HYPOTHESIS Download: 11| View: 14| Comments: 0 | doi:10.20944/preprints202004.0101.v1
Online: 7 April 2020 (12:07:22 CEST)
On March 11, 2020, the World Health Organization declared the coronavirus outbreak a pandemic. Since December 2019, the world has experienced an outbreak of coronavirus disease 2019 (COVID-19). Epidemiology, risk factors, and clinical characteristics of patients with COVID-19 have been reported but the factors affecting the immune system against COVID-19 have not been well described. In this article, we provide a novel hypothesis to describe how an increase in cellular adenosine triphosphate (c-ATP) can potentially improve the efficiency of innate and adaptive immune systems to either prevent and fight off COVID-19.
REVIEW Download: 25| View: 27| Comments: 0 | doi:10.20944/preprints202004.0097.v1
Subject: Life Sciences, Microbiology Keywords: convalescent plasma; serology; pathogen reduction technologies; pathogen inactivation; COVID-19; SARS-CoV2
Online: 7 April 2020 (11:47:15 CEST)
Convalescent blood product therapy has been introduced since early 1900s to treat emerging infectious disease based on the evidence that polyclonal neutralizing antibodies can reduce duration of viremia. Recent large outbreaks of viral diseases for whom effective antivirals or vaccines are still lacking has revamped the interest in convalescent plasma as life-saving treatments. This review summarizes historical settings of application, and surveys current technologies for collection, manufacturing, pathogen inactivation, and banking, with a focus on COVID-19.
REVIEW Download: 43| View: 148| Comments: 0 | doi:10.20944/preprints202004.0091.v1
Subject: Life Sciences, Virology Keywords: Coronavirus; Pneumonia; COVID-19; Virus; Flu; Vaccine; Epidemic; Pandemic
Online: 7 April 2020 (11:15:55 CEST)
The SARS-CoV-2 is a recently identified positive sense single stranded RNA virus and member of the coronavirus family of viruses. It is thought to be the etiological factor for the ongoing COVID-19 pandemic. This virus is thought to have originated from bats and acquired ability of human-to-human transmission. While SARS-CoV-2 is relatively benign, it has infected more than half a million people (as of March 29th 2020) worldwide and the number of infected people continues to rise. More than 170 countries have reported COVID-19 positive cases. With a mortality rate of less than both the previous coronavirus outbreaks, COVID-19 has (conversely) caused the death of over 33,980 (as of 29th March, 2020 at 22.00 hours EDT) people worldwide and the number is increasing. Given the enormous impact of this virus on human health and wellbeing and consequent devastating impacts on world trade, economics and quality of life, it is important to understand this virus better and get insight into its pathogenic mechanisms which will aid in devising effective measure to curb its spread and predict future pattern of its interaction with humans. Though very little is known about this SARS-CoV-2 but its mechanisms and patterns of spread can be speculated (with caution, nevertheless) from what we know about its closest relatives SARS-CoV-1 (responsible for SARS-2002 epidemic) and MERS-CoV (responsible for MERS-2012 epidemic). In the present review, we aim at bringing together the coherent and peer reviewed literature about the SARS-CoV-2 and its close relatives and try to understand its infection patterns and reconstruct its pathogenic mechanisms with anecdotes on diagnosis and future directions. We hope that this paper will serve the purpose of being a reliable source of information to scientists, clinicians and general public.
SHORT NOTE Download: 10| View: 15| Comments: 0 | doi:10.20944/preprints202004.0089.v1
Subject: Life Sciences, Other Keywords: Sars-CoV-2; Homology modelling; Envelope Membrane glycoprotein; Bat; Pangolin; Sars-CoV
Online: 7 April 2020 (11:09:23 CEST)
The Coronavirus disease (COVID-19) is a new viral infection caused by severe acute respiratory coronavirus 2 (SARS-CoV-2) that was initially reported in city of Wuhan, China and afterwards spread globally. Genomic analyses revealed that SARS-CoV-2 is phylogenetically related to severe acute respiratory syndrome-like (SARS-like) Pangolin and Bat coronavirus specific isolates. In this study we focused on two proteins of Sars-CoV-2 surface: Envelope protein and Membrane protein. Sequences from Sars-CoV-2 isolates and other closely related virus were collected from the GenBank through TBlastN searches. The retrieved sequences were multiply aligned with MAFFT. The Envelope protein is identical to the counterparts from Pangolin CoV MP798 isolate and Bat CoV isolates CoVZXC21, CoVZC45 and RaTG13. However, a substitution at position 69 where an Arg replace for Glu, and a deletion in position 70 corresponding to Gly or Cys in other Envelope proteins were found. The Membrane glycoprotein appears more variable with respect to the SARS CoV proteins than the Envelope: a heterogeneity at the N-terminal position, exposed to the virus surface, was found between Pangolin CoV MP798 isolate and Bat CoV isolates CoVZXC21, CoVZC45 and RaTG13. Mutations observed on Envelope protein are drastic and may have significant implications for conformational properties and possibly for protein-protein interactions. Mutations on Membrane protein may also be relevant because this protein cooperates with the Spike during the cell attachment and entry. Therefore, these mutations may influence interaction with host cells. The mutations that have been detected in these comparative studies may reflect functional peculiarities of the Sars-CoV-2 virus and may help explaining the epizootic origin the COVID-19 epidemic.
REVIEW Download: 6| View: 14| Comments: 0 | doi:10.20944/preprints202004.0080.v1
Subject: Life Sciences, Biotechnology Keywords: cancer-related viruses; CRISPR-Cas diagnostic tools; DETECTR; infectious disease; SHERLOCKv2
Online: 7 April 2020 (09:43:22 CEST)
Sensitive and precise nucleic acid detection is critical for clinical diagnostics and biotechnological advancements. Diagnostic in infectious disease field is very unique from diagnosing any other disease, that is time is of the essence; in outbreaks people die even with each passing hour in some cases, if the correct diagnosis wasn't make; for example Zika in particularly is a very challenging virus to diagnose, because it's in very few numbers of copies in the infected person, so it need high sensitive diagnostic approach to spot it, In particular, the advanced tools SHERLOCKv2 and DETECTR, give almost an immediate detection of attomolar amounts of pathogenic nucleic acids with specificity similar to that of PCR but with slight technical settings and that will guide the correct intervention for the patient. SHERLOCKv2 and DETECTR technologies are game changers for our ability to identify infectious disease and rapid detection of tumor DNA or cancer-related viruses with ultra-sensitive tests that don’t require a lot of complicated processing to go through. In this paper, we will review cutting-edge infectious disease diagnosis by CRISPR-Cas systems.
BRIEF REPORT Download: 10| View: 26| Comments: 0 | doi:10.20944/preprints202004.0076.v1
Online: 7 April 2020 (02:27:40 CEST)
Combating viral disease outbreaks has doubtlessly been one of the major public health challenges for the 21st century. Here, the host entry machinery required for COVID-19 (SARS-CoV-2) infection was examined for the gene expression profiles and polymorphism. The four human population groups of Europeans, Africans, Asians, and Americans had specific and also a shared pool of variants for the X-linked locus of ACE2 receptor. Several specific and common ACE2 variants were of the utmost importance to the viral entry and infection. In the absence of gender bias for the gene expression profiles, the hemizygous rare variants of ACE2 describe the observed higher mortality rate in males. Finally, a personalized medicine strategy is conceived for isolating high-risk individuals in epidemic circumstances.
CASE REPORT Download: 24| View: 46| Comments: 1
Subject: Life Sciences, Virology Keywords: COVID-19; coronavirus; fulminant myocarditis; infection; echocardiography.
Online: 7 April 2020 (01:03:22 CEST)
Background: Coronavirus Disease 2019 (COVID-19) has been demonstrated to be the cause of pneumonia. Nevertheless, it has not been reported as the cause of acute myocarditis or fulminant myocarditis. Case presentation: A 63-year-old male was admitted with pneumonia and cardiac symptoms. He was genetically confirmed as having COVID-19 according to sputum testing on the day of admission. He also had elevated troponin I (Trop I) level (up to 11.37 g/L) and diffuse myocardial dyskinesia along with a decreased left ventricular ejection fraction (LVEF) on echocardiography. The highest level of interleukin-6 was 272.40 pg/ml. Bedside chest radiographs showed typical ground-glass changes indicative of viral pneumonia. Laboratory test results for viruses that cause myocarditis were all negative. The patient conformed to the diagnostic criteria of the Chinese expert consensus statement for fulminant myocarditis. After receiving antiviral therapy and mechanical life support, Trop I was reduced to 0.10 g/L, and interleukin-6 was reduced to 7.63 pg/ml. Moreover, the LVEF of the patient gradually recovered to 68%. The patient died of aggravation of secondary infection on the 33rd day of hospitalization. Conclusion: COVID-19 patients may develop severe cardiac complications such as myocarditis and heart failure. This is the first report of COVID-19 complicated with fulminant myocarditis. The mechanism of cardiac pathology caused by COVID-19 needs further study.
Mon, 6 April 2020
ARTICLE Download: 41| View: 160| Comments: 0 | doi:10.20944/preprints202004.0068.v1
Subject: Life Sciences, Biotechnology Keywords: coronavirus; COVID-19; hACE-2; MPro; multi-target-directed ligand; protease inhibito; RdRp; SARS-CoV-2 virus
Online: 6 April 2020 (15:35:33 CEST)
The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from the Coronaviridae family. The disease has infected more than 1 million individuals worldwide with a mortality rate ranging from 5 to 10 %. It has also imposed extreme challenges on global health, economy, and social behavior. Due to the unavailability of therapeutics, several efforts are going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (MPro) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of MPro, we have performed phylogenetic and SSN analysis, that depicted divergence of Coronaviridae MPro in five clusters specific to viral hosts. This clustering was also corroborated with the structural comparison of MPro structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. This conservation can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 MPro. In agreement with this, we performed screening of the custom-made library of ~ 7000 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 MPro as the primary target. It has been observed that natural molecules like d-Viniferin, Myricitrin, Taiwanhomoflavone A, Lactucopicrin 15-oxalate, Nympholide A, Biorobin, Phyllaemblicin B and other several molecules show strong binding with the SARS-CoV-2 MPro. Most of the predicted lead molecules are from Vitis vinifera, also reported for anti-tussive and/or antiviral activities. These molecules also showed strong binding with other main targets RdRp and hACE-2. We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection.
ARTICLE Download: 37| View: 95| Comments: 0 | doi:10.20944/preprints202004.0066.v1
Subject: Life Sciences, Biotechnology Keywords: mitigation strategy; COVID-19; epidemics; health policy; public and global health; demographics; social distancing
Online: 6 April 2020 (15:20:55 CEST)
COVID-19 severity is heterogeneously distributed over age strata, but current mitigation strategies are homogeneously applied to all population. Social-distancing and stay-home are effective conservative approaches but lack economical sustainability on long term. Conversely, herd-immunity is a nonrestrictive strategy which can cost remarkable number of human lives and can melt the healthcare system down.Here I propose an Age Adaptive Social Distancing (AASD) engineering strategy to mitigate COVID-19 outbreak. AASD is based on the scientific evidence that the fatality rate grows nonlinearly with age, hence also the containing strategy should adapt nonlinearly. Essentially, AASD suggests that ‘silent spreaders’ (age 0-39) should avoid/minimize direct and indirect contacts with individuals in ‘dangerous zone’ (age 40+). The rationale is: 0-19 should follow parents strategy, healthy 20-39 (low fatality rate) might conduct screened life under active surveillance, to sustain economy and acquire rational immunity; 40-59 should respect social distancing (waiting a therapy); 60+ should stay at home (waiting a vaccine). This might save human lives, reduce healthcare demand and improve economical sustainability. The final take-home message is that future studies should design precision and personalized strategies for specific contagious diseases that integrate different social constrains, active surveillance and contact tracing.
ARTICLE Download: 5| View: 15| Comments: 0 | doi:10.20944/preprints202004.0064.v1
Subject: Life Sciences, Virology Keywords: erythroparvovirus, tetraparvovirus, protein sequence analyses, overlapping genes, overlapping reading frames VP1, capsid
Online: 6 April 2020 (14:20:35 CEST)
30 years ago, researchers noticed that the capsid (VP1) gene of B19 parvovirus might encode a second protein, called "X", in an overlapping reading frame. Since then, experimental approaches failed to detect it. In contrast, sequence analyses can reliably predict whether a protein is expressed from an overlapping frame, provided that it is beneficial to the virus and thus under selection pressure. We used a dedicated software, Synplot2, to identify regions of VP1 likely to encode functional proteins in overlapping frames. Synplot2 detected the X open reading frame and confirmed it is under highly significant selection pressure. We discovered that the X protein is homologous to the ARF1 protein of human parvovirus 4, another suspected protein encoded in a frame overlapping VP1. These findings provide compelling evidence that the X protein must be expressed and functional. We predict that it contains a predicted transmembrane region. We found that the X frame contains a potential AUG start codon in parvovirus B19 and in all related species. Yet no currently known viral transcript has the potential to encode the X protein in a monocistronic fashion. Therefore, the X protein is probably expressed either from an unmapped monocistronic mRNA, or translated by a non-canonical mechanism from the VP1 mRNA or from a short transcript, R3, which has no currently known function. Finally, Synplot2 also detected proteins likely to be expressed from a frame overlapping VP1 in species distantly related to parvovirus B19: porcine parvovirus 2 and bovine parvovirus 3.
HYPOTHESIS Download: 45| View: 128| Comments: 0 | doi:10.20944/preprints202004.0060.v1
Subject: Life Sciences, Immunology Keywords: COVID-19; coronavirus; cytokine storm; immunity; ADE; cross-reactive antibody; rapamycin; mTOR inhibotors
Online: 6 April 2020 (14:03:00 CEST)
COVID-19 has become a severe global public health concern. The critical illness has a mortality rate of 61.5%, and thus, reducing the severity and mortality is top priority. Currently, inflammatory storms are considered as the cause of critical illness and death due to COVID-19. However, After systematical review of the literature, we proposed that cross-reactive antibodies-associated antibody-dependent enhancement (ADE) may actually be the cause of cytokine storms. If the activation of memory B cells can be selectively inhibited in high-risk patients at an early stage of COVID-19 to reduce the production of cross-reactive antibodies of the virus, we speculate that the ADE can be avoided and severe symptoms can be prevented. The mammalian target of rapamycin (mTOR) inhibitors satisfy such conditions. We recommend that pharmaceutical companies conduct clinical trials urgently.
ARTICLE Download: 8| View: 17| Comments: 0 | doi:10.20944/preprints202004.0053.v1
Subject: Life Sciences, Genetics Keywords: calcium signaling; chemokine signaling; gap junction; NOD-like receptor signaling; oli-neu cells; pannexin1; PI3K-Akt pathway; thyroid hormone pathway
Online: 6 April 2020 (12:36:20 CEST)
We profiled the transcriptomes of primary mouse cortical astrocytes cultured alone or co-cultured with immortalized precursor oligodendrocytes. The experimental set-up (insert systems) prevented formation of gap junction channels but allowed free exchange of the two culture media. The study complements our previously published reports that the genomic fabrics of major functional pathways in oligodendrocytes are substantially remodeled by the proximity of non-touching astrocytes. Here, we present new analysis indicating that the transcriptomic landscape of astrocytes likewise changes significantly in the proximity of non-touching oligodendrocytes. The research was stimulated by the reported transcriptomic similarity between the brains of Cx43KO and Cx32KO mice, both substantially different from that of the Cx36KO mice. Since the three connexins are expressed in different cell types (Cx43 in astrocytes, Cx32 in oligodendrocytes and Cx36 in neurons), altogether these findings support the idea of a “panglial transcriptomic syncytium” in the mouse brain. Going further, our results suggest that integration in a heterocellular tissue modulates not only the expression profile but also the expression control and networking of the genes in each cell phenotype.
ARTICLE Download: 13| View: 45| Comments: 0 | doi:10.20944/preprints202004.0050.v1
Subject: Life Sciences, Biophysics Keywords: Banach–Tarski paradox; brain; power law; fractal; oscillations; information
Online: 6 April 2020 (11:36:49 CEST)
Neuroscientists are able to detect physical changes in information entropy in available neurodata. However, the information paradigm is inadequate to fully describe nervous dynamics and mental activities such as perception. This paper provides an effort to build explanations to neural dynamics alternative to thermodynamic and information accounts. We recall the Banach–Tarski paradox (BTP), which informally states that, when pieces of a ball are moved and rotated without changing their shape, a synergy between two balls of the same volume is achieved instead of the original one. We show how and why BTP might display this physical and biological synergy meaningfully, making it possible to tackle nervous activities. The anatomical and functional structure of the central nervous system’s nodes and edges allows to perform a sequence of moves inside the connectome that doubles the amount of available cortical oscillations. In particular, a BTP-based mechanism permits scale-invariant nervous oscillations to amplify and propagate towards far apart brain areas. Paraphrasing the BPT’s definition, we could state that: when a few components of a self-similar nervous oscillation are moved and rotated throughout the cortical connectome, two self-similar oscillations are achieved instead of the original one. Furthermore, based on topological structures, we illustrate how, counterintuitively, the amplification of scale-free oscillations does not require information transfer.
