ARTICLE | doi:10.20944/preprints202009.0758.v1
Subject: Life Sciences, Biochemistry Keywords: Enterococcus faecalis; Proteus mirabilis; Polymicrobial; Biofilm; Catheter; Urinary Tract Infection
Online: 30 September 2020 (16:39:51 CEST)
Indwelling urinary catheters are common in healthcare settings and can lead to catheter-associated urinary tract infection (CAUTI). Long-term catheterization causes polymicrobial colonization of the catheter and urine, for which the clinical significance is poorly understood. Through prospective assessment of catheter urine colonization, we identified Enterococcus faecalis and Proteus mirabilis as the most prevalent and persistent co-colonizers. Clinical isolates of both species successfully co-colonized in a murine model of CAUTI, and they were observed to co-localize on catheter biofilms during infection. We further demonstrate that P. mirabilis preferentially adheres to E. faecalis during biofilm formation, and that contact-dependent interactions between E. faecalis and P. mirabilis facilitate establishment of a robust biofilm architecture that enhances antimicrobial resistance for both species. E. faecalis may therefore act as a pioneer species on urinary catheters, establishing an ideal surface for persistent colonization by more traditional pathogens such as P. mirabilis.
REVIEW | doi:10.20944/preprints202009.0754.v1
Subject: Life Sciences, Biochemistry Keywords: human body segments; body dimensions; biomechanical modeling; anthropometry
Online: 30 September 2020 (14:54:14 CEST)
The knowledge of human body proportion and segmental properties of limbs, head and trunk are of fundamental importance in biomechanical research. As many methods are employed, it is important to know which they are currently available, which data on human body masses, lengths, center of mass (COM) location, weights and moment of inertia are available and which methods are most suitable for a specific research purposes. The present review examines the literature concerning human body segments properties for biomechanical purposes. It emerges that data obtained in studies on cadaveric specimens are still the most accurate, whilst technological tools currently available are manifolds, each one with proper advantages and disadvantages. Classical studies were focused mainly on white men, while in recent year the available data of body segments has been extended to children, woman, and other races. Also, data on special population (obese, pregnant women) are starting to appear in the scientific literature.
ARTICLE | doi:10.20944/preprints202009.0740.v1
Subject: Life Sciences, Biochemistry Keywords: balance training; real-time visual feedback; smart wearable devices; center of pressure
Online: 30 September 2020 (11:00:33 CEST)
This study aims to explore the effect of real-time visual feedback (VF) information of the pres-sure of center (COP) provided by intelligent insoles on balance training in a one leg stance (OLS) and tandem stance (TS) posture. Thirty healthy female college students were randomly assigned to the visual feedback balance training group (VFT), non-visual feedback balance training group (NVFT), and control group (CG). The balance training includes: OLS, tandem Stance (dominant leg behind, TSDL), tandem stance (non-dominant leg behind, TSNDL). The training lasted 4 weeks, the training lasts 30 minutes at an interval of 1 days. There was a sig-nificant difference in the interaction effect between Groups*Times of the COP parameters (p<0.05) for OLS. There was no significant difference in the interaction effect between Groups*Times of the COP parameters (p>0.05) for TS. The main effect of the COP parameters was a significant difference in Times (p<0.05). The COP displacement, velocity, radius, and area in VFT significantly decreased after training (p < 0.05). Therefore, the visual feedback technology of intelligent auxiliary equipment during balance training can enhance the benefit of training. The use of smart wearable devices in OLS balance training may improve the visual and physical balance integration ability.
REVIEW | doi:10.20944/preprints202009.0727.v1
Subject: Life Sciences, Biochemistry Keywords: vitamin D; muscle; parathyroid hormone; vitamin D-binding protein
Online: 30 September 2020 (08:11:15 CEST)
Vitamin D, unlike the micronutrients, vitamins A, E and K, is largely obtained, not from food, but by the action of solar UV light on its precursor, 7-dehydrocholesterol, in skin. With the decline in UV light intensity in winter, most skin production of vitamin D occurs in summer. Because no defined storage organ or tissue has been found for vitamin D, it has been assumed that adequate vitamin D status in winter can only be maintained by oral supplementation. Skeletal muscle cells have now been shown to incorporate the vitamin D-binding protein (DBP) from blood into the cell cytoplasm where it binds to cytoplasmic actin. This intracellular DBP provides an array of specific binding sites for 25-hydroxyvitamin D (25(OH)D) which diffuses into the cell from the extracellular fluid. When intracellular DBP undergoes proteolytic breakdown, the bound 25(OH)D is then released and diffuses back into blood. This uptake and release of 25(OH)D by muscle, accounts for the very long half-life of this metabolite in the circulation. As 25(OH)D concentration in blood declines in winter, its cycling in and out of muscle cells appears to be upregulated. Parathyroid hormone is the most likely factor enhancing the repeated cycling of 25(OH)D between skeletal muscle and blood. This mechanism appears to have evolved to maintain adequate vitamin D status in winter.
CONCEPT PAPER | doi:10.20944/preprints202009.0723.v1
Subject: Life Sciences, Biochemistry Keywords: Glycogen Storage Disease Type 1a, Glucose-6-phosphatase Catalytic Subunit (G6PC), Glucose-6-phosphatase (G6Pase), prime editing, mRNA delivery, CRISPR
Online: 30 September 2020 (08:05:17 CEST)
One of the rare diseases throughout the world is Glycogen Storage Disease, which appears due to problems in glycogen metabolism. Among various subtypes of GSD, GSD Type 1a is the most abundant one of GSD Type 1, seen in approximately 80% and caused by different kinds of mutations in the Glucose-6-Phosphatase Catalytic Subunit (G6PC) gene in human chromosome 17q21. G6PC gene encodes for glucose-6-phosphatase (G6Pase) protein, which cleaves glucose-6-phosphate into glucose and inorganic phosphate (Pi), and GSD Type 1a patients fail to breakdown glucose-6-phosphate due to several mutations in the G6PC gene. In our study, we aim to create new therapeutic approaches for GSD 1a. We collected mutation data of 57 GSD Type 1a patients from Turkey. According to the data, 16 types of mutations were observed in the G6PC gene. Allele frequencies of these mutations are calculated as 59% for R83C/H, 11% for W160*, 7% for G270V, and 28% for others which have less frequency. Up to now, the tertiary protein structure of G6Pase has not been structured yet. To understand the possible impacts of these mutations, we statistically obtained possible tertiary structure predictions of G6Pase by running 5 different tools. At the end of the study, we suggest two effective and promising gene therapy methods for GSD Type 1a, Prime Editing for R83C/H mutations, and mRNA delivery for other mutations, in addition to a promising, commercially available drug suggestion for patients with W160*, W86*, and S15* mutations, although the drug belongs to another disease.
Tue, 29 September 2020
REVIEW | doi:10.20944/preprints202009.0709.v1
Subject: Life Sciences, Biochemistry Keywords: Escherichia coli; Clostridium perfringens; broiler; antibiotic-free; production; chicken
Online: 29 September 2020 (12:46:00 CEST)
United States is the largest producer and the second largest exporter of broiler meat in the world. In the U.S, broiler production is largely converting to antibiotic-free programs which has caused an increase in morbidity and mortality within broiler farms. Escherichia coli and Clostridium perfringens are two important pathogenic bacteria readily found in the broiler environment and result in annual billion-dollar losses from colibacillosis, gangrenous dermatitis, and necrotic enteritis. Broiler industry is in search of non-antibiotic alternatives including novel vaccines, prebiotics, probiotics, and housing management strategies to mitigate production losses due to these diseases. This review provides an overview of the broiler industry and antibiotic free production, current challenges, and emerging research on antibiotic alternatives to reduce pathogenic microbial presence and improve bird health.
ARTICLE | doi:10.20944/preprints202009.0707.v1
Subject: Life Sciences, Biochemistry Keywords: antimicrobial alternatives; fermented defatted ‘alperujo’; intestinal health; olive oil by-products; Salmonella Typhimurium.
Online: 29 September 2020 (10:47:47 CEST)
Salmonella spp. contaminates egg and poultry meat leading to foodborne infections in humans. The emergence of antimicrobial-resistant strains limit the use of antimicrobials. We aimed to determine the effects of the food supplement, fermented defatted ‘alperujo’, a modified olive-oil by-product, on Salmonella Typhimurium colonisation in broilers. One hundred and twenty 1-day-old broilers were divided into four experimental groups: 2 control groups and 2 treated groups, and challenged with S. Typhimurium at day 7 or 21. On days 7, 14, 21, 28, 35 and 42 of life, duodenum and caecum tissue samples were collected for histopathological and histomorphometric studies. Additionally, cecum content was collected for Salmonella spp. detection by culture and qPCR, and for metagenomic analysis. Our results showed a significant reduction of Salmonella spp. in the cecum of 42-day-old broilers, suggesting that fermented defatted ‘alperujo’ stimulates Salmonella Typhimurium clearance in that cecum and may contribute to diminishing the risk of carcass contamination at the time of slaughter. Additionally, the improvement of the mucosal integrity suggests that enhancing intestinal health helps to limit Salmonella spp. colonisation in the host, mitigating production losses. These results could provide evidence that FDA would contribute to prophylactic and therapeutic measures to reduce salmonellosis prevalence in poultry farms.
COMMUNICATION | doi:10.20944/preprints202009.0702.v1
Subject: Life Sciences, Biochemistry Keywords: SARS-CoV-2; influenza vaccine; systematic review; infection; severity; risk
Online: 29 September 2020 (09:14:03 CEST)
We reviewed the association between seasonal influenza vaccination and the risk of SARS-CoV-2 infection or complicated illness or poor outcome (e.g. severe disease, need for hospitalization or ventilatory support, or death) among COVID-19 patients. None of the studies that were reviewed (n=12) found a significant increase in the risk of infection or in the illness severity or lethality, while some reported significantly inverse associations. Our findings support measures aimed at raising influenza vaccination coverage in the coming months.
REVIEW | doi:10.20944/preprints202009.0696.v1
Subject: Life Sciences, Biochemistry Keywords: Beauveria bassiana; cuticle degrading enzymes; entomopathogenic fungi; pathogenesis; virulence
Online: 29 September 2020 (08:57:33 CEST)
Intensive crop production and extensive use of harmful synthetic chemical pesticides create numerous socio-economic problems worldwide. Therefore, sustainable solutions are needed for insect pest control, such as biological control agents. The fungal insect pathogen Beauveria bassiana has shown considerable potential as a biological control agent against a broad range of insects. The insights into virulence mechanism of B. bassiana is essential to show the robustness of its use. B. bassiana has several determinants of virulence, including the production of cuticle-degrading enzymes (CDEs), such as proteases, chitinases, and lipases. CDEs are essential in the infection process as they hydrolyze the significant components of the insect's cuticle. Moreover, B. bassiana has evolved effective antioxidant mechanisms that include enzyme families that act as ROS scavengers, e.g., superoxide dismutases, catalases, peroxidases, and thioredoxins. In B. bassiana, the number of CDEs and antioxidant enzymes characterized in recent years. The enzymatic activities are crucial for the biological control potential and significantly advanced our understanding of the infection mechanism of B. bassiana. This review focuses on the progress detailed in the studies of these enzymes and provides an overview of enzymatic activities and their contributions to virulence.
Mon, 28 September 2020
ARTICLE | doi:10.20944/preprints202009.0681.v1
Subject: Life Sciences, Biochemistry Keywords: phosphorus solubilization; plant growth promotion; biofertilizers; sustainable agriculture; phosphorus solubilizing bacteria; rhizobacteria
Online: 28 September 2020 (07:37:59 CEST)
Phosphorus (P) is the second-most important element after nitrogen that is required for plant growth. Although this element is abundant in most soils, it is rarely available in plant-accessible forms since most of it normally exists in soil in insoluble forms such as phosphates. In conventional agriculture, P is normally supplied as chemical fertilizer to satisfy plant P requirements. This, to a large extent, boosts plant production. However, chemical fertilizers are costly, have a huge carbon footprint, and are environmentally-unsustainable owing to the high energy requirements during their synthesis. Besides, P-containing agricultural run-offs contribute hugely to the eutrophication of water bodies and environmental degradation. Moreover, plants can consume only a small amount of chemically-supplied P since between 75 and 90% of this form of P normally get precipitated into complexes and rapidly become fixed in soil. These issues and concerns necessitate research into alternative and viable ways of supplying P to plants. Rhizobacteria have for decades been investigated in vivo and in planta as suitable tools in sustainable agriculture due to the plant-growth-promoting activities such as nutrients’ solubilization, nitrogen fixation, and production of phytohormones. Although a lot of research has been done on different nutrients-solubilizing rhizobacteria and their potential in sustainable agriculture, their mechanisms of action and prospects in sustainable agriculture remain to be fully understood. This review particularly focuses on the P solubilizing rhizobacteria and evaluates their diversity, mechanisms of action, and prospects in sustainable agriculture based on the present and future scenario of their application. Such information is useful in determining their potential and evaluating their prospects in promoting sustainable agricultural systems.
ARTICLE | doi:10.20944/preprints202005.0040.v2
Online: 28 September 2020 (03:19:50 CEST)
To address the expression pattern of the SARS-CoV-2 receptor ACE2 and the viral priming protease, TMPRSS2, in the respiratory tract, this study investigated RNA sequencing transcriptome profiling of samples of airway and oral mucosa. As shown, ACE2 has medium levels of expression in both small airway epithelium and masticatory mucosa, and high levels of expression in nasal epithelium. The expression of ACE2 is low in mucosal associated invariant T (MAIT) cells, and can’t be detected in alveolar macrophages. TMPRSS2 is highly expressed in small airway epithelium and nasal epithelium, and has lower expression in masticatory mucosa. Our results provide the molecular basis that the nasal mucosa is the most susceptible locus in the respiratory tract for SARS-CoV-2 infection and consequently for subsequent droplet transmission and should be the focus for protection against SARS-CoV-2 infection.
Sun, 27 September 2020
ARTICLE | doi:10.20944/preprints202009.0679.v1
Subject: Life Sciences, Biochemistry Keywords: Consciousness Field; cosmic consciousness network; default mode network; EEG; Fara-darmani; Fara-therapist; gamma wave; Mind-body
Online: 27 September 2020 (11:58:42 CEST)
Mind-body interaction and its manifestations at the brain level has been studied extensively in the field of consciousness research. Fara-darmani Consciousness Field, as claimed by Mohammad Ali Taheri (the founder), is a method of connecting with the Cosmic Consciousness Network through human mind and his brain has a detective role in this process. As a result of this connection, the scanning process of the state of a being, e.g., the health status of the cells and consequently organs is performed. This study was conducted to evaluate the effects of the Fara-darmani Consciousness Field connection on electroencephalogram (EEG) features as an important biomarker of the brain functioning. The results showed that there was a significant increase in the gamma2 frequency band (35-40 Hz) power in the frontal lobe in medial frontal gyrus (BA6) and paracentral lobule (BA31) of the brain during the task condition compared to the rest condition in a Fara-therapist population. Considering the cortical electrical activity of Fara-therapist’s brain during Fara-darmani Consciousness Field connection, characterizing increase in the power of gamma wave and the activity of the areas affecting on memory, attention, perception and default mode network intrinsic activity. This manifestation distinguishes Fara-darmani Consciousness Field connection from other known methods dealing with the mind-body interaction criterion mainly different types of mediation.
ARTICLE | doi:10.20944/preprints202009.0665.v1
Subject: Life Sciences, Biochemistry Keywords: fencing kinematics; lunge velocity; technique development
Online: 27 September 2020 (05:04:27 CEST)
The teaching of the lunge technique in fencing is critical in the developmental age. The relations of anthropometrics with kinematics of lunge was studied only in adult fencers, and no study exist in young considering the different level of experience. Our aims were to assess, in young fencers, which factors, between the anthropometric and the kinematics, were mostly connected with lunge performance (speed and excursion) in different genders and expertise levels. Fifteen young fencers participated in this study. Lunge kinematics, anthropometric characteristics and force expressed in vertical jump tests were collected. Maximal lunge velocity resulted mainly correlated with the posterior knee’s extension ((r=0.56, p=0.031). The lunge distance and mean hip velocity were mostly correlated with fencers’ height (r=0.85, p=0.000 and r=0.76, p=0.001) and FFM (r=0.8, p=0.000 and r=0.73, p=0.002). Experts and non-experts show significant differences in fat free mass, area of upper arm, and of thighs (Effect Size = 1,27 – 1,33, p= 0,021-0,035). From our results it emerges that, in this age range, the analysed aspects of lunge performance are mainly correlated with participant’s anthropometry. Moreover, it is already possible in this age span, to find technical differences linked to the experience.
