pH 5.5), which was attributed mainly due to better performance of the antioxidant defense and glyoxalase systems. Interestingly, seedlings grown at pH 5.5 showed a significant increase in morphophysiological attributes compared with extreme acidic (pH 4.0)- and strong alkaline (pH 8.5)-stress treatments, which indicates the tolerance of wheat to the acidic condition.
ARTICLE | doi:10.20944/preprints201811.0318.v1
Subject: Engineering, Chemical Engineering Keywords: Sewage sludge, P bio-availability, P species, SMT protocol
Online: 13 November 2018 (15:07:58 CET)
The species and bio-availability of phosphorus (P) in primary, secondary and digested sludge were fractionated and further analyzed in this study. Results showed that inorganic P (IP) was the primary P fraction in the secondary sludge and digested sludge, in which non-apatite IP (NAIP) amounted to 91.6% and 69.3% of IP, respectively. Organic P (OP), accounting for about 71.7% of total P (TP), was the dominant P composition in primary sludge. The content of bio-available P was about 9.7, 43.4, 29.8 mg-P/g-TS in primary sludge, secondary sludge and digested sludge, respectively, suggesting secondary sludge is the optimal choice when land application of sewage sludge is taken into consideration, followed by digested sludge and primary sludge. Polyphosphate and orthophosphate, comprising approximately 54.3% and 89.2% of TP, was the dominant P species in the secondary sludge and digested sludge, respectively. Monoester-P (54.6% of TP in extract) and diester- P (24.1%) were identified as OP species in primary sludge by Phosphorus-31 nuclear magnetic resonance (31PNMR). The present results would be helpful for P recovery and recycle from sewage sludge in wastewater treatment plant.
ARTICLE | doi:10.20944/preprints201810.0426.v1
Subject: Biology And Life Sciences, Forestry Keywords: acacia species; allometric equation; above ground biomass; carbon stock
Online: 18 October 2018 (15:58:15 CEST)
Allometric equations are used to estimate accurate biomass and carbon stock of forests. However, in Ethiopia only few allometric equations as compared to its floral diversity and species-specific allometric equations for Acacia species are still not developed in Ethiopia. The numbers of tree marked for sampling are Fifty-four (54) using preferential sampling. Diameter at breast height, wood density and tree height were collected as independent variables to predict species specific dry biomass of Acacia species. The new species-specific allometric models have been performed using linear regression analysis in the R software. The Above ground biomass (AGB) have been validated using quantitative statically using the pantropic model. Six candidate models have been developed for each species and four best models for each species of dry biomass was selected based on goodness-of-fit statistics and equation performance analysis of the candidate models. The best model for predicting above ground biomass for Acacia seyal is 0.20636*((DBH2)Hρ) 0.53167, for Acacia polyacantha is 7.26982((DBH)2Hρ)0.21750, for Acacia ethibcia is 29.01898*((DBH)2Hρ)0.21518 and for Acacia toritolis is 3.82427*((DBH)2Hρ)0.16748. The selected models are the best performing (P> 0.01) and higher adjusted R2 (>80%) and has lower Akaike’s Information Criteria (AIC) and residual standard error (RSE) values as comparing the rest of the model. The validation of new developed biomass model using Tukey test indicated that significant variation of mean biomass (P<0.05) between the new developed model and the generalized model. The statistics model performance analysis of Nash-Sutcliffe efficiency (NSE) value is approaching to one, indicating that the new developed model has better performance model as compared with generalized model. Moreover, the percent bias of the new developed models is close to zero which indicates that the site-specific biomass models have more accurate estimator and the generalized biomass models have overestimated biomass for the four Acacia species.
