REVIEW | doi:10.20944/preprints202108.0141.v1
Online: 5 August 2021 (11:04:09 CEST)
Tomato leaf curl disease (TLCD) is the most common viral disease in the tomato plant. It is caused by begomoviruses, which are viruses that cause plant development to be slowed. Many of the traditional disease management methods are still in use. They are, however, ineffective and out of date. Modern biotechnology is being used to detect illness in tomato plants as early as possible, thus reducing damage to the plants. Through genetic engineering, the spread of viruses may be controlled or prevented entirely. Here reviewed many methods for decreasing or eliminating the viral influence on crop growth through biotechnology and genomics. We also investigated the possibility of genetic engineering to reduce or remove the virus TLCD impact on tomato crop development.
Wed, 4 August 2021
REVIEW | doi:10.20944/preprints202108.0124.v1
Subject: Biology, Anatomy & Morphology Keywords: rhizoremediation; plant growth promoting rhizobacteria; petroleum hydrocarbon-degrading bacteria; salix; contaminated soils; alkanes; polycyclic aromatic hydrocarbons
Online: 4 August 2021 (22:30:31 CEST)
Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern in the word due to intensification of industrial activities. This creates a serious environmental issue, therefore there is a need to find solutions, including application of efficient remediation technologies, or to improve current techniques. Rhizoremediation is a sub-category of the phytoremediation which refers to Phytomanagement that uses plants and their associated microbiota. These green technologies have received a global attention as a cost-effective and possible efficient remediation technique that can be applied to cleanup PHCs-polluted soils. The mechanism of rhizoremediation process is that plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is much complex because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the progress made on rhizoremediation approaches that can overcome the limitations and improve the efficiency of PHCs-contaminated soils. The addressed approaches in this review include: 1) selecting plants with desired characteristics suitable for rhizoremediation, 2) the exploitation and manipulation of plant microbiome by using inoculant containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms, and 3) enhancement of the understanding of how host-plant assembles a beneficial microbiome, and how it functions, under pollutant stress.
ARTICLE | doi:10.20944/preprints202108.0106.v1
Subject: Biology, Anatomy & Morphology Keywords: hormones; Carpathian Indigenus Buffalo; FTAI; sexed semen; OvSynch
Online: 4 August 2021 (10:02:50 CEST)
Although artificial insemination can mean a slow and progressive improvement of animal genetics, in buffalo-cow its practical application is difficult the results are incomparably lower then cattle. The purpose of this article is to develop a new methodology, a well-known technique to make AI biotechnology more applicable to the buffalo, in order to improve the conception rate. The protocol we follow is to stimulate hormonal ovarian activity, inducing the dominant follicle, causing ovulation and scheduling the moment of sexed artificial insemination deep in the uterine horn only ipsilateral to the ovary that will ovulate. The experiment was performed on 40 primiparous buffaloes-cows in two groups for AI separated by two bulls whit 2 Millions female sperm straws. The groups was compiled after a thorough gynecological examination, and subsequently the OvSynch therapeutic protocol was started. The results were 82,5% buffaloes (33/40) had dominant follicle (DF) and inseminated, on hot/cold seasons the distribution was 75%vs90%. The conception rate was 63,6% (21/33), on hot/cold seasons 60%vs66,6%, and after calving 92.5% (20/21) female cattle were obtained. Thus, by implementing UcFTAI protocol, we state that the goal of increasing the genetic potential of CIB by becomes achievable and can be extended to a larger scale. Our Improved Protocol (UcFTAI) aims to reduce waste and maximize OvSynch hormone therapy.
ARTICLE | doi:10.20944/preprints202108.0104.v1
Subject: Biology, Anatomy & Morphology Keywords: quantitative metagenomics; microbiome; obesity; gut microbiota; microbial DNA extraction; sequencing; Simulation; Oxford Nanopore Technologies; MinION
Online: 4 August 2021 (09:44:24 CEST)
Background: The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenges. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Results: Here, we propose a computational and experimental protocol for whole genome quantitative metagenomics studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatic protocol to analyse ONT sequences taxonomically and functionally and optimized pre-analytic protocols including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence alignment and classification. Our protocol was evaluated using simulations of metagenomic communities which reflect naturally occuring compositional variations. Next, we validated both protocols using stool samples from a bariatric surgery cohort, sequenced with ONT, Illumina and SOLiD technologies. Results revealed similar diversity and microbial composition profiles. Conclusion: This protocol can be implemented in the clinical or research setting, bringing rapid personalized whole genome profiling of target microbiome species.
Tue, 3 August 2021
REVIEW | doi:10.20944/preprints202108.0097.v1
Subject: Biology, Anatomy & Morphology Keywords: Goat population; Goat milk; Milk production; Milk composition; Goat cheese; Therapeutic properties
Online: 3 August 2021 (15:57:07 CEST)
Since the 1980s, a growing interest in goat milk was noticed due to the nutritional values and health benefits of this milk, which resulted in increasing goat populations and milk production worldwide. This comprehensive review elaborates on goat milk composition compared to other types of milk. It is also an overview of goat milk production, properties, nourishment-value, applications in dairy products, and potential health benefits. Goat milk composition and its characteristics are slightly different from other types of milk and can be utilized to manufacture many dairy products. Fresh goat milk and goat milk products (e.g., yogurt and kefir were found to provide various potential health benefits, such as anti-inflammatory, prevent cardiovascular disease, anti-diabetic and antihypertensive, strengthen bones, boost immunity, and improve metabolism.
ARTICLE | doi:10.20944/preprints202108.0092.v1
Subject: Biology, Anatomy & Morphology Keywords: petroleum; metagenomics; core microbiota, functional potential, oil fields
Online: 3 August 2021 (15:29:57 CEST)
Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to deci-pher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301,2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 MAGs of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to ar-chaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1,690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with lower level of intervention were the most similar to the potential functional core, while the oil fields with longer history of water in-jection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical trans-formations in these ecosystems.
REVIEW | doi:10.20944/preprints202108.0082.v1
Subject: Biology, Anatomy & Morphology Keywords: vaccines; vaccination; bovine respiratory disease; antigen; adjuvants
Online: 3 August 2021 (13:39:11 CEST)
Vaccination is widely regarded as a cornerstone in animal or herd health and infectious disease management. Nineteen vaccines against the major pathogens implicated in bovine respiratory disease are registered for use in the UK by the Veterinary Medicines Directorate (VMD). However, despite annual prophylactic vaccination, bovine respiratory disease is still conservatively estimated to cost the UK economy approximately £80 million per annum. This review examines the vaccine types available, discusses the surrounding literature and scientific rationale of the limitations and assesses the potential of novel vaccine technologies.
ARTICLE | doi:10.20944/preprints202108.0078.v1
Subject: Biology, Anatomy & Morphology Keywords: biodiversity; insolation, biogeography; lidar; point-cloud; multi-spectral imagery; spatial prediction model; forest canopy
Online: 3 August 2021 (13:05:43 CEST)
Incident solar radiation (insolation) passing through the forest canopy to the ground surface is either absorbed or scattered. This phenomenon, known as radiation attenuation, is measured using the extinction coefficient (K). The amount of radiation at the ground surface of a given site is effectively controlled by the canopy’s surface and structure, determining its suitability for plant species.Menhinick’s and Simpson biodiversity indexes were selected as spatially explicit response variables for the regression equation using canopy structure metrics as predictors. Independent variables include modeled area solar radiation, LiDAR derived canopy height, effective leaf area index data derived from multi-spectral imagery, and canopy strata metrics derived from LiDAR point-cloud data. The results support the hypothesis that, 1.) canopy surface and strata variability may be associated with understory species diversity due to habitat partitioning and radiation attenuation, and that, 2.) such a model can predict both this relationship and biodiversity clustering.The study data yielded significant correlations between predictor and response variables and was used to produce a multiple-linear model comprising canopy relief, texture of heights, and vegetation density to predict understory plant diversity. When analyzed for spatial autocorrelation, the predicted biodiversity data exhibited non-random spatial continuity.
ARTICLE | doi:10.20944/preprints202108.0077.v1
Subject: Biology, Anatomy & Morphology Keywords: arboviruses; Dengue; Chikungunya; molecular biology; qRT-PCR; Aedes aegypti; Burkina Faso
Online: 3 August 2021 (12:48:01 CEST)
Abstract: In 2016, we conducted an entomological survey in a railway transect between Banfora and Ouagadougou, Burkina Faso. The aim was to evaluate the risk factors for arbovirus epidemics, including vector infection status, in areas representative of the country. Aedes aegypti mosquitoes were collected at larval stage from four study sites and reared until adult stage and kept in RNAlater for detection of arbovirus RNA. In the laboratory, the mosquito specimens were screened for dengue virus (DENV) and chikungunya virus (CHIKV) using one step real-time qRT-PCR. We detected one DENV-2 positive pool from Ouagadougou, giving a minimum infec-tion rate (MIR) of 16.67, and 6 CHIKV positive pools, giving a MIR of 66.67 from Ouagadougou, but also in Banfora and Boromo. The qRT-PCR is a useful tool for the surveillance of arboviruses of public health importance in Burkina Faso and may be incorporated into disease surveillance and control programs in Burkina Faso.
Mon, 2 August 2021
ARTICLE | doi:10.20944/preprints202108.0059.v1
Subject: Biology, Anatomy & Morphology Keywords: Ballota nigra; salinity; antioxidant; enzyme activity; phytochemical composition
Online: 2 August 2021 (16:31:13 CEST)
Black horehound (Ballota nigra L.) is one of the important medicinal plants, which is a rich source of health-promoting essential oils. Salinity stress affects plant development and alters the quality and quantity of plants extracts and their composition. This study was aimed to investigate the effect of salinity on morphological, physiological characteristics, and secondary metabolites of B. nigra under greenhouse, and in vitro culture conditions. The plants were treated with different concentrations of NaCl (25, 50, 75, 100 mM) and fresh and dry weight of leaf and stem were measured as well as morphological characteristics of the plant. Plant growth was reduced with the increased salinity concentrations. The results showed that all growth-related traits and SPAD were decreased both in vivo and in vitro. Additionally, increased salt concentration affected the cell membrane integrity. Total phenolics content of plants growing in the greenhouse, increased by 21% at 50 mM NaCl, but at higher stress levels (100 mM NaCl), the amounts were decreased significantly. Total flavonoids contents followed similar patterns, with a slight difference. In addition, the maximum and minimum total phenolics contents of plants growing under in vitro condition were observed at 50 mM NaCl and control treatments, respectively. Increasing the salt concentration significantly affected the total flavonoids content, and as a result, the highest amount was observed in 50 and 75 mM NaCl treatments. Antioxidant activity was also measured. Among the NaCl treatments, the highest DPPH scavenging activities (IC50) under greenhouse and in vitro conditions were detected at 50 mM and 25 mM concentrations, respectively. In general, based on the results, with increasing the salinity level to 75 mM, the activities of CAT and APX were significantly upregulated in both greenhouse and in vitro culture conditions. A correlation between total phenolics and flavonoids contents as well as antioxidant activity were obtained. With shifting salinity stress, the type and the amount of the identified essential oil compounds changed. Compounds such as styrene, tridecanol, germacrene-D, beta-Ionone, beta-bisabolene, and caryophyllene oxide increased compared to the controlled treatment.
ARTICLE | doi:10.20944/preprints202107.0439.v2
Subject: Biology, Anatomy & Morphology Keywords: capital return rate deficiency; expected value; carbon storage; carbon rent; albedo effect
Online: 2 August 2021 (13:28:23 CEST)
Two sets of initial conditions are used in the investigation of capital return rate and carbon storage in boreal forests. Firstly, a growth model is applied in young stands as early as the inventory-based model is applicable. Secondly, the growth model is applied to observed wooded stands. Four sets of thinning schedules are investigated in either case. First, the capital return rate is aspired without any restriction. Second, the number of thinnings is restricted to at most one. Third, thinnings are restricted to the removal of only trees thicker than 237 mm. Fourth, commercial thinnings are omitted. The two sets of initial conditions yield similar results. The capital return rate is a weak function of rotation age, which results in variability in the optimal number of thinnings. Reducing the number of thinnings to one increases timber stock but induces a capital return rate deficiency. The deficiency per excess volume unit is smaller if the severity of any thinning is restricted by the removal of large trees only. Omission of thinnings best applies to spruce-dominated stands with stem count less than 2000/ha. Restricted thinning intensity applies to deciduous stands and dense pine stands. The albedo effect increases the benefits of restricted thinnings and increased clearcuttings instead of contradicting the carbon storage.
COMMUNICATION | doi:10.20944/preprints202108.0036.v1
Subject: Biology, Anatomy & Morphology Keywords: Acinetobacter baumannii, H-NS, natural transformation, naturally competent, DNA acquisition
Online: 2 August 2021 (12:58:22 CEST)
Most Acinetobacter baumannii strains are naturally competent. Although some information is available about factors that enhance or reduce the frequency of transformation of this bacterium, the regulatory elements and mechanisms are barely understood. In this article, we describe studies on the role of H-NS in the regulation of expression of genes related to natural competency and the ability to uptake foreign DNA. The expression levels of the natural transformation-related genes pilA, pilT, pilQ, comEA, comEC, comF, and drpA were significantly increased in a Δhns derivative of Acinetobacter baumannii A118. Complementation of the mutant with a recombinant plasmid harboring hns restored expression levels of six of these genes (pilT remained expressed at high levels) to those of the wild-type strain. The transformation frequency of the A. baumannii A118 Δhns strain was significantly higher than that of the wild-type. Similar, albeit not identical, effects occurred when hns was deleted from the hypervirulent A. baumannii AB5075 strain. Reduction of gene expression in a few cases was not as pronounced as to reach wild-type levels, and expression of comEA was enhanced further. In conclusion, the expression of all seven transformation-related genes was enhanced after deleting hns in A. baumannii A118 and AB5075, and these modifications are accompanied by an increase in the cells’ transformability. The results demonstrate a role of H-NS in A. baumannii’s natural competence.
ARTICLE | doi:10.20944/preprints202108.0002.v1
Online: 2 August 2021 (08:43:20 CEST)
Human Rhinovirus (HRV) is the most common cause of upper respiratory infections and exacerbations of asthma. In this work, we selected 14 peptides (6 from HRV A and 8 from HRV C) encompassing potential CD4 T cell epitopes. Peptides were selected for being highly conserved in HRV A and C serotypes and predicted to bind to multiple HLA II molecules. We found positive T cell recall responses by IFNγ-ELISPOT assays to 8 peptides, validating 7 of them (3 from HRV A and 4 from HRV C) as CD4 T cell epitopes through intracellular cytokine staining assays. Additionally, we verified their promiscuous binding to multiple HLA II molecules by quantitative binding assays. According to their experimental HLA II binding profile, the combination of all these 7 epitopes could be presented and recognized by > 95 % of the world population. We actually determined IFNγ responses to a pool encompassing these CD4 T cell epitopes by intracellular cytokine staining, finding positive responses in 29 out of 30 donors. The CD4 T cell epitopes identified in this study could be key to monitor HRV infections and to develop peptide-based vaccines against most HRV A and C serotypes.
Fri, 30 July 2021
ARTICLE | doi:10.20944/preprints202107.0693.v1
Subject: Biology, Anatomy & Morphology Keywords: Citrullus lanatus; grafting tool; rootstock regrowth; scion growth; vegetable grafting
Online: 30 July 2021 (09:56:14 CEST)
Grafting is an effective way to increase plant tolerance to biotic and abiotic stressors, it is widely used in watermelon production. However, grafting is labor intensive due to the additional time is required, such as the management of rootstock regrowth. This study used a new grafting tool to destroy (remove) the epidermis of pumpkin and bottle gourd rootstock cotyledon base during grafting, we called this a new grafting method. Compared with the traditional grafting (100%), the new grafting method had significantly lower rate of rootstock regrowth (2-23%), higher watermelon scion dry weight and leaf area. In addition, the time used for the new hole insertion and one cotyledon grafting method to destroy (remove) the epidermis of rootstock cotyledon base (4.2 s/plant, 4.2 s/plant) is significantly shorter than the time required to remove the rootstock regrowth manually in the traditional grafting (9.3 s/plant, 8.8 s/plant). Thus, this study developed a new grafting method for watermelon to inhibit rootstock regrowth and enhance scion growth, and this new method is cost-effective for grafted watermelon seedlings.
ARTICLE | doi:10.20944/preprints202107.0689.v1
Subject: Biology, Anatomy & Morphology Keywords: canine, carbohydrates, grain-free, pet food, pharmacokinetic mathematical modelling, acetaminophen tracking.
