ARTICLE | doi:10.20944/preprints202103.0203.v1
Subject: Biology, Anatomy & Morphology Keywords: Antimicrobial activity; Characterization; GC-MS analysis; FTIR analysis; Red lily; Secondary metabolites
Online: 5 March 2021 (21:42:00 CET)
The members of the Liliaceae family have been regarded as an excellent source of biologically active compounds. However, the work on antimicrobial potential and characterization of the bioactive fractions of Lilium philadelphicum flower is limited and needs to be explored. The present study reports the antimicrobial potential, anti-inflammatory and anticancer potential of the bioactive fraction extracted from the flower of L. philadelphicum (Red Lily) and characterization of these bioactive compounds. The antimicrobial activity was tested against nine different Gram-positive and Gram-negative bacterial strains. The minimum inhibitory concentration (MIC) values of methanolic extract of L. philadelphicum flower against Acinetobacter bouvetii, Achromobacter xylosoxidans, Bacillus subtilis MTCC 121, Candida albicans MTCC 183, Klebsiella pneumoniae MTCC 3384, and Salmonella typhi MTCC 537 were 25, 50, 12.5, 50, 100 and 50 μg mL-1, respectively. The phytochemical analysis of the extract reveals the presence of phenols, flavonoids, tannins, terpenoids, glycosides, coumarins, and quinones. The cytotoxicity of the partially purified compound against the HepG2 cell line in MTT assay demonstrates up to 90% cell viability with a bioactive compound concentration of 50 μg/ml. However, with the increase in bioactive compound concentration up to 1000 μg/ml results into nearly 80% cell viability, just a minor decline in cell viability suggests the importance of bioactive compounds for suitable therapeutic applications. Spectroscopic studies of the bioactive compound by UV-Visible spectroscopy, FT-Infra Red spectroscopy, Gas Chromatography-Mass Spectrometry (GCMS) as well as its phytochemical analysis suggests the presence of terpenoids moiety, responsible for the antimicrobial property of L. philadelphicum flower.
ARTICLE | doi:10.20944/preprints202103.0196.v1
Subject: Biology, Anatomy & Morphology Keywords: Single cell RNA-seq; spatial reconstruction; development; coalescent embedding
Online: 5 March 2021 (21:21:59 CET)
Single cell RNA-seq (scRNA-seq) profiles conceal temporal and spatial tissue developmental information. De novo reconstruction of single cell temporal trajectory has been fairly addressed, but reverse engineering single cell 3D spatial tissue localization is hitherto landmark based, and de novo spatial reconstruction is a compelling computational open problem. Here we show that a new algorithm - named D-CE - for coalescent embedding of single cell transcriptomic networks can address this open problem. We rely merely on the spatial information encoded in the expression patterns of developmental signal transcription factor (DST) genes, and we find that D-CE of cell-cell association DST-transcriptomic networks reliably reconstructs the Geo-seq or single cell samples’ 3D spatial tissue distribution. Comparison to the novoSpaRC and CSOmap (recent and only available de novo 3D spatial reconstruction methods) on 16 datasets and 681 reconstructions, reveals a significantly distinctive superior performance of D-CE.
Thu, 4 March 2021
ARTICLE | doi:10.20944/preprints202103.0164.v1
Subject: Biology, Anatomy & Morphology Keywords: Pelagornithidae; Teratornithidae; takeoff airspeed; paleo-air density; extinction
Online: 4 March 2021 (14:12:04 CET)
Three genera of very large volant birds existed for most of the Pliocene: the Pelagornithidae seabirds; the large North American Teratornithidae and the stork Leptoptilos falconeri in Africa and Asia. All became extinct around 3 Ma. The reasons for their demise are puzzling, as the Pelagornithidae had a world-wide evolutionary history of more than 50 Ma, smaller teratorns were still extant in the Holocene and smaller stork species are still globally extant. Extant large birds have a common critical takeoff airspeed suggesting a biomechanical limit in terms of power, risk and launch speed, and simulations of the flight of these extinct species suggest that at 1 bar they would have exceeded this value. Estimates for the Late Pliocene atmospheric density are derived from marine and terrestrial isotopes as well as resin chemistry, both approaches suggesting a value of about 1.2 bar, which drops to present levels during the period 3.3 to 2.6 Ma, thus a loss in atmospheric density may have caused biomechanical and ecological stress contributing to their extinction and/or development of smaller forms. This hypothesis is examined in terms of a possible mechanism of atmospheric mass loss and how this would be seen in the geological record. At 1.2 bar all the extinct species present takeoff airspeeds similar to large extant volant birds and which match the expected power and kinetic energy levels.
REVIEW | doi:10.20944/preprints202103.0154.v1
Subject: Biology, Anatomy & Morphology Keywords: β-glucans; polysaccharides; flavonoids; anthocyanins; antioxidants; biological role of pigments; gene families
Online: 4 March 2021 (11:19:12 CET)
Cereal crops, such as oats and barley, possess a number of valuable properties that meet the requirements for functional diet components. This review summarized the available information about bioactive compounds of oat and barley grain. The results of studying the structure and physicochemical properties of the cell wall polysaccharides of barley and oat are presented. The main components of the flavonoids formation pathway are shown and data, concerning anthocyanins biosynthesis in various barley tissues, are discussed. Moreover, we analyzed the available information about structural and regulatory genes of anthocyanin biosynthesis in Hordeum vulgare L. genome, including β-glucan biosynthesis genes in Avena sativa L species. However, there is not enough knowledge about genes responsible for biosynthesis of β-glucans and corresponding enzymes and plant polyphenols. The review also covers contemporary studies about collections of oat and barley genetic resources held by VIR. This review intended to provide information on the processes of biosynthesis of biologically active compounds in cereals that will promote further researches devoted to transcription factors controlling expression of structural genes and their role in other physiological processes in higher plants. Found achievements will allow breeders to create new highly productive varieties with the desirable properties.
ARTICLE | doi:10.20944/preprints202008.0621.v2
Subject: Biology, Anatomy & Morphology Keywords: Clustering; Mutation; Amino acid substitution; Structural proteins; Biochemical properties; Functional sub-domains
Online: 4 March 2021 (10:17:15 CET)
SARS-CoV-2 is mutating and creating divergent variants across the world. An in-depth investigation of the amino acid substitution in the genomic signature of SARS-CoV-2 proteins is highly essential for understanding its host adaptation and infection biology. A total of 9587 SARS-CoV-2 structural protein sequences collected from 49 different countries are used to characterize protein-wise variants, substitution pattern (type and location), and major substitution changes. The majority of the substitutions are distinct, occurred mostly in a particular location, and leads to a change in amino acid's biochemical properties. In terms of mutational changes, Envelope (E) and Membrane (M) proteins are relatively stable than Nucleocapsid (N) and Spike (S) proteins. Several co-occurrence substitutions are observed, particularly in S and N proteins. Substitution specific to active sub-domains reveals that Heptapeptide Repeat, Fusion peptides, Transmembrane in S protein, and N-terminal and C-terminal domains in N protein are remarkably mutated, and also found few deleterious mutations in these domains.
ARTICLE | doi:10.20944/preprints202103.0146.v1
Subject: Biology, Anatomy & Morphology Keywords: ultrasonic vocalization; mice; masculine behavior; testosterone
Online: 4 March 2021 (09:16:50 CET)
: Testosterone masculinizes male sexual behavior through an organizational effect during the perinatal period. We previously reported that the emission of ultrasonic vocalizations (USVs) in male mice was dependent on the organizational effects of testosterone; females treated with testosterone in the perinatal period had increased USV emissions compared to males. Recently, it was revealed that male USVs have various acoustic characteristics and these variations were related to behavioral interactions with other mice. In this regard, the detailed acoustic character changes induced by testosterone have not been fully elucidated. Here, we revealed that testosterone administered to female mice during the perinatal period modulated the acoustic characteristics of USVs. There was no clear difference in acoustic characters between males and females. Call frequencies were higher in TP-treated males and females compared to control males and females. When the calls were classified into nine types, there was also no distinctive difference between males and females, but TP increased the number of calls with a high frequency, and decreased the number of calls with a low frequency and short duration. The transition analysis by call type revealed that even though there was no statistically significant difference, TP-treated males and females had a similar pattern of transition to control males and females, respectively. Collectively, these results suggest that testosterone treatment can enhance the emission of USVs in females, but the acoustic characteristics are not the same as those of intact males.
REVIEW | doi:10.20944/preprints202103.0144.v1
Subject: Biology, Anatomy & Morphology Keywords: bioluminescence; molecular evolution; photoproteins; photobiology
Online: 4 March 2021 (09:14:17 CET)
Bioluminescence – i.e., the emission of visible light by living organisms - is defined as a biochemical reaction involving, at least, a luciferin substrate, an oxygen derivative, and a specialised luciferase enzyme. In some cases, the enzyme and the substrate are durably associated and form a photoprotein. While this terminology is educatively useful to explain bioluminescence, it gives a false idea that all luminous organisms are using identical or homologous molecular tools to achieve light emission. As usually observed in biology, the reality is more complicated. To date, 11 different luciferins have indeed been discovered, and several non-homologous luciferases lato sensu have been identified which, all together, confirms that bioluminescence emerged independently multiple times in evolution. While some phylogenetically related organisms may use non-homologous luciferases (e.g., at least four convergent luciferases found in Pancrustacea), it has also been observed that phylogenetically distant organisms may use homologous luciferases (e.g., parallel evolution observed in some cnidarians, tunicates and echinoderms that are sharing a homologous luciferase-based system). The evolution of luciferases then appears puzzling. The present review takes stock of the diversity of known “bioluminescent proteins”, their evolution and potential evolutionary origins. A total of 134 luciferase and photoprotein sequences have been investigated (from 75 species and 11 phyla), and our analyses identified 12 distinct types – defined as a group of homologous bioluminescent proteins. These analyses indicated that genes coding for luciferases and photoproteins have potentially emerged as new genes or have been co-opted from ancestral non-luciferase/photoprotein genes. In this latter case, the homologous gene’s co-options may occur independently in phylogenetically distant organisms.
Wed, 3 March 2021
ARTICLE | doi:10.20944/preprints202103.0134.v1
Subject: Biology, Anatomy & Morphology Keywords: Bacillus subtilis; NRPS/PKS; amicoumacins; heterologous expression; bioactivities
Online: 3 March 2021 (14:08:28 CET)
Abstract: Bacillus subtilis fmb60, which has broad-spectrum antimicrobial activities was isolated from plant straw compost. A hybrid NRPS/PKS cluster was screened from the genome. Sixteen secondary metabolites produced by the gene cluster were isolated and identified using LC-HRMS and NMR. Three lipoamides D–F (1-3) and two amicoumacin derivatives, amicoumacins D, E (4, 5), were identified, and are reported here for the first time. Lipoamides D–F exhibited strong antibacterial activities against harmful foodborne bacteria, with the MIC ranging from 6.25 to 25 µg/mL. Amicoumacin E scavenged 38.8% of ABTS+ radicals at 1 mg/mL. Direct cloning and heterologous expression of the NRPS/PKS and ace gene cluster identified its importance for the biosynthesis of amicoumacins. This study demonstrated that there is a high potential for biocontrol utilization of B. subtilis fmb60, and genome mining for clusters of secondary metabolites of B. subtilis fmb60 has revealed a greater biosynthetic potential for the production of novel natural products than previously anticipated.
ARTICLE | doi:10.20944/preprints202012.0773.v2
Subject: Biology, Anatomy & Morphology Keywords: secondary data analysis; PARP/PARG; transcriptomics; biotrophy-necrotrophy transition
Online: 3 March 2021 (10:15:08 CET)
Key genes needed for maintenance and growth for the two pathogens, Fusarium graminearum and Magnaporthe oryzae, were identified. These are genes that are induced in response to maintenance requirements (stress) and growth requirements. The processes involved are synthesizing arginine, synthesis of DNA-bases, nitric oxide synthesis needing arginine, autophagy, DNA synthesis, and DNA repair. A simplified regulatory network for these key genes for both organisms was constructed as a hypothesis for the work, and procedures previously developed to use sets of downloaded transcriptomic data were used to test hypotheses concerning what time under the course of infection of plants the key genes are expressed. The analysis shows that the transcription efforts (costs) to maintain the fungal cells (maintenance) are high before infection and during early infection. During the following biotrophic stage, maintenance activities drop, followed by a dramatic increase in the necrotrophic stage transition. Finally, in the necrotrophic stage, maintenance is again lower despite the high growth rate that can also cause stress. All identified genes' expressions behaved almost similar with an increased expression in the biotrophy-necrotrophy transition for both fungi except the DNA repair genes PARP/PARG that was not responding or absent (PARG) in the mainly clonal M. oryzae. This PARG expression pattern might indicate that M. oryzae is more subject to evolution by point mutations than F. graminearum, where sexual reproduction is frequent. The potential consequences of this in the development and the accelerated breakage of host species resistance in a Red Queen dynamics scenario are discussed. The analysis demonstrates the possibility of using large transcriptome datasets and co-regulations between key genes to test hypotheses. This technique's advantages complement molecular techniques that employ knockouts and over-expression of target genes to suggest that genes' roles are discussed.
Tue, 2 March 2021
ARTICLE | doi:10.20944/preprints202103.0100.v1
Subject: Biology, Anatomy & Morphology Keywords: Amphistegina lobifera; Red Sea; pH microsensor; global warming; thermal stress; ocean acidification; large benthic foraminifera; coral reef; LC-MS/MS proteomics; photosymbiotic calcifier
Online: 2 March 2021 (15:52:01 CET)
Reef-dwelling calcifiers face numerous environmental stresses associated with anthropogenic carbon dioxide emissions, including ocean acidification and warming. Photosymbiont-bearing calcifiers, such as large benthic foraminifera, are particularly sensitive. To gain insight into their resistance and adaptive mechanisms to climate change, Amphistegina lobifera from the Gulf of Aqaba were cultured under elevated pCO2 (492, 963, and 3182 ppm) fully-crossed with elevated temperature (28°C and 31°C) for two months. Differential protein abundances in host and photosymbionts amongst treatments were investigated alongside physiological responses and microenvironmental pH variations. Over 1000 proteins were identified, of which one-third varied significantly between treatments. Thermal stress induced protein depletions, along with reduced holobiont growth. Elevated pCO2 caused only minor proteomic alterations and color changes. However, combined stressors reduced pore sizes and increased microenvironmental pH, indicating adaptive modifications to gas exchange. Notably, substantial proteomic variations at moderate-pCO2 and 31°C indicate cellular stress, while stable physiological performance at high-pCO2 and 31°C is scrutinized by putative decreases in test stability. Our experiment shows that the effects of climate change can be missed when stressors are assessed in isolation, and that physiological responses should be assessed across organismal levels to make more realistic predictions for the fate of reef calcifiers.
ARTICLE | doi:10.20944/preprints202103.0098.v1
Subject: Biology, Anatomy & Morphology Keywords: substituted esters metabolism; wine fermentation; MGL2; YJU3; histone acetylation
Online: 2 March 2021 (15:05:19 CET)
Esters constitute a wide family of volatile compounds impacting the organoleptic properties of many beverages including wine and beer. They can be classified according to their chemical structure. Higher Alcohols Acetate differ from Fatty Acids Ethyl Esters whereas a third group, Substituted Ethyl Esters, contributes to the fruitiness of red wines. Derived from yeast metabolism, the biosynthesis of Higher Alcohols Acetates and Fatty Acids Ethyl Esters has been widely in-vestigated at the enzymatic and genetic level. In this work, we confirmed their effective contri-bution in the fruity perception in young red wines by evaluating the effect of their depletion by chemical and sensorial analyses. As previously reported, two pairs of esterases respectively en-coded by the paralogue genes (ATF1, ATF2) and (EEB1 and EHT1) are mostly involved in the bi-osynthesis of Acetate of Higher alcohols and Fatty Acids Ethyl Esters. However, those esterases have a moderate effect on the biosynthesis of Substituted Ethyl Esters that depends to another pair of genes, MGL2 and YJU3 encoding for mono-acyl lipases. These new findings complete our un-derstanding of esters metabolism in the context of wine alcoholic fermentation. In order to evaluate the sensorial impact of esters we attempted to produce a red wine without esters by generating a multiple deletion strain. Surprisingly, we failed to abolish all the esterase activities revealing unsuspected physiological consequences of ester biosynthesis routes. A preliminary RNA-seq analysis depicted the overall impact of the multiple deletion of ATF1, ATF2, EEB1 and EHT1 that triggers the expression shift of 1124 genes involved in nitrogen and lipid metabolism but also chromatin organization and histone acetylation, suggesting an unsuspected regulatory role of ester metabolism
Subject: Biology, Anatomy & Morphology Keywords: Crustacea; Anomura; Brachyura; Carcinization; Phylogeny; Convergent evolution; Morphological integration
Online: 2 March 2021 (12:43:52 CET)
A fundamental question in biology is whether phenotypes can be predicted by ecological or genomic rules. At least five cases of convergent evolution of the crab-like body plan (with a wide and flattened shape, and a bent abdomen) are known in decapod crustaceans, and have, for over 140 years, been known as ‘carcinization’. The repeated loss of this body plan has been identified as ‘decarcinization’. In reviewing the field, we offer phylogenetic strategies to include poorly known groups, and direct evidence from fossils, that will resolve the history of crab evolution and the degree of phenotypic variation within crabs. Proposed ecological advantages of the crab body are summarized into a hypothesis of phenotypic integration suggesting correlated evolution of the carapace shape and abdomen. Our premise provides fertile ground for future studies of the genomic and developmental basis, and the predictability, of the crab-like body form.
