ARTICLE | doi:10.20944/preprints202106.0535.v1
Subject: Biology, Anatomy & Morphology Keywords: biodiversity; sinkhole; Chironomidae; Copepoda; Trombidiformes; Cladocera, Ostracoda, Yucatan Peninsula
Online: 22 June 2021 (09:09:09 CEST)
This study is focused to the aquatic environments of the Sian Ka’an reserve, a World Heritage Site. We applied protocols recently developed for the rapid assessment of most animal taxa inhabiting any freshwater system, by using light traps, and DNA barcodes, represented by the mitochondrial gene Cytochrome Oxidase I (COI). We DNA barcoded 1037 specimens of mites, crustaceans, insects, and fish larvae from 13 aquatic environments close or inside the reserve, with a success rate of 99.8%. In total, 167 Molecular Operational Taxonomic Units (MOTU’s) were detected. From them we identified 43 species. All others remain as a MOTU. For analyzing the adult fish communities, we applied the non-invasive method of environmental DNA (eDNA), and identified the sequences obtained with the Barcode of Life Database (BOLD). We found 25 fish species, and other terrestrial vertebrates from this region. No alien species was found. After a comparison of the MOTU’s from all systems, we found that each water body was unique respect the communities observed. The reference library presented here represents the first step for future programs to detect any change in these ecosystems, including invasive species, or improve knowledge of freshwater zooplankton, because most of the MOTU’s are possibly new species to science.
Mon, 21 June 2021
ARTICLE | doi:10.20944/preprints202106.0519.v1
Subject: Biology, Anatomy & Morphology Keywords: Polyethylene terephthalate; Microbial degradation; Sustainable development
Online: 21 June 2021 (14:52:03 CEST)
Plastics are extensively used due to their versatility, durability, and low cost. PET stands for Polyethylene terephthalate. PET plastic is widely used all over the world and has many applications ranging from water bottles to fabrics like polyester and many things in between. But its unrestrained use in every field is resulting in heaps and piles of non-biodegradable materials causing damage to the environment and causing pollution. The idea being proposed is to degrade the PET plastic biologically using different bacteria. The bacteria used in this process are Ideonella sakaiensis, Acetobacterium woodii, Pelotomaculum and Methanospirillum hungatei. PET plastic is degraded, yielding Terephthalic Acid (TPA) and Ethylene Glycol (EG) by the action of the bacterium I. sakaiensis. Degradation of EG by A. woodii results in the formation of acetate and ethanol. TPA is degraded by the action of the coculture of Pelotomaculum and M. hungatei thereby yielding methane and acetate. All these products formed have significant commercial uses in various industries. The complete process that is to be carried out can help in achieving sustainability by fulfilling various Sustainable Development Goals set by the United Nations.
ARTICLE | doi:10.20944/preprints202106.0517.v1
Subject: Biology, Anatomy & Morphology Keywords: Harvest index; total biomass; fruit number; fruit length
Online: 21 June 2021 (14:22:35 CEST)
Pollination is the process by which pollen grains are exchanged in plant flowers to allow for fertilisation and production to take place. However, challenges occur when crops are grown under protected structures where there are minimal activities of natural pollination agents such as wind and animals which are responsible for transferring pollen grains from the anther to the stigma. Therefore, the study objective was to determine the effect on hand pollination on the yield of African horned cucumber grown under greenhouse and shade net environment. A factorial experiment with two factors (hand pollinated and non-hand pollinated/control) was conducted under two different growing environments (greenhouse and shade net). African horned cucumber plants were hand self-pollinated in the morning. Pollen were manually transferred with a hand using the new earbud from the male to the female flowers on the same plant (selfing). Results showed that hand pollinated African horned cucumber plants increased total biomass from 0.93 to 2.23 kg under greenhouse environment. Hand pollinated plants increased harvest index from 0.07 to 0.35 under shade net environment. It can thus, be deduced that hand pollination increases African horned cucumber yield in the greenhouse and shade net environments.
REVIEW | doi:10.20944/preprints202106.0515.v1
Subject: Biology, Anatomy & Morphology Keywords: inositol; inositol transporters; vacuole; stress tolerance
Online: 21 June 2021 (14:12:29 CEST)
Inositol transporter (INT) is reputed as the pivotal transporter for vital metabolites like lipids, minerals, and sugars particularly. These transporters play important role in transitional metabolism and various signaling pathways in plants through regulating the transduction of messages from hormones, neurotransmitters, and immunologic and growth factors. Extensive studies have been conducted on animal INT with promising outcomes. However, few recent studies have highlighted the importance and the complexity of INT genes in the regulation of plant physiology stages including growth and tolerance to stress conditions. The present review sum-up the most recent findings on the role of INT or inositol genes in plant metabolisms and the responsive mechanisms that cope with external stressors. Moreover, we highlighted the emerging role of vacuoles and vacuolar inositol transporters in plant molecular transition and their related roles in plant growth and development. Inositol transporters are the essential mediator for the inositol uptake and its intracellular broadcasting for various metabolic pathways where they play crucial roles. Also, so far characterized only in animals, we reported evidence on Na+/inositol transporters H+/inositol symporters and suggested their roles and operating mode in plants. Thus, understanding the INT functioning system, the coordinated movement of inositol, and the relation between inositol generation and other important plant signaling pathways would be an excellent asset for advancement in researches on plant stress adaptation.
REVIEW | doi:10.20944/preprints202106.0504.v1
Subject: Biology, Anatomy & Morphology Keywords: Microbiota; Microbiome; Mosquitoes; Behavior; Oviposition; Larval habitat; Life History Traits; Nutrition; Development; Survival
Online: 21 June 2021 (11:22:15 CEST)
Mosquitoes are considered one of the most important threats worldwide due to their ability to vector pathogens. They are responsible for the transmission of major pathogens such as Malaria, dengue, Zika or Chikungunya. Due to the lack of treatments or prophylaxis against many of the transmitted pathogens and an increasing prevalence of mosquito resistance to insecticides and drugs available, alternative strategies are now being explored. Some of these involve the use of microorganisms as promising agent to limit the fitness of mosquitoes, attract or repel them and decrease the replication and transmission of pathogenic agents. In recent years, the importance of microorganisms colonizing the habitat of mosquitoes has particularly been investigated since they appeared to play major roles in their development and diseases transmission. In this issue we will synthesize researches investigating how microorganisms present within water habitats may influence breeding site selection and oviposition strategy of gravid mosquito females. We will also highlight the impact, effect of such microbes on the fate of females’ progeny during their immature stages with a specific focus on egg hatching, development rate and larvae of pupae survival.
REVIEW | doi:10.20944/preprints202106.0494.v1
Subject: Biology, Anatomy & Morphology Keywords: adaptive significance; evolution of gall insects; gall-inducing insects; gall formation mechanism; insect effectors
Online: 21 June 2021 (09:34:51 CEST)
Galls are characteristic plant structures formed by hypertrophy (excessive increase in cell size) and/or hyperplasia (cell proliferation) induced by parasitic or pathogenic organisms. Insects are a major inducer of galls, and insect galls can occur on plant leaves, stems, floral buds, flowers, fruits, or roots. Many of these exhibit unique shapes, providing shelter and nutrients to the insects. To form unique gall structures, all-inducing insects are believed to secrete certain effector molecules and hijack host developmental programs. However, the molecular mechanisms of insect gall induction and development is still largely unknown because of the difficulty of studying non-model plants in the wild. Recent progress in next-generation sequencing has allowed us to determine the structure of biological processes in non-model organisms, including gall-inducing insects and their host plants. In this review, we first summarize the evolutionary aspects of gall-inducing life histories and their adaptive significance for insects and plants. Then, we briefly summarize recent progress regarding the molecular aspects of insect gall formation.
Fri, 18 June 2021
ARTICLE | doi:10.20944/preprints202106.0473.v1
Subject: Biology, Anatomy & Morphology Keywords: bleaching; coral reef; environmental stress; Google Earth Engine; monitoring; remote sensing; satellite
Online: 18 June 2021 (10:43:50 CEST)
Coral reefs are critical ecosystems globally for marine fauna, biodiversity and through the services they provide to humanity. However, they are significantly threatened by anthropogenic stressors, such as climate change. By combining 9 environmental variables and ecological and health-based thresholds obtained from the available literature, we develop, using fuzzy logic (discontinuous functions), a Coral Reef Stress Exposure Index (CRSEI) for remotely monitoring coral reef exposure to environmental stressors. Our approach capitalises on the abundance of readily available satellite Earth Observation (EO) data available in the Google Earth Engine (GEE) cloud-based geospatial processing platform. CRSEI values from 3157 distinct reefs were generated and mapped across 12 important coral reef ecosystem regions. Quantitative analyses indicated that the index detected significant temporal differences in stress and was, therefore, able to capture historic change at a global scale. We also applied the CRSEI to three case-study reef ecosystems, previously well-monitored for stress and disturbance using other methods. PCA analysis indicated that depth, current, sea surface temperature (SST) and SST anomaly accounted for the greatest contribution to the variance in stress in these three regions. The CRSEI corroborated temporal and spatial differences in stress exposure from known disturbances within these reference regions, in addition to identifying the potential drivers of inter- and intra-region differences in stress, namely depth, degree heating weeks and SST anomaly. We discuss how the index can be further improved in future with site-specific thresholds for each stress variable, and the incorporation of additional variables not currently available in GEE. This index provides an open access tool, built around a free and powerful processing platform, that has broad potential to assist in the regular monitoring of our increasingly imperilled coral reef ecosystems, and, in particular, those that are remote or inaccessible.
Thu, 17 June 2021
Subject: Biology, Anatomy & Morphology Keywords: mitochondria; mitochondrial DNA; nervous tissue, OxPhos complexes; bioenergetics; genomics; proteomics; mitochondrial diseases
Online: 17 June 2021 (15:12:01 CEST)
Oxidative phosphorylation (OxPhos) is the basic function of mitochondria although the land-scape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding de-tails to the mitochondrial proteome and defining novel metabolic cellular interrelations, espe-cially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition as ‘mitoexome’, ‘mitoproteome’ and ‘mitointeractome’ have entered the field of ‘mitochondrial medicine’. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic determination of the OxPhos complexes is one of the reasons for the complexity of the geno-type-phenotype correlation when facing human diseases associated with mitochondria defects; clinically, are characterized by extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the fu-ture directions of the multi-omics study of human brain disorders.
ARTICLE | doi:10.20944/preprints202106.0463.v1
Subject: Biology, Anatomy & Morphology Keywords: jellyfish; sting; first aid; vinegar; seawater; nematocyst discharge; Pelagia noctiluca; Carybdea marsupualis.
Online: 17 June 2021 (14:39:50 CEST)
Although the jellyfish species that inhabit the Mediterranean coastal waters are not lethal, their sting can cause severe pain and systemic effects that pose a health risk to humans. Despite the frequent occurrence of jellyfish stings, currently no consensus exists regarding the most appropriate first aid protocol among the scientific community. Over the years, several different rinse solutions have been proposed of which vinegar, or acetic acid, is one of the most noticeable as a rinse solution with efficacy data published. We investigated the effect of vinegar and seawater on the nematocyst discharge process in species representative of the Mediterranean region such as Pelagia noctiluca (Scyphozoa) and Carybdea marsupialis (Cubozoa) by means of: (1) direct observation on the nematocyst discharge by light microscope (Tentacle solution assay) and (2) the quantification of hemolytic area (Tentacle skin blood agarose assay). The nematocyst discharge of both species was not stimulated by seawater, and it was classified as a neutral solution. In P. noctiluca, vinegar produced nematocyst discharge per ser while inhibiting the nematocyst discharge of C. marsupilais. These results suggest that the use of vinegar cannot be universally recommended. While in case of a cubozoan C. marsupialis sting, the inhibitory effect of vinegar makes it the best rinse solution par excellence, in case of a scyphozoan P. noctiluca sting, its application can be counterproductive, worsening the pain and discomfort of the stung area.
HYPOTHESIS | doi:10.20944/preprints202010.0004.v9
Subject: Biology, Anatomy & Morphology Keywords: carbon-based entity; driving force; energy; evolution; fitness; mechanism; natural selection; speciation; thermodynamics; theory
Online: 17 June 2021 (11:56:15 CEST)
It is desirable to upgrade previous evolutionary theories, which have remained incomplete and controversial for decades. Here we employ the concept of carbon-based entities (CBEs), which include methane, amino acids, proteins, organisms, and other entities containing relatively many carbon atoms. We deduce the driving force, mechanisms, steps, modes, tempos of CBE evolution, through integration of biology, physics, and chemistry using logics for complex issues. We hence establish the Carbon-Based Evolutionary Theory (CBET). The CBET suggests that evolution is the increase in hierarchy, diversity, fitness of CBEs under natural selection and driven by thermodynamics due to the chemical effect of the thermodynamic features of the Earth on CBEs. It provides better explanations for life origin, macroevolution events, natural selection, sympatric speciation, and evolution tempos than previous evolutionary theories. It reveals the evolutionary basis of multiple important social notions, including diversity, collaboration, altruism, obeying rules, and proper increase in freedom. It refutes some wrong notions in thermodynamics, including negative entropy (negentropy) and that biological order is equal to thermodynamic order, which have misled many people. The CBET is supported by its deduction and application. It could be a rare bridge linking laws of thermodynamics, evolution of life, and development of human society, and could have great significance in various sciences.
Wed, 16 June 2021
ARTICLE | doi:10.20944/preprints202106.0445.v1
Subject: Biology, Ecology Keywords: allelopathy; leaf litter; condensed tannins; mangrove forests; natural regeneration
Online: 16 June 2021 (12:43:27 CEST)
Kandelia obovata (Ko) and Aegiceras corniculatum (Ac) are common and dominant plant species in mangrove wetlands in South China, and distribute in the similar tidal zones along the coastline. The present study aimed to determine the allelopathic effects of leaf litter leachates (LLLs) from Ko and their purified condensed tannins (PCTs) on the germination and growth of Ac by mangrove microcosms. Replicate pots containing five different levels of LLLs and PCTs were separately prepared and propagules of Ac were placed in each treatment. Both LLLs and PCTs significantly inhibited the germination and growth of Ac, especially in high levels. The final germination rates of roots, stems, and the number of fine roots declined continuously while other growth indicators, including the lengths of fine roots, nutritive roots, the biomasses of roots, stems, leaves, increased firstly and then decreased with increasing levels. These results indicated that LLLs from the leaf litter of Ko, in particular, their PCTs exerted an inhibition effect on propagule germination and seedling growth of Ac, and the inhibitory effects were concentration dependent. This study suggested that condensed tannins from leaf litter, acting as allelochemicals, could regulate the natural regeneration of a mangrove forest.
ARTICLE | doi:10.20944/preprints202106.0443.v1
Online: 16 June 2021 (12:07:30 CEST)
Studies have shown that stress such as hypoxia, chemotherapy, radiotherapy can lead to polyploidization of tumor cells, which play an important role in tumor heterogeneity and malignant phenotype. Paclitaxel (PTX) treatment promoted polyploid cancer cells (PCCs) formation, and miR-378d is sharply reduced in PCCs of esophageal squamous cell carcinomas (ESCC) cells, but miR-378d participation PCCs formation and the impact on the biological behavior of ESCC remains unclear. We analyzed the PCCs formation and biological behavior of ESCC cells in vivo and in vitro, and the related proteins regulated by miR-378d. Results showed that miR-378d expression was associated with good prognosis in ESCC patients. miR-378d inhibition promoted PCCs formation, heterogenicity, chemo-resistance, monoclonal formation, EMT, migration, invasion, stemness and metastasis of ESCC cells. miR-378d can target downregulated AKT1, and inactivating the AKT-β-catenin signaling pathway, miR-378d and AKT can also regulated RhoA expression. AKT and RhoA regulated polyploidization and depolyploidization. Therefore, miR-378d expression is a good prognostic factor of ESCC patients and regulates polyploidization and malignant phenotype of tumor cells through AKT and RhoA.