ARTICLE | doi:10.20944/preprints202009.0663.v1
Subject: Life Sciences, Biochemistry Keywords: ORFV; PCR; Sanger method; B2L gene; Phylogenetic analysis
Online: 27 September 2020 (04:58:03 CEST)
Aim: Despite the endemic nature of contagious ecthyma in Nigeria, there is limited report on the molecular characterization of the isolates responsible for disease outbreaks. The aim of this study was to molecularly characterize ORFV isolated from clinical infections in goats in Sokoto metropolis. Materials and Methods: Seronegative embryonated chicken eggs were used to isolate ORFV via the chorio allantoic membrane (CAM) route according to the established protocol. Viral DNA was extracted from infected CAM and the full coding region of B2L gene was amplified by PCR and subsequently sequenced by Sanger’s method. The nucleotide sequence results were blasted for identification and phylogenetically analyzed using MEGA and Bioedit softwares. Results and Discussion: The results showed that B2L gene sequences of the ORFV UDUS/01/19/More strain showed slight variability (96- 98.7%) with the reference sequences. Our isolate clustered within the same clade with Korean strain signifying a close genetic relationship. Unique amino acid substitutions were noted in our isolate when compared with other references. This is arguably the first genetic characterisation of B2L gene of ORFV circulating in Nigeria. Conclusion: Our study has provided in sight into the genetic diversity of ORFV in the study area. This is crucial for the design of effective vaccines against the disease which are currently lacking in the country.
BRIEF REPORT | doi:10.20944/preprints202009.0655.v1
Subject: Life Sciences, Biochemistry Keywords: urinary tract infections; multi-drug resistance; biofilm; virulence genes; WGS
Online: 27 September 2020 (02:40:41 CEST)
Background: Extraintestinal pathogenic Escherichia coli (ExPEC) is the most common cause of urinary tract infections (UTIs). They are often multidrug-resistant (MDR), making them challenging to treat. Additionally, virulence mechanisms as biofilm formation are associated with persistent UTIs. Aims: To reveal a possible association between patients’ risk factors and UTIs caused by MDR or biofilm-forming ExPECs and characterize ExPECs causing asymptomatic bacteriuria, community- (CA), or hospital-acquired (HA) UTIs in hospitalized patients in Brazil. Methods: Bacterial DNA was extracted from the urine of 63 hospitalized patients and sequenced using short-read sequencing. Antibiotic susceptibility was evaluated using VITEK-2, and the biofilm-forming, adhesion, and invasion abilities were quantitatively assessed. Results: Antibiotic resistance rates were high, and the majority of UTIs were complicated CA-UTIs. Most MDR- and ESBL-producing E. coli isolates belonged to high-risk lineages and were associated with UTIs in patients with comorbidities and over 60 years of age. The mortality rate of patients infected with MDR-isolates was higher than of those infected with non-MDR isolates. Most isolates were biofilm-forming, but no association with patients’ risk factors was found. Conclusions: Complicated UTIs caused by MDR- and biofilm-forming bacteria are frequently found in hospitalized patients in Brazil suffering from a UTI and are associated with high-risk lineages.
Sat, 26 September 2020
ARTICLE | doi:10.20944/preprints202009.0653.v1
Subject: Life Sciences, Biochemistry Keywords: ionizing radiation; radiation resistance; genetic mechanisms; microorganisms
Online: 26 September 2020 (17:24:56 CEST)
Nuclear pollution is an urgent environmental issue as a consequence of rapid industrialization and nuclear accidents in the past. Remediation of nuclear polluted sites using microbial vital activity (bioremediation) is a promising approach to recover contaminated areas in an environmentally friendly and cost-saving way. At the same time, the number of known bacterial and archaeal species able to withstand extremely high doses of ionizing radiation is steadily growing every year, together with growing knowledge about mechanisms of radioresistance. This opens up new opportunities for developing new biotechnological solutions. However, these data are often not systemized and it can be difficult to access. Here, we present the Determinants of Radioresistance Database, or DetR DB (http://extremebiolab.com/detr-db/), gathering a comprehensive catalog of radioresistant microbes and their molecular and genetic determinants of enhanced ionizing radiation tolerance. The database provides search tools including taxonomy, common gene name, and BLAST. DetR DB will be a useful tool for research community by facilitating the extraction of the necessary information to help further analysis of radiation-resistant mechanisms.
REVIEW | doi:10.20944/preprints202009.0650.v1
Subject: Life Sciences, Biochemistry Keywords: biofertilizers; sustainable agriculture; plant growth-promoting rhizobacteria; microbial formulations
Online: 26 September 2020 (16:48:22 CEST)
The world’s population is increasing and so are agricultural activities to match the growing demand for food. Conventional agricultural practices generally employ artificial fertilizers to increase crop yields, but these have multiple environmental and human health effects. For decades, environmentalists and sustainability researchers have focused on alternative crop fertilization mechanisms to address these challenges, and biofertilizers have constantly been researched, recommended, and even successfully-adopted for several crops. Biofertilizers are microbial formulations made of indigenous plant growth-promoting rhizobacteria (PGPR) which can naturally improve plant growth either directly or indirectly, through the production of phytohormones, solubilization of soil nutrients, and production of iron-binding metabolites; siderophores. Biofertilizers, therefore, hold immense potential as tools for sustainable crop production especially in the wake of climate change and global warming. Despite the mounting interest in this technology, their full potential has not yet been realized. This review updates our understanding of the PGPR biofertilizers and sustainable crop production. It evaluates the history of these microbial products, assesses their present state of utilization, and also critically propounds on their future prospects for sustainable crop production. Such information is desirable to fully evaluate their potential and can ultimately pave the way for their increased adoption for crop production.
ARTICLE | doi:10.20944/preprints202009.0648.v1
Subject: Life Sciences, Biochemistry Keywords: sustainable development; systemic sustainable transport development; systemic development
Online: 26 September 2020 (16:23:05 CEST)
The concept of sustainability and sustainable development, especially systemic sustainable development, still raises controversy in literature. The article makes an attempt to re-examine these concepts from a systems perspective, seeking foundations and applications in the selected sector. It is becoming increasingly clear that sustainability and sustainable development are aimed at integrated economic, social, cultural, political, and ecological factors [1[, (pp.641-642). This causes that the constructive approach to the issue is required, taking into account all the actors, areas and dimensions involved in the pursuit of systemic sustainable development. As a result, both local and global dimensions and the way they interact must be explored in a multi-faceted manner in order to offer a perspective more useful than other analytical approaches, because the systems view is a way of thinking in terms of connectedness, relationships, and context . The article aims to review selected publications and studies so as to form the general idea of systemic sustainable development and define the systemic development of sustainable transport, including in particular the perspective of the actors of the sector, transport providers (passenger, urban) and transport development program, implemented both by local governments and on the European scale. An attempt was made to identify elements of the systemic sustainable development model, setting it in the reality of the following subcategories: “Society”, “Economy” and “Environment” in sectoral terms. It is supposed that, systemic sustainable development is a conglomerate of public administration entities, companies operating in the sector, individual and corporate customers, acting in certain conditions for economic, social and environmental well-being, and a number of their initiatives of major or minor significance, grouped in six sub-areas, undertaken to achieve systemic value in the examined sector, with a positive or negative business/economic, social and environmental impact.
ARTICLE | doi:10.20944/preprints202009.0642.v1
Subject: Life Sciences, Biochemistry Keywords: copper; mercury; cadmium; oxidative stress; protein carbonylation; translation factors; oxidative stress biomarkers
Online: 26 September 2020 (14:46:39 CEST)
The impact of metals bioaccumulation on marine organisms is under investigation. This study was designed to determine the association of oxidative stress in mussels Mytilus galloprovincialis induced by seawater enriched with trace metals with protein synthesis. Mussels were exposed to 40 μg/L Cu, 30 μg/L Hg, or 100 μg/L Cd for 5 and 15 days, and the pollution effect was evaluated by measuring established oxidative biomarkers. The results showed damage on the protein synthesis machine integrity and specifically, on translation factors and ribosomal proteins expression and modifications. Exposure of mussels to all metals caused oxidative damage that was milder in the cases of Cu and Hg, and more pronounced for Cd. However, after prolonged exposure of mussels to Cd (15 days), the effects receded. These changes that perturb protein biosynthesis can serve as a great tool for elucidating the mechanisms of toxicity and could be integrated in biomonitoring programs.
ARTICLE | doi:10.20944/preprints202009.0637.v1
Online: 26 September 2020 (13:44:40 CEST)
Malassezia is lipid-dependent commensal yeast of the human skin. The different culture media and skin sampling methods used to grow these fastidious yeasts are a source of heterogeneity in culture-based epidemiological study results. This study aimed to compare the performances of three methods of skin sampling, and two culture media for the detection of Malassezia yeasts by culture from the human skin. Three skin sampling methods, namely sterile gauze, dry swab and TranswabTM with transport medium, were applied on 10 healthy volunteers. Each sample was further inoculated onto either the novel FastFung medium or the reference Dixon agar for the detection of Malassezia spp. by culture. At least one colony of Malassezia spp. grew on 93/300 (31%) of the cultures, corresponding to 150 samplings. The positive culture rate was 67%, 18%, and 15% (P < 10-3), for samples collected with sterile gauze, TranswabTM, and dry swab, respectively. The positive culture rate was 62% and 38% (P < 0.003) by using the FastFung and the Dixon media, respectively. Our results showed that sterile gauze rubbing skin sampling followed by inoculation on FastFung medium should be implemented in the routine clinical laboratory procedure for Malassezia spp. cultivation.
ARTICLE | doi:10.20944/preprints202009.0634.v1
Subject: Life Sciences, Biochemistry Keywords: compound 3K; ovarian cancer; pyruvate kinase M2; autophagy; apoptosis
Online: 26 September 2020 (13:34:05 CEST)
Ovarian cancer is the common cause of death among gynecological cancers. Although ovarian cancer initially responds to chemotherapy, the frequent recurrence in patients remains a therapeutic challenge. Pyruvate kinase M2 (PKM2) plays a pivotal role in regulating cancer cell survival. However, its therapeutic roles remain unclear. Here, we investigated the anticancer effects of compound 3K, a specific PKM2 inhibitor, on autophagic and apoptotic pathway regulation in SK-OV-3 (PKM2-overexpressing human ovarian adenocarcinoma cell line). The anticancer effect of compound 3K was examined using the MTT and colony formation assay in SK-OV-3. The results of tissue microarray showed that PKM2 expression positively correlated with the severity of the tumor. Moreover, the expression of pro-apoptotic proteins increased in SK-OV-3 following compound 3K treatment. Compound 3K induced AMPK activation, which was accompanied by the inhibition of mTOR. Additionally, this compound inhibited glycolysis, resulting in reduced proliferation in SK-OV-3. Compound 3K treatment suppressed tumor progression in vivo xenograft model. Our findings suggest that the inhibition of PKM2 by compound 3K affected Warburg effects and induced autophagic cell death. Therefore, the use of specific PKM2 inhibitors to block the glycolytic pathway and target cancer cell metabolism represents a promising therapeutic approach for treating PKM2-overexpressing ovarian cancer.
ARTICLE | doi:10.20944/preprints202009.0631.v1
Subject: Life Sciences, Biochemistry Keywords: COVID-19; SARS-CoV-2; In silico; Immunoinformatics; Vaccine designing
Online: 26 September 2020 (13:01:26 CEST)
As the number of infections and deaths caused by the recent COVID-19 pandemic is increasing dramatically day-by-day, scientists are rushing towards developing possible counter-measures to fight the deadly virus, SARS-CoV-2. Although many efforts have already been put forward for designing and developing potential vaccines, however, most of them are proved to possess negative consequences. Therefore, in this study, the methods of immunoinformatics were exploited to design novel epitope-based subunit vaccine against the SARS-CoV-2, targeting four essential proteins of the virus i.e., spike glycoprotein, nucleocapsid phosphoprotein, membrane glycoprotein, and envelope protein. The highly antigenic, non-allergenic, non-toxic, non-human homolog and 100% conserved (across other isolates from different regions of the world) epitopes were used for constructing the vaccine. In total, fourteen CTL epitopes and eighteen HTL epitopes were used to construct the vaccine. Thereafter, several in silico validations i.e., the molecular docking, molecular dynamics simulation (including the RMSF and RMSD studies), and immune simulation studies were also performed which predicted that the designed vaccine should be quite safe, effective, and stable within the biological environment. Finally, in silico cloning and codon adaptation studies were also conducted to design an effective mass production strategy of the vaccine. However, more in vivo and in vitro studies are required on the predicted vaccine to finally validate its safety and efficacy.
Subject: Life Sciences, Biochemistry Keywords: DNA methylation; epialleles; epiRILs; epigenetics; Epigenome-Wide Association Studies.
Online: 26 September 2020 (08:08:27 CEST)
Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Further, the development of epigenetic recombinant inbred lines (epi-RILs) in the model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can facilitate epigenetic based molecular breeding of important crop plants.
Fri, 25 September 2020
REVIEW | doi:10.20944/preprints202009.0604.v1
Subject: Life Sciences, Biochemistry Keywords: Nucleus; Nuclear envelope; Lamins; Genome organization; Chromatin; Gene expression
Online: 25 September 2020 (11:03:59 CEST)
Nuclear lamins are type V intermediate filament proteins that form a filamentous meshwork beneath the inner nuclear membrane. Additionally, a sub-population of A-type and B-type lamins is localized in the nuclear interior. The nuclear lamina protects the nucleus from mechanical stress and mediates nucleo-cytoskeletal coupling. Lamins form a scaffold that partially tethers chromatin at the nuclear envelope. The nuclear lamina also stabilizes protein-protein interactions involved in gene regulation and DNA repair. The lamin-based protein sub-complexes are implicated in both nuclear and cytoskeletal organization, the mechanical stability of the nucleus, genome organization, transcriptional regulation, genome stability, and cellular differentiation. Here we review recent research in the field of nuclear lamins and their role in modulating various nuclear processes and their impact on cell function.
REVIEW | doi:10.20944/preprints202008.0379.v2
Subject: Life Sciences, Other Keywords: hormone; quorum sensing; receptor; bacteria; fungi; metazoa; plants; microbiota; evolution
Online: 25 September 2020 (10:40:10 CEST)
Cellular communications play pivotal roles in multi-cellular species, but they do so also in uni-cellular species. Moreover, cells communicate with each other not only within the same individual but also with cells in other individuals belonging to the same or other species. These communications occur between two unicellular species, two multicellular species, or between unicellular and multicellular species. The molecular mechanisms involved exhibit diversity and specificity, but they share common basic features which allow common pathways of communication between different, and sometimes very different species. These interactions have been made possible by the high degree of conservation of the basic molecular mechanisms of interaction of many ligand-receptor pairs in evolutionary remote species. These inter-species cellular communications played crucial roles during Evolution and must have been positively selected, particularly when collectively beneficial in hostile environments. We think that communications between cells did not arise after their emergence but was part of the very nature of first cells. Synchronization of populations of non-living protocells through chemical communications may have been a mandatory step towards their emergence as populations of living cells and explain the large commonality of cell communication mechanisms among microorganisms, plants, and animals.