REVIEW | doi:10.20944/preprints202103.0085.v1
Subject: Biology, Anatomy & Morphology Keywords: Abiotic Stress; Ethylene; Jasomic acid; Mineral solubilization; Phytostimulants
Online: 2 March 2021 (12:17:01 CET)
This review presents a comprehensive and systematic study of the field of bacterial plant biostimulants and considers the fundamental and innovative principles underlying this technology. Plant biostimulants are an important tool for modern agriculture as part of an integrated crop management (ICM) system; helping make agriculture more sustainable and resilient. Plant biostimulants contain substance(s) and/or microorganisms whose function when applied to plants or the rhizosphere, is to stimulate natural processes to enhance plant nutrient uptake, nutrient use efficiency, tolerance to abiotic stress, biocontrol, and crop quality. The use of plant biostimulants has gained substantial and significant heed worldwide as an environment-friendly alternative for sustainable agricultural production. Presently, there is an increasing curiosity of industry and researchers in microbial biostimulants especially, bacterial plant biostimulants (BPBs) to improve crop growth and productivity. The BPBs that are based on PGPR (plant growth-promoting rhizobacteria) play plausible roles to promote/stimulate the crop plant growth through several mechanisms that include, i) nutrient acquisition by nitrogen (N2) fixation and solubilization of insoluble minerals (P, K, Zn), organic acids and siderophores, ii) antimicrobial metabolites and various lytic enzymes, iii) action of growth regulators and stress-responsive/induced phytohormones, iv) ameliorating abiotic stress like drought, high soil salinity, extreme temperatures, oxidative stress, and heavy metals by using different modes of action, and v) plant defense induction modes. Presenting here is a brief review emphasizing the applicability of BPBs as an innovative exertion to fulfill the current food crisis.
ARTICLE | doi:10.20944/preprints202103.0076.v1
Subject: Biology, Anatomy & Morphology Keywords: Faba bean; Farmers soil; Fertilizer; Fertile soil; Infertile soil; Production constraint; Yield
Online: 2 March 2021 (11:13:47 CET)
Understanding the soil fertility management practices is indispensable to improve faba bean productivity. However, little effort has been made to assess the soil fertility management practices of faba bean producing farmers of Wolaita Zone, southern Ethiopia. The study was conducted in Damot Gale and Sodo Zuria districts in Wolaita Zone to assess farmers’ soil fertility management practices for faba bean production, in 2019 on 310 framers. Faba bean productivity in the studied districts is majorly constrained by the scarcity of arable land, poor soil fertility, and soil acidity. These cumulative effects have caused negative consequences on soil fertility and faba bean productivity. In most soil fertility, management practices in faba bean farm did not significantly vary among the studied districts. The soil management practices by farmers were inadequate to improve soil fertility and to enhance faba bean productivity. Consequently, the average grain productions of both fertilized and unfertilized faba bean farm were far less than the national average. Therefore, intensive soil fertility management interventions such as faba bean residue management, crop rotation, application of sufficient and balanced fertilizers, adequate lime application, screening acidity tolerant varieties are required to improve faba bean productivity. in the studied districts.
REVIEW | doi:10.20944/preprints202103.0070.v1
Subject: Biology, Anatomy & Morphology Keywords: Genome; gene families; Transposable elements; Entamoeba histolytica
Online: 2 March 2021 (10:11:58 CET)
Entamoeba histolytica, like other Organismes, is characterized by diversity and heterogeneity in its genetic content, which is one of the most important reasons for survival, and the increase in susceptibility to infection.Non-condensation of chromosomes during the process of cell division and the ambiguity of the chromosomal ploidy makes predicting the exact chromosomal number difficult. Genes distributed across 14 chromosomes as well as many extra-chromosome elements. Most Genes composed of one axon only, with Introns in 25% of Genes. This genome is characterized by the presence of Polymorphic internal repeat regions, and several gene families, one of these large families encoding Transmembrane kinas, Cysteine protease (CP), SREHP protein, and others.
REVIEW | doi:10.20944/preprints202103.0066.v1
Subject: Biology, Anatomy & Morphology Keywords: GRAS protein, DELLA, Intrinsically Disordered Proteins, Arbuscular Mycorrhizal association, abiotic stress
Online: 2 March 2021 (10:01:42 CET)
The GAI‐RGA ‐ and ‐SCR (GRAS) proteins belong to the plant-specific transcription factor gene family and involved in several developmental processes, phytohormone and phytochrome signaling, symbiosis, stress responses etc. GRAS proteins have a conserved GRAS domain at C-terminal and hypervariable N-terminal. The C-terminal conserved domain directly affects the function of the GRAS proteins. For instance, in Arabidopsis, mutations in this domain in Slender rice 1 (SLR1) and Repressor of GA (RGA) proteins cause significant phenotypic changes. GRAS proteins have been reported in more than 30 plant species and till now it has been divided into 17 subfamilies. This review highlighted GRAS protein's importance during several biological processes in plants, structural features of GRAS proteins, their expansion and diversification in the plants, GRAS-interacting proteins complexes and their role in biological processes. We also summarized available recent research that utilized CRISPR-Cas9 technology to manipulate GRAS genes in a plant for different traits. Further, the exploitation of GRAS genes in crop improvement programs has also been discussed
ARTICLE | doi:10.20944/preprints202103.0048.v1
Subject: Biology, Anatomy & Morphology Keywords: Taste; Sugar-aversion; German cockroach; Glucose; Saliva; Salivary digestion; Feeding behavior; Bait; Pest control
Online: 2 March 2021 (09:14:36 CET)
Saliva has diverse functions in feeding behavior of animals. However, the impact of salivary digestion of food on insect gustatory information processing is poorly documented. Glucose-aversion (GA) in the German cockroach, Blattella germanica, is a highly adaptive heritable behavioral resistance trait that protects the cockroach from ingesting glucose-containing-insecticide-baits. In this study, we confirmed that GA cockroaches rejected glucose, but they accepted oligosaccharides. However, whereas wild-type cockroaches that accepted glucose also satiated on oligosaccharides, GA cockroaches ceased ingesting the oligosaccharides within seconds, resulting in significantly lower consumption. We hypothesized that saliva might hydrolyze oligosaccharides, releasing glucose and terminating feeding. By mixing artificially collected cockroach saliva with various oligosaccharides, we demonstrated oligosaccharide-aversion in GA cockroaches. Acarbose, an alpha-glucosidase inhibitor, prevented the accumulation of glucose and rescued the phagostimulatory response and ingestion of oligosaccharides. Our results indicate that pre-oral and oral hydrolysis of oligosaccharides by salivary alpha-glucosidases released glucose, which was then processed by the gustatory system of GA cockroaches as a deterrent and caused the rejection of food. We suggest that the genetic mechanism of glucose-aversion support an extended aversion phenotype that includes glucose-containing oligosaccharides. Salivary digestion protects the cockroach from ingesting toxic chemicals and thus could support the rapid evolution of behavioral and physiological resistance in cockroach populations.
ARTICLE | doi:10.20944/preprints202103.0047.v1
Subject: Biology, Anatomy & Morphology Keywords: Sustainable agriculture; allelopathy; biocidal potential; phytotoxic effects; weed management.
Online: 2 March 2021 (09:12:01 CET)
Along with climate change, the native forest replacement by exotic species, such as Eucalyptus globulus, is contributing to a highly fire-prone environment. Since E. globulus detains several post-fire regeneration strategies, sustainable practices are needed to manage eucalyptus stands. Thus, eucalyptus allelopathic potential can be used for weed control. Therefore, this study aimed at assessing the herbicidal potential of post-fire regenerated E. globulus leaves in Portulaca oleracea, and unraveling the main physiological processes disturbed by biocide application. For this, an aqueous extract prepared with fresh leaves (FLE; 617 gfresh weightL-1) and other with oven-dried leaves (DLE; 250 gdry weightL-1) were prepared and foliar-sprayed twice-a-week at different dilutions in 7-days-old purslane plants. As positive control, glyphosate was used. After five weeks, results revealed that DLE at the highest dose detained the greatest herbicidal activity against P. oleracea. To understand how DLE impacted weed physiology, several biochemical and redox-related parameters were evaluated in purslane plants treated with DLE highest dose. Results suggested an overproduction of hydrogen peroxide, causing severe oxidative damage in roots. Overall, this study showed that young E. globulus dried leaves had powerful herbicidal properties against P. oleracea and can represent a feasible approach for weed management, while reducing fire hazard.
ARTICLE | doi:10.20944/preprints202103.0046.v1
Online: 2 March 2021 (09:10:51 CET)
Application of native PGPR as bio inoculant is an alternative sustainable agricultural practice to enhance crop productivity, grain quality, and soil fertility. In this view, a study was to examine the effect of either individual or consortium PGPR inoculation on growth, yield, and grain nutrient uptake of two teff varieties. The pot experiment was carried out in (CRD) three replication and 10 treatments. The PGPR inoculants used in this study were Pseudomonas fluorescens biotype G, Enterobacter cloacae ss disolvens, and Serratia marcescens ss marcescen and their consortium. Dukem and Magna varieties were used in this study. The results of the analysis of variance showed significant differences (P ≤ 0.001) among the treatment and most of the agronomic traits except number of fertile tillers and also significant different (P ≤ 0.01) for grain P and N uptake. The variety was significantly affected grain Mg, Zn and Fe uptake at 5 % probability level and did not significantly influence all agronomic traits of the two varieties. Furthermore, interaction effects of two factors (TM*VT) were significant differences (P ≤ 0.05) for plant height and panicle length. Individual treatments mean comparison results showed that inoculation of native PGPR consortium significantly affected most of the PGP traits at (P ≤ 0.05). The maximum traits like plant height (189cm), panicle length (66.7cm), shoot dry biomass (9.98g), root dry biomass (2.90g) and grain yield per plant (4.55g) were observed from Dz-01-196. It could be concluded that the consortium of native PGPR inoculants for plant growth, yield and grain nutrient uptake improvement performed better than their individual strain.
Mon, 1 March 2021
REVIEW | doi:10.20944/preprints202103.0037.v1
Subject: Biology, Anatomy & Morphology Keywords: olfactory; olfaction; glia; ensheathing cells; primary olfactory; cell-based; therapy
Online: 1 March 2021 (17:42:19 CET)
Olfactory ensheathing cells (OECs) are the glial cells that accompany axons from the olfactory epithelium to their targets in the olfactory bulb. They possess unique features that have made them the subject of much study as being potentially useful in cell-based therapeutic approaches to CNS repair. Investigation of OECs has demonstrated antigenic and morphological heterogeneity in their population. No marker specific to and selective for OECs have yet been identified, and many of the markers used are variably expressed by other glial cells. Even among OECs, these markers appear to vary in vivo (depending on their anatomical location, contact with other cells, and developmental timing) and in vitro. The variation across the population of OECs has compromised their isolation and characterization. It has also made the task of identifying meaningful subpopulations - with greater or lesser therapeutic utility - dependent on identifying the source of their variability. Such information would aid in both the harvest and experimental manipulation of OECs to optimize their therapeutic effect. One way to understand the nature of this variability is to seek its potential causes in vivo. This must begin with an examination of the structure of the olfactory nerve. Here, the structure and development of the primary olfactory projection are thoroughly reviewed with an emphasis on OECs and the cells with which they make contact. The relevant experimental results are also discussed. The weight of anatomical evidence indicates that the structural variations described in different locations and across species are mostly the result of spatiotemporal developmental factors. As such, the formation of the olfactory projection is mediated primarily by the source tissue, the olfactory epithelium. Cell-autonomous development is common elsewhere, and suits the evolutionary age and importance of olfaction, as well as its continued regenerative capacity. Our findings provide a more systematic anatomical understanding of this nerve. That understanding indicates that variation in axon ensheathment by OECs is an inherent feature arising from the flexibility of the ensheathing program. This perspective, along with the anatomical data reviewed here, can inform more carefully controlled laboratory investigations designed to uncover the detailed mechanisms governing OEC biology.
TECHNICAL NOTE | doi:10.20944/preprints202103.0030.v1
Subject: Biology, Anatomy & Morphology Keywords: Marine invertebrates; RNA extraction by LiCl precipitation; electron microscopy of blood cells; cytology stains; tunicate culture
Online: 1 March 2021 (14:19:14 CET)
Marine invertebrates are model organisms in several areas of biological sciences, being a source of massive biological information. Although, the scientific relevance of marine invertebrates, the research with them can be limited for their tissue characteristics and troubles for the replication of physical and chemical properties of seawater. Thence, the main goal of this laboratory workflow is to provide a useful methodological approach to reduce the experimental limitations during the study of marine invertebrates. The present study describes experimental methodologies for the collection, transport, and maintenance of sessile tunicates. Also, an approach to observe and characterize, a diverse population of blood cells in marine invertebrates, by several cytological stains and electron microscopy. Lastly, suggestions and protocols to extract quality RNA from samples with high concentrations of salts, pigments, secondary metabolites, and polysaccharides. This methodological approach can be easily adapted to other marine invertebrates, moreover uses low-cost reagents and widely available laboratory equipment. Making possible the study of different types of marine animals in diverse locations.
Fri, 26 February 2021
Subject: Biology, Anatomy & Morphology Keywords: Hypoxia Inducible Factor; HIF; Ischemia; Hypoxia; Adaptation; Alzheimer’s Disease; Parkinson Disease; Neurodegeneration
Online: 26 February 2021 (15:34:31 CET)
Hypoxia is one of the most common pathological conditions which results from ischemic injury, trauma, inflammatory conditions, tumors, The adaptation of the body to hypoxia is a phenomenon that is of great importance both in normal conditions and in Most of the cellular response’ reactions to hypoxia is associated with a family of transcription factors called hypoxia-inducible factors (HIF). They induce the expression of a wide range of genes that help cells adapt to a hypoxic HIF functions are currently being extensively studied. In 2019, William G. Kaelin and Gregg Semenza from the USA and Sir Peter J. Ratcliffe from the UK received the Nobel Prize in Physiology or Medicine for the discovery of the basic mechanisms of adaptation to hypoxia and investigation of the role of HIF factor in the regulation of the hormone erythropoietin Based on its pivotal physiological importance, the HIF factor attracts more and more attention as a new potential target for treating a large number of diseases associated with Most of the experimental work dealing with the HIF factor is focused on its role in liver and However, increasing amount of experimental results clearly demonstrates that the HIF factor-based response represents an universal adaptation mechanism for all kinds of tissues, including the nervous system where HIF is critical for regulating neurogenesis, nerve cell differentiation, and neuronal This review provides actual overview about the complex role of HIF-1 in the adaptation of nerve cells to hypoxia with the focus on its potential role by various neuronal
ARTICLE | doi:10.20944/preprints202102.0623.v1
Subject: Biology, Anatomy & Morphology Keywords: history of biology; history of zoology; taxonomy; biological nomenclature; metazoans
Online: 26 February 2021 (15:32:17 CET)
The great Greek philosopher Aristotle (384–322 BCE) is almost unanimously acclaimed as the founder of zoology. There is a consensus that he was interested in attributes of animals, but whether or not he tried to develop a zoological taxonomy remains controversial. Fürst von Lieven and Humar compiled a data matrix and showed, through a parsimony analysis published in 2008, that these data produced a hierarchy that matched several taxa recognized by Aristotle. However, their analysis leaves some questions unanswered because random data can sometimes yield fairly resolved trees. In this study, we update the scores of many cells and add four new characters to the data matrix (147 taxa scored for 161 characters) and quote passages from Aristotle’s Historia animalium to justify these changes. We confirm the presence of a phylogenetic signal in these data through a test using skewness in length distribution of a million random trees, which shows that many of the characters discussed by Aristotle were systematically relevant. Our parsimony analyses on the updated matrix recover far more trees than reported by Fürst von Lieven and Humar, but their consensus includes many taxa that Aristotle recognized and apparently named for the first time, such as selachē (selachians) and dithyra (Bivalvia). This study suggests that even though taxonomy was clearly not Aristotle’s chief interest in Historia animalium, it was probably among his secondary interests. These results may pave the way for further taxonomic studies in Aristotle’s zoological writings in general. Despite being almost peripheral to Aristotle’s writings, his taxonomic contributions are clearly major achievements.
REVIEW | doi:10.20944/preprints202102.0619.v1
Subject: Biology, Anatomy & Morphology Keywords: Nanotechnology 1; Nanomedicine 2; organic and inorganic nanoparticles 3; drug delivery 4; antitumour therapy5; tissue engineering 6.