Online: 30 July 2021 (09:29:05 CEST)
Gastric emptying rate (GER) may impact diabetes and obesity in humans and could provide a method to reduce canine weight gain. Starch, the most common source of carbohydrates (CHOs) in pet food, is classified as rapidly or slowly digestible, or resistant to digestion. This study investigated starch source effects in commercial extruded dog foods on the GER of 11 healthy adult Siberian Huskies (5.63±0.72 years; mean±SEM). Test diets were classified as traditional, grain-free, whole-grain, and vegan. Dogs received each diet once, a glucose control twice, and acetaminophen (Ac) as a marker for GER in a randomized, partially-replicated, 6x6 Latin square design. Pre- and post-prandial blood samples were collected at 16 timepoints from -15 to 480 minutes. Serum Ac concentrations were assessed via standard spectrophotometric assays and fitted with a mathematical model to estimate parameters of GER. Data was analyzed using a repeated measures ANOVA, followed by a Tukey-Kramer post-hoc test when significant (p<0.05). More total emptying (p= 0.0430) occurred at faster rate (p=0.0668) in dogs fed the grain-free diet, which contained the lowest total starch (34.03 ± 0.23%) and highest resistant starch (0.52 ± 0.007%). This research may benefit future diet formulations to reduce the prevalence of canine weight gain.
Thu, 29 July 2021
ARTICLE | doi:10.20944/preprints202107.0665.v1
Subject: Biology, Anatomy & Morphology Keywords: cannabinoid receptor; inflammation; astrocytes; immunohistochemistry
Online: 29 July 2021 (14:11:55 CEST)
HIV-associated neurocognitive disorders (HAND) persist despite the advent of antiretroviral therapy (ART), suggesting underlying systemic and central nervous system (CNS) inflammatory mechanisms. The endogenous cannabinoid receptors 1 and 2 (CB1 and CB2) modulate inflammatory gene expression and play an important role in maintaining neuronal homeostasis. Cannabis use is disproportionately high among people with HIV (PWH) and may provide a neuroprotective effect for those on ART due to its anti-inflammatory properties. However, expression profiles of CB1 and CB2 in the brains of PWH on ART with HAND have not been reported. In this study, biochemical and immunohistochemical analyses were performed to determine CB1 and CB2 expression in brain specimens of HAND donors. Immunoblot revealed CB1 and CB2 were differentially expressed in frontal cortices from HAND brains compared to neurocognitively unimpaired (NUI) brains from PWH. CB1 expression levels negatively correlated with memory and information processing speed. CB1 was primarily localized to neuronal soma in HAND brains versus a more punctate distribution on neuronal processes of NUI brains. CB1 expression was increased in cells with glial morphology and showed increased colocalization with an astroglial marker. These results suggest that targeting the endocannabinoid system may be a potential therapeutic strategy for HAND.
Wed, 28 July 2021
COMMUNICATION | doi:10.20944/preprints202107.0633.v1
Subject: Biology, Anatomy & Morphology Keywords: Biofortification; Agro-biodiversity; HarvestPlus; Hidden Hunger; Orphan Crops; Wild edibles
Online: 28 July 2021 (16:18:29 CEST)
Biofortification refers to the increase in the amount of essential vitamins or provitamins or minerals in crops to improve the nutritional status of the people, which is largely intended to alleviate the problem of micronutrient malnutrition. I argue that biofortification may not be an effective weapon to fight against the hidden hunger since it demonstrates limited capacity on nutritional enhancement and can negatively impact the socio-economic fabric of the society in many different ways. Finally, I suggest a couple of alternatives that might meet the challenge more efficiently than biofortified crops.
Tue, 27 July 2021
Subject: Biology, Anatomy & Morphology Keywords: Magnesium transporter; Comparative analysis; Malvaceae; Theobroma, Gossypium; Corchorus; Expression analysis; Gene structure; Phylogenetic analysis.
Online: 27 July 2021 (22:49:36 CEST)
Magnesium (Mg) is a vital element, which involves in various key cellular processes in plants. Mg transporter (MGT) genes play an important role in magnesium distribution and ionic balance maintenance. Here, MGT family members were identified and characterized in three species of the plant family Malvaceae, including Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum to improve our understanding of their structure, regulatory systems, functions, and possible interactions. We identified 18, 41, and 16 putative non-redundant MGT genes from the genome of T. cacao, G. hirsutum, and C. capsularis, respectively, which were clustered into five groups within maximum likelihood tree. Several segmental/tandem duplication events were determined between MGTs genes. It seems that MGTs were slowly evolving and have been evolved under a purifying selection. Analysis of gene promoter regions showed that MGTs have a high potential to respond to biotic/abiotic stresses as well as hormones. The expression patterns of MGT genes revealed their possible T. cacaorole in response to P. megakarya fungi in T. cacao, whereas MGT genes showed differential expression in various tissues and respond to several abiotic stresses, including cold, salt, drought, and heat stress in G. hirsutum. Besides, the co-expressions network of MGTs indicated that genes involved in auxin responsive, lipid metabolism, cell wall organization, and photoprotection can interact with MGTs.
REVIEW | doi:10.20944/preprints202107.0610.v1
Online: 27 July 2021 (15:28:35 CEST)
In contrast to animals, adult organs in plants are not determined during embryogenesis but gen-erated from meristematic cells as plants advance through development. Plant development in-volves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can re-verse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant’s phenotype and development have been shown to control phase transitions. How develop-mental and environmental cues interact to epigenetically alter gene expression and influence these transitions are not well understood and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic con-sequences for perennial plants in natural and agricultural ecosystems. Here we review studies focussing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress.
REVIEW | doi:10.20944/preprints202107.0602.v1
Subject: Biology, Anatomy & Morphology Keywords: epigenetic mechanisms of disease; fetal programming; obstructive sleep apnea; DNA methylation; histone modifications; chronic disease
Online: 27 July 2021 (11:45:08 CEST)
Pediatric obstructive sleep apnea (OSA) has significant negative effects on health and behavior in childhood including depression, failure to thrive, neurocognitive impairment, and behavioral issues. It is strongly associated with an increased risk for chronic adult disease such as obesity and diabetes, accelerated atherosclerosis, and endothelial dysfunction. Accumulating evidence suggests that adult-onset non-communicable diseases may originate from early life through a process by which an insult applied at a critical developmental window causes long-term effects on the structure or function of an organism. Recently, much attention has been paid to the role of epigenetic mechanisms in the pathogenesis of adult disease susceptibility. Epigenetic mechanisms that influence adaptive variability include histone modifications, non-coding RNAs, and DNA methylation. This review will highlight what is currently known about the phenotypic associations of epigenetic modifications in pediatric OSA and will emphasize the importance of epigenetic changes as both modulators of chronic disease and potential therapeutic targets.
Mon, 26 July 2021
ARTICLE | doi:10.20944/preprints202107.0572.v1
Subject: Biology, Anatomy & Morphology Keywords: CFPHV; ChHV5; phylogenetics; phylogenomics; viral evolution and diversity; marine turtles; fibropapillomatosis
Online: 26 July 2021 (11:58:37 CEST)
The spreading global sea turtle fibropapillomatosis (FP) epizootic is threatening some of Earth’s ancient reptiles, adding to the plethora of threats faced by these keystone species. Understanding this neoplastic disease, and its likely aetiological pathogen, chelonid alphaherpesvirus 5 (ChHV5), is crucial to understand how the disease impacts sea turtle populations and species and the future trajectory of disease incidence. We generated 20 ChHV5 genomes, from three sea turtle species, to better understand the viral variant diversity and gene evolution of this oncogenic virus. We revealed previously underappreciated genetic diversity within this virus (with an average of 2,035 single nucleotide polymorphisms [SNPs], 1.54% of the ChHV5 genome) and identified genes under the strongest evolutionary pressure. Furthermore, we investigated the phylogeny of ChHV5 at both genome and gene level, confirming the propensity of the virus to be interspecific with related variants able to infect multiple sea turtle species. Finally, we revealed unexpected intra-host diversity, with up to 0.15% of the viral genome varying between ChHV5 genomes isolated from different tumours concurrently arising within the same individual. These findings offer important insights into ChHV5 biology and provide genomic resources for this oncogenic virus.
Subject: Biology, Anatomy & Morphology Keywords: Fish size; otolith shape; head side; Sargocentron spiniferum; Red Sea; asymmetry
Online: 26 July 2021 (10:55:07 CEST)
Otolith morphology analysis is one of the main tools used for fish or fish stock identification. Moreover, otolith shape can also be used in fish dietary studies (stomach content) for the identi-fication of prey fishes and their size according to the relationship between fish and otolith sizes. In the present study, the relationship between fish length and otolith morphological dimensions was investigated for the sabre squirrelfish, Sargocentron spiniferum (Forsskål, 1775) (family: Hol-ocentridae). Samples of 185 fish were collected from the coast of the Red Sea, Egypt. To analyze the relationship between fish and otolith, otolith morphometric measurements (length, width, area, perimeter, weight, sulcus, and ostium) and shape factors (aspect ratio, compactness, form factor, rectangularity, roundness, ellipticity, squareness) describing outline shape were extracted using image analysis. Generalized linear models were applied for the relationship between body length and each otolith morphology feature. From the relationships between the total length of fish and fourteen morphology features, only otolith length, caudal length, and squareness were significantly correlated with fish size. Our results provide more information for the relationship between fish length and otolith morphometric features.
ARTICLE | doi:10.20944/preprints202107.0558.v1
Subject: Biology, Anatomy & Morphology Keywords: KwaZulu-Natal grassland soils; P deficiency; Vachellia nilotica; N- fixing bacteria; Mesorhizo-bium
Online: 26 July 2021 (09:49:12 CEST)
Vachellia nilotica (L.) Willd. Ex Del. is multipurpose leguminous tree which is common in grass-land and savanna ecosystems in southern and eastern Africa. These ecosystem soils are reported to be acidic and nutrient limited, specifically with regards to nitrogen (N) and phosphorus (P). The presence of this plant in these terrestrial ecosystems improves soil fertility benefiting the sur-rounding vegetation due to its ability fix atmospheric N. This study seeks to understand the mi-crobial symbiosis and physiological adaptations of V. nilotica in these acidic and nutrient defi-cient KZN soils. The soils used for this study were collected from the Ukulinga Grassland Nutri-ent Experiment located at the Ukulinga research farm of the University of KwaZulu-Natal, Pie-termaritzburg, South Africa. Due to long-term soil nutrient addition treatments, these soils of-fered a diverse nutrient variation for better understanding the effects of acidity and nutrient var-iation on microbial symbiosis, plant nutrition and biomass accumulation of V. nilotica. V. nilotica was able to maintain growth by relying on both atmospheric and soil derived N across all treat-ments decreasing carbon (C) growth costs. There was an increased reliance on atmospheric de-rived N of un-nodulated high N treated plants. The plants grown in high N+P soils were able to nodulate with various species from the Mesorhizobium genus which resulted in an increased bio-mass compared to other plants. The results of this study show that V. nilotica can alter N sources to reduce C growth costs. Also, free-living N2 fixing bacteria play an important role under P deficient conditions.
Fri, 23 July 2021
CONCEPT PAPER | doi:10.20944/preprints202107.0546.v1
Subject: Biology, Anatomy & Morphology Keywords: Bacterial nomenclature; taxonomy; microbial genomics
Online: 23 July 2021 (14:22:59 CEST)
The remarkable success of taxonomic discovery, powered by culturomics, genomics and metagenomics, creates a pressing need for new bacterial names, while holding a mirror up to the slow pace of change in bacterial nomenclature. Here, I take a fresh look at bacterial nomenclature, exploring how we might create a system fit for the age of genomics, playing to the strengths of current practice, while minimising difficulties. Adoption of linguistic pragmatism, obeying the rules while treating recommendations as merely optional will make it easier to create names derived from descriptions, from people or places or even arbitrarily. Simpler protologues and a relaxed approach to recommendations will also remove much of the need for expert linguistic quality control. Automated computer-based approaches will allow names to be created en masse before they are needed, while also relieving microbiologists of the need for competence in Latin. The result will be a system that is accessible, inclusive and digital, while also fully capable of naming the unnamed millions of bacteria.
ARTICLE | doi:10.20944/preprints202107.0540.v1
Subject: Biology, Anatomy & Morphology Keywords: polymeric spiral-wound membrane; microfiltration; transmembrane pressure; diafiltration; micellar casein concentrate
Online: 23 July 2021 (11:05:17 CEST)
Micellar Casein Concentrate (MCC) is manufactured from microfiltration (MF) of skim milk utilizing ceramic or polymeric membrane filtration. While ceramic filtration has higher efficiency, use of polymeric is cost effective and the process is familiar to several US dairy processors. The aim of the present study was to develop an optimized membrane filtration process to produce MCC using spiral wound polymeric membrane filtration (SW MF) system by systematic selection of transmembrane pressure (TMP) and level of diafiltration (DF). Using skim milk as feed material, preliminary lab-scale MF experiments were conducted using 0.5 µm polyvinylidene fluoride (PVDF) membrane. Three TMP (34.5, 62.1, and 103.4 kPa) and three levels of DF (70, 100, and 150%) along with a process without DF as control were used in the study. Effect of TMP and effectiveness of DF on flux rates, SP removal, casein to total protein (CN/TKN) ratio, casein to true protein (CN/TP) ratio, rejection of casein (rej CN) and SP (rej SP) were evaluated. At all TMP values used in the study, the overall flux (O Flux) increased with the level of DF. Highest O Flux of 30.77 liter per meter square per hour (LMH) was obtained with 34.5 kPa pressure and 150% DF. The impact of DF was more pronounced at lower pressures than at the higher pressures used in the study. With controlled DF, instantaneous flux was maintained within 80% of initial flux for the entire process run. For all the experiments, casein has a rejection of 0.97 to 1.0, while serum protein has the lowest rejection of 0.10 at 34.5 kPa pressure and 150% DF level. Use of 34.5 kPa and DF level of 150 % contributed to 81.45% SP removal, and casein to true protein ratio of 0.96. SP removal data from the lab-scale experiments were fitted into a mathematical model using DF and square of TMP as factors. The model predicts SP removal within 90-95% of actual SP removal got from the pilot plant experiments.
ARTICLE | doi:10.20944/preprints202107.0534.v1
Subject: Biology, Anatomy & Morphology Keywords: governance; social-ecological system; tropical cyclone; urban forest; urban tree canopy
Online: 23 July 2021 (10:31:50 CEST)
Urban Tree Canopy (UTC) greatly enhances the livability of cities by reducing urban heat buildup, mitigating stormwater runoff, and filtering airborne particulates, among other ecological services. These benefits, combined with the relative ease of measuring tree cover from aerial imagery, have led many cities to adopt management strategies based on UTC goals. In this study, we conducted canopy analyses for the 300 largest cities in Florida to assess the impacts of development practices, urban forest ordinances, and hurricanes on tree cover. Within the cities sampled, UTC canopy ranged from 5.9% to 68.7% with a median canopy coverage of 32.3% Our results indicate that the peak gust speeds recorded during past hurricanes events were a significant predictor of canopy coverage (P-value = <0.001) across the sampled cities. As peak gust speeds increased from 152 km/h (i.e., a lower-intensity Category 1 storm) to 225 km/h (lower-intensity Category 4 and the maximum gusts captured in our data), predicted canopy in developed urban areas decreased by 7.7%. Beyond the impacts of hurricanes and tropical storms, we found that historic landcover and two out of eight urban forest ordinances were significant predictors of existing canopy coverage (P-landcover <0.001; P-tree preservation ordinance = 0.02, P-heritage tree ordinance = 0.03). Results indicate that local policies and tree protections can protect or enhance urban tree canopy, even in the face of rapid development and periodic natural disturbances.
ARTICLE | doi:10.20944/preprints202107.0531.v1
Subject: Biology, Anatomy & Morphology Keywords: A.thaliana; HaloTag; RNA-binding proteins; RNA pulldown assay; RNA-protein complexes; cold shock domain protein
Online: 23 July 2021 (09:32:28 CEST)
Study of RNA-protein interactions and identification of RNA targets are among the key aspects of understanding the RNA biology. Currently, various methods are available to investigate these interactions, in particular, RNA pulldown assay. In the present paper, a method based on the HaloTag technology is presented that is called Halo-RPD (HaloTag RNA PullDown). The proposed protocol uses plants with stable fusion protein expression and the MagneBeads magnetic beads to capture RNA-protein complexes directly from the cytoplasmic lysate of transgenic A. thaliana plants. The key stages described in the paper are as follows: 1) preparation of the magnetic beads 2) tissue homogenization and collection of control samples 3) precipitation and wash of RNA-protein complexes; 4) evaluation of protein binding efficacy; 5) RNA isolation; 6) analysis of the obtained RNA. Recommendations for better NGS assay designs are provided.