Thu, 24 September 2020
ARTICLE | doi:10.20944/preprints202009.0585.v1
Subject: Life Sciences, Biochemistry Keywords: Geobaccilus thermoleovorans IT-08; β-D-xylosidase; GbtXyl43A; kinetic characteristics
Online: 24 September 2020 (14:15:50 CEST)
GbtXyl43A, a β-xylosidase that is isolated from Geobacillus thermoleovorans IT-08 and grouped in GH43 family. The substitution of 121Asp residue with Asn in GbtXyl43A caused decrease the enzyme activity. The aim of this study, determine the kinetic characteristics of wild-type GbtXyl43A and D121N variant using Vmax, KM, kcat, and kcat/KM. These parameters indicated catalytic mechanism of GbtXyl43A and its derivative. All of them were produced in Escherichia coli BL21 star. The purification of wild-type GbtXyl43A using affinity chromatography, but D121N variant also required anion-exchange chromatography. The specific activity of wild-type GbtXyl43A and D121N variant were 0.471 U mg-1 in purity level 55,44 and 0.012 U mg-1 in purity level 2,407, respectively. Both enzymes had same molecular weight, ~58 kDa. The kinetic parameters of wild-type GbtXyl43A were KM: 2.845 mM, kcat: 0.033 s-1, Vmax: 0.0033 mM min-1and kcat/KM: 0.0115 s-1mM-1. Furthermore, the KM, kcat, Vmax, and kcat/KM values of D121N variant were 4.565 mM, 1.01 × 10-4 mM min-1, 0.140 × 10-4 s-1, and 0.0307 s-1mM-1, respectively. The KM value of the D121N variant was higher than its wild type and showed the affinity of D121N variant was lower than GbtXyl43A
ARTICLE | doi:10.20944/preprints202009.0584.v1
Subject: Life Sciences, Microbiology Keywords: fungal community; gut mycobiota; diversity; ITS metabarcoding; intestinal parasites; children; Mali
Online: 24 September 2020 (12:24:53 CEST)
Eukaryotic enteric pathogens (EEP) are a public health issue in tropical areas. Yet, their interactions with the gut mycobiota remain poorly understood. We conducted a cross-sectional study in Malian children to analyze the impact of EEP on the gut fungal community. EEP were assessed by qPCR and the gut mycobiota was characterized by ITS1-2 metabarcoding in stool samples collected from 296 children. The 100 controls, in whom no EEP was detected, were compared to: a) 196 children with ≥1 EEP; b) 91 with only Blastocystis; c) 35 with only Giardia intestinalis; and d) 12 with another (<1% each) EPP. The gut fungal community structure was homogenous in each children’s group. Linear size-effect discriminant analysis highlighted five relatively more abundant species, including Fusarium longipes and Penicillium caseifulvum, in children with ≥1 EEP, whereas 28, including Aspergillus sydowii and Microdochium colombiense were more abundant in controls. Fusarium, Pyxidiophora, and Stereum abundance was higher in Blastocystis-infected children, whereas Ogataea and Allocryptovalsa were more abundant in controls. Sordariales and Mortierellales abundance was higher in Giardia intestinalis-infected children, whereas Agaricales and Capnodiales abundance was higher in controls. In conclusion, EEP do not significantly alter the gut fungal community structure, and further studies are warranted to confirm our findings that particular taxa are associated with susceptibility or resistance to specific EEP.
Subject: Life Sciences, Molecular Biology Keywords: COVID-19; SARS-CoV-2; RT-PCR; control strategy; Morocco
Online: 24 September 2020 (10:45:21 CEST)
Since March 2nd, 2020, date of the first SARS-COV-2 detected case in Morocco; multiples activities were adopted as COVID-19 control strategies. If the first period of COVID-19 noticed a few numbers of cases and deaths, the second half from July until today is marked with an exponential increase of the number of cases and a spread in almost all provinces with more intensive care needs and more deaths. The fatality rate of this disease is mainly compared with the highest developed countries in Europe and America. Instead of comparing the strategy and the deaths, with similar Arabic, African or Asiatic Middle-Income countries like Tunisia, Jordan, Cote d’Ivoire, Uzbekistan; that socio-demographic situation, behaviours, population density, and individual vulnerabilities create less confounding factors to make fair comparisons. Thus, this report has the aim to present how the COVID-19 pandemic was dealt in Morocco during this 200 days, by highlighting some discrepancies with corrective advice to get better future control results against COVID-19 and afford a possible comparison with other countries.The policy analysis approach was followed as a method to defines the pitfalls themes and to compare with the updated available international information about was it work and what is not needed to do. In conclusion, molecular biology represented by q-RT-PCR is the immediate action to do to enhance the diagnostic and the overall control strategy by knowing how to interpret its results following the time progress of cycle quantification values.
REVIEW | doi:10.20944/preprints202009.0565.v1
Subject: Life Sciences, Virology Keywords: Coronavirus; SARS-CoV-2; COVID-19; Immunobiochemical aspects; pathogenesis; diagnosis; management
Online: 24 September 2020 (04:39:38 CEST)
Background: A new coronavirus (SARS-CoV-2) that emerged from Wuhan, Hubei Province, China, has spread throughout the world and is declared a pandemic by the World Health Organization (WHO). A lot remains to be understood of SARS-CoV-2 and the disease (COVID-19). SARS-CoV-2 has until recently been identified as responsible for both asymptomatic and serious life-threatening infections. The unavailability of specific therapeutic agents is a major hurdle in the treatment and management of COVID-19 patients. The present review attempts to evaluate the immunobiochemical aspects of the pathogenesis, diagnosis, and management of SARS-CoV-2 infection. Main Body: This review is a comprehensive evaluation of the data collected through various sources, including Google Scholar, PubMed, and Scopus. The articles were searched and selected using key words such as “Coronavirus disease (COVID-19)”, “Diagnosis of COVID-19”, Pathogenesis of Covid-19”, “management of COVID-19”, “Immunology of COVID-19”, and “Complications of COVID-19”. The study noted that the novel Coronavirus infection could result in an exaggerated immune response, causing a cytokine storm and damaging several organs of the body. The infected patients develop several complications, including immunological, hematological, and biochemical alterations. Consequently, COVID-19 patients may develop cardiovascular, liver, renal, and neurological complications, among others. Conclusion: An increased understanding of the immunobiochemical aspects of the disease may contribute to better management of SARS-CoV-2-infected persons, as evidenced from the available literature. A holistic approach to the management of COVID-19 patients taking into consideration the effect of COVID-19 infection on various organs of the body assumes increased significance in patient management.
ARTICLE | doi:10.20944/preprints202009.0564.v1
Subject: Life Sciences, Other Keywords: air pollution; skin; nutraceutical; natural compound; polyphenols; antioxidant; skin barrier; anti-agein; clinical trial
Online: 24 September 2020 (04:38:10 CEST)
Repeated air pollution exposure is one of the major threats to skin health. Air pollution causes skin damage and accelerates skin ageing mainly through oxidative stress mechanisms. Since it is difficult to minimize skin exposure from air pollutants, especially in urban areas, strategies to protect the skin are needed. On the other hand, plant phenolic compounds have been found to be effective in attenuating cellular oxidative stress and inflammation induced by different air pollutants. Therefore, we conducted a 12-week randomized, placebo-controlled, double blind study to assess the efficacy of a polyphenol-enriched dietary supplement (comprised of olive leaf, lemon verbena, rosemary and Sophora japonica extracts) in reducing pollution-induced oxidative stress and in improving different skin parameters related to skin ageing of Caucasian and Asian volunteers living in a polluted urban European area (Milan). One hundred healthy women were recruited and randomized in the placebo or in the test dietary supplement treatment arms. To assess the efficacy of the dietary supplement, the total antioxidant capacity on saliva (FRAP) was determined, as well as the oxidative damage on skin (lipoperoxides content), the skin moisture (corneometry), the trans-epidermal water loss (Tewameter), the skin radiance and the skin colour, (spectrophotometry), the skin elasticity (cutometry), the skin sebum content (sebumeter), and the skin roughness (image analysis). As a result, both inter-group and intra-group analysis proved that the dietary supplement improved all clinical and biochemical monitored parameters, in both Caucasian and Asian individuals. In conclusion, the results of the study indicate a reduced oxidative stress-induced skin damage in both Asian and Caucasian women living in a polluted urban area.
ARTICLE | doi:10.20944/preprints202009.0563.v1
Subject: Life Sciences, Other Keywords: plant development rate; temperature-dependent; landscape; multi-location trials
Online: 24 September 2020 (04:33:34 CEST)
Understanding the detailed timing of crop phenology and their variability enhances grain yield and quality by providing precise scheduling of irrigation, fertilization, and crop protection mechanisms. Advances in information and communication technology (ICT) provide a unique opportunity to develop agriculture-related tools that enhance wall-to-wall upscaling of data outputs from point-location data to wide-area spatial scales. Because of the heterogeneity of the worldwide agro-ecological zones where crops are cultivated, it is unproductive to perform plant phenology research without providing means to upscale results to landscape-level while safeguarding field-scale relevance. This paper presents an advanced, reproducible, and open-source software for plant phenology prediction and mapping (PPMaP) that inputs data obtained from multi-location field experiments to derive models for any crop variety. This information can then be applied consecutively at a localized grid within a spatial framework to produce plant phenology predictions at the landscape level. This software supports the development of process-oriented and temperature-driven plant phenology models by intuitively and interactively leading the user through a step-by-step progression to the production of spatial maps for any region of interest. Maize (Zea mays L.) was used to demonstrate the robustness, versatility, and high computing efficiency of the resulting modeling outputs of the PPMaP. The framework is implemented in R, providing a flexible and easy‐to‐use GUI interface. Since this allows appropriate scaling to the larger spatial domain, the software can effectively be used to determine the spatially explicit length of growing period (LGP) of any variety.
ARTICLE | doi:10.20944/preprints202009.0559.v1
Subject: Life Sciences, Virology Keywords: porcine astroviruses; linear antigenic epitopes; recombination; glycosylation; whole genome sequences; East Africa
Online: 24 September 2020 (03:26:44 CEST)
Astroviruses (AstVs) are occurs globally and are common causes of gastroenteritis in human and animals. The genetic diversity and epidemiology of AstVs in Africa is not well known, hence, we aimed to genetically characterize astroviruses in asymptomatic smallholder piglets in East Africa. Twenty-four samples randomly selected from 446 piglets (<6 months old), initially collected for rotavirus study, was sequenced for metagenomic analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of 7 strains with complete (or near complete) genome revealed variable nucleotide and amino acid sequence identities with known PoAstV strains. The U083 and K321 strains had nucleotide sequence similarities ranging from 66.4 to 75.4 % to the known PoAstV2 strains, nucleotide sequence similarity of U460 strain with known PoAstV3 ranged 57.0 to 65.1 % to the, while K062, K366, K451, and K456 strains showed nucleotide sequence similarities of 63.5 to 80 % to the known PoAstV4 strains. The low sequence identities (<90 %) indicate that novel genotypes of PoAstVs are circulating in the study area. Multiple recombination events were detected in our PoAstV4 strains, indicating that the genetic diversity observed in these strains may be due to recombination. Importantly, we identified potential candidate epitopes with conserved peptides in our PoAstV strains that could aid in the design of immune diagnosis tools and subunit vaccines. Our data provide new intuitions into the genetic structure of porcine astroviruses in East African.
Wed, 23 September 2020
REVIEW | doi:10.20944/preprints202009.0548.v1
Subject: Life Sciences, Biotechnology Keywords: genome-scale metabolic model; microbial community; optimization; design; engineering; computational methods; synthetic microbial consortia
Online: 23 September 2020 (09:52:17 CEST)
Microbes do not live in isolation but in microbial communities. The relevance of microbial communities is increasing due to the awareness about their biotechnological influences in a huge number of environmental, health and industrial processes. Hence, being able to control and engineer the output of both natural and synthetic communities would be of great interest. However, most of the available methods and biotechnological applications (both in vivo and in silico) have been developed in the context of isolated microbes. In vivo microbial consortia development, i.e. to reproduce the community life conditions in the wet-lab, is extremely difficult and expensive requiring of computational approaches to advance knowledge about microbial communities, mainly with descriptive modelling, and further with engineering modelling. In this review we provide a detailed compilation of available examples of engineered microbial communities as a launch pad for an exhaustive and historical revision of those computational methods devoted so far toward the better understanding, and rational engineering of natural and synthetic microbial communities.
REVIEW | doi:10.20944/preprints202009.0547.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: cardiovascular disease; ischemic disease; therapeutic angiogenesis; endothelial colony forming cells; signaling pathways; genetic modification; pharmacological conditioning
Online: 23 September 2020 (09:42:46 CEST)
Cardiovascular disease (CVD) comprises a group of heart and circulatory disorders, which are regarded as a global medical issue with high prevalence and mortality rates. Currently, vascular regenerative surgery represents the most employed therapeutic option to treat ischemic disorders, even though not all the patients are amenable to surgical revascularization. Therefore, more efficient therapeutic approaches are urgently required to promote neovascularization. Therapeutic angiogenesis represents an emerging strategy that aims at reconstructing the damaged vascular network by stimulating local angiogenesis and/or promoting de novo blood vessel formation according to a process known as vasculogenesis. Circulating endothelial colony forming cells (ECFCs), in turn, represent truly endothelial precursors able to aggregate into bidimensional tube networks and to originate patent vessels. Accordingly, ECFCs provide the most rationale and promising cellular candidate for therapeutic purposes. The current review provides a brief outline on the origin and characterization of ECFCs and a summary of the progress in preclinical studies aiming at assessing their efficacy in a variety of ischemic disorders, including AMI, PAD, ischemic brain disease and retinopathy. We also describe how to enhance the vasoreparative potential of ECFCs by boosting specific pro-angiogenic signalling pathways either pharmacologically or through gene manipulation. Taken together, these observations suggest that ECFCs represent a useful strategy to treat ischemic diseases.
ARTICLE | doi:10.20944/preprints202009.0531.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: polystyrene; tissue culture; cell membrane stability
Online: 23 September 2020 (03:46:57 CEST)
Unanticipated errors in scientific research data can be attributed to the unwarranted assumption of uniformity in the polystyrene surface that is ubiquitously used in tissue culture flasks and dishes. We have shown that when adherent cells are subjected to fluid shear force, equivalent to rinsing the culture with a balanced salt solution, cells on some areas of the polystyrene surface will immediately rupture while still adherent on the surface. This heterogeneity on the polystyrene surface can cause unexpected variability in experimental results and in replicating experiments among labs. In this paper a novel quantitative method is described to measure the degree of heterogeneity on the polystyrene surface of tissue culture flasks. The results show significant variation among several brands of tissue culture flasks as well as large variability within the production lot of a manufacturer. The assay method involves loading the cells with a fluorescent marker that is released upon membrane rupture. Cell membrane rupture also causes the loss of marker proteins used in Westernblots. This novel assay method can be used to monitor the batch consistency and the manufacturing process of flasks and dishes. It may also be used to test new biomaterials.
REVIEW | doi:10.20944/preprints202009.0526.v1
Subject: Life Sciences, Virology Keywords: COVID-19 testing; molecular diagnostics; immunological testing; RT-qPCR; ELISA; pool PCR; lateral flow assay; rapid assay
Online: 23 September 2020 (03:33:12 CEST)
Accurate diagnosis at an early stage of infection is essential for the successful management of any contagious disease. The COVID-19, caused by the SARS-CoV-2 virus is a pandemic that has affected 214 countries affecting more than 30.8 million people causing 0.957 million deaths as of third week of September, 2020. The primary diagnosis of the infection is done either by the molecular technique of RT-qPCR by detecting portions of the RNA of the viral genome or through immunodiagnostic tests by detecting the viral proteins or the antibodies produced by the host. As the demand for the test increased rapidly many naive manufacturers entered the market with novel kits and more and more laboratories also entered the diagnostic arena making the test result more error-prone. There are serious debates globally and regionally on the sensitivity and specificity of these tests and about the overall accuracy and reliability of the tests for decision making on control strategies. The significance of the test is also complexed by the presence of asymptomatic carriers, re-occurrence of infection in cured patients as well as by the varied incubation periods of the infection and shifting of the viral location in the host tissues. In this paper, we review the techniques available for SARS-CoV-2 diagnosis and probable factors that can reduce the sensitivity and specificity of the different test methods currently in vogue. We also provide a check-list of factors to be taken care to avoid fallacious practices to reduce false positive and false negative results by the clinical laboratories
Tue, 22 September 2020
REVIEW | doi:10.20944/preprints202009.0198.v2
Subject: Life Sciences, Virology Keywords: coronavirus; aquatic organisms; fish; marine mammals; frogs; birds
Online: 22 September 2020 (11:45:01 CEST)
Coronaviruses are pathogens recognized for having an animal origin, commonly associated with terrestrial environments. However, although in a few cases, there are reports of their presence in aquatic organisms like fish, frogs, waterfowls and marine mammals. None of these cases has led to human health effects when contact with these infected organisms has taken place, whether they are alive or dead. Aquatic birds seem to be the main group carrying and circulating these types of viruses among healthy bird populations. Although the route of infection for CoVID-19 by water or aquatic organisms has not yet been observed in the wild, the relevance of its study is highlighted because there are cases of other viral infections known to have been transferred to humans by aquatic biota. It is encouraging to know that aquatic species, such as fish, marine mammals, and amphibians, shows very few cases of coronaviruses and that some other aquatic animals may also be a possible source of cure or treatment against then, as some evidence with algae and marine sponges suggest.
Subject: Life Sciences, Microbiology Keywords: Quorum sensing; Quorum quenching; AHL molecules; 16S rRNA
Online: 22 September 2020 (09:43:55 CEST)
N-Acyl-homoserine lactones, the Quorum sensing signaling molecules predominantly found in gram-negative bacteria, which regulate several bacterial genes including virulence and antibiotic resistant genes. The study was aimed to identify and characterize QS and QQ bacteria from different samples. 5 samples with different ecological background were collected from soil and 10 samples from hospital setup. 31 different bacteria were isolated with either QS or QQ activities all together. CV026 and A136 biosensor strains were used for the detection of QS and QQ positive strains. QS activity was observed by cross streaking test of bacteria against CV026, it was affirmed that 13 isolates from the soil and 5 from hospital equipment’s showed positive QS activity. QQ activity of each isolate was tested by well diffusion assay, C6-HSL and C12-HSL were our candidate AHL molecules. The AHL molecule degradation was detected in 4 isolates of soil and none from the samples obtained from hospital setup. The total of 6 strongly positive QS and QQ isolates were identified and selected for 16S rRNA gene sequencing. The phylogenetic analysis revealed that these isolates were closely related to Pseudomonas, Bacillus and Exiguobacterium genera. In contrast, 1 Gram positive bacterial isolate was also purified with QS potential.