Online: 26 February 2021 (13:31:45 CET)
Nanotechnology is an emerging field of modern science based on the use of nanoparticles (NPs) with a huge potential in many sectors, including nanomedicine. Their small size confers them unique properties because they are subject to physical laws that are in the middle between classical and quantum physics. In this context, NPs project plays a pivotal role because the composition, size, shape and surface proprieties need to be carefully considered for their optimal design and application. As reported in this review, NPs are classified in inorganic (metallic NPs; quantum dots; carbon-based nanostructures; mesoporous silica nanoparticles) and organic (liposomes and micelles, dendrimers and polymer nanoparticles) ones. Here, we report an accurate description of the potential of each NPs type focusing on their multiple areas of application like theranostics drug delivery, imaging, tissue engineering, antimicrobial techniques and nanovaccines, and therefore they represent a promise to revolutionize the new era of nanomedicine, especially in cancer research.
REVIEW | doi:10.20944/preprints202102.0609.v1
Subject: Biology, Anatomy & Morphology Keywords: cold acclimation; vernalization; frost tolerance; dehydrins; COR14b; growth chambers; field trials
Online: 26 February 2021 (11:09:15 CET)
Low temperatures in the autumn induce enhanced expression/relative accumulation of several cold-inducible transcripts/proteins with protective functions from Late-embryogenesis-abundant (LEA) superfamily including dehydrins. Several studies dealing with plants grown under controlled conditions revealed a correlation (significant quantitative relationship) between dehydrin transcript/protein relative accumulation and plant frost tolerance. However, to apply these results in breeding, field experiments are necessary. The aim of the review is to provide a summary of the studies dealing with the relationships between plant acquired frost tolerance and COR/LEA transcripts/proteins relative accumulation in cereals grown in controlled and in the field conditions. The impacts of cold acclimation and vernalization processes on the ability of winter-type Triticeae to accumulate COR/LEA proteins are discussed. The factors determining dehydrin relative accumulation under controlled cold acclimation treatments versus field trials during winter seasons are discussed. In conclusion, it can be stated that dehydrins could be used as suitable indicators of winter surival in field-grown winter cereals but only in plant prior to the fullfilment of vernalization requirement.
Subject: Biology, Anatomy & Morphology Keywords: RSV; BRD4; AP-MS; PPI; AP1; Wnt; Innate Immune Response
Online: 26 February 2021 (09:26:24 CET)
Respiratory Syncytial Virus (RSV) causes severe inflammation and airway pathology in children and the elderly by infecting the epithelial cells of the upper and lower respiratory tract. RSV replication is sensed by intracellular pattern recognition receptors upstream of the IRF and NF-B transcription factors. These proteins coordinate an innate inflammatory response via Bromodomain containing protein 4 (BRD4), a protein that functions as a scaffold for unknown transcriptional regulators. To better understand the pleiotropic regulatory function of BRD4, we examine the BRD4 interactome and identify how RSV infection dynamically alters it. To accomplish these goals, we leverage native immunoprecipitation and Parallel Accumulation – Serial Fragmentation (PASEF) mass spectrometry to examine BRD4 complexes isolated from human alveolar epithelial cells in the absence or presence of RSV infection. In addition, we explore the role of BRD4’s acetyl-lysine binding bromodomains in mediating these interactions by using a highly selective competitive bromodomain inhibitor. We identify 101 proteins that are significantly enriched in the BRD4 complex and are responsive to both RSV-infection and BRD4 inhibition. These proteins are highly enriched in transcription factors and transcriptional coactivators. Among them, we identify members of the AP1 transcription factor complex, a complex important in innate signaling and cell stress responses. We independently confirm the BRD4/AP1 interaction in primary human small airway epithelial cells. We conclude that BRD4 recruits multiple transcription factors during RSV infection in a manner dependent on acetyl-lysine binding domain interactions. This data suggests that BRD4 recruits transcription factors to target its RNA processing complex to regulate gene expression in innate immunity and inflammation.
Thu, 25 February 2021
ARTICLE | doi:10.20944/preprints202102.0584.v1
Subject: Biology, Anatomy & Morphology Keywords: controlled atmosphere (CA) storage; crop load; internal browning disorders; receiver operating characteristic (ROC)
Online: 25 February 2021 (13:45:54 CET)
Physiological storage disorders continue to cause sizable economic losses in a range of commercially important pomefruit cultivars. Given similar storage regimes, the incidence and severity of browning disorders in the apple cultivar ‘Braeburn’ can vary in different years in a way that can be explained by the interaction of preharvest seasonal and orchard factors. Over a three-year period (2016 to 2019) at the Kompetenzzentrum Obstbau-Bodensee (KOB) in Southwest Germany a range of orchard and storage treatments were conducted for: air temperature during cell division for three weeks post petalfall or during four weeks preharvest, calcium orchard sprays, crop load and harvest timings. Following controlled atmosphere (CA) storage, the disorder incidence for internal browning and cavity formation varied markedly over the three different growing seasons. Crop load treatments strongly influenced the expression of browning disorders in all years. Differences in air temperatures (△ +/- 2 °C compared to ambient) during the cell division period showed little effect on browning incidence. Warm night temperatures (>10 °C) prior to harvest can reduce internal browning in ‘Braeburn’ apples during CA storage and shelf-life.
ARTICLE | doi:10.20944/preprints202102.0579.v1
Subject: Biology, Anatomy & Morphology Keywords: Pseudomonas aeruginosa, Reverse vaccinology, Subtractive proteomics, Vaccine candidates, Chimeric vaccine, Druggable targets.
Online: 25 February 2021 (12:06:13 CET)
Pseudomonas aeruginosa is a critical healthcare challenge due to its ability to cause persistent infections and the acquisition of antibiotic resistance mechanisms. Lack of preventive vaccines and rampant drug resistance phenomenon has rendered patients vulnerable. As new antimicrobials are in the preclinical stages of development, mining for the unexploited drug targets is also crucial. Here, we designed a chimeric vaccine against P. aeruginosa using a subtractive proteomics approach and identified nine unique enzymes as novel drug targets in PAO1 proteome. A total of five unique proteins were selected as potential vaccine candidates based on essentiality, extracellular localization, virulence, antigenicity, pathway association, protein-protein interaction analysis, hydrophilicity, and low molecular weight. These include two outer membrane porins OprF (P13794) and OprD (P32722), a protein activator precursor pra (G3XDA9), a probable outer membrane protein precursor PA1288 (Q9I456), and a conserved hypothetical protein PA4874 (Q9HUT9). These proteins were further analyzed using a reverse vaccinology approach to identify immunogenic and antigenic T cell and B cell epitopes. The best scoring epitopes qualifying for all set criteria were then further subjected to the construction of a polypeptide multi-epitope vaccine construct with cholera toxin B (CtxB) subunit as an adjuvant. The identified drug targets qualifying the screening criteria were: UDP-2-acetamido-2-deoxy-d-glucuronic acid 3-dehydrogenase WbpB (G3XD23), aspartate semialdehyde dehydrogenase (Q51344), 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (Q9HV71), 3-deoxy-D-manno-octulosonic-acid transferase (Q9HUH7), glycyl-tRNA synthetase alpha chain (Q9I7B7), riboflavin kinase/FAD synthase (Q9HVM3), aconitate hydratase 2 (Q9I2V5), probable glycosyltransferase WbpH (G3XD85) and UDP-3-O-[3-hydroxylauroyl] glucosamine N-acyltransferase (Q9HXY6). For druggability and pocketome analysis crystal and homology structures of these proteins were retrieved and developed. A sequence-based search was performed in different databases (ChEMBL, Drug Bank, PubChem and Pseudomonas database) for the availability of reported ligands and tested drugs for the screened targets. These predicted targets may provide a basis for the development of reliable antibacterial preventive and therapeutic options against P. aeruginosa.
ARTICLE | doi:10.20944/preprints202102.0528.v2
Subject: Biology, Anatomy & Morphology Keywords: Fermentation; Honey processes; Principal component analysis; Organoleptic properties
Online: 25 February 2021 (10:40:39 CET)
It is widely accepted that the post-harvest processes of coffee are key factors in determining the final quality of the product. In the department of Cauca in Colombia, this stage is carried out empirically by the farmers of the region, using old methods that do not assure consistent quality. We propose a study to determine the best conditions of temperature and time in post-harvest for the coffee produced in the region. For this purpose, we carried the fermentation and honey process out on different samples of coffee of the Coffea Arabica species of the Castillo variety. Subsequently, the quality of the samples was determined through sensory evaluation by experts. Finally, descriptive statistical techniques applied to the resulting data, and component 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 fermentation condition.
Wed, 24 February 2021
ARTICLE | doi:10.20944/preprints202102.0560.v1
Subject: Biology, Anatomy & Morphology Keywords: Trachymene incisa; Apiaceae; Chemotype; -Selinene; Bicyclogermacrene; -Bisabolene; -Pinene; -Caryophyllene; Essential oil; Chemical composition.
Online: 24 February 2021 (17:10:21 CET)
Trachymene incisa subsp. incisa is an Australian endemic taxon that varies greatly in the abundance and length of the leaf trichomes. The essential oil composition of five populations of this subspecies, three corresponding to the typical glabrous form and two of the particularly hairy variant, has been analyzed in an attempt to determinate if that variability is also reflected in their composition. The oils have been extracted by hydrodistillation and analysed by Gas Chromatography (GC) and Gas Chromatography coupled to Mass Spectrometry (GC-MS). The essential oils of T. incisa subsp. incisa were characterized by the high amount of sesquiterpenes that were the major fraction. The sesquiterepene hydrocarbons were significantly higher in the hairy variant in comparison to the glabrous one. According to the main compound three different chemotypes were found: I.- -selinene + bicyclogermacrene and II.- -bisabolene + -pinene for the typical glabrous variant and III.- bicyclogermacrene + -caryophyllene for the hairy variant.
REVIEW | doi:10.20944/preprints202102.0548.v1
Subject: Biology, Anatomy & Morphology Keywords: Huanglongbing, Candidatus Liberibacter, Asian citrus psyllid, blotchy mottle, visual symptoms
Online: 24 February 2021 (11:45:39 CET)
Citrus Greening, which is mainly caused by bacteria, is one of the severe citrus diseases affecting all citrus cultivars and causing the deliberate abolition of trees worldwide. This infectious disease cannot be spread by wind, rain, or contact by contaminated personnel. The primary vector that spreads this disease through feeding citrus leaves is the Asian citrus psyllid (ACP), a minuscule insect. The management of citrus greening is also very costly as there is no fruitful technique is developed to cure this disease except removing all infected plants from good ones to eliminate the dissemination of the pathogen. Citrus greening identification is also the most difficult job, as the symptoms are similar to other citrus diseases and nutrient deficiency. Asymmetrical blotchy mottling patterns on leaves are the main symptoms to detect this disease. Here we have discussed some visual signs of citrus greening, which will ultimately help root level farmers to identify and prevent this disease before it drastically impacts citrus plants. Whether it is affected by citrus greening or lack of nutrients, we have also discussed the pen test method of determining the symptoms as symmetrical or asymmetrical across the mid-vein.
ARTICLE | doi:10.20944/preprints202102.0539.v1
Subject: Biology, Anatomy & Morphology Keywords: Rhus chinensis Mill; Syzygium aromaticum; Rice sheath blight; Antifungal activity
Online: 24 February 2021 (10:05:28 CET)
Plant diseases reduce crop yield and quality, hampering the development of agriculture. Fungicides, which restrict chemical synthesis, are the strongest controls for plant diseases. However, the harmful effects on the environment due to continued and uncontrolled utilization of fungicides has become a major challenge in recent years. Plant-sourced fungicides are a class of plant antibacterial substances or compounds that induce plant defenses. They can kill or inhibit the growth of target pathogens efficiently with no or low toxicity, degrade readily, do not prompt development of resistance, which has led to their widespread use. In this study, the growth inhibition effect of 24 plant-sourced ethanol extracts on rice sprigs was studied. Ethanol extract of gallnuts and cloves inhibited the growth of rice sprites by up to 100%. Indoor toxicity measurement results showed that the gallnut and glove constituents inhibition reached 39.23 μg/mL and 18.82 μg/mL, respectively. Extract treated rice sprigs were dry and wrinkled. Gallnut caused intracellular swelling and breakage of mitochondria , disintegration of nuclei, aggregation of protoplasts, and complete degradation of organelles in hyphae and aggregation of cellular contents. Protection of Rhizoctonia solani viability reached 46.8% for gallnut and 37.88% for clove in water emulsions of 1,000 μg/mL gallnut and clove in the presence of 0.1% Tween 80. The protection by gallnut was significantly stronger than that of clove. The data could inform the choice of plant-sourced fungicides for the comprehensive treatment of rice sprig disease. The studied extract effectively protected rice sprigs and could be a suitable alternative to commercially available chemical fungicides. Further optimized field trials are needed to effectively sterilize rice paddies.
Tue, 23 February 2021
ARTICLE | doi:10.20944/preprints202102.0528.v1
Subject: Biology, Anatomy & Morphology Keywords: Fermentation; Honey processes; Principal component analysis; Organoleptic properties
Online: 23 February 2021 (15:57:35 CET)
It is widely accepted that the post-harvest processes of coffee are key factors in determining the final quality of the product. In the department of Cauca in Colombia, this stage is carried out empirically by the farmers of the region, using old methods that do not assure consistent quality. We propose a study to determine the best conditions of temperature and time in post-harvest for the coffee produced in the region. For this purpose, we carried the fermentation and honey process out on different samples of coffee of the Coffea Arabica species of the Castillo variety. Subsequently, the quality of the samples was determined through sensory evaluation by experts. Finally, descriptive statistical techniques applied to the resulting data, and component 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 fermentation condition.
REVIEW | doi:10.20944/preprints202101.0110.v2
Subject: Biology, Anatomy & Morphology Keywords: Amphiploidy; Disomic Polyploidy; Plant Genome Evolution; Neo-polyploidy; Polysomic Polyploidy
Online: 23 February 2021 (14:25:28 CET)
Polyploidy means having more than two basic sets of chromosomes. Polyploid plants may be artificially obtained through chemical, physical and biological (2n gametes) methods. This approach allows an increased gene scope and expression, thus resulting in phenotypic changes such as yield and product quality. Nonetheless, breeding new cultivars through induced polyploidy should overcome deleterious effects that are partly contributed by genome and epigenome instability after polyploidization. Furthermore, shortening the time required from early chromosome set doubling to the final selection of high yielding superior polyploids is a must. Despite these hurdles, plant breeders have successfully obtained polyploid bred-germplasm in broad range of forages after optimizing methods, concentration and time, particularly when using colchicine. These experimental polyploids are a valuable tool for understanding gene expression, which seems to be driven by dosage dependent gene expression, altered gene regulation and epigenetic changes. Isozymes and DNA-based markers facilitated the identification of rare alleles for particular loci when compared with diploids, and also explained their heterozygosity, phenotypic plasticity and adaptability to diverse environments. Experimentally induced polyploid germplasm could enhance fresh herbage yield and quality, e.g. leaf protein content, leaf total soluble solids, water soluble carbohydrates and sucrose content. Offspring of experimentally obtained hybrids should undergo selection for several generations to improve their performance and stability.
ARTICLE | doi:10.20944/preprints202102.0508.v1
Subject: Biology, Anatomy & Morphology Keywords: Swine; Archaea; Energy Metabolism; CAZyme genes; ARGs
Online: 23 February 2021 (09:54:38 CET)
Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n=76), Denmark (n=100), and France (n=100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (P<0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus Methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus Methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32%, 11.67%, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being: AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.
REVIEW | doi:10.20944/preprints202102.0500.v1
Subject: Biology, Anatomy & Morphology Keywords: Glioblastoma; Neurodegeneration; Injury; Regeneration; Drosophila
Online: 23 February 2021 (08:15:48 CET)
The c-Jun N-terminal Kinase (JNK) signalling pathway is a conserved response to a wide range of internal and external cellular stress signals. Besides the stress response, the JNK pathway is involved in a series of vital regulatory mechanisms during development and adulthood that are critical to maintain tissue homeostasis. These mechanisms include the regulation of apoptosis, growth, proliferation, differentiation, migration and invasion. The JNK pathway has such a diverse functionality and cell-tissue specificity, that it has emerged as a key player in regeneration, tumorigenesis and other pathologies such as neurodegenerative diseases. The JNK pathway is highly active in the central nervous system (CNS), and plays a central role for the cells to cope with pathophysiological insults during both development and adulthood. Among the many mechanisms described in the literature, in this review we focus on the JNK pathway functions in pathologies of the CNS. More specifically, we discuss some newly identified examples and mechanisms of JNK-driven tumor progression in glioblastoma, regeneration/repair after an injury in the CNS, neurodegeneration, and neuronal cell death. Recent studies have shown that the JNK pathway regulates matrix metalloproteinases (MMPs) production in response to cytoneme/tumor microtubes formation and Wingless (Wg)/WNT pathway activation in glioblastoma cells. Thus, JNK pathway is essential for glioblastoma progression, infiltration and non-autonomous induction of neurodegeneration. In regeneration, the JNK pathway controls Draper (Drpr) expression in glial cells that mediate engulfment and regeneration of the CNS upon injury.