Thu, 22 July 2021
ARTICLE | doi:10.20944/preprints202107.0522.v1
Subject: Biology, Anatomy & Morphology Keywords: Biogeographic Chocó; Carbon balance; Nutritional limitation; Nitrogen; Phosphorus; Potassium
Online: 22 July 2021 (14:14:30 CEST)
Tropical rainforests have the highest rates of net primary productivity (NPP) of the world. Hypotheses about the effect of edaphic nutrient contents, especially the availability of P, propose that they limit NPP of tropical forests or promote the redistribution of its above and belowground components. However, these hypotheses have not been tested experimentally in highly rainy tropical forests. To test such hypotheses, the effects of soil fertilization on the above and belowground NPP were evaluated in forests of two localities of Chocó (Colombia), one of the rainiest regions of the world. Five fertilization treatments (N, P, K, NPK and Control) were applied, and the above and belowground NPP were determined in permanent plots. There were no significant effects of treatments on total NPP; only the application of N significantly increased litter NPP. Additionally, a redistribution of the above and belowground NPP was found with the application of P, which increased the proportion of fine roots and litter, and decreased the woody components of forest NPP. This change of carbon allocation is interpreted as an ecophysiological mechanism to capture additional nutrients in soils with very low content of available P.
ARTICLE | doi:10.20944/preprints202107.0518.v1
Subject: Biology, Anatomy & Morphology Keywords: Chronobiotics; geroprotectors; cryptochrome; KL001; KS15; Drosophila melanogaster
Online: 22 July 2021 (13:39:54 CEST)
Chronobiotics is a group of drugs utilized to modify circadian rhythms targeting clock-associated molecular mechanisms. The circadian clock is known as a controller of numerous processes standing behind aging. Hypothesis: KL001 and KS15 targeting CRY, affect lifespan, locomotor activity and circadian rhythm of Drosophila melanogaster. We observed a slight (2%, p<0.001) geroprotective effect on median lifespan (5 µM solution of KL001 in 0.1% DMSO) and a 14% increase in maximum lifespan in the same group. KS15 10 µM solution extended males’ median lifespan by 8% (p <0.05). The statistically significant positive effects of KL001 and KS15 on lifespan were not observed in female flies. KL001 5 µM solution improved locomotor activity in young male imagos (p<0.05) and elevated morning activity peak in aged imagos and modified robustness of circadian rhythms, leaving the period intact. KS15 10 µM solution decreased the locomotor activity in constant darkness and minimized the number of rhythmic flies. KL001 5 µM solution improved by 9% the mean starvation resistance in male flies (p<0.01), while median resistance was elevated by 50% (p<0.0001). This phenomenon may suggest the presence of the mechanism associated with improvement of fat body glucose depos’ utilization in starvation conditions which is activated by dCRY binding KL001.
ARTICLE | doi:10.20944/preprints202107.0509.v1
Subject: Biology, Anatomy & Morphology Keywords: Perilla crop; genetic resources; morphological traits; principal component analysis; SSR marker; genetic variation
Online: 22 July 2021 (08:04:28 CEST)
Using morphological characteristics and SSR markers, we evaluated the morphological and genetic variation of 200 Perilla accessions collected from the five regions of South Korea and other region. In morphological characteristics analysis, particularly, leaf color, stem color, degree of pubescence, leaf size were found to be useful for distinguishing the characteristics of native Perilla accessions cultivated in South Korea. A total of 137 alleles were identified in the 20 simple sequence repeat (SSR) markers, and the number of alleles per locus ranged from 3 to 13, and the average number of alleles per locus was 6.85. The average gene diversity (GD) was 0.649, with a range of 0.290-0.828. From analysis of SSR markers, accessions from the Jeolla-do and Gyeongsang-do regions showed comparatively high genetic diversity values compared with those from other regions in South Korea. In the unweighted pair group method with arithmetic mean (UPGMA) analysis, the 200 Perilla accessions were found to cluster into three major groups and an outgroup with a genetic similarity of 42%, and did not showed a clear geographic structure from the five regions of South Korea. Therefore, it is believed that landrace Perilla seeds are frequently exchanged by farmers through various routes between the five regions of South Korea. The results of this study are expected to provide useful information for conservation of these genetic resources and selection of useful resources for the development of varieties for seeds and leafy vegetables of cultivated var. frutescens of Perilla crop in South Korea.
Wed, 21 July 2021
Subject: Biology, Anatomy & Morphology Keywords: Wild Edible Plants; antimicrobial effect; Mediterranean plant; Gram+ bacteria; Gram- bacteria; extraction protocols; bioactive compounds; essential oils
Online: 21 July 2021 (10:05:22 CEST)
Introduction. Bacterial resistance to antibiotics is estimated to cause the major number of deaths by 2050 if we do not find strategies to slow down the rise of drug resistance . Reviews on Mediterranean Wild Edible Plants (MWEPs) with antimicrobial properties are scarce in the mean databases (Pubmed, Scopus and WoS). Hence, we proceeded to a new review of the studies on MWEPs. Methods. We used Wild Edible Plant and Antimicrobial as keywords. We only included the Mediterranean plants, and studies in non-Mediterranean countries, but for plants growing in Mediterranean basin. Exclusion criteria were the document type, studies not concerning plant, plants not edible, not antimicrobial properties, or totally out of topic. Results. Finally, the number of studies reviewed, starting from one hundred and ninety-two, was thirty-eight (19,8%), concerning the antimicrobial properties of seventy-four MWEPs species, be-longing to twenty-five Families. Fifty-seven (77%) out of seventy-four species, proved to be antimicrobial with a stringent threshold selection. Conclusions. The studies are still very heterogeneous. We still know too little about MWEPs properties, but what we already know seriously recommends continuing.
Tue, 20 July 2021
Subject: Biology, Anatomy & Morphology Keywords: Bovine respiratory disease; Pasteurella multocida; resistance; tolerance; satP.
Online: 20 July 2021 (14:48:06 CEST)
Under the pressure of fluoroquinolones, Pasteurella multocida (PM) can easily develop resistance to fluoroquinolones mediated by QRDR target mutation. It is imperative to find new drug resistance inhibitor targets to combat the rapid development of drug resistance. In order to overcome these problems, we sequenced the transcriptome of PM with different levels of resistance to ENR(0.03 μg/mL; 8 μg/mL; 32μg/Ml, Enrofloxacin). The results showed that with the increase of resistance to fluoroquinolones, the expression of satP gene was significantly up-regulated. The satP gene deletion strain and replenishment strain were constructed, and their drug resistance and tolerance were determined. The results showed that the deletion of satP gene did not affect the resistance of PM to fluoroquinolones, rather affected the time when PM developed resistance to fluoroquinolones. After 10 generations of drug induction, the MIC (minimum inhibitory concentration) of fluoroquinolones for wild strain was 64 μg/mL, while the MIC for satP gene deletion strain was only 8 μg/mL. The MDK99 test (time to kill 99% bacteria),agar diffusion test and mutation frequency test showed that the tolerance of satP gene deletion strain was significantly lower than that of wild strain. At the same time, the virulence of gene deletion strain and wild strain was tested, and about 400 times decreased virulence was observed for satP gene deletion strain. The mouse infection model confirmed that mice infected with satP gene deletion strains were more likely to be treated with ENR than mice infected with wild-type bovine PM strains. The results show that satP has potential to be a target of fluoroquinolone resistance inhibitors.
ARTICLE | doi:10.20944/preprints202107.0444.v1
Subject: Biology, Anatomy & Morphology Keywords: cyanobacteria; Phormidium; culture growth; light; salinity; phycocyanin; pigments
Online: 20 July 2021 (11:35:05 CEST)
A strain of the filamentous non N-fixing cyanobacterium Phormidium sp. isolated from the Messolonghi (W. Greece) saltworks, was cultured in the laboratory at 6 different combinations of salinity (20-40-60 ppt) and illumination (low-2000 lux and high-8000 lux). At salinities of 60 and 40 ppt and in high illumination (XL-8000 lux) the growth rate (μmax) presented the highest values (0.491 and 0.401 respectively) compared to the corresponding at 20 ppt (0.203). In general and at all salinities, the higher illumination (XL) gave the highest growth rates and shorter dublication time (tg) in comparison to the lower illumination (L). On the contrary, phycocyanin, phycoerythrin and allophycocyanin production was extremely increased in the lower illumination (L) in all salinities, from ~14fold at 40 and 60 ppt to 269fold at 20 ppt of those corresponding to higher illumination (XL). Similar analogies were also recorded for the other two billiproteins. Chlorophyll-a content was also higher in lower illumination at all salinities in contrast to total carotenoids that did not exhibit such a pattern. The high growth rate and high phycocyanin content along with the rapid sedimentation of its cultured biomass can set this marine Phormidium species as a promising canditate for mass culture.
Mon, 19 July 2021
Subject: Biology, Anatomy & Morphology Keywords: Cannabis sativa; Germplasm preservation; Droplet vitrification; Conventional vitrification; Tissue culture
Online: 19 July 2021 (18:13:48 CEST)
Cannabis has developed into a multi-billion dollar industry that relies on clonal propagation of elite genetics with desirable agronomic and chemical phenotypes. While the goal of clonal propagation is to produce genetically uniform plants, somatic mutations can accumulate during growth and compromise long-term genetic fidelity. Cryopreservation is a process in which tissues are stored at cryogenic temperatures, halting cell division and metabolic processes to facilitate high fidelity germplasm preservation. In this study, a series of experiments were conducted to optimize various stages of cryopreservation and develop a protocol for long-term germplasm storage of Cannabis sativa. The resulting protocol uses a standard vitrification procedure to cryopreserve nodal explants from in vitro shoots as follows: Nodes were cultured for 17 hours in a pre-culture solution (PCS), followed by a 20 minute treatment in a loading solution (LS), and a 60 minute incubation in plant vitrification solution 2 (PVS2). The nodes were then flash frozen in liquid nitrogen, re-warmed in an unloading solution at 40°C, and cultured on basal MS culture medium in the dark for 5 days followed by transfer to standard culture conditions. This protocol was tested across 13 genotypes to assess the genotypic variability. The protocol was successful across all 13 genotypes, but significant variation was observed in tissue survival (43.3-80%) and regrowth of shoots (26.7-66.7%). Plants grown from cryopreserved samples were morphologically and chemically similar to control plants for most major traits, but some differences were observed in the minor cannabinoid and terpene profiles. While further improvements are likely possible, this study provides a functional cryopreservation system that works across multiple commercial genotypes for long-term germplasm preservation.
ARTICLE | doi:10.20944/preprints202107.0418.v1
Subject: Biology, Anatomy & Morphology Keywords: herbicide efficacy; glutamine synthetase; reactive oxygen species; enzyme turnover; mode of action; Palmer amaranth
Online: 19 July 2021 (16:10:12 CEST)
Glufosinate, a glutamine synthetase (GS) inhibitor, often provides variable weed control depending on environmental conditions such as light, temperature and humidity at the time of application. Midday applications normally provide improved efficacy compared to applications at dawn or dusk. We investigated the physiological, molecular, and biochemical basis for the time-of-day effect on glufosinate efficacy in Amaranthus palmeri. GS1 and GS2 gene expression and protein abundance were assessed in different parts (young leaves, old leaves, and roots) of plants incubated in the dark compared to those in the light. The turnover of GS total activity was also evaluated overtime following glufosinate treatment at midday compared to dusk application. The results suggest that GS in A. palmeri is less expressed and less abundant in the dark compared to in the light. Midday application of glufosinate under intense light conditions in the hours following application provide full control of A. palmeri plants. Consequently, these plants are unable to recover GS activity by de novo protein synthesis. Full activity of GS is required for complete inhibition by the irreversible inhibitor glufosinate. Therefore, glufosinate applications should always be performed in the middle of the day when sunlight is intense, to prevent weed escapes from the herbicide treatment.
ARTICLE | doi:10.20944/preprints202107.0416.v1
Subject: Biology, Anatomy & Morphology Keywords: Epilepsy; VOCs; Attention seeking behaviours; Remote Odour Delivery Mechanism (RODM)
Online: 19 July 2021 (14:30:08 CEST)
Abstract Epilepsy is a disorder of the brain and a seriously debilitating condition, which has been associated with injury, social stigmatisation and in some cases, sudden unexpected and premature death. A sense of profound isolation is felt by many individuals with epilepsy, and this community has expressed an urgent desire for an early warning system to allow them time to prepare for seizure onset. Surveys of dog owners with epilepsy have previously reported that some dogs can predict the onset of a seizure. The current study used an experimental design to investigate the alleged propensity of untrained pet dogs to react to human epileptic seizures. We hypothesised that seizures are associated with specific volatile organic compounds resulting in detectable odours which are the biomarker that triggers these reported behavioural changes in the dogs. Here we provide details of the first empirical test to demonstrate that pet dogs display several significant behavioural changes when they are exposed to seizure-related odours that apparently emanate from their owners. Using a repeated measures design experiment, recordings were made of the reactions of 19 untrained pet dogs to odours from sweat samples provided by three people with epilepsy and by two people without epilepsy (controls). The seizure-associated sweat samples were captured pre-seizure, during seizure and post-seizure. All samples were randomly delivered to individual dogs in a test area, using two bespoke pieces of apparatus called Remote Odour Delivery Mechanisms (RODM). One RODM delivered only experimental odours, the other delivered only control odours. Behavioural changes by the dogs on encountering the odour samples were recorded by video for later analysis. Consistent with our hypothesis, seizure-associated odours evoked significant behavioural changes in the dogs which were affiliative in nature and directed at their owners.
ARTICLE | doi:10.20944/preprints202106.0389.v2
Subject: Biology, Anatomy & Morphology Keywords: Tomatoes; Night low temperature; Physiological traits; Fruit yield; Tomato breeding; 28 correlation coefficients
Online: 19 July 2021 (10:01:59 CEST)
Tomato is exposure to diverse abiotic stresses. Cold stress is one of harsh environmental stresses and abnormal low temperature affects tomato growth and development including physio- logical disorders, flower drops, and abnormal fruit morphology, causing the decrease of tomato yield and a fruit quality. It is important to identify low temperature-(LT) tolerant tomato (Solanum lycopersicum L.) cultivars relying on different fruit types. This study focused on analyzing physiological traits of 35 tomato accessions with three different fruit types (cherry, medium, and large sizes) under night temperature set-points of 15°C for normal temperature (NT) and 10°C for LT, respectively. Plant heights (PH) of most tomato accessions in LT were remarkably decreased compared to those in NT. The growth of leaf length (LL) and leaf width (LW) was reduced depending on the genotypes under LT. In addition, the number of fruits (NFR), fruit set (FS), fruit yield (FY), and marketable yield (MY) were negatively affected in LT. The variation was further investigated by the correlation analysis, the principal component (PCA), and the cluster analysis. Interestingly, positive correlations between different vegetative and reproductive traits were uncovered. Multivariate analysis including the PCA and hierarchical clustering classified LT-treated 35 tomato accessions into four major groups. The identified accessions were associated with vegetative and reproductive parameters on positive directions and might be utilized for breeding programs on selecting LT-tolerant cultivars.
Fri, 16 July 2021
REVIEW | doi:10.20944/preprints202107.0384.v1
Subject: Biology, Anatomy & Morphology Keywords: miRNAs, valvulopathy, aortic stenosis, calcification, delivery systems
Online: 16 July 2021 (15:26:09 CEST)
Micro-RNAs have been recently investigated in preclinical and clinical research as regulators of valvulopathies pathogenesis, diagnostic biomarkers and therapeutical targets. Evidences from in-vivo and in-vitro studies demonstrated stimulatory or inhibitory roles in mitral valve prolapse, aortic leaflet fusion and calcification pathways, specifically osteoblastic differentiation and transcription factors modulation. Tissue expression assessment and comparison between physiological and pathological phenotypes or different disease entities, including mitral valve prolapse and mitral chordae tendineae rupture, emerged as the best strategies to address mi-RNAs over or under-representation. In this review we discuss the fundamental intracellular homeostatic and cardiogenetic pathways regulated by mi-RNAs leading to defects in mitral and aortic valves, congenital heart diseases and the possible therapeutical strategies targeting them. Mi-RNAs inhibitors comprise antisense oligonucleotides and sponge vectors while mi-RNA mimics, mi-RNA expression vectors and small molecules are possible practical strategies to increase their activity. Advantages and technical limitations, including instability and complex pharmacokinetics are also presented. Novel strategies, such as nanoparticles and liposomes, are conclusively described to improve knowledge on these molecules delivery and establish future personalized treatment directions.