REVIEW | doi:10.20944/preprints202009.0513.v1
Subject: Life Sciences, Molecular Biology Keywords: PIP2; membrane dynamics; disease; actin dynamics; phosphoinositides; signaling
Online: 22 September 2020 (09:04:28 CEST)
In this review we summarize the recent development in understanding the role of PIP2 in cellular function and signaling. We first discuss the effect of PIP2 on actin binding proteins addressing the mechanism of the actin cytoskeletal dynamics such as polymerization or depolymerization of the filamentous network or the coupling to membrane to generate forces. Next, we outline the role of PIP2 in membrane dynamics. We summarized how the membrane organization depends upon PIP2 in the presence of ions or transmembrane proteins that are sensitive to membrane curvature. We discuss how clathrin coated pits interact with adaptor proteins during the endocytosis process, which is facilitated by PIP2. Finally, we discuss the role of PIP2 in cell signaling and diseases.
Mon, 21 September 2020
ARTICLE | doi:10.20944/preprints202009.0494.v1
Online: 21 September 2020 (04:26:52 CEST)
Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is a serious-global public health issue. A total of 292 E. coli isolates obtained from fecal samples of pigs in Central (n = 103) and Northeastern (n = 189) provinces of Thailand were included in this study. Eighty-six E. coli isolates were phenotypically confirmed to be β-lactamase producers (29.5%) and screened for the presence of β-lactamase genes. The genes in CTX-M family was most frequently found (90.7%). The blaCTX-M-15 gene (59.3%) was predominantly identified CTX-M genotype, followed by blaCTX-M-14 (31.4%) and blaCTX-M-4 (25.6%). The blaTEM-1 gene was prevalent (75.6%). The blaCTX-M-4 and blaCTX-M-14 genes were located on conjugative plasmid. The results highlight healthy pigs as reservoirs of ESBL-producing E. coli carrying ESBL genes that could be horizontally transferred.
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; signaling pathway; molecular alteration
Online: 21 September 2020 (04:17:24 CEST)
Emerging viruses description have grown at an unprecedented rate since the beginning of the 21st century. The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its related illness, Coronavirus Disease 2019 (COVID-19) has been reported as the third highly pathogenic coronavirus introducing itself into human population in the current era after the SARS-CoV and Middle East Respiratory Syndrome (MERS-CoV). Molecular and cellular studies considering the pathogenesis of this novel coronavirus are still in the early stages of research, however, regarding the similarity of SARS-CoV-2 and other coronaviruses, it could be hypothesized that the NF-κB, Cytokine regulation, ERK, and TNF-α signaling pathways are the more likely causes of inflammation upon onset of COVID-19. There are several drugs prescribed and used to alleviate the activity of these inflammatory cellular signaling pathways which might be beneficial for developing novel therapeutic modalities against COVID-19. In this review, we briefly summarized the alteration of cellular signaling pathways affected by coronavirus infection, particularly SARS-CoV and MERS-CoV and tabulated the current therapeutic agents approved for previous human diseases.
ARTICLE | doi:10.20944/preprints202009.0487.v1
Online: 21 September 2020 (03:35:15 CEST)
The age-related mortality and morbidity risk of COVID-19 has been considered speculative without enough scientific evidence. This study aimed to collect more evidence on the association between patient age and risk of severe disease state and/or mortality from SARS-CoV-2 infection. Genomic dataset along with metadata (3608 samples) retrieved from GISAID from different geographical regions were grouped into 10 age groups (0-10, 11-20, 21-30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100 years) as well as high-risk or low-risk according to patient clinical status. Genomic sequences were aligned and analyzed using MAFFT and FASTTREE to build a phylogenetic tree in order to identify age-risk associations based on phylogenetic clustering. Case fatality rates (CFR), as well as the Odds ratio (OR) for high-risk outcomes, were calculated for different age groups. Results revealed that individuals aged between 25-50 years have the best immune response to the infection. On the other hand, disease fatality was higher in patients aging above 50 years. We created an application to calculate the OR of being at high risk given a certain age threshold from GISAID datasets. OR values increased between ages 1-10 years (1.271) and 11-20 years (1.313) but reduced at age range 21-30 years (1.290) and increased again for 61-70 years (2.465). CFR calculated for each of the age groups had peak values at 90-100 years (26.8%) and the lowest at 0-10 years (0%). The CFR for ages above 50 years was about twice greater (11.6%-26.8%) than that for ages below (0-6.6%). The phylogenetic analysis revealed that the majority of samples obtained from India showed low-risk among different age groups and were defined as clade GH. Another cluster from Singapore visualization showed unfavorable patient outcome across several age groups and were classified under clade O. To conclude, this study analyses showed a variety of age-risk associations. As scientists from different countries upload more genomes to globally shared databases, more evidence will reinforce mortality risk associations in COVID-19 patients.
ARTICLE | doi:10.20944/preprints202009.0486.v1
Subject: Life Sciences, Immunology Keywords: COVID-19; comorbidity; SARS-CoV-2; leukemia; NAFLD; psoriasis; cancer; type II diabetes
Online: 21 September 2020 (03:32:58 CEST)
Background: Comorbidities have been frequently reported in COVID-19 patients, which often lead to more severe outcomes. The underlying molecular mechanisms behind these clinical observations have not yet been explained. Herein, we investigated the disease-specific gene expression signatures that may induce susceptibility to SARS-CoV-2 infection. Methods: We studied 30 frequently occurring acute, chronic, or infectious diseases of recent times that have shown comorbidity in one or another respiratory disease(s) caused by pathogenic human infecting coronaviruses, especially SARS-CoV-2. We retrieved array-based gene expression data for each disease and control from relevant datasets. Subsequently, all the datasets were quantile normalized, and log-2 transformed data was used for analysis. Results The expression of ACE2 receptor and host proteases, namely FURIN and TMPRSS2 that are essential for cellular entry of SARS-CoV-2, was upregulated in all six studied subtypes of leukemia (hereafter, referred as leukemia). The expression of ACE2 was also increased in psoriasis, lung cancer, Non-alcoholic fatty liver disease (NAFLD), breast cancer, and pulmonary arterial hypertension patients. The expression of FURIN was higher in psoriasis, NAFLD, lung cancer, and in type II diabetic liver, whereas it was lowered in breast cancer. Similarly, the expression of TMPRSS2 was increased during lung cancer and type II diabetes; it was decreased during psoriasis, NAFLD, lung cancer, breast cancer, and cervical cancer.Furthermore, a heightened expression of genes that are involved in immune response was observed in leukemia patients, as shown by the higher expression of IFNA2, IFNA8, IFNA10, IFNA14, IFNA16, IFNA21, IFNB1, CXCL10, and IL6. The expression of JAK1, STAT1, IL6, and CXCL10 was higher in NAFLD. Besides, JAK1 and STAT1 were upregulated in type II diabetic muscles. In addition, most of the upregulated genes in COVID-19 patients showed a similar trend in leukemia, NAFLD, and psoriasis. Furthermore, SARS-CoV-2, SARS-CoV and MERS CoV, were found to commonly alter two genes, namely, CARBONIC ANHYDRASE 11 and CLUSTERIN.Conclusions: The genes that may confer susceptibility to SARS-CoV-2 infection are mostly upregulated in leukemia patients; hence, leukemia patients are relatively more susceptible to develop COVID-19, followed by other chronic disorders, such as, NAFLD, type II diabetes, psoriasis, and hypertension. This study identifies key genes that are altered in the studied diseases types, which may aid in the infection of SARS-CoV-2 and underlie COVID-19 associated comorbidities.
Sun, 20 September 2020
ARTICLE | doi:10.20944/preprints202009.0485.v1
Subject: Life Sciences, Microbiology Keywords: Characterisation; Epidemiology; ESBL; Escherichia coli
Online: 20 September 2020 (15:46:21 CEST)
.The emergence and spread of antimicrobial resistance genes and resistant bacteria does not recognized animal, human or geographic borders. Addressing this threat requires a combination of multidisciplinary approach involving human, animal and environmental health (One Health). Because antimicrobial agents used in veterinary medicine maybe the same or like those in human medicine. Extended-spectrum beta lactamase (ESBL) E. coli is a growing public health problem worldwide, and the Agri-Food industry is constantly becoming sources of clinically important ESBL bacteria. Accordingly, the aim of this study was to investigate the occurrence and characteristics of ESBL-producing E. coli from dairy cattle, milk, and the farm environment. E. coli isolates were identified by their 16sRNA and their ESBL production was confirmed by ESBL-CHROMagar media and double disk diffusion method. Genotypes of ESBL producers were characterised using mPCR assay. Among the examined samples, 18(4.8 %) were positive for ESBL-producing E. coli. Of these, 66.7% were from milk, 27.8% and 5.5% were from farm environment and faecal samples respectively. Predominant ESBL Genotype identified were a combination of both TEM and CTX-M in eight out of 18 (44.4%) isolates. Four (22.2%) isolates produced CTX-M gene, two (11.1%) isolates produced TEM gene and four (22.2%) remaining isolates produced ESBL genes other than TEM, SHV, CTX-M and OXA. The SHV and OXA gene were not detected in all 18 isolates. The occurrence of these genotype in indicator organisms from dairy cattle, milk, and farm environment further re-enforced the potentials of food-animals as sources of infection for humans via the food chain. Thus, consolidating the need for the adoption of tripartite One Health approach in surveillance and monitoring antimicrobial resistance
ARTICLE | doi:10.20944/preprints202009.0473.v1
Subject: Life Sciences, Molecular Biology Keywords: antioxidant enzymes; DNA methylation; epigenetics; plant resistance; root-knot nematodes; ROS; tomato
Online: 20 September 2020 (14:35:29 CEST)
Two wild-type field populations of root-knot nematodes (Mi-Vfield, Mj-TunC2field), and two isolates selected for virulence in laboratory on resistant tomato cultivars (SM2V, SM11C2), were used to induce a resistance reaction in tomato to the soil-borne parasites. Epigenetic and metabolic mechanisms of resistance were detected and compared with those occurring in partially or fully successful infections. The activated epigenetic mechanisms in plant resistance, as opposed to those activated in infected plants, were detected by analysing the methylated status of total DNA, by ELISA methods, and the expression level of key genes involved in the methylation pathway, by qRT-PCR. DNA hypo-methylation and down-regulation of two methyl-transferase genes (CMT2, DRM5), characterized the only true resistant reaction obtained by inoculating the Mi-1.2-carrying resistant tomato cv Rossol with the avirulent field population Mi-Vfield. On the contrary, in the roots into which nematodes were allowed to develop and reproduce, total DNA was generally found to be hyper-methylated and methyl-transferase genes up-loaded. DNA hypo-methylation was considered to be the upstream mechanism that triggers the general gene over-expression observed in plant resistance. Gene silencing induced by nematodes may be obtained through DNA hyper-methylation and methyl-transferase gene activation. Plant resistance is also characterized by an inhibition of the anti-oxidant enzyme system and activation of the defence enzyme chitinase, as opposed to the activation of such a system and inhibition of the defence enzyme glucanase in roots infested by nematodes.
REVIEW | doi:10.20944/preprints202009.0471.v1
Subject: Life Sciences, Microbiology Keywords: Burkholderia pseudomallei; Mycobacterium tuberculosis; Multi nucleated giant cell; persistence; chronic infection
Online: 20 September 2020 (14:31:03 CEST)
This review provides a snapshot of chronic bacterial infections through the lens of Burkholderia pseudomallei; detailing its ability to establish multi-nucleated giant cells (MNGC) within the host, leading to the formation of pyogranulomatous lesions. We explore the role of MNGC in melioidosis disease progression and pathology by comparing the similarities and differences of melioidosis to tuberculosis, outlining the concerted events in pathogenesis that lead to MNGC formation, discussing the factors that influence MNGC formation and how they fit into clinical findings reported in chronic cases. Finally, we speculate about future models and techniques that can be used to delineate the mechanisms of MNGC formation and function.
Subject: Life Sciences, Virology Keywords: JC virus; polyomavirus; SV40; progressive multifocal leukoencephalopathy
Online: 20 September 2020 (14:08:01 CEST)
The polyomaviruses are small, non-enveloped DNA tumor viruses that cause serious disease in immunosuppressed people, including progressive multifocal leukoencephalopathy (PML) in patients infected with JC polyomavirus, but the molecular events mediating polyomavirus entry are poorly understood. Through genetic knockdown approaches, we identified phosphoinositide 3’ kinase γ (PI3Kγ) and its regulatory subunit PIK3R5 as cellular proteins that facilitate infection of human SVG-A glial cells by JCPyV, but not by adenovirus, an unrelated small, non-enveloped DNA tumor virus. PI3Kα appears less important for polyomavirus infection than PI3Kγ. CRISPR/Cas9-mediated knockout of PIK3R5 or PI3Kγ inhibited infection by authentic JCPyV and by JC pseudovirus. PI3Kγ knockout also inhibited infection by BK and Merkel Cell pseudoviruses, other pathogenic human polyomaviruses, and SV40, an important model polyomavirus. Reintroduction of the wild-type PI3Kγ gene into the PI3Kγ knock-out SVG-A cells rescued the JCPyV infection defect. Disruption of the PI3Kγ pathway did not block binding of JCPyV to cells or virus internalization, implying that PI3Kγ facilitates some intracellular step(s) of infection. These results imply that agents that inhibit PI3Kγ signaling may have a role in managing polyomavirus infections.
Sat, 19 September 2020
ARTICLE | doi:10.20944/preprints202009.0450.v1
Subject: Life Sciences, Molecular Biology Keywords: COVID-19; rRT-PCR; dilution; viral diagnosis; RNA extraction
Online: 19 September 2020 (08:27:13 CEST)
Although rRT-PCR is the gold standard method for SARS-CoV-2 detection, some factors, such as amplification inhibitors presence, lead to false-negative results. Here we describe differences between rRT-PCR results for SARS-CoV-2 infection in normal and diluted samples, simulating the need for dilution due to amplification inhibitors presence. Viral RNA extraction of nasopharyngeal swabs samples from 20 patients previously detected as 'Negative' and 21 patients detected as 'Positive' for SARS-CoV-2 was realized with the EasyExtract DNA-RNA (Interprise®) for extraction. rRT-PCR was realized with OneStep/COVID-19 (IBMP) kit with normal and diluted (80µl of H₂O RNAse free) samples, totaling 82 tests. The results indicate that there is an average variation (ɑ < 0.05) delaying Ct between the amplification results of internal control (IC), N Gene (NG), and ORF-1ab (OF) of 1.811Ct, 3.840Ct, and 3.842Ct, respectively. The extraction kit does not completely purify the inhibitor compounds, therefore non-amplification by inhibitors may occur. In this study, we obtained a 19.04% false-negative diagnosis after sample dilution, and this process reduces the efficiency of rRT-PCR to 29.8% for detecting SARS-CoV-2. Knowing the rRT-PCR standards of diluted samples can help in the identification of false-negative cases, and consequently avoid a wrong diagnosis.
Subject: Life Sciences, Virology Keywords: origin of viruses; phylogenetic reconstruction; reductive evolution; obligate intracellular parasites; Varidnaviria; Bamfordvirae; Nucleocytoviricota
Online: 19 September 2020 (03:51:15 CEST)
The extension of virology beyond its traditional medical, veterinary or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on earth. In particular, virus isolation studies involving unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure and morphology, genome size and gene content, or mode of replication. Complemented by large-scale metagenomic analyzes, these discoveries have rekindled interest in the enigma of the evolutionary origin of viruses, for which no simple definition encompassing all of their diversity is still unanimous. Several laboratories have repeatedly tackled the deep reconstruction of the evolutionary history of viruses, using various methods of molecular phylogeny applied to the few shared genes detected in certain virus groups (e.g. the Nucleocytoviricota). Beyond the practical difficulties of establishing reliable homology relationships from extremely divergent sequences, I present here purely conceptual arguments highlighting several fundamental limitations plaguing the reconstruction of the deep evolutionary history of viruses, and even more the identification of their unique of multiple origin (s). Those limitations are direct consequences of the particularly random mechanisms which govern the reductive evolution of obligate intracellular parasites.