Fri, 3 April 2020
REVIEW Download: 123| View: 293| Comments: 3 | doi:10.20944/preprints202004.0040.v1
Subject: Life Sciences, Virology Keywords: Dengue; COVID-19; SARS-CoV-2; epidemiology; infection; mortality; cross-protection; Dengue vaccine; ELISA; Dengvaxia
Online: 3 April 2020 (15:48:36 CEST)
We observed that global severity maps of ongoing dengue epidemic and COVID-19 pandemic do not overlap. Countries where dengue is highly endemic (>1.5 million cases/year) appear to be less hit by COVID-19 pandemic in terms of infection and transmission. Other evidences also support our proposition that pre-exposure to other wide-spread viral infections like dengue may thwart the spread of the COVID-19 pandemic.
REVIEW Download: 50| View: 115| Comments: 1 | doi:10.20944/preprints202004.0019.v2
Online: 3 April 2020 (15:23:50 CEST)
OBJECTIVE: Recent worldwide outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of respiratory coronavirus disease 2019 (COVID-19), is a current, ongoing life-threatening crisis and international public health emergency. The early diagnosis and management of the disease remains a major challenge. In this review, we aim to summarize the updated epidemiology, causes, clinical manifestation and diagnosis, as well as prevention and control of the novel coronavirus SARS-CoV-2.MATERIALS AND METHODS: A broad search of the literature was performed in “PubMed” “Medline” “Web of knowledge”, and “Google Scholar” World Health Organization-WHO” using the keywords “severe acute respiratory syndrome coronavirus”, “2019-nCoV”, “COVID-19, “SARS”, “SARS-CoV-2” “Epidemiology” “Transmission” “Pathogenesis” “Clinical Characteristics”. We reviewed and documented the information obtained from literature on epidemiology, pathogenesis and clinical appearances of SARS-CoV-2 infection.RESULTS: The global cases of COVID-19 as of April 2, 2020 have risen to more than 900,000 and morbidity has reached more than 47,000. The incidence rate for COVID-19 has been predicted to be higher than the previous outbreaks of other coronavirus family members, including those of SARS-CoV and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The main clinical presentation of SARS-CoV-2 infection ranges from asymptomatic stages to severe lower respiratory infection in the form of pneumonia. Most of the patients also presented with fever, cough, sore throat, headache, fatigue, myalgia and breathlessness.Individuals at higher risk for severe illness include elderly people and patients with a weakened immune system or that are suffering from a underlying chronic medical condition like hypertension, diabetes, cancer, respiratory illness or cardiovascular diseases.CONCLUSIONS: SARS-Cov-2 has emerged as a worldwide threat, currently affecting 170 countries and territories across the globe. There is still much to be understood regarding SARS-CoV-2 about its virology, epidemiology and clinical management strategies; this knowledge will be essential to both manage the current pandemic and to conceive comprehensive measures to prevent such outbreaks in the future.
BRIEF REPORT Download: 77| View: 225| Comments: 0 | doi:10.20944/preprints202004.0024.v1
Subject: Life Sciences, Virology Keywords: COVID-19; SARS-nCoV-2; vaccine; antibody; immune escape; variant; spike protein; genomic drift; convalescent plasma
Online: 3 April 2020 (04:24:52 CEST)
New coronavirus (SARS-CoV-2) treatments and vaccines are under development to combat the COVID-19 disease. Several approaches are being used by scientists for investigation including 1) various small molecule approaches targeting RNA polymerase, 3C-like protease, and RNA endonuclease and 2) exploration of antibodies obtained from convalescent plasma from patients who have recovered from COVID-19. The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. As the disease has grown to become a pandemic, new B-cell and T-cell epitopes predicted from SARS coronavirus have been reported. Using the epitope information along with variants of the virus, we have found several variants which might cause drifts. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries such as the Netherlands, Switzerland and France.
COMMUNICATION Download: 74| View: 130| Comments: 0
Subject: Life Sciences, Virology Keywords: anti-viral; COVID-19, SARS-CoV-2; autophagy; chloroquine; hydroxychloroquine; immunology; infection; inflammation; lysophagy; microbiology; Plaquenil; SARS; virophagy
Online: 3 April 2020 (03:57:49 CEST)
At a time when the world faces an emotional breakdown, crushing our dreams if not taking our lives, we realize that together we must fight the war against the COVID-19 outbreak even if almost the majority of the scientific community finds itself confined to home. Every day, like everyone else, we, scientists, listen to the latest news with its promises and announcements. Across the world, a surge of clinical trials trying to cure or slow down the coronavirus pandemic has been launched to bring hope instead of fear and despair. One of the most recent has drawn worldwide hype to the possible benefit of chloroquine (CQ), a well-known and broadly used anti-malarial drug, in the treatment of patients infected by the recently emerged deadly coronavirus (SARS-CoV-2). We should consider this information in the light of the long-standing anti-inflammatory and anti-viral properties of CQ-related drugs. Yet, none of these articles evoked a possible molecular or cellular mechanism of action that could account for any efficacy. Here, given the interaction of viruses with macroautophagy (hereafter referred to as autophagy), a CQ-sensitive anti-viral safeguard pathway, we would like to discuss some pros and cons concerning the current therapeutic options targeting this process.
Thu, 2 April 2020
REVIEW Download: 57| View: 85| Comments: 0 | doi:10.20944/preprints202004.0019.v1
Online: 2 April 2020 (12:20:19 CEST)
OBJECTIVE: Recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), another member of coronavirus family is an ongoing worldwide life-threatening crisis. The early diagnosis and management of the disease remains a major challenge. In this review, we aim to summarize the updated epidemiology, causes, clinical manifestation and diagnosis, as well as prevention and control of the novel coronavirus SARS-CoV-2. MATERIALS AND METHODS: A broad search of the literature was performed in “PubMed” “Medline” “Web of knowledge”, and “Google Scholar” World Health Organization-WHO” using the key words “severe acute respiratory syndrome coronavirus”, “SARS”, “SARS-CoV-2” “Epidemiology” “Transmission” “Pathogenesis” “Clinical Characteristics”. We reviewed and documented the information attained from literature on epidemiology, pathogenesis and clinical appearances of SARS-CoV-2 infection. RESULTS: The global cases of COVID-19 till 30th March 2020 have rose more than 700,000 and morbidity has gone more than 37,000. The infection rate for COVID-19 has been predicted to be higher than the previous outbreaks of same family members, that includes the SARS-CoV and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The main clinical presentation ranges from asymptomatic stages to severe lower respiratory infection in the form of pneumonia. Most of the patients also presented with fever, cough, sore throat, headache, fatigue, myalgia and breathlessness. High risk includes elderly people and patients with weak immune system or suffering from chronic medical condition like hypertension, diabetes, cancer, respiratory illness and cardiovascular diseases. CONCLUSIONS: SARS-Cov-2 has emerged as a worldwide threat, affecting almost each and every country on globe. As there is still growing understanding of SARS-CoV-2 in relation to its virology, epidemiology and clinical management strategies, we need to learn our lessons to conceive comprehensive measures to prevent such outbreaks in future.
REVIEW Download: 435| View: 1064| Comments: 0 | doi:10.20944/preprints202004.0018.v1
Subject: Life Sciences, Virology Keywords: COVID-19 response; MERS-CoV; Saudi Arabia; travel restrictions; Pandemic preparedness
Online: 2 April 2020 (12:08:33 CEST)
Nearly three months have passed since the emergence of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which caused the rapidly spreading Coronavirus Disease 2019 (COVID-19) pandemic. To date, there have been more than 550,000 confirmed cases and more than 25,000 deaths globally caused by COVID-19. Chinese health authorities, where the virus emerged, have taken prompt strict public health measures to control and prevent the spread of the outbreak. In the kingdom of Saudi Arabia, unprecedented precautionary strict measures were applied to slow virus entry and to mitigate the risk of the outbreak. Here, we review the experience learned during the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) epidemic in Saudi Arabia, which has been in the country since 2012, and is expected to have helped the country to be well prepared for the current COVID-19 pandemic. We also discuss the country readiness, improvement in research and development, and the unprecedented rapid precautionary measures that have been taken by the Saudi government thus far.
ARTICLE Download: 27| View: 32| Comments: 0 | doi:10.20944/preprints202004.0016.v1
Subject: Life Sciences, Other Keywords: glaucoma; retina ganglion cell degeneration; microarray; genes coordination; notch signaling pathway; complement cascade
Online: 2 April 2020 (11:59:28 CEST)
Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the retinal ganglion cells (RGCs). There has been little progress in developing efficient strategies for neuroprotection in glaucoma. We profiled the retina transcriptome of Lister Hooded rats at 2 weeks after optic nerve crush (ONC) and applied systems biology approaches to better understand the molecular mechanisms related with the retinal remodeling after induction of RGC degeneration. We observed a higher Relative Expression Variability after ONC. Gene expression stability was used as a measure of transcription control and disclosed a robust reduction in the number of very stably expressed genes. Enrichment analysis showed that Complement cascade and Notch signaling pathway were the main affected pathways after ONC. To expand our studies of these two pathways, we examined the coordination of gene expressions within each pathway and with the entire transcriptome. ONC increased the number of synergistically coordinated pairs of genes and the number of similar profiles. This study provided novel findings beyond the regulation of individual gene expression and disclosed changes in the control of expression by Complement cascade and Notch signaling functional pathways important for both RGC degeneration and remodeling of the retinal tissue after ONC.
HYPOTHESIS Download: 127| View: 230| Comments: 0 | doi:10.20944/preprints202004.0014.v1
Online: 2 April 2020 (11:28:57 CEST)
Severe acute respiratory syndrome coronavirus 2 (SARS coronavirus 2 or SARS-CoV2) is the cause of the respiratory infection known as COVID-19. From an immunopathological standpoint, coronaviruses such as SARS-CoV2 induce an increase in a variety of T-helper 1 (Th1) and inflammatory cytokines and chemokines including interleukins IL-1, IL-6, CCL2 protein and CXCL10 protein. In the absence of proven antiviral agents or an effective vaccine, substances with immunomodulatory activity may be able to inhibit inflammatory and Th1 cytokines and/or yield an anti-inflammatory and/or Th2 immune response to counteract COVID-19 symptoms and severity. This report briefly describes four unconventional but commercially accessible immunomodulatory agents that could be employed in clinical trials to evaluate their effectiveness at alleviating disease symptoms and severity: Low-dose oral interferon-alpha, microdose DNA, low-dose thimerosal and phytocannabinoids.
COMMUNICATION Download: 60| View: 120| Comments: 1 | doi:10.20944/preprints202003.0395.v2
Subject: Life Sciences, Biotechnology Keywords: Novel coronavirus (SARS-CoV-2); RdRp; HCV; beclabuvir; in silico; molecular docking
Online: 2 April 2020 (11:25:57 CEST)
Recent emergence of novel coronavirus (SARS-CoV-2) all over the world has resulted more than 33,106 global deaths. To date well-established therapeutics modules for infected patients are unknown. In this present initiative, molecular interactions between FDA-approved antiviral drugs against the Hepatitis-C virus (HCV) have been investigated theoretically against the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. HCV and SARS-CoV-2 are both +ssRNA viruses. At 25o C beclabuvir, a non-nucleoside inhibitor of the RdRpHCV can efficiently bind to RdRp SARS-CoV-2 (ΔGAutoDock = -9.95 kcal mol-1) with an inhibition constant of 51.03 nM. Both the ΔGLondon and ΔGGBVI / WSA values were - 9.06 and - 6.67 kcal mol-1, respectively for binding of beclabuvir to RdRpSARS-CoV-2. In addition, beclabuvir has also shown better binding free energy with RdRpSARS-CoV-2 (ΔGvina = -8.0 kcal mol-1) than that observed with the Thumb 1 domain of RdRpHCV (ΔGvina = -7.1 kcal mol-1). InterProScan has suggested the RNA-directed 5'-3' polymerase activity exists within 549th to 776th amino acid residues of RdRpSARS-CoV, where the major amino acid residues interacting being I591, Y621, C624, D625, A690, N693, L760, D762, D763, and E813-N817. Molecular interaction suggests occupancy of beclabuvir inside the active site environment of the RdRpSARS-CoV-2, the enzyme essential for viral RNA synthesis. In conclusion, results suggest beclabuvir may serve as an anti-SARS-CoV-2 drug.
HYPOTHESIS Download: 74| View: 523| Comments: 1 | doi:10.20944/preprints202003.0419.v2
Subject: Life Sciences, Other Keywords: origin of genetic codes; ATP-hypothesis; solar energy driven synthesis of chemicals; informatization; structuralization
Online: 2 April 2020 (05:16:09 CEST)
The origin of genetic codes is the key to reveal life’s origin on the earth as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of genetic codes, while their origin is still one of the greatest mysteries. Are the origins of genetic codes really unknowable? Do they really require external design? Here, I present an ATP-hypothesis that explains how the genetic codes came into being with the coevolution of biochemical system. ATP has several properties that make it suitable as the initiator of the origin of genetic codes. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as carriers of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between them, and eventually mediating prebiotic biochemical transaction from energy to information. This hypothesis shows how primitive life emerged through a series of processes from energy to information mediated by ATP. Informatization (processes of creating and managing information) was inevitably coupled with structuralization (processes of organizing or incorporating into a cellular structure), making polynucleotides and polypeptides be cyclized into a system of reciprocal causation. The triplet codon might just be for stereo-chemical handing of amino acid through e.g. Watson–Crick pairing interactions. It is an evolutionary completion for genetic codes from RNA to DNA, only which, a reverse to the Central Dogma, marked the dawn of cellular life when Darwinian evolution began to operate. ATP-hypothesis shades lights on the origin of life, together with the formations of both photosynthesis and biochemical systems, which have been largely unknown so far.
REVIEW Download: 14| View: 14| Comments: 0
Subject: Life Sciences, Biochemistry Keywords: RecG; SSB; stalled DNA replication fork; DNA repair; DNA replication; helicase; atomic force microscopy; OB-fold; SH3 domain; PXXP motif
Online: 2 April 2020 (04:26:52 CEST)
In E. coli DNA replication forks stall on average once per cell cycle. When this occurs, replisome components disengage from the DNA, exposing an intact, or nearly intact fork. Consequently, the fork structure must be regressed away from the initial impediment so repair can occur. Regression is catalyzed by the powerful, monomeric DNA helicase, RecG. During this reaction, the enzyme couples unwinding of fork arms to rewinding of duplex DNA resulting in the formation of a Holliday junction. RecG works against large opposing forces enabling it to clear the fork of bound proteins. Following subsequent processing of the extruded junction, the PriA helicase mediates reloading of the replicative helicase DnaB leading to the resumption of DNA replication. The single-strand binding protein (SSB) plays a key role in mediating PriA and RecG functions at forks. It binds to each enzyme via linker/OB-fold interactions and controls fork loading sites in a substrate-dependent manner that involves helicase remodeling. Finally, it is displaced by RecG during fork regression. The intimate and dynamic SSB-helicase interactions play key roles in ensuring fork regression and DNA replication restart.
ARTICLE Download: 42| View: 56| Comments: 0 | doi:10.20944/preprints202004.0008.v1
Subject: Life Sciences, Biophysics Keywords: bottom-up synthetic biology; motor proteins; pattern formation; self-organization
Online: 2 April 2020 (04:02:53 CEST)
Cortical actomyosin flows, among other mechanisms, scale up spontaneous symmetry breaking and thus play pivotal roles in cell differentiation, division, and motility. According to many model systems, myosin motor-induced local contractions of initially isotropic actomyosin cortices are nucleation points for generating cortical flows. However, the positive feedback mechanisms by which spontaneous contractions can be amplified towards large-scale directed flows remain mostly speculative. To investigate such a process on spherical surfaces, we reconstituted and confined initially isotropic minimal actomyosin cortices to the interfaces of emulsion droplets. The presence of ATP leads to myosin-induced local contractions that self-organize and amplify into directed, large-scale actomyosin flows. By combining our experiments with theory, we found that the feedback mechanism leading to a coordinated, directional motion of actomyosin clusters can be described as asymmetric cluster vibrations, caused by intrinsic non-isotropic ATP consumption, in conjunction with spatial confinement. By tracking individual actomyosin clusters, we identified fingerprints of vibrational states as the basis of directed motions. These vibrations may represent a generic key driver of directed actomyosin flows under spatial confinement in vitro and in living systems.