ARTICLE | doi:10.20944/preprints202106.0468.v2
Subject: Biology, Anatomy & Morphology Keywords: Pollinator; landscape; land use; urban rural gradient; Japanese honeybee; honey; pollen; nutrition.
Online: 16 July 2021 (13:04:52 CEST)
Pollinators are being threatened globally by urbanisation and agricultural intensification, driv-en by a growing human population. Understanding these impacts on landscapes and pollinators is critical to ensuring a robust pollination system. Remote sensing data on land use attributes have previously linked honeybee nutrition to land use in the Western Honeybee (Apis mellifera L.). Here, we instead focus on the less commonly studied Apis cerana japonica – the Japanese Honeybee. Our study presents preliminary data comparing forage (honey and pollen) with land use across a rural-urban gradient from 22 sites in Kyushu, southern Japan. Honey samples were collected from hives between June 2018 and August 2019. Pollen were collected and biotyped from hives in urban and rural locations (n = 4). Previous studies of honey show substantial vari-ation in monosaccharide content. Our analysis of A. cerana japonica honey found very little varia-tion in glucose and fructose (which accounted for 97% of monosaccharides), despite substantial differences in surrounding forage composition. As expected, we observed temporal variation in pollen foraged by A. cerana japonica, likely dependent on flowering phenology. These prelimi-nary results suggest that the forage and nutrition of A. cerana japonica may not be negatively af-fected by urban land use. This highlights the need for further comparative studies between A. cerana japonica and A. mellifera as it could suggest a resilience in pollinators foraging in their na-tive range.
Subject: Biology, Anatomy & Morphology Keywords: Arabidopsis; HY2; salt stress; seed germination; proteome; DRPs
Online: 16 July 2021 (13:04:26 CEST)
Phytochromobilin (PΦB) participates in the regulation of plant growth and development as an important synthetase of photoreceptor phytochromes (phy). And Arabidopsis Long Hy-pocotyl 2 (HY2) appropriately works as a key PΦB synthetase. However, whether HY2 takes part in plant stress response signal network remains unknown. Here, we described the func-tion of the HY2 in NaCl signaling. The hy2 mutant was NaCl-insensitive, whereas HY2-overexpressing lines showed NaCl-hypersensitive phenotypes during seed germination. The exogenous NaCl induced the transcription and the protein level of HY2 which positively mediated the expression of downstream stress-related genes of RD29A, RD29B and DREB2A. Further quantitative proteomics showed the patterns of 7,391 proteins under salt stress. HY2 was then found to specifically regulate 215 differentially regulated proteins (DRPs) which, according to GO enrichment analysis, were mainly involved in ion homeostasis, flavonoid biosynthetic & metabolic, hormone response (SA, JA, ABA, ethylene), reactive oxygen spe-cies (ROS) metabolic, photosynthesis and detoxification pathway to respond to salt stress. More importantly, ANNAT1-ANNAT2-ANNAT3-ANNAT4 and GSTU19-GSTF10-RPL5A-RPL5B-AT2G32060, two protein interaction networks specifi-cally-regulated by HY2, jointly participated in the salt stress response. These results direct the pathway of HY2 participating in salt stress, and provide new insights for the plant to re-sist salt stress.
REVIEW | doi:10.20944/preprints202107.0367.v1
Subject: Biology, Anatomy & Morphology Keywords: Fever; Beneficial fever; Infections; WHO; Fever Management; Guidelines; Antipyretic; Mortality; Heat Shock; Inflammation; COVID-19; Respiratory diseases; Paracetamol
Online: 16 July 2021 (09:40:35 CEST)
Fever remains an integral part of the acute clinical diseases management, esp. viral, for which effective therapeutics remain desired. However, the presence of often confusing fever reduction recommendations for COVID-19 in the public domain during the pandemic, as late as 28 April 2021, seems to suggest the reduction of any ‘uncomfortable’ fever ranging from 37.8 - 39oC, as opposed to WHO fever reduction guidelines (≥39oC), urgently need attention. The confusion could percolate down into different agencies who look up to these agencies for guidance in framing their own, denying the benefits of fever to populations, and effectively undo whatever successive WHO’s guidelines have achieved in the last two decades. The existence of conflicting guidelines in public domains which are open to interpretations has consequences to public health and the healthcare infrastructure, on implementation. For controlling acute infectious diseases, esp. viral, the fever remains the most important enabler. Historically, our chief obstacles to harnessing the benefits of fever in acute clinical diseases with limited therapeutics had been: a) widespread myths about ‘fevers’ arising from a general misunderstanding of basic facts; b) presence of confusing guidelines by different agencies which are open to alternate interpretation. The article attempts to briefly indicate the benefits of fever in disease resolution, dispel myths, underline vagueness in illustrative national guidelines and the need to align them with evidence-based WHO guidelines, as it has the potential to perpetuate myths/confusion in masses leading to adverse impact on disease management – more morbidity and mortality from diseases including COVID-19.
Subject: Biology, Anatomy & Morphology Keywords: Chlamydia; bacteria community; cryo-soft X-ray tomography; segmentation
Online: 16 July 2021 (08:57:06 CEST)
The impact of the cell community on its individual components in the prokaryotic realm is often overlooked. However, in the case of intracellular pathogens, where each infected cell can be considered as a single community, understanding how a population adapts to its environment to evolve and successfully propagate is key. Chlamydia infections are characterised by a silent propagation of the bacteria within individual hosts and the wider population. Chlamydia are strict intracellular pathogens residing within a specialised membrane-bound compartment called the inclusion. The life cycle of Chlamydia involves altering between the invasive elementary bodies (EBs) and replicative reticulate bodies (RBs). We have used cryo-soft X-ray tomography to observe individual inclusions, combining excellent resolution (40 nm) and large volume imaging (up to 16 µm). Combined with a semi-automated segmentation pipeline, we were able to consider each inclusion as an individual bacterial niche. Within the inclusion, we identified and classified different forms of the bacteria and confirmed the recent finding that RBs have a variety of volumes (small, large and abnormal). Moreover, we demonstrate that the proportions of these different RB forms depend on the bacterial concentration in the cell demonstrating the impact of the group on its individual component. We conclude that each inclusion operates as an autonomous community which regulates the characteristics of individual bacteria within the inclusion
Thu, 15 July 2021
ARTICLE | doi:10.20944/preprints202107.0356.v1
Subject: Biology, Anatomy & Morphology Keywords: airway cell exosomes; viral infection; microglia; mitochondria; reactive oxygen species
Online: 15 July 2021 (11:12:49 CEST)
Viral infections induce exosomes containing viral material and inflammatory factors. During respiratory tract infection, exosomes can easily cross the blood-brain barrier and transmit the inflammatory signal to the brain; however, such a hypothesis has no experimental evidence. The study investigated whether exosomes from virus mimetic poly (I:C)-primed airway cells enter the brain and interact with brain immune cells microglia. Airway cells were isolated from Wistar rats and BALB/c mice; microglial cell cultures - from Wistar rats. Exosomes from poly (I:C)-stimulated airway cell culture medium were isolated by precipitation, visualised by transmission electron microscopy, and evaluated by nanoparticle analyser; exosomal markers CD81 and CD9 were determined by ELISA. For in vitro and in vivo tracking, exosomes were loaded with Alexa Fluor 555-labelled RNA. Intracellular reactive oxygen species (ROS) were evaluated by DCFDA fluo-rescence and mitochondrial superoxide - by MitoSOX. The exosomes from poly (I:C)-primed airway cells entered the brain within an hour after intranasal introduction, were internalised by microglia, and induced intracellular and intramitochondrial ROS production. There was no ROS increase in microglial cells was after treatment with exosomes from airway cells untreated with poly (I:C). The data indicate that virus-primed airway cell exosomes might enter the brain and induce the activation of microglial cells.
ARTICLE | doi:10.20944/preprints202107.0352.v1
Subject: Biology, Anatomy & Morphology Keywords: Fusarium oxysporum f. sp. cubense; Panama disease; epidemiology; disease impact; loss; yield; management.
Online: 15 July 2021 (10:12:43 CEST)
The effective management of Fusarium wilt of bananas (FW) depends on the knowledge of the disease dynamics in time and space. The objectives of this work were: To estimate disease intensity and impact, and to investigate the spatial and temporal dynamic of FW. Fields planted with Silk (n = 10), Pome (n = 17) or Cavendish (n = 3) banana subgroups were surveyed in Brazil, totaling 95 ha. In each field, all plants were visually assessed and diseased plants were georeferenced. The incidence of FW and the impact of the disease on yield on a regional scale were estimated. Spatial patterns were analyzed using quadrat- and distance-based methods. FW incidence ranged from 0.09 to 41.42%, being higher in Silk fields (median = 14.26%). Impacts of epidemics on yield ranged from 18.4 to 8,192.5 kg.ha-1.year-1, with a median of 935.2 kg.ha-1.year-1. The higher economic impact of the disease was observed on Silk cultivar with a median loss of US$ 910.5 ha-1.year-1. Overall, estimated losses increased on average by US$ 109.8 ha-1.year-1 at each 1% of incidence. Aggregation of FW was detected by all analytical methods in 13 fields (1 of Cavendish, 11 of Pome and 1 of Silk). In the other 17 fields, at least one analytical method did not reject the null hypothesis of randomness. One field (5 ha), composed of six plots, was selected for spatial and temporal studies during two years with bi-monthly assessments. A sigmoidal curve represented the FW progress and the Gompertz model best fitted disease progress. The level of aggregation varied over time, and evidence of secondary infection to neighboring and distant plants were detected. FW is a widespread problem in Brazil and yield losses can be of high magnitude. Epidemiology-based management strategies can now be better established.
ARTICLE | doi:10.20944/preprints202107.0348.v1
Subject: Biology, Anatomy & Morphology Keywords: pepper; heat tolerance; photosynthesis; proline; electrical conductivity; fruit; yield
Online: 15 July 2021 (09:42:13 CEST)
Understanding the mechanism for heat tolerance is important for the hot pepper breeding program to develop heat-tolerant cultivars in changing climate. This study was conducted to investigate physiological and biochemical parameters related to heat tolerance and to determine leaf heat damage levels critical for selecting heat-tolerant genotypes. Seedlings of two commercial cultivars, heat-tolerant ‘NW Bigarim’ (NB) and susceptible ‘Chyung Yang’ (CY), were grown in 42 °C for ten days. Photosynthesis, electrolyte conductivity, proline content were measured among seedlings during heat treatment. Photosynthetic rate was significantly reduced in ‘CY’ but not in ‘NB’ seedlings in 42 °C. Stomatal conductivity and transpiration rate was significantly higher in ‘NB’ than ‘CY’. Proline content was also significantly higher in ‘NB’. After heat treatment, leaf heat damages were determined as 0, 25, 50 and 75% and plants with different leaf heat damages were moved to a glasshouse (30–32/22–24 °C in day/night). The growth and developmental parameters were investigated until 70 days. ‘NB’ was significantly affected by leaf heat damages only in fruit yield while ‘CY’ was in fruit set, number and yield. ‘NB’ showed fast recovery after heat stress compared to ‘CY’. These results suggest that constant photosynthetic rate via increased transpiration rate as well as high proline content in heat stress condition confer faster recovery from heat damage of heat-tolerant cultivars in seedlings stages.
ARTICLE | doi:10.20944/preprints202107.0344.v1
Subject: Biology, Anatomy & Morphology Keywords: Phytoremediation; Petroleum hydrocarbon-degrading bacteria; Salix; Eleocharis; Alkanes; Polycyclic aromatic hydrocarbons; Plant growth promoting rhizobacteria
Online: 15 July 2021 (09:27:25 CEST)
Phytoremediation, a method of phytomanagement using the plant holobiont to clean up polluted soils, is particularly effective for degrading organic pollutants, such as alkanes and polycyclic aromatic hydrocarbons (PAHS). However, the respective contributions of host plants and their associated microbiota within the holobiont to the efficiency of phytoremediation is poorly understood. Identification of plant-associated bacteria capable of efficiently utilizing these compounds as carbon source while stimulating plant-growth, is a keystone for phytomanagement engineering in order to improve the efficiency of pollutant removal. In this study, we sampled the rhizosphere and the surrounding bulk soil of Salix purpurea and Eleocharis obusta from the site of a former petrochemical plant in Varennes, QC, Canada. Our objectives were to: (i) isolate and identify indigenous bacteria inhabiting these biotopes; (ii) assess the ability of isolated bacteria to utilize alkanes (dodecane and hexadecane) and PAHs (naphthalene, phenanthrene and pyrene) as the sole carbon source, and (iii) determine the plant growth-promoting (PGP) potential of the isolates using five key traits. A total of 438 morphologically different bacterial isolates were obtained, purified, preserved and identified through PCR and 16S rRNA gene sequencing. Identified isolates represent 62 genera, including taxa such as Acinetobacter, Arthrobacter, Bacillus, Enterobacter, Nocardia, Pseudomonas, Rhodococcus, Streptomyces and Variovorax. Approximately, 32% of bacterial isolates, including Arthrobacter, Pseudomonas, Streptomyces, Enterobacter, Nocardia, Acinetobacter and Microbacterium, were able to utilize all five different hydrocarbons compounds. Additionally, 5% of tested isolates belonging to genera Pseudomonas, Acinetobacter, Serratia, Klebsiella, Microbacterium, Bacillus and Stenotrophomonas possessed all five of the tested PGP functional traits. This culture collection of diverse, petroleum-hydrocarbon degrading bacteria, with multiple PGP traits, represents a valuable resource for future use in environmental bio- and phyto-technology applications, including phytoremediation of petroleum hydrocarbons contaminated soils and phytomanagement of anthropized areas.
Wed, 14 July 2021
REVIEW | doi:10.20944/preprints202107.0339.v1
Subject: Biology, Anatomy & Morphology Keywords: Blood feeding; Vertebrate host; transovarial transmission; vectorial capacity.
Online: 14 July 2021 (14:46:58 CEST)
The aim of the work was to update the distribution range of Aedes (Stegomyia) albopictus Skuse in the Americas, review the blood feeding patterns and compare the minimum infection rate (MIR) between studies of vertical and horizontal transmission of arboviruses. The current distribution of Ae. albopictus encompasses 21 countries in the Americas. In eleven published papers on the blood feeding pattern of Ae. albopictus, DNA from 16 species of mammals and five species of avian species was found. The most common host is humans, and dogs. We found 24 published papers on the identification of arboviruses in wild populations of Ae. albopictus with the potential to infect humans and animals. Eight arboviruses have been isolated in different studies carried out in Brazil, USA, Mexico, Colombia, and Costa Rica. Fifty-eight percent (14/24) of the publications reported vertical transmission of arbovirus. Positive pools were higher in vertical (8.45%) compared to horizontal transmission (0.97%). This was supported by the MIR, which was 3 times greater in vertical (MIR=3.21) than horizontal transmission (MIR= 1.08). In conclusion, Ae. albopictus is an invasive mosquito with wide phenotypic plasticity to adapt to broad and new areas, high vectorial competence to transmit several arboviruses mainly by transovarial transmission, it can participate in the endemic transmission, and serve as a bridge vector for emerging arboviruses between sylvan, rural, and urban areas.
Subject: Biology, Anatomy & Morphology Keywords: uremia; uremic toxins; microbiome; chronic kidney disease
Online: 14 July 2021 (13:04:35 CEST)
Uremic toxins are the compounds that emerge in the blood when kidney excretory function is impaired. The cumulative detrimental effect of uremic toxins results in numerous health problems and eventually death during acute or chronic uremia, especially in end-stage renal disease. More than 100 different solutes rise during uremia; however, the exact origin for most of them is still discussable. There are 3 main sources for such compounds: exogenous ones are consumed with food, whereas endogenous are produced by host metabolism or by symbiotic microbiota metabolism. In this article, we identified uremic toxins presumably of gut microbiota origin. We analyzed various databases to get information on enzymatic reactions in bacteria and human organism potentially yielded uremic toxins and to determine what toxins could be synthetized in bacteria residing in human gut. We selected biochemical pathways resulting in uremic toxins synthesis related to specific bacterial strains, and revealed links between toxin concentration in uremia and the proportion of different bacteria species, which can synthesize it. Moreover, we defined the relative abundance of human toxin-generating enzymes as well as the possibility of a particular toxin synthesis by the human metabolism. Finally, we analyzed which bacteria are potentially producing the biggest number of uremic toxins as well as which bacteria are decomposing them. Our study presents a bioinformatics-based approach for both elucidation of the origin of uremic toxins and search of the most likely human microbiome producers of toxins that can be targeted and used for the therapy of adverse consequences of uremia.