Fri, 18 September 2020
REVIEW | doi:10.20944/preprints202009.0361.v2
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; foodborne viruses; enteric viruses; fecal-oral transmission; fresh produce, berries, fruits, hepatitis A virus, Norovirus, ready-to-eat foods.
Online: 18 September 2020 (10:35:33 CEST)
Background:Although highly strict social distancing and viral spread protection guidelines are in force, the reported numbers of COVID-19 cases across the world are still increasing. This indicates that we are still unable to completely understand the transmission routes of SARS-CoV-2. One of the possible routes that can play a significant role is the fecal-oral transmission since SARS-CoV-2 can replicate in the intestines as demonstrated by isolation of infectious virus from fecal samples of COVID-19 cases. Scope and approach:In this review, we compare the characteristics of SARS-CoV-2 with the distinctive characteristics of enteric foodborne viruses. We also discuss and respond to the arguments given in some reports that downplay the importance of foodborne transmission route of SARS-CoV-2. Key findings and conclusions:Enteric viruses such as human noroviruses (HuNoVs) and hepatitis A virus (HAV) are known to transmit through foods such as fresh produce and berries, leading to frequent multistate foodborne disease outbreaks all over the world. SARS-CoV-2 was found to share four distinctive characteristics of foodborne viruses that allow them to transmit through foods. This similarity in characteristics, recent report of detecting SARS-CoV-2 particles from frozen food packages in China, and recent suspected foodborne COVID-19 case in New Zealand, indicate that foodborne transmission of SARS-CoV-2 is more evident than previously thought possible. To support or deny this route of transmission, urgent research needs to be undertaken to answer two primary questions and many secondary ones as described in this review.
Thu, 17 September 2020
HYPOTHESIS | doi:10.20944/preprints202009.0407.v1
Subject: Life Sciences, Genetics Keywords: Centromere; karyotype evolution; centromere drive; Mus musculus domesticus
Online: 17 September 2020 (12:13:03 CEST)
The companion paper (Rice 2020) found that the centromeric repeats of the Western European house mouse (Mus musculus domesticus) have unusual structure: i) despite moderate pairwise sequence divergence (average = 5.9%), no monomer sequence was common and many hundreds of monomer sequences were observed, ii) local sequence divergence among neighboring monomers was nearly as high as genome-wide divergence, and iii) matching sequences were rare between side-by-side monomers. Here I integrate information from many published studies to formulate a hypothesis for the evolution of this structure. Non-matching sequences of neighboring centromeric monomers is hypothesized to be selectively favored in the context of molecular drive because it reduces the rate of monomer deletion during repair of double strand breaks (DSBs) via the Single Strand Annealing (SSA) pathway. The foundation for the hypothesis is the observation that centromeres of most populations of M. m. domestics reside close to the telomere, i.e., all their chromosomes are telocentrics. This proximity influences repair of centromeric DSBs because it places at least part of the centromere within the Telomere-Affected Repair Region (TARR; a location with increased concentrations of the shelterin-complex proteins that bind telomeres, especially TRF2). Shelterin proteins increase the level of 5’→3’ end resection at DSBs and thereby: i) decrease the frequency of repair via the c- NHEJ pathway, and ii) increase the frequency of homology-directed repair (HD-repair) –including the SSA repair pathway. It is hypothesized that certain ‘trigger’ events (e.g., sub-telomeric deletions) occur in local populations that increase the influence of TARR on the centromere. This increase elevates the occurrence of SSA repair of centromeric DSBs to a level that causes centromeres to begin to gradually shrink. Chronic shrinkage leads to coevolution between centromere size and karyotype number. Once centromeres shrink to a size below a critical minimum (that causes substantially reduced kinetochore size), fusions between non- homologous telocentrics with undersized centromeres produces metacentrics with an expanded centromere size (and a corresponding ‘quantum-jump’ in kinetochore size). These metacentrics: i) accumulate to fixation because they are favored by centromere drive, and ii) are released from the influence of TARR and thereby gradually recover larger centromere size. Fission of metacentrics with enlarged centromeres can next plausibly regenerate pairs of telocentrics with sufficiently large centromeres (which recruit normal-sized kinetochores) to be favored by centromere drive and accumulate to fixation. This fixation completes a cycle of coevolution within genomes that oscillate between two extremes: i) high karyotype number (2N = 40; all telocentrics) with larger centromeres, and ii) low karyotype number (2N << 40; mainly metacentrics) with initially small centromeres that gradually increase in size.
REVIEW | doi:10.20944/preprints202009.0405.v1
Subject: Life Sciences, Microbiology Keywords: horizontal gene transfer; bacterial conjugation; phenotypic conversion; drug-resistance dissemination; bacterial biofilms; mobile plasmids; F plasmid
Online: 17 September 2020 (12:00:29 CEST)
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism where the DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic life-style, virulence, biofilm formation, or resistance to heavy metals and, most importantly, resistance to antibiotics. These properties make of conjugation a fundamentally important process at the center of extensive study. Here, we review the key steps of conjugation by following the life-cycle of the F plasmid during transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.
REVIEW | doi:10.20944/preprints202009.0395.v1
Subject: Life Sciences, Virology Keywords: Spike protein, V483A, substitution mutation, virus-host cell interaction, high transmission, infectivity.
Online: 17 September 2020 (10:43:02 CEST)
Exploring the biological significance of mutations in SARS-CoV-2 coronavirus, causing the COVID–19 pandemic, has recently become an area of paramount interest for many researchers, who are pouring their tremendous efforts, in cracking the COVID–19 pandemic code. One of many such mutations that have occurred in the viral genome is V483A mutation, which is a part of the receptor-binding motif (RBM), present in the S1 domain of the spike protein. V483A mutant virus is becoming popular in North America with 36 cases so far, due to its frequent occurrences in recent days. In this review, we have assembled all information, currently available on V483A mutation, and have made a critical analysis based on the perspectives of many researchers all around the world. Comparison is made between the wild type and the V483A mutants to analyze certain factors like the type of interaction between the virus and host cell interface, binding affinity, stability, partition energy, hydrophobicity, occurrence rate, and transmissibility. Insilico dynamic analysis shows minimal alteration in the receptor-binding domain (RBD) of V483A mutant protein in free-state and no significant change of mutant tertiary structure of RBM upon binding to the ACE2 receptor. Comprehensive details about infectivity and evasion of the immune system by the virus are discussed. This information can in turn be of monumental importance in the field of vaccine and drug development because the mutants are becoming resistant to the vaccines and monoclonal antibodies.
ARTICLE | doi:10.20944/preprints202009.0383.v1
Subject: Life Sciences, Molecular Biology Keywords: Methylglyoxal; Glyoxalase system; AGEs; glutathione; hyperglycemia
Online: 17 September 2020 (07:45:11 CEST)
Chronic high glucose (HG) exposure increases methylglyoxal (MG)-derived AGEs and is involved in the onset of pathological conditions, such as diabetes, atherosclerosis and chronic‐degenerative diseases. Under physiologic condition the harmful effects of MG are contrasted by glyoxalase system that is involved in the detoxification of Reactive Carbonyl Species (RCS) and maintain the homeostasis of the redox environment of the cell. Polyphenols are the most abundant antioxidants in the diet and present various health benefits. The study aimed at investigating the role of polyphenols extracted from an apple high in polyphenols (Calville White Winter), on glyco-oxidative stress induced by chronic HG-exposure. Intestinal Caco-2 cells were treated in physiological glucose condition (25mM) as a control and in HG condition (50mM) with or without apple extract for one week. Our data demonstrated that HG-treatment triggers glyco-oxidation stress with a significantly increase in ROS, lipid peroxidation, AGEs and Glyoxalase I (GlxI) activity with a significant decrease in total antioxidant intracellular defense. Treatment with polyphenols under HG condition restores to the control levels GlxI activity, decreases Glyoxalase II (GlxII) in relation to the control and induces a drop of glyco-oxidative damage. This paper seeks to highlight the roles of polyphenols in glyco-oxidative stress.
ARTICLE | doi:10.20944/preprints202009.0381.v1
Subject: Life Sciences, Biotechnology Keywords: high throughput screening; rapid phenotyping; model-based experimental design; Escherichia coli; automated bioprocess development
Online: 17 September 2020 (07:34:19 CEST)
In bioprocess development, the host and the genetic construct for a new biomanufacturing process are selected in the early developmental stages. This decision, made at the screening scale with very limited information about the performance of the selected cell factory in larger reactors, has a major influence on the performance of the final process. To overcome this, scaledown approaches are essential to run screenings that show the real cell factory performance at industrial like conditions. We present a fully automated robotic facility with 24 parallel mini-bioreactors that is operated by a model based adaptive input design framework for the characterization of clone libraries under scale-down conditions. The cultivation operation strategies are computed and continuously refined based on a macro-kinetic growth model that is continuously re-fitted to the available experimental data. The added value of the approach is demonstrated with 24 parallel fed-batch cultivations in a mini-bioreactor system with eight different Escherichia coli strains in triplicate. The 24 fed-batches ran under the desired conditions generating sufficient information to define the fastest growing strain in an environment with varying glucose concentrations similar to industrial scale bioreactors.
Subject: Life Sciences, Biophysics Keywords: non-ionizing radiation; millimeter waves; novel biomedical applications; yeast; non-invasive devices
Online: 17 September 2020 (07:08:47 CEST)
Nonionizing millimeter-waves (MMW) are reported to interact with cells in a variety of ways. Possible mechanisms of the inhibited cell division effect were investigated using 85-105 GHz MMW irradiation within the ICNIRP (International Commission on Non-Ionizing Radiation Protection) non-thermal 20 mW/cm2 safety standards. ~1.0 mW/cm2 exposure over 5-6 hours treatment on 50 cells/μl samples of Saccharomyces cerevisiae model organism, resulted in 62% growth rate reduction compared to control (sham). The effect was specific for 85-105 GHz range and energy dose and cell density dependent. Irradiation of wild type and Δrad52 (DNA damage repair gene) deletion cells presented no differences of colony growth profiles indicating non-thermal MMW treatment does not cause genetic alterations. Dose versus response relations studied using a standard horn antenna (~1.0 mW/cm2) and compared to that of a compact waveguide (17.17 mW/cm2) for increased power delivery resulted in complete termination of cell division via non-thermal processes supported by temperature rise measurements. Combinations of MMW mediated Structure Resonant Energy Transfer (SRET), membrane modulations eliciting signaling effects, and energetic resonance with biomolecules were indicated to be responsible for the observations reported. Our results provide novel mechanistic insights enabling innovative applications of nonionizing radiation procedures for eliciting targeted biomedical outcomes.
ARTICLE | doi:10.20944/preprints202009.0374.v1
Subject: Life Sciences, Other Keywords: aldosterone; apoptosis; cardiac myocyte; eplerenone; fibrosis; finerenone; G protein-coupled receptor kinase (GRK)-5; mineralocorticoid receptor; mineralocorticoid receptor antagonist (MRA); signal transduction
Online: 17 September 2020 (05:24:29 CEST)
Background: In the heart, aldosterone (Aldo) binds the mineralocorticoid receptor (MR) to exert damaging, adverse remodeling-promoting effects. We recently showed that G protein-coupled receptor (GPCR)-kinase (GRK)-5 blocks the cardiac MR by directly phosphorylating it, thereby repressing its transcriptional activity. MR antagonist (MRA) drugs block the cardiac MR reducing morbidity and mortality of advanced human heart failure. Non-steroidal MRAs, such as finerenone, may provide better cardio-protection against Aldo than classic, steroidal MRAs, like spironolactone and eplerenone. Herein, we sought to investigate potential differences between finerenone and eplerenone at engaging GRK5-dependent cardiac MR phosphorylation and subsequent blockade. Methods: We used the cardiomyocyte cell line H9c2 and neonatal rat ventricular myocytes (NRVMs). Results: GRK5 phosphorylates the MR in H9c2 cardiomyocytes in response to finerenone but not to eplerenone. Unlike eplerenone, finerenone alone potently and efficiently suppresses cardiac MR transcriptional activity, thus displaying inverse agonism. GRK5 is necessary for finerenone`s inverse agonism, since GRK5 genetic deletion renders finerenone incapable of blocking cardiac MR transcriptional activity. Eplerenone alone does not fully suppress cardiac MR basal activity regardless of GRK5 expression levels. Finally in NRVMs, GRK5 is necessary for the anti-apoptotic and anti-fibrotic effects of both finerenone and eplerenone against Aldo, as well as for the higher efficacy and potency of finerenone at blocking Aldo-induced apoptosis and fibrosis. Conclusions: Finerenone, but not eplerenone, induces GRK5-dependent cardiac MR inhibition, which underlies, at least in part, its higher potency and efficacy, compared to eplerenone, as an MRA in the heart. GRK5 acts as a co-repressor of the cardiac MR and is essential for efficient MR antagonism in the myocardium.
Wed, 16 September 2020
REVIEW | doi:10.20944/preprints202009.0348.v1
Subject: Life Sciences, Genetics Keywords: DNA methylation; epialleles, epiRILs; epigenetics; Epigenome-Wide Association Studies.
Online: 16 September 2020 (05:11:28 CEST)
Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Further, the development of epigenetic recombinant inbred lines (epi-RILs) in the model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can facilitate epigenetic based molecular breeding of important crop plants.
COMMUNICATION | doi:10.20944/preprints202009.0343.v1
Subject: Life Sciences, Other Keywords: Poincaré–Weyl gauge theory; super-early Universe; effective cosmological constant
Online: 16 September 2020 (03:27:49 CEST)
The stage of a super-early scale-invariant Universe is considered on the basis of the Poincaré–Weyl gauge theory of gravity in a Cartan–Weyl space-time. An approximate solution has been found that demonstrates an inflationary behavior of the scale factor and, at the same time, a sharp exponential decrease in the effective cosmological constant from a huge value at the beginning of the Big Bang to an extremely small (but not zero) value in the modern era, which solves the well-known “cosmological constant problem”.
ARTICLE | doi:10.20944/preprints202009.0342.v1
Subject: Life Sciences, Biotechnology Keywords: [email protected]; periodic mesoporous silica; omega-3; anchovy; fish oil
Online: 16 September 2020 (03:25:43 CEST)
Fish oil rich in docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), vitamin D3 and natural astaxanthin sustainably extracted from anchovy fillet leftovers using biobased limonene only, can be conveniently stabilized by adsorption on periodic mesoporous silicas. The simplicity of the process, the high load of entrapped fish oil, and the biocompatible nature of silica support numerous forthcoming applications of this new class of “[email protected]” materials.
Tue, 15 September 2020
ARTICLE | doi:10.20944/preprints202009.0338.v1
Subject: Life Sciences, Virology Keywords: COVID-19; vaccine hesitancy; vaccine attitudes; vaccine development; SARS-CoV-2
Online: 15 September 2020 (10:32:28 CEST)
The COVID-19 pandemic continues to ravage the world, with the United States being highly affected. A vaccine provides the best hope for a permanent solution to controlling the pandemic. However, to be effective, a vaccine must be accepted and used by a large majority of the population. Structural equation modelling was used to analyze the relationships of several factors with attitudes toward potential COVID-19 vaccination. The survey was administered to 316 respondents across the United States by a survey corporation. Prior vaccine usage and attitudes predicted attitudes towards COVID-19 vaccination. Assessment of the severity of COVID-19 for the United States was also predictive. Approximately 68% of all respondents were supportive of being vaccinated for COVID-19, but side effects, efficacy, and length of testing remained concerns. Longer testing, increased efficacy and development in the United States were significantly associated with increased vaccine acceptance. Messages promoting COVID-19 vaccination should seek to alleviate the concerns of those who are already vaccine-hesitant. Messaging directed at the benefits of vaccination for the United States as a country would address the second predictive factor. Enough time should be taken to allay concerns about both short and long-term side effects before a vaccine is released.