Wed, 1 April 2020
COMMUNICATION Download: 366| View: 545| Comments: 0 | doi:10.20944/preprints202004.0006.v1
Online: 1 April 2020 (09:30:36 CEST)
The novel coronavirus, COVID-19 is now officially declared as a pandemic by the World Health Organization (WHO), and most parts of the world are taking drastic measures to restrict human movements to contain the infection. Like millions of others around the world, I am wondering, is there anything that could be done, other than keeping high personal hygiene, and be vigilant of symptoms, to reduce the chances of infection, or at least to reduce the burden of the disease. So far, the National and International health agencies, including the National Institutes of Health (NIH), the Centers for Disease Control and Prevention (CDC), and the WHO have provided clear guidelines for both preventive and treatment suggestions. In this opinion-based article, I want to discuss, why keeping the adequate micronutrient balance might enhance the host response and be protective of viral infections. A detailed in-depth discussion of various micronutrients is not the purpose of this article, I will mostly emphasize on the role of zinc in viral infection.
REVIEW Download: 975| View: 1069| Comments: 0 | doi:10.20944/preprints202004.0005.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Coronavirus; Pandemic; Viral Genomics
Online: 1 April 2020 (09:22:38 CEST)
The COVID-19 pandemic is due to infection caused by the novel SARS-CoV-2 that impacts the lower respiratory tract. The spectrum of symptoms ranges from asymptomatic infections to mild respiratory symptoms to the lethal form of COVID-19 which is associated with severe pneumonia, acute respiratory distress and fatality. At present, the global case fatality rate of COVID-19 laboratory confirmed cases is ~4.7% ranging from ~0.3-0.4% in Chile and Israel to ~10.8% in Italy. To address this global crisis, up-to-date information on the viral genomics and transcriptomics is crucial for understanding the origins and global dispersal of the virus, providing insight into viral pathogenicity, transmission and epidemiology, and enabling strategies for therapeutic interventions, drug discovery and vaccine development. Therefore, this review provides a comprehensive overview of COVID-19 epidemiology, genomic etiology, findings from recent transcriptomic map analysis, viral-human protein interactions, molecular diagnostics, and the current status of vaccine and novel therapeutic intervention development. Moreover, we provide an extensive list of resources that will help the scientific community access numerous types of databases related to SARS-CoV-2 OMICs and approaches to therapeutics related to COVID-19 treatment.
BRIEF REPORT Download: 260| View: 408| Comments: 1 | doi:10.20944/preprints202004.0004.v1
Subject: Life Sciences, Virology Keywords: COVID-19, Pakistan, Economic Losses, Disease Spread, SARS-CoV-2
Online: 1 April 2020 (09:19:30 CEST)
As of 26 March 2020, Pakistan had 1179 cases of COVID-19, with most 421 cases from Sindh, 394 cases, 131 cases, 123 cases, 84 cases, 25 cases and 01 cases from Punjab, Balochistan, Khyber Pakhtunkhwa, Gilgit-Baltistan, Islamabad Capital Territory, and Azad Jammu and Kashmir respectively. Travel-related cases were the main source of SARS-CoV-2 infection during the early phase of the pandemic in Pakistan. Nevertheless, cases of local virus transmission are increasing day by day. As of 26 March 2020, nine deaths have been reported from COVID-19. The case fatality rate is 0.8%, which is less compare to China, Italy, USA, and Iran. The SIR (Susceptible-Infected-Recovered) model of epidemiological analysis predicts that almost 90 million population will be infected in the coming days with 5% critical cases that need health care facilities. However, the Pakistan health care system cannot provide services to this much population. Hence, we need to act timely to reduce this number by restricting local transmission of the disease. This can be done by mass testing, quarantine, isolation and social distancing of the active coronavirus cases in Pakistan. Moreover, better communication between the authorities is very much required to control disease transmission.
Tue, 31 March 2020
HYPOTHESIS Download: 37| View: 64| Comments: 0 | doi:10.20944/preprints202003.0459.v1
Subject: Life Sciences, Biophysics Keywords: topological quantum brain; quantum computing; Majorana Zero modes; qualia; consciousness
Online: 31 March 2020 (10:41:35 CEST)
Controversial hypotheses to explain consciousness exist in many fields of science, psychology and philosophy. Recent experimental findings in quantum cognition and magnetic resonance imaging have added new controversies to the field, suggesting that the mind may be based on quantum computing. Quantum computers process information in quantum bits (qubits) using quantum gates. At a first glance, it seems unrealistic or impossible that the brain can meet the challenges to provide either of these. Nevertheless, we show here why the brain has the incredible ability to perform quantum computing and how that may be realized.
ARTICLE Download: 35| View: 83| Comments: 0 | doi:10.20944/preprints202003.0448.v1
Subject: Life Sciences, Microbiology Keywords: Escherichia coli; ESBL; hybrid pathotype; ExPEC; EPEC; MDR; ST10; O153; Enterobase
Online: 31 March 2020 (09:51:05 CEST)
Different surveillance studies (2005-2015) on the presence of ESBL-producing E. coli in the northwest Spain revealed that eae-positive isolates of serotype O153:H10 were periodically detected in meat (of beef, chicken and pork), and also implicated in human diarrhea. This study aimed: i) to characterize the degree of relatedness between human and animal isolates; ii) to know if this was a geographically restricted or disseminated genetic lineage. Thirty-two isolates were conventionally typified as O153:H10-A-ST10 fimH54, fimAvMT78, traT and eae-beta1, being 21 of those CTX-M-32 or SHV-12 producers. PFGE comparison of their macrorestriction profiles showed high similarity (>85%). The plasmidome analysis revealed a stable combination of IncF (F2:A-:B-), IncI1 (STunknown) and IncX1 plasmid types, together with non-conjugative Col-like. Besides, the core genome investigation based on the cgMLST scheme from Enterobase, proved close relatedness between isolates of human and animal origin. Our results demonstrate that a hybrid MDR aEPEC/ExPEC of clonal group O153:H10-A-ST10 (CH11-54) would be playing a successful role in spreading ESBLs (CTX-M-32) in our region within different hosts, including wildlife. It would be potentially implicated in human diarrhea via food (meat) transmission. Importantly, we proved genomic evidence of a related hybrid aEPEC/ExPEC in other countries.
BRIEF REPORT Download: 198| View: 502| Comments: 0 | doi:10.20944/preprints202003.0446.v1
Online: 31 March 2020 (05:08:29 CEST)
The COVID-19 pandemic caused by SARS-COV-2 has infected over 500,000 people causing over 25,000 deaths in the last 10 weeks. A key host cellular protein required for the virus entry is angiotensin-converting enzyme 2 (ACE2). Recent studies have reported that patients with hypertension and diabetes treated with ACE inhibitors or angiotensin receptor blockers might be at a higher risk of COVID-19 infection as these drugs have been reported to increase ACE2 expression. This has raised the need to systematically investigate the effect of different drugs including antihypertensives on modulating ACE2 expression. Here, we analyzed a publicly available CMAP dataset of pre/post transcriptomic profiles for drug treatment in cell lines for over 20,000 small molecules. We show that only one subclass of antihypertensives drugs - ACE inhibitors, are significantly enriched for drugs up-regulating ACE2 expression. Studying the effects of the 672 clinically approved drugs in CMAP, we chart the drug categories that affect ACE2 expression. Specifically, we find that panobinostat (an HDAC inhibitor) confers the highest up-regulation of ACE2 expression while isotretinoin (a vitamin A derivative) is its strongest down-regulator. Our results provide initial candidates guiding further in vitro and in vivo studies aimed at assessing drug effects on ACE2 expression.
ARTICLE Download: 18| View: 35| Comments: 1 | doi:10.20944/preprints202001.0157.v3
Subject: Life Sciences, Biochemistry Keywords: pectin; antioxidant; lemon; flavonoids; hydrodynamic cavitation; IntegroPectin
Online: 31 March 2020 (05:00:13 CEST)
Lemon pectin extracted along with water-soluble flavonoids and other phytochemicals from citrus industry’s waste lemon peel via hydrodynamic cavitation in water, directly at pre-industrial scale and further isolated via freeze drying, shows exceptionally high antioxidant and non-cytotoxic activity. Preliminary investigation indicates also significant antimicrobial activity. These findings open the route to the development of new nutraceutical and healthcare application of a versatile biopolymer endowed with new functionality, rapidly and conveniently obtained from an abundant by-product of the agrofood industry.
Mon, 30 March 2020
BRIEF REPORT Download: 83| View: 164| Comments: 1 | doi:10.20944/preprints202003.0394.v2
Online: 30 March 2020 (08:25:51 CEST)
The recent outbreak of novel coronavirus (SARS-CoV-2 or 2019-nCoV) and its spread to the whole world is currently posing one of the major threats to human health and the world economy. It has been suggested that SARS-CoV-2 is similar to SARS-CoV based on the genome sequence comparison. Despite the genomic similarity between SARS-CoV and SARS-CoV-2, the spike glycoprotein and receptor binding domain in SARS-CoV-2 shows considerable difference compared to SARS-CoV, due to the presence of several point mutations. We analyzed the receptor binding domain (RBD) from recently published 3D structure of spike glycoprotein of SARS-CoV-2 and compared with RBD of SARS-CoV. The observations highlight few important features of RBD in the light of the recently published findings from the 3D structures of spike glycoprotein and its complex with human angiotensin-converting enzyme 2 (ACE2) (Yan, R., et al. (2020); Wrapp, D., et al. (2020); Walls, A. C., et al. (2020)).
ARTICLE Download: 352| View: 767| Comments: 0 | doi:10.20944/preprints202003.0440.v1
Subject: Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; 2019-nCoV; novel corona virus; drug repurposing; chloroquine; high-risk group; asymptomatic
Online: 30 March 2020 (07:24:16 CEST)
COVID-19 (2019-nCoV) is a pandemic disease with an estimated mortality rate of 3.4% (estimated by the WHO as of March 3, 2020). Until now there is no antiviral drug and vaccine for COVID-19. The current overwhelming situation by COVID-19 patients in hospitals is likely to increase in the next few months. About 15 percent of patients with serious disease in COVID-19 require immediate health services. Rather than waiting for new anti-viral drugs or vaccines that take a few months to years to develop and test, several researchers and public health agencies are attempting to repurpose medicines that are already approved for another similar disease and have proved to be fairly effective. This study aims to identify FDA approved drugs that can be used for drug repurposing and identify biomarkers among high- risk and asymptomatic groups. In this study gene-disease association related to COVID-19 reported mild, severe symptoms and clinical outcomes were determined. The high-risk group was studied related to SARS-CoV-2 viral entry and life cycle by using Disgenet and compared with curated COVID-19 gene data sets from the CTD database. The overlapped gene sets were enriched and the selected genes were constructed for protein-protein interaction networks. Through interactome, key genes were identified for COVID-19 and also for high risk and asymptomatic groups. The key hub genes involved in COVID-19 were VEGFA, TNF, IL-6, CXCL8, IL10, CCL2, IL1B, TLR4, ICAM1, MMP9. The identified key genes were used for drug-gene interaction for drug repurposing. The chloroquine, lenalidomide, pentoxifylline, thalidome, sorafenib, pacitaxel, rapamycin, cortisol, statins were proposed to be probable drug repurposing candidates for the treatment of COVID-19. However, these predicted drug candidates need to be validated through randomized clinical trials. Also, a key gene involved in high risk and the asymptomatic group were identified, which can be used as probable biomarkers for early identification.
SHORT NOTE Download: 43| View: 111| Comments: 1 | doi:10.20944/preprints202002.0289.v4
Subject: Life Sciences, Biochemistry Keywords: COVID-19; proton affinity; calcium oxalate; isoleucine; valine; glycine; prophylactic approach
Online: 30 March 2020 (04:56:42 CEST)
The current pneumonia epidemic in China could evolve into a pandemic on a global scale if not effectively contained. The COVID-19 possesses a 61-amino acid open reading frame resembling SARS-CoV virulence factor - ORF6 peptide. The isoleucine content is 15.9% in ORF6 of SARS-CoV versus 16.4% of that in COVID-19. Given the proton affinity in the carbonyl oxygen in isoleucine, augmented proton traffic can enhance proton-ion antiport and prompt cell swelling. Calorie restriction has been confirmed in animal studies to extend lifespan, and its underlying mechanism is not fully known. As the content of essential amino acids in the open reading frame of COVID-19 reaches 57.4%, a starch/vitamin diet served for short period of time does not give rise to essential amino acids and halts virion production, which could be adopted as prophylactic approach of many viral infections. Plant-based diet or fasting/boiled rice water can also minimize the intake of essential amino acids or all amino acids respectively. Furthermore, several proteins of COVID-19 possess high valine plus glycine content which is implicated in heart disease, justifying the aforementioned approaches.
ARTICLE Download: 95| View: 211| Comments: 0 | doi:10.20944/preprints202003.0437.v1
Online: 30 March 2020 (03:34:26 CEST)
All RNA viruses deliver their genomes into target host cells through processes distinct from normal trafficking of cellular RNA transcripts. The delivery of viral RNA into most cells hence triggers innate antiviral defenses that recognize viral RNA as foreign. In turn, viruses have evolved mechanisms to subvert these defenses, allowing them to thrive in target cells. Therefore, drugs activating defense to foreign or exogenous RNA could serve as broad-spectrum antiviral drugs. Here we show that transcriptional signatures associated with cellular responses to the delivery of a non-viral exogenous RNA sequence into human cells predicts small molecules with broad-spectrum antiviral activity. In particular, transcriptional responses to the delivery of cas9 mRNA into human hematopoietic stem and progenitor cells (HSPCs) highly matches those triggered by small molecules with broad-spectrum antiviral activity such as emetine, homoharringtonine, pyrvinium pamoate and anisomycin, indicating that these drugs are potentially active against other RNA viruses. Furthermore, these drugs have been approved for other indications and could thereby be repurposed to novel viruses. We propose that the antiviral activity of these drugs to SARS-CoV-2 should therefore be determined as they have been shown as active against other coronaviruses including SARS-CoV and MERS-CoV. These drugs could also be explored as potential adjuvants to COVID-19 vaccines in development due to their potential effect on the innate antiviral defenses that could bolster adaptive immunity when delivered alongside vaccine antigens.
Sun, 29 March 2020
ARTICLE Download: 70| View: 121| Comments: 0 | doi:10.20944/preprints202003.0429.v1
Subject: Life Sciences, Other Keywords: Blumeria graminis; hexaploid bread wheat; Magnaporthe oryzae; Mlo; plant disease resistance; powdery mildew; TALEN; TILLING; Zymoseptoria tritici
Online: 29 March 2020 (09:10:52 CEST)
Barley mlo mutants are well known for their profound resistance against powdery mildew disease. Recently, mlo mutant plants were generated in hexaploid bread wheat (Triticum aestivum) with the help of transgenic (transcription-activator-like nuclease, TALEN) and non-transgenic (targeted induced local lesions in genomes, TILLING) biotechnological approaches. While full gene knockouts in the three wheat Mlo (TaMlo) homoeologs, created via TALEN, confer full resistance to the wheat powdery mildew pathogen (Blumeria graminis f.sp. tritici), the currently available TILLING-derived Tamlo missense mutants provide only partial protection against powdery mildew attack. Here we studied the infection phenotypes of TALEN- and TILLING-derived Tamlo plants to the two hemibiotrophic pathogens Zymoseptoria tritici, causing Septoria leaf blotch in wheat, and Magnaporthe oryzae pv. Triticum (MoT), the causal agent of wheat blast disease. While Tamlo plants showed unaltered outcomes upon challenge with Z. tritici, we found allele-specific levels of enhanced susceptibility to MoT, with stronger powdery mildew resistance correlated with more invasive growth by the blast pathogen. Surprisingly, unlike barley mlo mutants, young wheat mlo mutant plants do not show undesired pleiotropic phenotypes such as spontaneous callose deposits in leaf mesophyll cells or signs of early leaf senescence. In conclusion, our study provides evidence for allele-specific levels of enhanced susceptibility of Tamlo plants to the hemibiotrophic wheat pathogen MoT.
HYPOTHESIS Download: 137| View: 170| Comments: 0 | doi:10.20944/preprints202003.0428.v1
Subject: Life Sciences, Biophysics Keywords: COVID-19; SARS-CoV-2; furin cleavage site (FCS); salt bridging analysis
Online: 29 March 2020 (08:54:42 CEST)
One notable features of the SARS-CoV-2 genome is that the spike protein of SARS-CoV-2 has a functional polybasic (furin) cleavage site (RRAR) at the S1–S2 boundary through the insertion of 12 nucleotides encoding PRRA. To date, the furin cleavage site (FCS) remains an experimentally uncharted territory both structurally and functionally. For instance, whether or not FCS is actually cleaved, before or after viral cell entry or exit, still remains to be experimentally investigated. With currently available structural data, this article presents a computational structural characterization of the FCS inserted into SARS-CoV-2 spike glycoprotein, and puts forward a set of structural hypothesis against the hypothesis of SARS-CoV-2 from purposeful manipulation: (1), the inserted FCS does not alter, neither stabilize nor de-stabilize, the overall structure of SARS-CoV-2 spike glycoprotein; (2), the net structural consequence of FCS is the insertion of a furin cleavage site into SARS-CoV-2 spike glycoprotein, whose S1 and S2 subunits will still be bonded together even if the FCS is actually cleaved by furin protease.