ARTICLE | doi:10.20944/preprints202107.0333.v1
Subject: Biology, Anatomy & Morphology Keywords: Dsup; tardigrade; UV-C; Oxidative stress; DNA repair; transcription factors
Online: 14 July 2021 (12:49:11 CEST)
The Ramazzottius varieornatus tardigrade is an extremotolerant terrestrial invertebrate belonging to the phylum of Tardigrada. At a length of 0.1-1.0 mm, tardigrades are small animals with an exceptional tolerance to extreme conditions such as high pressure, chemicals and irradia-tion. These properties have been attributed to the recently-discovered Dsup protein. Dsup is a nucleosome-binding protein that prevents DNA damage against X-ray and oxidative stress without impairing cell life, also in Dsup-transfected animal and plant cells. However, the precise “protective” role of this protein is still under study. We performed experiments on human cells and shows that, as compared to control cells, Dsup+ cells are more resistant to UV-C exposure and H2O2. Real-time PCR identified different expression patterns of endogenous genes involved in apoptosis, cell survival and DNA damage repair in Dsup+ cells in response to H2O2 and UV-C. While H2O2 treatment in Dsup+ cells only marginally involved the activation of pathways responsible for DNA repair reinforcing the idea of a direct protective effect of the protein on DNA, in UV-C exposed cells, Dsup efficiently upregulates DNA damage repair genes. In conclusion, our data may help to delineate the different mechanisms by which the Dsup protein operates in response to different insults.
REVIEW | doi:10.20944/preprints202107.0313.v1
Subject: Biology, Anatomy & Morphology Keywords: Pig; PRRS; PRRS virus; immune response; disease resistance; disease control
Online: 14 July 2021 (09:40:20 CEST)
The control of Porcine Reproductive and Respiratory Syndrome (PRRS) is still a major issue worldwide in the pig farming sector. Despite extensive research efforts and the practical experience gained so far, the syndrome still heavily affects farmed pigs worldwide and challenges established beliefs in veterinary virology and immunology. The clinical and economic repercussions of PRRS are based on concomitant, additive features of virus pathogenicity, host susceptibility and influence of environmental, microbial and non-microbial stressors. This makes a case for integrated, multi-disciplinary research efforts in which the three types of contributing factors are critically evaluated toward the development of successful disease control strategies. These could be definitely eased by the definition of reliable markers of disease risk and virus pathogenicity. As for the host’s susceptibility to PRRSV infection and disease onset, the roles of both innate and adaptive immune responses are still ill-defined. In particular, the overt discrepancy between passive and active immunity and the uncertain role of adaptive immunity vis-à-vis an established PRRSV infection should prompt the scientific community to the development of novel research schemes, in which apparently diverging and contradictory findings could be reconciled, and eventually brought to a satisfactory conceptual framework.
Tue, 13 July 2021
ARTICLE | doi:10.20944/preprints202107.0311.v1
Online: 13 July 2021 (15:11:54 CEST)
The SnRK gene family is a key regulator playing an important role in plant stress response by phosphorylating the target protein to regulate the signalling pathways. The function of SnRK gene family has been reported in many species but is limited to Triticum asetivum. In this study, SnRK gene family in the wheat genome was identified and its structural characteristics were described. One hundred forty-seven SnRK genes distributed across 21 chromosomes were identified in the Triticum aestivum genome and categorised into three subgroups (SnRK1/2/3) based on phylogenetic analyses and domain types. The gene intron-exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication between the wheat, Arabidopsis, rice and barley genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. SnRK genes showed differential expression patterns in leaves, roots, spike, and grains. Redundant stress-related cis-elements were also found in the promoters of 129 SnRK genes and their expression levels varied widely following drought, ABA and light regulated elements. In particular, TaSnRK2.11 had higher and increased expression under the abiotic stresses and can be a candidate gene for the abiotc stress tolerance. The findings will aid in the functional characterization of TaSnRK genes for further research.
REVIEW | doi:10.20944/preprints202107.0307.v1
Online: 13 July 2021 (12:18:20 CEST)
The study of the development of the vertebrate retina can be addressed from several perspectives: from purely qualitative to a more quantitative approach that takes into account its spatiotemporal features, its three dimensional structure and also the regulation and properties at the systems level. Here we review the ongoing transition towards a full four-dimensional characterization of the developing vertebrate retina, focusing on the challenges at the experimental, image acquisition, image processing and quantification. Using the developing zebrafish retina, we illustrate how quantitative data extracted from these type of highly dense three-dimensional tissues depends strongly on the image quality, image processing and algorithms used to segment and quantify. Therefore, we propose that the scientific community that focuses on developmental systems could strongly benefit from a more detailed disclosure of the tools and pipelines used to process and analyze images from biological samples.
ARTICLE | doi:10.20944/preprints202107.0305.v1
Subject: Biology, Anatomy & Morphology Keywords: Dioscorea spp.; flow cytometry; chromosome counting; ploidy level; DArTseq
Online: 13 July 2021 (11:29:47 CEST)
Yam (Dioscorea spp.) is a monocotyledonous herbaceous vine plant grown in the tropics and subtropics. It is a multi-species plant with varied intra- and interspecific ploidy levels. Of the 600 species, 11 are cultivated staple supporting the livelihood of over 300 million people. The paucity of information on ploidy and the genomic constitution is a significant challenge to the crop’s genetic improvement through crossbreeding. The objective of this study was to investigate the ploidy levels of 236 accessions across six cultivated and two wild species using chromosome counting, flow cytometry and genotyping-based ploidy determination methods. Results obtained from chromosome counting and genotyping-based ploidy determination were in agreement. In majority of the accessions, chromosome counting and flow cytometry were congruent, allowing future rapid screening of ploidy levels using flow cytometry. Among cultivated accessions, 168 (71%) were diploid, 50 (21%) were triploid, and 12 (5%) were tetraploid. Two wild species included in the study were diploids. Resolution of ploidy level in yams offers opportunities for implementing successful breeding programmes through intra- and inter-specific hybridization.
COMMUNICATION | doi:10.20944/preprints202107.0302.v1
Subject: Biology, Anatomy & Morphology Keywords: Aedes aegypti; Insecticides resistance; kdr mutations; Nigeria
Online: 13 July 2021 (11:26:32 CEST)
The outbreak of yellow fever transmitted by Aedes aegypti has been of major concern in Nigeria, this mosquito also transmits several other arboviruses globally. The control of many of the Aedes aegypti borne diseases relies heavily on the use of insecticides. Therefore, constant monitoring of insecticide resistance status and associated mechanisms in crucial within the local population. Here, we determined the resistance profile of adult Aedes aegypti from Ikorodu Local Government Area of Lagos State, Nigeria to different classes of insecticides using WHO procedures. The presence of kdr mutations F1534C, S989P and V1016G were also determined among resistant populations using molecular methods. High level of resistance to DDT and pyrethroid was rec-orded in Aedes aegypti in this study, though possible resistance to deltamethrin was reported in one of the locations. Resistance to bendiocarb was recorded in Majidun community while Aedes aegypti in both locations were susceptible to malathion. The presence of F1534C mutation associated with resistance in Aedes aegypti was detected for the first time in Nigeria, and the presence of S989P mutation was detected singly and in co-occurrence with F1534C for the first time in Africa. The role of these mutations in resistance phenotype expressed in Aedes aegypti in this study area need to established.
ARTICLE | doi:10.20944/preprints202107.0286.v1
Subject: Biology, Anatomy & Morphology Keywords: axial canal; reef-building coral; high resolution micro-computed tomography; Acropora muricata; calcium transport; deposit
Online: 13 July 2021 (10:02:33 CEST)
In Acropora, the complex canals in a coral colony connect all polyps into a holistic network to collaborate in performing biological processes. There are various types of canals, including calice, axial canals, and other internal canals, with structures that are dynamically altered during different coral growth states due to internal calcium transport. However, few studies have considered the regulation of calcium transport in Acropora. In this study, we investigated the morphological changes of the axial canal in six Acropora muricata samples by high resolution micro-computed tomography, observing the patterns of the axial canal during the processes of new branch formation and truncated branch rebuilding. We visualized the formation of a new branch from a calice and deposition of the iconic hexactin skeletons in the axial canal. Furthermore, the diameter and volume changes of the axial canal in truncated branches during rebuilding processes were calculated, revealing that the volume ratio of calcareous deposits in the axial canal exhibit significant increases within the first three weeks, returning to levels in the initial state in the following week. This work indicates that the axial canal can transport calcium to form hexactin skeletons in a new branch and rebuild the tip of a truncated branch. The calcium transport along canal network regulates various growth processes, including budding, branching, skeleton forming, and self-rebuilding of an Acropora colony. Understanding the changes in canal function under normal and extreme conditions will provide theoretical guidance for restoration and protection of coral reefs.
Mon, 12 July 2021
ARTICLE | doi:10.20944/preprints202107.0275.v1
Subject: Biology, Anatomy & Morphology Keywords: Genome sequencing; de novo Assembly; Scaffolding; Chromosome-scale; Nanopore sequencing; Long reads; Optical maps; Bionano Genomics; Hi-C; Omni-C; Pore-C; Plant genomes
Online: 12 July 2021 (22:55:37 CEST)
With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Indeed, sequencing techniques but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome-scale is now feasible at the laboratory scale. Current technologies, and especially long-range technologies, are numerous and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range techniques, optical mapping, Omni-C and Pore-C sequencing libraries commercialized by Bionano Genomics, Dovetail Genomics and Oxford Nanopore Technologies respectively, or a combination of the three, in order to evaluate the capability of each technology.
REVIEW | doi:10.20944/preprints202107.0273.v1
Subject: Biology, Anatomy & Morphology Keywords: Plastisphere; Plastic biofilms; Microbial communities; Marine plastic pollution; Plastic biodegradation
Online: 12 July 2021 (22:12:28 CEST)
The microbial colonisers of plastics – the ‘plastisphere’ – can affect all interactions that plastics have with their surrounding environments. While only specifically characterised within the last 10 years, at the beginning of 2021 there were 140 primary research and 65 review articles that investigate at least one aspect of the plastisphere. We gathered information on the locations and methodologies used by each of the primary research articles, highlighting several aspects of plastisphere research that remain understudied: (i) the non-bacterial plastisphere constituents; (ii) the mechanisms used to degrade plastics by marine isolates or communities; (iii) the capacity for plastisphere members to be pathogenic or carry antimicrobial resistance genes; and (iv) meta-OMIC characterisations of the plastisphere. We have also summarised the topics covered by the existing plastisphere review articles, identifying areas that have received less attention to date – most of which are in line with the areas that have fewer primary research articles. Therefore, in addition to providing an overview of some fundamental topics such as biodegradation and community assembly, we discuss the importance of eukaryotes in shaping the plastisphere, potential pathogens carried by plastics and the impact of the plastisphere on plastic transport and biogeochemical cycling. Finally, we summarise the future directions suggested by the reviews that we have evaluated and suggest other key research questions.
ARTICLE | doi:10.20944/preprints202107.0239.v1
Subject: Biology, Anatomy & Morphology Keywords: Probiotics; Canine; Lactobacilli; Feed supplementation; Infectious diseases
Online: 12 July 2021 (10:13:26 CEST)
Antibiotics are commonly used to treat infectious diseases. However, massive and inappropriate antibiotics usage cause many problems including the emergence and spread of antibiotic-resistant bacteria. To avoid this issue, in modern countries the interest of using probiotics in feed supplementation to promote health and prevent or treat intestinal infectious diseases in companion animals like dogs has been increasing. We evaluate the probiotic potential of Lactobacilli isolated from healthy dogs faeces. The isolated Lactobacilli were first confirmed by 16SrRNA sequencing, then in vitro tests were conducted to assess survival potential of Lactobacilli under simulated gastrointestinal conditions and adhesion ability to gut epithelia, effects on epithelial barrier function, anti-inflammatory activities, effects on defensin peptides (beta-defensin 3) and inhibitory effects on common pathogens. Lactobacilli showed considerable potential to survive in simulated gastrointestinal environmental conditions, low pH, high bile salt concentrations along with good adhesion properties with MODE-K cells. Pathogenic bacterial growth and their adhesion to MODE-K cells was significantly inhibited by Lactobacilli. Real-time PCR analyses further demonstrated that L. acidophilus strain AR1 and AR3 inhibit Salmonella-induced proinflammatory cytokines (IL-6, IL-8, 1ꞵ) production and reinforce expression of tight junction protein (occludin). None of the strain induce mRNA expression of beta-defensin 3 in MODE-K cells. Based on in vitro results the L. acidophilus strain AR1 has potential to be supplemented in canine feed. However, further in vivo studies investigating health-promoting effects are awaited.
Thu, 8 July 2021
ARTICLE | doi:10.20944/preprints202107.0194.v1
Subject: Biology, Anatomy & Morphology Keywords: Tillage; trencher; sugarcane plantation; energy consumption; conservation agriculture.
Online: 8 July 2021 (10:52:17 CEST)
An efficient design of conservation tillage trencher (CTT) saves time, natural resources, and conserves soil health by avoiding vigorous soil disturbance of tillage operations. A two-wheel tractor operated CTT has constructed with modified rotary shafts, toolbar frames, depth control bars, bed shapers and chisel ploughs for conservation tillage operation of sugarcane plantation. The performance evaluation of developed CTT was tested for comparing the suitability with small-scale farmer’s practice (SFP) and large farm practice (LFP). Finally, the CTT is applied for preparing sugarcane farmland in different conservation tillage methods of i) bed cum trenching (BT), ii) zero-tillage trenching (ZT) and iii) strip-tillage (ST). The performance of effective field capacities of CTT were 0.14 ha h-1, 0.12 ha h-1 and 0.14 ha h-1 for BT, ZT and ST, respectively. Developed CTT saved time 80% and 26-37% over SFP and LFP, and required 96% and 26-36% less labour than SFP and LFP, respectively. Conservation tillage required 7-10 l ha-1diesel whereas SFP and LFP required 25 l ha-1and 65 l ha-1, which reduced CO2 emission by 60-72% and 85-89% compared to SFP and LFP, respectively. Ultimately, newly developed CTT saved sugarcane land preparation costs by 86% to 90% compared to conventional tillage systems.
Wed, 7 July 2021
ARTICLE | doi:10.20944/preprints202107.0168.v1
Subject: Biology, Anatomy & Morphology Keywords: lizard; autotomy; tail; locomotion; performance; temperature; predation
Online: 7 July 2021 (08:00:27 CEST)
Caudal autotomy is a dramatic adaptation used by many lizard species to evade predators. Most studies to date indicate that caudal autotomy impairs lizard locomotor performance. Surprisingly, some species bearing the longest tails show negligible impacts of caudal autotomy on sprint speed. Part of this variation has been attributed to lineage effects. For the first time, we model the effects of caudal autotomy on the locomotor performance of a gymnophthalmid lizard, Micrablepharus atticolus, characterized by a long and bright blue tail. To improve model accuracy, we incorporated the effects of several covariates. We found that body temperature, pregnancy, mass, collection site, and the length of the regenerated portion of the tail were the most important predictors of locomotor performance in Micrablepharus atticolus. However, sprint speed was unaffected by tail loss. Apparently, the long tail of M. atticolus is more useful when using undulation amidst the leaf litter and not when using quadrupedal locomotion on a flat surface. Our findings highlight the intricate relationships among physiological, morphological, and behavioral traits. We suggest that future studies about the impacts of caudal autotomy among long-tailed lizards should consider the role of different microhabitats/substrates on locomotor performance, using laboratory conditions that closely mimic their natural environments.
Tue, 6 July 2021
COMMUNICATION | doi:10.20944/preprints202107.0160.v1
Online: 6 July 2021 (14:58:24 CEST)
Exosomes are associated with cancer progression, pregnancy, cardiovascular diseases, central nervous system–related diseases, immune responses and viral pathogenicity. However, study on the role of exosomes in the immune response of teleost fish, especially antiviral immunity, is limited. Herein, serum-derived exosomes from mandarin fish were used to investigate antiviral effect for the exosomes of teleost fish. Exosomes were isolated from mandarin fish serum by ultracentrifugation could internalize into Mandarin fish fry (MFF-1) cells and inhibited Infectious spleen and kidney necrosis virus (ISKNV) infection. To further investigated the underlying mechanisms of exosomes in inhibiting ISKNV infection. The protein composition of serum-derived exosomes was by analysis mass spectrometry and found that myxovirus resistance 1 (Mx1) was incorporated in the exosomes. Furthermore, the scMx1 protein was proved transferred to the recipient cells though the exosomes. Our results found that the serum-derived exosomes from mandarin fish could inhibit ISKNV replication and suggested an underlying mechanism of the serum-derived exosomes antivirus is that serum-derived exosomes incorporation of the Mx1 protein into exosomes and delivery into recipient cells. This study provided an evidence for the important antiviral role of exosomes in the immune system of teleost fish.