ARTICLE | doi:10.20944/preprints202009.0331.v1
Subject: Life Sciences, Other Keywords: milk lactose; automatic milking system; smart farming; dairy cows
Online: 15 September 2020 (04:51:45 CEST)
In this study pH, temperature of the contents of the forestomach of cows and cow activity were measured using specific smaXtec boluses manufactured for animal care. Rumination time, body weight, milk yield, milk fat/protein ratio, milk lactose, milk somatic cell count, milk electrical conductivity and conception of concentrates were registered with the help of Lely Astronaut® A3 milking robots. The following parameters were obtained: base excess in blood, partial carbon dioxide pressure, partial oxygen pressure, bicarbonate, hydrogen potential, total carbon dioxide carbon, base excess in extracellular fluid, sodium, calcium, potassium, packed cell volume, chlorides, hemoglobin concentration and lactate. According to the concentration of lactose in milk, cows were grouped into two groups: group 1 - milk lactose <4.70% (n = 20), group 2 - milk lactose ≥ 4.70% (n = 15). Data of cows were also divided by milk fat and protein ratio: F/P<1.2 (class 1), F/P=1.2 (class 2) and F/P>1.2 (class 3). According our results we can conclude that inline registered milk lactose concentration can be used as indicator for the health status of fresh dairy cows. Cows with higher lactose concentration (≥ 4.70%) developed more activity (54.47%) and had less risk of mastitis (lover milk EC, and SCC) and metabolic disorders according to F/P. Cows with higher lactose concentration showed higher glucose concentrations. Low level of lactose can be used as indicator of mastitis (milk SCC ≥ 100 thousand/ml) and metabolic disorders according to F/P.
ARTICLE | doi:10.20944/preprints202009.0327.v1
Online: 15 September 2020 (04:24:17 CEST)
In regions lacking genomic data, analysis of sequences from the early stages of an outbreak can provide important insights into the diversity of pathogens present. Following the detection of the first imported case of COVID-19 in the Northern sector of Ghana on 13th March 2020, we have now molecularly characterized and phylogenetically analysed sequences including three (3) complete genomes of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) isolated from nine (9) patients observed in Ghana. Eight (8) of these patients reported with a recent history of foreign travel and one (1) with no history of foreign travel. We performed high throughput sequencing for 9 samples following the determination of high concentration of viral RNA. In addition, we estimated the potential impact that long distance transportation of samples to testing centres may have on sequencing outcomes. Here, two samples that were closest in terms of viral RNA concentration but transported from sites which are over 400km apart were assessed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Complete genomes were obtained for three (3) sequences and with another near complete genome with a coverage of 95.6%. Sequences with coverage in excess of 80% were found to belong to three lineages namely A, B.1 and B.2. Our sequences clustered in two different clades with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23 which was collected 9km compared with sample TTH6 which was collected and transported over a distance of 400km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be the need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.
ARTICLE | doi:10.20944/preprints202009.0324.v1
Subject: Life Sciences, Virology Keywords: MERS-CoV; camel; seroprevalence; transmission; ELISA; RT-qPCR; slaughterhouse
Online: 15 September 2020 (03:54:34 CEST)
Background: MERS-CoV is a zoonotic virus that have emerged in humans in 2012 and caused severe respiratory illness with mortality rate of 34.4%. Since its appearance, MERS-CoV have been reported in 27 countries and most of these cases were in Saudi Arabia. So far, dromedaries are considered to be the intermediate host and the only known source of human infection. Method: This study was designed to determine the seroprevalence and the infection rate of MERS-CoV in slaughtered food-camels in Riyadh, Saudi Arabia. A total of 171 nasal swabs along with 161 serum samples were collected during the winter; from January to April 2019. Nasal swabs were examined by Rapid test and RT-qPCR to detect MERS-CoV RNA, while serum samples were tested primarily using S1-based ELISA Kit to detect MERS-CoV (IgG) antibodies and subsequently by MERS pseudotyped viral particles (MERSpp) neutralization assay for confirmation. Genetic diversity of the positive isolates was determined based on the amplification and sequencing of the spike gene. Results: Our results showed high prevalence (38%) of MERS-CoV infection in slaughtered camels and high seropositivity (70.81%) during the time of the study. These data indicate previous and ongoing MERS-CoV infection in camels. Phylogenic analysis revealed relatively low genetic variability among our isolated samples. When these isolates were aligned against published spike sequences of MERS-CoV, deposited in global databases, there was sequence similarity of 94%. Conclusion: High seroprevalence and high genetic stability of MERS-CoV in camels indicating that camels pose a public health threat. The widespread of MERS-CoV infections in camels increases the risk of future zoonotic transmission into people with direct contact with these infected camels. This study confirms re-infections in camels, highlighting a challenge for vaccine development when it comes to protective immunity.
Sun, 13 September 2020
REVIEW | doi:10.20944/preprints202009.0301.v1
Subject: Life Sciences, Immunology Keywords: Atherosclerosis; Phospholipases; Macrophages; T cells; Lipins
Online: 13 September 2020 (23:45:55 CEST)
Phospholipases are a family of lipid altering enzymes that can either reduce or increase bioactive lipid levels. Bioactive lipids elicit signaling responses, activate transcription factors, promote g-coupled protein activity, and modulate membrane fluidity that mediate cellular function. Phospholipases and the bioactive lipids they produce are important regulators on immune cell activity, dictating both pro-inflammatory and pro-resolving activity. During atherosclerosis, pro-inflammatory and pro-resolving activities govern atherosclerosis progression and regression respectively. This review will look at the interface of phospholipase activity, immune cell function, and atherosclerosis.
Subject: Life Sciences, Other Keywords: World Trading signals; Fruits; WTO; Foreign Trade Research; Policies
Online: 13 September 2020 (15:53:54 CEST)
Fruits play an important role in human diet and to maintain better health. Globally, India ranks second in fruits production after China. Grapes, mangoes, bananas and oranges were the selected fruit crops for study purpose. The study period is from 1990 to 2018. The present study analyzed the growth rates, instability and elasticity of export quantity, prices of selected fruit crops from major producing countries in the world and also dealt with the major export destinations of Indian fruits. The results showed that an exporting countries should export grapes to Peru, Spain and Chile; bananas to the Panama, Philippines and Ecuador; mangoes to Italy, Egypt and Australia; and, oranges to Thailand, Philippines and Mexico for generating higher revenue because in global market those countries were associated with highest export price with the stability. Globally, the export price elasticity was inelastic in all countries of grapes, oranges and bananas except Italy in oranges and panama in bananas. The study found that export price elasticity of mangoes was marginally higher in the Spain and the Netherlands. The study showed that the major destinations for Indian fruits are; USA, Germany and Netherlands for grapes; USA, Belgium and Germany for bananas; USA, the Netherlands and Viet Nam for mangoes; and, Germany, France and Netherlands for oranges. Globally, the current study gave useful data to comprehend competition of prices for fruits to importing countries. This study may assist in preparing major price strategies and policies on fruits and also assisted in foreign earnings for all nations.
ARTICLE | doi:10.20944/preprints202009.0283.v1
Subject: Life Sciences, Molecular Biology Keywords: Decapod Crustaceans; dsRNA transport; Gene silencing mechanism; Serum dsRNA binding proteins; Systemic RNAi
Online: 13 September 2020 (12:09:03 CEST)
RNA interference (RNAi) has become a widely utilised method to study gene function, yet despite this, many of the mechanisms surrounding RNAi remain elusive. The core RNAi machinery is relatively well understood, however many of the systemic mechanisms, particularly double stranded RNA (dsRNA) transport, are not. Here, we demonstrate that dsRNA binding proteins in the serum contribute to systemic RNAi, and may be the limiting factor in RNAi capacity for species such as spiny lobsters where gene silencing is not functional. Incubating serum from a variety of species across phyla with dsRNA led to a gel mobility shift in species where systemic RNAi has been observed, with this response being absent in species where systemic RNAi has never been observed. Proteomic analysis suggested lipoproteins may be responsible for this phenomenon, and may transport dsRNA to spread the RNAi signal systemically. Following this, we identified the same gel shift in the slipper lobster Thenus australiensis and subsequently silenced the insulin androgenic gland hormone, marking the first time RNAi has been performed in any lobster species. These results pave the way for inducing RNAi in spiny lobsters, and better understanding the mechanisms of systemic RNAi in Crustacea, as well as across phyla.
Sat, 12 September 2020
ARTICLE | doi:10.20944/preprints202009.0273.v1
Subject: Life Sciences, Microbiology Keywords: Chromobacterium vaccinii; biofilm; sharing goods; social cheater; bog microbiome; bacterial genome, violacein, cold adaptation, IDBac, QS mutant
Online: 12 September 2020 (12:04:38 CEST)
Chromobacterium species are common in tropical and subtropical zones in environmental water samples and believed to «tropical» species. Here we describe an environmental case of resident Chromobacterium vaccinii in biofilms associated with Carex spp. roots in Moscow region, Russia (warm-summer humid continental climate zone). We performed broad characterization of individual properties as well as surrounding context for better understanding the premise of C. vaccinii survival during winter season. Genome properties of isolated strains propose some insights into adaptation to habit and biofilm mode of life, including social cheaters carrying ΔluxR mutation. Isolated C. vaccinii differs with previously described strains in some biochemical properties and some basic characteristics like fatty acid composition as well as unique genome features. Despite potential to modulate membrane fluidity and presence of several genes responsible for cold shock response, isolated C. vaccinii didn`t survive during exposure to 4 °C, while in initial complex biofilm it was able to survive for months in vitro at 4 °C. Surrounding bacterial community within the same biofilm with C. vaccinii represented a series of psychrophilic bacterial species which may share resistance to low temperatures with other species within biofilm and provide C. vaccinii opportunity to survive during cold winter season.
ARTICLE | doi:10.20944/preprints202009.0269.v1
Subject: Life Sciences, Microbiology Keywords: escherichia coli; dogs; virulence genes; antibiotic resistance; WGS; ST372; clonal structure
Online: 12 September 2020 (09:56:27 CEST)
Under one-health perspective and the worldwide antimicrobial resistance concern, we investigate extraintestinal pathogenic Escherichia coli (ExPEC), uropathogenic E. coli (UPEC), and multidrug resistant (MDR) E. coli from 197 isolates recovered from healthy dogs in Spain between 2013 and 2017. Ninety-one (46.2%) isolates were classified as ExPEC and/or UPEC including 50 clones, among which (i) four clones were dominant (B2-CH14-180-ST127, B2-CH52-14-ST141, B2-CH103-9-ST372 and F-CH4-58-ST64815) and (ii) 15 had been shown to be displayed by previously published isolates causing extraintestinal infections in humans. Twenty-eight (14.2%) isolates were classified as MDR, associated with B1, D and E phylogroups and included 24 clones, of which eight had also been identified among human isolates causing infections. We selected 23 ST372 strains, 21 healthy dogs faecal isolates and two human clinical isolates for whole genome sequencing and built a SNP-tree with these 23 genomes and 174 genomes (128 from canine strains and 46 from human strains) obtained from public databases. The analysis of these 197 genomes allowed to identify six clusters. Cluster 1 comprised 74.6% of the strain genomes that were mostly composed of canine strain genomes (P < 0.00001). Clusters 4 and 6 also included canine strain genomes, while clusters 2, 3 and 5 were significantly associated with human strain genomes. All these findings suggest that dogs are reservoirs of ExPEC, UPEC and MDR E. coli isolates with zoonotic potential.
ARTICLE | doi:10.20944/preprints202009.0266.v1
Subject: Life Sciences, Microbiology Keywords: hypogenous ectomycorrhizal fungi; truffles; soil nutrient; fungal community
Online: 12 September 2020 (08:04:07 CEST)
Truffles contribute to crucial dynamics in the soil systems, being involved in plentiful ecological functions important for ecosystems. Despite this, the interactions between truffles and surrounding mycobiota remain unknown. Here, we aimed to shed light on how much truffle species could affect its surrounding soil mycobiota. Using traditional chemical analysis and Illumina ITS amplicon sequencing, we compared soil nutrients and mycobiota surrounding two truffle species: Tuber indicum (Ti) and T. pseudohimalayense (Tp) inhabit in the same Pinus armandii forest in southwestern China. Tp soil was more acidic and had higher nutrients (total C, N, P contents) than Ti soil. Fungal richness and diversity of truffle ascomata and surrounding soils were significantly higher in Tp than in Ti. Redundancy analysis showed relationships between soil fungal taxa and soil properties had changed from negative (Tp) to positive (Ti) and shifted from a moisture-driving (Tp) to a total N-driving (Ti). Overall, our results showed that the interactions between truffle and soil system had been altered with species variation, although the causative peculiarity of these associations needs to be further studied.
REVIEW | doi:10.20944/preprints202009.0263.v1
Subject: Life Sciences, Biotechnology Keywords: marine fisheries; aquatic organisms; brachyura; anomura; commercial crab species; red king crab; Kamchatka crab; processing waste; hepatopancreas; waste recycling; enzymes; proteases; hyaluronidase
Online: 12 September 2020 (04:02:24 CEST)
Since the early 1980s, a large number of research works on enzymes from the red king crab hepatopancreas have been conducted. These studies have been relevant both from a fundamental point of view for studying the enzymes of marine organisms and in terms of the rational management of nature to obtain new and valuable products from the processing of crab fishing waste. Most of these works were performed by Russian scientists due to the area and amount of waste of red king crab processing in Russia (or the Soviet Union). However, the close phylogenetic kinship and the similar ecological niches of commercial crab species and the production scale of the catch provide the bases for the successful transfer of experience in the processing of red king crab hepatopancreas to other commercial crab species mined worldwide. This review describes the value of recycled commercial crab species, discusses processing problems, and suggests possible solutions to these problems. The main emphasis is placed on the enzymes of the hepatopancreas as the most highly salubrious product of waste processed from red king crab fishing.
Fri, 11 September 2020
ARTICLE | doi:10.20944/preprints202009.0252.v1
Subject: Life Sciences, Other Keywords: Water saving; Irrigation; Water productivity; Grain yield; Rice
Online: 11 September 2020 (09:22:02 CEST)
Tanzania with 945 million hectares of land area and annual rainfall of 300 mm on 67% of its territorial land is considered as a semi-dry region in the world. Rice production in Tanzania needs to be increased to feed a growing population, whereas water for irrigation is getting scarce. One way to decrease water consumption in paddy fields is to change the irrigation regime for rice production and to replace continuous flooding with alternate wetting and drying. In order to investigate the effect of different regimes of irrigation and nitrogen fertilizer on yield and water productivity of hybrid rice, two greenhouse pot experiments comprising soils from upland and lowland production ecologies were conducted at Sokoine University of Agriculture, Tanzania during crop seasons of 2019. The experiment was arranged in split plots based on randomized completely block design with 3 replications. Water regimes were the main factor comparing continuous flooding (CF) and alternate wetting and drying (AWD) with nitrogen fertilizer levels as the sub-factor including absolute control , 0, 60, 90, 120 and 150 kg/ha. Alternate wetting and drying (AWD) improved water productivity in both upland and lowland production ecologies compared to CF. AWD increased yield under lowland production by 13.3% while in upland there was 18.5% decrease in yield. The average water use varied from 31.5 to 84 L pot-1 under upland trials, while in lowland trials it was 36 to 82.3 L. Higher yield and lower water application led to an increase in WP varying from 1.2 to 1.8 kg cm-3 under upland trials, and 0.6 to 1.5 kg cm-3 under lowland trials. The variation in water productivity among treatments was mainly due to the differences in the yield, water and nitrogen levels used in the production process. Both sets of trials recorded water saving up to 34.3% and 17.3% under lowland and upland trials, respectively. Under upland trials, the yield varied from 39.9 to 124.1 g pot-1 and in lowland trials yield ranged from 20.6 to 118.2 g pot-1 representing paddy rice. The measurements showed that less water can be used to produce more crops under alternative rice growing practices. The results are important for water-scarce areas, providing useful information to policy makers, farmers, agricultural departments, and water management boards in devising future climate-smart adaptation and mitigation strategies.
HYPOTHESIS | doi:10.20944/preprints202003.0419.v9
Subject: Life Sciences, Molecular Biology Keywords: ATP hypothesis; origin of genetic code; life’s building block; probiotic “soup”; coevolution; biochemical system; missing “matchmaker”; energy transformation; informatization; structuralization; precellular selection; photo- chemical origin of life; virus; anti-life form; 2019-nCoV
Online: 11 September 2020 (08:39:39 CEST)
A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored the energetic driving force, its relation to the biochemical system, and most importantly, the missing “matchmaker” between proteins and nucleic acids. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by driving the coevolution of the genetic code with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced e.g. by photochemical reactions in a protocell that derived from a lipid vesicle enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically form and elongate chains of both polynucleotides and polypeptides, thus acting a “matchmaker” between these two bio-polymers and eventually mediating precellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthesis system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of permanently recording the genetic information by DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis assumes or supports the photochemical origin of life, shedding light on the origins of both photosynthetic and biochemical systems, which remains largely unknown thus far. Based on ATP hypothesis, virus (like the new coronavirus) could not be the earliest life on Earth, as it has neither biochemical systems nor lipid bilayer membrane that provided relatively isolated environment for the development of protobiochemical reactions, although it owns the genetic code of a cellular life. Virus could not be a bridge between life and non-life, but is an anti-life substance, as it depletes cellular material for its own replication, and then spreads by destroying the host cells. It can be imagined that if cellular life are completely wiped out by the virus, the complete destruction of life on Earth would be inevitable.