ARTICLE Download: 39| View: 53| Comments: 0 | doi:10.20944/preprints202003.0424.v1
Subject: Life Sciences, Genetics Keywords: primary congenital glaucoma; exome sequencing; GUCA1C; GCAP3; zebrafish; CRISPR/Cas9
Online: 29 March 2020 (06:33:17 CEST)
Primary congenital glaucoma (PCG) is a heterogeneous, inherited, and severe optical neuropathy caused by apoptotic degeneration of the retinal ganglion cell layer. Whole-exome sequencing analysis of one PCG family identified two affected siblings who carried a low-frequency homozygous nonsense GUCA1C variant (c.52G>T/p.Glu18Ter/rs143174402). This gene encodes GCAP3, a member of the guanylate cyclase activating protein family, involved in phototransduction and with a potential role in intraocular pressure regulation. Segregation analysis supported the notion that the variant was coinherited with the disease in an autosomal recessive fashion. GCAP3 was detected immunohistochemically in the adult human ocular ciliary epithelium and retina. To evaluate the ocular effect of GUCA1C loss-of-function, a guca1c knockout zebrafish line was generated by CRISPR/Cas9 genome editing. Immunohistochemistry demonstrated the presence of GCAP3 in the non-pigmented ciliary epithelium and retina of adult wild-type fishes. Knockout animals presented up-regulation of the glial fibrillary acidic protein in Müller cells and evidence of retinal ganglion cell apoptosis, indicating the existence of gliosis and glaucoma-like retinal damage. In summary, our data provide evidence for the role of GUCA1C as a candidate gene in PCG and offer new insights into the function of this gene in the ocular anterior segment and the retina.
HYPOTHESIS Download: 107| View: 372| Comments: 1 | doi:10.20944/preprints202003.0419.v1
Subject: Life Sciences, Other Keywords: origin of genetic codes; ATP-hypothesis; solar energy driven synthesis of chemicals; informatization; structuralization
Online: 29 March 2020 (04:08:22 CEST)
The origin of genetic codes is the key to reveal life’s origin on the earth as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of genetic codes, while their origin is still one of the greatest mysteries. Are the origins of genetic codes really unknowable? Do they really require external design? Here, we present an ATP-hypothesis that explains how the genetic codes came into being with the coevolution of biochemical system. ATP has several properties that make it suitable as the initiator of the origin of genetic codes. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as carriers of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between them, and eventually mediating prebiotic transaction from energy to information. This hypothesis shows how primitive life emerged through a series of processes from energy to information. Informatization (processes of creating and managing information) was inevitably coupled with structuralization (processes of organizing or incorporating into a cellular structure), making polynucleotides and polypeptides be cyclized into a system of reciprocal causation. The triplet codon might just be for stereo-chemical handing of amino acid through e.g. Watson–Crick pairing interactions. This hypothesis shades lights on the origin of life, together with the formations of both photosynthesis and biochemical systems, which have been largely unknown so far.
Fri, 27 March 2020
BRIEF REPORT Download: 178| View: 416| Comments: 0 | doi:10.20944/preprints202003.0409.v1
Subject: Life Sciences, Virology Keywords: angiotensin-converting enzyme 2; SARS-CoV-2; spike protein
Online: 27 March 2020 (11:37:06 CET)
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has high infectivity in humans, attributed to the strong affinity of its spike (S) protein to angiotensin-converting enzyme 2. Here, we analysed the structural similarity of the S protein between SARS-CoV-2 and other SARS-related coronaviruses. The S1 domain of the unclassified coronavirus RaTG13 was structurally very similar to that of SARS-CoV-2, implying that RaTG13 could be the origin of SARS-CoV-2.
CONCEPT PAPER Download: 34| View: 29| Comments: 0 | doi:10.20944/preprints202003.0401.v1
Subject: Life Sciences, Biophysics Keywords: SNAP25; linker; protein lipid interaction; acceptor complex; exocytosis; fusion
Online: 27 March 2020 (02:56:59 CET)
A recent paper demonstrates the importance of the linker region joining the two SNARE motifs of the neuronal t-SNARE SNAP25 for maintaining rates of secretion with roles for distinct segments in speeding fusion pore expansion (Shaaban et al., 2019, Elife. 8). Remarkably, lipid perturbing agents rescue a palmitoylation-deficient phenotype that includes slow fusion pore expansion, suggesting that protein-protein interactions have a role not only in bringing together the granule or vesicle membrane with the plasma membrane but also in orchestrating protein-lipid interactions leading to the fusion reaction. Furthermore, biochemical investigations demonstrate the importance of the C-terminal domain of the linker in the formation of the plasma membrane t-SNARE acceptor complex for synaptobrevin2 (Jiang, et al., 2019, FASEB J. 33:7985-7994;Shaaban et al., 2019, Elife. 8). This insight, together with biophysical and optical studies from other laboratories (Wang, et al., 2008, Molecular Biology of the Cell. 19:3944-3955; Zhao, et al., 2013, Proc Natl Acad Sci U S A. 110:14249-14254) suggests that the plasma membrane SNARE acceptor complex between SNAP25 and syntaxin and the resulting trans SNARE complex with the v-SNARE synaptobrevin form just milliseconds before fusion.
SHORT NOTE Download: 78| View: 163| Comments: 1 | doi:10.20944/preprints202003.0077.v3
The Ongoing COVID-19 Epidemic Curves Indicate Initial Point Spread in China With Log-Normal Distribution of New Cases per Day With a Predictable Last Date of the Outbreak Version 3: Test for When After a Peak in Daily Cases the Predicted Equation Becomes Reliable and Use of the Derivative of the Equation to Detect Time of Key Changes Determining the Length of the Outbreak
Online: 27 March 2020 (02:22:11 CET)
During an epidemic outbreak it is useful for planners and responsible authorities to be able to plan ahead to estimate when an outbreak of an epidemic is likely to ease and when the last case can be predicted in their area of responsibility. Theoretically this could be done for a point source epidemic using epidemic curve forecasting. The extensive data now coming out of China makes it possible to test if this can be done using MS Excel a standard spreadsheet program available to most offices. The available data is divided up for whole China and the different provinces. This and the high number of cases makes the analysis possible. Data for new confirmed infections for Hubei, Hubei outside Wuhan, China excluding Hubei as well as Zhejiang and Fujian provinces all follow a log-normal distribution that can be used to make a rough estimate for the date of the last new confirmed cases in respective areas. In the version 2 continuation work, 9 additional days were added for the Chinese data to evaluate the previous predictions. The extra data then available from China follows the previous predicted trend supporting the usefulness of this simple technique. In the version 2 we also tested the feasibility for a non-specialist to make similar predictions using additional data from S Korea now available. In this third continuation the predictions for Version 2 are evaluated for S Korea and fits well the beginning of the decline but it seems to be difficult to bring down numbers of cases per day under about 100 new cases per day, potential reasons for this is discussed. To further evaluate when in a prediction becomes reliable the Chinese data was used to evaluate to make predictions for each day around the peak in number of cases and after2-3 consecutive days of decreasing new cases per day the prediction becomes reliable. In version 3 data for Italy just reaching this point was used to make further predictions for that country. A second new analysis was also added to use the fitted equation to detect when the acceleration of new cases per day stopped increasing exponentially. In the Chinese case this measured point coincides with the date of the complete Hubei lockdown and in the new Italian analysis it coincides with the mandatory Italian lockdown. Predicted dates for the end of the Italian outbreak is also added.
Thu, 26 March 2020
BRIEF REPORT Download: 93| View: 215| Comments: 0 | doi:10.20944/preprints202003.0394.v1
Online: 26 March 2020 (15:12:34 CET)
The recent outbreak of novel coronavirus (2019-nCoV or SARS-CoV-2) and its spread to the whole world is currently posing one of the major threat to human health and the world economy. It has been suggested that 2019-nCoV is similar to SARS-CoV based on the genome sequence comparison. Despite the genomic similarity between SARS-CoV and SARS-CoV-2, the spike glycoprotein and receptor binding domain in SARS-CoV-2 shows considerable difference compared to SARS-CoV, due to the presence of several point mutations. We analyzed the receptor binding domain (RBD) from recently published 3D structure of spike glycoprotein of SARS-CoV-2 and compared with RBD of SARS-CoV. The observations highlight few important features of RBD in the light of the recently published findings from the 3D structures of spike glycoprotein and its complex with human angiotensin-converting enzyme 2 (ACE2) (Yan, R., et al. (2020); Wrapp, D., et al. (2020); Walls, A. C., et al. (2020)).
ARTICLE Download: 139| View: 209| Comments: 1 | doi:10.20944/preprints202003.0393.v1
Subject: Life Sciences, Biophysics Keywords: SARS-CoV2; RNA depended RNA polymerase; Valproic acid Co-A; drug repurposing
Online: 26 March 2020 (15:04:22 CET)
SARS-CoV2 RNA depended RNA polymerase is an essential enzyme for the survival of the virus in hosts as it helps in the replication of viral RNA. There are no human polymerases that share either sequence or structural homology with viral RNA depended RNA polymerase. These make it a good target for inhibitor discovery, as a specific inhibitor cannot cross-react with the human polymerases. We have used virtual screening, docking, binding energy calculation and simulation to show that valproic acid Co-A, a metabolite from prodrug valproic acid, forms stable interaction with nsP12 of CoV. Our results suggest valproic acid Co-A could be a potential inhibitor of nsP12 of SARS-CoV2.
SHORT NOTE Download: 21| View: 49| Comments: 0 | doi:10.20944/preprints202003.0390.v1
Subject: Life Sciences, Biochemistry Keywords: Warburg effect; Protons; Calcium oxalate; Antagonization
Online: 26 March 2020 (14:20:51 CET)
The Warburg effect refers to the phenomenon that cancer cells produce energy via glycolysis instead of cellular respiration. Glycolysis generated no net protons. The Warburg effect may be malignant cells’ built-in mechanism to antagonize the buildup of protons via Krebs cycle and other pathways with compromised cellular respiration. Data described in this study indicated that cancer cells were less sensitive to the presence of oxalate than non-cancer model cell lines 16HBE14o- and HaCaT. Malignant cells may resort on organic acids such as oxalate and their calcium salts to antagonize strong acids. This experiment sheds light on the role of Warburg effect in cancer cell metabolism and homeostasis.
ARTICLE Download: 382| View: 827| Comments: 1 | doi:10.20944/preprints202003.0386.v1
Subject: Life Sciences, Virology Keywords: hesperidin; COVID-19; pectin; flavonoids; hydrodynamic cavitation; IntegroPectin
Online: 26 March 2020 (13:59:28 CET)
Computational studies suggest that hesperidin, a flavonoid abundant in citrus peel, binding the three main cellular receptors of SARS-CoV-2 virus can act in the prophylaxis and treatment of COVID-19. Herein we urge the uptake of hydrodynamic cavitation industrial-scale reactors based on the low cost, reliable Venturi tube for the extraction of citrus pectin rich in hesperidin (and in other bioflavonoids including naringing) by very fast processing of waste orange peel or waste lemon peel in water only. A device able to process up to 500 kg of waste peels per session, similar to the one lately deployed in Italy for hydrodynamic cavitation-assisted brewing, is capable to provide 36,000 doses of 1000 mg hesperidin per day.
Wed, 25 March 2020
ARTICLE Download: 42| View: 67| Comments: 0 | doi:10.20944/preprints202003.0371.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: matrix metalloproteinase 3 (MMP3); extracellular vesicles (EVs); tumoroid; tumor organoid; tumorigenesis; three-dimensional (3D) culture system
Online: 25 March 2020 (05:25:09 CET)
The tumor organoid (tumoroid) model in three-dimensional (3D) culture systems has been developed to reflect more closely the in vivo tumors than 2D-cultured tumor cells. Notably, extracellular vesicles (EVs) are efficiently collectible from the culture supernatant of gel-free tumoroids. Matrix metalloproteinase (MMP) 3 is a multi-functional factor playing crucial roles in tumor progression. However, roles of MMP3 within tumor growth and EVs have not unveiled. Here, we investigated the protumorigenic roles of MMP3 on integrities of tumoroids and EVs. We generated MMP3-knockout (KO) cells using the CRISPR/Cas9 system from rapidly metastatic LuM1 tumor cells. Moreover, we established fluorescent cell lines with palmitoylation signal-fused fluorescent proteins (tdTomato and enhanced GFP). Then we confirmed the exchange of EVs between cellular populations and tumoroids. LuM1-tumoroids released large EVs (300-1000 nm) and small EVs (50-200 nm) while the knockout of MMP3 resulted in the additional release of broken EVs from tumoroids. The loss of MMP3 leads to a significant reduction in tumoroid size and to the development of the necrotic area within tumoroids. MMP3 and CD9 (a category-1 EV marker tetraspanin protein) were significantly down-regulated in MMP3-KO cells and their EV fraction. These weakened phenotypes by MMP3 KO were markedly rescued by the addition of MMP3-rich EVs or conditioned medium (CM) collected from LuM1-tumoroids, which caused a dramatic rise in the expression of MMP3, CD9, and Ki-67 (a marker of proliferating cells) in the MMP3-null/CD9-low tumoroids. Notably, MMP3 enriched in tumoroids-derived EVs and CM deeply penetrated into recipient MMP3-KO tumoroids, resulting in a remarkable enlargement of solid tumoroids, while MMP3-null EVs did not. These data demonstrate that EVs can mediate molecular transfer of MMP3 resulting in increasing the proliferation and CD9+ tumorigenesis, indicating crucial roles of MMP3 in tumor progression.
Tue, 24 March 2020
REVIEW Download: 995| View: 2285| Comments: 1 | doi:10.20944/preprints202003.0362.v1
Online: 24 March 2020 (14:46:29 CET)
With the current rapid spread of COVID-19, global health systems are increasingly overburdened by the sheer number of people that need diagnosis, isolation and treatment. Shortcomings are evident across the board, from staffing, facilities for rapid and reliable testing to availability of hospital beds and key medical-grade equipment. The scale and breadth of the problem calls for an equally substantive response not only from frontline workers such as medical staff and scientists, but from skilled members of the public who have the time, facilities and knowledge to meaningfully contribute to a consolidated global response. Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) currently being developed and deployed to bolster access to personal protective equipment (PPE), patient treatment and diagnostics.
ARTICLE Download: 1042| View: 2727| Comments: 1 | doi:10.20944/preprints202003.0360.v1
Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; transcriptional inhibition; COVID-19; drug repurposing; TMPRSS2
Online: 24 March 2020 (14:26:57 CET)
There is an urgent need to identify effective therapies for COVID-19 given that a broadly available and effective vaccine is likely at least one year away. Here, we identify compounds that transcriptionally inhibit host proteins required for SARS-CoV-2 entry and should be evaluated for efficacy in SARS-CoV-2 viral infection assays. Recognizing the need for immediately available treatment options, we focused particular attention on FDA-approved drugs that could be immediately repurposed to treat COVID-19 patients. By mining publicly available gene expression data, we identify several compounds that down-regulate TMPRSS2, a protein required for SARS-CoV-2 entry that has emerged as a promising therapeutic target. Among these, we find twenty independent studies that implicate estrogen-related and androgen-related compounds as transcriptional modulators of TMPRSS2 expression, suggesting that these drugs and others acting on the pathway may be promising therapeutic candidates for COVID-19 for further testing. It is also noteworthy that TMPRSS2 has highly variable and skewed expression in humans, spanning two orders of magnitude with a small minority of individuals having extremely high expression. Combined with literature showing that TMPRSS2 loss-of-function in mouse is protective against SARS while anti-estrogen treatment predicted to increase TMPRSS2 expression exacerbates SARS, this observation raises the hypothesis that TMPRSS2 expression may positively correlate with severity in COVID-19.
ARTICLE Download: 33| View: 40| Comments: 0 | doi:10.20944/preprints202003.0357.v1
Subject: Life Sciences, Molecular Biology Keywords: Benzo[a]pyrene; Microtubule; Neuroblastoma; Cell cycle arrest, Neuropeptide Y
Online: 24 March 2020 (08:41:53 CET)
Benzo[a]pyrene (B[a]P), is a family member of polycyclic aromatic hydrocarbons and a widespread environmental pollutant and neurotoxicant that contribute to the development of cancer. Microtubules are polymers of tubulin that form part of the cytoskeleton and target for anticancer drugs. Furthermore, NPY significantly increased the percentage of cells in S and G2/M phases. However, little is known about the specific role of NPY in proliferation and the underlying protective mechanism remains unclear. Hence, the aim of this work was to investigate the effect of B[a]P on SH-SY5Y neuroblastoma cells and to explore the potential mechanism for alteration of tubulin-microtubule equilibrium causing mitotic arrest and NPY expression. The present findings showed B[a]P treatment significantly increase number of SH-SY5Y cells in S and G2/M phase as compared to G1 phase and provokes cell cycle arrest that correlated with significant decrease in G0/G1 cells. Immunofluorescence study showed significantly distorted tubulin arrangement from metaphasic plate in formation of bipolar mitotic spindle apparatus. Further, higher doses of B[a]P treatment lead to chromosomal abnormalities accompanied by DNA damage due ROS causing oxidative stress showing significant decrease in tubulin protein around spindle. The results of present study demonstrated that NPY exerts a proliferative and protective effect on B[a]P-induced oxidative stress in a dose-dependent manner in vitro and importantly, these effects may be mediated via mitotic arrest and involved in spindle arrangement during cell division. Our findings addresses a novel pathological outcomes of B[a]P-induced NPY expression by oxidative stress through spindle abnormalities leading to microtubule disruption.
