REVIEW | doi:10.20944/preprints202005.0519.v1
Subject: Life Sciences, Molecular Biology Keywords: Angiotensin-Converting Enzyme 2; Spike glycoprotein; TMPRESS2; Furin; Malayan pangolin
Online: 31 May 2020 (21:41:44 CEST)
The outbreak of a novel coronavirus (SARS-CoV2) associated with acute respiratory disease called COVID-19 marked the introduction of the third spillover of an animal CoV to humans in the last 2 decades. The SARS-CoV2 genome analysis with various bioinformatics tools revealed that it belongs to beta CoVs genera, with highly similar genome as bat coronavirus and receptor binding domain (RBD) of spike glycoprotein as Malayan pangolin coronavirus. Based on its genetic proximity, SARS-CoV2 is likely to be originated from bat derived CoV and transmitted to humans via an unknown intermediate mammalian host, probably Malayan pangolin. Further spike protein S1/S2 cleavage site of SARS-CoV2 has acquired polybasic furin cleavage site which is absent in bat and pangolin suggesting natural selection either in an animal host before zoonotic transfer or in humans following zoonotic transfer. In the current review, we recapitulate a preliminary opinion about the disease, origin and life cycle of SARS-CoV2, roles of virus proteins in pathogenesis, commonalities and differences between different corona viruses. We have also highlighted the evidences regarding the potential drugs and vaccine candidates with their modes of action to cope with this viral outbreak. Our review provides comprehensive up-dated information on molecular aspects of the SARS-CoV2.
REVIEW | doi:10.20944/preprints202005.0518.v1
Subject: Life Sciences, Biophysics Keywords: virus; extracellular vesicles; COVID-19; SARS-CoV-2; membrane vesicluation
Online: 31 May 2020 (21:35:23 CEST)
Within the micro and nano world, tiny membrane-enclosed bits of material are more or less free to move and act as communication tools within cells, between cells, between different tissues and between organisms in global environment. Based on the mechanism of membrane budding and vesiculation that includes all types of cells, in this review, we attempted to present a review on SARS-CoV-2 virus actions in compartments of different scales (cells and their surroundings, tissues, organisms and society). Interactions of the virus with cells on a molecular level, with neural system, endothelium, hematopoietic system, gastrointestinal system and genitourinary system. Transmission route between organisms and between mother and fetus are considered. Also, transmission of virus through contact with materials and with environment, the suggested measures to prevent contamination with the virus and to support the organism against the disease are given.
BRIEF REPORT | doi:10.20944/preprints202005.0515.v1
Subject: Life Sciences, Virology Keywords: Covid-19; Herd Immunity Threshold; Corona Virus; Innate immunity; flattening the curve; serological survey
Online: 31 May 2020 (21:14:05 CEST)
We have analysed the death and recovery rate of Covid-19 disease progression. From the analysis, we have argued that the pandemic is over in certain countries (labelled as group-A) and for other countries (labelled as group-B) the disease appears to remain as endemic. Taking into account the serological survey (sero-survey) test results obtained by certain groups and comparing it with herd immunity threshold value one can infer that the low number of infection for group-B is either due to acquired immunity by some previous infection by other coronavirus or due to innate immunity towards this infection. This effect is stronger for group-B to slow the progress of the disease to such an extent resulting in flattening of the disease progression curve compared to group-A.
ARTICLE | doi:10.20944/preprints202005.0505.v1
Subject: Life Sciences, Virology Keywords: COVID-19; Viral Co-infection; SARS-CoV-2; Influenza A virus; Human Immunodeficiency virus
Online: 31 May 2020 (20:36:28 CEST)
In December 2019, pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection emerged in Wuhan City, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused epidemic disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be the sixth international public health emergency. Cellular co-infection is a critical determinant of both viral fitness and infection outcome and plays a crucial role in shaping the host immune response to infections. In this study, sixty-eight public next-generation sequencing libraries from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Using an alignment-free method based on K-mer mapping and extension, SARS-CoV-2 was identified in all except three patients. Influenza A H7N9 (3/68), Human immunodeficiency virus 1 (1/68), Spodoptera frugiperda rhabdovirus isolate (3/68), Human metapneumovirus (1/68), coronaviruses NL63 (1/68), Sri Lankan cassava mosaic virus (1/68), Indian cassava mosaic virus (1/68), Parvovirus (1/68), Simian virus 40 (1/68), Woodchuck hepatitis virus (1/68), Saccharomyces 20S RNA narnavirus (2/68), and Autographa californica nucleopolyhedrovirus (2/68) genome sequences were detected in SARS-CoV-2 infected patients.