Subject: Biology, Anatomy & Morphology Keywords: Real-time PCR; peanut; food allergen; chloroplast marker; DNA isolation
Online: 16 June 2021 (11:33:10 CEST)
Peanut (Arachis hypogaea) contains allergenic proteins, which make it harmful to the sensitised population. The presence of peanut in foods must be indicated on label, to prevent accidental consumption by allergic population. In this work, we use chloroplast markers for specifically detection of peanut by real-time PCR, in order to increase the assay sensitivity. Binary mixtures of raw and processed peanut flour in wheat were performed at concentrations ranging from 100000 to 0.1 mg/kg. DNA isolation from peanut, mixtures and other legumes was carried out following three protocols for obtaining genomic and chloroplast-enrich DNA. Quantity and quality of DNA was evaluated, obtaining better results for protocol 2. Specificity and sensitivity of the method has been assayed with specific primers for three chloroplast markers (mat k, rpl16 and trnH-psbA) and Ara h 6 peanut allergen-coding region was selected as nuclear low-copy target and TaqMan probes. Efficiency and linear correlation of calibration curves were within the adequate ranges. Mat k chloroplast marker yielded the most sensitive and efficient detection for peanut. Moreover, detection of mat K in binary mixtures of processed samples was possible up to 10 mg/kg even after boiling, and autoclave 121°C 15 min, with acceptable efficiency and linear correlation. Applicability of the method has been assayed in several commercial food products.
Tue, 15 June 2021
ARTICLE | doi:10.20944/preprints202106.0412.v1
Subject: Biology, Plant Sciences Keywords: Carbohydrate; heat stress; hydrogen sulphide; hypotaurine; melatonin
Online: 15 June 2021 (15:21:54 CEST)
Photosynthesis is a pivotal process that determines the synthesis of carbohydrates required for sustaining growth under normal or stress situation. Stress exposure reduces the photosynthetic potential owing to the excess synthesis of reactive oxygen species that disturb the proper functioning of photosynthetic apparatus. This decreased photosynthesis is associated with disturbances in carbohydrate metabolism resulting in reduced growth under stress. We evaluated the importance of melatonin in reducing heat stress-induced severity in wheat plants (Triticum aestivum L.). The plants were subjected to 25 ˚C (optimum temperature) or 40 ˚C (heat stress) for 15 days at 6 hours time duration and then developed the plants for 30 days. Heat stress led to oxidative stress with increased production of TBARS and H2O2 content and reduced accrual of total soluble sugars, starch and carbohydrate metabolism enzymes which are reflected in reduced photosynthesis. Application of melatonin not only reduced oxidative stress through lowering TBARS and H2O2 content, through augmenting the activity of antioxidative enzymes but also increased the photosynthesis in plant and carbohydrate metabolism that is needed to provide energy and carbon skeleton to the developing plant under stress. However, the increase in these parameters with melatonin was mediated via hydrogen sulfide (H2S), as the inhibition of H2S by hypotaurine (HT; H2S inhibitor) reversed the ameliorative effect of melatonin. This suggests a crosstalk of melatonin and H2S in protecting heat stress-induced photosynthetic inhibition via regulation of carbohydrate metabolism.
ARTICLE | doi:10.20944/preprints202106.0410.v1
Subject: Biology, Anatomy & Morphology Keywords: highly pathogenic avian influenza viruses, pathogenicity factors.
Online: 15 June 2021 (14:29:26 CEST)
The H7 subtype of avian influenza viruses (AIV) stands out among other AIV. The H7 viruses cir-culate in ducks, poultry, equine and have repeatedly caused outbreaks of disease in humans. In or-der to study the pathogenicity factors of H7N1 viruses, several variants were obtained, starting with laboratory strain, with a history of 12 passages through chicken embryos. This strain, A/chicken/Rostock/R0p/1934(H7N1) (R0p) had only 3 substitution in HA relatively A/Chicken/Rostock/45/34(H7N1), substitution Arg140Gly among them. 10 variants of this strain was obtained and studied to ascertain its biological property, genome stability and factors of patho-genicity. Strain R0p had decreased virulence for chicken, comparing with described in literature virulence of A/FPV Rostock/34 and A/chicken/Rostock/34 viruses. After 10 passages through the chicken lungs variant was obtained much more pathogenic than the starting R0p. The study of in-termediate passages through the chicken lungs showed that the jump in pathogenicity had occurred sharply between the fifth and sixth passage. By cloning these variants, a pair of strains (R5p and R6p) were obtained, and the complete genomes of these strains were sequenced. Single amino acid substitution was revealed, namely reversion Gly140Arg in HA1. This amino acid is located at the head part of the hemagglutinin, adjacent to the receptor-binding site. In addition to the increased pathogenicity for chicken and mice, R6p differs from R5p in the pattern of foci in cell culture and an increased affinity for a negatively charged receptor analogue, while maintaining a pattern of recep-tor binding specificity and the pH optimum of the HA conformational change.
ARTICLE | doi:10.20944/preprints202106.0397.v1
Online: 15 June 2021 (11:23:33 CEST)
Little phylogeographic structure is presumed for highly mobile species in pelagic zones. Lake Tanganyika is a unique ecosystem with a speciose and largely endemic fauna famous for its remarkable evolutionary history. In bathybatine cichlid fishes, the pattern of lake-wide population differentiation differs among species. We tested the magnifying glass hypothesis for their parasitic flatworm Cichlidogyrus casuarinus. Lake-wide population structure of C. casuarinus ex Hemibates stenosoma was assessed based on a portion of the mtCOI gene combined with morphological characterisation. Additionally, intraspecific mitogenomic variation among 80 individuals within one spatially constrained parasite metapopulation sample was assessed using shotgun NGS. While no clear geographic genetic structure was detected in parasites, both geographic and host-related phenotypic variation was apparent. The incongruence with the genetic north-south gradient observed in the host may be explained by the broad host range of this flatworm as some of its other host species previously showed no lake-wide restriction of gene flow. Our results are consistent with host driven morphological variation without genetic differentiation of the parasite, and highlight the importance of integratively approaching parasites` potential as “tags” for their hosts. We present the first parasite mitogenome from Lake Tanganyika and propose a methodological framework for studying intraspecific mitogenomic variation of dactylogyrid monogeneans.
ARTICLE | doi:10.20944/preprints202106.0391.v1
Subject: Biology, Anatomy & Morphology Keywords: catalase; flavonoids; hydrogen peroxide; proline, soluble sugars
Online: 15 June 2021 (09:25:13 CEST)
The role of plant growth-promoting rhizobacteria (PGPR) on enhancing tolerance of plants to abiotic stresses is well reported, but the effects of RGPRs on plants under salinity stress are not widely studied in the literature. Our study aimed to investigate the effect of Halomonas sp. and Azotobacter sp. on antioxidant activity, secondary metabolites, and biochemicals changes of purple basil under salinity stress conditions. The applied salt concentrations in this study were 50, 100, and 150 mM sodium chloride (NaCl). Salinity stress had a negative effect on plant growth parameters. Moreover, a reduction in some of the osmolytes and oxidative stress markers was observed. Inoculated plants ameliorated the oxidative damage by reducing the hydrogen peroxide (H2O2) contents and by increasing osmolytes (proline, total proteins, and soluble sugars), antioxidant enzymes activities (catalase, ascorbate peroxidase) and secondary metabolites (flavonoids). Overall, among treatments, plants inoculated with Azotobacter showed a better impact on physiological attributes to alleviate the adverse effects of 150 mM NaCl salinity stress on basil growth.
ARTICLE | doi:10.20944/preprints202106.0390.v1
Subject: Biology, Anatomy & Morphology Keywords: tomato; low night temperature; flower; fruit; chlorophyll content, electrolyte conductivity; proline; photosynthesis
Online: 15 June 2021 (09:22:19 CEST)
Low night temperature (LNT) can be a practical and economical target in tomato breeding programs in terms of energy saving in greenhouses. This study was conducted to investigate the physiological responses to LNT using four tomato accessions of cherry and large fruit types with LNT tolerance and sensitivity grown in two greenhouses with night temperature set-points of 10 and 15°C for heating. LNT significantly reduced plant height regardless of fruit types and LNT tolerance. The number of flowers were significantly reduced in 10°C in cherry but not in large fruit types. Fruit set in 10°C was significantly lower in LNT sensitive accessions than tolerant ones regardless of fruit types, which was due to abnormal flower morphology in 10°C. Proline accumulation patterns between 10 and 15°C significantly differed between fruit types as well as between LNT tolerant and sensitive accessions. Chlorophyll content in 10 °C was significantly higher at later growth stages in LNT tolerant accessions than sensitive ones in both fruit types. No clear difference in photosynthetic parameters was observed between fruit types or tolerance and sensitive accessions except for photosynthetic rate, which was significantly lower in tolerant than sensitive accessions during early growing period. These results suggest that different tomato fruit types may have different mechanisms for LNT tolerance.
ARTICLE | doi:10.20944/preprints202106.0389.v1
Subject: Biology, Anatomy & Morphology Keywords: Tomatoes; Night low temperature; Physiological traits; Fruit yield; Tomato breeding; 28 correlation coefficients
Online: 15 June 2021 (09:03:49 CEST)
Tomato is exposure to diverse abiotic stresses. Cold stress is one of harsh environmental 12 stresses. Abnormal low temperature affects tomato growth and development including physiolog- 13 ical disorders, flower drops, and abnormal fruit morphology, causing the decrease of tomato yield 14 and a fruit quality. It is important to identify low temperature-(LT) tolerant tomato (Solanum lyco- 15 persicum L.) cultivars. This study focused on analyzing physiological traits of thirty-five tomato ac- 16 cessions with three fruit types (cherry, medium, and large sizes) under night temperature set-points 17 of 15°C for normal temperature (NT) and 10°C for LT, respectively. Plant heights (PH) of most to- 18 mato accessions in LT were remarkably decreased compared to those in NT. The growth of leaf 19 length (LL) and leaf width (LW) was reduced depending on the genotypes under LT. The number 20 of fruits (NFR), fruit set (FS), fruit yield (FY), and marketable yield (MY) was negatively affected in 21 LT. The FS in LT was significantly correlated with FY in LT in total populations (n = 35), cherry fruit 22 sub-populations (n = 20), and medium fruit sub-populations (n = 11). Moreover, the relevance of 23 NFL in LT with FY in LT was related to total populations (n = 35), cherry fruit sub-populations (n = 24 20), but not medium fruit sub-populations (n = 11). The results indicate the physiological traits of 25 FS in LT and FY in LT are crucial factors for selecting and determining LT-tolerant cultivars for 26 breeding programs in tomato plants depending on different fruit types.
REVIEW | doi:10.20944/preprints202106.0386.v1
Subject: Biology, Anatomy & Morphology Keywords: polymorphism; hyphal morphogenesis; hyphal activation; signal transduction pathways; cell cycle regulation
Online: 15 June 2021 (08:54:43 CEST)
Candida albicans is a major fungal pathogen of humans, accounting for 15% of nosocomial infections with an estimated attributable mortality of 47%. C. albicans is usually a benign member of the human microbiome in healthy people. Under constant exposure to highly dynamic environmental cues in diverse host niches, C. albicans has successfully evolved to adapt to both commensal and pathogenic lifestyles. The ability of C. albicans to undergo a reversible morphological transition from yeast to filamentous forms is a well-established virulent trait. Over the past few decades, a significant amount of research has been carried out to understand the underlying regulatory mechanisms, signaling pathways, and transcription factors that govern the C. albicans yeast-to-hyphal transition. This review will summarize our current understanding of well-elucidated signal transduction pathways that activate C. albicans hyphal morphogenesis in response to various environmental cues and the cell cycle machinery involved in the subsequent regulation and maintenance of hyphal morphogenesis.
CONCEPT PAPER | doi:10.20944/preprints202106.0384.v1
Subject: Biology, Anatomy & Morphology Keywords: Salmonella enterica; food safety; genome; theory; single nucleotide polymorphisms; recombination; serotype
Online: 15 June 2021 (07:43:34 CEST)
Adenine and thymine homopolymer strings of at least 8 nucleotides (AT 8+mers) were charac-terized in Salmonella enterica subspecies I and other Eubacteria. Incidence of the motif differed between Eubacteria but not between Salmonella enterica serotypes. Of 481 AT 8+mers loci in serovars Typhimurium, Enteritidis, and Gallinarum, 35 (12.3%) had mutations. We propose that the AT 8+mer motif identifies genomes with optimal gene content and provides self-recognition that facilitates efficient genome repair. A theory that genome regeneration accounts for both serovar diversity and persistence of predominant Salmonella serovars associated provides a new framework for investigating root causes of foodborne illness.
Mon, 14 June 2021
REVIEW | doi:10.20944/preprints202106.0377.v1
Subject: Biology, Anatomy & Morphology Keywords: aa = amino acids, ACE-2 = receptor angiotensin-converting enzyme 2, cDNA = complementary DNA, mRNA = messenger RNA, orf = open reading frame, RBD = receptor binding protein
Online: 14 June 2021 (15:41:00 CEST)
The SARS (severe acute respiratory syndrome)-CoV (Coronavirus)-2 S(spike)-protein mRNA/cDNA currently being used as vaccines are antigenic but not antigens against SARS-CoV-2, that causes COVID (Coronavirus Disease) -19. Furthermore, the mRNA and cDNA antigenic vaccines also have potentials for homologous as well as heterologous recombination, primarily into the somatic cell DNA of the vaccine recipients. On the contrary, a SARS-CoV-2 RBD-protein antigen, a part of the S-protein, will directly stimulate antibody production against SARS-CoV-2. Hence, a vaccine composed of SARS-CoV-2 RBD-protein as a safer, fast acting, and effective vaccine against SARS-CoV-2 and thus against COVID-19. This is also useful for some immune compromised individuals.
ARTICLE | doi:10.20944/preprints202106.0374.v1
Subject: Biology, Anatomy & Morphology Keywords: Mesenchymal Stem Cells 1; Cell Migration 2; Xenogeneic Wound Repair 3.
Online: 14 June 2021 (15:06:48 CEST)
Bone marrow derived adult human mesenchymal stem cells (hMSCs) possess therapeutic qualities that enable them to enhance wound repair. However, the mechanisms by which this occurs remains poorly understood. Basic mechanisms may include the directed migration of delivered cells to target sites and/or the production and release of soluble factors that act at a distance. Allogeneic and even xenogeneic cells may effectively participate in wound repair. Labeled hMSCs were delivered to full-thickness skin wounds that were created in immunologically competent mice. The delivery occurred on day 3 post-wounding using two different carriers; one which released cells and one which retained cells. The fates of the delivered cells were tracked for up to 25 days. During this period, released cells migrated as a tight cohort deep into the wound to reach the subdermal vascular plexus. Simultaneously, enhanced formation of granulation tissue was evident. This migration of hMSCs was not essential in that enhanced granulation tissue formation and wound contraction occurred when cells were retained in the carrier matrix. This provided further evidence for the release of therapeutic factors by hMSCs to sites of injury.
REVIEW | doi:10.20944/preprints202106.0363.v1
Subject: Biology, Anatomy & Morphology Keywords: Traditional food crops; Climate change; Food security; Omics; Translational genomics; Gene editing
Online: 14 June 2021 (13:02:24 CEST)
The indigenous communities across the globe especially in the rural areas consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many of the traditional food plants are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. TFPs are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in times of pandemics and other situations like COVID-19. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realising the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of traditional food plants for their improvements, further cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in few TFPs. This suggests that there is ample scope of integrated use of modern omics and editing tools/techniques for improvement of TFPs and their use for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.
ARTICLE | doi:10.20944/preprints202106.0345.v1
Subject: Biology, Anatomy & Morphology Keywords: warming; freshening; salinity fluctuation; multiple stressors; stock holding
Online: 14 June 2021 (10:28:26 CEST)
We investigated the response of the Manila clam Venerupis philippinarum to possible temperature and salinity changes in a holding facility. First, clams were exposed to four temperatures for 15 days. Valve closure and survival of clams exposed to seawater at 18℃ were higher than that of those exposed to seawater at 24℃. Second, clams were exposed to six salinities for 15 days. Survival of clams exposed to two salinity fluctuation conditions (24–30 and 27–24 psu) was lower than that of clams exposed to constant 30 psu conditions. Valve closures of clams exposed to constant low salinity conditions (24 psu) and two salinity fluctuation conditions (24–30 and 27–24 psu) were higher than of those exposed to constant 30 psu conditions. Lastly, clams were exposed to two different temperatures and three different salinities conditions for 8 days. Valve closure and survival decreased significantly under the combination of 24℃ and 18 psu. These results suggest that an increase in temperature or a wider range of salinity fluctuations are detrimental to the survival of the Manila clam. The synergistic effect of temperature and salinity stressors may decrease the survival period of clams compared to the effect of a single stressor.