Mon, 22 February 2021
REVIEW | doi:10.20944/preprints202102.0491.v1
Subject: Biology, Anatomy & Morphology Keywords: mTORC1; mTORC2; rapamycin; rapalog; aging; lifespan; longevity
Online: 22 February 2021 (15:34:25 CET)
Inhibition of mTORC1 (mechanistic Target Of Rapamycin Complex 1) signaling promotes health and longevity in diverse model organisms. Over the past decade, excitement has built over the possibility that treatment with the mTORC1 inhibitor rapamycin can be utilized to treat or prevent age-related disease in humans. However, concerns over the side effects of rapamycin on immunity and metabolism have precluded the routine use of rapamycin as a geroprotective therapy. Here, we discuss the evidence that these negative side effects of rapamycin are largely mediated by off-target inhibition of a second mTOR Complex (mTORC2). Further, we discuss how intermittent treatment with rapamycin, specific dietary regimens, and new molecules may provide routes to the safer and more selective inhibition of mTORC1. We conclude that the time is ripe for the development of therapies based on the safe and selective inhibition of mTORC1 for the treatment or prevention of diseases of aging.
ARTICLE | doi:10.20944/preprints202102.0474.v1
Online: 22 February 2021 (13:26:18 CET)
Transposable elements (TE) function as one of the major effectors to respond to biological or environmental stress. The mobility of TEs, which is heavily controlled under normal conditions, may be activated by stress. LncRNAs are emerging as a crucial tool in the regulation of TEs. This study focuses on the gene expression of THAP9, a domesticated transposon and lncRNA THAP9-AS1 (THAP9-antisense1), which form a sense and antisense gene pair with a promoter overlap of approximately 350bp. Under basal conditions, THAP9 is preferentially transcribed while THAP9-AS1 is heavily down-regulated. In the S-phase of the cell cycle, THAP9 expression exhibits stress-specific effects ranging from moderate enhancement to no change. On the other hand, THAP9-AS1, which has previously been reported to be upregulated in several cancers, always demonstrates enhanced expression under stress. Moreover, THAP9-AS1 is transcriptionally favoured during stress since the stress-induced fold-increase of THAP-AS1 expression is always higher than THAP9. Interestingly, the expression of both THAP9 and THAP9-AS1 exhibit a striking periodicity throughout the S-phase, reminiscent of cell cycle regulated genes. Thus, this study sets the stage to further explore the relationship between THAP9 and THAP9-AS1 and investigate THAP9-AS1’s potential regulatory role during stress.
ARTICLE | doi:10.20944/preprints202102.0461.v1
Subject: Biology, Anatomy & Morphology Keywords: Dead pericarps; salinity; short episodes of high temperature; stress response; reproductive phase; seed abortion; Phyohormones; Climate change; Brassica juncea
Online: 22 February 2021 (11:48:15 CET)
Climate change is expected to increase the frequency and severity of abiotic stresses that lead to loss of crop yield. We investigated the effect of salinity (S), short episodes of high temperature (HS) and combination of S+HS at the reproductive phase on dead pericarps properties and yield of the crop plant Brassica juncea. Three intervals of HS resulted in massive seed abortion; seeds from salt-treated plants germinated poorly. Pericarp extracts of salt-treated plants reduced seed germination of B. juncea; all pericarp extracts completely inhibited seed germination of tomato and Arabidopsis; removal of pericarp extracts restored seed germination. HS reduced all metabolites accumulated in dead pericarps, except for upregulation of isomaltose and cellobiose. Salt induced alteration in metabolite levels including increase in proline, reduction in TCA intermediates and changes in phytohormone levels. Proteome analysis revealed hundreds of proteins stored in dead pericarps whose levels and composition were altered under salt stress. The integration of metabolic and proteomic data showed that changes in metabolites were highly correlated with changes in proteins involved in their biosynthetic pathways. Thus, besides providing a physical shield for seed/embryo protection dead pericarps store beneficial substances whose levels, composition and biological function are altered under stress, further highlighting the elaborated function of dead organs enclosing embryos in seed biology and ecology. The detrimental effect of HS on crop production might have implications for global food security in the face of climate change.
Thu, 18 February 2021
REVIEW | doi:10.20944/preprints202011.0256.v2
Subject: Biology, Anatomy & Morphology Keywords: marmoset; Neotropical; Brazil; biomedical; arbovirus; conservation; hybridization; biological invasion
Online: 18 February 2021 (15:52:32 CET)
We provide here a current overview of marmoset (Callithrix) evolution, hybridization, species biology, basic/biomedical research, and conservation initiatives. Composed of two subgroups, the aurita group (C. aurita and C. flaviceps) and the jacchus group (C. geoffroyi, C. jacchus, C. kuhlii and C. penicillata), this relatively young primate radiation is endemic to the Brazilian Cerrado, Caatinga, and Atlantic Forest biomes. Significant impacts on Callithrix within these biomes resulting from anthropogenic activity include: (1) population declines, particularly for the aurita group; (2) widespread geographic displacement, biological invasions, and range expansions of C. jacchus and C. penicillata; (3) anthropogenic hybridization; and (4) epizootic Yellow Fever and Zika viral outbreaks. A number of Brazilian legal and conservation initiatives are now in place to protect the threatened aurita group and increase research about them. Due to their small size and rapid life history, marmosets are prized biomedical models. As a result, there are increasingly sophisticated genomic Callithrix resources available and burgeoning marmoset functional, immuno-, and epi- genomic research. In both the laboratory and the wild, marmosets have given us insight into cognition, social group dynamics, human disease, and pregnancy. Callithrix jacchus and C. penicillata are emerging Neotropical primate models for arbovirus disease, including Dengue and Zika. Wild marmoset populations are helping us understand sylvatic transmission and human spillover of Zika and Yellow Fever viruses. All of these factors are positioning marmosets as preeminent models to facilitate understanding of facets of evolution, hybridization, conservation, human disease, and emerging infectious diseases.
REVIEW | doi:10.20944/preprints202102.0416.v1
Subject: Biology, Anatomy & Morphology Keywords: zoo animals; visitor attitudes; wildlife encounters; wildlife tourism; selfie
Online: 18 February 2021 (12:13:24 CET)
In the twenty-first century– an era of increasing domestic and international tourism- there are boundless opportunities to encounter wild animals both in their home countries and ex situ in zoological facilities around the world. Tourism activity– especially at accredited zoos and sanctuaries –plays a crucial role in the conservation of wild animal populations, and influences the welfare of individuals within involved species. Unfortunately, not all zoos and sanctuaries prioritize the conservation and welfare of their animals, such as those who promote irresponsible and mutually-harmful visitor-animal encounters for economic profit. While the relationship between visitors and animals at zoological facilities has shifted over time to match evolving morals and sentiments towards animals, there is still a storied tendency of visitors preferring close encounters with charismatic wild species. Since the 1970s, researchers’ attention has increasingly focused on assessing the influence of the visitor effect, which refers to the impact that viewing, touching, feeding, holding, and riding captive wildlife has on the animals. Many wildlife attractions promote such encounters, despite research suggesting that close interactions with visitors can cause stress and harm to involved species. Such activities are further promoted through the “selfie tourism” phenomenon, in which visitors capture images of themselves in too-close proximity to wild animals to be shared on social media. In this commentary, we consider the challenge of “selfie tourism”, and how it can promote unethical relationships between humans and wildlife and lead to deleterious implications for the animals’ conservation and welfare.
Wed, 17 February 2021
BRIEF REPORT | doi:10.20944/preprints202101.0254.v2
Online: 17 February 2021 (12:18:07 CET)
Although working memory (WM) is crucial for intellectual abilities, not much is known about its brain underpinnings, especially the structural connectivity. We used diffusion tensor imaging (DTI) to look across the whole brain for the white matter integrity correlates of the individual differences in the reading span (verbal WM capacity during reading) in healthy adults. Right-handed healthy native Russian speakers (N = 67) underwent DTI on a 3T Philips Ingenia scanner. Verbal WM was assessed with the Daneman-Carpenter reading span test (Russian version). Fractional anisotropy maps from each participant were entered into the group tract-based spatial statistics analysis with the reading span as a covariate; the results were TFCE-corrected. After taking into account effects of age, sex, education and handedness, reading span positively correlated with the white matter integrity in multiple sites: the body, the genu and the splenium of corpus callosum; bilateral corona radiata (anterior, posterior, and superior); bilateral superior longitudinal fasciculus; several tracts in the right hemisphere only, including the internal and external capsule; bilateral superior parietal and frontal white matter. Although the left hemisphere is central for verbal processing, we revealed the important role of the right hemisphere white matter for the verbal WM capacity. Our finding indicates that larger verbal working memory span may originate from additional processing resources of the right hemisphere.
ARTICLE | doi:10.20944/preprints202102.0383.v1
Online: 17 February 2021 (11:57:41 CET)
Shark unprovoked attacks consist of fatal and non-fatal cases. Numerous cases have been reported involving shark species from Carcharhinus melanopterus with length of 145.5 cm to half-ton Carcharodon carcharias. Currently there are more (P < 0.05) unprovoked non-fatal cases with the average is 28.46 cases/shark species (95%CI: 3.86-53.1) than unprovoked fatal cases, which the average is 5.12 cases /shark species (95%CI: -0.075-10.3). Hence this paper seeks to select the best shark size model that correlates with the unprovoked fatal and non-fatal cases. The studied sharks consist of 24 shark species with the average length is 268.18 cm (95%CI: 230-306 cm) and the average weight is 225.42 kg (95%CI: 128-323 kg). Based on the model and as described by low values of AIC and the highest values of R2 and adjusted R2 , shark weight followed by combinations of shark weight and length produced unprovoked fatal and non-fatal cases best models. The model for explaining unprovoked fatal cases is the shark weight with high numbers of cases observed in large size shark (weight⁓fatal cases, AIC = 165.359, R2 = 0.72, Adj. R = 0.71). While for non-fatal cases, the best model is also the shark weight (weight⁓non fatal cases, AIC = 246.93, R2 = 0.63, Adj. R = 0.59).
ARTICLE | doi:10.20944/preprints202102.0375.v1
Subject: Biology, Anatomy & Morphology Keywords: Gas exchanges; LMA; rare species; Salvia ceratophylloides Ard.; VOC; within-plant plasticity
Online: 17 February 2021 (10:31:07 CET)
Salvia ceratophylloides (Ard.) is an endemic, rare, threatened plant species recently rediscovered in very few individuals in two different sites of South Italy. The study of within-plant variation more than among-plant one is fundamental to understand the plant adaptation to the local conditions, especially in rare species, and consequently to preserve plant biodiversity. Here, we reported the variation of the morpho-ecophysiological and metabolic traits between the sessile and petiolate leaf of S. ceratophylloides plants in two different sites for understanding the adaptation strategies for surviving in these habitats. The S. ceratophylloides individuals exhibited different net photosynthetic rate, maximum quantum yield, light intensity for the saturation of the photosynthetic machinery, stomatal conductance, transpiration rate, leaf area, fractal dimension and some VOCs between the different leaf types. This within-plant morpho-physiological and metabolic variation was depended on the site. These results provide empirical evidence of sharply within-plant variation of the morpho-physiological traits and VOCs profiles in S. ceratophylloides which could be because of adaptation to the local conditions.
Subject: Biology, Anatomy & Morphology Keywords: machine learning; deep learning; bioinformatics; phylogenetics; cancer evolution
Online: 17 February 2021 (09:40:45 CET)
The exponential growth of biomedical data in recent years urged the application of numerous machine learning techniques to address emerging problems in biology and clinical research. By enabling automatic feature extraction, selection and generation of predictive models, these methods can be used to efficiently study complex biological systems. Machine learning techniques are frequently integrated with bioinformatic methods, as well as curated databases and biological networks, to enhance training and validation, identify the best interpretable features, and enable feature and model investigation. Here, we review recently developed methods that incorporate machine learning within the same framework with techniques from molecular evolution, protein structure analysis, systems biology and disease genomics. We outline the challenges posed for machine learning, and in particular, deep learning in biomedicine and suggest unique opportunities for machine learning techniques integrated with established bioinformatics approaches to overcome some of these challenges.
REVIEW | doi:10.20944/preprints202102.0351.v1
Subject: Biology, Anatomy & Morphology Keywords: telomeres; shelterins; telomere biology diseases; cancer; dyskeratosis
Online: 17 February 2021 (09:34:55 CET)
Telomeres are crucial structures that preserve genome stability. Their progressive erosion over rounds of DNA duplication determines senescence of cells and organisms. In a classic view, telomere biology impinges on intracellular signaling pathways regulating DNA damage repair and cell cycle arrest, but new roles of telomeric proteins and transcripts emerge from recent literature. Telomere biology diseases are human disorders associated to telomere attrition. This review wants to overview the recent findings in the field of telomere’s metabolism and to deepen molecular mechanisms of inherited and acquired telomeropathies, explaining new critical connections between telomeric factors and disease pathogenesis
ARTICLE | doi:10.20944/preprints202102.0347.v1
Subject: Biology, Anatomy & Morphology Keywords: Ulmus pumila; salt stress; salt-tolerance; antioxidants; osmolytes; gas-exchange
Online: 17 February 2021 (09:22:23 CET)
Elevated salinity is one of the major environmental limitation factors of plant growth and development and salinity stress compromises the production and survival of plantation and urban forests and agricultural crops in the arid, semi-arid, and intertidal zones. Ulmus pumila, a salt- indigenous tree species in Asia and is widely deployed in salt-affected areas in China, and U.pumila is promising for multi-varietal forestry in plantation and urban forests. The comprehensive mechanism of the intraspecific salt tolerance is still not clear yet. Here, we investigated the physiological responses of the salinity stress based on the antioxidant enzyme activities, osmotic adjustments, and gas exchange among salt-tolerant U. pumila genotypes for 100 days under five different NaCl levels (0%, 0.3%, 0.5%, 0.7%, and 0.9% w/v) with natural surroundings and rain shade at age-2. Salt stress decreased height (HR), ground diameter (DR), and dry weight (biomass) were significantly different among genotypes. HR and performance indices were positively correlated with photosynthesis rate (Pn), apparent mesophyll conductance (AMC), and chlorophyll (CHLL) with (r= 0.7 - 0.8 ***), but were negatively related to the free proline, sugar, and protein accumulation (r=-0.5 ~ -0.7***). We found that high accumulation of sugars and more activities of SOD enzyme in leaf tissue contribute to the osmotic adjustment and ROS scavenging system under salinity treatment; the sugar content and SOD activity play key roles in U. pumila’s tolerance to salt stress, and are promising indicators for U. pumila species ex vitro selections. The ex vitro selection results align with the previous in vitro studies  and is promising for the MVF development.
Tue, 16 February 2021
ARTICLE | doi:10.20944/preprints202102.0335.v1
Subject: Biology, Anatomy & Morphology Keywords: IQGAP1; MST2; LATS1, YAP1, Hippo, Bile acid, hepatocellular carcinoma.
Online: 16 February 2021 (14:08:12 CET)
The Hippo pathway regulates a complex signalling network which mediates several biological functions including cell proliferation, organ size and apoptosis. Several scaffold proteins regulate the crosstalk of the members of the pathway with other signalling pathways and play an important role in the diverse output controlled by this pathway. In this study we have identified the scaffold protein IQGAP1 as a novel interactor of the core kinases of the Hippo pathway, MST2 and LATS1. Our results indicate that IQGAP1 scaffolds MST2 and LATS1, supresses their kinase activity, and YAP1-dependent transcription. Additionally, we show that IQGAP1 is a negative regulator of the non-canonical pro-apoptotic pathway and may enable the crosstalk between this pathway and the ERK and AKT signalling modules. Our data also show that bile acids regulate the IQGAP1-MST2-LATS1 signalling module in hepatocellular carcinoma cells which could be necessary for the inhibition of MST2-dependent apoptosis and hepatocyte transformation.
Subject: Biology, Anatomy & Morphology Keywords: Zika virus; ER stress; unfolded protein response; apoptosis; CHOP
Online: 16 February 2021 (13:48:02 CET)
Zika virus (ZIKV) is an emerging mosquito-borne flavivirus considered as a threat to human health due to large epidemics and serious clinical outcomes such as microcephaly in newborns. Like all flaviviruses, ZIKV relies on the cellular machinery to complete its viral cycle, with the endoplasmic reticulum (ER) being the critical site of viral replication factories. The sudden high protein load in the ER induces an ER stress to which the cell responds with an appropriate unfolded protein response (UPR) in an attempt to restore its disturbed homeostasis. When the restoration fails, the cell signaling leads to a programmed cell death by apoptosis with the upregulation of the UPR-induced C/EBP homologous protein (CHOP) which acts as the main trigger for this fatal outcome. Our previous studies have shown the ability of ZIKV to manipulate various cellular responses in order to optimize virus production. ZIKV is able to delay apoptosis to its benefit and although ER stress is induced, the UPR is not complete. Here we discovered that ZIKV impairs the expression of CHOP/DDIT3, the main factor responsible of ER-stress driven apoptosis. Surprisingly, the mechanism does not take place at the transcriptional level but at the translational level.
ARTICLE | doi:10.20944/preprints202102.0325.v1
Subject: Biology, Anatomy & Morphology Keywords: Hazel Grouse; Bohemian Forest; Long-Term Monitoring; Population Trend; TRIM.