Online: 31 May 2020 (18:28:15 CEST)
Dengue is one of the life-threatening common neglected tropical diseases of the world, yet to develop any therapeutic for its treatment and prevention. Although there is a licensed vaccine reported, but becomes less efficacious due to the presence of multiple serovars of the dengue virus (DENV). Thus, an efficacious dengue vaccine potent to work against all the serovars is very crucial and time-demanding. Here we used a comprehensive hierarchical reverse vaccinology approach to design an epitope-based vaccine, targeted against multiple serovars of the DENV. Conservancy and population coverage analysis of the promiscuous epitopes revealed the robust immune response against multiple serovars of the DENV and various ethnicities. Final vaccine constructs comprising of B and T-cell epitopes, Universal pan-HLA DR or PADRE (AKFVAAWTLKAAA) sequence, and an adjuvant (β-defensin) at N-terminal of the construct with suitable linkers. Physiochemical properties and secondary structure profiling of the vaccine protein secured its hydrophilic, thermostable, and other structural nature. Molecular docking analysis indicates the deep binding of the proposed vaccine in the binding groove of the human immune TLR4 receptor present on the dendritic cell. In addition, disulfide engineering was coped to extend its stability. Furthermore, molecular dynamics simulation of the modeled vaccine-TLR8 complex showed minimum deformability. Finally, in silico cloning approach of the vaccine construct within an expression vector (pET28a+) assure good expression. Proposed vaccine may give novel insights for treatment of dengue patients.
HYPOTHESIS | doi:10.20944/preprints202005.0480.v1
Subject: Life Sciences, Virology Keywords: endothelial; infection; basement membrane; fibroblast; fibrosis; nsp7; hypothesis; pathogenesis; COVID-19; SARS-CoV2
Online: 31 May 2020 (16:28:19 CEST)
Severe COVID-19 is associated with viraemia and multiple organ disease. Similar clinicopathological features have been previously seen in SARS and MERS. Clinically, the severity of SARS, MERS and COVID-19 has been associated with the presence of SARS-CoV, MERS-CoV or SARS-CoV2 viraemia in affected patients. In vitro work has looked at the pattern of viral entry and release from polarised epithelial cells infected by coronaviruses. This work has demonstrated a correlation between the severity of a coronavirus infection and the ability of the virus to reach and infect the basal surface of host cells. It has been postulated that this ability helps the virus invade the bloodstream of the host, resulting in a systemic infection with multiple organ involvement. Here we propose that basal surface release and entry of COVID-19 into and out of cells at epithelial-endothelial interface plays a key pathogenic role in severe COVID-19 disease.
ARTICLE | doi:10.20944/preprints202005.0471.v1
Subject: Life Sciences, Genetics Keywords: DNA oligomers; harmonic progression; hyperbolic rules; matrices; tensor product; quantum informatics; oligomer sums method; genomes; genes; viruses
Online: 31 May 2020 (15:19:29 CEST)
The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of rhythmically repeating deviations from model hyperbolic sequences; these deviations are associated with DNA triplets and should be systematically analyzed for a deeper understanding the genetic coding system. The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.
Fri, 29 May 2020
Subject: Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; variant; low pathogenicity; Singapore
Online: 29 May 2020 (12:47:07 CEST)
Number of confirmed cases of COVID-19 caused by SARS-CoV-2 exceeded 5 million as of May 21, 2020. Global average of the case fatality rate of COVID-19 is about 7% so far. There exist variations in case fatality rates among countries. Particularly, Singapore and Qatar have exceptionally low case fatality rates with 0.1% while France’s rate is almost 20%. Since no magic bullet treatment for COVID-19 exists, we investigated SARS-CoV-2 strains specific to Singapore in this study to identify a clade with low pathogenicity. Variant analysis revealed that a clade with variants ORF1ab L3606F, A4489V, S2015R, T2016K, and N P13L is common in Singapore. Based on our analysis of variants and historical case statistics, the clade is dominant in a recent surge. Therefore, we suggest that low case fatality rate of Singapore possibly is attributed to the clade. Although contribution of each variant to the low pathogenicity is not clear, L3606F alone does not accomplish such low pathogenicity from the comparison with case fatality data from Japan, where L3606F is dominant. Further investigation is necessary to conclude to validate this finding.