ARTICLE | doi:10.20944/preprints202106.0340.v1
Subject: Biology, Anatomy & Morphology Keywords: Axial canal; reef-building coral; high resolution micro-computed tomography; Acropora muricata; calcareous transportation
Online: 14 June 2021 (09:21:47 CEST)
In Acropora, the complex canals in a coral colony connect all polyps into a holistic network to collaborate in performing biological processes, while axial canal is the largest canal amongst the network and distributes at the center of a coral branch. However, previous studies indicated that, in the non-radial symmetry transport system of Acropora, axial canal do not play a major role in the transport of hydroplasm, and the action of axial canal in coral growth is still obscure. In this study, we reconstructed six Acropora muricata samples by high resolution micro-computed tomography to investigate the growth patterns of axial canals during the processes of new branch forming and truncated branch rebuilding. We found that the axial canal of a new branch is transformed from a calice and the polyps in the new branch are budded from the polyp in the axial canal. Meanwhile, the axial canal can transport the calcareous skeletons to rebuild the tip of a truncated branch, which represents as the change in the diameter of axial canal and calcareous deposition/reduction in it. This work indicate the regulation of axial canal in the growth processes including budding, branching, and mineralising of an Acropora colony.
Fri, 11 June 2021
ARTICLE | doi:10.20944/preprints202106.0317.v1
Subject: Biology, Anatomy & Morphology Keywords: Cannabis sativa; potency; ultraviolet; indoor; sole source; terpene
Online: 11 June 2021 (11:31:18 CEST)
It is commonly believed that exposing Cannabis sativa (cannabis) plants to ultraviolet (UV) radiation can enhance Δ9-tetrahydrocannabinol (Δ9-THC) concentrations in female inflorescences and associated foliar tissues. However, a lack of published scientific studies has left knowledge-gaps in the effects of UV on cannabis that must be elucidated before UV can be utilized as a horticultural management tool in commercial cannabis production. In this study we investigated the effects of UV exposure level on photosynthesis, growth, inflorescence yield, and secondary metabolite composition of two indoor-grown cannabis cultivars: ‘Low Tide’ (LT) and ‘Breaking Wave’ (BW). After growing vegetatively for 2 weeks under a canopy-level photosynthetic photon flux density (PPFD) of ≈225 μmol·m–2·s–1 in an 18-h light/6-h dark photoperiod, plants were grown for 9 weeks in a 12-h light/12-h dark “flowering” photoperiod under a canopy-level PPFD of ≈400 µmol·m–2·s–1 and 3.5 h·d–1 of supplemental UV radiation with UV photon flux densities (UV-PFD) ranging from 0.01 to 0.8 μmol·m–2·s–1 provided by light-emitting diodes (LEDs) with a peak wavelength of 287 nm (i.e., biologically-effective UV doses of 0.16 to 13 kJ·m–2·d–1). The severity of UV-induced morphology (e.g., whole-plant size and leaf size reductions, leaf malformations, and stigma browning) and physiology (e.g., reduced leaf photosynthetic rate and reduced Fv/Fm) symptoms worsened as UV exposure level increased. While the proportion of dry inflorescence yield that was derived from apical tissues decreased in both cultivars with increasing UV exposure level, total dry inflorescence yield only decreased in LT. The equivalent Δ9-THC and cannabidiol (CBD) concentrations also decreased in LT inflorescences with increasing UV exposure level. While the total terpene content in inflorescences decreased with increasing UV exposure level in both cultivars, the relative concentrations of individual terpenes varied by cultivar. The potential for using UV to enhance cannabis quality must still be confirmed before it can be used as a production tool for modern, indoor-grown cannabis cultivars.
CASE REPORT | doi:10.20944/preprints202106.0311.v1
Subject: Biology, Anatomy & Morphology Keywords: Honey bees; Apis mellifera; acaricides; pesticides; Toxic Unit; Varroa destructor; Nosema ceranae; bee viruses; tau-fluvalinate; coumaphos
Online: 11 June 2021 (09:55:42 CEST)
In this Case Report we analyze the possible causes of the poor health status of a professional Apis mellifera iberiensis apiary located in Gajanejos (Guadalajara, Spain). Several factors that potentially favor colony collapse were identified, including Nosema ceranae infection, alone or in combination with other factors (eg, BQCV and DWV infection), and the accumulation of acaricides commonly used to control Varroa destructor in the beebread (coumaphos and tau-fluvalinate). Based on the levels of residues, the average toxic unit estimated for the apiary, suggests a possible increase in vulnerability to infection by N. ceranae due to the presence of high levels of acaricides. These data highlight the importance of evaluating these factors in future monitoring programs, as well as the need to adopt adequate preventive measures as part of national and international welfare programs aimed at guaranteeing the health and fitness of bees.
Thu, 10 June 2021
ARTICLE | doi:10.20944/preprints202106.0279.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Blood-Brain Barrier, Penetrating Peptides, Machine learning techniques, Drug delivery, Therapeutic peptides
Online: 10 June 2021 (08:13:15 CEST)
Blood-brain-barrier is a major obstacle in treating brain-related disorders as it does not allow to deliver drugs in the brain. In order to facilitate delivery of drugs in brain, we developed a method for predicting blood-brain-barrier penetrating peptides. These blood-brain barriers penetrating peptides (B3PPs) can act as therapeutic as well as drug delivery agents. We trained, tested, and evaluated our models on blood-brain-barrier peptides obtained from the B3Pdb database. First, we compute a wide range of peptide features then we select relevant peptide features. Finally, we developed numerous machine learning-based models for predicting blood-brain-barrier peptides using selected features. Our model based on random forest performed best on the top 80 selected features and achieved a maximum 85.08% accuracy with 0.93 AUROC. We also developed a web server, B3pred that implements our best models. It has three major modules that allow users to; i) predict B3PPs, ii) scanning B3PPs in a protein sequence, and iii) designing B3PPs using analogs. Our web server and standalone software is freely available at https://webs.iiitd.edu.in/raghava/b3pred/.
Wed, 9 June 2021
ARTICLE | doi:10.20944/preprints202106.0257.v1
Subject: Biology, Other Keywords: Extracellular vesicles (EVs); mRNA; fungal pathogen; plant pathogen; Ustilago maydis
Online: 9 June 2021 (10:59:36 CEST)
Extracellular vesicles (EVs) can transfer diverse RNA cargo for intercellular signalling. EV-associated RNAs have been found in diverse fungi and were proposed to be relevant for pathogenesis in animal hosts. In plant-pathogen interactions, small RNAs are exchanged in a cross-kingdom RNAi warfare and EVs were considered to be a delivery mechanism. To extend the search for EV-associated molecules involved in plants-pathogen communication, we have characterised the repertoire of EV-associated mRNAs secreted by the maize smut pathogen, Ustilago maydis. For this initial survey, EVs were isolated from axenic filamentous cultures that mimic infectious hyphae. The EV-associated RNAs were resistant to degradation by RNases and the presence of intact mRNAs was evident. The set of mRNAs enriched inside EVs relative to the fungal cells are functionally distinct from those that are depleted from EVs, particularly overrepresented in metabolic enzyme activities. Intriguingly, mRNAs of some known effectors and other proteins linked to virulence were found in EVs. Furthermore, several mRNAs enriched in EVs are also upregulated during infection, suggesting that EV-associated mRNAs may participate in plant-pathogen interaction.
ARTICLE | doi:10.20944/preprints202106.0256.v1
Online: 9 June 2021 (10:58:20 CEST)
Abstract: Oxidative metabolism is crucial for leukemic stem cell (LSC) function and drug resistance in acute myeloid leukemia (AML). Mitochondrial metabolism also affects the immune system and therefore the antitumor response. Modulation of oxidative phosphorylation (OxPHOS) has emerged as a promising approach to improve therapy outcome for AML patients. However, the effect of mitochondrial inhibitors on the immune compartment in the context of AML is yet to be explored. Immune checkpoints such as the ecto-nucleotidase CD39 and programmed dead ligand 1 (PD-L1) have been reported to be expressed in AML and linked to chemoresistance and poor prognosis. In the present study, we first demonstrated that a novel selective electron transfer chain complex (ETC) I inhibitor, EVT-701, decreased OxPHOS metabolism of murine and human cytarabine (AraC)-resistant leukemic cell lines. Furthermore, we showed that, while AraC induced immune response regulation by increasing CD39 expression and by reinforcing interferon-γ/PD-L1 axis, EVT-701 reduced CD39 and PD-L1 expression in vitro in a panel of both murine and human AML cell lines, especially upon AraC treatment. Altogether, this work uncovers a non-canonical function of ETCI in controlling CD39 and PD-L1 immune checkpoints, thereby improving the anti-tumor response in AML.
Tue, 8 June 2021
COMMUNICATION | doi:10.20944/preprints202106.0238.v1
Subject: Biology, Anatomy & Morphology Keywords: Immunoinformatics; Molecular dynamics simulation; mutation; SARS-CoV-2; Spike protein; Virus structure
Online: 8 June 2021 (13:57:03 CEST)
It has been more than a year since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was found. This coronavirus has infected more than 110 million people worldwide by the end of February, 2021, and several virulent as well as more spreadable mutant forms of SARS-CoV-2 have emerged subsequently. In the latter group, three variants B.1.1.7, B.1.351, and P1 lineages, have been reported. Using computer simulation, the present paper investigates the structural differences between the wild type SARS-CoV-2 spike protein and its Asn501Tyr (N501Y) mutant variant. Time-based structural changes between the receptor binding domains of these two species are also examined. The N501Y mutation is common to all the three aforesaid mutant variants.
Subject: Biology, Anatomy & Morphology Keywords: Quercus; oak, canopy; fogging; new species; inventory; Norway
Online: 8 June 2021 (13:16:34 CEST)
(1) We document the invertebrate fauna collected from 24 oak canopies in east and west Norway as a contribution to the Norwegian Biodiversity Information Centre’s “The Norwegian Taxonomy Initiative”. (2) A snap-shot inventory of the canopies was recorded by means of emitting a mist of synthetic pyrethroid into the canopies at night using a petrol-driven fogger, collecting the specimens in butterfly nets spread on the ground under the canopy. (3) Almost the entire catch of more than 6800 specimens was identified to 722 species. Out of 92 species new to the Norwegian fauna, 21 were new to science and additionally 15 were new to the Nordic fauna. Diptera alone constituted nearly half of the species represented with 61 new records (18 new species). Additionally, 24 Hymenoptera (one new species), six oribatid mites (two new species) and one Thysanoptera were new to the Norwegian fauna. (4) Our study emphasis the importance of oak tree as habitat both for a specific fauna and occasional visitors and it demonstrates that the canopy fogging technique is an efficient way to find the ‘hidden fauna’ of Norwegian forests. The low number of red listed species found reflects how poor the Norwegian insect fauna is still studied. Moreover, the implication of the IUCN red list criteria for new described or newly observed species is discussed.
ARTICLE | doi:10.20944/preprints202106.0229.v1
Subject: Biology, Other Keywords: The Gulf of Mottama Wetland, Morphometric measurement, catch weight, size group
Online: 8 June 2021 (13:15:52 CEST)
The present study was conducted the status of sea bass from Kokko and Kyuntone of The Gulf of Motttama Wetland (GoMW) area in Thanatpin Township in Bago Region Myanmar from September 2019 to August 2020. Fifty specimens were monthly collected, measured and weighed. Invoices of sea bass were collected for the depot and fish sellers by monthly. In Kokko, mean value of standard length and body weight were highest in March (32.70±1.58, 660.7±112.23). The mean value of standard length was peak in January (31.39±7.16) but peak of body weight was in March (963.24±280.86) in Kyuntone villages. The lowest mean value of standard length and body weight were found in June at both study areas. According to the invoice data revealed that monthly catch weight of sea bass is most abundance in October (829.92) kg in Kokko, (339.12) kg in Kyuntone. Based on price of relations to size group, small size C < 300g (41%) was mostly abundance in Kokko and in Kyuntone small size C < 300g (35%) was second abundance. Specimens were not landed in April and May. In June, young specimens were very rarely seen in both study sites. The important roles of wetland fishes, the economic valuation of GOMW in Myanmar and samples of fishing gear and value chain of sea bass in Myanmar was expressed in this study.
ARTICLE | doi:10.20944/preprints202106.0214.v1
Subject: Biology, Anatomy & Morphology Keywords: formae speciales; horizontal gene transfer; endophytic; pathogenic; Fusarium; RNAseq; comparative genomics; vanilla
Online: 8 June 2021 (11:37:26 CEST)
Members of the Fusarium oxysporum species complex (FOSC) has the capacity to specialize into host-specific pathogens known as formae speciales through horizontal gene transfer between pathogenic and endophytic individuals. To this day, the origin of these formae speciales and the genetic determinants dictating the switch from endophytic to pathogenic Fusarium oxysporum (Fox) are still unknown. F. oxysporum f. sp. vanillae (Fov), member of FOSC, is the causal agent of root and stem rot disease, representing the main phytosanitary problem in vanilla plantations worldwide. Here we analyzed the RNA-seq libraries resulting from the interaction vanilla-Fov at early and late stages of the infection, and what we initially identified as control in a previous study, detecting the presence of Fox endophytes. We identified virulence, hypervirulence, sporulation, conidiation, necrosis, and production of fusaric acid as key processes taking place during Fov-vanilla interaction. Through comparison with endophytic Fox, we found that Fov can infect vanilla thanks to the presence of pathogenicity islands and genomic regions associated with supernumerary chromosomes. These play a central role as carriers of genes involved with pathogenic activity and could have being obtained by Fov through horizontal gene transfer. We also found that, unlike other pathogenic members of FOSC, Fov do not use Secreted in Xylem proteins (SIX) to infect vanilla.
ARTICLE | doi:10.20944/preprints202106.0198.v1
Subject: Biology, Anatomy & Morphology Keywords: Postharvest storage; fruit firmness; total soluble solids; apple cultivars; apple packaging; apple maturity
Online: 8 June 2021 (09:15:30 CEST)
This research was conducted to understand changes of physicochemical properties of fruits of three apple cultivars as influenced by stage of maturity and packaging types over storage period of three weeks. The research was designed to replicate practices by the producers and along the value chains and to assess the fruit quality under the conditions of the major markets in the region. All the measured physicochemical parameters significantly varied with the cultivars, maturity stage at harvest and packaging types. Higher firmness was recorded for the samples harvested about two weeks before the optimal maturity, usually practiced by significant number of producers to gain market advantage. Lower total soluble solids corresponded to the early harvested samples regardless of cultivars and packaging types. The firmness was observed decreasing over the storage periods whereas the total soluble solids increased, which is associated to improving sensorial quality for the early harvested cultivars as the soluble solids are mainly sugars. The early harvesting resulted in fruits of inferior desirability including extreme hardness, firmness and low total soluble solids that may have high sourness and less sweet taste. Awareness creation for the producers on the quality and advantages of harvesting their produces at optimal maturity and practicing good postharvest management is required.
Mon, 7 June 2021
Subject: Biology, Animal Sciences & Zoology Keywords: convolutional neural networks; horse emotion recognition; horse emotion
Online: 7 June 2021 (12:42:05 CEST)
Creating intelligent systems capable of recognizing emotions is a difficult task, especially when looking at emotions in animals. This paper describes the process of designing a “proof of concept” system to recognize emotions in horses. This system is formed by two elements, a detector and a model. The detector is a fast region-based convolutional neural network that detects horses in an image. The model is a convolutional neural network that predicts the emotions of those horses. These two elements were trained with multiple images of horses until they achieved high accuracy in their tasks. 400 images of horses were collected and labeled to train both the detector and the model while 80 were used to validate the system. Once the two components were validated, they were combined into a testable system that would detect equine emotions based on established behavioral ethograms indicating emotional affect through head, neck, ear, muzzle and eye position. The system showed an accuracy of between 69% and 74% on the validation set, demonstrating that it is possible to predict emotions in animals using autonomous intelligent systems. Such a system has multiple applications including further studies in the growing field of animal emotions as well as in the veterinary field to determine the physical welfare of horses or other livestock.