ARTICLE Download: 1577| View: 4783| Comments: 2 | doi:10.20944/preprints202003.0356.v1
Subject: Life Sciences, Genetics Keywords: COVID-19; SARS-CoV-2; host genetics; genetics; polygenic risk score
Online: 24 March 2020 (08:36:20 CET)
The global pandemic of COVID-19 accounts for more than 14,000 deaths worldwide. However, little is known about the host genetics interaction with infection and COVID-19 progression. To better understand the role of host genetics, we review the current literature, aggregate readily available genetic resources, and provide some updated analysis relevant to COVID-19 and associated phenotypes. Using the unrelated individuals in UK Biobank (total n = 337,579 across 5 populations), we aggregate human leukocyte antigen and ABO blood type frequencies. We find significant and consistent risk reduction of blood group O reported in Zhao et al. and encourage broad sharing of ABO blood type frequencies that are readily accessible across COVID-19 with mild, moderate, and severe/critical symptoms for robust inferences at https://tinyurl.com/abo-covid19. In addition, we generate polygenic risk scores (PRSs) weights for 29 blood measurements, including clinically relevant haematological measurements for COVID-19, such as lymphocyte count and percentage. Focusing on the 8 most COVID-19 clinically relevant blood measurements, we performed PRS-PheWAS analysis across 44 disease antigen measurements (n = 6,643 unrelated individuals in White British group), infectious diseases and acute respiratory infections (n = 20,928 cases and 349,000 controls across 3 population groups) and deaths (n = 1,846 cases and 368,082 controls), recorded in hospital inpatient record and death registry data, respectively, in UK Biobank, and find host genetic PRS associations with disease risk. Taken together, we anticipate these resources (https://github.com/rivas-lab/covid19) will aid in improving our understanding of host genetic risk factors playing a role in SARS-CoV-2 infection and COVID-19 disease severity.
Mon, 23 March 2020
REVIEW Download: 48| View: 106| Comments: 0 | doi:10.20944/preprints202003.0351.v1
Subject: Life Sciences, Biotechnology Keywords: Conventional method; Clustered Regularly Interspaced Short Palindromic Sequence; Genome editing; RNA Interference; TALEN
Online: 23 March 2020 (10:23:45 CET)
Conventional plant breeding has contributed enormously towards feeding the world and has played crucial roles in the development of modern society. The conventional method creates variation by transferring genes between or within the species. In general, these methods are more expensive and takes more time, to overcome these limitations, new technology is required. Genome editing is a powerful tool for biotechnology applications, with the capacity to alter the function of any gene. With the availability of gene information for the majority of the traits, genome editing emerged as a potential to create a new variation with the introduction of any transgene. The important genome editing tools used nowadays are ZFNs, TALEN, Pentatricopeptide repeats protein, adenine base editor, RNA interference, and CRISPR/Cas9. These tools have opened a new era for crop improvement. Due to the complex genetic architecture of most traits, it is challenging to edit genes controlling them. To overcome these challenges, genome editing provides a broader perspective. Among the above-mentioned tools, CRISPR/Cas9 is the most powerful tool for gene editing. These technologies are being used to create abiotic and biotic resistance crop varieties.
HYPOTHESIS Download: 256| View: 597| Comments: 1 | doi:10.20944/preprints202003.0042.v2
Subject: Life Sciences, Other Keywords: Flue; Virus; COVID19; SARS CoV-2; Spike Protein; Virtual Screening; dgitoxin; anthracycline; rolitetracycline; E-155
Online: 23 March 2020 (10:19:17 CET)
The novel coronavirus (SARS-CoV-2) is a human pathogen recently emerged in China, causing a global pandemic of severe respiratory illness (COVID19). SARS-CoV-2 makes entry into human cells through its spike (S) protein that binds to cell surface receptors. Widespread of SARS-CoV-2 has been attributed to high affinity of S protein to its receptor. A homology model of the receptor binding domain of SARS-CoV-2 S protein (RBD) was built. RBD- receptor docking and published molecular dynamics data were used to map the key RBD-receptor interaction hotspot (RBDhp) on the RBD. Primary virtual screening was carried out against RBDhp using more than 3300 compounds approved by U.S Food and Drug Administration (FDA) and other authorities for human use. Compounds that bind to hpRBD with a binding energy ≤ - 6.5 kcal/mol were subjected to secondary screening using a recently published cryo EM (2.9 Å) structure of RBD. A cardiac glycoside (dgitoxin), two anthracyclines (zorubicin and aclarubicin), a tetracycline derivative (rolitetracycline), a cephalosporin (cefoperazone) and a food dye (E-155) were predicted to be most potent inhibitors of RBD – receptor interaction. An anti-asthmatic drug (zafirlukast) and several other drugs (itrazol, fazadinium, troglitazone, gliquidone, Idarubicin, Oxacillin) were found to be high affinity binders that may have a potential to inhibit RBD – receptor interaction.
ARTICLE Download: 520| View: 915| Comments: 0 | doi:10.20944/preprints202003.0349.v1
Subject: Life Sciences, Biotechnology Keywords: novel coronavirus; COVID-19; protease; molecular docking; drug designing; ADME; drug repurposing
Online: 23 March 2020 (09:47:49 CET)
The Novel Coronavirus (COVID-19) is a positive-sense single-stranded RNA ((+)ssRNA) virus. The COVID-19 Main Proteases play very important role in the propagation of the Novel Coronavirus (COVID-19). It has already killed more than 8000 people around the world and thousands of people are getting infected every day. Therefore, it is very important to identify a potential inhibitor against COVID-19 Main Proteases to inhibit the propagation of the Novel Coronavirus (COVID-19). We have applied a drug repurposing approach of computational methodology, depending on the synergy of molecular docking and virtual screening techniques, aimed to identify possible potent inhibitors against Novel Coronavirus (COVID-19) from FDA approved antiviral compounds and from the library of active phytochemicals. On the basis of recently resolved COVID-19 Main Protease crystal structure (PDB:6LU7), the library of 100 FDA approved antiviral compounds and 1000 active components of Indian Medicinal Plants extracted for screening against COVID-19 Main Protease. The compounds were further screened using Pyrex virtual screening tool and then best inhibitors, top 19 compounds optimally docked to the COVID-19 Main Protease structure to understand the participation of specific amino acids with inhibitors at active sites. Total 19 best compounds were identified after screening based on their highest binding affinity with respect to the other screened compounds. Out of 19, 6 best compounds were further screened based on their binding affinity and best ADME properties. Nelfinavir exhibited highest binding energy -8.4 kcal/mol and strong stability with the TRP207, ILE281, LEU282, PHE3, PHE291, GLN127, ARG4, GLY283, GLU288, LYS5, LYS137, TYR126, GLY138, TYR126, SER139 and VAL135 amino acid residues of COVID-19 Main Protease participating in the interaction at the binding pocket. In addition to Nelfinavir (-8.4), Rhein (-8.1), Withanolide D (-7.8), Withaferin A (-7.7), Enoxacin (-7.4), and Aloe-emodin (-7.4) also showed good binding affinity and best ADME properties. Our findings suggest that these compounds can be used as potential inhibitors against COVID-19 Main Protease, which could be helpful in inhibiting the propagation of the Novel Coronavirus (COVID-19). Moreover, further in vitro and in vivo validation of these findings would be very helpful to bring these inhibitors to next level study.
HYPOTHESIS Download: 310| View: 892| Comments: 0 | doi:10.20944/preprints202003.0341.v1
Subject: Life Sciences, Virology Keywords: Aetiology; Treatment; Cytokine Storm; ICU; COVID-19; ACE2; Irinotecan; Etoposide
Online: 23 March 2020 (06:56:57 CET)
We present the AI-discovered aetiology of COVID-19, based on a precise disease model of COVID-19 built under five weeks that best matches the epidemiological characteristics, transmission dynamics, clinical features, and biological properties of COVID-19 and consistently explains the rapidly expanding COVID-19 literature. We present that SARS-CoV-2 implements a unique unbiased survival strategy of balancing viral replication with viral spread by increasing its dependence on (i) ACE2-expressing cells for viral entry and spread, (ii) PI3K signaling in ACE2-expressing cells for viral replication and egress, and (iii) viral-non-structural-and-accessory-protein-dependent immunomodulation to balance viral spread and viral replication. We further propose the combination of irinotecan (an in-market topoisomerase I inhibitor) and etoposide (an in-market topoisomerase IIinhibitor) could potentially be an exceptionally effective treatment to protect critically ill patients from death caused by COVID-19-specific cytokine storms triggered by sepsis, ARDS, and other fatal comorbidities.
ARTICLE Download: 25| View: 46| Comments: 0 | doi:10.20944/preprints202003.0336.v1
Subject: Life Sciences, Virology Keywords: Manihot esculenta Crantz; potexvirus; Cassava common mosaic virus; genomics
Online: 23 March 2020 (05:46:35 CET)
The complete genomic sequence of a Cassava common mosaic virus Linggao isolate (CsCMV-LG) was determined from cassava (Manihot esculenta Crantz) with mild leafy mosaic symptom to no symptom in China. Excluding the poly(A) tail, the CsCMV-LG genome (GenBank accession No. MT038420) is 6374 nucleotides (nts) in length, with five major open reading frames encoding a 1450-amino acids (aa) RNA-dependent RNA polymerase (RdRp), three triple gene block (TGB) proteins (231-aa, 110-aa and 95-aa), and a 229-aa coat protein (CP). Phylogenetic analysis indicated that the complete genome of the CsCMV-LG is closely related to that of CsCMV-Brazilian which has been assigned to the genus Potexvirus, but the sequence identity shared only 88.0%. Notable, the mild CsCMV-LG isolate can also infect Nicotiana benthamiana in laboratory through rub inoculation causing mild vein yellowing at 15-day post inoculation. This is the first full-length genome sequence of a distinct isolate of Cassava common mosaic virus (CsCMV) infecting cassava in Hainan, China.
REVIEW Download: 90| View: 87| Comments: 0 | doi:10.20944/preprints202003.0329.v1
Subject: Life Sciences, Microbiology Keywords: membrane remodeling; membrane biosynthesis, membrane curvature; phospholipids; inner membrane; evolution
Online: 23 March 2020 (03:09:35 CET)
Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of certain membrane proteins hijack these regulation networks, leading to the formation of impressive intracellular membrane structures in both prokaryotic and eukaryotic cells. The proteins triggering membrane proliferation share two major common features: 1) they promote the formation of highly curved membrane domains and 2) they lead to an enrichment in anionic, cone-shaped phospholipids (cardiolipin or phosphatidic acid) in the newly formed membranes. Taking into account the available examples of membrane proliferation upon protein overproduction, together with the latest biochemical, biophysical and structural data, we explore the relationship between protein synthesis and membrane biogenesis. We propose a mechanism for the formation of these non-physiological intracellular membranes that shares similarities with natural inner membrane structures found in α-proteobacteria, mitochondria and some viruses-infected cells, pointing towards a conserved feature through evolution. We hope that the information discussed in this review will give a better grasp of the biophysical mechanisms behind physiological and induced intracellular membrane proliferation, inspiring new biotechnological applications.
ARTICLE Download: 351| View: 614| Comments: 0 | doi:10.20944/preprints202003.0325.v1
Online: 23 March 2020 (01:30:06 CET)
The pandemic threat SARS-CoV-2 is now beyond control though the country of origin of this virus had already been limited for the new infection. Number of infected people and countries have been increasing day by day. Considering the previous pandemic flues, it is hypothesizing that COVID-19 will be reduced with warming the global environmental temperature. Therefore, the current study was aimed to analyze the effect of temperature and relative humidity (RH) on spreading of SARS-CoV-2 infection. The COVID-19 confirmed cases of 31 different states in China and 70 cities of 11 countries were obtained from several online databases. The real time temperature and humidity of the respective regions were taken from an online weather forecasting data source. Correlation analyses showed that SARS-CoV-2 infectivity and spreading negatively correlated with temperature of most of the states of China or cities of the world or in a country. The effect of humidity on COVID-19 was found to be positively correlated inside the China and difference of humidity was not found among countries and/or various regions of the world. Moreover, a minimum number of COVID-19 cases have been confirmed in the temperate regions compared to regions/countries compared to regions/countries with relatively low temperature. In conclusion, the SARS-CoV-2 infection has been found in a wide range of temperatures. It might be hypothesized that comparatively elevated air temperature could play a detrimental effect for SARS-CoV-2 spread.
CONCEPT PAPER Download: 59| View: 67| Comments: 0 | doi:10.20944/preprints202003.0321.v1
Subject: Life Sciences, Biotechnology Keywords: bookmark; CRISPR/Cas9; complementation; clostridium; knock-out
Online: 23 March 2020 (00:50:23 CET)
Phenotypic complementation of gene knock-outs is an essential step in establishing function. Here we describe a simple strategy for ‘gold standard’ complementation in which the mutant allele is replaced in situ with a wild type (WT) allele in a procedure that exploits CRISPR/Cas9. The method relies on the prior incorporation of a unique 24 nucleotide (nt) ‘bookmark’ sequence into the mutant allele to act as a guide RNA target during its Cas9-mediated replacement with the WT allele. The bookmark comprises a 23 nt Cas9 target sequence plus an additional nt to ensure the deletion is in-frame. Here, bookmarks are tailored to Streptococcus pyogenes CRISPR/Cas9, but could be designed for any CRISPR/Cas system. For proof of concept, 9 bookmarks were tested in Clostridium autoethanogenum. Complementation efficiencies reached 91%. As complemented strains are indistinguishable from their progenitors, concerns over contamination may be satisfied by incorporation of ‘watermark’ sequences into the complementing genes.
ARTICLE Download: 317| View: 497| Comments: 0 | doi:10.20944/preprints202003.0320.v1
Subject: Life Sciences, Virology Keywords: envelope protein; furin cleavage site; hydrophobic aggregation and rapid transmission; immediate ancestor; pangolins coronaviruses; SARS-CoV-2; spike protein
Online: 23 March 2020 (00:42:35 CET)
We are witnessing the severe third outbreak mediated by coronaviruses affecting global public health with unprecedented economic consequences. A better understanding of its phylogenetics, exploration of sequence features and mutational changes could unveil its genealogy to gain insights into the mechanism of transmission and development of possible interventions. Our comparative genomic analyses of >160 isolates of SARS-CoV-2 reveal phylogenetic kinship with other coronaviruses and emergence of evolutionary divergence in clinical isolates. t-SNE-based clustering revealed different clades but no continent specific clusters. Amino acid substitutions at RBD of spike protein provide possible reasons for rapid transmission. Few proteins specific to SARS-CoV-2 were identified which could have implications as therapeutic targets and diagnostic biomarkers. Virtual screening identified repurposed drugs, known nutraceuticals, for specific interventions. These phylogenetic observations reveal the ancestry and computational studies reveal the emergency measures to interject this emerging pathogen that pose threat to whole of mankind.
Fri, 20 March 2020
SHORT NOTE Download: 87| View: 253| Comments: 1 | doi:10.20944/preprints202002.0289.v3
Subject: Life Sciences, Biochemistry Keywords: COVID-19; proton affinity; calcium oxalate; isoleucine; valine; glycine; prophylactic approach
Online: 20 March 2020 (09:14:58 CET)
The current pneumonia epidemic in China could evolve into a pandemic on a global scale if not effectively contained. The SARS-CoV-2 possesses a 61-amino acid open reading frame resembling SARS-CoV virulence factor - ORF6 peptide. The isoleucine content is 15.9% in ORF6 of SARS-CoV versus 16.4% of that in SARS-CoV-2. Given the proton affinity in the carbonyl oxygen in isoleucine, augmented proton traffic can enhance proton-ion antiport and prompt cell swelling. Calorie restriction has been confirmed in animal studies to extend lifespan, and its underlying mechanism is not fully known. As the content of essential amino acids in the open reading frame of SARS-CoV-2 reaches 57.4%, a starch/vitamin diet served for short period of time does not give rise to essential amino acids and halts virion production, which could be adopted as prophylactic approach of many viral infections. Plant-based diet or fasting/boiled rice water can also minimize the intake of essential amino acids or all amino acids respectively. Furthermore, several proteins of SARS-CoV-2 possess high valine plus glycine content which is implicated in heart disease, justifying the aforementioned approaches.