Online: 16 February 2021 (13:33:25 CET)
The population dynamics of Hazel Grouse was studied by presence/ absence recording at stationary sites along fixed routes (110 km) during 1972-2019 in the central part of the Bohemian Forest (Šumava, Czech Republic). The 100-km² study area covered altitudes between 600 m (Rejstejn) and 1,253 m a.s.l., (mount Sokol). Our data base contained indices of Hazel Grouse occupancy: positive sites/ controlled sites for a yearly increasing number of Hazel Grouse occurrence sites (N = 134) for 48 years. We used a loglinear Poisson-regression method to analyze the long-term population trend for Hazel Grouse in the study area. In the period 1972 to 2006 we found a stable Hazel Grouse population (p = 0.83). From 2006-2007 to 2019, the population index dropped (-3.8% per year, p < 0.05) for the last 13 years. This decline is assumed to be influenced by habitat loss due to succession resulting in older, more open forest stands, by strongly increasing forestry and windstorm “Kyrill” followed by clear cutting, bark-beetle damage, and removal of pioneer trees in spruce plantations, which diminished buds and catkins, the dominant winter food. The influence of disturbance by increasing touristic activities and/or predation is discussed. Our results could help to optimize conservation efforts for Hazel Grouse in the Bohemian Forest.
ARTICLE | doi:10.20944/preprints202102.0321.v1
Subject: Biology, Anatomy & Morphology Keywords: Sundarbans; Fisheries; Natural disasters; Occupational changes; Climate change
Online: 16 February 2021 (13:20:45 CET)
The climate of Bangladesh has changed drastically which may put considerable adverse impacts on mangrove fishers but very few studies focused on this professional group. An attempt was made to perceive the impact and adaptation measures of the Sundarbans mangrove resource users, employing interviews and focus group discussions. A total of 150 respondents were randomly selected from the Sundarbans west under Shyamnagar Upazila of Satkhira District. It was revealed that the abundance of fishes, fuel woods, honey, golpata (Nypa fruticans), and shrimp post-larvae (PL) was reduced considerably. The resource users have adapted themselves by changing their occupation and becoming jobless and depending on the other family members. PL collection, honey collection, shrimp culture, and wood collection were found professional adapting strategies to adopt cyclone, flood, salinity intrusion, river erosion, and drought. Several recommendations are elicited, the implementation of which is important to ensure livelihood sustainability of the mangrove communities.
Fri, 12 February 2021
REVIEW | doi:10.20944/preprints202102.0300.v1
Subject: Biology, Anatomy & Morphology Keywords: Evolution of multicellularity; Amoebozoa; Dictyostelia; cAMP signalling; encystation; cell type evolution
Online: 12 February 2021 (11:15:40 CET)
Multicellularity evolved repeatedly in the history of life, but how it unfolded varies greatly between different lineages. Dictyostelid social amoebas offer a good system to study the evolution of multicellular complexity, with a well-resolved phylogeny and molecular genetic tools being available. We compare the life cycles of the Dictyostelids with closely related amoebozoans to show that complex life cycles were already present in the unicellular common ancestor of Dictyostelids. We propose frost resistance as an early driver of multicellular evolution in Dictyostelids and show that the cell signalling pathways for differentiating spore and stalk cells evolved from that for encystation. The stalk cell differentiation program was further modified, possibly through gene duplication, to evolve a new cell type, cup cells, in Group 4 Dictyostelids. Studies in various multicellular organisms including Dictyostelids, volvocine algae, and metazoans suggest as a common principle in the evolution of multicellular complexity that unicellular regulatory programs for adapting to environmental change serve as “proto-cell types” for subsequent evolution of multicellular organisms. Later, new cell types could further evolve by duplicating and diversifying the “proto-cell type” gene regulatory networks.
ARTICLE | doi:10.20944/preprints202102.0298.v1
Subject: Biology, Anatomy & Morphology Keywords: cellulase; evolution; gene duplication; intron; RNA interference; root-lesion nematode
Online: 12 February 2021 (11:03:57 CET)
Pratylenchus loosi is an important root-lesion nematode that cause damage to tea plantations in Iran and all over the world. The present study reports on the characterization and evolution of three ß-1,4-engoglucanase genes Pl-eng-2, Pl-eng-3 and Pl-eng-4. The gene structure of Pl-eng-2 was fully determined with the predicted signal peptide and devoid of the linker domain and carbohydrate-binding domain, while Pl-eng-3 and Pl-eng-4 were only partially sequenced. The transcription of Pl-eng-2 was localized in the secretory esophageal glands of all life stages, but it was upregulated in male and females stages. Exon/intron structures of Pl-eng-2, Pl-eng-3 and Pl-eng-4 confirmed that they resulted from gene duplication followed by sequence and gene structure diversification with loss of linker domain and carbohydrate-binding domain during evolution. Phylogenetic analysis further confirmed that nematode endoglucanases resulted from horizontal gene transfer of a bacterial gene as Pl-eng-3 showed sister relationships with CelB cellulase of Bacillus subtilis. Silencing Pl-eng-2 by in vitro RNA interference, produced a 60% decrease of the transcript level. The reproductive ability of silenced P. loosi showed a 35% reduction of eggs and larval stages compared to untreated nematodes suggesting that this gene is involved in the early steps of invasion.
ARTICLE | doi:10.20944/preprints202102.0294.v1
Subject: Biology, Anatomy & Morphology Keywords: Schizophyllum commune Fr.; Mushroom fruiting bodies; Schizophyllum commune Fr polysaccharide; β-glucan; β-glucan extraction method; FTIR Spectra
Online: 12 February 2021 (09:23:08 CET)
Schizophyllum commune Fr, a native mushroom of Thailand, has a high nutrition value and it classified as a mushroom with medicinal properties, which can neutralize the growth of many cancer cells. Thus, the aim of this research was studied effect of S. commune strain and the extraction method on the quantity and properties of β-glucan. The five S. commune Fr strains consisted of Chanthaburi, 85-022, 85-023, 85-031, and 85-043, which used in this research. The β-glucan extraction method compared two different extraction: hot water (M1) and hot alkali extraction (M2), with control (native-MR). It found that Chanthaburi strain has the highest in β-glucan content 49.20 + 0.35 % (w/w), and high potential antioxidant activity (79.14 +0.77 DPPH % and 50.92 + 0.48 ABTS %) (p < 0.05). The extraction methods had no effect on the yield of β-glucan, except antioxidant properties and chemical structure of extract substance. The extract substance from M2 has significant the highest potential antioxidant activity (80.22 + 0.51 drink mushroom juice in can by using 1-day-old MR and adjust pH more than 7 can increase antioxidant properties of product.
Thu, 11 February 2021
ARTICLE | doi:10.20944/preprints202102.0290.v1
Subject: Biology, Anatomy & Morphology Keywords: abiotic stress; strawberry; companion plants; phytoremediation
Online: 11 February 2021 (19:00:26 CET)
Strawberry is a saline sensitive plant adversely affected under slightly or moderately saline conditions. Growth and biochemical parameters of strawberry plants grown under NaCl (0-, 30-, 60-, and 90 mmol L-1) conditions with or without a halophytic companion plant (Portulaca oleracea L.) were investigated in a pot experiment. Salt stress negatively affected the growth, physiological (stomatal conductance, electrolyte leakage, total soluble solids) and biochemical parameters such as chlorophyll contents (chl-a and chl-b), proline, hydrogen peroxide, malondialdehyde, catalase, and peroxidase enzyme activities, lycopene, vitamin C contents along with the mineral uptake of strawberry plants. The companionship of P. oleacea increased fresh weight, dry weight, and fruit average weight and total fruit yield of strawberry plants along with the improvement of physiological and biochemical parameters. This study showed that cultivating of P. oleracea with strawberry plants under salt stress conditions effectively increased strawberry fruit yield and quality. We, therefore, that approaches towards the use of P. oleracea could be an environmentally friendly method that should be commonly practised where salinity is of great concern.
Subject: Biology, Anatomy & Morphology Keywords: T cell receptor; dolphin genome; TRB locus; TRBV; TRBJ; TRBD and TRBC genes; TRA and TRB gene expression analysis; multiple sequence alignments (MSA); 3D modelisation; IMGT
Online: 11 February 2021 (13:26:26 CET)
Bottlenose dolphin (Tursiops truncatus) belongs to the Cetartiodactyla and similarly to the other cetaceans represent the most successful mammalian colonization of the aquatic environment. Here we report a genomic, evolutionary and expression study of Tursiops truncatus T cell receptor beta (TRB) genes. Although the organization of the dolphin TRB locus is similar to that of the other artiodactyl species, with three in tandem D-J-C clusters located at its 3’ end, its uniqueness is given by the reduction of the total length due essentially to the absence of duplications and to the deletions that have drastically reduced the number of the germline TRBV genes. We have analyzed the relevant mature transcripts from two subjects. The simultaneous availability of rearranged TRA and TRB cDNA from the peripheral blood of one of the two specimens, and the human/dolphin amino acids multi sequence alignments, allowed us to calculate the most likely interactions at the protein interface between the alpha/beta heterodimer in complex with major histocompatibility class I (MH1) protein. Interacting amino acids located in the CDR-IMGT of the dolphin variable V alpha and beta domains were identified. According to comparative modelisation, the atome pair contact sites analysis between the human MH1 grove (G) domains and the TR V domains confirms conservation of the structure of the dolphin TR/pMH.
Wed, 10 February 2021
ARTICLE | doi:10.20944/preprints202102.0270.v1
Subject: Biology, Anatomy & Morphology Keywords: MPDB2.0,; medicinal plant; medicinal plant database of Bangladesh; folk medicine
Online: 10 February 2021 (16:29:00 CET)
Medicinal plants are generally defined as rare herbals with potent medicinal activities that can be used as an alternative treatment for diseases. Recent studies exploring novel medicine developments, originating from folk-medicinal practices challenges this notion and suggests that both the circumference of the term medicinal plant and their potential application covers a substantially extensive verse than previously suggested. While medicinal plants are not limited to the borders of any country, Bangladesh and its south-east Asian neighbors do boast a huge collection of potent medicinal plants with considerable folk-medicine history compared to most other countries of the world. MPDB 2.0 is the continuation of MPDB 1.0, it serves as both a data repertoire for medicinal of Bangladesh and a user-friendly interface for researchers, health practitioners, drug developers, and students who wish to study the various medicinal & nutritive plants scattered around Bangladesh and the underlying phytochemicals contributing to their efficacy in folk medicine. While in developing MPDB 2.0 human diseases have been highly focused upon, the information in this database is not limited in its application for human diseases or diseases only, as many of the plants indexed here can serve in developing biofuel or bioremediation technologies or nutritive diets or cosmetics, etc. MPDB 2.0 comprises a collection of more than five hundred medicinal plants from Bangladesh along with a record of their corresponding scientific, family, and local names together with their utilized parts, information regarding ailments, active compounds, and PubMed ID of related publications.
Subject: Biology, Anatomy & Morphology Keywords: epithelial mesenchymal plasticity (EMP); epithelial mesenchymal transition (EMT); mesenchymal epithelial transition (MET); E/M Hybrid; partial EMT; computational biology; mathematical modeling; cancer
Online: 10 February 2021 (15:04:19 CET)
The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of elements of cancer progression, facilitated by epithelial mesenchymal plasticity (EMP). We review here evidence for the presence, prognostic significance, and therapeutic potential of the E/M hybrid state in carcinoma. We further assess modelling predictions and validation studies to demonstrate stabilised E/M hybrid states along the spectrum of EMP, as well as computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based techniques.
ARTICLE | doi:10.20944/preprints202102.0254.v1
Subject: Biology, Anatomy & Morphology Keywords: Chemical composition; Dry matter digestibility; Gas test
Online: 10 February 2021 (12:32:21 CET)
This investigation was conducted to determine the chemical composition and nutritional value of five plant species commonly used as ruminant feeds namely: Artemisia herba-alba, Acer monspessulanum, Amygdalus lycoides, Amygdalus scoparia, and Atriplex leucoclada. After the collecting samples, the chemical compositions of plants included dry matter (DM), organic matter (OM), crude protein (CP), ether extract (EE), ash (CA), cell wall (NDF), and non-lignin cell wall (ADF) were determined according to standard methods. For degradation testing, the nylon bag technique was applied using three native Sistani fistula calves. Organic matter digestibility (OMD) and metabolisable energy (ME) were determined through the gas production technique. The CP value ranged from 5.30 (Amygdalus scoparia) to 11.72% (Atriplex leucoclada) while NDF value ranged from 52.62 (Amygdalus lycoides) to 69.05% (Amygdalus scoparia). The range of OMD, DOMD, and ME was from 36.67 to 53.27%, 34.67 to 49.11%, and 5.57 to 8.08 (MJ/kg), respectively. The results showed a positive correlation between cell wall composition and dry matter digestibility in plant species. The nutritional value of Amygdalus lycoides, Atriplex leucoclada, Acer monspessulanum, and Artemisia herba-alba was acceptable composition and digestibility.
ARTICLE | doi:10.20944/preprints202102.0249.v1
Subject: Biology, Anatomy & Morphology Keywords: spontaneous plants; metabolites; insecticidal; identification; quantification
Online: 10 February 2021 (10:12:15 CET)
Spontaneous plants metabolites are more widespread for their properties and biological functions. Also, natural products have reminded diverse scientists to take a delight in their medical and insecticidal applications linked to the environmental. A variety of metabolites have a defensive function for the plants. Thus, three spontaneous plants: Caroxylon imbricatum, Tetraena alba and Cotula cinerea collected from two ecotypes and analyzed by two known conventional methods:Gas Chromatography‐Mass Spectrometry GC QTOF(quadrupole time of flight )_MS and Liquid Chromatography-Mass spectrometry LCQTOF(quadrupole time of flight )_MS. The investigation conducted out on the identification and quantification of metabolites revealed the main metabolites which have biological activities as a part of an alternative to synthetic insecticides. The chemical study showed the presence of N-Butylbenzensulfonamide and Sulfoxycaprylicacid in the three plants. N-Carboxy-methionineresidue, Butanoicacid and Valine were found in those of Cotula cinerea and Caroxylon imbricatum (Forssk.). Artomunoxanthentrione, Glycoaldehyde, Indoline, ,Benzensulfonamide and Oxoproline were detected in extracts of Caroxylon imbricatum (Forssk.) and Tetraena alba (L.f.) In addition, Pyrroline is the only compound common in Cotula cinerea and Tetraena alba (L.f.).
Tue, 9 February 2021
REVIEW | doi:10.20944/preprints202102.0244.v1
Subject: Biology, Anatomy & Morphology Keywords: microbial communities; synergistic interactions; ecosystem processes; multi-omics
Online: 9 February 2021 (16:59:36 CET)
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used to define the building blocks to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
ARTICLE | doi:10.20944/preprints202102.0241.v1
Subject: Biology, Anatomy & Morphology Keywords: plant-growth-promoting bacteria; spore-forming bacteria; Bacillus vallismortis; Macrophomina phaseolina; phenotypic and genotypic characterization; Biocontrol agents
Online: 9 February 2021 (15:09:32 CET)
In the last decades, intensive crop management has involved excessive use of pesticides or fertilizers, compromising environmental integrity and public health. Accordingly, there has been worldwide pressure to find an eco-friendly and safe strategy to ensure agricultural productivity. Recently, Plant Growth-Promoting (PGP) rhizobacteria are receiving increasing attention as suitable biocontrol agents against agricultural pests. In the present study, 22 spore-forming bacteria were selected among a salt-pan rhizobacteria collection for their PGP traits and their antagonistic activity against the plant pathogen fungus Macrophomina phaseolina. Based on the higher antifungal activity, strain RHFS10, identified as Bacillus vallismortis, was furtherly examined and cell-free supernatants assays, column purification, and tandem mass spectrometry employed to purify and preliminarily identify the antifungal metabolites. Interestingly, the minimum inhibitory concentration assessed for the fractions active against M. phaseolina, resulted 10 times lower and more stable than the one estimated for the commercial fungicide pentachloronitrobenzene. These results suggest the use of B. vallismortis strain RHFS10 as a potential Plant Growth Promoting Rhizobacteria to efficiently control phytopathogenic fungus M. phaseolina, in alternative to chemical pesticides.
ARTICLE | doi:10.20944/preprints202102.0240.v1
Subject: Biology, Anatomy & Morphology Keywords: auxin; ethanolammonium p-aminobenzoate; fluorescence; Arabidopsis; cucumber; tomato; Hirshfeld surfaces; homology model; molecular docking; auxin receptor TIR1
Online: 9 February 2021 (14:38:39 CET)
The phytohormone auxin is involved in almost every process of a plant’s life, from germination to plant development. Nowadays, auxin research connects synthetic chemistry, plant biology, and computational chemistry in order to develop innovative and safe compounds to be used in sustainable agricultural practice. In this framework, we developed new environmentally-friendly fluorescent compounds, ethanolammonium p-aminobenzoate (HEA-pABA) and p-nitrobenzoate (HEA-pNBA), and investigated their auxin-like behavior on two main commercial vegetables cultivated in Europe, cucumber (Cucumis sativus) and tomato (Solanum lycopersicum), in comparison to the model plant Arabidopsis (Arabidopsis thaliana). Moreover, the binding modes and affinities of two organic salts in relation to the natural auxin indole-3-acetic acid (IAA) into TIR1 auxin receptor were investigated by computational approaches (homology modeling and molecular docking). Both experimental and theoretical results highlight HEA-pABA as a fluorescent compound with auxin-like activity both in Arabidopsis and the commercial cucumber and tomato. Therefore, alkanolammonium benzoates have a great potential as promising sustainable plant growth stimulators to be efficiently used in vegetable crops.