REVIEW | doi:10.20944/preprints202106.0163.v1
Subject: Biology, Other Keywords: white biotechnology; metabolic engineering; non-conventional yeast; oleaginous yeast; cell factory; heterologous expression; biodiversity; Yarrowia lipolytica; Yarrowia clade; GMO
Online: 7 June 2021 (10:50:26 CEST)
Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.
ARTICLE | doi:10.20944/preprints202106.0160.v1
Subject: Biology, Anatomy & Morphology Keywords: Silverleaf disease; Chondrostereum purpureum; Prunus salicina; Japanese plum
Online: 7 June 2021 (09:30:58 CEST)
Silverleaf is an important trunk disease of fruit crops, like Japanese plum. It is known that Chondrostereum purpureum produces wood discoloration, leaves silvering and tree decline, however, the information about the effects on fruit production is scarce. Therefore, the objectives of this study were to determine C. purpureum pathogenicity on Prunus salicina and effects on physiology, fruit yield and quality, in Chile, in 2019 and 2020. Wood samples from affected plum trees were collected in the Chilean plum productive area. Fungi were isolated plating wood sections from the necrosis margin on culture media. Isolates colonies morphological and molecular characteristics accorded to C. purpureum (98%). Representative isolates were inoculated on healthy plum plants and after 65-d incubation, wood necrotic lesions and silver leaves were visible. Fungi were reisolated, fulfilling Koch’s postulates. To determine Silverleaf effects, water potential, and fruit yield and quality were measured in healthy and Silverleaf diseased plum plants cv. ‘Angeleno’. Water potential was altered on diseased trees, and their yield was reduced in 51% (2019) and 41% (2020), compared to fruit from healthy plants. Moreover, cover-colour, equatorial-diameter and weight were reduced, and fruit were softer, failing to meet the criteria to be properly commercialized and exported to demanding markets.
ARTICLE | doi:10.20944/preprints202106.0159.v1
Subject: Biology, Anatomy & Morphology Keywords: run off; deep leakage; Soil water; plant growth; Soil Water Resource Use Limit by plants; Soil Water Carrying Capacity for Vegetation; key period of plant water relationship regulation; sustainable use of soil water resources
Online: 7 June 2021 (09:29:51 CEST)
There is a balanced plant-water relationship in the primary vegetation of desert area. With the increase of population and social development in desert areas, people’s need for forest vegetation ecosystem’s goods and service have been changed. To meet the growing demand for plant community goods and services, more original vegetation has been changed into non-native vegetation such as in China loess plateau. However, with the plant growth, sometime soil drying happens and then becomes gradually serious with times in most of desert regions. Serious drying of soil eventually result in soil degradation, vegetation decline and agriculture failure，which influence the produce and supply of forest vegetation goods and service in market in dry year or waste of soil water resources in wet year, which wastes precious nature resources. In order to solve these problems, the soil water resources have to be used in sustainable way and plant-water relationship have to be regulated on Carrying Capacity of Soil Water for Vegetation in the key period of plant water relationship regulation, to carry out sustainable use of nature resources, high-quality and sustainable development of forest and grass or high-quality produce of fruit and crop in desert re-gions.
ARTICLE | doi:10.20944/preprints202106.0147.v1
Subject: Biology, Anatomy & Morphology Keywords: Abscisic acid; Brassica juncea; Nitrogen; Salinity; Oxidative stress; Photosynthetic functions
Online: 7 June 2021 (07:47:12 CEST)
The present study assessed the effect of abscisic acid (ABA; 25 µM) and/or nitrogen (N; 10 mM) in minimization of salinity (NaCl; 100mM)-impact on growth, photosynthetic efficiency, Rubisco activity, nitrogen and sulfur assimilation, oxidative stress (H2O2), lipid peroxidation measured as thiobarbituric acid reactive substances, (TBARS), osmolyte (Proline) content, and the activity of antioxidant enzymes (superoxide dismutase, SOD glutathione reductase, GR; ascorbate peroxidase, APX) in cultivar RH0-749 of Brassica juncea L. NaCl stress caused significant elevations in H2O2 and TBARS, and differentially modulated proline content, the activity of antioxidant enzymes, and impaired growth and photosynthetic functions. Exogenously applied 25 µM ABA negatively affected plant growth and photosynthesis in B. juncea without NaCl. In contrast, exogenously applied 25 µM ABA and 10 mM N, alone or in combination minimized oxidative stress, and maintained a fine-tuning between proline content and the activity of antioxidant enzymes, and thereby improved plant growth and photosynthetic functions in NaCl exposed B. juncea.
Fri, 4 June 2021
COMMUNICATION | doi:10.20944/preprints202106.0139.v1
Subject: Biology, Anatomy & Morphology Keywords: Vegetation indices; precision agriculture; RGB images
Online: 4 June 2021 (11:25:04 CEST)
Here, we report the prediction of vegetative stages variables of canary bean crop by means of RGB and multispectral images obtained from UAV during the ripening stage, correlating the vegetation indices with biometric variables measured manually in the field. Results indicated a highly significant correlation of plant height with eight RGB image vegetation indices for the canary bean crop, which were used for predictive models, obtaining a maximum correlation of R2 = 0.79. On the other hand, the estimated indices of multispectral images did not show significant correlations.
SHORT NOTE | doi:10.20944/preprints202106.0121.v1
Subject: Biology, Anatomy & Morphology Keywords: SARS-CoV-2 origin; Furin Cleavage Site; Arginine Codon Usage; Bioinformatics
Online: 4 June 2021 (08:00:03 CEST)
The furin cleavage site, with an arginine doublet (RR), is one of the clues of the SARS-CoV-2 origin. This furin-RR is encoded by the CGG-CGG sequence. Because arginine can be encoded by six codons, in a previous work we found that in SARS-CoV-2, CGG was the minority arginine codon (3%). Also, analyzing the RR doublet from a large sample of furin cleavage sites of several kinds of viruses, we found that none of them were encoded by CGG-CGG. Here, we come back to the core of the matter, but from the perspective that in the human genome, in contrast, CGG is the majoroty arginine codon (21%). Here, we highlighted that the 6 arginine codons provide genetic markers to a traceability on the RR origin in the furin site, as well as, to weigh the probability of the theories about the origin of the virus.
Thu, 3 June 2021
REVIEW | doi:10.20944/preprints202106.0085.v2
Online: 3 June 2021 (13:36:26 CEST)
Kenyan coffee is ranked among the best in the world and 99% is exported mainly to Germany, Sweden and Belgium, the USA and Saudi Arabia. Kenya produces quality Arabica beans which are generally recognized and upgraded with other relatively lower brands. In 1937, the Kenya Planters Cooperative Union (KPCU) was formed to represent small farmers' interests. In 1944, in the Coffee Board of Kenya (CBA) the law required smallholders to join local growing cooperatives run by government to reduce the power of large estates to control the board. Many reforms in the coffee industry have been initiated. This review explores evolution and existing coffee varieties in Kenya, the coffee value chain and the regions that grow coffee in Kenya. Additionally, the variety agronomics and appearance that encompass; quality potential at different altitudes, yield potential and nematodes susceptibility.
Subject: Biology, Forestry Keywords: Pinus tabulaeformis; Space instead of time; stand area; compatibility; combination prediction method
Online: 3 June 2021 (11:26:41 CEST)
The study of the area model of Pinus tabulaeformis forest provides an important reference for improving the management of Pinus tabulaeformis and revealing the growth law of Pinus tabulaeformis. According to the classification method proposed by Munro, stand growth and harvest prediction models are divided into three categories: full stand model, single wood model and diameter distribution model. Based on the fixed sample data of Shangluo Pinus tabulaeformis, the spatial instead of time method is used to process the data, and the weight coefficient of each model in the combined prediction model is calculated by using the optimal weighting method. The single wood model, the whole forest model and the diameter distribution model are combined by the combined prediction method to integrate the fault area prediction of Pinus tabulaeformis forest. The results show that the combined prediction method is more accurate than the single model (single wood model, whole forest model and diameter distribution model). At the same time, the method can improve the compatibility of the forest break area prediction model, ensure the consistency of the forest break area prediction, and provide a new direction for the research of forest resource monitoring and investigation.
Subject: Biology, Anatomy & Morphology Keywords: glioblastoma; MGMT; lomeguatrib; radiosensitivity; radiotherapy
Online: 3 June 2021 (10:44:21 CEST)
Background: Treatment resistance of glioblastoma multiforme to chemo- and radiotherapy remains a challenge yet to overcome. Especially MGMT promoter unmethylated patients have only little benefit from chemotherapy treatment using temozolomide since MGMT counteracts its therapeutic efficacy. Therefore, new treatment options in radiotherapy need to be developed to inhibit MGMT and increase radiotherapy response. Methods: Lomeguatrib, a highly specific MGMT inhibitor was used to inhibit MGMT protein expression in vitro. Radiosensitivity of established human glioblastoma multiforme cell lines in combination with lomeguatrib was investigated using the clonogenic survival assay. Inhibition of MGMT was analyzed using Western Blot. Cell cycle distribution and apoptosis were investigated to determine the effects of lomeguatrib alone as well as in combination with ionizing radiation. Results: Lomeguatrib significantly decreased MGMT protein expression and reduced radiation-induced G2/M arrest. A radiosensitizing effect of lomeguatrib was observed when administered at 1 µM and increased radioresistance at 20 µM. Conclusion: Low concentrations of lomeguatrib elicit radiosensitization, while high concentrations mediate a radioprotective effect.
ARTICLE | doi:10.20944/preprints202106.0095.v1
Subject: Biology, Anatomy & Morphology Keywords: antioxidants; Brassica juncea; ethylene; nitrogen assimilation; proline metabolism; sulfur assimilation
Online: 3 June 2021 (09:55:26 CEST)
In the present study, the potential of ethylene as ethephon (an ethylene source) was investigated individually or with a combination of the split dosage of nitrogen (N) and sulfur (S) soil treatments for the removal of damaging effects of salt stress (100 mM NaCl) in mustard (Brassica juncea L.). Plants were grown with 50 mg N plus 50 mg S kg−1 soil at sowing time and an equivalent dosage at 20 days after sowing ([N50 + S50]0d + [N50 + S50]20d). Ethephon at 200 μL L‒1 was applied to combined split dosage of N and S with or without NaCl. Plants subjected to NaCl showed a deceased in growth and photosynthetic characteristics as well as N and S assimilation, though, proline metabolism and antioxidants increased. The application of ethephon to plants grown with split N and S dosages significantly enhanced the photosynthetic efficiency by increasing the assimilation of N and S, improving the content of proline and induction of the antioxidant system with or without NaCl. The regulation of ethylene and/or split form N and S application may be the potential tools for overcoming salt stress effects in this species and in related Brassicaceae.
Wed, 2 June 2021
REVIEW | doi:10.20944/preprints202106.0085.v1
Online: 2 June 2021 (15:03:43 CEST)
Kenyan coffee is ranked among the best in the world and 99% is exported mainly to Germany, Sweden and Belgium, the USA and Saudi Arabia. Kenya produces quality Arabica beans which are generally recognized and upgraded with other relatively lower brands. In 1937, the Kenya Planters Cooperative Union (KPCU) was formed to represent small farmers' interests. In 1944, in the Coffee Board of Kenya (CBA) the law required smallholders to join local growing cooperatives run by government to reduce the power of large estates to control the board. Many reforms in the coffee industry have been initiated. This review explores evolution and existing coffee varieties in Kenya, the coffee value chain and the regions that grow coffee in Kenya.
ARTICLE | doi:10.20944/preprints202106.0084.v1
Subject: Biology, Anatomy & Morphology Keywords: Vitis spp.; interspecific hybrid grapes; cultivar evaluation; Integrated Pest Management; disease resistance.
Online: 2 June 2021 (15:01:26 CEST)
Susceptibility to economically-important diseases of grapes is critical to the evaluation of germplasm recommended for commercial production and for development of sustainable production systems. In 2018-2019, nine cold-hardy grape cultivars including ‘Brianna’, ‘Crimson Pearl’, ‘Itasca’, ‘Louise Swenson’, ‘Marechal Foch’, ‘Marquette’ ‘Petite Pearl’, ‘St. Pepin’, and ‘Verona’ were evaluated on non-treated vines for susceptibility to downy mildew, powdery mildew, black rot, anthracnose, Phomopsis leaf spot and fruit rot, and Botrytis bunch rot. No cultivars were consistently disease-free, and all exhibited some degree of black rot and powdery mildew infection. Relative susceptibility to disease was not consistent across both years, but ‘Brianna’ had greater incidence of black rot and ‘Louise Swenson’ showed lower incidence of powdery mildew in both years. The relatively new cultivars ‘Crimson Pearl’ and ‘Verona’ exhibited comparatively moderate disease susceptibility overall. Growers typically manage diseases with fungicides on commercial farms, so cultivar susceptibility is just one component of a sustainable pest management and production system.
ARTICLE | doi:10.20944/preprints202106.0079.v1
Subject: Biology, Anatomy & Morphology Keywords: Environmental heterogeneity; Habitat; Anthropization; Chiropterans
Online: 2 June 2021 (12:47:01 CEST)
Bats play important ecosystem roles. Anthropogenic activities cause the decrease and loss of biological diversity and, consequently, the loss of these ecosystem services. One way of measuring local habitat conditions and relating the landscape to biodiversity. Our objective is to investigate how the bat community is influenced by this change in the landscape. Collections were carried out at five points and 76 individuals of 12 species are sampled. Although the points present a high variation in relation to land use, we did not observe any correlation between species richness and guilds with land use. However, the difference in the composition of the guilds is related to the variation in land use, in which 74% of the variation in the abundance of guilds is related to the different patterns of land use. At SENAI, even though it was the place with the greatest anthropic impact, it was the one with the greatest abundance of species, while the points Module two and Sítio Jaburu had the greatest abundance of guilds. This result corroborates the idea that ecosystem services are dependent on habitat maintenance, since the greater the heterogeneity the greater the difference in the composition of the trophic guilds.
REVIEW | doi:10.20944/preprints202106.0060.v1
Subject: Biology, Anatomy & Morphology Keywords: SARS-CoV-2; COVID-19; variants; vaccines; immune dysregulated; comorbidities; antibody; Spike protein; biomolecules; coronavirus
Online: 2 June 2021 (09:56:14 CEST)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of the coronavirus disease 2019 (COVID-19) pandemic which has been a topic of major concern to global human health. The challenge to restrain the COVID-19 pandemic is further compounded by the emergence of several SARS-CoV-2 variants viz. B.1.1.7, B.1.351, P1 and, B.1.617., which show in-creased transmissibility and resistance towards vaccines and therapies. Importantly, the likelihood of susceptibility to SARS-CoV-2 infection among individuals with dysregulated immune response or comorbidities needs greater attention. Herein, we provide a comprehensive perspective regarding ongoing vaccine (mRNA, protein-based, viral vector based etc.) and therapeutic (mono-clonal antibodies, small molecules, plasma therapy, etc.) modalities designed to curb the COVID-19 pandemic. We also discuss in detail the challenges posed by different SARS-CoV-2 variants of concern (VOC) identified across the globe and their effects on therapeutic and prophylactic interventions.
ARTICLE | doi:10.20944/preprints202106.0049.v1
Subject: Biology, Anatomy & Morphology Keywords: Agroecology; territorial agroecologycal food systems.
Online: 2 June 2021 (07:20:43 CEST)
The health emergency caused by Covid 19 highlighted the food dependency of many cities in the world and Cali and the cities of Valle del Cauca were no exception as they depended on food flows from other regions and countries, so these Entities are part of the corporate food system, to which their rulers delegated food security for their inhabitants. In the same territory and for the last nine years, a second-level organization has been consolidating that brings together 14 peasant agroecological markets and that despite strict confinement measures was able to continue supplying food to consumers in the municipalities of influence that have supported this initiative. The foregoing leads to think that said organization can become a platform for an agroecological food system of regional scope, for which the characteristics that said system should have according to a model based on the principles of agroecology were evaluated.