ARTICLE | doi:10.20944/preprints202107.0142.v1
Subject: Biology, Anatomy & Morphology Keywords: Arabidopsis thaliana; indole-3-acetic acid; jasmonic acid; plant hormone crosstalk; transcriptional regulation; wound response; biotic stress; growth-defense trade-off
Online: 6 July 2021 (12:20:15 CEST)
The indole-3-pyruvic acid pathway is the major route for auxin biosynthesis in higher plants. Tryptophan aminotransferases (TAA1/TAR) and members of the YUCCA family of flavin-containing monooxygenases catalyze the conversion of L-tryptophan via indole-3-pyruvic acid into indole-3-acetic acid (IAA). It has been described that locally produced jasmonic acid (JA) in response to mechanical wounding, triggers de novo-formation of IAA through the induction of two YUCCA genes, YUC8 and YUC9. Here, we report the direct involvement of a small number of basic helix-loop-helix transcription factors of the MYC family in this process. We show that the JA-mediated regulation of YUC8 and YUC9 gene expression depends on the abundance of MYC2, MYC3, and MYC4. In support of this observation, seedlings of myc knockout mutants displayed a strongly reduced response to JA-mediated IAA formation. In addition, transactivation assays provided experimental evidence for the binding of the MYC transcription factors to a particular tandem G-box motif abundant in the promoter regions of YUC8 and YUC9, but not in those of the other YUCCA genes. Moreover, we clearly demonstrate that YUC8ox and YUC9ox overexpressing plants show less damage after spider mite infestation, thereby underlining a role of auxin in plant responses toward biotic stress cues.
REVIEW | doi:10.20944/preprints202107.0135.v1
Subject: Biology, Anatomy & Morphology Keywords: epigenetics; epigenetic variation; chromatin changes; omics; climate-resilient crops
Online: 6 July 2021 (11:32:11 CEST)
Climate change has had a significant impact on many ecosystems worldwide, prompting native population species to adapt to the current weather patterns eventually. Pre-existing genetic variation in populations explains part of this adaptation. Still, recent studies have shown that new stable phenotypes can be generated through epigenetic modifications in just a few generations, thereby contributing to the stability and survival of plants in their natural habitat as they eventually adjust to the surrounding impacts. The state of chromatin inside plant cells varies, allowing cells to fine-tune their transcriptional profiles to better adapt to stimuli from the external environment. Within a cell, chromatin state changes such as post-transcriptional histone modifications and variations, DNA methylation, and non-coding RNA activity are all examples of chromatin state alterations that may epigenetically dictate certain transcriptional outputs. Recent advances in the field of ‘Omics’ in major crops has made it easier to identify epigenetic changes and their impact on plant responses to environmental stresses. These epigenetic mechanisms thus play an important role in improving crop adaptation and resilience to changing environments. This variation that has emerged can thus be exploited in crop breeding, ultimately leading to the generation of stable climate-resilient genotypes.
ARTICLE | doi:10.20944/preprints202107.0130.v1
Subject: Biology, Anatomy & Morphology Keywords: Arbutus unedo; Bacillus cereus; Bacteria endophytes; Biological control; Phytophthora cinnamomi
Online: 6 July 2021 (09:42:41 CEST)
Arbutus unedo L. is a resilient tree with a circum-Mediterranean distribution. Besides its ecological relevance, it is vital for local economies as a fruit tree. Several microorganisms are responsible for strawberry tree diseases leading to production constrictions. Thus, the development of alternative plant protection strategies is necessary and bacteria endophytes may increase their host overall fitness and productivity. As agricultural practices are a driving factor of microbiota, this paper aimed to isolate, identify and characterize endophytic bacteria from strawberry tree leaves from plants growing spontaneously in a natural environment as well as from plants growing on orchards. 62 endophytes were isolated from leaves and identified as Bacillus, Paenibacillus, Pseudomonas, Sphingomonas and Staphylococcus. Although a slightly higher number of species was found in wild plants, no differences in terms of diversity indexes were found. Sixteen isolates were tested in vitro for their antagonistic effect against A. unedo mycopathogens. B. cereus was the most effective antagonist causing a growth reduction of 20% in Glomerella cingulata and 40% in Phytophthora cinnamomi and Mycosphaerella aurantia. Also, several endophytic isolates exhibited plant growth-promoting potential. This study provides insights into the diversity of endophytic bacteria in A. unedo leaves and their potential role as growth-promoters and pathogen antagonists.
ARTICLE | doi:10.20944/preprints202107.0123.v1
Subject: Biology, Anatomy & Morphology Keywords: Sitophilus oryzae; Natural insecticides; Pandanus amaryllifolius; Azadirachta indica
Online: 6 July 2021 (08:07:57 CEST)
The aim of this study was to determine the effect of Pandanus (Pandanus amaryllifolius 20 Roxb.) and Neem (Azadirachta indica) leaves powder on the repellency, mortality, and weight loss 21 of grains due to Sitophilus oryzae. The methodes of this study used a completely randomized design 22 (CRD) with 7 treatments and 4 replications. The results of this study indicate that the best treat- 23 ment in terms of causing repellency was the treatment of 10 grams of pandanus with a percentage 24 of 87.5%, while the best treatment in terms of causing pest mortality and was also able to reduce 25 the risk of rice weight loss due to Sitophilus oryzae was treatment 10 gram of neem with a mortality 26 percentage of 76.25% and weight loss of rice 3.14%. This research showed that neem leaf com- 27 pounds are better in terms of causing mortality, while Pandanus compounds are better in terms of 28 causing mortality of Sitophilus oryzae.
Mon, 5 July 2021
ARTICLE | doi:10.20944/preprints202107.0115.v1
Subject: Biology, Anatomy & Morphology Keywords: Controlled drainage; Water content; Salinity (EC); Mineral nitrogen; Nitrogen loss; Yield of oilseed sunflower
Online: 5 July 2021 (16:06:58 CEST)
Controlled drainage (CD) is an important agricultural measure for maintaining soil moisture and nutrients, controlling groundwater level, and increasing crop yield. In arid regions, CD can be used to improve the water supply in agriculture and reduce environmental pollution. In this study, we investigated the effect of CD, including a drainage depth of 40 cm (CWT1) and 70 cm (CWT2) during the plant growth period, free drainage (FD), and open ditch drainage (OD) on the migration of water, nutrients, and salts in the soil; the dynamics of groundwater level; the loss of soil nitrogen; and the growth of oilseed sunflower plants. Compared with FD, CD increased the water and nutrient content in the soil, reduced nitrogen loss, and enhanced the ability of the soil to continuously supply nitrogen to the oilseed sunflower plants, which benefited plant growth at later growth stages and reduced environmental pollution. During the period between irrigation at the budding stage and harvest stage, the average soil water content in the 0–20 cm soil layer in CWT1 increased by 3.67%, 4.78%, and 0.55%, respectively, compared with that in CWT2, FD, and OD. The soil mineral content in CWT1 was 25.17%, 35.05%, and 17.78% higher than that in CWT2, FD, and OD, respectively, indicating that higher soil salinity occurred at the later stage of plant growth in CWT1, which actually had little effect on the plants due to their enhanced salt tolerance and increased need for water and nutrients at that stage. In addition, CD delayed the decline in groundwater level, which allowed the plants to use groundwater at later growth stages, and as a result the yield and water use efficiency were improved. CWT1 significantly increased oilseed sunflower yield by 4.52–11.14% and increased water use efficiency by 1.16–10.8%. Moreover, CWT1 also increased the survival rate of the oilseed sunflower plants by 2.62–2.92%, and the plants demonstrated good growth. Therefore, under CD conditions, plants used soil water and nitrogen more efficiently and, as a result, their productivity was increased, and the water quality was improved.
ARTICLE | doi:10.20944/preprints202107.0111.v1
Subject: Biology, Anatomy & Morphology Keywords: untargeted approach; metabolites; drought stress; mulberry, LC-MS
Online: 5 July 2021 (15:47:17 CEST)
Mulberry is an economically significant crop for the sericulture industry worldwide. Stresses such as drought exposure have a significant influence on plant survival. Metabolome directly reflects plant physiological status; thus, a way to assess this impact is to perform a global metabolomic analysis. This study investigated the effect of drought stress on mulberry Yu-711 metabolic balance using a liquid chromatography-mass spectrometry (LC-MS) based on an untargeted metabolomic approach. For this objective, Yu-711 leaves were subjected to two weeks of drought stress treatment and control without drought stress. Multivariate and univariate statistical analyses highlighted numerous differentially-accumulated metabolic elements as a function of time and treatment. Drought stress led to a more differentiated metabolites response than the control. We found that the levels of total lipids and galactolipids, and phospholipids (PC, PA, PE) were significantly altered, producing 48% of the total differentially expressed metabolites. Fatty acyls were the most abundant lipids expressed and decreased considerably by 73.6%. Prenol lipids class of lipids increased in drought leaves. Other classes of metabolites, including polyphenols( flavonoids and cinnamic acid), organic acid (amino acids), carbohydrates, benzenoids, and organoheterocyclic, all had a dynamic trend in response to the drought stress. However, their levels under drought stress generally decreased significantly compared to the control. These results provide an overview of the metabolic profile of the mulberry plant through differentially-accumulated compounds and provide a better understanding of global plant metabolic changes in defense mechanisms.
REVIEW | doi:10.20944/preprints202107.0082.v1
Subject: Biology, Anatomy & Morphology Keywords: Nucleic Acid sensors; TREX1; cGAS; STING; RIG-I; Tumor angiogenesis; vascular normalization; vascular inflammation; endothelial cells; tumor microenvironment
Online: 5 July 2021 (09:31:26 CEST)
Endothelial cells form a powerful interface between tissues and immune cells. In fact, one of the underappreciated roles of endothelial cells is to orchestrate immune attention to specific sites. Tumor endothelial cells have a unique ability to dampen the immune responses and thereby maintain an immunosuppressive microenvironment. Recent approaches to trigger immune responses in cancers have focused on activating nucleic acid sensors such as cGAS/STING in combination with immunotherapies. In this review, we present a case for targeting nucleic acid sensing pathways within the tumor vasculature to invigorate tumor immune responses. We introduce two specific nucleic acid sensors, the DNA sensor TREX1 and the RNA sensor RIG-I and discuss their functional roles in the vasculature. Finally, we present perspectives on how these nucleic acid sensors in the tumor endothelium can be targeted in an antiangiogenic and immune activation context. We believe understanding the role of nucleic acid sensing in the tumor vasculature can enhance our ability to design more effective therapies targeting the tumor microenvironment.
BRIEF REPORT | doi:10.20944/preprints202107.0075.v1
Subject: Biology, Anatomy & Morphology Keywords: DNA methylation; epigenetic aging; bottlenose dolphin; chronological age
Online: 5 July 2021 (07:59:15 CEST)
Epigenetics, specifically DNA methylation, allows for estimation of animal age from blood or remotely sampled skin. This multi tissue epigenetic aging clock uses 110 longitudinal samples from 34 Navy bottlenose dolphins (Tursiops truncatus), identifying 195 cytosine-phosphate-guanine sites associated with chronological aging via leave-one-individual-out-cross-validation (R2=0.95). With a median absolute error of 2.5 years this clock improves age estimation capacity in wild dolphins, expanding conservation efforts, enabling better understanding of population demographics.
Fri, 2 July 2021
ARTICLE | doi:10.20944/preprints202107.0043.v1
Subject: Biology, Anatomy & Morphology Keywords: mitogenome; biogeography; intraspecific variation; Caucasian lynx; Balkan lynx; Himalayan lynx; Anatolian refugium
Online: 2 July 2021 (09:27:04 CEST)
Phylogenetic and phylogeographic assessments of species should ideally include individuals of all known populations. However, this is difficult for species with large distribution areas. Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed that the subspecies L. l. isabellinus harbours the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbours the second-most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species. Genetic variation present in southern Palearctic populations of Lynx lynx is clearly important for elucidating the evolutionary history of this species.
Thu, 1 July 2021
ARTICLE | doi:10.20944/preprints202107.0020.v1
Subject: Biology, Anatomy & Morphology Keywords: IBV; infectious bronchitis; variants; whole-genome sequencing, enteric tropism; runting-stunting syndrome
Online: 1 July 2021 (11:25:48 CEST)
Abstract: Infectious bronchitis virus (IBV) induces respiratory and urogenital disease in chickens. Although IBV replicates in the gastrointestinal tract, enteric lesions are uncommon. We have reported a case of runting-stunting syndrome in commercial broilers from which an IBV variant was isolated from the intestines. The isolate, CalEnt, demonstrated an enteric tissue tropism in chicken embryos and SPF chickens experimentally. Here, we determined the full genome of CalEnt and compared it to other IBV strains, in addition to comparing the pathobiology of CalEnt and M41 in commercial broilers. Despite the high whole-genome identity to other IBV strains, CalEnt is rather unique in nucleotide composition. The S gene phylogenetic analyses showed great similarity between CalEnt and Cal 99. Clinically, vent staining was slightly more frequent in CalEnt-infected birds than those challenged with M41. Furthermore, IBV IHC detection was more evident and the viral shedding in feces was overall higher with the CalEnt challenge compared with M41. Despite underlying intestinal lesions caused by coccidiosis and salmonellosis vaccination, microscopic lesions in CalEnt-infected chickens were more severe than in M41-infected chickens or controls, supporting the enteric tropism of CalEnt. Further studies in SPF chickens are needed to determine the pathogenesis of the virus, its molecular mechanisms for the enteric tropism, and its influence in intestinal health.
ARTICLE | doi:10.20944/preprints202107.0003.v1
Subject: Biology, Anatomy & Morphology Keywords: Conventional agriculture; sustainable agriculture; compost tea; bacteria; biodiversity; Illumina MiSeq sequencing; plant growth; soybean
Online: 1 July 2021 (07:59:55 CEST)
Soil bacteria drive key ecosystem functions, including nutrient mobilization, soil aggregation and crop bioprotection against pathogens. Bacterial diversity is thus considered a key component of soil health. Conventional agriculture reduces bacterial diversity in many ways. Compost tea has been suggested as a bioinoculant that may restore bacterial community diversity and promote crop performance under conventional agriculture. Here, we conducted a field experiment to test this hypothesis in a soybean-maize rotation. Compost tea application had no influence on bacterial diversity or community structure. Plant growth and yield were also unresponsive to compost tea application. Combined, our results suggest that our compost tea bacteria did not thrive in the soil, and that the positive impacts of compost tea applications reported elsewhere may be caused by different microbial groups (e.g., fungi, protists, nematodes) or by abiotic effects on soil (e.g., contribution of nutrients and dissolved organic matter). Further investigations are needed to elucidate the mechanisms through which compost tea influences crop performance.
Wed, 30 June 2021
ARTICLE | doi:10.20944/preprints202102.0528.v3
Subject: Biology, Anatomy & Morphology Keywords: Fermentation; Honey production; Principal component analysis; Organoleptic characteristics; Coffea arabica
Online: 30 June 2021 (12:50:43 CEST)
The post-harvest processes of coffee are widely accepted as key factors in determining the quality of the product. In the Cauca department, Southwestern Colombia, this stage is carried out empirically by farmers in the region, using old methods that do not assure consistent quality. This study proposes to determine the best post-harvest temperature and time conditions for coffee produced in the region. For this purpose, we carried the fermentation and honey process out on different coffee samples of the Coffea Arabica species of the Castillo variety. Subsequently, the cup profile quality of the coffee samples was determined by a sensory evaluation by experts. Finally, we applied descriptive statistical techniques to the resulting data and principal component analysis and hierarchical cluster analysis to find similarities between the samples. The results suggest that the honey process gets better evaluations in the cup profile over any condition of temperature and fermentation time.