BRIEF REPORT Download: 571| View: 2331| Comments: 0
Subject: Life Sciences, Cell & Developmental Biology Keywords: SARS-CoV2; spike; receptor–ligand docking; super infection
Online: 20 March 2020 (08:30:40 CET)
SARS-CoV2 (corona virus) has spread globally at an unprecedented rate; so far, increasing SARS-CoV2-infected individuals have been identified. Although the situation in China is improving and is currently under control, the outbreak in other countries and its pandemic management is only beginning to develop. Based on 154 SARS-CoV2 genome sequence analyses, we used receptor–ligand docking to identify one potential point mutation (V354F) on the spike structure which enhances spike binding to ACE2 receptors underlying potential super infection. Importantly, the V354F site on spike S1 had been identified in 5/10 infected French patients living in Paris, who sharing 100% identical SARS-CoV2 genomes. With Covid-19 cases increasing rapidly in France that could lead to a new explosion, we suggest that the French government should identify all potential super spreaders and treat them accordingly. In summary, our study provides on of the measures to avoid the potential second worldwide explosion of SARS-CoV2.
ARTICLE Download: 293| View: 1921| Comments: 0 | doi:10.20944/preprints202003.0307.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: COVID-19; influenza; SARS-CoV-2; ACE2; risk factor
Online: 20 March 2020 (06:56:25 CET)
Coronavirus disease 2019 (COVID-19) is caused by infection with the 2019 novel coronavirus 2 (2019-nCoV, now referred to as SARS-CoV-2). COVID-19 has become a global pandemic since its outbreak at the end of Dec 2019. COVID-19 could lead to severe acute respiratory disease, especially to those who have reduced immunity. Binding of the viral Spike protein (S) to its receptor ACE2 (Angiotensin Converting Enzyme 2) on the surface of target cells has been proven to be key for virus entry and infection. Although ACE2 expression in the respiratory system is necessary for pneumonia infection by SARS-CoV-2, the regulation of ACE2 gene expression remains poorly investigated, especially for patients that are in pre-pathological conditions. Here, by analyzing The Gene Expression Omnibus (GEO) database, we investigated the expression regulation of ACE2 in various kinds of primary epithelial cells from the respiratory system after influenza A or respiratory Syncytial Virus (RSV) infection. Our analyses reveal that infection of influenza A, RSV or influenza vaccines greatly increased ACE2 expression, suggesting that influenza viral infection could represent a high risk factor for developing COVID-19. We also found that the regulatory effect of influenza A virus on ACE2 expression is associated with activation of the interferon beta-induced pathway and viral RNA-activated host response. Together, our data provide a theoretical framework for clinical classification for SARS-CoV-2 infection susceptibility and could be used for future prevention and therapy treatment for COVID-19.
ARTICLE Download: 28| View: 87| Comments: 0
Subject: Life Sciences, Biotechnology Keywords: sulfite oxidase; molybdenum; tungsten; sulfite toxicity; tomato; SO expression
Online: 20 March 2020 (04:16:41 CET)
Plant sulfite oxidase )SO( is a molybdo-enzyme responsible for the oxidation of excess SO2/sulfite into non-toxic sulfate. The effect of toxic sulfite level on leaves and fruits was studied in tomato plants with different SO expression levels: wild-type (WT), SO overexpression (OE) and SO RNA interference (Ri) plants. Leaf discs and ripe fruit of plants lacking SO were more susceptible, whereas SO OE plants were more resistant as revealed by remaining chlorophyll content and tissue damage levels. Application of molybdenum further enhanced the tolerance of leaf discs to sulfite by enhancing SO activity in SO OE lines, but not in WT or Ri plants. Notably, incubation with tungsten, the molybdenum antagonist, overturned the effect of molybdenum spray in SO OE plants, revealed by remaining chlorophyll content and SO activity. The results indicate that SO determines, in tomato leaves and ripe fruits, the resistance to toxic sulfite and the application of molybdenum enhances sulfite resistance in OE plants by increasing SO activity. The results suggest that overexpressing SO mechanism can be employed in agriculture with or without molybdenum application, for the development of more tolerate crops and vegetables to higher concentrations of sulfite/SO2 containing postharvest treatments.
Thu, 19 March 2020
ARTICLE Download: 52| View: 56| Comments: 0 | doi:10.20944/preprints202003.0296.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: retinol binding protein 4 receptor 2; RBP4; Rbpr2; STRA6; all-trans retinol transport; photoreceptor cell; vision; retinoids; zebrafish
Online: 19 March 2020 (03:16:19 CET)
Dietary vitamin A/all-trans retinol/ROL plays a critical role in human vision. ROL circulates bound to the plasma retinol-binding protein (RBP4) as RBP4-ROL. In the eye, the STRA6 membrane receptor binds to circulatory RBP4 and internalizes ROL. STRA6 is however not expressed in systemic tissues, where there is high-affinity RBP4 binding and ROL uptake. We tested the hypothesis, that the second retinol-binding protein 4 receptor 2 (Rbpr2) which is highly expressed in systemic tissues of zebrafish and mouse, contains a functional RBP4 binding domain, critical for ROL transport. As for STRA6, modeling and docking studies confirmed three conserved RBP4 binding residues in zebrafish Rbpr2. In cell culture studies, disruption of the RBP4 binding residues on Rbpr2 almost completely abolished uptake of exogenous vitamin A. CRISPR generated rbpr2-RBP4 domain zebrafish mutants showed microphthalmia, shorter photoreceptor outer segments, and decreased opsins, that were attributed to impaired ocular retinoid content. Injection of WT-Rbpr2 mRNA into rbpr2 mutant or all-trans retinoic acid treatments rescued the mutant eye phenotypes. In conclusion, zebrafish Rbpr2 contains a putative extracellular RBP4-ROL ligand-binding domain, critical for yolk vitamin A transport to the eye for ocular retinoid production and homeostasis, for photoreceptor cell survival.
Wed, 18 March 2020
REVIEW Download: 82| View: 111| Comments: 0 | doi:10.20944/preprints202003.0290.v1
Subject: Life Sciences, Molecular Biology Keywords: Histone PTM; RNA Polymerase II; ChIP-seq; chromatin; epigenetics; transcriptional interference; plant; Transcription Cycle; Transcription
Online: 18 March 2020 (17:14:28 CET)
Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNAPII transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin Immuno-precipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM “readers”, “writers” and “erasers”, with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may in part rely on the characteristic histone PTMs profiles that distinguish transcription stages.
REVIEW Download: 76| View: 56| Comments: 0 | doi:10.20944/preprints202003.0288.v1
Subject: Life Sciences, Other Keywords: surveying microglia; amoeboid microglia; P2X receptors; P2Y receptors; P1 receptors; CD39; CD73; microglia-neuron cross talk; phagocytosis; microglial products; neuroinflammation
Online: 18 March 2020 (16:52:28 CET)
Microglial cells, the resident macrophages of the CNS, exist in a process-bearing, ramified/surveying phenotype under resting conditions. Upon activation by cell damaging factors they get transformed to an amoeboid phenotype releasing various cell products including pro-inflammatory cytokines, chemokines, proteases, reactive oxygen/nitrogen species and the excytotoxic ATP and glutamate. In addition, they engulf pathogenic bacteria or cell debris and phagocytose them. However, already resting/surveying microglia has a number of important physiological functions in the CNS; they e.g. shield small disruptions of the blood-brain barrier by their processes, dynamically interact with synaptic structures and clear surplus synapses during development. In neurodegenerative illnesses they aggravate the original disease by a microglia-based compulsory neuroinflammatory reaction. Therefore, the blockade of this reaction improves the outcome of Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, amyotrophic lateral sclerosis, etc. The function of microglia is regulated by a whole array of purinergic receptors classified as P2Y12, P2Y6, P2Y4, P2X4, P2X7, A2A, A3, and being targets for endogenous ATP, ADP, or adenosine. ATP is sequentially degraded by the ecto-nucleotidases and 5’-nucleotidase enzymes to the weak adenosine agonist inosine as an end-product. The appropriate selective agonists/antagonists for purinergic receptors as well as the respective enzyme inhibitors may profoundly interfere with microglial functions and reconstitute the homeostasis of the CNS disturbed by neuroinflammation.
ARTICLE Download: 36| View: 57| Comments: 1 | doi:10.20944/preprints202001.0157.v2
Subject: Life Sciences, Biochemistry Keywords: pectin; antioxidant; lemon; flavonoids; hydrodynamic cavitation; IntegroPectin
Online: 18 March 2020 (02:37:32 CET)
Lemon pectin extracted along with water-soluble flavonoids and other phytochemicals from citrus industry’s waste lemon peel via hydrodynamic cavitation in water, directly at pre-industrial scale and further isolated via freeze drying, shows exceptionally high antioxidant and non-cytotoxic activity. Preliminary investigation indicates also significant antimicrobial activity. These findings open the route to the development of new nutraceutical and healthcare application of a versatile biopolymer endowed with new functionality, rapidly and conveniently obtained from an abundant by-product of the agrofood industry.
Tue, 17 March 2020
ARTICLE Download: 49| View: 87| Comments: 0 | doi:10.20944/preprints202003.0263.v1
Subject: Life Sciences, Microbiology Keywords: pectin; antibacterial; lemon; flavonoids; hydrodynamic cavitation; IntegroPectin
Online: 17 March 2020 (03:43:39 CET)
Pectin extracted via hydrodynamic cavitation in water only from waste lemon peel and further isolated via freeze drying displays significant antibacterial activity against Staphylococcus aureus, a Gram positive pathogen which easily contaminates food. The antibacterial effect of the new IntegroPectin is largely superior to that of commercial citrus pectin, opening the way to advanced applications of a new bioproduct now obtainable in large amounts and at low cost from citrus juice industry’s waste.
ARTICLE Download: 28| View: 47| Comments: 1 | doi:10.20944/preprints201911.0301.v2
Subject: Life Sciences, Genetics Keywords: genetic code; DNA; alphabet; amino acids; hypercomplex numbers; doubly stochastic matrix; binary numbers; dyadic groups; tensor product; palindrome
Online: 17 March 2020 (03:02:27 CET)
The article shows materials to the question about algebraic features of the genetic code and about the dictatorial influence of the DNA and RNA molecules on the whole organism. Presented results testify in favor that the genetic code is an algebraic code related with a wide class of algebraic codes, which are a basis of noise-immune coding of information in communication technologies. Structural features of the genetic systems are associated with hypercomplex double (or hyperbolic) numbers and with bisymmetric doubly stochastic matrices. The received results confirm that represented matrix approaches are effective for modeling genetic phenomena and revealing the interconnections of structures of biological bodies at various levels of their organization. This allows one to think that living organisms are algebraically encoded entities where structures of genetic molecules have the dictatorial influence on inherited structures of the whole organism. New described algebraic approaches and results are discussed.
Mon, 16 March 2020
REVIEW Download: 50| View: 63| Comments: 0 | doi:10.20944/preprints202003.0254.v1
Subject: Life Sciences, Immunology Keywords: zebrafish; inflammation; tumour initiation; macrophage; neutrophil; cancer; pre-neoplastic; live imaging; tumourigenesis; tumour model
Online: 16 March 2020 (01:31:28 CET)
The zebrafish is now an important model organism for cancer biology studies and provides some unique and complementary opportunities in comparison to the mammalian equivalent. The translucency of zebrafish has allowed in vivo live imaging studies of tumour initiation and progression at the cellular level thus providing novel insights into our understanding of cancer. Here we summarise and discuss available transgenic zebrafish tumour models and what we have gleaned from them with respect to cancer inflammation. In particular, we focus on the host inflammatory response toward transformed cells during the pre-neoplastic stage of tumour development. We discuss features of tumour associated macrophages and neutrophils in mammalian models and present evidence which supports the idea that these inflammatory cells promote early stage tumour development and progression. Direct live imaging of tumour initiation in zebrafish models has shown that the intrinsic inflammation induced by pre-neoplastic cells is tumour promoting. Signals mediating leukocyte recruitment to pre-neoplastic cells in zebrafish correspond to signals mediating leukocyte recruitment in mammalian tumours. The activation state of macrophages and neutrophils recruited to pre-neoplastic cells appears to be heterogenous, as seen in mammalian models, which provides an opportunity to study the plasticity of innate immune cells during tumour initiation. Although several potential mechanisms are described that might mediate the trophic function of innate immune cells during tumour initiation in zebrafish, there are several unknowns that are yet to be resolved. Rapid advancement of genetic tools and imaging technologies for zebrafish will facilitate research into the mechanisms that modulate leukocyte function during tumour initiation and identify targets for cancer prevention.
Sun, 15 March 2020
ARTICLE Download: 614| View: 1048| Comments: 0 | doi:10.20944/preprints202003.0242.v1
Subject: Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; spike protein; multiepitope vaccine; molecular modeling
Online: 15 March 2020 (12:45:54 CET)
The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the world health organization declared it pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. In this urgency situation, development of SARS-CoV-2 based vaccines is immediately required. Immunoinformatic and molecular modelling are generally used time-efficient methods to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines is proved to be a promising immunization strategy against viruses and pathogens, which induce more comprehensive protective immunity. The current study demonstrated a comprehensive in-silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in-silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in E. Coli. Despite this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can present to be a better prophylactic solution against COVID-19.
COMMUNICATION Download: 37| View: 39| Comments: 0 | doi:10.20944/preprints202003.0234.v1
Subject: Life Sciences, Other Keywords: astrocytes; calcineurin; GLAST; protein synthesis; protein degradation; proteostasis
Online: 15 March 2020 (01:39:55 CET)
Alterations in the expression of glutamate/aspartate transporter (GLAST) have been associated with several neuropathological conditions including Alzheimer’s disease and epilepsy. However, the mechanisms by which GLAST expression is altered are poorly understood. Here we used a combination of pharmacological and genetic approaches coupled with quantitative PCR and Western blot to investigate the mechanism of the regulation of GLAST expression by a Ca2+/calmodulin-activated phosphatase calcineurin (CaN). We show that treatment of cultured hippocampal mouse and fetal human astrocytes with a CaN inhibitor FK506 resulted in a dynamic modulation of GLAST protein expression, being downregulated after 24-48 h, but upregulated after 7 days of continuous FK506 (200 nM) treatment. Protein synthesis, as assessed by puromycin incorporation in neo-synthesized polypeptides, was inhibited already after 1 h of FK506 treatment, while the use of a proteasome inhibitor MG132 (1 μM) shows that GLAST protein degradation was only suppressed after 7 days of FK506 treatment. In astrocytes with constitutive genetic ablation of CaN both protein synthesis and degradation were significantly inhibited. Taken together, our data suggest that, in cultured astrocytes, CaN controls GLAST expression at a posttranscriptional level through regulation of GLAST protein synthesis and degradation.
Fri, 13 March 2020
ARTICLE Download: 38| View: 41| Comments: 0 | doi:10.20944/preprints202003.0230.v1
Subject: Life Sciences, Molecular Biology Keywords: Ixeris dentate; lactobacillus, salivation; xerostomia
Online: 13 March 2020 (10:18:15 CET)
Dry mouth, hyposalivation, or xerostomia is a significant problem in diabetic patients; however, there was no way to relieve these symptoms. This study was aimed to evaluate the effects of Ixeris dentata (IXD) in combination with lactobacillus extract on the salivation rate in diabetes-induced dry mouth, and its mechanism was also investigated. In the streptozotocin-induced diabetes model, dry mouth condition was established as a model. Both control and diabetic rats were treated with a sublingual spray of either water or IXD and subsequently treated with or without a spray of lactobacillus extract. In diabetes condition, the salivary flow rate, amylase activity, and aquaporin-5 and Na+/H+ exchanger (NHE-1) expressions were markedly decreased, whereas they were more significantly recovered in the sequential treatment of IXD-lactobacillus extract than each single treatment. Furthermore, oxidative stress and its related ER stress response were especially regulated in the IXD/lactobacillus extract condition, where the following anti-oxidative enzymes; GSH:GSSG ratio, superoxide dismutase (SOD), and glutathione peroxidase (GPx) were involved. This study suggests that the combination of IXD and lactobacillus would be a potential alternative medicine against diabetes-induced hyposalivation and xerostomia.
Thu, 12 March 2020
ARTICLE Download: 38| View: 54| Comments: 0 | doi:10.20944/preprints202003.0216.v1
Subject: Life Sciences, Other Keywords: Aflatoxin treated corn; Aspergillus flavus; atoxigenic aflatoxin; bee community; biological pesticide; saprophytic soil fungus
Online: 12 March 2020 (14:18:11 CET)
A saprophytic soil fungus, Aspergillus flavus, produces aflatoxin (toxigenic strains) in the kernels of corn (Zea mays L.) and seeds of many other crops. Many strains of A. flavus do not produce toxigenic aflatoxin, and soil application of these atoxigenic strains is a suppressive control tactic to assist in controlling toxigenic conspecifics. Effects of atoxigenic A. flavus applications on honey bees (Apis mellifera L.) and other bees are unknown, and basic information on bee occurrences in corn fields treated with and without this biological pesticide is needed to inform integrated pest management in corn. Fields with atoxigenic A. flavus applications were compared to nearby control fields in three counties in corn production regions in eastern Texas. In each corn field, twenty bee bowl traps were deployed along four equal transects located between corn rows, with contents of the bowls (i.e. bees) retrieved after 24 hours. Eleven bee genera from four families were collected from corn fields, with only two honey bees collected and zero honey bees observed in transects. The sweat bee genus Agapostemon (primarily composed of the Texas-striped sweat bee A. texanus) was most abundant in corn fields (44% of the total number of bees collected) followed by long-horned bees (Melissodes spp., 24%). The southernmost county (i.e. San Patricio) produced over 80% of the total number of bees collected. Bee communities occurring in corn production fields with applications of atoxigenic A. flavus applications were not significantly different from nearby control fields. While little is known of bee resource use in corn production systems in Texas, the abundant yet variable bee communities across latitudes in this study suggests a need to investigate the influence of farming practices on bee resources in regional corn production systems.