ARTICLE | doi:10.20944/preprints202106.0047.v1
Online: 2 June 2021 (07:19:08 CEST)
A field experiment was conducted during Kharif 2018, laid out in Randomized Block Design with three replications having seven treatments viz. N omission (T1), N applied as basal and AT (T2), N as basal, AT and PI (T3), N as basal and top dressing at NDVI threshold of 0.75 (T4), at NDVI threshold of 0.8 (T5), at SPAD threshold of 35.0 (T6) and SPAD threshold of 37.5 (T7) with Rice variety Sahabhagidhan.The study revealed that application of 30 kg N/ha as basal dose and top dressing of 20 kg N/ha twice at 35 and 63 DAS guided by NDVI threshold value of 0.8 (T5) was found to be superior over other treatments with respect to productivity. T5 recorded highest grain yield of 4438 kg/ha which was 17.0% higher than that top dressed at NDVI threshold of 0.75 (T4) and 7.1% higher than that top dressed at SPAD threshold value of 37.5 (T7). In case of SPAD meter, nitrogen top dressed at threshold value of 37.5 (T7) produced grain yield of 4143 kg/ha which was 15.0% higher than T6. T5 produced maximum dry matter of 8678 kg/ha with highest grain yield (4438 kg/ha), straw yield (5092 kg/ha) and harvest index 46.0%.
Mon, 31 May 2021
REVIEW | doi:10.20944/preprints202105.0779.v1
Subject: Biology, Anatomy & Morphology Keywords: Lineage Plasticity; Tumor Progression; Metastasis; Therapy Resistance; Epithelial-Mesenchymal Plasticity
Online: 31 May 2021 (13:48:08 CEST)
Lineage plasticity, the switching of cells from one lineage to another has been recognized to be a cardinal property essential for embryonic development, tissue repair and homeostasis. However, such a highly regulated process goes awry when cancer cells exploit this inherent ability to their advantage, resulting in tumorigenesis, relapse, metastasis and therapy resistance. In this review, we summarize our current understanding on the role of lineage plasticity in tumor progression and therapeutic resistance in multiple cancers. Lineage plasticity can be triggered by treatment itself and is reported across various solid as well as liquid tumors. Here we focus on the importance of lineage switching in tumor progression and therapeutic resistance of solid tumors such as the prostate, lung, hepatocellular and colorectal carcinoma and the myeloid and lymphoid lineage switch observed in leukemias. Besides this, we also discuss the role of Epithelial-Mesenchymal Transition (EMT) in facilitating the lineage switch in biphasic cancers such as aggressive carcinosarcomas. We also discuss the mechanisms involved, current therapeutic approaches and challenges that lie ahead in taming the scourge of lineage plasticity in cancer.
CONCEPT PAPER | doi:10.20944/preprints202105.0767.v1
Subject: Biology, Animal Sciences & Zoology Keywords: evidential integration; causal explanation; early animal evolution; phylogenetics; macroevolution; evolutionary scenario; cross-disciplinary research
Online: 31 May 2021 (12:25:44 CEST)
Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have collectively transformed our understanding of the evolutionary history of animals. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and traditional phylogenies. Here, I argue that tackling this multifaceted problem lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent developments in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence and theory. I then argue that integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond.
ARTICLE | doi:10.20944/preprints202105.0746.v1
Subject: Biology, Anatomy & Morphology Keywords: ABC transporter; ABCB1; P-glycoprotein; taxol; drug recognition
Online: 31 May 2021 (11:27:14 CEST)
The multidrug efflux transporter ABCB1 is clinically important for drug absorption and distribution and can be a determinant of chemotherapy failure. Recent structure data shows that three glutamines donate hydrogen bonds to co-ordinate taxol in the drug binding pocket. This is consistent with earlier drug structure-activity relationships that implicated the importance of hydrogen bonds in drug recognition by ABCB1. By replacing the glutamines with alanines we have tested whether any or all of Q347, Q725 and Q990 are important for the transport of three different drug classes. Flow cytometric transport assays show that Q347A and Q990A act synergistically to reduce transport of Calcein-AM, BODIPY-verapamil and OREGON GREEN-taxol bisacetate but the magnitude of the effect was dependent on the test drug and no combination of mutations completely abrogated function. Surprisingly, Q725A mutants generally improved transport of Calcein-AM and BODIPY-verapamil, suggesting that engagement of the wild-type Q725 in a hydrogen bond is inhibitory for the transport mechanism. To test transport of unmodified taxol, stable expression of Q347/725A and the triple mutant was engineered and shown to confer equivalent resistance to the drug as the wild-type transporter, further indicating that none of these potential hydrogen bonds between transporter and transport substrate are critical for function of ABCB1. The implications of the data for plasticity of the drug binding pocket are discussed.
ARTICLE | doi:10.20944/preprints202105.0733.v1
Subject: Biology, Anatomy & Morphology Keywords: conditioning; high-intensity functional training; methods; performance; physical fitness
Online: 31 May 2021 (10:36:00 CEST)
The purpose of the present study was to compare heart rate (HR), blood lactate and training load between different CrossFit® workouts, with equalized total volume in men and women. The study included 23 individuals (13 men and 10 women) experienced in CrossFit® training, who performed two workouts with different training types (as many reps as possible - AMRAP and for time) but equalized volume. Measurements of lactate, HR and rating of perceived exertion (RPE) were performed. The results showed that there was no HR interaction between workout time and sex (p = 0.822; η2 = 0.006] and between workout type and sex (p = 0.064, η2 = 0.803). HR significantly differed during each workout type (p <0.001, η2 = 0.621), but not between the two workout types (p = 0.552, η2 = 0.017). Lactate showed no difference between the workout types (p = 0.474, η2 = 0.768), although the training load was higher (p = 0.033, η2 = 0.199) in women when they performed AMRAP. Altogether, HR was not significantly different between training types or sex, while RPE, lactate and training load showed small differences depending on the group (women or men) or workout type (AMRAP or 'for time').
Fri, 28 May 2021
ARTICLE | doi:10.20944/preprints202105.0697.v1
Subject: Biology, Anatomy & Morphology Keywords: nitrate-alkaline pulp; Black Mustard; Camelina; tensile index; chemical analysis
Online: 28 May 2021 (11:32:38 CEST)
To investigate this suitability of Black Mustard (Brassica Nigra L.) and Camelina (Camelina Sativa L.) for pulp manufacturing the nitrate-alkaline method was used. The non-wood plants were characterized by chemical analysis, especially lignin, cellulose, ash, extractives and alpha-, beta-, gamma-cellulose. The pulp was cooked in 6% nitric acid and then underwent the extraction by 5% sodium-hydroxide and neutralized by 1% acetic acid. The cooked pulp was characterized by delignification degree – Kappa number. The laboratory sheets were made from this cooked pulp and they were characterized by tensile index, breaking length, smoothness and compared with commonly available papers.
ARTICLE | doi:10.20944/preprints202104.0382.v2
Subject: Biology, Anatomy & Morphology Keywords: Real-time PCR; peanut; food allergen; chloroplast marker; DNA isolation
Online: 28 May 2021 (11:05:58 CEST)
Peanut (Arachis hypogaea) contains allergenic proteins, which make it harmful to the sensitised population. The presence of peanut in foods must be indicated on label, to prevent accidental consumption by allergic population.. In this work, we use chloroplast markers for specifically detection of peanut by real-time PCR, in order to increase the assay sensitivity. Three different protocols of DNA isolation were evaluated, for total and organelle-DNA extraction. Binary mixtures of raw and processed peanut flour in wheat were performed at concentrations ranging from 100000 to 0.1 mg/kg. DNA isolation from peanut, mixtures and other legumes was carried out following three protocols for obtaining genomic and chloroplast-enrich DNA. Quantity and quality of DNA was evaluated, obtaining better results for protocol 2. Specificity and sensitivity of the method has been assayed with specific primers for three chloroplast markers (mat k, rpl16 and trnH-psbA) and Ara h 6 peanut allergen-coding region was selected as nuclear low-copy target and TaqMan probes. Efficiency and linear correlation of calibration curves were within the adequate ranges. Moreover, the influence of pressure and thermal processing on the peanut detectability was analyzed.
Thu, 27 May 2021
ARTICLE | doi:10.20944/preprints202105.0680.v1
Subject: Biology, Anatomy & Morphology Keywords: Protists; cyanobacteria; rotifers; crustacea; hypersalinity; Messolonghi saltworks
Online: 27 May 2021 (14:17:02 CEST)
During a survey in 2015 an impressive assemblage of organisms were found in a hypersaline pond of the Messolonghi saltworks. The salinity ranged between 50 and 180 ppt and the organisms recorded fell in the categories of Cyanobacteria (17 species), Chlorophytes (4 species), Diatoms (23 species), Dinoflagellates (1 species), Protozoa (40 species), Rotifers (8 species), Copepods (1 species), Artemia sp., one nematode and Alternaria sp. (Fungi). Fabrea salina was the most prominent protist in all samples and salinities. This ciliate has the potential to be a live-food candidate for marine fish larvae. Asteromonas gracilis proved a sturdy microalga performing excellently in a broad spectrum of culture salinities ies. Most of the specimens were identified only to the genus level and, based on their morphology, as there are no relevant records in Greece, there is a possibility for some of them to be either new species or strikingly different strains of certain species recorded elsewhere.
COMMUNICATION | doi:10.20944/preprints202105.0679.v1
Online: 27 May 2021 (14:14:20 CEST)
The study aimed to identify different molds that grow on various food surfaces. As a result, we conducted a case study for the detection of mold on food surfaces based on the “you only look once (YOLO) v5” principle. In this context, a dataset of 2050 food images with mold growing on their surfaces was created. The dataset was trained using the pre-trained YOLOv5 algorithm. In comparison to YOLOv3 and YOLOv4, this current YOLOv5 model had better precision, recall, and average precision (AP), which were 98.10%, 100%, and 99.60%, respectively. The YOLOv5 algorithm was used for the first time in this study to detect mold on food surfaces. In conclusion, the proposed model successfully recognizes any kind of mold present on the food surface. Using YOLOv5, we are currently conducting research to identify the specific species of the detected mold.
ARTICLE | doi:10.20944/preprints202105.0653.v1
Subject: Biology, Anatomy & Morphology Keywords: monarch butterfly; Danaus plexippus; Arthropods; community structure; survivorship
Online: 27 May 2021 (07:58:52 CEST)
The eastern migratory population of the monarch butterfly (Danaus plexippus) in North America has declined by over 80% in the last 20 years, prompting the implementation of numerous conservation strategies. However, there is little information on the survivorship of first-generation monarchs in the core area of occupancy in Texas, Oklahoma, and Louisiana where overwinter population recovery begins. The purpose of this study was to determine the survivorship of first-generation eggs to third instars at a site in north Texas and to evaluate host plant arthropods for their effect on survivorship. Survivorship to third instar averaged 13.4% and varied from 11.7% to 15.6% over three years. The host plants harbored 77 arthropod taxa, including 27 predatory taxa. Despite their abundance, neither predator abundance nor predator richness predicted monarch survival. However, host plants upon which monarchs survived often harbored higher numbers of non-predatory arthropod taxa and more individuals of non-predatory taxa. These results indicate that indirect top-down effects improved monarch survival in our study. The creation of diverse functional arthropod communities should be considered for effective monarch conservation, particularly in southern latitudes.
Wed, 26 May 2021
ARTICLE | doi:10.20944/preprints202105.0648.v1
Subject: Biology, Anatomy & Morphology Keywords: herpes simplex virus type 1 (HSV-1); bovine herpesvirus 1 (BoHV-1); Krüppel–like factor 15 (KLF15); infected cell protein 0 (ICP0); BoHV-1 ICP0 (bICP0)
Online: 26 May 2021 (15:10:59 CEST)
Expression of Krüppel–like factor 15 (KLF15), a stress induced transcription factor, is induced during bovine herpesvirus 1 (BoHV-1) reactivation from latency, and KLF15 stimulates BoHV-1 replication. Transient transfection studies revealed KLF15 and glucocorticoid receptor (GR) cooperatively transactivate the BoHV-1 immediate early transcription unit 1 (IEtu1), herpes sim-plex virus type 1 (HSV-1) infected cell protein 0 (ICP0), and ICP4 promoter. The IEtu1 promoter drives expression of bICP0 and bICP4, two key BoHV-1 transcriptional regulatory proteins. Based on these studies, we hypothesized infection is a stressful stimulus that increases KLF15 ex-pression and enhances productive infection. New studies demonstrated that silencing KLF15 impaired HSV-1 productive infection and KLF15 steady state protein levels were increased at late stages of productive infection. KLF15 was primarily localized to the nucleus following in-fection of cultured cells with HSV-1, but not BoHV-1. When cells were transfected with a KLF15 promoter construct and then infected with HSV-1, promoter activity was significantly increased. The ICP0 gene and to a lesser extent bICP0 transactivated the KLF15 promoter in the absence of other viral proteins. In contrast, BoHV-1 or HSV-1 encoded VP16 had no effect on KLF15 pro-moter activity. Collectively, these studies revealed HSV-1 and BoHV-1 productive infection in-creased KLF15 steady state protein levels, which correlated with increased virus production.
Tue, 25 May 2021
ARTICLE | doi:10.20944/preprints202105.0606.v1
Subject: Biology, Anatomy & Morphology Keywords: Chi-squared; Genetic ratios; Progenies; Selfing; Variability analysis
Online: 25 May 2021 (10:34:35 CEST)
The present cultivated enset clonal landraces in Ethiopia originated from few wild progenitors. However, enset has a mixed mode of reproduction in which, the wild enset reproduces sexually through seeds, while cultivated enset is generally propagated vegetatively. The objective of this study was to understand the genetic structures of enset cultivars and estimate their genetic variability by evaluating the morphological data generated from progenies of cultivated and wild enset clones. Hence, seeds collected from six cultivated and four wild enset genotypes were used for this study. Data on four qualitative and six quantitative morphological traits were recorded from the progenies of the 10 enset genotypes. Progenies of seven enset genotypes segregated with 3:1 genetic ratio while progenies of the remaining genotypes segregated differently for the qualitative traits considered. With regard to the quantitative traits, the progenies of the 10 enset genotypes differed significantly for five of the six traits except pseudostem length. Generally the cultivated clones performed better than the wild types. This study demonstrated the possibility of creating genetic variation through selfing of the existing clones of enset for traits of interest and makes improvements either through selection or crossing the elite types to develop novel cultivar
Mon, 24 May 2021
REVIEW | doi:10.20944/preprints202105.0572.v1
Subject: Biology, Other Keywords: microalgae; marine bacteria; quorum sensing signals; alkyl quinolones; microbial loop
Online: 24 May 2021 (13:34:11 CEST)
Quorum sensing (QS) describes a process by which bacteria can sense the local cell density of their own species, thus enabling them to coordinate gene expression and physiological processes on a community-wide scale. Small molecules called autoinducers or QS signals, which act as intraspecies signals, mediate quorum sensing. As our knowledge of QS has progressed, so too has our understanding of the structural diversity of QS signals, along with the diversity of bacteria conducting QS and the range of ecosystems in which QS takes place. It is now also clear that QS signals are more than just intraspecies signals. QS signals mediate interactions between species of prokaryotes, and between prokaryotes and eukaryotes. In recent years, our understanding of QS signals as mediators of algae–bacteria interactions has advanced such that we are beginning to develop a mechanistic understanding of their effects. This review will summarize the recent efforts to understand how different classes of QS signals contribute to the interactions between planktonic microalgae and bacteria in our oceans, primarily N-acyl-homoserine lactones, their degradation products tetramic acids, and 2-alkyl-4-quinolones. In particular, this review will discuss the ways in which QS signals alter microalgae growth and metabolism, namely as direct effectors of photosynthesis, regulators of the cell cycle, and as modulators of other algicidal mechanisms. Furthermore, the contribution of QS signals to nutrient acquisition is discussed, and finally how microalgae can modulate these small molecules to dampen their effects.