Online: 29 May 2020 (03:41:50 CEST)
The outbreak of COVID-19 has caused a global public health crisis. The spread of SARS-CoV-2 by contact is widely accepted, but the relative importance of aerosol transmission for the spread of COVID-19 is controversial. Here we characterize the distribution of SARA-CoV-2 in 123 aerosol samples, 63 masks, and 30 surface samples collected at various locations in Wuhan, China. The positive percentages of viral RNA included 21% of the aerosol samples from an intensive care unit and 39% of the masks from patients with a range of conditions. A viable virus was isolated from the surgical mask of one critically ill patient while all viral RNA positive aerosol samples were cultured negative. The SARS-CoV-2 detected in masks from patients, ambient air, and respirators from health workers compose a chain of emission, transport, and recipient of the virus. Our results indicate that masks are effective in protecting against the spread of viruses, and it is strongly recommended that people throughout the world wear masks to break the chain of virus transmission and thus protect themselves and others from SARS-CoV-2.
Thu, 28 May 2020
REVIEW | doi:10.20944/preprints202005.0460.v1
Subject: Life Sciences, Other Keywords: extracellular vesicles; exosomes; neural tissue repair; neuroregeneration; non-human primates; hydrogels; neural tissue engineering; stroke; cortical injury
Online: 28 May 2020 (13:08:32 CEST)
Neural tissue engineering, nanotechnology and neuroregeneration are diverse biomedical disciplines that have been working together in recent decades to solve the complex problems linked to central nervous system (CNS) repair. It is known that the CNS demonstrates a very limited regenerative capacity because of a microenvironment that impedes effective regenerative processes, making development of CNS therapeutics challenging. Given the high prevalence of CNS conditions such as stroke that damage the brain and place a severe burden on afflicted individuals and on society, it is of utmost significance to explore the optimum methodologies for finding treatments that could be applied to humans for restoration of function to pre-injury levels. Extracellular vesicles (EVs), also known as exosomes, when derived from mesenchymal stem cells, are one of the most promising approaches that have been attempted thus far, as EVs deliver factors that stimulate recovery by acting at the nanoscale level on intercellular communication while avoiding the risks linked to stem cell transplantation. At the same time, advances in tissue engineering and regenerative medicine have offered the potential of using hydrogels as bio-scaffolds in order to provide the stroma required for neural repair to occur, as well as the release of biomolecules facilitating or inducing the reparative processes. This review introduces a novel experimental hypothesis regarding the benefits that could be offered if EVs were to be combined with biocompatible injectable hydrogels. The rationale behind this hypothesis is presented, analyzing how a hydrogel might prolong the retention of EVs and maximize the localized benefit to the brain. This sustained delivery of EVs would be coupled with essential guidance cues and structural support from the hydrogel until neural tissue remodeling and regeneration occur. Finally, the importance of including non-human primate (NHP) models in the clinical translation pipeline, as well as the added benefit of multi-modal neuroimage analysis to establish non-invasive, in vivo, quantifiable imaging-based biomarkers for CNS repair are discussed, aiming for more effective and safe clinical translation of such regenerative therapies to humans.
REVIEW | doi:10.20944/preprints202004.0097.v6
Subject: Life Sciences, Microbiology Keywords: convalescent plasma; serology; pathogen reduction technologies; pathogen inactivation; COVID-19; SARS-CoV2
Online: 28 May 2020 (11:52:38 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.