ARTICLE | doi:10.20944/preprints202009.0244.v1
Subject: Life Sciences, Virology Keywords: Myxomatosis; recombinant myxoma virus; ha-MYXV; European rabbit; Oryctolagus cuniculus algirus; species jump; spillover
Online: 11 September 2020 (08:03:18 CEST)
In late 2018, an epidemic myxomatosis outbreak emerged on the Iberian Peninsula leading to high mortality in Iberian hare populations. Soon, a recombinant virus (MYXV-Tol or ha-MYXV) was identified, harboring a 2.8 kb insertion containing evolved duplicates of M060L, M061L, M064L, and M065L from MYXV. Since 2017, 1616 rabbits and 82 hares were tested by a qPCR directed to M000.5L/R gene, conserved in MYXV and MYXV-Tol/ ha-MYXV strains. A subset (20%) of the positive samples was tested for the insert with MYXV being detected in rabbits and recombinant MYXV in hares. Recently, two wild rabbits found dead in South Portugal, showing skin oedema and pulmonary lesions tested positive for the 2.8 Kb insert. Sequencing showed 100% similarity with the insert sequences described in Iberian hares from Spain. Viral particles were observed in the lungs of both rabbits by electron microscopy, and isolation in RK13 cells showed virus infectivity. Despite the analysis of recombinant MYXV genomes may predict its ability to infect rabbit, routine analyses showed species segregation for the circulation of MYXV and recombinant MYXV in wild rabbit and in Iberian hares, respectively. This study demonstrates, however, that recombinant MYXV can effectively infect and cause myxomatosis in wild rabbits and domestic rabbits, which raises serious concerns for the future of the Iberian wild leporids and emphasizes the need to continue monitoring MYXV and recombinant MYXV in both species.
Wed, 9 September 2020
ARTICLE | doi:10.20944/preprints202009.0207.v1
Online: 9 September 2020 (10:48:24 CEST)
Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It also has been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler— SMARTdenovo, which is an SMS assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a fast assembler that did not require highly accurate raw reads for error correction, unlike other, contemporaneous SMS assemblers. It has performed well for evaluating congeneric assemblers and has been successful for a variety of assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015, and here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.
ARTICLE | doi:10.20944/preprints202008.0529.v2
Subject: Life Sciences, Biophysics Keywords: membrane potential; Nernst; Bernstein; action potential; propagation; theory
Online: 9 September 2020 (09:24:15 CEST)
Man has always been interested in animal electricity, which seems to be measured in every living cell. He has been fascinated by trying to elucidate the mechanisms by which this potential is created and maintained. Biology is the science that seeks to explain this mystery. Biology is based on basic sciences such as physics or chemistry. The latter, in turn, make systematic use of mathematics to measure, evaluate and predict certain phenomena and to develop "laws" and models that are as general as possible while respecting, as closely as possible, observations and facts. The Nernst equation was one of the pillars of electrochemistry. Biology also uses this same equation as one of the indispensable bases for the computation of membrane potential. Man has established a cellular model that highlights this equation in several forms. However, we are going to show by various means that this model is inadequate or even inapplicable.
REVIEW | doi:10.20944/preprints202009.0198.v1
Subject: Life Sciences, Virology Keywords: coronavirus; aquatic organisms; fish; marine mammals; crustaceans; birds
Online: 9 September 2020 (04:04:12 CEST)
Coronaviruses are pathogens recognized for having an animal origin and commonly associated with terrestrial environments. However, although in few cases, there are reports of their presence in aquatic organisms like fish, crustaceans, waterfowls and marine mammals. None of these cases have even led to human health effects, when contact with these infected organisms, whether they are alive or dead. Aquatic birds seem to be the main group in carrying and circulating these types of viruses in healthy bird populations and play an important role in these environments. Although the route of infection for CoVID-19 (Coronavirus disease 2019) by water or aquatic organisms, has not yet been observed in the wild, the relevance of its study is highlighted , because there are cases of other viral infections (no coronavirus), which are known to have been transferred to the human by aquatic biota. What is even better, it becomes encouraging to know that aquatic species shows very few cases in fishes, marine mammals, and crustaceans, and some other aquatic animals may also be a possible source of cure or treatment against coronaviruses, as some evidence with algae and marine sponges suggests.
ARTICLE | doi:10.20944/preprints202009.0194.v1
Subject: Life Sciences, Molecular Biology Keywords: Oenothera biennis; Evening primrose; Oxidative stress; Cell death; Nrf2/HO-1
Online: 9 September 2020 (03:29:52 CEST)
Background: Oenothera biennis (evening primrose) produces bioactive substances with a diverse range of pharmacological functions. However, it is currently unknown whether extract prepared from the aerial parts of O. biennis (APOB) can protect the skin against oxidative stress. To investigate the protective effects of APOB against oxidative stress-induced damage in human skin keratinocytes (HaCaT) and elucidate the underlying mechanisms. Methods: We pretreated HaCaT cells with various concentrations of APOB or the antioxidant N-acetyl-L-cysteine before applying H2O2. We then compared the cell viability, intracellular reactive oxygen species (ROS) production, and DNA and mitochondrial damage between pretreated and untreated control cells using a range of assays, flow cytometry, and Western blot analysis and also examined the reducing power and DPPH free radical-scavenging activity of APOB. Results: APOB pretreatment significantly increased cell viability, effectively attenuated H2O2-induced comet tail formation, and inhibited H2O2-induced phosphorylation of the histone γH2AX, as well as the number of apoptotic bodies and Annexin V-positive cells. APOB was found to have a high reducing power and DPPH radical-scavenging activity and also exhibited scavenging activity against intracellular ROS accumulation and restored the loss of mitochondrial membrane potential caused by H2O2. APOB pretreatment almost totally reversed the enhanced cleavage of caspase-3, the degradation of poly (ADP-ribose)-polymerase (PARP), DNA fragmentation that usually occurs in the presence of H2O2 and increased the levels of heme oxygenase-1 (HO-1), a potent antioxidant enzyme that is associated with the induction of nuclear factor-erythroid 2-related factor 2 (Nrf2). Conclusions: APOB can protect HaCaT cells from H2O2-induced DNA damage and cell death by blocking cellular damage related to oxidative stress via a mechanism that affects ROS elimination and by activating the Nrf2/HO-1 signaling pathway.
ARTICLE | doi:10.20944/preprints202009.0192.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: connexin 43; gap junctions; cancer; intercellular communication; breast cancer; cell signaling; tunneling nanotubes; cell–cell communication; tumor microtubes
Online: 9 September 2020 (03:09:50 CEST)
Connexin 43 (Cx43) forms gap junctions that mediate the direct intercellular diffusion of ions and small molecules between adjacent cells. Cx43 displays both pro- and anti-tumorigenic properties, but the mechanisms underlying these characteristics are not fully understood. Tunneling nanotubes (TNTs) are long and thin membrane projections that connect cells, facilitating the exchange of not only small molecules, but also larger proteins, organelles, bacteria, and viruses. Typically, TNTs exhibit increased formation under conditions of cellular stress and are more prominent in cancer cells, where they are generally thought to be pro-metastatic and to provide growth and survival advantages. Cx43 has been described in TNTs, where it is thought to regulate small molecule diffusion through gap junctions. Here, we developed a high-fidelity CRISPR/Cas9 system to knockout (KO) Cx43. We found that loss of Cx43 expression was associated with significantly reduced TNT length and number in breast cancer cell lines. Notably, secreted factors present in conditioned medium stimulated TNTs more potently when derived from Cx43-expressing cells than from KO cells. Moreover, TNT formation was significantly induced by inhibition of several key cancer signaling pathways that both regulate Cx43 and are regulated by Cx43, including RhoA kinase (ROCK), protein kinase A (PKA), focal adhesion kinase (FAK), and p38. Intriguingly, drug-induced stimulation of TNTs was more potent in Cx43 KO cells than in wild-type cells. In conclusion, this work describes a novel non-canonical role for Cx43 in regulating TNTs, identifies key cancer signaling pathways that regulate TNTs in this setting, and provides mechanistic insight into a pro-tumorigenic role of Cx43 in cancer.
Tue, 8 September 2020
COMMUNICATION | doi:10.20944/preprints202009.0186.v1
Online: 8 September 2020 (11:04:34 CEST)
Vibrio is a bacterial genus widely distributed in natural aquatic systems. Some Vibrio species are pathogenic and can cause severe diseases in both marine organisms and humans. Previous studies revealed a link between the current climate change and increased incidence of the Vibrio-associated diseases recently causing sanitary, economic and/or ecological problems worldwide. The conventional culture-based methods (e.g. cultivation of TCBS agar) used to monitor the presence of Vibrio spp. in environmental samples are not always straightforward and can underestimate the number of cells, especially if the microbial population contains a fraction of ‘dormant’ cells (e.g. cells in Viable but not Culturable (VBNC) state). However, this problem can be overcome by using alternative culture-free approaches such as Catalyzed Reporter Deposition-Fluorescence In situ Hybridization (CARD-FISH). To optimize CARD-FISH for efficient and reliable detection of Vibrio spp. in environmental samples, we have used both computer-assisted and experimental approaches. Our results demonstrate that the use of the optimized protocol along with a very specific probe, ViB572a, can offer the high sensitivity and selectivity of CARD-FISH detection of marine vibrios in natural seawater.
ARTICLE | doi:10.20944/preprints202009.0185.v1
Subject: Life Sciences, Endocrinology & Metabolomics Keywords: eel luteinizing hormone receptor; constitutively activating mutation; inactivating mutation; cyclic adenosine monophosphate response; cell surface loss of receptor
Online: 8 September 2020 (10:56:48 CEST)
We analyzed signal transduction of three constitutively activating mutants (M410T, L469R, and D590Y) and two inactivating mutants (D417N and Y558F) of the eel luteinizing hormone receptor (eel LHR), known to occur in human LHR. The objective of this study was to assess the functional effects of these mutations in signal transduction and cell surface loss of receptor. Mutant receptors were transiently expressed in Chinese hamster ovary (CHO-K1) cells. Eel LH-stimulated accumulation of cyclic adenosine monophosphate (cAMP) was measured by homogeneous time-resolved fluorescence (HTRF) assays. The loss of receptors from the cells surface was measured using an enzyme-linked immunosorbent assay (ELISA) in human embryonic kidney (HEK) 293 cells. The cAMP response in cells expressing the wild type eel LHR was increased in a dose-dependent manner using eel LH ligand stimulation. Compared with the wild type, cells expressing the activating mutants (M410T, L469R, and D590Y), exhibited a 4.0-, 19.1-, and 7.8-fold increase in basal cAMP response without agonist stimulation, respectively. Their maximal responses to agonist stimulation were approximately 65%, 52%, and 98%, respectively, of those of the wild type. The inactivating mutants (D417N and Y558F) did not completely impair signal transduction, and their maximal responses were only 33% and25 % of those of wild type. These data clearly showed that the eel LHR-L469R and D590Y, activating mutants enhanced the rate of the loss of cell surface receptors following treatment with eel LH. Thus, the loss of cell surface receptors in cells expressing mutant eel LHRs was consistent with the eel LH agonist-induced production of cAMP. Our results suggested that the activation of the eel LHR requires appropriate loss of LHR-ligand complexes from the cell surface.
REVIEW | doi:10.20944/preprints202009.0178.v1
Online: 8 September 2020 (07:50:29 CEST)
A strategy to propose solutions to health-related problems recognizes that people, animals, and the environment are interconnected. Fusarium and Neocosmospora are an example of this interaction due to the capable of infecting plants, animals, and human. This review provides information on various aspects of these relations and proposes how to approach fusariosis with a One Health methodology. Here we give a framework to understand infection pathogenesis, through the epidemiological triad and explain how the broad utilization of fungicides in agriculture may play a role in the treatment of human fusariosis. We assess how plumbing systems and hospital environments might play a role as a reservoir for animal and human infections. We explain the role of antifungal resistance mechanism in both humans and agriculture. Our review emphasizes the importance of developing interdisciplinarity research studies where aquatic animals, plants, and human disease interactions can be explored through coordination and collaborative actions.
Subject: Life Sciences, Other Keywords: Pomegranate; Punica granatum L.; Pomegranate skin extract; Pomegranate fruit extract; Nutraceutical properties; Biological properties
Online: 8 September 2020 (05:05:55 CEST)
The pomegranate, an ancient plant native to Central Asia, cultivated in different geographical areas including the Mediterranean basin and California, consists of flowers, roots, fruits and leaves. Presently, it is utilized not only for the exterior appearance of its fruit but above all, for the nutritional and health characteristics of the various parts composing this last one (carpellary membranes, arils, seeds and bark). The fruit, the pomegranate, is rich in numerous chemical compounds (flavonoids, ellagitannins, proanthocyanidins, mineral salts, vitamins, lipids, organic acids) of high biological and nutraceutical value that make it the object of study for many research groups, particularly in the pharmaceutical sector. Its interest is mainly addressed to the knowledge of its biological and functional properties and the research of new formulations to apply it in a wide range of diseases such as neoplastic, cardiovascular, viral, inflammatory, metabolic, microbial, intestinal, reproductive and skin diseases. In this review we highlight the health-promoting properties of pomegranate and its bioactive compounds against human diseases.
Mon, 7 September 2020
Subject: Life Sciences, Microbiology Keywords: Computational methods; machine learning; microbiome-host interactions
Online: 7 September 2020 (14:50:42 CEST)
The microbiome, by virtue of its interactions with the host, is implicated in various host functions including its influence on inflammation, nutrition, and homeostasis. Although driven by a complex combination of intrinsic and extrinsic factors, many chronic diseases such as diabetes, cancer, Inflammatory Bowel Disease among others are characterized by a disruption of microbial communities in at least one biological niche/organ system. Various molecular mechanisms between microbial and host components such as proteins, RNAs, metabolites etc have recently been elucidated, thus filling many gaps in our understanding of how the microbiome modulates host processes. Concurrently, high throughput technologies have enabled the profiling of heterogeneous datasets capturing community level changes in the microbiome as well as the host responses. However, due to pragmatic limitations with respect to parallel sampling and analytical procedures, big gaps still exist in terms of how the microbiome mechanistically influences host functions at a systems and community level. In the past decade, various computational biology and machine learning methodologies and approaches have been developed with an aim to fill these existing gaps. Due to the agnostic nature of the tools, they have been applied in various disease contexts to analyze and infer the interactions between the microbiome and host molecular components, and in the case of a few selected tools, on downstream host processes. Generally, most of the tools are enabled by frameworks to statistically or mechanistically integrate different types of -omic and meta -omic datasets followed by functional/biological interpretation. In this review, we provide an overview of the landscape of computational approaches for investigating mechanistic microbiome-host interactions and their potential benefit for basic and clinical research. These could include but are not limited to the development of activity and mechanism based biomarkers, uncovering mechanisms for therapeutic interventions and generating integrated signatures to stratify patients.
REVIEW | doi:10.20944/preprints202008.0369.v2
Subject: Life Sciences, Other Keywords: Extreme capsule; uncinate fasciculus; IFOF; ventral pathway of language; bottle neck; DTI
Online: 7 September 2020 (10:26:24 CEST)
On review of neuroscience literature extreme capsule considered as a whiter matter tract. Nevertheless it is not clear that extreme capsule itself is a association fiber pathway or is o bottleneck for passing other association fiber. By a systematic search with investigating anatomical position, dissection, connectivity and cognitive role of extreme capsule it can be argued that extreme capsule probably is a bottleneck for passing uncinated fasciculus (UF) and inferior fronto – occipital fasciculus(IFOF), And its different role of language processing is duo to different tract that passing it.
Subject: Life Sciences, Virology Keywords: COVID-19; thermal inversion; PM2.5 air pollution; desert dust intrusions
Online: 7 September 2020 (04:28:12 CEST)
A probe of a patient, seeking help in an emergency ward of a French hospital in late December 2019 because of Influenza like symptoms, was retrospectively tested positive to COVID-19. Despite the early appearance of the virus in Europe, the prevalence and virulence appeared to be low for several weeks, before the spread and severity of symptoms increased exponentially, yet with marked spatial and temporal differences. Here, we compare the possible linkages between peaks of fine particulate matter (PM2.5) and the sudden, explosive increase of hospitalizations and mortality rates in the Swiss Canton of Ticino, and the Greater Paris and London regions. We also discuss the influence of Saharan dust intrusions on the COVID-19 outbreak observed in early 2020 on the Canary Islands. We find that high PM2.5 concentrations – possibly favored by air temperature inversions or Saharan dust intrusions – are not only modulating but even more so boosting severe outbreaks of COVID-19. We conclude that the overburdening of the health services and hospitals as well as the high over-mortality observed in various regions of Europe in spring 2020 can be linked to peaks of PM2.5 and likely particular weather situations that have favored the spread and enhanced the virulence of the virus. In the future, we recommend to monitor not only the prevalence of the virus, but also to consider the occurrence of weather situations that can lead to sudden, very explosive COVID-19 outbreaks.