ARTICLE | doi:10.20944/preprints202105.0560.v1
Subject: Biology, Anatomy & Morphology Keywords: ae mutant; amylose; breeding potential; maize; SBEIIb
Online: 24 May 2021 (10:44:31 CEST)
Maize varieties with high amylose proportion are more valuable for starch industry. The SBEⅡb gene encodes one of the starch branching isozymes (SBEⅠ, SBEⅡa, and SBEⅡb). Its recessive mutant amylose-extender (ae/sbe2b) decreases the total activities of SBEs and increases amylose proportion up to 60%. Here, the breeding potential of introduced germplasm line GEMS-0067 was evaluated by genotyping and phenotyping. The deletion of the ninth exon of the SBEⅡb gene, high amylose proportion, and the typical irregular granules suggested that this germplasm line was derived from the same resource of high amylose line AE11. The gelatinization and thermal properties, and degree of polymerization of starch chain showed its advantages used for high amylose breeding. However, the negative correlation between amylose proportion and starch content, as well as ker-nel filling characteristics should be overcome during breeding process.
ARTICLE | doi:10.20944/preprints202105.0553.v1
Subject: Biology, Anatomy & Morphology Keywords: mushroom; organic-debris; fruiting bodies; diversity; frequency
Online: 24 May 2021 (10:22:51 CEST)
A The present investigation was undertaken in foothill regions of Uttarakhand from July-2016 up to December-2018. A total of thirty four different sites ranging from the roadside areas, grasslands to forests were studied and Mushroom fruiting bodies were collected. A total of One Hundred sixty six fruiting counts were obtained and 68 mushroom genera belonging to 15 orders and 43 families were identified. During collection visits mushroom were apparent from organic debris of diversified habitats ranging from humid soil; grassland; leaf litter; living tree trunk; dead wood log of forest zone. Maximum fruiting bodies (75%) were obtained between July to September and minimum i.e. 6% between November – February. Among the collected mushroom Stereum rugosum, Crepidotus variabilis, Laccaria laccata, Schizophyllum commune, Ganoderma applantum, Cantharellus cibarius were more prevalent. Out of all collected mushroom sample the frequency of Mushroom belonging to order Agaricales was 45.18% followed by Polyporales i.e., 27.7%. The collected mushroom were cultured on PDA medium and their mycelial forms were preserved for further studies.
ARTICLE | doi:10.20944/preprints202105.0538.v1
Subject: Biology, Anatomy & Morphology Keywords: Lophelia pertusa; Haplosporidia; Vibrio; Rickettsiales-like organisms; Histology; PCR; Pathogen; Cold-water corals
Online: 24 May 2021 (08:20:11 CEST)
Temperature and pH can expedite the ability of pathogens to cause diseases in cold-water corals (CWCs). The present study employed a combination of histology and polymerase chain reaction diagnostic techniques to investigate potential pathogens present in the CWCs Lophelia pertusa and Madrepora oculata in the Porcupine Bank Canyon (PBC), NE Atlantic. No pathogen was observed in the Madrepora samples. Neither histology nor standard PCR detected Vibrio spp. in the corals, although using Illumina technology, V. shilonii was observed in some L. pertusa samples in low abundances (0.22%). A Rickettsiales-like organisms (RLOs) occurred at a prevalence of 8.0% and at a low infection intensity of 1 - 4. Lophelia showed a few RLOs infection from the PBC canyon head (2.7%) and high infections in the south branch (5.3%). Similarly, unidentified cells observed in L. pertusa from the south branch (4.0%) were more common than those found in the canyon head (1.3%) with a prevalence of 5.3%. Although the route of pathogen infection is unclear, a likely mode of entry could be associated with particulate availability and the feeding strategies of the scleractinian corals. This suggest that L. pertusa invests energy into an enhanced immune function and reduced susceptibility to global pathogens despite a changing ocean environment.
ARTICLE | doi:10.20944/preprints202105.0536.v1
Subject: Biology, Anatomy & Morphology Keywords: Argan biosphere reserve; Climate change; Rainfall; Temperature; Woodland regression
Online: 24 May 2021 (07:44:25 CEST)
This paper explores the effect of climate change on the regression of the Argan tree (Argania spinosa L. Skeels) woodland, focusing on the Argan Biosphere Reserve and especially in the Souss plain (Western Morocco). Rainfall and temperature data of four sites within the Argan Biosphere Reserve were analyzed over the last 60 years to assess any climatic change. Regression curves applied to the dataset showed an important decrease in rainfall (18 to 26 %) in the four locations as well as an increase in temperature (1 to 2 °C). These changes may have a detrimental effect on the Argan woodland although human factors have been reported to be the main factor of its regression. It can therefore be concluded that the reduction in rainfall and the increase in temperature should now be considered as factors of Argan woodland regression.
Fri, 21 May 2021
ARTICLE | doi:10.20944/preprints202105.0527.v1
Subject: Biology, Anatomy & Morphology Keywords: Phenylpropanoid pathway; Caffeoylquinic acid; BAHDs; hydroxycinnamoyl-coenzyme A: quinate hydroxycinnamoyl transferase; hydroxycinnamoyl-coenzyme A: shikimate/quinate hy droxycinnamoyl transferase;
Online: 21 May 2021 (15:13:15 CEST)
The phenylpropanoid pathway is a major secondary metabolite pathway that helps plants overcome biotic and abiotic stress and produces various by-products that promote human health. Its byproduct, chloroquinic acid (CQA), is a soluble phenolic compound present in many angiosperms. Hy-droxycinnamate-CoA shikimate/quinate transferase(BAHDs superfamily enzyme) is a significant en-zyme that plays a role in accumulating CQA biosynthesis. This study analyzed transcriptome-wide identification of the phenylpropanoid to chloroquinic acid biosynthesis candidate genes in A. spathulifolius flowers and leaves. Transcriptomic analyses of the flowers and leaves showed a differential expression of the PPP and CQA biosynthesis regulated unigenes. An analysis of PPP captive unigenes revealed the following: the major duplication of the key enzyme, PAL, 120 unigenes in leaves and 76 in flowers; the gene encoding C3’H, 169 unigenes in leaves and 140 unigenes in flowers; duplicated unigenes of 4CL, 41 in leaves and 27 in flowers. In addition, C4H unigenes had 12 unigenes in the leaves of A. spathulifolius and four in the flowers. The characterization of the BAHDs superfamily members identified 82 in leaves and 72 in flowers. Among them, phylogenetic analysis showed that five unigenes encoded HQT and three en-coded HCT in A. spathulifolius. The three HQT are common to both leaves and flowers, whereas the two HQT were specialized for leaves. The pattern of HQT synthesis was upregulated in flowers, whereas HCT was expressed strongly in the leaves of A. spathulifolius. Overall, 4CL, C4H, and HQT are expressed strongly in flowers, and caffeic acid and HCT show more expression in leaves. Therefore, CQA biosynthesis occurs in the flowers of A. spathulifolius rather than leaves.
Thu, 20 May 2021
REVIEW | doi:10.20944/preprints202105.0476.v1
Subject: Biology, Anatomy & Morphology Keywords: Histone Methylation, DNA repair, homologous recombination, Non homologous end joining
Online: 20 May 2021 (10:26:07 CEST)
Packaging of the eukaryotic DNA genome with histone and other proteins forms a chromatin structure that regulates the outcome of all DNA mediated processes. The cellular pathways that ensure genomic stability detect and repair DNA damage through mechanisms which are critically dependent upon chromatin structures established by histones and, particularly, transient histone post-translational modifications . Though subject to a range of modifications, histone methylation is especially crucial for DNA damage repair as the methylated histones often form platforms for subsequent repair protein binding at damaged sites. In this review, we highlight and discuss how histone methylation impacts the maintenance of genome integrity through effects related to DNA repair and repair pathway choice.
ARTICLE | doi:10.20944/preprints202102.0122.v2
Subject: Biology, Anatomy & Morphology Keywords: tomato; temperature; damage; seedling; plant; root; weight; photosynthesis; proline; electrical conductivity
Online: 20 May 2021 (09:45:18 CEST)
High temperature (HT) significantly affects the crop physiological traits and reduces the 12 productivity in plants. To increase yields as well as survival of crops under HT, developing heat13 tolerant plants is one of the main targets in crop breeding programs. The present study attempted 14 to investigate the linkage of the heat tolerance between the seedling and the reproductive growth 15 stages of tomato cultivars ’Dafnis‘ and ’Minichal’. This research was undertaken to evaluate heat 16 tolerance under two experimental designs such as screening at seedling stage and screening from 17 reproductive traits in greenhouses. Survival rate and physiological responses in seedlings of 18 tomatoes with 4-5 true leaf were estimated under HT (40 °C, RH 70%, day/night, respectively) and 19 under two control and HT greenhouse conditions (day time 28 °C and 40 °C, respectively). Heat 20 stress significantly affected physiological-chemical (photosynthesis, electrolyte conductivity, 21 proline) and vegetative parameters (plant height, shoot fresh weight, root fresh weight) in all 22 tomatoes seedlings. The finding revealed that regardless of tomato cultivars the photosynthesis, 23 chlorophyll, total proline and electrical conductivity parameters were varied in seedlings during the 24 heat stress period. The heat tolerance rate of tomatoes in the seedling stage might not be associated 25 always with reproductive parameters. HT reduced the fruit parameters likeas fruit weight (31.9%), 26 fruit length (14.1%), fruit diameter (19.1%) and fruit hardness (9.1%) in compared to NT under HT 27 in heat susceptible tomato cultivar ‘Dafnis’, while in heat tolerant cultivar ‘Minichal’ fruit length 28 (7.1%) and fruit diameter (12.1%) was decreased by the affect of HT but on the contrary fruit weight 29 (3.6%) and fruit hardness (8.3%) were increased. In conclusion, screening and selection for tomatoes 30 should be evaluated at the vegetative and reproductive stages with consideration of reproductive 31 parameters.
ARTICLE | doi:10.20944/preprints202105.0460.v1
Subject: Biology, Anatomy & Morphology Keywords: Bacteria; community composition; growth stage; rhizosphere; root nodule; soybean; 16S rRNA gene
Online: 20 May 2021 (09:13:15 CEST)
Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max L.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.
Tue, 18 May 2021
ARTICLE | doi:10.20944/preprints202105.0400.v1
Online: 18 May 2021 (09:31:15 CEST)
Dracunculiasis (also known as Guinea worm disease) is caused by Dracunculus medinensis parasite and it spreads by drinking water containing Larvae of Guinea worm. The lack of safe water facilities, preventions and treatments resulted in highly dangerous consequences in its endemic regions. The economy of the affected regions totally falls down due to less production which is the result of agricultural field worker’s bad health. In this study, a multi epitope vaccine was designed against Dracunculus medinensis by using immune-informatics. The vaccine was designed by using T-Cell and B-Cell epitopes derived from Dracunculus medinensis proteins (Lactamase-B domain-containing protein, G-Domain containing protein and Ferrochelatase) in addition to Adjuvants and Linkers. The tertiary structure, physiochemical properties and immunogenic elements of vaccine were achieved. The validation of tertiary structure was accessed, and quality was achieved. In addition, the world coverage of parasite’s CTL and HTL epitopes is 95.61%. The stability of the chimeric vaccine was achieved through disulfide engineering. The molecular docking with Toll Like Receptor 4 (TLR-4) of vaccine showed its binding efficiency followed by Molecular Dynamic Simulation. The immune simulation suggested the mediated cell immunity and repeated antigen clearance. At the end, the optimized codon was used in in silico cloning to ensure vaccine’s higher exposure in bacterium E. coli strain K12. With further assessments, it is believed that the proposed multi epitope vaccine has strong immunogen to control Dracunculus medinensis which may result in better social and economic conditions of endemic regions.
Mon, 17 May 2021
REVIEW | doi:10.20944/preprints202105.0398.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: intellectual property; intellectual property protection; plant variety protection, plant breeders’ rights, essentially derived variety; utility patent; plant breeding; biotechnology.
Online: 17 May 2021 (17:03:30 CEST)
This review examines the categorization of Essentially Derived Varieties (EDV) introduced in the 1991 revision of the Convention of the Union internationale pour la protection des obtentions végétales (UPOV). Challenges in the implementation of the concept and progress made on a crop-by-crop basis to provide greater clarity and more efficient implementation are reviewed. The current approach to EDV remains valid provided i) clarity on thresholds can be achieved including through resource intensive research on an individual crop species basis and ii) that threshold clarity does not lead to perverse incentives to avoid detection of essential derivation. However, technological advances leading to new varieties resulting from the simultaneous introduction or change in expression of more than “a few” genes will so challenge the concept to require a new Convention. Revision could include deletion of the concept of essential derivation and revision on a crop-by-crop basis of the breeder exception. Countries that allow utility patents for individual plant varieties per se should consider removing that possibility unless plant breeders utilize those encouragements for risk taking and investment to broaden the germplasm base upon which the long-term sustainability of plant breeding resides.
ARTICLE | doi:10.20944/preprints202105.0394.v1
Subject: Biology, Other Keywords: Modularity; Protein-to-protein interaction networks; Spectral characterization; Tree of life
Online: 17 May 2021 (16:56:57 CEST)
Modularity and organizational hierarchy are important concepts in understanding the structure and evolution of interactions in complex biological systems. In this work, we introduce and use a spectral characterization measure (Spectral Entropy) to quantify modularity in protein-to-protein interaction (PPI) networks in species across the tree of life. We evaluated the relation between the size of a PPI network and its (Spectral Entropy-based) modularity, and found a sigmoidal response between the two. We also found significant differences in the distribution of Spectral Entropy values among the three domains of life (Bacteria, Archaea, Eukaryotes). To explore further correlations with biological traits, we focused solely on bacterial PPI networks, which are the most numerous among the three domains and had associated trait metadata, and investigated how modularity impacts or is impacted by growth, aerobicity, selection and location on the tree of life. We found no relation between maximal growth rate and Spectral Entropy, but a strong dependence between G-C content (a proxy for selection) and Spectral Entropy. We also discovered that Spectral Entropy is negatively affected by phylogenetic placement (evolutionary distance from the last universal common ancestor). The general nature of the Spectral Entropy measure of hierarchical modularity in networks suggests that it will be useful in other settings where structural properties of real-world networks are being compared.
COMMUNICATION | doi:10.20944/preprints202105.0380.v1
Subject: Biology, Anatomy & Morphology Keywords: Analgesia; local anesthetic; sheep; lignocaine; elastrator; husbandry; rubber ring
Online: 17 May 2021 (10:03:53 CEST)
Use of local anesthesia at the time of ring castration and tail docking can improve lamb welfare. However, few local anesthetics are registered for sheep, and data on their duration of effect is limited. Three studies were conducted to evaluate the efficacy of procaine (P), lidocaine (L) and bupivacaine (B) in terms of observed alleviation of behavioral responses to castration and/or tail docking in 10-min blocks in the first 60 min post treatment. In each study, comparisons were made between two groups of lambs castrated and/or tail docked with rubber rings and either receiving the agent using the NUMNUTS® instrument (N) or receiving no anesthetic agent (RR). Acute pain behavior was lower in NL (n = 28) than RRL (n = 15) males in the first 10 min post procedure (P < 0.05); lower in NB (n = 16) than RRB (n = 16) males in periods 10-20 min (0.05 < P < 0.01), 20-30 min (P < 0.05) and 40-50 min (0.05 < P < 0.01); lower in NB (n = 16) than RRB (n = 16) females between 20 and 40 min post-procedure (0.05 < P < 0.01); lower in NP (n = 8) than RRP (n = 7) males in period 10-20 min (0.05 < P < 0.01), and lower in NP (n = 9) than RRP (n = 9) females in periods 0-10 min (0.05 < P < 0.01), and 10-40 min (P < 0.05). Analgesic benefits were modest, and the effects of procaine appear to last longer than lidocaine, while bupivacaine is slower to take effect than either procaine or lidocaine but may provide longer lasting analgesia. The duration of action of local anesthetics is short in sheep, and detailed behavioral evaluations are required in the first hour post procedure to establish efficacy.