ARTICLE | doi:10.20944/preprints202106.0731.v1
Subject: Biology, Anatomy & Morphology Keywords: mitochondria; physiological uncoupling; permeability transition; reversibility
Online: 30 June 2021 (11:37:53 CEST)
Abstract: The Saccharomyces cerevisiae mitochondrial unspecific pore (ScMUC) is an uncoupling unspecific pore that shares some similarities with the mammalian permeability transition pore (mPTP). When open, both channels deplete ion and proton gradients across the inner mitochon-drial membrane. However, the role of mPTP is to reversibly open to protect cells against stress. If mPTP remains stuck in the open position the cell dies. In contrast, ScMUC is probably dedicated to deplete oxygen from the medium in order to kill competing organisms. Such O2 depletion would be better achieved if oxidative phosphorylation is at least mildly uncoupled. Still, when oxida-tive phosphorylation is needed ScMUC should be able to close. To test this, the reversible opening and closing of ScMUC in the presence of different effectors was tested in isolated mitochondria from S. cerevisiae. Evaluations were conducted at different incubation times, monitoring the rate of O2 consumption, mitochondrial swelling and the transmembrane potential. It was observed that ScMUC did remain reversibly open for minutes. A low energy charge (ATP/ADP) closed the chan-nel. In addition, high Ca2+ promoted closing and it was a highly powerful effector.
ARTICLE | doi:10.20944/preprints202106.0724.v1
Subject: Biology, Anatomy & Morphology Keywords: sperm production; sperm competition; testes; socio-sexual environment
Online: 30 June 2021 (09:43:14 CEST)
Theoretic and empirical studies show that social surroundings experienced by male insects during their larval or adult stage can influence their testicular investment in diverse ways. Although insect pupae do not feed and crawl, they can communicate using sex-specific and/or non-sex specific cues. Yet, it is unknown, in any insect, whether and how male pupae can fine-tune their resource allocation to sperm production and testis size in response to socio-sexual environment. We investigated this question using a moth, Ephestia kuehniella, which produces fertile eupyrene sperm and unfertile apyrene sperm. We held male pupae individually or in groups with different sex ratios, and dissected adults upon eclosion, measured their testis size, and counted both types of sperm. We demonstrated that after exposure to conspecific pupal cues regardless of sex, male pupae increased production of eupyrenes and apyrenes at the same rate but kept testis size unchanged. We suggest that testis size is fixed after pupation because most morphological traits are formed during the larval stage, allowing little room for pupae to adjust testis size. Like adults, male pupae with fully grown testes have sufficient resources to produce more sperm of both types according to the perceived increase of sperm competition risk.
Tue, 29 June 2021
ARTICLE | doi:10.20944/preprints202106.0705.v1
Online: 29 June 2021 (12:54:42 CEST)
Phenotypes are necessary for genomic evaluations and management. Sometimes genomics can be used to measure phenotypes when other methods are difficult or expensive. Prolificacy of bulls used in multiple-bull pastures for commercial beef production is an example. A retrospective study of 79 bulls aged 2-year-old and older used 141 times in 4-5 pastures across 4 years was used to estimate repeatability from variance components. Traits available before each season’s use were tested for predictive ability. Sires were matched to calves using individual genotypes and evaluating exclusions. A lower cost method of measuring prolificacy was simulated for 5 pastures using the bulls’ genotypes and pooled genotypes to estimate average allele frequencies of calves and of cows. Repeatability of prolificacy was 0.62 ± 0.09. A combination of age-class and scrotal circumference accounted for less than 5 % of variation. Simulated estimation of prolificacy by pooling DNA of calves was accurate. Adding pooling of cow DNA or actual genotypes both increased accuracy about the same. Knowing a bull’s prior prolificacy would help predict future prolificacy for management purposes and could be used in genomic evaluations and research with coordination of breeders and commercial beef producers.
REVIEW | doi:10.20944/preprints202106.0701.v1
Subject: Biology, Anatomy & Morphology Keywords: retina; neurodegeneration; AMD; aging; neurogenesis; development; transcription factor
Online: 29 June 2021 (12:41:56 CEST)
Age-related macular degeneration (AMD) is a complex, multifactorial neurodegenerative disease that constitutes the most common cause of irreversible blindness in the elderly in developed countries. Incomplete knowledge about its pathogenesis prevents the search for effective methods of prevention and treatment of AMD, primarily its “dry” type, which is by far the most common (90% of all AMD cases). In recent years, AMD became younger: late stages of the disease are now detected in relatively young people. It is known that AMD pathogenesis—according to the age-related structural and functional changes in the retina—is linked with inflammation, hypoxia, oxidative stress, mitochondrial dysfunction, and an impairment of neurotrophic support, but the mechanisms that trigger the conversion of normal age-related changes to the pathological process as well as the reason for early AMD development remain unclear. In the adult mammalian retina, de novo neurogenesis is very limited. Therefore, the structural and functional features that arise during its maturation and formation can exert long-term effects on further ontogenesis of this tissue. The aim of this review is to discuss possible contributions of the changes/disturbances in retinal neurogenesis to the early development of AMD.
ARTICLE | doi:10.20944/preprints202106.0699.v1
Subject: Biology, Anatomy & Morphology Keywords: pollen, pollen classes, determination, 3D, laser scanning microscopy
Online: 29 June 2021 (11:45:54 CEST)
Pollen analysis as a part of palynology deals with the morphological determination of pollen and spores. Different technologies with different resolutions varying from simple light microscopy to highly elaborate electron microscopy are used for the examination, depending on the area of application (e.g. sedimentology, melissopalynology, forensic palynology, etc.). To answer the question of whether laser scanning microscopy (LSM) can replace scanning electron microscopy (SEM) for the determination of pollen species, 168 species were examined using LSM. It was concluded that LSM is both efficient and easy to handle. After preparing the fresh pollen, a 3D laser scan takes 5-10 minutes and unlike using SEM, the pollen does not have to be sputtered or processed. The 3D scans can be measured quickly and easily with the integrated software and there were no observable artifacts. At magnifications up to 8545x, the image quality is comparable to that of a sputtered SEM sample whereas at higher magnifications, the SEM method is superior. Overall, pollen display by LSM is much less time consuming and more cost effective than with the SEM method.
REVIEW | doi:10.20944/preprints202106.0692.v1
Subject: Biology, Anatomy & Morphology Keywords: Ryanodine receptor; skeletal muscle; cardiac muscle; exercise and injury; heart function; diet
Online: 29 June 2021 (08:37:53 CEST)
The ryanodine receptor (RyR) is a Ca2+ release channel in the sarcoplasmic reticulum of skeletal and cardiac muscles and plays a key role in excitation-contraction coupling. The activity of the RyR is regulated by many intracellular factors such as divalent cations (Ca2+ and Mg2+), nucleotides, associated proteins, and reactive oxygen species. Since these intracellular factors change depending on the condition of the muscle, e.g., exercise, fatigue, or disease states, the RyR channel activity will be altered accordingly. In this review, we describe how the RyR channel is regulated under various conditions and discuss the possibility that the RyR acts as a sensor for change in the cellular environment of muscles.
Mon, 28 June 2021
ARTICLE | doi:10.20944/preprints202106.0675.v1
Subject: Biology, Anatomy & Morphology Keywords: pharmacogenes; transcripts; sex-bias; drug metabolism; sex differences
Online: 28 June 2021 (15:08:38 CEST)
Individual response to drugs is highly variable and largely influenced by genetic variants and gene-expression profiles. Also, it has been shown that response to drugs is strongly sex-dependent, both in terms of efficacy and toxicity. To expand current knowledge on sex differences in the expression of genes relevant for drug response, we generated a catalogue of differentially expressed human transcripts encoded by 289 genes in 41 human tissues from 838 adult individuals of the Genotype-Tissue Expression project (GTEx, v8 release) and focused our analysis on relevant transcripts implicated in drug response. We have detected significant sex-differentiated expression of 99 transcripts encoded by 59 genes in the tissues most relevant for human pharmacology (Liver, Lung, Kidney, Small intestine terminal ileum, Skin not sun-exposed, and Whole Blood). Among them, as expected, we observed significant differences in the expression of transcripts encoded by the cytochromes in the liver, CYP2B6, CYP3A7, CYP3A5, and CYP1A1. Our systematic investigation on differences between male and female in the expression of drug response related genes, reinforce the need to overcome the sex bias of clinical trials.
ARTICLE | doi:10.20944/preprints202106.0659.v1
Subject: Biology, Anatomy & Morphology Keywords: Neonatal mortality; husbandry practices; cage inspection; pup counting method; social environment; cannibalistic behaviour; asynchrony breeding; mouse welfare, 3Rs principle.
Online: 28 June 2021 (14:02:37 CEST)
Perinatal mortality is a major issue in laboratory mouse breeding. We compared a counting method using daily checks (DAILY_CHECK) with a method combining daily checks with detailed video analyses to detect cannibalisms (VIDEO_TRACK) for estimating the number of C57BL/6 pups born, died and weaned in 193 litters from trios with (TRIO-OVERLAP) or without (TRIO-NO_OVERLAP) the presence of another litter. Linear mixed models were used at litter level. To understand if cannibalism was associated with active killing (infanticide), we analysed VIDEO_TRACK recordings of 109 litters from TRIO-OVERLAP, TRIO-NO_OVERLAP or SOLO (single dams). We used Kaplan-Meier method and logistic regression at pup level. For DAILY_CHECK, the mean litter size was 35% smaller than for VIDEO_TRACK (P<0.0001) and the number of dead pups was twice lower (P<0.0001). The risk of pup loss was higher for TRIO-OVERLAP than TRIO-NO_OVERLAP (P<0.0001). A high number of pup losses occurred between birth and the first cage checking. Analyses of VIDEO_TRACK data indicated that pups were clearly dead at the start of most of the cannibalism events and infanticide was rare. As most pups die and disappear before the first cage check, many breeding facilities are likely to be unaware of their real rates of mouse pup mortality.
REVIEW | doi:10.20944/preprints202106.0657.v1
Subject: Biology, Anatomy & Morphology Keywords: mitochondria, dynamics, transport, mitophagy, cell proliferation, stemness, fate acquisition
Online: 28 June 2021 (13:55:59 CEST)
Mitochondria are essential to cell homeostasis, and alterations in mitochondrial distribution, segregation or turnover have been linked to complex pathologies such as neurodegenerative diseases or cancer. Understanding how these functions are coordinated in specific cell types is a major challenge to discover how mitochondria globally shape cell functionality. In this review, we will first describe how mitochondrial transport and dynamics are regulated throughout the cell cycle in yeast and in mammals. Second, we will explore the functional consequences of mitochondrial transport and partitioning on cell proliferation, fate acquisition, stemness, and on the way cells adapt their metabolism. Last, we will focus on how mitochondrial clearance programs represent a further layer of complexity for cell differentiation, or in the maintenance of stemness. Defining how mitochondrial transport, dynamics and clearance are mutually orchestrated in specific cell types may help our understanding of how cells can transition from a physiological to a pathological state.
Fri, 25 June 2021
COMMUNICATION | doi:10.20944/preprints202106.0616.v1
Subject: Biology, Anatomy & Morphology Keywords: olive-oil mill wastewater; wastewater; microalgae; Chlorella sp.; phenolic compounds
Online: 25 June 2021 (11:42:54 CEST)
The Mediterranean diet has among its cornerstones the use of olive oil for its nutraceutical and organoleptic properties. Despite the numerous merits, olive-oil mill wastewater (OMWW), which is generated by the olive-oil extraction process, is one of the most serious environmental pollutants in the Mediterranean countries. The polluting potential of OMWW is due to its high content of tannins, polyphenols, polyalcohols, pectins and lipids. In this experiment, we tested the ability of five microalgae of the Chlorella group (SEC_LI_ChL_1, CL-Sc, CL-Ch, FB and Idr) in lowering the percentage of total phenolic compounds in vegetation water. In order to close the recovery cycle of a fortified citrus olive oils previously developed, we tested the vegetation wa-ter obtained with three different extraction processes (conventional, lemon and orange peels) at three concentrations each (10%, 25% and 50%). Results showed that strains Idr, FB and CL-Sc from the Lake Massaciuccoli can tolerate vegetation water from conventional and lemon peels extraction up to 25%; these strains can also reduce the phenolic compounds within the tests. The results demonstrate that the application of microalgae for OMWW treatment represent an inter-esting opportunity, and an eco-friendly low-cost solution to be developed within the companies as a full-scale approach.
ARTICLE | doi:10.20944/preprints202106.0611.v1
Subject: Biology, Anatomy & Morphology Keywords: Within-host modeling; Dengue fever; immune response; antibodies; viral load; Antibody-Dependent Enhancement
Online: 25 June 2021 (09:21:23 CEST)
Dengue fever is a viral mosquito-borne infection, a major international public health concern. With 2.5 billion people at risk of acquiring the infection around the world, disease severity is influenced by the immunological status of the individual, seronegative or seropositive, prior to natural infection. Caused by four antigenically related but distinct serotypes, DENV-1 to DENV-4, infection by one serotype confers life-long immunity to that serotype and a period of temporary cross-immunity (TCI) to other serotypes. The clinical response on exposure to a second serotype is complex with the so-called Antibody-Dependent enhancement (ADE) process, a disease augmentation phenomenon when pre-existing antibodies to previous dengue infection do not neutralize but rather enhance the new infection, used to explain the etiology of severe disease. In this paper, we present a minimalistic mathematical model framework developed to describe qualitatively the dengue immunological response mediated by antibodies. Three models are analyzed and compared: i) primary dengue infection, ii) secondary dengue infection with the same (homologous) dengue virus and iii) secondary dengue infection with a different (heterologous) dengue virus. We explore the features of viral replication, antibody production, and infection clearance over time. The model is developed based on body cells and free virus interactions resulting in infected cells activating antibody production. Our mathematical results are qualitatively similar to the ones described in the empiric immunology literature, providing insights on the immunopathogenesis of severe disease. Results presented here are of use for future research directions to evaluate the impact of dengue vaccines.
ARTICLE | doi:10.20944/preprints202106.0610.v1
Subject: Biology, Anatomy & Morphology Keywords: phylogenomic analyses; exon sequence; Gadiformes; Lota lota
Online: 25 June 2021 (09:13:35 CEST)
Our understanding of phylogenetic relationships among Gadiformes fish is obtained through the analysis of a small number of genes, but uncertainty remains around critical nodes. A series of phylogenetic controversial exists at the suborder, family, subfamily, and species levels. A total of 1105 orthologous exon sequences and translated amino acid sequences from 36 genomes and 12 transcriptomes covering 33 species were applied to investigate the phylogenetic relationships within Gadiformes and address these problems. Phylogenetic trees reconstructed with the amino acid data set using different tree-building methods (RAxML and MrBayes) showed consistent topology. The monophyly of Gadifromes was confirmed in our study. However, the three suborders Muraenolepidoidei, Macrouroidei, and Gadoidei were not well recovered by our phy-logenomic study, rejecting the validity of suborder Muraenolepidoidei. Four major lineages were revealed in this study. The family Bregmacerotidae forming clade I was the basal lineage of Gadiformes. The family Merluciidae formed clade II. Clade III contained families Melanonidae, Muraenolepididae, Macrouridae (with subfamilies Trachyrincinae, Macrourinae, and Bathygadinae), and Moridae. Clade IV contained at least three families of suborder Gadoidei, i.e., Gadidae, Phycidae, and Ranicipitidae. The subspecies of Lota lota from Amur River were confirmed, indicating that exon markers were a valid high-resolution method for delimiting subspecies or distinct lineages within species level. The PSMC analysis of different populations of L. lota suggests a continuous decline since 2 Myr.
Thu, 24 June 2021
REVIEW | doi:10.20944/preprints202106.0594.v1
Subject: Biology, Anatomy & Morphology Keywords: autophagy, glycogen, lysosome, glycophagy, Atg8, Stbd1, Gabarapl1
Online: 24 June 2021 (08:48:36 CEST)
Macro-autophagy is an essential cellular process involved in degradation of aberrant organelles and proteins. Initially proposed to be a ‘bulk’ degradation pathway, a more nuanced appreciation of selective autophagy pathways has emerged in recent years. The discovery of a glycogen-selective autophagy pathway (‘glycophagy’) has highlighted the importance of autophagy in regulating cellular metabolic homeostasis and identified a novel non-canonical major pathway of glycogen flux. The field of glycogen autophagy research is at an early evolutionary stage, but already it is clear that the implications of these discoveries are far-reaching and provide scope for multi-disciplinary investigations into the role of glycophagy in health and disease. With potential cognate protein partners identified, the opportunities for targeted intervention have become viable. Here we review the current evidence relating to specific protein mediators involved in glycophagy, and highlight areas of uncertainty that provide opportunity for further investigation.