ARTICLE | doi:10.20944/preprints202102.0234.v1
Subject: Biology, Anatomy & Morphology Keywords: Principal Component Analysis, RNA-seq, prostate cancer, biomarkers, RNA genes
Online: 9 February 2021 (10:26:47 CET)
Prostate cancer (Pca) is a highly heterogeneous disease and the second more common tumor in males. Molecular and genetic profiles have been used to identify subtypes and guide therapeutic intervention. However, roughly 26% of primary Pca are driven by unknown molecular lesions. We use Principal Component Analysis (PCA) and custom RNAseq-data normalization to identify a gene expression signature which segregates primary PRAD from normal tissues. This Core-Expression Signature (PRAD-CES) includes 33 genes and accounts for 39% of data complexity along the PC1-cancer axis. The PRAD-CES is populated by protein-coding (AMACR, TP63, HPN) and RNA-genes (PCA3, ARLN1) sparsely found in previous studies, validated/predicted biomarkers (HOXC6, TDRD1, DLX1), and/or cancer drivers (PCA3, ARLN1, PCAT-14). Of note, the PRAD-CES also comprises six over-expressed LncRNAs without previous Pca association, four of them potentially modulating driver’s genes TMPRSS2, PRUNE2 and AMACR. Overall, our PCA capture 57% of data complexity within PC1-3. GO enrichment and correlation analysis involving major clinical features (i.e., Gleason Score, AR Score, TMPRSS2-ERG fusion and Tumor Cellularity) suggest that PC2 and PC3 gene signatures might describe more aggressive and inflammation-prone transitional forms of PRAD. Of note, surfaced genes may entail novel prognostic biomarkers and molecular alterations to intervene. Particularly, our work uncovered RNA genes with appealing implications on Pca biology and progression.
Subject: Biology, Anatomy & Morphology Keywords: Tropical Andes; Manu Biosphere Reserve; Astroblepus; Trichomycterus; Mauritia flexuosa
Online: 9 February 2021 (10:14:20 CET)
Our study analyzes the ecology and distribution of fish communities related to the environmental variables of the Alto Madre de Dios River, an Andean-Amazon watershed of southern Peru, between 300 and 2811 m a.s.l. within the Manu Biosphere Reserve. We provide new ecological and diversity data for these highly unknown rivers and new data for palm swamp habitats. With electric fishing techniques, we collected a total of 1934 fish specimens belonging to 78 species, 42 genera and 15 families. To assess main patterns of diversity we combined SIMPER and ANOSIM with canonical correspondence analysis to obtain an overview of the community structure of fish and their distribution related to aquatic habitats. Our results show an important shift on fish diversity at 700 m a.s.l. separating headwater and middle-lowland communities. Electrofishing was a hindrance due to the depth, flow and low conductivity of the rivers, but also allowed us to capture fish not observed with other techniques. We also compared the use of elevation with slope as an alternative variable for statistical analysis. Our results show that slope offers a solid and equivalent explanation for fish distribution variability, avoids redundance, and instead of giving geographical data offers ecologically solid information.
ARTICLE | doi:10.20944/preprints202102.0226.v1
Subject: Biology, Anatomy & Morphology Keywords: Antarctica; cold adaptation; hemocyanin; amphipod; transcriptome
Online: 9 February 2021 (09:20:04 CET)
We here report the de novo transcriptome assembly and functional annotation of Eusirus cf. giganteus clade g3, providing the first database of expressed sequences from this giant Antarctic amphipod. RNA-sequencing, carried out on the whole-body of a single juvenile individual likely undergoing molting, revealed the dominant expression of hemocyanins. The mRNAs encoding these oxygen-binding proteins cumulatively accounted for about 40% of the total transcriptional effort, highlighting the key biological importance of high hemocyanin production in this Antarctic amphipod species. We speculate that this observation may mirror a strategy previously described in Antarctic cephalopods, which compensate the decreased ability to release oxygen to peripheral tissues at sub-zero temperatures by massively increasing total blood hemocyanin content compared with temperate species. These preliminary results will undoubtedly require confirmation through proteomic and biochemical analyses aimed at characterizing the oxygen-binding properties of E. cf. giganteus clade g3 hemocyanins, and at investigating whether other Antarctic arthropod species exploit similar adaptations to cope with the challenges posed by the extreme conditions of the polar environment.
Mon, 8 February 2021
Subject: Biology, Anatomy & Morphology Keywords: Food; feeding; diets; macro-micronutrients; feeding behavior; pellet-animal performances
Online: 8 February 2021 (14:10:19 CET)
A number of studies have investigated different crustacean food stuffs, feeding methods, 18 and feeding behavior, but little attention has been given to the interaction between these aspects in 19 crustaceans. The aim of the present review is to update knowledge, and examine challenges and 20 opportunities in the development of formulated diets, as pelleted feed, which is vital for developing 21 better quality of seed or broodstock in hatcheries, and adaptation of hatchery product to the aqua- 22 culture environment, and production systems.
REVIEW | doi:10.20944/preprints202102.0193.v1
Subject: Biology, Anatomy & Morphology Keywords: mild cognitive impairment (MCI); mild dementia; Alzheimer’s disease; Ginkgo biloba (EGb761®); Tebonin; anti-dementia drugs; randomized controlled trials
Online: 8 February 2021 (11:37:05 CET)
Mild cognitive impairment (MCI) and mild dementia are a clinically relevant health problem in the elderly and Alzheimer's disease being the most common neurodegenerative disorder. Furthermore, MCI and mild dementia are characterized by a deterioration of cognitive function and their diagnosis is mainly based on cognitive examination and, the prognosis of the disease seems to be an essential reason for the diagnosis, because there is a high risk of cognitive decline in the two syndromes. This review describes the effectiveness of Ginkgo biloba (EGb761®) leaf extract for the treatment of dementia syndrome and EGb761® combination therapy with other medications for symptomatic dementia. Tebonin® is a drug of plant origin based on the active ingredient “Ginkgo biloba”. This drug has shown encouraging results, improving cognitive function, neuropsychiatric disorders and consequent reduction of caregiver stress and maintenance of autonomy in patients with age-related cognitive decline, MCI and mild dementia. Nowadays, there is little evidence to support the efficacy of EGb761® combination therapy with anti-dementia drugs and, therefore, more evidence is needed to evaluate the role of EGb761® in mixed therapy.
Subject: Biology, Anatomy & Morphology Keywords: elevated CO2; nitrogen-fixing plants; herbivores; total phenolic compounds; C:N ratio
Online: 8 February 2021 (10:32:07 CET)
Many studies have found that future predicted CO2 levels (< 800 ppm) can increase plant mass but dilute N content in leaves, impacting antiherbivore compounds. Nitrogen-fixing plants may balance leaf C:N ratio under elevated CO2, counteracting this dilution effect. The aim of this study was to look at how nitrogen-fixing plants grow and respond to herbivore damage at different CO2 levels. Alnus incana ssp. rugosa was grown at 400, 800, or 1600 ppm CO2 in soil collected from the field, inoculated with Frankia and exposed to herbivores (Orgyia leucostigma). Elevated CO2 increased nodulated plant biomass and stimulated the nitrogen fixation rate in the early growth stage. However, nitrogen-fixing plants were not able to balance the C:N ratio under elevated CO2 after grown 19 weeks. When plant were grown at 400 and 1600 ppm CO2, herbivores preferred to feed on leaves of nodulated plants. At 800 ppm CO2, nodulated plants accumulated more total phenolic compounds in response to herbivore damage than plants in the non-Frankia and non-herbivore treatments. Our results suggest that plant leaf defence, not leaf nutritional content, is the dominant driver of herbivory and nitrogen fixing plants have limited ability to balance C:N ratios at elevated CO2 in natural soil.
Fri, 5 February 2021
ARTICLE | doi:10.20944/preprints202012.0814.v2
Subject: Biology, Anatomy & Morphology Keywords: biosystems; order-stability; classical versus quantum entropy; open quantum systems; quantum channel; entanglement
Online: 5 February 2021 (22:04:17 CET)
This paper is our attempt on the basis of physical theory to bring more clarification on the question ``What is life?'' formulated in the well-known book of Schr\"odinger in 1944. According to Schr\"odinger, the main distinguishing feature of biosystem's functioning is the ability to preserve its order structure or, in the mathematical terms, to prevent increasing of entropy. Since any biosystem is fundamentally open, it is natural to use open system's theory. However, Schr\"odinger's analysis shows that the classical theory is not able to adequately describe the order-stability in a biosystem. Schr\"odinger should also appeal to the ambiguous notion of negative entropy. We suggest to apply the quantum theory. As is well-known, behaviour of the quantum von Neumann entropy crucially differs from behaviour of the classical entropy. We consider a complex biosystem $S$ composed of many subsystems, say proteins, or cells, or neural networks in the brain, i.e., $S=(S_i).$ We study the following problem: if the composed system $S$ can preserve the ``global order'' in the situation of increase of local disorder and if $S$ can preserve its entropy while some of $S_i$ increase their entropies We show that within quantum information theory the answer is positive. The significant role plays entanglement of the subsystems states. In the absence of entanglement, increasing of local disorder generates disorder increasing in the compound system $S$ (as in the classical regime).
REVIEW | doi:10.20944/preprints202102.0168.v1
Subject: Biology, Anatomy & Morphology Keywords: aquaculture; shellfish; future food; nursery stage; mud crab; juvenile; seed production; hatchery; crablet; breeding
Online: 5 February 2021 (16:18:19 CET)
This study attempted to explain the definition, objectives, and key stages in mud crab nursery activities. The nursery stages of Scylla spp was started from megalopa stage to several crablet instar stages or started from earlier crablet stage to several crablet stages. Direct stocking of megalopa into ponds is not recommended due to their sensitivity. Instead, nursery rearing is needed to produce mud crab of larger size before stocking. Individual nursery rearing results in higher survival rate (up to 100%), but with reduced growth rate, and a more complicated maintenance process compared with communal rearing. Nursery of mud crab can be done indoors, or outdoors, with adequate shelter and feed required to obtain good survival and growth performance. Artemia nauplii are the main, established nursery feed, particularly at megalopa stage, while survival rate may be improved if combined with artificial feed, such as micro bound diet formulations. Water quality parameters, identical to those proposed in tiger shrimp culture, can followed. Crablets may be transported to the pond location with, or without water. The provision of monosex seeds from mud crab hatcheries is expected to become more common, increasing seed price, and thus improving income of farmers. Numerous aspects of mud crab nursery, including nutrition, feeding strategies, understanding of their behaviour, i.e., cannibalism, control of environmental factors, and practical rearing techniques, still need further improvement.
ARTICLE | doi:10.20944/preprints202102.0159.v1
Subject: Biology, Anatomy & Morphology Keywords: Enterovirus; Coxsackievirus; 2A protease; polyclonal antibody; type 1 diabetes
Online: 5 February 2021 (11:34:57 CET)
The need for antiserum for immunohistochemical (IHC) detection of enterovirus (EV) in formaldehyde fixed and paraffin-embedded (FFPE) specimens is increasing. The standard monoclonal antibody against EV-envelope protein (VP1), clone 5D8/1, was proven to cross-react with other proteins. Another candidate marker of EV proteins is 2A protease (2Apro), which is coded by the EV gene and translated by host cells during EV replication. We raised polyclonal antiserum by immunizing rabbits with an 18-mer peptide of Coxsackievirus B1 (CVB1)-2A protease (2Apro) and examined the specificity and sensitivity for EV on FFPE tissue samples. ELISA study showed a high titer of antibody for CVB1-2Apro. IHC demonstrated that antiserum against 2Apro reacted with CVB1-infected Vero-cells. Confocal microscopy demonstrated that 2Apro labelled by the antibody located in the same cell with VP1 stained with 5D8/1. IHC demonstrated dense positive reactions pancreatic islets of EV-associated fulminant type 1 diabetes (FT1DM), and located in the same cell stained positive with 5D8/1. Specificity of IHC staining FT1DM pancreas was confirmed by absorption with an excessive concentration of immunized peptide. In conclusion, our study provides a new polyclonal antiserum against CVB1 2Apro which may be useful for detection of EV-infected human tissues stored as archive of FFPE tissue samples.
Thu, 4 February 2021
REVIEW | doi:10.20944/preprints202102.0145.v1
Subject: Biology, Anatomy & Morphology Keywords: Biodiversity Conservation, Sharks, Sustainable Shark Fishing, Fisheries, Shark Fin Trade
Online: 4 February 2021 (15:50:54 CET)
A detailed analysis of fishing records has shown that the shark species accessible to global fisheries have been systematically depleted for decades. They were already fished to about 10 percent of their former levels by 2003. Now one species after another is being listed on the IUCN Red List of Threatened Species as their numbers drop towards extinction. Shark depletion has not been well documented and a large proportion of shark mortality has been bycatch, the target species being teleost fish. But with the rise in value of shark fins due to the shark fin trade, at the same time as teleost fish stocks have become severely overfished, sharks, along with tuna, have become the most valuable catches. Fishing on the high seas is scarcely profitable, and so is heavily supported by subsidies. But the shark fin trade, in which organized crime is heavily involved, is driven by enormous profits and provides a powerful demand for the fins of all sharks. Thus it is now being supplied by fisheries around the world. There is no interest in sustainability in consumer countries, and neither the will nor the resources to manage the trade exist. Although some shark fisheries might have been managed sustainably in some regions for certain species for meat, such fisheries are increasingly dependent on the shark fin trade.. The rising global demand for shark fins, coupled with the increasing depletion of the animals supplying that demand, makes commercial fishing for sharks unsustainable. Given their high ecological value across the aquatic ecosystems they inhabit, it is important that they receive more effective measures of protection going far beyond the currently existing ones. In particular, protection of all sharks, manta rays, devil rays and rhino rays through an Appendix I CITES listing should be effected immediately due to the scale of the global take of the shark fin trade and the state of shark depletion amply documented in the literature.
Wed, 3 February 2021
ARTICLE | doi:10.20944/preprints202102.0122.v1
Subject: Biology, Anatomy & Morphology Keywords: tomato; temperature; damage; seedling; plant; root; weight; photosynthesis; proline; electrical conductivity
Online: 3 February 2021 (15:57:33 CET)
High temperature seriously effects on plant vegetative and reproductive development and reduces productivity of plants, while to increase crop yield is the main target in most crop heat stress tolerance improvement breeding programs, not just survival, under high temperature. Our aim was to compare temperature stress tolerance in two commercial tomato cultivars “Dafnis” (big fruit size) and “Minichal” (cherry fruit size) to develop early screening methods and find out survival rate and physiological responses of tomato cultivars on high temperature (40°C and within 70% RH, day/night) in 4-5 true leaf seedling stage- (4LS) and identifies the linkage of heat tolerance with fruit set and leaf heat damage rates (LHD) in seedling stage with subsequent vegetative traits at recovery. Results showed that heat stress significantly affected on physiological-chemical and vegetative parameters of seedlings regardless of tomato cultivars. Survival and the threshold level of high temperature tolerance in the seedlings of cv. “Dafnis” and “Minichal” were identified on days 7 and 9, respectively. Our findings revealed that photosynthesis (PN, Gs, Ci, Tr) parameters were increased and CHL content persisted steady value in cv. “Minichal” during heat stress period, however EC and RPL rates were lower than cv. “Dafnis”. Heat stress reduced the SFW in both cultivars in seedling stage, but PH and RFW were significantly decreased in the heat tolerant cv. “Minichal”, whereas this parameters were not significantly ranged in the heat susceptible cv. “Dafnis”. Additionally, there no found linkage between vegetative parameters with decreasing of PN and CHL rates during HT of seedlings. In plants of cv. “Minichal” with LHD-25, 50 and 75% were no found significant differences in PH, whereas in cv. “Dafnis” significant differences were determined in plants with LHD-75%, and the significant differences in rates of SFW and RFW were observed in plants of cv. “Dafnis” having LHD-75% for 28 days of recovery at NT condition. Taken together, we concluded that heat stress affected on physiological parameters regardless of tolerance level, and to identify heat tolerant genotype in tomato breeding program, screening and selection genotypes have to be evaluated at the vegetative and reproductive stages with consideration fruit size types. Since we could not find linkage between heat tolerances in seedling stage with fruit set at the reproductive stage and fruit set cannot be used as a general predictor of heat tolerance.
Tue, 2 February 2021
ARTICLE | doi:10.20944/preprints202102.0090.v1
Subject: Biology, Anatomy & Morphology Keywords: Carbon dioxide; Chilling injury; Ethylene response factor; Ripening; Tomato
Online: 2 February 2021 (14:26:34 CET)
The effect of CO2 pre-treatments on tomato quality prior to cold storage was investigated using physiochemical and transcriptome changes. Three hours CO2 treated fruits were firmer than untreated fruits and had a good appearance even after being transferred from 4°C storage to 20°C for 8 d. CO2 pretreatment with cold storage showed a synergistic effect on delayed ripening through reduced respiration; these tomatoes exhibited a lower lycopene content than untreated fruit under cold storage. Tomatoes treated with 30% CO2 had fewer pits than untreated fruits subjected to chilling temperatures, even after being transferred to 20°C for 8 d. Functional enrichment analyses from transcriptome and metabolome commonly showed that CO2-responsive genes or metabolites were involved in the sucrose and starch and biosynthesis of secondary metabolisms. The most frequently detected domain, ethylene-responsive factor domain and reduced glycolysis provide insights into the mechanism that CO2 regulates tomato quality.