Subject: Biology, Anatomy & Morphology Keywords: winter wheat; mycotoxins; Fusarium; resistance; ergosterol; trichothecenes; zearalenone
Online: 17 May 2021 (09:56:21 CEST)
Fusarium head blight (FHB) can cause contamination of cereal grain with mycotoxins. Winter wheat is also infected with FHB. It is more resistant than durum wheat to head infection and less than other small grain cereals. The aim of this study was to identify winter wheat lines that combine low head infection and kernel damage with low toxin contamination. Resistance to FHB of 27 winter wheat lines and cultivars was evaluated over a three-year experiment established in two locations. At the anthesis stage, heads were inoculated with Fusarium culmorum isolates. The FHB index was scored and the percentage of Fusarium-damaged kernels (FDKs) assessed. The grain was analysed for type B trichothecenes (deoxynivalenol and derivatives, nivalenol) and zearalenone content. The average FHB index was 12.9%. The proportion of FDK was 6.9% (weight) and 8.5% (number). An average content of deoxynivalenol amounted to 3.543 mg/kg and nivalenol to 2.115 mg/kg. In total, it was 5.804 m/kg of type B trichothecenes. The zearalenone content in the grain was 0.214 mg/kg. Relationships between FHB index, FDK and mycotoxin contents were highly significant for wheat lines; however, they were stronger for FDK versus mycotoxins. Breeding lines combing all types of FHB resistance were found, and five of them had resistance similar to that of wheat lines with the Fhb1 gene.
REVIEW | doi:10.20944/preprints202105.0366.v1
Subject: Biology, Anatomy & Morphology Keywords: Hibiscus sabdariffa L.; agricultural wastes; anthocyanins; ruminant nutrition; milk and meat production; fat milk and meat quality
Online: 17 May 2021 (07:52:05 CEST)
The objective was to analyze the effects of adding anthocyanin delphinidin-3-O-sambubioside and cyanidin-3-O-sambubioside of Hibiscus sabdariffa L. in animal diets. Scientific articles published before 2021 in clinics, pharmacology, nutrition, and animal production were included. The grains/concentrate, metabolic exigency, and caloric stress contribute to increasing the reactive oxygen species (ROS); the excess of ROS unbalance the oxidants and antioxidants. Cyanidin-3-O-sambubioside and delphinidin-3-O-sambubioside have antioxidant, antibacterial, antiviral, and anthelmintic activities. In the rumen, anthocyanin might show interactions and/or synergisms with substrates, microorganisms, and enzymes which could reduce the fiber degradability, but increase the potential methane (CH4) emissions; since anthocyanin interferes in the biohydrogenation of fats, they increase the fat milk and meat quality. Anthocyanins reduce plasma oxidation and deposit in tissues, increasing the milk and meat antioxidant activities. Cyanidin-3-O-sambubioside and delphinidin-3-O-sambubioside act as inhibitors of the angiotensin-converting enzyme (ACEi) and rennin expression which may improve milk yield (there is not enough evidence in ruminants, though). Polyphenols affect the reproductive potential. Sub products of HS contain as many amounts of polyphenols as calyces, and their inclusion in diets would positively affect the average daily gain and fat meat quality. Including HS in ruminant diets can improve the meat and milk quality.
Fri, 14 May 2021
ARTICLE | doi:10.20944/preprints202105.0351.v1
Subject: Biology, Anatomy & Morphology Keywords: cytoprotection; cytotoxicity; ferns; oxidative stress; Polypodiaceae; Polypodium vulgare L.; medicinal plants
Online: 14 May 2021 (16:03:00 CEST)
Pteridophytes, represented by ferns and allies, are an important phytogenetic bridge between lower and higher plants (gymnosperms and angiosperms). Ferns have evolved independently of any other species in the plant kingdom being its secondary metabolism a reservoir of phytoconstituents characteristic of this taxon. The study of the possible medicinal uses of Polypodium vulgare L. (Polypodiaceae), PV, has increased particularly when in 2008 the European Medicines Agency published a monograph about the rhizome of this species. Thus, our objective is to provide scientific knowledge on the methanolic extract from the fronds of P. vulgare L., one of the main ferns described in the Prades Mountains, to contribute to the validation of certain traditional uses. Specifically, we have characterized the methanolic extract of PV fronds (PVM) by HPLC-DAD and investigated its potential cytotoxicity, phototoxicity, ROS production and protective effects against oxidative stress by using in vitro methods. Our results show that PVM is not cytotoxic against the different cell lines assessed, but we found potential cytoprotective and cellular repair activity in 3T3 fibroblast cells. This biological activity could be attributed to the high content of polyphenolic compounds; thus, this extract is positioned as a potential candidate for pharmaceutical uses.
ARTICLE | doi:10.20944/preprints202105.0348.v1
Subject: Biology, Anatomy & Morphology Keywords: Pistacia atlantica leaves; L. infantum; L. major; promastigote; antileishmanial; Masticadienonic acid, 3-Methoxycarpachromene; molecular docking.
Online: 14 May 2021 (15:36:40 CEST)
This study aimed to identify new drug molecules against Leishmania parasites, leishmaniasis's causal agent, using Pistacia atlantica leaves as source. The evaluation of the anti-leishmania potential against the promastigote form of Leishmania. infantum and Leishmania. major was performed. A new in silico study was accomplished using molecular docking, with Autodock vina program, to find the binding affinity of two important phytochemical compounds from this plant (Masticadienonic acid, 3-Methoxycarpachromene) towards the trypanothione reductase as target drugs, responsible for defence mechanism against oxidative stress and virulence of this parasites. Results: Several concentrations showed a significant decrease in cell viability (P<0.0001), with IC50 values of 0.3 mg/ mL for L. infantum and 0.12 mg/ mL L. major; The molecular docking confirms the significant relationship between Leishmania survival and the inhibition of this crucial enzyme. There were promising and new positive results on binding modes of selected ligands and the trypanothione reductase for the first time. Through this work, we propose 3-Methoxycarpachromene and Masticadienonic acid as anti Trypanosomatidae species drug.
ARTICLE | doi:10.20944/preprints202105.0347.v1
Subject: Biology, Anatomy & Morphology Keywords: Tuberculosis; Mycobacterium tuberculosis; mRNA expression; Cytokine; Human FFPE tissue
Online: 14 May 2021 (15:33:20 CEST)
In the present study, we aimed to investigate whether an automated molecular diagnostic method based on PCR-reverse blot hybridization assay can discriminate between human Mycobacterium tuberculosis (MTB)-positive and -negative FFPE tissues and to compare the relative mRNA expression levels of various host immune markers between MTB-infected and uninfected human tissues using quantitative reverse transcription (qRT) PCR. A total of 52 human FFPE tissue samples from various regions of the body, including the lungs, lymph nodes, tendons, colon, and appendix, were collected and used for the molecular identification of Mycobacterium species and analysis of cytokine mRNA expression. As a result, IFN-γ, TNF-α, IP-10, CXCL9, CXCL11, and GM-CSF mRNA expression levels in MTB-infected tissues were significantly higher than those in uninfected samples. Additionally, the differences in the mRNA expression levels of IFN-γ, CXCL9, and GM-CSF between MTB-infected and uninfected tissues were statistically significant were statistically significant (p < 0.05). Correlation curve analysis indicated that the mRNA expression of IFN-γ was inversely proportional to that of IP-10 and that the mRNA expression levels of IFN-γ, TNF-α, CXCL9, CXCL11, GM-CSF, and TNFR were proportional and well-correlated. Furthermore, to establish marker profiles for detecting MTB infection, the statistically significant expression levels of three markers were combined. We confirmed that the combined profile of IFN-γ, CXCL9, and GM-CSF expression levels was statistically significant (P < 0.001). Although the mRNA expression patterns of host immune markers may vary according to MTB infection status, these patterns may be highly correlated and can be simultaneously used as an additional indicator for diagnosing TB.
ARTICLE | doi:10.20944/preprints202105.0339.v1
Subject: Biology, Anatomy & Morphology Keywords: Modeling; forest structure; silviculture; pine; oaks; juniper
Online: 14 May 2021 (14:05:32 CEST)
Tree biomass and diversity relationship in mixed forest impacts on forest ecosystem services provisions. Tree biomass yield is driven by several aspects such as species identity, site condition, stand density, tree age as well as tree diversity expressed as species mingling and structural diversity. By comparing diverse degrees of tree mixture in natural forests we can insight on the ecosystem services provision level and dynamic. Two monitoring sites in the Castilian Northern Plateau (Spain) have been analyzed to disentangle the relationships between biodiversity levels and tree biomass yield. Two permanent one ha squared plots were established at Llano de San Marugan and Valdepoza. In each plot all individual trees were measured (diameter and height), georeferenced and its species identity defined. Tree species in the two sites were Pinus sylvestris, Pinus nigra, Pinus pinea, Quercus pyrenaica, Quercus ilex, Quercus faginea and Juniperus thurifera. From these datasets ten diversity indices that fall in three categories (species richness indices, species compositional/mingling indices and vertical structural indices) were used as predictor variables to fit several candidate models. By merging the trees by site (without considering the species identity) selected models include individual tree basal area as explanatory variable combining by addition or interaction with diversity indices. When species are analyzed independently structural diversity impacts on biomass yield in combination (additive or multiplicative) with tree size is negative Pinus nigra and positive for the other species.
REVIEW | doi:10.20944/preprints202105.0326.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: organic; conventional; potato; quality; disease
Online: 14 May 2021 (11:44:40 CEST)
Interest in organic foods is increasing at a moment when humanity is facing a range of health challenges including the concern that some conventionally produced foods may pose possible adverse effects on human and livestock health. With the increasing human population, intensive production is increasingly trending towards high-input systems that aim to close yield gaps, increase crop yields, and develop new crop varieties with higher yield potential and tolerance to biotic and abiotic stresses, all within the context of incorporating specific traits to satisfy consumer demand. Potato (Solanum tuberosum L.) is one of the most consumed foods under different cultural diets, however its production faces some challenges related to soilborne diseases, marketable yield and quality, sugars and dry matter content of the produced tubers, tuber content in terms of nitrate, minerals, vitamins, bioactive compounds and antioxidants, and consumer appreciation regarding the sensory characteristics of tubers and processed products. Different studies have been investigating some of these challenges, with sometimes straightforward and sometimes connflicting results. This variability in research results indicates the general non-transferability of the results from one location to another under the same management practices in addition to differences in plant material. This review compares some characteristics of raw or boiled potato and processed products from potato tubers grown organically and conventionally. Ideally, such information may be of benefit in decision making by consumers in their dietary choices, by potato growers in their selection of crop management practices, and by scientists looking at potential areas for future research on potatoes.
ARTICLE | doi:10.20944/preprints202105.0322.v1
Subject: Biology, Anatomy & Morphology Keywords: Virus; plant virus; long noncoding RNA; replication; positive sense RNA virus
Online: 14 May 2021 (11:01:56 CEST)
Long noncoding RNAs (lncRNAs) of virus origin accumulate in cells infected by many positive strand (+) RNA viruses to bolster viral infectivity. Their biogenesis mostly utilizes exoribonucleases of host cells that degrade viral genomic or subgenomic RNAs in the 5’-to-3’ direction until being stalled by well-defined RNA structures. Here we report a viral lncRNA that is produced by a novel replication-dependent mechanism. This lncRNA corresponds to the last 283 nucleotides of the turnip crinkle virus (TCV) genome, hence is designated tiny TCV subgenomic RNA (ttsgR). ttsgR accumulated to high levels in TCV-infected Nicotiana benthamiana cells when the TCV-encoded RNA-dependent RNA polymerase (RdRp), also known as p88, was overexpressed. Both (+) and (-) strand forms of ttsgR were produced in these cells in a manner dependent on the RdRp functionality. Strikingly, templates as short as ttsgR itself were sufficient to program ttsgR amplification, as long as the TCV-encoded replication proteins, p28 and p88, were provided in trans. Consistent with its replicational origin, ttsgR accumulation required a 5’ terminal G3(A/U)4 motif shown by others to be crucial for the replication of a TCV satellite RNA. More importantly, introducing a new G3(A/U)4 motif elsewhere in the TCV genome was alone sufficient to cause the emergence of another lncRNA. Collectively our results unveil a replication-dependent mechanism for the biogenesis of viral lncRNAs, thus suggesting that multiple mechanisms, individually or in combination, may be responsible for viral lncRNA production.
Thu, 13 May 2021
ARTICLE | doi:10.20944/preprints202105.0308.v1
Subject: Biology, Anatomy & Morphology Keywords: Indonesia; biodiversity; novel antibiotics; drug screening; bioactivity; gene cluster networking; GNPS
Online: 13 May 2021 (14:05:00 CEST)
Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two-thirds of all clinically used antibiotics. Thus, exploiting Indonesia’s microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Besides, eight putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.
ARTICLE | doi:10.20944/preprints202105.0286.v1
Subject: Biology, Anatomy & Morphology Keywords: 21st Century Skills/Thinking Skills; Computational Thinking; Critical Thinking; Robotics for Education
Online: 13 May 2021 (11:34:37 CEST)
A new teaching method under the name of STEM, integrating the disciplines of Science, Technology, Engineering, and Mathematics, is now taught by teachers in their classes. Considering that the generation that grows up in the 21st-century has grown up with technology, it is thought that integrating technology into lessons helps students learn the subject. The study aims to develop five STEM activities for the human body systems lesson by integrating the coding-based Arduino into STEM education. The activities were implemented to 6th-grade students for seven weeks and the effects on students' skills of establishing a cause-effect relationship. The study method was pre-test-post-test quasi-experimental design, and the cause-effect relationship scale was used as a data collection tool. As a result of the study, a significant difference was found between the Arduino-supported STEM activities developed and the students' skills of establishing a cause-effect relationship.
ARTICLE | doi:10.20944/preprints202105.0283.v1
Online: 13 May 2021 (11:20:29 CEST)
Wheat (Triticum aestivum L.) being a staple food crop is an important nutritional source providing protein and minerals. It is important to fortify staple cereals like wheat with essential minerals to overcome the problems associated with malnutrition. The experiment was designed to evaluate the status of 11 micronutrients including grain iron (GFe) and zinc (GZn) in 62 wheat cultivars released between 1911 and 2016 in Pakistan. Field trials were conducted over two years and GFe and GZn were quantified by both inductively coupled plasma optical emission spectroscopy (ICP-OES) and energy dispersive X-ray fluorescence spectrophotometer (EDXRF). The GZn ranged from 18.4 to 40.8 mg/kg by ED-XRF and 23.7 to 38.8 mg/kg by ICP-OES. Similarly, GFe ranged from 24.8 to 44.1 mg/kg by ICP-OES and 26.8 to 36.6 mg/kg by EDEXR. The coefficient of correlation was higher for GZn (r=0.90), compared to GFe (r=0.68). Modern cultivars like Zincol-16 and AAS-2011 showed higher GFe and GZn along with improved yield components. Old wheat cultivars WL-711, C-518 and Pothowar-70 released before 1970 also exhibited higher value of GFe and GZn, however their agronomic performance was poor. Multivariate analysis using ten micronutrients (Al, Ca, Cu, K, Mg, Mn, Na and P) along with agronomic traits, and genome-wide SNP markers identified the potential cultivar with improved yield, biofortification trait and wider genetic diversity. Genetic gain analysis identified significant increase in grain yield (0.4% year-1), while there was negative gain for GFe (-0.11% year-1) and GZn (-0.15% year-1) over the span of 100 years. The Green Revolution Rht-B1 and Rht-D1 genes had strong association with plant height, and grain yield (GY), while semi-dwarfing alleles had negative effect on GFe and GZn contents. This study provided a valuable insight into biofortification status of wheat cultivars deployed historically in Pakistan and is a valuable source to initiate a breeding strategy for simultaneous improvement in wheat phenology and biofortification.
Wed, 12 May 2021
Subject: Biology, Anatomy & Morphology Keywords: floral meristem; polystemony; numerous stamens; evo-devo; ring meristem
Online: 12 May 2021 (10:49:13 CEST)
Floral meristems are dynamic systems that generate floral organ primordia at their flanks and, in most species, terminate while giving rise to the gynoecium primordia. However, we find species with floral meristems that generate additional ring meristems repeatedly throughout angiosperm history. Ring meristems produce only stamen primordia, resulting in polystemous flowers (having stamen numbers more than double that of petals or sepals), and act independently of the floral meristem activity. Most of our knowledge on floral meristem regulation is derived from molecular genetic studies of Arabidopsis thaliana, a species with a fixed number of floral organs and as such of only limited value to understand ring meristem function, regulation, and ecological value. This review provides an overview of the main molecular players regulating floral meristem activity in A. thaliana, and summarizes our knowledge of ring primordia morphology and occurrence in dicots. Our work provides a first step towards understanding the significance and molecular genetics of ring meristem regulation and evolution.