Wed, 23 June 2021
Subject: Biology, Anatomy & Morphology Keywords: Goats; Heat stress; Saccharomyces cerevisiae; Clostridium butyricum; Rumen fermentation, Growth performance
Online: 23 June 2021 (13:18:38 CEST)
Heat stress had adverse effects on rumen fermentation and growth performance of goats. This study was to evaluate the effects of Saccharomyces cerevisiae (SC), Clostridium butyricum (CB) and their combination on rumen fermentation and growth performance of heat-stressed goats. Probiotics treatment were control (with no probiotics), 0.60%SC, 0.05%CB, and 0.60%SC + 0.05%CB (CG, SC, CB, and COM), respectively. Heat-stressed goats (n = 12, 20.21 ± 2.30 kg) were assigned to a 4 × 3 incomplete Latin square study. The dry matter intake (DMI) and body weight of goats were recorded daily. And the rumen contents and feces were collected for fermentation parameters and feed digestibility analysis, respectively. The rumen pH; rumen cellulolytic enzyme (avicelase, CMCaes, cellobiase, and xylanase) activities; the concentrations of rumen total volatile fatty acid, acetic acid, propionic acid, and acetic acid to propionic acid ratio; the DMI, average daily gain (ADG), and the digestibility of dry matter (DM), neutral detergent fiber (NDF), and acidic detergent fibe (ADF) were significantly increased (p < 0.05); while the rumen oxidation-reduction potential (ORP) was significantly decreased with SC, CB and their combination supplementation (p < 0.05) compared with that of CG. These results indicated that the supplementation with these probiotics were beneficial for rumen fermentation and growth performance of heat-stressed goats.
Subject: Biology, Anatomy & Morphology Keywords: monarch butterfly; Danaus plexippus; arthropods; community structure; survivorship
Online: 23 June 2021 (11:48:42 CEST)
Based on surveys of winter roost sites, the eastern migratory population of the monarch butterfly (Danaus plexippus) in North America appears to have declined in the last 20 years and this has prompted the implementation of numerous conservation strategies. However, there is little information on the survivorship of first-generation monarchs in the core area of occupancy in Texas, Oklahoma, and Louisiana where overwinter population recovery begins. The purpose of this study was to determine the survivorship of first-generation eggs to third instars at a site in north Texas and to evaluate host plant arthropods for their effect on survivorship. Survivorship to third instar averaged 13.4% and varied from 11.7% to 15.6% over three years. The host plants harbored 77 arthropod taxa, including 27 predatory taxa. Despite their abundance, neither predator abundance nor predator richness predicted monarch survival. However, host plants upon which monarchs survived often harbored higher numbers of non-predatory arthropod taxa and more individuals of non-predatory taxa. These results suggest that ecological processes may have buffered the effects of predators and improved monarch survival in our study. The creation of diverse functional arthropod communities should be considered for effective monarch conservation, particularly in southern latitudes.
ARTICLE | doi:10.20944/preprints202106.0558.v1
Subject: Biology, Anatomy & Morphology Keywords: Chronic obstructive pulmonary disease (COPD); Pulmonary Rehabilitation; Vegetables; DNA damage; Genomic Instability; Oxidative stress; Inflammation.
Online: 23 June 2021 (10:08:20 CEST)
Chronic obstructive pulmonary disease (COPD) is a respiratory disease associated with airways inflammation and lung parenchyma fibrosis. The primary goals of COPD treatment are to re-duce symptoms and risk of exacerbations, therefore pulmonary rehabilitation is considered the key component of managing COPD patients. Oxidative airway damage, inflammation and re-duction of endogenous antioxidant enzymes are known to play a crucial role in the pathogenesis of COPD. Natural antioxidants have also recently been considered as they play an important role in metabolism, DNA repair and fighting the effects of oxidative stress. In this paper we evaluated the response of 105 elderly COPD patients to pulmonary rehabilitation (PR), based on high or low vegetable consumption, by analyzing clinical parameters and biological measure-ments at baseline and after completion of the three weeks PR. We found that high vegetable in-take in normal diet, without any specific intervention, can increase the probability to success-fully respond to rehabilitation (65.4% of responders ate vegetables daily vs. 40.0% of Non-Responders, p=0.033). Three weeks of pulmonary rehabilitation are probably too short to reveal a reduction of the oxidative stress and DNA damage, but are enough to show an im-provement in the patient's inflammatory state.
Tue, 22 June 2021
ARTICLE | doi:10.20944/preprints202106.0551.v1
Subject: Biology, Anatomy & Morphology Keywords: Pinus sylvestris var. mongolica; stable carbon isotope (δ13C); ecological stoichiometry; environmental factors
Online: 22 June 2021 (14:36:01 CEST)
The decline in Pinus sylvestris var. mongolica in the introduction area has had a high profile in recent years. For the ecological restoration, management and silvicultural design of Mongolian pines in the introduction area, it is necessary to conduct a comprehensive and in-depth study on the ecological adaptation mechanism of Mongolian pines in provenances. The ecological process of water and nutrient accumulation as well as the influence of environmental factors on the photosynthetic physiology are the key to revealing the ecological adaptation mechanism of Mongolian pines. According to the differences of climate in the distribution area of Mongolian pines, sampling sites were set up, the effects of environmental factors on leaf δ13C and the relationship between leaf δ13C and nutrient content were analyzed. The results showed that leaf δ13C values were ranging from - 29.7 ‰ to - 23.76 ‰. The ecological stoichiometry, including LC (522.81 mg·g-1), LN (16.04 mg·g-1), LP (1.19 mg·g-1) and L-N:P (13.56), indicated that leaf photosynthesis and water use efficiency is greatly affected by environmental conditions, Mongolian pines had strong ability of carbon fixation, and its growth was obviously restricted by nitrogen. Although there was no significant correlation between δ13C with stoichiometric parameters in leaf, photosynthesis was the key link in the process of carbon fixation. It also showed that Pinus sylvestris var. mongolica was a stomatal limited plant. Leaf δ13C had significant correlation with climatic factors. VPD is the dynamic factor affecting the photosynthetic physiological process in leaves. Air and soil moisture are the dominate factors affecting the leaf stomatal conductance and determines leaf δ13C value, while other factors indirectly affect leaf δ13C by its impact on relative humidity or soil water content. Soil phosphorus content affected by clay is a key factor affecting soil water availability and soil nutrient cycling. Photosynthetic process in leaf is the dynamic process affecting the nutrient accumulation.
ARTICLE | doi:10.20944/preprints202106.0535.v1
Subject: Biology, Anatomy & Morphology Keywords: biodiversity; sinkhole; Chironomidae; Copepoda; Trombidiformes; Cladocera, Ostracoda, Yucatan Peninsula
Online: 22 June 2021 (09:09:09 CEST)
This study is focused to the aquatic environments of the Sian Ka’an reserve, a World Heritage Site. We applied protocols recently developed for the rapid assessment of most animal taxa inhabiting any freshwater system, by using light traps, and DNA barcodes, represented by the mitochondrial gene Cytochrome Oxidase I (COI). We DNA barcoded 1037 specimens of mites, crustaceans, insects, and fish larvae from 13 aquatic environments close or inside the reserve, with a success rate of 99.8%. In total, 167 Molecular Operational Taxonomic Units (MOTU’s) were detected. From them we identified 43 species. All others remain as a MOTU. For analyzing the adult fish communities, we applied the non-invasive method of environmental DNA (eDNA), and identified the sequences obtained with the Barcode of Life Database (BOLD). We found 25 fish species, and other terrestrial vertebrates from this region. No alien species was found. After a comparison of the MOTU’s from all systems, we found that each water body was unique respect the communities observed. The reference library presented here represents the first step for future programs to detect any change in these ecosystems, including invasive species, or improve knowledge of freshwater zooplankton, because most of the MOTU’s are possibly new species to science.
Mon, 21 June 2021
ARTICLE | doi:10.20944/preprints202106.0519.v1
Subject: Biology, Anatomy & Morphology Keywords: Polyethylene terephthalate; Microbial degradation; Sustainable development
Online: 21 June 2021 (14:52:03 CEST)
Plastics are extensively used due to their versatility, durability, and low cost. PET stands for Polyethylene terephthalate. PET plastic is widely used all over the world and has many applications ranging from water bottles to fabrics like polyester and many things in between. But its unrestrained use in every field is resulting in heaps and piles of non-biodegradable materials causing damage to the environment and causing pollution. The idea being proposed is to degrade the PET plastic biologically using different bacteria. The bacteria used in this process are Ideonella sakaiensis, Acetobacterium woodii, Pelotomaculum and Methanospirillum hungatei. PET plastic is degraded, yielding Terephthalic Acid (TPA) and Ethylene Glycol (EG) by the action of the bacterium I. sakaiensis. Degradation of EG by A. woodii results in the formation of acetate and ethanol. TPA is degraded by the action of the coculture of Pelotomaculum and M. hungatei thereby yielding methane and acetate. All these products formed have significant commercial uses in various industries. The complete process that is to be carried out can help in achieving sustainability by fulfilling various Sustainable Development Goals set by the United Nations.
ARTICLE | doi:10.20944/preprints202106.0517.v1
Subject: Biology, Anatomy & Morphology Keywords: Harvest index; total biomass; fruit number; fruit length
Online: 21 June 2021 (14:22:35 CEST)
Pollination is the process by which pollen grains are exchanged in plant flowers to allow for fertilisation and production to take place. However, challenges occur when crops are grown under protected structures where there are minimal activities of natural pollination agents such as wind and animals which are responsible for transferring pollen grains from the anther to the stigma. Therefore, the study objective was to determine the effect on hand pollination on the yield of African horned cucumber grown under greenhouse and shade net environment. A factorial experiment with two factors (hand pollinated and non-hand pollinated/control) was conducted under two different growing environments (greenhouse and shade net). African horned cucumber plants were hand self-pollinated in the morning. Pollen were manually transferred with a hand using the new earbud from the male to the female flowers on the same plant (selfing). Results showed that hand pollinated African horned cucumber plants increased total biomass from 0.93 to 2.23 kg under greenhouse environment. Hand pollinated plants increased harvest index from 0.07 to 0.35 under shade net environment. It can thus, be deduced that hand pollination increases African horned cucumber yield in the greenhouse and shade net environments.
REVIEW | doi:10.20944/preprints202106.0515.v1
Subject: Biology, Anatomy & Morphology Keywords: inositol; inositol transporters; vacuole; stress tolerance
Online: 21 June 2021 (14:12:29 CEST)
Inositol transporter (INT) is reputed as the pivotal transporter for vital metabolites like lipids, minerals, and sugars particularly. These transporters play important role in transitional metabolism and various signaling pathways in plants through regulating the transduction of messages from hormones, neurotransmitters, and immunologic and growth factors. Extensive studies have been conducted on animal INT with promising outcomes. However, few recent studies have highlighted the importance and the complexity of INT genes in the regulation of plant physiology stages including growth and tolerance to stress conditions. The present review sum-up the most recent findings on the role of INT or inositol genes in plant metabolisms and the responsive mechanisms that cope with external stressors. Moreover, we highlighted the emerging role of vacuoles and vacuolar inositol transporters in plant molecular transition and their related roles in plant growth and development. Inositol transporters are the essential mediator for the inositol uptake and its intracellular broadcasting for various metabolic pathways where they play crucial roles. Also, so far characterized only in animals, we reported evidence on Na+/inositol transporters H+/inositol symporters and suggested their roles and operating mode in plants. Thus, understanding the INT functioning system, the coordinated movement of inositol, and the relation between inositol generation and other important plant signaling pathways would be an excellent asset for advancement in researches on plant stress adaptation.
REVIEW | doi:10.20944/preprints202106.0504.v1
Subject: Biology, Anatomy & Morphology Keywords: Microbiota; Microbiome; Mosquitoes; Behavior; Oviposition; Larval habitat; Life History Traits; Nutrition; Development; Survival
Online: 21 June 2021 (11:22:15 CEST)
Mosquitoes are considered one of the most important threats worldwide due to their ability to vector pathogens. They are responsible for the transmission of major pathogens such as Malaria, dengue, Zika or Chikungunya. Due to the lack of treatments or prophylaxis against many of the transmitted pathogens and an increasing prevalence of mosquito resistance to insecticides and drugs available, alternative strategies are now being explored. Some of these involve the use of microorganisms as promising agent to limit the fitness of mosquitoes, attract or repel them and decrease the replication and transmission of pathogenic agents. In recent years, the importance of microorganisms colonizing the habitat of mosquitoes has particularly been investigated since they appeared to play major roles in their development and diseases transmission. In this issue we will synthesize researches investigating how microorganisms present within water habitats may influence breeding site selection and oviposition strategy of gravid mosquito females. We will also highlight the impact, effect of such microbes on the fate of females’ progeny during their immature stages with a specific focus on egg hatching, development rate and larvae of pupae survival.
REVIEW | doi:10.20944/preprints202106.0494.v1
Subject: Biology, Anatomy & Morphology Keywords: adaptive significance; evolution of gall insects; gall-inducing insects; gall formation mechanism; insect effectors
Online: 21 June 2021 (09:34:51 CEST)
Galls are characteristic plant structures formed by hypertrophy (excessive increase in cell size) and/or hyperplasia (cell proliferation) induced by parasitic or pathogenic organisms. Insects are a major inducer of galls, and insect galls can occur on plant leaves, stems, floral buds, flowers, fruits, or roots. Many of these exhibit unique shapes, providing shelter and nutrients to the insects. To form unique gall structures, all-inducing insects are believed to secrete certain effector molecules and hijack host developmental programs. However, the molecular mechanisms of insect gall induction and development is still largely unknown because of the difficulty of studying non-model plants in the wild. Recent progress in next-generation sequencing has allowed us to determine the structure of biological processes in non-model organisms, including gall-inducing insects and their host plants. In this review, we first summarize the evolutionary aspects of gall-inducing life histories and their adaptive significance for insects and plants. Then, we briefly summarize recent progress regarding the molecular aspects of insect gall formation.
Fri, 18 June 2021
ARTICLE | doi:10.20944/preprints202106.0473.v1
Subject: Biology, Anatomy & Morphology Keywords: bleaching; coral reef; environmental stress; Google Earth Engine; monitoring; remote sensing; satellite
Online: 18 June 2021 (10:43:50 CEST)
Coral reefs are critical ecosystems globally for marine fauna, biodiversity and through the services they provide to humanity. However, they are significantly threatened by anthropogenic stressors, such as climate change. By combining 9 environmental variables and ecological and health-based thresholds obtained from the available literature, we develop, using fuzzy logic (discontinuous functions), a Coral Reef Stress Exposure Index (CRSEI) for remotely monitoring coral reef exposure to environmental stressors. Our approach capitalises on the abundance of readily available satellite Earth Observation (EO) data available in the Google Earth Engine (GEE) cloud-based geospatial processing platform. CRSEI values from 3157 distinct reefs were generated and mapped across 12 important coral reef ecosystem regions. Quantitative analyses indicated that the index detected significant temporal differences in stress and was, therefore, able to capture historic change at a global scale. We also applied the CRSEI to three case-study reef ecosystems, previously well-monitored for stress and disturbance using other methods. PCA analysis indicated that depth, current, sea surface temperature (SST) and SST anomaly accounted for the greatest contribution to the variance in stress in these three regions. The CRSEI corroborated temporal and spatial differences in stress exposure from known disturbances within these reference regions, in addition to identifying the potential drivers of inter- and intra-region differences in stress, namely depth, degree heating weeks and SST anomaly. We discuss how the index can be further improved in future with site-specific thresholds for each stress variable, and the incorporation of additional variables not currently available in GEE. This index provides an open access tool, built around a free and powerful processing platform, that has broad potential to assist in the regular monitoring of our increasingly imperilled coral reef ecosystems, and, in particular, those that are remote or inaccessible.
Thu, 17 June 2021
Subject: Biology, Anatomy & Morphology Keywords: mitochondria; mitochondrial DNA; nervous tissue, OxPhos complexes; bioenergetics; genomics; proteomics; mitochondrial diseases
Online: 17 June 2021 (15:12:01 CEST)
Oxidative phosphorylation (OxPhos) is the basic function of mitochondria although the land-scape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding de-tails to the mitochondrial proteome and defining novel metabolic cellular interrelations, espe-cially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition as ‘mitoexome’, ‘mitoproteome’ and ‘mitointeractome’ have entered the field of ‘mitochondrial medicine’. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic determination of the OxPhos complexes is one of the reasons for the complexity of the geno-type-phenotype correlation when facing human diseases associated with mitochondria defects; clinically, are characterized by extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the fu-ture directions of the multi-omics study of human brain disorders.
ARTICLE | doi:10.20944/preprints202106.0463.v1
Subject: Biology, Anatomy & Morphology Keywords: jellyfish; sting; first aid; vinegar; seawater; nematocyst discharge; Pelagia noctiluca; Carybdea marsupualis.
Online: 17 June 2021 (14:39:50 CEST)