REVIEW | doi:10.20944/preprints202102.0088.v1
Subject: Biology, Anatomy & Morphology Keywords: Microbiome; sound exposure; noise pollution; microalgae; artificial light; bioacoustics; ecosystem health; light pollution; photo-sonic restoration hypothesis
Online: 2 February 2021 (13:12:10 CET)
Globally, anthropogenic sound and artificial light pollution have increased to alarming levels. Evidence suggests that these can disrupt critical processes that impact ecosystems and human health. However, limited focus has been given to the potential effects of sound and artificial light pollution on microbiomes. Microbial communities are the foundations of our ecosystems. They are essential for human health and provide myriad ecosystem services. Therefore, disruption to microbiomes by anthropogenic sound and artificial light could have important ecological and human health implications. In this mini-review, we provide a critical appraisal of available scientific literature on the effects of anthropogenic sound and light exposure on microorganisms and discuss the potential ecological and human health implications. Our mini-review shows that a limited number of studies have been carried out to investigate the effects of anthropogenic sound and light pollution on microbiomes. However, based on these studies, it is evident that anthropogenic sound and light pollution have the potential to significantly influence ecosystems and human health via microbial interactions. Many of the studies suffered from modest sample sizes, suboptimal experiments designs, and some of the bioinformatics approaches used are now outdated. These factors should be improved in future studies. This is an emerging and severely underexplored area of research that could have important implications for global ecosystems and public health. Finally, we also propose the photo-sonic restoration hypothesis: does restoring natural levels of light and sound help to restore microbiomes and ecosystem stability?
Subject: Biology, Anatomy & Morphology Keywords: reflectance; hyperspectral imaging; pigments; damages; apple fruit
Online: 2 February 2021 (12:58:42 CET)
Reflected light carries ample information about biochemical composition, tissue architecture, and physiological condition of plants. Recent technical progress brought about affordable imaging hyperspectrometers (IH) providing spatially resolved spectral data on plants. The extraction of sensible information from hyperspectral reflectance images is difficult due to inherent complexity of plant tissue and canopy optics, especially when recorded by IH under ambient sunlight. We aimed at obtaining a deeper insight into plant optics as perceived by IH since there is a high demand for algorithms for fruit harvesting and grading systems equipped with computer vision and robotic systems capable of working in orchard. We report on the characteristic changes in hyperspectral reflectance accompanying the accumulation of anthocyanins in healthy fruit, pigment breakdown during sunscald and phytopathogen attacks. The measurements made outdoors with a snapshot IH were compared with traditional “point” reflectance measured with a conventional spectrophotometer under controlled illumination conditions. Most of the spectral features and patterns of plant reflectance were evident in the IH-derived reflectance images. As a step forward, a novel index for highlighting tissue damages on the background of the anthocyanin absorption, BRI-M = (1/Rorange – 1/Rred + 1/RNIR), is suggested. Difficulties of the interpretation of fruit hyperspectral reflectance images recorded in situ are discussed with possible implications for plant physiology and precision horticulture practices.
ARTICLE | doi:10.20944/preprints202102.0079.v1
Subject: Biology, Anatomy & Morphology Keywords: Faba Bean; Farmyard Manure (FYM); Nodulation; NPS Fertilizers; Rhizobium; Yield
Online: 2 February 2021 (09:40:58 CET)
Faba bean (Vicia faba L) is the first grain legume in terms of hectarage, total production and foreign exchange earnings in Ethiopia. The current study was designed to evaluate effect of NPS and bio-organic fertilizers on the yield and yield components of faba bean in Debre Markos University research farm. A total of 16 treatments were made from the factorial combination of four levels NPS (0, 50, 100 and 150 kg ha-1) and four levels bio-organic fertilizer (Nil BOF (Bio(Nil)), rhizobium (Bio(IR)), 10 t ha-1 FYM (Bio(FYM)) and FYM+Rhizobium (Bio(FYM+IR))) in randomized complete block design (RCBD) with three replications. The Walki (EH 96049-2) variety, which is high yielding, moderate disease resistant and water-logging tolerant used as test crop. The result experiment showed that, plot treated with Bio(FYM+IR)+NPS100 treatment gave statically maximum effective number of tillers (2.73), maximum number of pods per plant (20.30), hundred seeds weight (76.11g), grain yield (5.62 t ha-1), biomass yield (10.94 t ha-1) and Harvest index (59.91%) than over other treatments received NPS fertilizer with and without bio-organic fertilizers. Therefore, the combined use of 100kg ha-1 NPS with 10 tha-1 FYM and rhizobium inoculation is superior for optimum production of faba bean in study area.
Mon, 1 February 2021
ARTICLE | doi:10.20944/preprints202102.0060.v1
Subject: Biology, Anatomy & Morphology Keywords: Escherichia coli; magnetite nanoparticles; metals; antibiotics; genomics; pleiotropy; cell morphology
Online: 1 February 2021 (15:58:10 CET)
Experimental evolution was utilized to produce 5 magnetite nanoparticle-resistant (FeNP1-5) populations of Escherichia coli. The control populations were not exposed to magnetite nanoparticles. The 24-hour growth of these replicates was evaluated in the presence of increasing concentrations magnetite NPs as well as other ionic metals (gallium III, iron II, iron III, silver I) and antibiotics (ampicillin, chloramphenicol, rifampicin, sulfanilamide, tetracycline). Scanning electron microscope was utilized to determine cell size and shape in response to magnetite nanoparticle selection. Whole genome sequencing was carried out to determine if any genomic changes that resulted from magnetite nanoparticle resistance. After 25 days of selection magnetite resistance was evident in the FeNP treatment. The FeNP populations also showed a highly significantly (p < 0.0001) greater 24-growth as measured by optical density in metals (Fe (II), Fe (III), Ga (III), Ag and Cu II); as well as antibiotics (ampicillin, chloramphenicol, rifampicin, sulfanilamide, and tetracycline). The FeNP resistant populations also showed a significantly greater cell length compared to controls (p < 0.001). Genomic analysis of FeNP identified both polymorphisms and hard selective sweeps in the RNA polymerase genes rpoA, rpoB, and rpoC. Collectively, our results show that E. coli can rapidly evolve resistance to magnetite nanoparticles and that this result is correlated resistances to other metals and antibiotics. There were also changes in cell morphology resulting from adaptation to magnetite NPs. Thus, the various applications of magnetite nanoparticles could result in unanticipated changes in resistance to both metal and antibiotics.
ARTICLE | doi:10.20944/preprints202102.0045.v1
Subject: Biology, Anatomy & Morphology Keywords: Burkina Faso; Candida albicans; ERG11; virulence; susceptibility; Fluconazole; Galleria mellonella
Online: 1 February 2021 (14:31:17 CET)
The aim of this study is to have an idea on the molecular mechanisms of C. albicans resistance to fluconazole in Burkina Faso, by studying the polymorphism of the ERG11 gene, and its implication in the C. albicans virulence and resistance in vivo according to the Galleria mellonella model; (2) Methods: Ten (10) clinical strains including, 5 resistant and 5 susceptible and 1 virulent and susceptible reference strain SC5314 are used. For the estimation of virulence, the larvae were inoculated with 10 μL of C. albicans cell suspension at variable concentrations: 2,5.105, 5.105, 1.106, and 5.106 CFU/larva of each strain. For the in vivo efficacy study, fluconazole was administered at 1, 4 and 16 mg/kg respectively to G. mellonella larvae, after infection by inoculum 5.106 CFU / larvae of each strain; (3) Results: Six (6) non-silent mutations in the ERG11 gene (K143R, F145L, G307S, S405F, G448E, V456I on ERG11p) were found in 4 resistant isolates. Larval mortality depended on fungal burden and strain. The inoculum 5.106 CFU caused 100% mortality in 2 days for the 2 CAAL-1 and CAAL-2 strains carrying the F145L mutation, in 3 days for the reference strain SC5314, in 4 days for the ensemble of resistant strains, and in 5 days for the ensemble of susceptible strains. The comparison of the mortality due to the reference strain SC5314 CFU / larva and the average mortality due to the two mutant F145L strains, shows a significant difference (P <0.05).Fluconazole significantly protected (P> 0.05) the larvae from infection by susceptible strains and the reference strain. However, 100% mortality in 6 days after injection of the resistant strains, was observed (4) Conclusions: Certain mutations in the ERG11 gene such as the F145L mutation are thought to be a source of increased virulence in Candida albicans. Fluconazole effectively protected larvae from infection by susceptible strains in vivo, unlike resistant strain
ARTICLE | doi:10.20944/preprints202102.0037.v1
Subject: Biology, Anatomy & Morphology Keywords: Biomineralization; Finnish blue mussel; Interfacial matrix protein; Chitin
Online: 1 February 2021 (13:56:20 CET)
Studying various marine biomineralized ultrastructures reveals the appearance of common architectural designs and building blocks in materials with fascinating mechanical properties that match perfectly to their biological tasks. Advanced mechanical properties of biological materials are attributed to evolutionary optimized molecular architectures and structural hierarchy. One example which has not yet been structurally investigated in great detail is the shell of Mytilus edulis L. (Finnish blue mussel) found in the archipelago of SW-Finland. Through a combination of various state-of-the-art techniques such as high-resolution electron microscopy imaging, Fourier-transformed infrared spectroscopy, powder X-ray diffraction, synchrotron wide-angle X-ray diffraction, nanoindentation and protein analysis, both the inorganic mineralized components as well as the organic-rich matrix were extensively characterized. We found very similar ultra-architecture across the shell of M. edulis L. as compared to the widely studied and closely related M. edulis. However, we also found interesting differences, for instance in the thickness and degree of orientation of the mineralized layers indicating dissimilar properties and related alterations in the biomineralization processes. Our results show that the shell of M. edulis L. has a gradient of mechanical properties, with the increase in the stiffness and the hardness from anterior to the posterior region of the shell. The shell is made from distinct and recognizable mineralized layers each varying in thickness and microstructural features. At posterior regions of the shell, moving from dorsal to ventral side, these layers are an oblique prismatic layer, a prismatic layer and a nacreous layer, in which the oblique prismatic layer is found to be the main and thickest mineralized layer of the shell. Probing the calcified rods in the oblique prismatic layer using high resolution SEM imaging revealed opening of channels with a diameters of 40-50 nm and lengths up to a micrometer extending through the rods. The chitin and protein have been found to be the main component of the organic-rich interfacial matrix as expected. Protein analysis showed two abundant proteins with sizes around 100 kD and 45 kD which likely not only regulates biomineralization and adhesion of the crystals but also governing the intrinsic-extrinsic toughening in the shell. Overall, this detailed analysis provides new structural insights into biomineralization of marine shells in general.
REVIEW | doi:10.20944/preprints202102.0030.v1
Subject: Biology, Anatomy & Morphology Keywords: AEA; 2-AG; CB1; CB2; endocannabinoid; regeneration; neurodevelopment; invertebrate
Online: 1 February 2021 (13:16:51 CET)
Cannabis has long been used for its medicinal and psychoactive properties. With the relatively new adoption of formal medicinal cannabis regulations worldwide, the study of cannabinoids, both endogenous and exogenous, has similarly flourished in more recent decades. In particular, research investigating the role of cannabinoids in regeneration and neurodevelopment has yielded promising results in vertebrate models. However, regeneration-competent vertebrates are few, whereas a myriad of invertebrate species have been established as superb models for regeneration. As such, this review aims to provide a comprehensive summary of the endocannabinoid system, with a focus on current advances in the area of endocannabinoid system contributions to invertebrate neurodevelopment and regeneration.
REVIEW | doi:10.20944/preprints202102.0018.v1
Subject: Biology, Anatomy & Morphology Keywords: Food; feeding; diets; macro-micronutrients; feeding behavior; pellet-animal performances
Online: 1 February 2021 (12:08:54 CET)
There are several literatures that cover different views of crustacean food, feeding and behavior aspects, but little was known on its interaction between them and it's also shown a different perspective. Thus, a better understanding of the interactions between food, feeding and diets in crustaceans is vital for developing better quality of seed or broodstock produced in hatchery and its adaptation to the aquaculture environment and system. The aim of the present review is to update the state of the art and to explicit the knowledge regarding food, feeding and diets in crustaceans and challenges and opportunities in the development of formulated diets.
ARTICLE | doi:10.20944/preprints202102.0004.v1
Subject: Biology, Anatomy & Morphology Keywords: Equine theileriosis; Theileria haneyi; enzyme-linked immunosorbent assay (ELISA), serology
Online: 1 February 2021 (09:41:24 CET)
The apicomplexan parasite Theileria haneyi is one of two known causative agents of equine theileriosis. It causes milder clinical disease than its more virulent counterpart, Theileria equi, in experimentally infected horses, and can superinfect T. equi-positive horses. The current EMA1-based competitive ELISA used in the U.S. to detect equine theileriosis detects T. equi but not T. haneyi, and the complexity of molecular assays precludes widespread use for epidemiologic studies. In order to facilitate urgently needed studies on the prevalence of T. haneyi, the goal of this study was to develop a sensitive and specific serologic assay for the diagnosis of T. haneyi based on the equi mero-zoite antigen 11 (ThEMA11). To achieve this objective, ThEMA11 was recombinantly expressed in eukaryotic cells and its antigenicity assessed using sera from T. haneyi-experimentally infected horses. Confirmation of sera reactiv-ity enabled design and optimization of an indirect ELISA. Specificity of the ELISA for T. haneyi was assessed using a cohort of sera from horses experimentally infected and confirmed PCR-positive for either T. equi or T. haneyi. Data from field samples further demonstrate that the ThEMA11 ELISA is capable of identifying T. haneyi antibodies in horses from multiple continents around the world.
Fri, 29 January 2021
REVIEW | doi:10.20944/preprints202101.0626.v1
Subject: Biology, Anatomy & Morphology Keywords: BTB and CNC homology 1 BACH1; mitochondrial metabolism; glycolysis; heme oxygenase 1 (HMOX1); mitochondrial electron transport chain (ETC); Nrf2 (encoded by Nfe2l2); metformin; hemin; breast cancer; lung cancer
Online: 29 January 2021 (13:57:41 CET)
BTB domain and CNC homology 1 (BACH1) is a highly expressed transcription factor in tumors including breast and lung, relative to their non-tumor tissues. BACH1 is known to regulate multiple physiological processes including heme homeostasis, oxidative stress response, senescence, cell cycle, and mitosis. In a tumor, BACH1 promotes invasion and metastasis of cancer cells, and the expression of BACH1 presents a poor outcome for cancer patients including breast cancer patients. Recent studies identified novel functional roles of BACH1 in the regulation of metabolic pathways in cancer cells. BACH1 inhibits mitochondrial metabolism through transcriptional suppression of mitochondrial membrane genes. In addition, BACH1 suppresses activity of pyruvate dehydrogenase (PDH), a key enzyme that converts pyruvate to acetyl-CoA for the citric acid (TCA) cycle through transcriptional activation of pyruvate dehydrogenase kinase (PDK). Moreover, BACH1 increases glucose uptake and lactate secretion in aerobic glycolysis through the expression of metabolic enzymes involved such as hexokinase 2 (HK2) and glyceraldehyde 3- phosphate dehydrogenase (GAPDH). Pharmacological or genetic inhibition of BACH1 could reprogramme metabolic pathways, subsequently rendering metabolic vulnerability of cancer cells. Furthermore, inhibition of BACH1 decreased antioxidant-induced glycolysis rates as well as reduced migration and invasion of cancer cells, suggesting BACH1 as a potentially useful cancer therapeutic target.
ARTICLE | doi:10.20944/preprints202101.0614.v1
Subject: Biology, Anatomy & Morphology Keywords: Durum wheat; Tunisian landraces; genetic diversity; population structure; phenotypic characterization
Online: 29 January 2021 (11:53:26 CET)
During the 1970s, Tunisian durum wheat landraces were replaced progressively by modern cultivars. These landraces are nowadays maintained by smallholder farmers in some ecological niches and are threatened gradually by extinction resulting on the narrowing of the genetic diversity. This study aims to investigate patterns of phenotypic variability using twelve quantitative traits in a panel of 189 durum wheat landraces and seven checks, based on farmer’s population name attribution and genetic structure. Our results showed high phenotypic variability among and within landraces and checks for the majority of the studied traits. The principal components analysis showed similar grouping using farmers name attribution and genetic structure using K = 6, which confirmed the identification of a new gene pool in the oases of Tunisia, represented by the sub-population Jenah Zarzoura and the robustness and high relationships between phenotypic and genome-wide genetic structure using DArTseq method. These findings will enhance the conservation efforts of these landraces and their use in breeding efforts at national and international levels to adapt to dry conditions.