Tue, 11 May 2021
ARTICLE | doi:10.20944/preprints202105.0247.v1
Subject: Biology, Anatomy & Morphology Keywords: IgLON; Lsamp; Ntm; Opcml; Negr1; alternative promoter; cell adhesion molecules; embryonic mouse brain; pallium
Online: 11 May 2021 (14:22:01 CEST)
The members of the IgLON superfamily of cell adhesion molecules facilitate fundamental cellular communication during brain development, maintain functional brain circuitry, and are associated with several neuropsychiatric disorders. Usage of alternative promoter-specific 1a and 1b mRNA isoforms in Lsamp, Opcml, Ntm and the single promoter of Negr1 in the mouse and human brain has been previously described. To determine the precise spatiotemporal expression dynamics of Lsamp, Opcml, Ntm isoforms and Negr1, in the developing brain, we generated isoform-specific RNA probes and carried out in situ hybridization in the developing (embryonic, E10.5, 13.5, 17; post natal, P0) and adult mouse brains. We show that promoter-specific expression of IgLONs is established early during pallial development (at E10.5), where it remains throughout its differentiation through adulthood. In the diencephalon, midbrain and hindbrain, strong expression patterns are initiated a few days later and begin fading after birth, being only faintly expressed during adulthood. Thus, the expression of specific IgLONs in the developing brain may provide the means for regionally specific functionality as well as for specific regional vulnerabilities. The current study will therefore improve the understanding of how IgLON genes are implicated in the development of neuropsychiatric disorders.
ARTICLE | doi:10.20944/preprints202105.0246.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: agriculture 4.0; chlorophyll; early diagnosis; fungal tree pathogens; mycology; plant disease; plant pathology; smart viticulture; vegetation indices; wine grapes
Online: 11 May 2021 (14:21:25 CEST)
The Armillaria genus represents one of the most common causes of chronic root rot disease in woody plants. The disease damage prompt assessment is crucial for pest management. However, the disease detection current methods are limited at the field scale. Therefore, an alternative approach that can enhance or supplement traditional techniques is needed. In this study, we investigated the potential of hyperspectral methods to identify the changes between fungi-infected and uninfected plants of Vitis vinifera in early detecting the Armillaria disease. The hyperspectral imaging sensor Specim-IQ was used to acquire images of leaves of the Teroldego Rotaliano grapevine cultivar. We analysed three groups of plants: healthy, asymptomatic, and diseased. Highly significant differences were found in the Near infrared (NIR) spectral region with a decreasing pattern from healthy to diseased plants attributable to internal leaf structure changes. Asymptomatic plants emerged from the other groups due to a smaller reflectance in the red-edge spectrum (around 705nm). Hypothetically associated with the presence of secondary metabolites involved in plant defence strategy. Furthermore, significant differences were observed in the wavelengths close to 550 nm in diseased plants versus asymptomatic. We used linear discriminant analysis from a machine learning context to classify the leaves based on the most significant variables (vegetation indices and single bands), with resulting overall accuracies of 85% and 84% respectively in healthy vs. diseased and healthy vs. asymptomatic. To our knowledge, this study represents the first report on the possibility of using hyperspectral data for root rot disease diagnosis on woody plants. Although further validation studies are required, it appears that the spectral reflectance technique, possibly implemented on unmanned aerial vehicles (UAV), could be a promising tool for a cost-effective, non-destructive method of Armillaria disease early diagnosis and mapping in the field, contributing to a significant step forward in precision viticulture.
REVIEW | doi:10.20944/preprints202105.0232.v1
Subject: Biology, Ecology Keywords: cyanobacteria, toxic, biotic factors, abiotic factors, interactions, allelopathy
Online: 11 May 2021 (10:36:33 CEST)
Environmental genetics-related modern methods are shown as important indicators of various cyanotoxins syntheses, and their knowledge and use are critically analyzed. Microcystins and other cyanotoxins loads and syntheses are related to different drivers, like various chemical elements and compounds (especially nutrients, such as nitrogen and phosphorus, and their ratio), then to the light, conductivity, temperature, and other climatical and hydrological factors, to which spatial and geographical features (such as the surface of the water bodies) have to be added. The biotic relationships include different specific and supraspecific, uni- and bilateral links between the cyanobacteria, and subsequently their synthesized toxins, and protozoans (or protoctists), chromists, macrophytes, different systematical and ecological groups of zooplankton, and others. The importance of, but also the gaps in, the knowledge and the scarcity of studies involving ectocrines mediated interactions between different groups of algae and plants are highlighted. The paper ends with an interesting classification of lakes' trophicity, illustrated with conceptual diagrams, based on possible scenarios of cyanobacteria behavior.
Subject: Biology, Anatomy & Morphology Keywords: Animal model; COVID-19; ferret; lipidomics; metabolomics; SARS-CoV-2; systems biology
Online: 11 May 2021 (10:20:03 CEST)
COVID-19 is a contagious respiratory disease that is causing significant global morbidity and mortality. Understanding the impact of a SARS-CoV-2 infection on the host metabolism is still in its infancy but of great importance. Herein, we investigated the metabolic response during viral shedding and post-shedding in an asymptomatic SARS-CoV-2 ferret model (n=6) challenged with two SARS-CoV-2 isolates. Virological and metabolic analyses were performed on (minimally invasive) collected oral swabs, rectal swabs, and nasal washes. Fragments of SARS-CoV-2 RNA were only found in the nasal wash samples in four of the six ferrets, and in the samples collected 3 to 9 days post-infection (referred to as viral shedding). Central carbon metabolism metabolites were analyzed during viral shedding and post-shedding periods using a dynamic MRM (dMRM) database and method. Subsequent untargeted metabolomics and lipidomics of the same samples were performed using an LC-QToF-MS methodology, building upon the identified differentiated central carbon metabolism metabolites. Multivariate analysis of the acquired data identified 29 significant metabolites and three lipids that were subjected to pathway enrichment and impact analysis. The presence of viral shedding coincided with the challenge dose administered and significant changes in the citric acid cycle, purine metabolism, and pentose phosphate pathways, amongst others, in the host nasal wash samples. An elevated immune response in the host was also observed between the two isolates studied. These results support other reported metabolomic-based findings found in clinical observational studies and indicate the utility of metabolomics applied to ferrets for further COVID-19 research that advances early diagnosis of asymptomatic and mild clinical COVID-19 infections, in addition to assessing the effectiveness of new or re-purposed drug therapies.
REVIEW | doi:10.20944/preprints202105.0228.v1
Subject: Biology, Anatomy & Morphology Keywords: Upland cotton (Gossypium hirsutum L.); Mercury stress; Phytotoxicity; Physiological and bio-chemical response
Online: 11 May 2021 (10:18:21 CEST)
Cotton is a potential and excellent candidate to balance both agricultural production and reme-diation of mercury-contained soil, as its main production fiber hardly involve into food chains. However, there is known rarely about the tolerance and response to Hg environments in cotton. In this study, The biochemical and physiological damages, in response to mercury (Hg), were investigated in upland cotton seedlings. The results on cottonseeds germination, indicated the germination rate were suppressed by high Hg levels, as the decrease of percentage was more than 10% at 1000 µM Hg. Shoots and roots’ growth were significantly inhibited above 10 µM Hg. The inhibitor rates (IR) in fresh weight were close between shoots and roots, whereas that in dry weight the root growth was more obviously influenced by Hg. In comparison of organs, the growth inhibition ranked as root > leaf > stem. The declining of translocation factor (TF) op-posed the Hg level even as low to 0.05 at 50 µM Hg. The assimilation of cotton plants was af-fected negatively by Hg toxicity, as evidenced from the performances on photosynthesis pig-ments (chlorophyll a and b) and gas exchange (Intercellular CO2 concentration (Ci), CO2 assimila-tion rate (Pn) and stomatal conductance (Gs)). Sick phenotypes on leaf surface included small white zone, shrinking and necrosis. Membrane lipid peroxidation and leakage were Hg dose-dependent as indicated by malondialdehyde (MDA) content and relative conductivity (RC) values in leaves and roots. More than 10 µM Hg damaged antioxidant enzyme system in both leaves and roots (P<0.05). Concludingly, 10 µM Hg post negative consequences to upland cotton plants in growth, physiology and biochemistry, whereas high phytotoxicity and damage ap-peared at more than 50 µM Hg concentration.
Mon, 10 May 2021
REVIEW | doi:10.20944/preprints202103.0144.v2
Subject: Biology, Anatomy & Morphology Keywords: bioluminescence; molecular evolution; photoproteins; photobiology
Online: 10 May 2021 (16:02:22 CEST)
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, reality is more complex. 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 during the evolution of living organisms. While some phylogenetically related organisms may use non-homologous luciferases (e.g., at least four convergent luciferases are 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. The literature review 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.
ARTICLE | doi:10.20944/preprints202105.0206.v1
Subject: Biology, Anatomy & Morphology Keywords: Simian Immunodeficiency Virus; SIVmac239; barcoded viruses; intravenous challenge; intrarectal challenge
Online: 10 May 2021 (15:01:31 CEST)
Little is known about how individual virus lineages replicating during acute Human Immunodeficiency Virus or Simian Immunodeficiency Virus (HIV/SIV) infection persist into chronic infection. In this study, we use molecularly barcoded SIV (SIVmac239M) to track distinct viral lineages for 12 weeks after intravenous and intrarectal challenge in macaques. Two Mafa-A1*063+ cynomolgus macaques (Macaca fascicularis) were challenged intravenously (IV), and two Mamu-A1*001+ rhesus macaques (Macaca mulatta) were challenged intrarectally (IR) with 200,000 Infectious Units (IU) of SIVmac239M. We deep sequenced the molecular barcode from all animals over 12 weeks to characterize the diversity and persistence of virus lineages, as well as the sequences of T cell epitopes during acute SIV infection. During the first three weeks post-infection, we found ~175-950 times more unique virus lineages circulating in the animals challenged intravenously than those challenged intrarectally, suggesting that challenge route is the primary driver restricting the transmission of individual viral lineages. Additionally, the emergence of escape variants can occur on multiple virus templates simultaneously, but elimination of some templates is likely a consequence of additional host factors. These data imply that virus lineages present during acute infection can be eliminated from the virus population even after initial T cell selection.
Subject: Biology, Anatomy & Morphology Keywords: highly pathogenic avian influenza viruses, pathogenicity factors.
Online: 10 May 2021 (14:22:23 CEST)
The H7 subtype of avian influenza viruses (AIV) stands out among other AIV. H7 viruses circulate in ducks, poultry, equine and have repeatedly caused outbreaks of disease in humans. In order to study the pathogenicity factors of H7N1 viruses, several laboratory variants of the A/FPV/Rostock/34 (H7N1) strain were obtained by passages in the chicken lungs. After 10 such passages, a variant was obtained that differed from the parent virus by amino acid substitutions Val109Phe in PB2, Gln621Lys in PB1, Thr32Ala and Leu586Phe in PA Gly140Arg in HA1 and Ala101Thr in HA2 (numbering by H3), Ser82Arg in M2, Arg118Lys and Met124Arg in NS1. No differences were found in proteins NA, NP, M1 and NS2. The resulting variant was hundreds of times more pathogenic for chickens than the original laboratory variant of the virus. The study of intermediate passages showed that the jump in pathogenicity occurs sharply between the fifth and sixth passage through the chicken lungs. By cloning these variants, a pair of strains (R5p and R6p) were obtained, and the complete genomes of these strains were sequenced. Single amino acid substitution was revealed, namely Gly140Arg in HA1. It is important to emphasize that this substitution is a reversion, since Arg is located in position 140 HA1 of original the A/FPV/Rostock/34 (H7N1) virus (GenBank). This amino acid is located at the head part of the hemagglutinin, adjacent to the receptor-binding site. In addition to the increased pathogenicity, R6p differs from R5p by an increased affinity for a negatively charged receptor analogue, an increased affinity for MDCK cells, while maintaining a receptor specificity profile.
REVIEW | doi:10.20944/preprints202105.0162.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Agroecology; Apoidea; Landscape; Pesticide; Sacrifice zones
Online: 10 May 2021 (10:33:00 CEST)
Industrial agriculture (IA) is the predominant model of food production since the Green Revolution in the 1950s. IA has been recognized among the main drivers of biodiversity loss, climate change and native pollinator decline. This is controversial, given that native agricultural pollinators are an important resource biota already contributing to crop yield, especially in areas defined as "world biodiversity hotspots” (WBH). These areas often overlap with agricultural zones hosting a significant proportion of cultivated land, mainly through intensive agricultural practices. Pollinator biodiversity and pollination services in these places are currently under threat due to the negative consequences of IA. The dual role of insects as key players allowing the maintenance of the natural ecosystem, as well as main crop pollinators, is particularly exacerbated and urgently requires conservation actions in WBH and food-producing zones. Here we summarize the known negative effects of IA on pollinator biodiversity and illustrate these problems by considering the case of Chile. Food exports represent a considerable part of the economy in this OECD “developing country” in the “Global South”, and a large part of its surface has been highlighted as a unique WBH. This area is currently being replaced by IA businesses at a fast pace, threatening local biodiversity. We present agroecological strategies for sustainable food production and pollinator conservation in food-producing WBHs like Chile. These alternatives recognize native pollinators as internal inputs that cannot be replaced by IA technological packages or external inputs and support the development of agroecological and biodiversity restoration practices to protect their existing biodiversity. We suggest a strategy that integrates four fundamental pillars for producing food in a sustainable way, recognizing biodiversity and local cultural heritage: 1) Share the land, restore and protect; 2) Ecological intensification; 3) Localized knowledge, research and technological development; and 4) Territorial planning and implementation of socio-agroecological policies. We suggest that this approach does not need greater modification of native pollination services that sustain the world with food and basic subsistence goods, but a paradigm change where the interdependency of nature and human wellbeing are recognized for ensuring the present and future of the world’s food security and sovereignty as well as considering the reduction of consumerism and food waste.
HYPOTHESIS | doi:10.20944/preprints202010.0004.v8
Subject: Biology, Anatomy & Morphology Keywords: carbon-based entity; driving force; energy; evolution; fitness; mechanism; natural selection; speciation; thermodynamics; theory
Online: 10 May 2021 (10:21:15 CEST)
The current evolutionary theories have remained incomplete, controversial, and stagnant for multiple decades. To solve this issue, we create the concept of carbon-based entities (CBEs) which include methane, amino acids, proteins, organisms, and other entities containing carbon atoms. We deduce from thermodynamics the driving force, the progressive mechanisms, and the major steps of evolution of CBEs, and hence establish a comprehensive evolutionary theory termed the CBE evolutionary theory (CBEET). The CBEET demonstrates 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, evolution tempos, animal group evolution, and human society development in a comprehensive and comprehensible way. It elucidates that collaboration, altruism, obeying rules with properly increased freedom are important throughout evolution of CBEs. It refutes thoroughly the wrong 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.
Fri, 7 May 2021
REVIEW | doi:10.20944/preprints202105.0131.v1
Subject: Biology, Anatomy & Morphology Keywords: rhizobia; legume; rhizobium-legume symbiosis; exopolysaccharide synthesis; quorum sensing (QS); nodulation; nod regulon; flavonoids; RosR/MucR; SyrM
Online: 7 May 2021 (09:29:45 CEST)
Abstract: Rhizobia are soil proteobacteria able to engage in a nitrogen-fixing symbiotic interaction with legumes which involves root rhizobial infection and bacterial invasion of new organs formed by the plant in response to the presence of appropriate bacterial partners. This interaction relies on a complex molecular dialogue between both symbionts. Bacterial N-acetyl-glucosamine oligomers called Nod factors are indispensable in most cases for early steps of the symbiotic interaction. In addition, different rhizobial surface polysaccharides, such as exopolysaccharides (EPS), may also be symbiotically relevant. EPS are acidic polysaccharides located out of the cell with little or no cell association that carry out important roles both in free-life and in symbiosis. EPS production is very complexly modulated and, frequently, co-regulated with that of Nod factors, but the type of co-regulation varies depending on the rhizobial strain. Many studies point out a signalling role of EPS-derived oligosaccharides in root infection and nodule invasion but, in certain symbiotic couples, EPS can be dispensable for a successful interaction. In summary, the complex regulation of the production of rhizobial EPS varies in different rhizobia and the relevance of this polysaccharide in symbiosis with legumes depends on the specific interacting couple.