ARTICLE Download: 78| View: 178| Comments: 0 | doi:10.20944/preprints202003.0215.v1
Subject: Life Sciences, Other Keywords: major depression; skin fibroblasts; mitochondria; bioenergetics; oxidative phosphorylation; adenosine triphosphate; calcium imaging; mitochondrial membrane potential; mitochondrial DNA copy number
Online: 12 March 2020 (14:11:25 CET)
Mitochondrial malfunction is supposed to be involved in the etiology and pathology of major depressive disorder (MDD). Here, we aimed to identify and characterize the molecular pathomechanisms related to mitochondrial disfunction in adult human skin fibroblasts which were derived from MDD patients or non-depressive control subjects. We found that MDD fibroblasts showed significantly impaired mitochondrial functioning: basal and maximal respiration, spare respiratory capacity, non-mitochondrial respiration and ATP-related oxygen consumption was lower. Moreover, MDD fibroblasts harbor lower ATP levels and showed hyperpolarized mitochondrial membrane potential. To investigate cellular resilience, we challenged both groups of fibroblasts with hormonal (dexamethasone) or metabolic (galactose) stress for one week, and found that both stressors increased oxygen consumption but lowered ATP content in MDD as well as in non-depressive control fibroblasts. Interestingly, the bioenergetic differences between fibroblasts from MDD or non-depressed subjects, which were observed under non-treated conditions, could not be detected after stress. Our findings support the hypothesis that altered mitochondrial function causes a bioenergetic imbalance which is associated with the molecular pathophysiology of MDD. The observed alterations in OXPHOS and other mitochondria-related properties represent a basis for further investigations of pathophysiological mechanisms and might open new ways to gain insight into antidepressant signaling pathways.
ARTICLE Download: 31| View: 38| Comments: 1 | doi:10.20944/preprints202002.0430.v2
Subject: Life Sciences, Biotechnology Keywords: Co-culture; Reduced-serum; Wound bed; Fibroblasts; Keratinocytes
Online: 12 March 2020 (13:24:46 CET)
Contact-based co-culture of fibroblasts and keratinocytes is important to study the structure and functions of the wound bed. Co-culture of these two cell types in direct contact with each other has been challenging, requiring high serum concentrations (up to 10%), feeder systems and a range of supplemental factors. These approaches are not only technically demanding, but also present scientific, cost and ethical limitations associated with high-serum concentrations. We have developed two reduced-serum approaches (1-2%) to support contact-based co-culture of human dermal fibroblasts (HDFa) and human epidermal keratinocytes (HaCaT). The two approaches include (1) Specialized cell culture media for each cell type mixed in a 1:1 ratio (KGM+FGM), and (2) Minimal media supplemented with cell-specific growth factors (MEM+GF). Co-culture could be successfully achieved by co-seeding (two cell types were introduced simultaneously), or in a layered fashion (keratinocytes seeded on top of confluent fibroblasts). With wound scratch assays, the co-cultured platforms could demonstrate cell proliferation, migration and wound closure. The reduced-serum conditions developed are simple, easy to formulate and adopt, and based on commonly-available media components. These contact-based co-culture approaches can be leveraged for wound and skin studies, and tissue bioengineering applications, potentially reducing concerns with high-serum formulations.
SHORT NOTE Download: 223| View: 368| Comments: 1 | doi:10.20944/preprints202003.0077.v2
The Ongoing COVID-19 Epidemic Curves Indicate Initial Point Spread in China with Log-Normal Distribution of New Cases Per Day with a Predictable Last Date of the Outbreak Version 2: Evaluation of Previous Prediction and Testing the Method for S Korea and the Use of the Method by an Unexperienced Person
Online: 12 March 2020 (05:04:52 CET)
During an epidemic outbreak it is useful for planners and responsible authorities to be able to plan ahead to estimate when an outbreak of an epidemic is likely to ease and when the last case can be predicted in their area of responsibility. Theoretically this could be done for a point source epidemic using epidemic curve forecasting. The extensive data now coming out of China makes it possible to test if this can be done using MS Excel a standard spreadsheet program available to most offices. The available data is divided up for whole China and the different provinces. This and the high number of cases makes the analysis possible. Data for new confirmed infections for Hubei, Hubei outside Wuhan, China excluding Hubei as well as Zhejiang and Fujian provinces all follow a log-normal distribution that can be used to make a rough estimate for the date of the last new confirmed cases in respective areas. In this continuation work 9 additional days were added for the Chinese data to evaluate the previous predictions. We also tested the feasibility for a non-specialist to make similar predictions using additional data from S Korea now available. The extra data now available from China follows the previous predicted trend supporting the usefulness of this simple technique.
REVIEW Download: 731| View: 1254| Comments: 0
Subject: Life Sciences, Immunology Keywords: immune system; viral infection; influenza; COVID-19; micronutrients; vitamins; omega-3 fatty acids; minerals; vitamin C; vitamin D
Online: 12 March 2020 (04:30:45 CET)
Public health practices including handwashing and vaccinations help reduce the spread and impact of infections. Nevertheless, the global burden of infection is high, and additional measures are necessary. Acute respiratory tract infections, for example, are responsible for approximately 2.65 million deaths per year. The role nutrition plays in supporting the immune system is well-established. A wealth of mechanistic and clinical data show that vitamins, including vitamins A, B6, B12, C, D, E, and folate; trace elements, including zinc, iron, selenium, magnesium, and copper; and the omega-3 fatty acids eicosapentaenoic acid and docosahexaenoic acid play important and complementary roles in supporting the immune system. Inadequate intake and status of these nutrients are widespread, leading to a decrease in resistance to infections and as a consequence an increase in disease burden. Against this background the following conclusions are made: 1) Supplementation with the above micronutrients and omega-3 fatty acids is a safe, effective, and low-cost strategy to help support optimal immune function; 2) Supplementation above the RDA, but within recommended upper safety limits, for specific nutrients such as vitamins C and D is warranted; and 3) Public health officials are encouraged to include nutritional strategies in their recommendations to improve public health.
BRIEF REPORT Download: 51| View: 41| Comments: 0 | doi:10.20944/preprints202003.0198.v1
Subject: Life Sciences, Virology Keywords: human cytomegalovirus; progenitor cell; hematopoietic stem cell transplant; myelosuppression; hematopoiesis; humanized mice
Online: 12 March 2020 (04:26:12 CET)
Human Cytomegalovirus (HCMV) infection is a serious complication in hematopoietic stem cell transplant (HSCT) recipients due to virus-induced myelosuppression and impairment of stem cell engraftment. Despite the clear clinical link between myelosuppression and HCMV infection, little is known about the mechanism(s) by which the virus inhibits normal hematopoiesis because of the strict species specificity and the lack of surrogate animal models. In this study, we developed a novel humanized mouse model system that recapitulates the HCMV-mediated engraftment failure after hematopoietic cell transplantation. We observed significant alterations in the hematopoietic populations in peripheral lymphoid tissues following engraftment of a subset of HCMV+ CD34+ HPCs within the transplant suggesting that a small proportion of HCMV-infected CD34+ HPCs can profoundly affect HPC differentiation in the bone marrow microenvironment. This model will be instrumental to gain insight into the fundamental mechanisms of HCMV myelosuppression after HSCT and provides a platform to assess novel treatment strategies.
ARTICLE Download: 47| View: 123| Comments: 0
Subject: Life Sciences, Biophysics Keywords: cytosolic phospholipase A2; electron microscopy; C2 domain; Golgi; membrane bending; membrane curvature; oligomerization
Online: 12 March 2020 (04:10:52 CET)
Group IV phospholipase A2α (cPLA2α) regulates the production of prostaglandins and leukotrienes via the formation of arachidonic acid from membrane phospholipids. The targeting and membrane binding of cPLA2α to the Golgi involves the N-terminal C2 domain whereas the catalytic domain produces arachidonic acid. Although most studies of cPLA2α concern its catalytic activity, it is also linked to homeostatic processes involving the generation of vesicles that traffic material from the Golgi to the plasma membrane. Here we investigate how membrane curvature influences the homeostatic role of cPLA2α in vesicular trafficking. The cPLA2α C2 domain is known to induce changes in positive membrane curvature, a process which is dependent on cPLA2α membrane penetration. We show that cPLA2α undergoes C2 domain-dependent oligomerization on membranes in vitro and in A549 cells. We found that the association of the cPLA2α C2 domain with membranes is limited to membranes with positive curvature, and enhanced C2 domain oligomerization was observed on vesicles ~50 nm in diameter. We demonstrated that the cPLA2α C2 domain generates cholesterol enriched Golgi-derived vesicles independently of cPLA2α catalytic activity. Our results therefore provide novel insight into the molecular forces that mediate C2 domain-dependent membrane localization in vitro and in cells.
Wed, 11 March 2020
HYPOTHESIS Download: 56| View: 55| Comments: 0 | doi:10.20944/preprints202003.0183.v1
Subject: Life Sciences, Biophysics Keywords: Ebolavirus glycoprotein; Electrostatic interaction; Salt bridging network; Two Achilles' heels
Online: 11 March 2020 (10:32:02 CET)
Ebolavirus has a membrane envelope decorated by trimers of a glycoprotein (GP), which is responsible for host cell attachment and membrane fusion. Therefore, GP is a primary target for antiviral drugs development. Here, this article reports the first, to my knowledge, set of structural analysis of all Ebolavirus GP structures as of March 10, 2020, and also a brief update of the structurally identified electrostatic features of the Ebolavirus GP structures in both apo (unliganded) state and also in bound states with a series of small compounds, including a variety of approved drugs. With this comprehensive set of structural analysis, this article puts forward a hypothesis of two Achilles' heels of Ebolavirus GP structure, where the formation of two interfacial salt bridges, instead of destabilizing the prefusion conformation of Ebolavirus GP, constitutes a positive contribution towards the structural rigidification of the prefusion conformation of the Ebolavirus GP structure, thereby acting against GP-mediated Ebolavirus cell entry and/or preventing fusion between the viral and endosome membranes.
CASE REPORT Download: 2947| View: 11206| Comments: 0 | doi:10.20944/preprints202003.0180.v1
Subject: Life Sciences, Virology Keywords: COVID-19; coronavirus; fulminant myocarditis; infection; echocardiography
Online: 11 March 2020 (04:57:10 CET)
Background: The Coronavirus Disease 2019 (COVID-19) has been demonstrated as the cause of pneumonia. Nevertheless, it has not been reported as the cause of acute myocarditis or fulminant myocarditis. Case Presentation: A 63-year-old male was admitted with pneumonia and cardiac symptoms. He was genetically confirmed as COVID-19 by testing sputum on the first day of admission. He also had an elevated troponin-I (Trop I) level and diffuse myocardial dyskinesia along with decreased left ventricular ejection fraction (LVEF) on echocardiography. The highest level of Interleukin 6 was 272.40pg/ml. Bedside chest radiograph had typical ground-glass changes of viral pneumonia. The laboratory test results of virus that can cause myocarditis are all negative. The patient conformed to the diagnostic criteria of Chinese expert consensus statement for fulminant myocarditis. After receiving antiviral therapy and mechanical life support, the Trop I reduced to 0.10 g/L, and Interleukin 6 was 7.63 pg/ml. Meanwhile the LVEF of the patient gradually recovered to 68%. Conclusion: COVID-19 patients may develop severe cardiac complications such as myocarditis and heart failure, and this is the first case of COVID-19 infection complicated with fulminant myocarditis. The mechanism of cardiac pathology caused by COVID-19 needs further study.
Tue, 10 March 2020
ARTICLE Download: 44| View: 45| Comments: 0 | doi:10.20944/preprints202003.0168.v1
Subject: Life Sciences, Molecular Biology Keywords: NF-kappaB; HIF; ARNT; TRAF6; Transcription; ChIP; Drosophila
Online: 10 March 2020 (11:14:37 CET)
NF-B signalling is crucial for cellular responses to inflammation but has also been associated with the hypoxia response. NF-B and HIF transcription factors possess an intense molecular crosstalk. Although it is known that HIF-1beta modulates NF-kappaB transcriptional response, very little is understood regarding how HIF-1beta contributes to NF-kappaB signalling. Here, we demonstrate that HIF-1beta is required for full NF-kappaB activation in cells following canonical and non-canonical stimuli. We found that HIF-1beta specifically controls TRAF6 expression in human cells but also in Drosophila melanogaster. HIF-1beta binds to the TRAF6 gene and controls its expression independently of HIF-1alpha. Furthermore, exogenous TRAF6 expression is able to rescue all of the cellular phenotypes observed in the absence of HIF-1beta. These results indicate that HIF-1beta is an important regulator of NF-kappaB with consequences for homeostasis and human disease.
ARTICLE Download: 44| View: 105| Comments: 0 | doi:10.20944/preprints202003.0166.v1
Subject: Life Sciences, Biochemistry Keywords: vimentin; zinc; cysteine; redox sensing; intermediate filaments; cysteine mutant; filament bundling; filament width; divalent cations; magnesium
Online: 10 March 2020 (11:07:05 CET)
The intermediate filament protein vimentin constitutes a critical sensor for electrophilic and oxidative stress. We previously showed that vimentin interacts with zinc, which affects its assembly and redox sensing. Here we have used vimentin wt and C328S, an oxidation-resistant mutant showing improved NaCl-induced polymerization, to assess the impact of zinc on soluble and polymerized vimentin by light scattering and electron microscopy. Zinc acts as a switch, reversibly inducing the formation of vimentin oligomeric species. High zinc concentrations elicit optically-detectable vimentin structures with a characteristic morphology depending on the support. These effects also occur in vimentin C328S, but are not mimicked by magnesium. Treatment of vimentin with micromolar zinc induces fibril-like particles that do not assemble into filaments, but form aggregates upon subsequent addition of NaCl. In contrast, when added to NaCl-polymerized vimentin, zinc increases the diameter or induces lateral association of vimentin wt filaments. Remarkably, these effects are absent or attenuated in vimentin C328S filaments. Therefore, the zinc-vimentin interaction depends on the chemical environment and on the assembly state of the protein, leading to atypical polymerization of soluble vimentin, likely through electrostatic interactions, or to broadening and lateral association of preformed filaments through mechanisms requiring the cysteine residue. Thus, impact of zinc on vimentin assembly and redox regulation is envisaged.
ARTICLE Download: 620| View: 1059| Comments: 0 | doi:10.20944/preprints202003.0161.v1
Subject: Life Sciences, Microbiology Keywords: coronaviruses receptors; angiotensin-converting enzyme 2 (ACE2); COVID-19; SARS-Cov-2; the Red Queen hypothesis; segmented filamentous bacteria
Online: 10 March 2020 (08:45:34 CET)
Understanding how the coronaviruses invade our body is an essential point, and the expression profile of coronaviruses receptor may help us to find where the coronavirus infects our body. We found that the coronavirus receptors, including angiotensin-converting enzyme 2 (ACE2) for SARS-CoV and SARS-Cov-2, are digestion-related enzymes in human enterocytes. Coronaviruses are continually altering the binding receptor and binding modes during their evolution, but the potential target cell in the small intestine is constant when in the lung is inconstant. Enterocytes may act as a conserved cell reservoir for coronaviruses, which may be partially explained by the Red Queen hypothesis. We also found that coronaviruses receptors could be elevated in the presence of both invasive bacteria and their counterpart, probiotics. We demonstrated here that enterocytes act as a conserved cell reservoir for coronaviruses during their evolutions, which should not be ignored in the investigation of coronavirus diagnosis and treatment strategies.