Thu, 28 January 2021
ARTICLE | doi:10.20944/preprints202101.0597.v1
Subject: Biology, Anatomy & Morphology Keywords: Vis/NIR; repeated longitudinal measurements; apple maturation; precision horticulture
Online: 28 January 2021 (22:24:35 CET)
Optical sensor data can be used to determine changes in anthocyanins, chlorophyll and soluble solids content (SSC) in apple production. In this study, visible and near-infrared spectra (729 to 975 nm) were transformed to SSC values by advanced multivariate calibration models i.e. partial least square regression (PLSR) in order to test the substitution of destructive chemical analyses through non-destructive optical measurements. Spectral field scans were carried out from 2016 to 2018 on marked ’Braeburn’ apples in Southwest Germany. The study combines an in-depth statistical analyses of longitudinal SSC values with horticultural knowledge to set guidelines for further applied use of SSC predictions in the orchard to gain insights into apple carbohydrate physiology. The PLSR models were investigated with respect to sample size, seasonal variation, laboratory errors and the explanatory power of PLSR models when applied to independent samples. As a result of Monte Carlo simulations, PLSR modelled SSC only depended to a minor extent on the absolute number and accuracy of the wet chemistry laboratory calibration measurements. The comparison between non-destructive SSC determinations in the orchard with standard destructive lab testing at harvest on an independent sample showed mean differences of 0.5 % SSC over all study years. SSC modelling with longitudinal linear mixed-effect (LME) models linked high crop loads to lower SSC values at harvest and higher SSC values for fruit from the top part of a tree.
REVIEW | doi:10.20944/preprints202101.0581.v1
Subject: Biology, Anatomy & Morphology Keywords: genetically encoded biosensors; live spatiotemporal imaging; multiparameter imaging; plant immune response; biotic stress; crops
Online: 28 January 2021 (12:33:42 CET)
Biosensors are indispensable tools to follow plant’s immunity as its spatiotemporal dimension is key in withstanding the complex plant immune signaling. The diversity of genetically encoded biosensors in plants is expanding, covering new analytes with ever higher sensitivity and robustness, but their assortment is limited in some aspects, such as their use to follow biotic stress response, employing more than one biosensor in the same chassis and their implementation into crops. In this review, we focused on the available biosensors that encompass these aspects. We show that in vivo imaging of calcium and reactive oxygen species is satisfactorily covered with the available genetically encoded biosensors, while on the other hand they are still underrepresented when it comes to imaging of the main three hormonal players of the immune response, salicylic acid, ethylene and jasmonic acid. Following more than one analyte in the same chassis, upon one or more conditions has so far been possible by using the most advanced genetically encoded biosensors in plants which allow to monitor calcium and two main hormonal pathways involved in plant development, auxin and cytokinin. These kinds of biosensors are also the most evolved in crops. In the last section, we gathered the challenges in the use of the biosensors and showed some strategies to overcome them.
HYPOTHESIS | doi:10.20944/preprints202010.0004.v7
Subject: Biology, Anatomy & Morphology Keywords: carbon-based entity; driving force; energy; evolution; fitness; mechanism; natural selection; speciation; thermodynamics; theory
Online: 28 January 2021 (12:25:54 CET)
Studies on evolution have made significant progress in multiple disciplines, but evolutionary theories remain incomplete, controversial and inadequate in explaining origin of life and macroevolution. Here we create the concept of carbon-based entities (CBEs) which include methane, amino acids, proteins, bacteria, animals, plants, and other entities containing carbon atoms. From thermodynamics, we deduce the driving force, the progressive mechanisms, and the major steps of CBE evolution, and hence establish a comprehensive evolutionary theory termed the CBE evolutionary theory (CBEET). CBEET highlights that evolution is driven hierarchy-wise by thermodynamics and favors fitness and diversity. It provides novel explanations for origin of life (abiogenesis), macroevolution, natural selection, sympatric speciation, and animal group evolution in a comprehensive and comprehensible way. It elucidates that collaboration, altruism, obeying rules with properly increased freedom are important throughout the CBE evolution. It refutes thoroughly the notion that negative entropy (negentropy) leads to biological order which is distinct from thermodynamic order. It integrates with research advances in multiple disciplines and bridges laws of physics, evolution in biology, and harmonious development of human society.
Wed, 27 January 2021
ARTICLE | doi:10.20944/preprints202101.0552.v1
Subject: Biology, Anatomy & Morphology Keywords: organoid; induced pluripotent stem cell; Parkinson’s disease; neurotransmission; neuroimmunity; neuroinflammation; chikungunya; neuroinvasive
Online: 27 January 2021 (10:31:06 CET)
Arboviruses of medical and veterinary significance have been identified on all 7 continents with every human and animal population at risk for exposure. Like arboviruses, chronic neurodegenerative diseases like Alzheimer’s and Parkinson’s disease are found wherever there are humans. Viral parkinsonism has been documented for a variety of human pathogens though there are few studies that evaluate the effects of viral infection on degenerative neurological diseases. Significant differences in baseline gene and protein expression have been determined between Human Induced Pluripotent Stem Cell lines derived from a non-Parkinson’s disease individual and from an individual with reported Parkinson’s disease. While the organoids generated from each cell line were physically indistinguishable, significant differences were observed in gene and protein expression for neurotransmission and immunity. It was hypothesized that these inherent differences would impact cerebral organoid responses to viral infection. In this preliminary observational study, cerebral organoids from a non-Parkinson’s and Parkinson’s patient were infected with Chikungunya virus and observed for 2 weeks. Parkinson’s organoids lost mass and exhibited a dysfunctional antiviral response. Neurotransmission data from both non-Parkinson’s and Parkinson’s organoids had dysregulation of IL-1, IL-10, IL-6. These cytokines are associated with mood and could be contributing to persistent depression seen in patients following CHIKV infection. Both organoid types had increased expression of CCR5 and CXCL10 which are linked to demyelination, highlighting a potential mechanism for virus-associated parkinsonism. The dysfunctional antiviral response of Parkinson’s organoids highlights the need for more research in neurotropic infections in a neurologically compromised host.
Tue, 26 January 2021
ARTICLE | doi:10.20944/preprints202101.0543.v1
Subject: Biology, Anatomy & Morphology Keywords: Blueberry; Pre-breeding; hybridization; V. elliottii; Fruit quality
Online: 26 January 2021 (15:55:14 CET)
Wild germplasm can be classified as the raw material essential for crop improvement. Introgression of wild germplasm is normally used in breeding to increase crop quality or resilience to evolving biotic and abiotic threats. Here, we explore the potential of introgressing Vaccinium elliottii into commercial blueberry germplasm. Vaccinium elliottii is a wild diploid blueberry species endemic to the southeastern United States that possesses highly desirable and economically important traits for blueberry breeding such as: short bloom to ripe period, adaptation to upland sandy soils, disease resistance, firmness, and pleasant flavor. To examine the potential of hybridization, we evaluated populations of interspecific hybrids across multiples stages of breeding (i.e., F1, F2, and backcrosses) in two crop seasons. We used our extensive pedigree data to generate breeding values for pre-breeding blueberry hybrid populations. Hybrid performance was evaluated considering fitness (i.e., plant vigor and plant height) in addition to evaluating six fruit-quality and marketable-related traits (i.e., size, firmness, acidity, soluble solids, weight, and yield). Overall, F2 and backcrosses rapidly achieved market thresholds, presenting values not significantly different from commercial blueberry germplasm. Our results confirmed the potential of exploiting the high genetic variability contained in V. elliotii for interspecific hybridization. Additionally, we developed germplasm resources that can be further evaluated and utilized in the breeding process, advancing selections for fruit quality and environmental adaptation.
ARTICLE | doi:10.20944/preprints202012.0689.v3
Subject: Biology, Anatomy & Morphology Keywords: Meme; memetic; culture; propagation; equilibrium; inheritance; extinction; resistance; evolution; natural selection; Fermi Paradox
Online: 26 January 2021 (10:24:54 CET)
Background: The term meme includes vertical trait transmission and laterally transmitted ideas that can be lasting or transient. Memes may sometimes follow the logic of population genetics, e.g. learned birdsong, but not when laterally transmitted. Much current work focuses on selection of memes rather than hosts. This paper investigates mathematically the interaction of behaviorally transmitted traits with host selection fitness. Methods: We analyze equilibrium between gene-meme and meme-meme competing propagators and consider whether a meme is linked to reproduction (e.g. vertical culture transmission), or not. We employ a genetic component and combined meme-induced fitness components for hosts, while memes have replication factors to distinguish from what’s good for the host (fitness). We use a Monte Carlo simulation roughly calibrated to the Industrial Revolution to study meme effects on population stability. Results: A basic effective calculus of memetic trait competition and interaction with genes is derived and analyzed. The transient nature of many lateral memes may be a defense against accumulation of deleterious memes. Laterally transmitted (panmictic) memes with high spreading rate will often not equalize with a genetic trait, spreading outside of natural selection of the hosts, presenting a cumulative existential threat. Vertical transmission reduces replication rate and allows group selection against deleterious memes. Competing mutually exclusive memes contribute to inequality and altruism, but compete through adverse fitness since exclusivity assumes low conversion. Conclusions: The advantage of a portfolio of groups or species may not accrue to a single group. This understanding elevates meme-risk to the level of a candidate solution to the so-called Fermi Paradox.
ARTICLE | doi:10.20944/preprints202101.0526.v1
Subject: Biology, Anatomy & Morphology Keywords: Asaia; paratransgenesis; symbiotic traits; Anopheles stephensi; genome features
Online: 26 January 2021 (08:19:00 CET)
Asaia bacteria commonly comprise part of the microbiome of many mosquito species in the genera Anopheles and Aedes, including important vectors of infectious agents. Their close association with multiple organs and tissues of their mosquito hosts enhances the potential for paratransgenesis for delivery of anti-malaria or anti-virus effectors. The molecular mechanisms involved in the interactions between Asaia and mosquito hosts, as well as Asaia and other bacterial members of the mosquito microbiome, remained unexplored. Here, we determined the genome sequence of the strain W12 isolated from Anopheles stephensi mosquitoes, compared them to other Asaia species associated with plants or insects, and investigated some properties of the bacteria relevant to their symbiosis with host mosquitoes. The assembled genome of strain W12 has a size of 3.94 MB, which is the largest among Asaia spp studied so far. At least 3,585 coding sequences were predicted. The insect-associated Asaia including strain W12 carried more glycoside hydrolase (GH) encoding genes (31 per genome) than those isolated from plants (22 per genome). W12 had the most predicted regulatory protein components (213) among the selected Asaia (ranging from 131 to 211), indicating its great capability to adapt to frequent environmental changes in the mosquito gut. Two complete operons encoding cytochrome bo3-type ubiquinol terminal oxidases (cyoABCD-1 and cyoABCD-2) were found in most of Asaia genomes, which possibly offer alternative terminal oxidases and allow the flexible transition of respiratory pathways. Genes involved in the production of acetoin and 2,3-butandiol have been identified in Asaia sp. W12.
REVIEW | doi:10.20944/preprints202101.0525.v1
Subject: Biology, Anatomy & Morphology Keywords: DNA Damage; Base Excision Repair; SMUG1; 5-hmdU; Cancer
Online: 26 January 2021 (08:17:11 CET)
Single-stand selective monofunctional uracil DNA glycosylase 1 (SMUG1) works to remove uracil and certain oxidized bases from DNA during base excision repair (BER). This review provides a historical characterization of SMUG1 and 5-hydroxymethyl-2'-deoxyuridine (5-hmdU) one important substrate of this enzyme. Biochemical and structural analyses provide remarkable insight into the mechanism of this glycosylase revealing SMUG1 has a unique helical wedge which influences damage recognition during repair. Rodent studies suggest that, while SMUG1 shares substrate specificity with another uracil glycosylase UNG2, loss of SMUG1 can have unique cellular phenotypes. This review highlights the multiple roles SMUG1 may play in preserving genome stability, and how the loss of SMUG1 activity may promote cancer. Finally, we discuss recent studies indicating SMUG1 has moonlighting functions beyond BER, playing a critical role in RNA processing including the RNA component of telomerase.
Mon, 25 January 2021
ARTICLE | doi:10.20944/preprints202101.0512.v1
Subject: Biology, Anatomy & Morphology Keywords: fish; functional data analysis; long-term monitoring; habitat; occupancy; modeling; California
Online: 25 January 2021 (15:11:52 CET)
Abundance of estuarine fish species has declined globally. In the San Francisco Estuary (SFE), long-term monitoring documented declines of many species including the anadromous species Longfin Smelt (Spirinchus thaleichthys). To improve management and recovery planning, we identified patterns in the timing, seasonal occupancy, and distribution of Longfin Smelt in a monitoring study (San Francisco Bay Study) for five regions of the SFE using a generalized additive model. We then investigated the year-to-year variability in the shape of the seasonal relationships using functional data analysis (FDA). FDA separated the variability due to population size from variability due to differences in occupancy timing. We found that Longfin Smelt have a consistent seasonal distribution pattern, that two trawl types were needed to accurately describe the pattern, and that the pattern is largely consistent with the hypothesized conceptual model. After accounting for variability in occupancy due to year-class strength, the timing of occupancy has shifted in three regions. The most variable period for the upstream regions Suisun Bay and Confluence was age-0 summer and for the downstream region Central Bay, was age-0 late fall. This manifested as a recent delay in the typical fall re-occupation of upstream regions, reducing Longfin Smelt abundance as calculated by another monitoring study (Fall Midwater Trawl); thus, a portion of recent reductions in Fall Midwater Trawl abundance of Longfin Smelt result from changes in behavior rather than a decline in abundance. The presence of multiple monitoring surveys allowed analysis of distribution from one data set to interpret patterns in abundance of another. Future investigations will examine environmental conditions as covariates during these periods and could improve our understanding of what conditions contribute to the shifting occupancy timing of Longfin Smelt, and possibly provide insight into the long-term quality of the San Francisco Estuary as habitat.
ARTICLE | doi:10.20944/preprints202101.0490.v1
Subject: Biology, Anatomy & Morphology Keywords: CD44; Cancer Stem Cells; Tumorigenesis; Drug Resistance; Immune Markers; Epithelial to Mesenchymal Transition; Therapeutic Targeting
Online: 25 January 2021 (12:23:49 CET)
One of the most used markers of cancer stem cells in several cancers, including colorectal cancer and breast cancer, is CD44. CD44 is a glycoprotein that traverses the cell membrane and binds to many ligands including hyaluronan resulting in activation of signaling cascades. Several reports have shown conflicting data on the expression of CD44 and that the expression depends on modes of investigations and subtypes of cancers. In addition, the correlation between CD44 expression and drug resistance, immune infiltration, EMT, metastasis and patients prognosis in several cancer types remains unclear. This study investigated CD44 expression in several cancers and explored its relationship with tumorigenesis using various publicly available databases, including The Cancer Genome Atlas, GEPIA, Oncomine, Genomics of Drug Sensitivity in Cancer and Tumor Immune Estimation Resource. Our analysis reveals that CD44 is differentially expressed in different cancers. CD44 expression is significantly associated with cancer patients’ survival in gastric, pancreatic and colorectal cancers. In addition, CD44 expression is closely linked with immune infiltration and immune suppressive features in pancreatic, colon adenocarcinoma and stomach cancer. High CD44 expression was significantly correlated with the expression of drug resistance-, EMT- and metastasis- linked genes. Tumors expressing high CD44 have higher mutation burden and afflict older patients than tumors expressing low CD44. Cell lines expressing high CD44 are more resistant to anti-cancer drugs compared to those expressing low CD44. Protein-protein interaction investigations and functional enrichment analysis showed that CD44 interacts with gene products related to cell-substrate adhesion, migration, platelet activation, and cellular response to stress. KEGG pathway analysis revealed that these genes play key roles in biological adhesion, cell component organization, locomotion, G-α-signaling and the response to stimulus. Overall, this investigation reveals that CD44 play significant roles in tumorigenesis, can be used as a prognostic biomarker in several cancers and can be therapeutically targeted in cancer therapy.
HYPOTHESIS | doi:10.20944/preprints202101.0486.v1
Subject: Biology, Anatomy & Morphology Keywords: reproductive isolation; MEN; Hmr; Rab GTPases; cholesterol; HyMEN
Online: 25 January 2021 (11:39:44 CET)
At the end of mitosis the Mitotic Exit Network (MEN) pathway triggers complex tasks which mainly include the spindle disassembly and the nuclear envelopes assembly. In the course of telophase, which often lasts less than an hour and corresponds to only about 2% of the entire cell cycle’s duration, spatial and temporal cues are integrated to ensure that cytokinesis occurs after the genome has partitioned between mother and daughter cells. From the end of anaphase through telophase, sequential components of a Ras-like GTPase signaling pathway are controlled by a set of different spatial and temporal signals. Successful propagation of these signals through multi-step transduction requires a remarkable sequential coordination. By considering that cells lacking proper MEN function fail to exit from mitosis, I argue that in a hybrid genome impaired coordination between two diverged MENs is prone to result in critical mitotic defects, from late anaphase through telophase. The so-called HyMEN model of hybrid incompatibility depicted here can be regarded as an extension of the Bateson-Dobzhansky-Muller model of speciation, centered on the MEN.
ARTICLE | doi:10.20944/preprints202101.0480.v1
Subject: Biology, Anatomy & Morphology Keywords: organoid; induced pluripotent stem cell; Parkinson’s disease; neurotransmission; neuroimmunity; neuroinflammation; viral infection
Online: 25 January 2021 (10:55:03 CET)