ARTICLE | doi:10.20944/preprints202009.0154.v1
Subject: Life Sciences, Biochemistry Keywords: COVID-19; Knowledge; Practices; Perception; Veterinarians students; Nigeria
Online: 7 September 2020 (03:52:58 CEST)
Background: The novel Coronavirus SARS-CoV-2 (COVID-19) is a global pandemic with an increasing public health concern. Due to the non-availability of a vaccine against the disease, non-pharmaceutical interventions constitute major preventive and control measures. However, inadequate knowledge about the disease and poor perception might limit compliance. Aim: This study examined COVID-19-related knowledge, practices, perceptions and associated factors amongst undergraduate veterinary medical students in Nigeria. Methods: A cross-sectional web survey was employed to collect data from 437 consenting respondents using pre-tested self-administered questionnaire (August 2020). Demographic factors associated with the knowledge and adoption of recommended preventive practices towards COVID-19 were explored using multivariate logistic regression at P ≤ 0.05.Results: The respondents’ mean knowledge and practice scores were 22.7 (SD ± 3.0) and 24.1 (SD ± 2.9), respectively with overall 63.4% and 88.8% displaying good knowledge and satisfactory practice levels. However, relatively lower proportions showed adherence to avoid touching face or nose (19.5%), face mask-wearing (58.1%), and social distancing (57.4%). Being in the 6th year of study (OR = 3.18, 95%CI: 1.62-6.26, P = 0.001) and female (OR = 2.22, 95% CI = 1.11-4.41, P = 0.024) were significant positive predictors of good knowledge and satisfactory practices, respectively. While only 30% of the respondents perceived the pandemic as a scam or a disease of the elites (24.0%), the respondents were worried about their academics being affected negatively (55.6%). Conclusion: The study revealed good knowledge and satisfactory preventive practices towards COVID-19 among Nigerian Veterinary students; albeit with essential gaps in the key non-pharmaceutical preventive measures recommended by the WHO. Therefore, there is a need to step up enlightenment and targeted campaigns about COVID-19 pandemic.
Sun, 6 September 2020
ARTICLE | doi:10.20944/preprints202009.0145.v1
Subject: Life Sciences, Genetics Keywords: NHEJ; Cernunnos; Cyren; pro-B cells; lymphocyte; genetic interaction
Online: 6 September 2020 (15:50:10 CEST)
Non-homologous end-joining (NHEJ) is a DNA repair pathway required to detect, process, and ligate DNA double-stranded breaks (DSBs) throughout the cell cycle. The NHEJ pathway is necessary for V(D)J recombination in developing B and T lymphocytes. During NHEJ, Ku70 and Ku80 form a heterodimer that recognizes DSBs and promotes recruitment and function of downstream factors PAXX, MRI, DNA-PKcs, Artemis, XLF, XRCC4, and LIG4. Mutations in several known NHEJ genes result in severe combined immunodeficiency (SCID). Inactivation of Mri, Paxx or Xlf in mice results in normal or mild phenotype, while combined inactivation of Xlf/Mri, Xlf/Paxx, or Xlf/Dna-pkcs leads to late embryonic lethality. Here, we describe three new mouse models. We demonstrate that deletion of Trp53 rescues embryonic lethality in mice with combined deficiencies of Xlf and Mri. Furthermore, Xlf-/-Mri-/-Trp53+/- and Xlf-/-Paxx-/-Trp53+/- mice possess reduced body weight, severely reduced mature lymphocyte counts, and accumulation of progenitor B cells. We also report that combined inactivation of Mri/Paxx results in live-born mice with modest phenotype, and combined inactivation of Mri/Dna-pkcs results in embryonic lethality. Therefore, we conclude that XLF is functionally redundant with MRI and PAXX during lymphocyte development in vivo. Moreover, Mri genetically interacts with Dna-pkcs and Paxx.
ARTICLE | doi:10.20944/preprints202009.0144.v1
Subject: Life Sciences, Genetics Keywords: Symbiosis; Opportunistic pathogens; Janthinobacterium sp.; Flavobacterium sp.; Genomes; Floc formation; Lubomirskia baikcalensis
Online: 6 September 2020 (15:45:20 CEST)
Endemic freshwater sponges (Demosponges, Lubomirskiidae) dominate in Lake Baikal and are multicellular filter-feeding animals represent a complex consortium of many species of eukaryotes and prokaryotes. In recent years, mass disease and death of the L. baicalensis have been an urgent problem of Lake Baikal. The etiology and ecology of these events remain unknown. Bacteria in microbiomes of diseased sponges of the families Flavobacteriaceae and Oxalobacteraceae were dominant. Both species are opportunistic pathogens common for freshwater ecosystems. The aim of our study is to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. The first one attacks the other cells using type VI secretion system, suppress gram-positive bacteria with violacein pigment and regulate its own activity via quorum sensing. It makes the floc and strong biofilm by exopolysaccharide biosynthesis and PEP‐CTERM proteins expression. The second one utilizes the fragments of cell walls produced of polysaccharides. Named two strains have noticeable difference in carbohydrates acquisition. We described the possible way of joint occupation of ecological niche into freshwater sponge microbial community. This study expands understanding about symbiotic relationship of microorganisms with freshwater Baikal sponges.
Sat, 5 September 2020
HYPOTHESIS | doi:10.20944/preprints202009.0140.v1
Subject: Life Sciences, Biochemistry Keywords: Insect decline; Tracheal system; Tracheole; Fine dust; Ultrafine particles
Online: 5 September 2020 (11:59:33 CEST)
Is the extensive decline of insects partially due to an insect-specific feature of their functional organization that is disadvantageous for living in an industrialized environment? The unique way in which gases are supplied in insect tissues is such a special trait. It exposes cells directly to the gas phase, via tracheae that end in micro-tubes, the tracheoles, which have diameters in the same range as particles of ultra-fine dust transported by air of industrialized countries. Number and volume of these particles – calculated to be inhaled by honeybees, e.g., – are indicative to locally impede O2-uptake and CO2-release and thus to restrain physiological activities.
REVIEW | doi:10.20944/preprints202009.0133.v1
Subject: Life Sciences, Other Keywords: Cognition; nutrition; metabolism; neurodegeneration; ketone bodies; glycaemia; nutrition therapy
Online: 5 September 2020 (08:29:52 CEST)
Although diet interventions are mostly related to metabolic disorders, nowadays they are used in wide variety of pathologies. From diabetes and obesity to cardiovascular diseases, through cancer or neurological disorders and stroke, nutritional recommendations applied to almost all diseases. Among those disorders, metabolic disturbances and brain function and/or diseases have recently been shown to be linked. Indeed, numerous neurological functions are often associated with perturbations of whole-body energy homeostasis. In this regard, specific diets are used in various neurological conditions such as epilepsy, stroke, or seizure recovery. In addition, Alzheimer’s disease or Autism Spectrum Disorders are also considered as putatively improved by diet intervention. Glycemic index diets are a novel developed indicator expected to anticipate the changes in blood glucose induced by specific foods, and how they can affect various physiological function. Several results provide indications of efficiency of low glycemic index diets in weight management, insulin sensitivity, but also cognitive function, epilepsy treatment, stroke, or neurodegenerative diseases. Overall, studies involving glycemic index could provide new insight in the relationship between energy homeostasis regulation and brain function or related disorders. Therefore, in this review we will summarize main evidences on glycemic index involvement in brain mechanisms of energy homeostasis regulation.
COMMUNICATION | doi:10.20944/preprints202009.0115.v1
Subject: Life Sciences, Microbiology Keywords: intramammary infection; spa typing; antimicrobial susceptibility; dairy cow
Online: 5 September 2020 (04:51:45 CEST)
In the present study, we aimed to determine the antimicrobial resistance and genetic structure of a population of S. aureus recovered from transient and persistent intramammary infections and nares/muzzles. We investigated the antimicrobial resistance of 189 S. aureus strains using a broad antimicrobial susceptibility profile. Furthermore, 107 S. aureus isolates were strain-typed using staphylococcal protein-A (spa) typing. Here, a great proportion of strains exhibited multidrug resistance to antimicrobials, including resistance to critically important antimicrobials, although no methicillin-resistant S. aureus strains were found. Our study did not strengthen the idea that extramammary niches (i.e., nares/muzzles) are an important source for S. aureus. A discrepancy in the antimicrobial resistance between S. aureus strains isolated from nasal/muzzles and milk samples was observed. Furthermore, S. aureus isolates from transient and persistent IMIs did not differ by spa typing, suggesting that the persistence of bovine IMIs was determined by cow factors. Thus, the high level of multidrug-resistant S. aureus found in the two herds studied together with the predominance of a well udder-adapted S. aureus strain may contribute to the history of the high prevalence of mastitis caused by S. aureus, leading to great animal and public health concerns.
ARTICLE | doi:10.20944/preprints202009.0108.v1
Subject: Life Sciences, Molecular Biology Keywords: Synuclein; CPT1A; MMP14; PYGL; Tfrc; Ireb2; Pgrmc1; Hmox1; Cyp46a1; Slc11a2; Slc25a37
Online: 5 September 2020 (03:54:37 CEST)
Iron deprivation activates mitophagy and extends lifespan in nematodes. In patients suffering from Parkinson’s disease (PD), PINK1-PRKN mutations via deficient mitophagy trigger iron accumulation and reduce lifespan. To evaluate molecular effects of iron chelator drugs as a potential PD therapy, we assessed fibroblasts by global proteome profiles and targeted transcript analyses. In mouse cells, iron shortage decreased protein abundance for iron-binding nucleotide metabolism enzymes (prominently XDH and ferritin homolog RRM2). It also decreased the expression of factors with a role for nucleotide surveillance, which associate with iron-sulfur-clusters (ISC), and are important for growth and survival. This widespread effect included prominently Nthl1-Ppat-Bdh2, but also mitochondrial Glrx5-Nfu1-Bola1, cytosolic Aco1-Abce1-Tyw5, and nuclear Dna2-Elp3-Pold1-Prim2. Incidentally, upregulated Pink1-Prkn levels explained mitophagy induction, the downregulated expression of Slc25a28 suggested it to function in iron export. The impact of PINK1 mutations in mouse and patient cells was pronounced only after iron overload, causing hyperreactive expression of ribosomal surveillance factor Abce1 and of ferritin, despite ferritin translation being repressed by IRP1. This misregulation might be explained by the deficiency of the ISC-biogenesis factor GLRX5. Our systematic survey suggests mitochondrial ISC-biogenesis and post-transcriptional iron regulation to be important in the decision, whether organisms undergo PD pathogenesis or healthy aging.
Fri, 4 September 2020
ARTICLE | doi:10.20944/preprints202009.0106.v1
Subject: Life Sciences, Microbiology Keywords: Fish pathogen; host-pathogen interaction; proteomics; infection assays; virulence factors
Online: 4 September 2020 (12:51:22 CEST)
Piscirickettsia salmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with numerous negative impacts in the Chilean salmon farming industry. Although transcriptomic studies of P. salmonis and its host have been performed, dual host-pathogen proteomic approaches during infection are still missing. Considering that gene expression not always corresponds with observed phenotype, and bacteriological culture studies inadequately reflect infection conditions, to improve the existing knowledge for the pathogenicity of P. salmonis we present here a global proteomic profiling of Salmon salar macrophage-like cell cultures infected with P. salmonis LF-89. The proteomic analyses identified several P. salmonis proteins from two temporally different stages of macrophages infection; some of them related to key functions for bacterial survival in other intracellular pathogens. Metabolic differences were observed in early-stage infection bacteria, compared to late-stage infections. Virulence factors related to membrane, LPS and surface component modifications, cell motility, toxins and secretion systems also varied between the infection stages. Pilus proteins, beta-hemolysin and the T6SS were characteristic of the early-infection stage, while fimbria, upregulation of 10 toxins or effector proteins, and the Dot/Icm T4SS were representative of the late-infection stage bacteria. Previously described virulence-related genes in P. salmonis plasmids were identified by proteomic assays during infection in SHK-1 cells, accompanied by an increase of mobile-related elements. By comparing the infected and un-infected proteome of SHK-1 cells, we observed changes in cellular and ROS homeostasis, innate immune response, microtubules and actin cytoskeleton organization and dynamics, alteration in phagosome components, iron transport and metabolism, and amino acids, nucleoside and nucleotide metabolism, together with an overall energy and ATP production alteration. Our global proteomic profiling and the current knowledge of the P. salmonis infection process allowed us to propose a model of the macrophage-P. salmonis interaction.
ARTICLE | doi:10.20944/preprints202009.0097.v1
Subject: Life Sciences, Genetics Keywords: orphan crop; genotyping-by-sequencing; inbreeding; pre-breeding; population genetics; DArTseq; isolation by distance
Online: 4 September 2020 (11:11:37 CEST)
Kersting’s groundnut is an important source of protein and essential nutrients that contribute to food security in West Africa. However, the crop is still underexploited by the populations and under-researched by the scientific community. This study aimed to investigate the genetic diversity and population structure of 217 Kersting’s groundnut accessions from five origins using 886 DArTseq markers. Gene diversity was low and ranged from 0.049 to 0.064. The number of private alleles greatly varied among populations (42–192) and morphotypes (40–339). Moderate to very high levels of selfing and inbreeding were observed among populations (s=56–85%, FIS=0.389–0.736) and morphotypes (s=57–82%, FIS=0.400–0.691). Moreover, little to very high genetic differentiations were observed among populations (0.006≤FIS≤0.371) and morphotypes (0.029≤FIS≤0.307). Analysis of molecular variance partitioned 38.5% of the genetic variation among and 48.7% within populations (P<0.001). Significant isolations by distance were detected between populations (R2=0.612, P=0.011) and accessions (R2=0.499, P<0.001). Discriminant analysis of principal components and neighbour joining consistently distinguished eight distinct clusters. These data provide a global picture of the existing genetic diversity for Kersting’s groundnut and will guide the choice of breeding strategies to increase production.
REVIEW | doi:10.20944/preprints202009.0091.v1
Subject: Life Sciences, Other Keywords: Evolutionary dynamics; life-history stages; mating systems; biotic interactions; climatic variability; ecological genomics
Online: 4 September 2020 (08:13:40 CEST)
Contemporary climate change is exposing plant populations to novel combinations of temperatures, drought stress, [CO2] and other abiotic and biotic conditions. These changes are rapidly disrupting the evolutionary dynamics of plants. Despite the multifactorial nature of climate change, most studies typically manipulate only one climatic factor. In this opinion piece, we seek to explore how climate change factors interact with each other and with biotic pressures to alter evolutionary processes. We first explore the ramifications of climate change for key life history stages (germination, growth and reproduction). We then examine how mating system variation influences population persistence under rapid environmental change and propose that mixed mating could be advantageous in future climates. Furthermore, we discuss how spatial and temporal mismatches between plants and their mutualists and antagonists could promote or constrain adaptive responses to climate change. For example, plant-virus interactions vary from highly pathogenic to mildly facilitative, and are partly mediated by temperature, moisture availability and [CO2]. Will host plants exposed to novel, stressful abiotic conditions be more susceptible to viral pathogens? Finally, we propose novel experimental approaches that could illuminate how plants will cope with unprecedented global change, such as resurrection studies combined with experimental evolution, genomics or epigenetics.
ARTICLE | doi:10.20944/preprints202009.0090.v1
Subject: Life Sciences, Other Keywords: age; coring sample; forest productivity; Nepal; P. roxburghii; stand structure
Online: 4 September 2020 (08:08:30 CEST)
Distinguishable annual growth rings produce in Pinus roxburghii are an asset to find out the age of individual tree. This paper aimed to determine the age of P. roxburghii through coring samples and test the relationship with forest production. The biomass estimated, girths measured at two different sections and heights measured which allowed to determine the rate of tapering of the stand. The regression analysis was performed to test the relationship between various variables. The mean age of the P. roxburghii stand was found to be 23.97 (~24 years). The result showed the significant (p<0.05) positive correlation coefficient has been seen between age with girth at breast height, biomass, volume and carbon stock. However, no significant (p>0.05) correlation (r = 0.08) was found between age and height of the stand. In contrast, a correlation between diameter at breast height (DBH) was significant (p<0.05) and positive with volume, biomass, but no significant (p>0.05) correlation (r = 0.14) found between DBH and height of the stand. However, height has a significant (p<0.0