ARTICLE Download: 253| View: 274| Comments: 0 | doi:10.20944/preprints202003.0160.v1
Subject: Life Sciences, Virology Keywords: influenza-like illness; 2019-nCoV; person-to-person transmission
Online: 10 March 2020 (05:18:19 CET)
The ongoing pandemic of the 2019 novel coronavirus disease (COVID-19) raises a global health crisis, which has resulted in 75,778 confirmed cases with 2130 deaths in China and beyond. Atypical symptom renders it challenging to earlier recognize the 2019-nCoV carrier with the potential ability of equivalent transmission. Therefore, it is needed to gain full spectrum of COVID-19. Here we report clustered COVID-19 cases of person-to-person transmission. The symptoms of typical pneumonia are shared by the two familial members, namely son (Patient 1) and father (Patient 2). Unexpectedly, an influenza-like illness (ILI) is also caused in Patient 3 having close contact with Patient 1 at personal dinner party. Combined with clinical and epidemiological study, chest computed tomography (CT) and molecular diagnosis demonstrate that all the three cases tested positive for COVID-19 with distinct symptoms by human-to-human transmission. To the best of knowledge, it closes in part (if not all), a missing gap of clinical repertoires of COVID-19 outbreaks and underlines the possibility that neglection of cryptic/asymptomatic/mild cold-like syndromes gives biased screen in the earlier stage of COVID-19 cases.
ARTICLE Download: 360| View: 268| Comments: 0 | doi:10.20944/preprints202003.0159.v1
Subject: Life Sciences, Microbiology Keywords: bat SARS-like CoV; SARS-CoV; 2019-nCoV; phylogeny; spike protein; viral and host fusion
Online: 10 March 2020 (03:49:10 CET)
A novel coronavirus (2019-nCoV) that is initially found to trigger human severe respiratory illness in Wuhan City of China, 2019, has been recognized as a public health emergency of international concern. In the past two months, this deadly agent has caused 77,785 cases with 2,666 deaths via rapid person-to-person transmission and reached at least 25 countries. However, its evolutionary origin is poorly understood. Here we show integrative evidence that 2019-nCoV is a possible progenitor for SARS-CoV with bat origin. Our finding underscores the importance of tracing origin in the efficient monitoring, and effectively preventing the interspecies transmission of such emerging/re-emerging coronaviruses.
Mon, 9 March 2020
ARTICLE Download: 47| View: 114| Comments: 0 | doi:10.20944/preprints202003.0148.v1
Subject: Life Sciences, Endocrinology & Metabolomics Keywords: osteosarcoma; cancer; tumor; vitamin D; vitamin D deficiency; vitamin D receptor; vdr; mitochondria; ROS; SOD; SOD1; SOD2; superoxide; superoxide dismutase
Online: 9 March 2020 (02:40:08 CET)
Superoxide, a form of reactive oxygen species (ROS), is catabolized by superoxide dismutase (SOD) and contributes to carcinogenesis via the oxidative damage it inflicts on cells. The aim of this research was to analyze the potential vitamin D-mediated regulation of the antioxidative “SOD1-to-SOD2 switch” within the human MG-63 osteosarcoma model. For this study; real-time PCR analysis was performed using MG-63 cells exposed to metabolically active 1,25(OH)2D3. Frist; a sustained statistically significant >2-fold suppression of proliferating cell nuclear antigen (PCNA) transcripts was observed after 10nM but not at 100nM of 1,25(OH)2D3 treatment; suggesting a cytostatic effect. In order to assess regulators of mitochondrial oxidative phosphorylation; gene expression of COX2 and COX4l1 of the mitochondrial complex IV and antioxidative enzymes (SOD1; SOD2 and Catalase (CAT)) were monitored. For COX2 and COX4l1; no changes in gene expression were observed. However; a concomitant decrease in CAT and SOD1 mRNA; and increase in SOD2 mRNA after 24 hours of 10nM 1,25(OH)2D3 treatment were observed. A ~8-fold increase in SOD2 mRNA was apparent after 48 hours. The significant increase in SOD2 activity in the presence of vitamin D indicates an antioxidant potential and sensitization of vitamin D during osteosarcoma transformation and mitochondrial detoxification over time.
Sun, 8 March 2020
ARTICLE Download: 377| View: 579| Comments: 0
Online: 8 March 2020 (17:14:57 CET)
3CLpro is the main protease of the novel coronavirus (SARS-CoV-2) responsible for their intracellular duplication. Based on virtual screening technology, we found 23 approved clinical drugs such as Carfilzomib, Saquinavir, Thymopentin and etc., which showed high affinity with the 3CLpro active sites. These findings suggest that 3CLpro inhibitors might be potential candidates for further activity detection and molecular modification.
ARTICLE Download: 34| View: 47| Comments: 0 | doi:10.20944/preprints202003.0142.v1
Subject: Life Sciences, Other Keywords: total knee arthroplasty; rehabilitation program; knee osteoarthritis; exercise rehabilitation; postoperative care
Online: 8 March 2020 (16:50:41 CET)
This multi-center, single-blinded, randomized controlled study assessed the efficacy of phased exercise rehabilitation programs in patients who underwent a total knee arthroplasty (TKA) and investigated suitable exercise types, intensities, and frequencies for patients undergoing postoperative rehabilitation. Between January and March 2018, 494 patients who had undergone TKA were treated at two medical centers. Patients were randomized and allocated to the rehabilitation group (n=330) or the control group (n=164; treated with postoperative care). The 100-mm Visual Analogue Scale (VAS), Western Ontario and McMaster Universities Arthritis Index (WOMAC), range of motion, and Short-Form 36 (SF-36) scores were assessed and compared between the two groups. The average WOMAC score was 84.40±15.20 in the rehabilitation group and 108.30±3.90 in the control group (p=0.009). The mean VAS score was 2.54±0.16 in the rehabilitation group and 2.87±0.31 in the control group (p=0.024). Furthermore, the range of motion was 125.02±6.20 in the rehabilitation group and 116.40±1.40 in the control group (p=0.017). The mean SF-36 score was 105.40±21.50 in the rehabilitation group and 83.70±5.01 in the control group (p=0.043). This study suggests that the phase rehabilitation program could be more effective at improving pain, knee function, and quality of life than condition postoperative care after TKA.
HYPOTHESIS Download: 723| View: 1861| Comments: 0 | doi:10.20944/preprints202003.0138.v1
Subject: Life Sciences, Virology Keywords: 2019-nCoV; SARS-CoV-2; COVID-19; ADE; antibody depedendent enhancement
Online: 8 March 2020 (15:35:27 CET)
Background: In 80% of patients, COVID-19 presents as mild disease1,2. 20% of cases develop severe (13%) or critical (6%) illness. More severe forms of COVID-19 present as clinical severe acute respiratory syndrome, but include a T-predominant lymphopenia3, high circulating levels of proinflammatory cytokines and chemokines, accumulation of neutrophils and macrophages in lungs, and immune dysregulation including immunosuppression4. Methods: All major SARS-CoV-2 proteins were characterized using an amino acid residue variation analysis method. Results predict that most SARS-CoV-2 proteins are evolutionary constrained, with the exception of the spike (S) protein extended outer surface. Results were interpreted based on known SARS-like coronavirus virology and pathophysiology, with a focus on medical countermeasure development implications. Findings: Non-neutralizing antibodies to variable S domains may enable an alternative infection pathway via Fc receptor-mediated uptake. This may be a gating event for the immune response dysregulation observed in more severe COVID-19 disease. Prior studies involving vaccine candidates for FCoV5,6 SARS-CoV-17-10 and Middle East Respiratory Syndrome coronavirus (MERS-CoV) 11 demonstrate vaccination-induced antibody-dependent enhancement of disease (ADE), including infection of phagocytic antigen presenting cells (APC). T effector cells are believed to play an important role in controlling coronavirus infection; pan-T depletion is present in severe COVID-19 disease3 and may be accelerated by APC infection. Sequence and structural conservation of S motifs suggests that SARS and MERS vaccine ADE risks may foreshadow SARS-CoV-2 S-based vaccine risks. Autophagy inhibitors may reduce APC infection and T-cell depletion12 13. Amino acid residue variation analysis identifies multiple constrained domains suitable as T cell vaccine targets. Evolutionary constraints on proven antiviral drug targets present in SARS-CoV-1 and SARS-CoV-2 may reduce risk of developing antiviral drug escape mutants. Interpretation: Safety testing of COVID-19 S protein-based B cell vaccines in animal models is strongly encouraged prior to clinical trials to reduce risk of ADE upon virus exposure.
ARTICLE Download: 23| View: 36| Comments: 0
Subject: Life Sciences, Genetics Keywords: genetic diversity; Dioscorea praehensilis; SSR markers; Ghana
Online: 8 March 2020 (14:55:19 CET)
Dioscorea praehensilis Berth is one of the wild yam species resistance to many yam disease (yam anthracnose disease and yam mosaic virus) grow in Ghana especially in the cocoa grown regions of the country. It is a crucial crop that has been known to contribute to poverty reduction and food gap. Genetic diversity in this yam species has been discovered to be eroding and neglected. In this study we evaluated the genetic diversity among 43 D. praehensilis collected from Ghana using simple sequence repeat (SSR). Using 11 SSR marker, a total of 99 number of alleles were generated with an average of 8.48 alleles per locus. The mean gene diversity was 0.81, mean polymorphism information content was 0.82 while mean Shannon information index was 1.94. Principal coordinate analysis (PCoA) revealed a contribution of 40.16% of the first three coordinate axes and grouped the 43 morphotypes into 2 groups while hierarchical cluster through UPGMA revealed the presence of 3 main clusters. Molecular variance (AMOVA) alongside the Fst revealed low genetic diversity and differentiation among accessions and population. Result of this study assess the genetic diversity and will facilitate the use D. praehensilis as sources of resistance gene into yam breeding program.
ARTICLE Download: 70| View: 315| Comments: 0 | doi:10.20944/preprints202003.0132.v1
Online: 8 March 2020 (04:40:36 CET)
Body temperature responses were recorded during phases of work (waiting to work in close proximity to search site, active work in a search site, and post-work recovery crated in vehicle) in human remains detection dogs during search training. State or federally certified human remains detection dogs (n = 8) completed eight iterations of searching, rotating through six different types of search environments to detect numerous scent sources including partial and complete, buried, hidden, or fully visible human remains. Internal temperature (Tgi) of the body was measured continuously using an ingestible thermistor in the gastrointestinal tract. Mean total phase times were: waiting to work: 9.17 minutes (± 2.27); active work: 8:58 minutes (± 2:49); and post work recovery: 24:04 minutes (± 10.59). Tgi was impacted by phase of work (P < 0.001) with a small increase during active work, with mean peak temperature 39.4 °C (± 0.34 ºC) during that period. Tgi continued to increase for a mean of 7:37 (± 6:04) minutes into the post-work recovery phase in the handler’s vehicle with a mean peak Tgi of 39.66 °C (± 0.41 ºC). No significant increase in temperature was measured during the waiting to work phase, suggesting anticipation of work did not appear to contribute to overall body temperature increase during the waiting to work recovery cycle. Continued increase of gastrointestinal body temperature several minutes after cessation of exercise indicates that risk of heat injury does not immediately stop when the dog stops exercising, although none of the dogs in this study reached clinically concerning body temperatures or displayed any behavioral signs suggestive of pending heat injury. More work is needed to better understand the impact of vehicle crating on post-work recovery temperatures in dogs.
Sat, 7 March 2020
ARTICLE Download: 60| View: 59| Comments: 0 | doi:10.20944/preprints202003.0124.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: horse; aynchronous embryo transfer; conceptus; endoemtrium; transcriptome; extracellular exosome; IGFBP3; Kininogen 1
Online: 7 March 2020 (16:11:52 CET)
Pre-implantation horse conceptuses require nutrients and signals from histotroph, the composition of which is regulated by luteal progesterone and conceptus-secreted factors. To distinguish progesterone and conceptus effects we shortened the period of endometrial progesterone-priming by asynchronous embryo transfer. Day 8 embryos were transferred to synchronous (day 8) or asynchronous (day 3) recipients, and RNA sequencing was performed on endometrium and conceptuses recovered 6 and 11 days later (embryo days 14 and 19). Asynchrony resulted in many more differentially expressed genes (DEGs) in conceptus membranes (3473) than endometrium (715). Gene ontology analysis identified upregulation in biological processes related to organogenesis and preventing apoptosis in synchronous conceptuses on day 14, and in cell adhesion and migration on day 19. Asynchrony also resulted in large numbers of DEGs related to ‘extracellular exosome’. In endometrium, genes involved in immunity, the inflammatory response, and apoptosis regulation were upregulated during synchronous pregnancy and, again, many genes related to extracellular exosome were differentially expressed. Interestingly, only 14 genes were differentially expressed in endometrium recovered 6 days after synchronous versus 11 days after asynchronous transfer (day 14 recipient in both). Among these, KNG1 and IGFBP3 were consistently up-regulated in synchronous endometrium. Furthermore bradykinin, an active peptide cleaved from KNG1, stimulated prostaglandin release by cultured trophectoderm cells. The horse conceptus thus responds to a negatively asynchronous uterus by extensively adjusting its transcriptome, whereas the endometrial transcriptome is modified only subtly by a more advanced conceptus.
ARTICLE Download: 33| View: 36| Comments: 0 | doi:10.20944/preprints202003.0119.v1
Subject: Life Sciences, Biotechnology Keywords: black rice; transcriptome sequencing; genic SSRs; genetic diversity
Online: 7 March 2020 (09:03:34 CET)
Study in black rice has gain prominence in recent times due to its high nutritive value, curative effect, and anti-oxidant properties. However, its poor agronomic traits, including low yield necessitates the incorporation of the colour-grain trait into elite varieties through plant breeding techniques. SSR markers play an important role in plant identification and breeding. Here, the generation of reference-based transcriptome, annotation of transcriptome datasets, and a large set of simple sequence repeat (SSR) markers derived from Black rice have been described. In all 28664 SSRs were predicted in 34978 (48.59%) expressed transcripts. However, 7068 (20.20%) transcripts were found to have more than one SSR. The identified SSRs were dominated by tri-nucleotide and tetra-nucleotide repeats representing about 54.11% and 33.31% respectively, of total SSRs. Validation of selected markers associated with anthocyanin trait performed across different black rice accessions established the reliability of the process used for mining SSR markers. The SSR markers identified in this study could be used to select varieties with desired traits, and to investigate the genetic mechanism underlying anthocyanin accumulation in the pericarps of black rice. Furthermore, the findings from this study may prove beneficial in future genetic diversity studies, primer development, and selective breeding programs.
ARTICLE Download: 58| View: 54| Comments: 0
Online: 7 March 2020 (03:05:56 CET)
Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior yield and biomass to parental lines and has been used to breed F1 hybrid cultivars in many crops. A similar level of heterosis in all F1 individuals is expected as they are genetically identical. However, we found variation of rosette size in individual F1 plants from a cross between C24 and Columbia-0 accessions of Arabidopsis thaliana. Big sized F1 plants had 26.1% larger leaf area in the 1st and 2nd leaves than medium sized F1 plants at 14 days after sowing in spite of the identical genetic background. We identified differentially expressed genes between big and medium sized F1 plants by microarray; genes involved in the category of stress response were overrepresented. We made transgenic plants overexpressing 21 genes, which were differentially expressed between the two size classes, some lines had increased plant size at 14 or 21 days after sowing but not at all time points. Change of expression levels in stress responsive genes among individual F1 plants, implying epigenetic changes, could generate the variation in plant size of individual F1 plants in A. thaliana.
Fri, 6 March 2020
ARTICLE Download: 42| View: 56| Comments: 0 | doi:10.20944/preprints202003.0106.v1
Subject: Life Sciences, Molecular Biology Keywords: purinergic P2X4 receptor; TM1 and TM2 segments; ethanol and agonist action; mutagenesis; molecular model
Online: 6 March 2020 (04:45:49 CET)
Mouse models of alcohol use disorder (AUD) revealed a subtype of purinergic receptors (P2X4Rs) as a promising target for AUD drug development. We have previously demonstrated that residues at the transmembrane (TM)-ectodomain interface and within TM1 segment contribute to the formation of an ethanol action pocket in P2X4Rs. In the present study, we tested the hypothesis that there are more residues in TM segments, which are important for ethanol sensitivity of P2X4Rs. Using site-directed mutagenesis and two-electrode voltage-clamp electrophysiology in Xenopus oocytes, we found that arginine at position 33 (R33) in the TM1 segment plays a role in ethanol sensitivity of P2X4Rs. Molecular models in both closed and open states provided evidence for interactions between R33 and aspartic acid at position 354 (D354) of the neighboring TM2 segment. Further work with mixtures of wild-type (WT) and reciprocal single (R33D:WT, D354R:WT) and double (R33D-D354R:WT) mutants confirmed the importance of this interaction for ethanol sensitivity, ivermectin action and channel function. Additionally, our findings suggest that valine at TM1 position 49 plays a role in P2X4R function by providing flexibility during channel opening. Collectively, these findings identified new activity sites, and suggest the importance of TM1-TM2 interaction for channel function and ethanol sensitivity of P2X4Rs.
ARTICLE Download: 65| View: 86| Comments: 0 | doi:10.20944/preprints202003.0097.v1
Subject: Life Sciences, Microbiology Keywords: base modification; methyltransferases; flavoenzymes; tRNA; rRNA; mycoplasmas; spiroplasmas; acholeplasmas; evolution; minimal cell; moonlighting function
Online: 6 March 2020 (02:28:12 CET)