ARTICLE | doi:10.20944/preprints201805.0270.v1
Subject: Biology And Life Sciences, Parasitology Keywords: biotrophic interactions; invasive species; colour polymorphism; harlequin ladybird; harmonine
Online: 21 May 2018 (11:41:07 CEST)
Harmonia axyridis is an invasive ladybird (Coleoptera, Coccinellidae) with the potential to outcompete native ladybird species in its invasive distribution area. It was introduced as a biological control agent in many countries but has also spread unintentionally in many others. Hesperomyces virescens (Ascomycota, Laboulbeniales) is a minute (200–400 µm in size) biotrophic fungus that infects over 30 species of ladybirds. The aim of this study was to evaluate whether elytral colour pattern, size, and sex of Ha. axyridis affect infection by H. virescens. Colouration in Ha. axyridis has been linked to the presence of an antimicrobial alkaloid (harmonine). In fall 2016, we collected 763 Ha. axyridis individuals in Cambridge, Massaschusetts, of which 119 (16%) bore H. virescens fruiting bodies. We analysed 160 individuals concerning prevalence and intensity of infection by H. virescens. Elytral sizes and colouration patterns were quantified using digital photography and analytical methods. Smaller ladybirds had a higher prevalence and higher intensity of parasitism. Additionally, male ladybirds bore more thalli compared to female ladybirds. Elytral colour patterns had an effect on neither prevalence nor intensity of infection by Laboulbeniales in our dataset. This suggests that development of Laboulbeniales may be unaffected by certain insect alkaloids.
ARTICLE | doi:10.20944/preprints201804.0267.v1
Subject: Business, Economics And Management, Economics Keywords: deforestation; environmental awareness; media consumption; sustainable development; species extinction
Online: 20 April 2018 (12:01:26 CEST)
This study inscribes itself in the global discussion about the issue of environmental awareness, beliefs and behaviors. Here we focus on the role that cultural differences and scientific media dieting play in explaining heterogeneities in students' awareness and expectations about the two environmental issues of deforestation and species (plant and animal) extinction in the Middle East and North America. To this end, we use the cross-sectional survey data of the OECD's Program for International Student Assessment (PISA) 2015, along with seemingly unrelated Bi-variate ordered Probit modeling techniques. The results show that compared to their North American Counterparts, students' in the Middle East are 14.2% less aware of, and 14.5% less optimistic about the issue of deforestation, while 38.9% less aware of, and 59.0% less optimistic about the issue of species extinction. In addition, we found that science club attendance and broad science reading in books are the two most effective communication media for raising students awareness about the two environmental issues. In fact, every one level increase in students' awareness is found to raise their optimism by 20.4% for the issue of deforestation, and 15.0% for the issue of plant and animal extinction. Therefore raising young people environmental awareness and optimism through proper communication strategies, could be invaluable for achieving an economic development in line with our need to preserve the natural environment and ecosystem services for generations to come.
ARTICLE | doi:10.20944/preprints201804.0146.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: species richness; latitudinal gradients; water-energy; habitat; animal richness
Online: 11 April 2018 (11:24:46 CEST)
Species data of 249 National Nature Reserves in China was used to identify potential underlying drivers of latitudinal gradients in plant diversity. We used generalized linear models (GLMs) to assess the correlations between predictor and response variables. We also used SAM (Spatial Analysis in Macroecology) to eliminate autocorrelation along each of the 249 studied locations. We used the Akaike information criterion (AICc; Montoya et al. 2007) to select the independent variables were those included in the best models from different combinations of climate, habitat and animal variables. Variance partitioning was used to decompose the variation in plant richness across different taxonomic levels among the three groups of predictors. We found that: Total plant species, gymnosperms, angiosperms and ferns showed significant latitudinal trends in richness (p < 0.001). Water-energy and habitat variables generally explained more variation in richness across different plant groups than did animal richness. Annual precipitation was selected as the best water-energy variable across different taxonomic plants groups, soil PH and elevation range were selected as the best habitat variables across different taxonomic plant groups. The independent effects of habitatvariables were higher than that of water-energy and animal variables across different taxonomic plants groups. Water-energy, habitat heterogeneity, and animal variables explain 48.8% of the variation in total species richness, 28.2% in gymnosperm richness, 44.2% in angiosperm richness, and 38.9% in fern richness.Plants showed significant latitudinal trends in richness (p < 0.001). Water-energy and habitat variables generally explained more variation in richness across different taxonomic plants groups than did animal variables. The independent effects of habitat variables were higher than those of water-energy and animal variables across different taxonomic plants groups.