Wed, 27 May 2020
ARTICLE | doi:10.20944/preprints202005.0450.v1
Subject: Life Sciences, Other Keywords: epidemiology; transmission dynamics; isolated population; Spain
Online: 27 May 2020 (09:05:14 CEST)
Background: Since March 2020, Spain is severely hit by the ongoing pandemic of coronavirus disease 19 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding and disrupting the early transmission dynamics of the infection is crucial for impeding sustained transmission. Methods: We recorded all COVID-19 cases and traced their contacts in an isolated rural community. We also sampled 10 households, 6 public service sites and the wastewater from the village sewage for environmental SARS-CoV-2 RNA. Results: The first village patient diagnosed with COVID-19-compatible symptoms occurred on March 3, 2020, twelve days before lockdown. A peak of 39 cases occurred on March 30. By May 15, the accumulated number of symptomatic cases was 53 (6% of the population), of which only 22 (41%) had been tested and confirmed by RT-PCR as SARS-CoV-2 infected, including 16 hospitalized patients. Contacts (n=144) were six times more likely to develop symptoms. Environmental sampling detected SARS-CoV-2 RNA in two households with known active cases and in two public service sites: the petrol station and the pharmacy. Samples from other sites and the wastewater tested negative. Conclusions: The low proportion of patients tested by RT-PCR calls for urgent changes in disease management. We propose that early testing of all cases and their close contacts would reduce infection spread, reducing the disease burden and fatalities. In a context of restricted testing, environmental RNA surveillance might prove useful for early warning and to identify high-risk settings enabling a targeted resource deployment.
REVIEW | doi:10.20944/preprints202005.0448.v1
Subject: Life Sciences, Virology Keywords: betacoronaviruses; genomics; SARS-CoV; MERS-CoV; SARS-CoV-2; COVID-19
Online: 27 May 2020 (08:50:46 CEST)
In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of betacoronaviruses in the aftermath of the 2002-03 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-20 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind, allowing the follow up of disease spread and transmission dynamics in near real time. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202005.0153.v2
Subject: Life Sciences, Microbiology Keywords: Escherichia coli; antimicrobial resistance; ESBL; MDR; frozen chicken meat; Bangladesh
Online: 27 May 2020 (08:31:20 CEST)
Escherichia coli is known as one of the most important foodborne pathogens in humans, and contaminated chicken meat is an important source of foodborne infection with this bacterium. The occurrence of extended-spectrum β-lactamase (ESBL)-producing E. coli (ESBL-Ec), in particular, in chicken meat is considered a global health problem. This study aimed to determine the magnitude of E. coli, with special emphasis on ESBL-Ec, along with their phenotypic antimicrobial resistance pattern in frozen chicken meat. The study also focused on the determination of ESBL-encoding genes in E. coli. A total of 113 frozen chicken meat samples were purchased from 40 outlets of nine branded supershops in five megacities in Bangladesh. Isolation and identification of E. coli were done based on cultural and biochemical properties, as well as PCR assay. The resistance pattern was determined by the disc diffusion method. ESBL-encoding genes were determined by multiplex PCR. The results showed that 76.1% of samples were positive for E. coli, of which 86% were ESBL producers. All the isolates were multidrug-resistant (MDR). Resistance to 9–11 and 12–13 antimicrobial classes was observed in 38.4% and 17.4% isolates, respectively, while only 11.6% were resistant to 3–5 classes. Possible extensive drug resistance (pXDR) was found in 2.3% of isolates. High single resistance was observed for oxytetracycline (93%) and amoxicillin (91.9%), followed by ampicillin (89.5%), trimethoprim–sulfamethoxazole, and pefloxacin (88.4%), and tetracycline (84.9%). Most importantly, 89.6% of isolates were resistant to carbapenems. All the isolates were positive for the blaTEM gene. However, the blaSHV and blaCTX-M-2 genes were identified in two ESBL-non producer isolates. None of the isolates carried the blaCTX-M-1 gene. This study provided evidence of the existence of MDR and pXDR ESBL-Ec in frozen chicken meat in Bangladesh, which may pose a risk to human health if the meat is not properly cooked or pickled raw only. This emphasizes the importance of the implementation of good slaughtering and processing practices by the processors.
ARTICLE | doi:10.20944/preprints202005.0440.v1
Subject: Life Sciences, Microbiology Keywords: Scrub typhus; qRT PCR; Quantitative PCR; real time PCR; IgM ELISA; North-East India
Online: 27 May 2020 (07:51:25 CEST)
Scrub typhus is a life-threatening infectious disease and always creating a diagnostic dilemma in terms of rapid turnaround time and accuracy, qRT PCR can become a very good option to achieve the desired result with the molecular level of accuracy and boost up the rapid patient management. This study was performed to evaluate the performance of qRT PCR in comparison to commonly used IgM ELISA and Weil-Felix tests to diagnose scrub typhus, as well as to look for the demographic and clinical profile of the disease in North-East India. It was a hospital-based prospective study conducted in a tertiary care hospital of north-east India, over a period of 1 year, in which all the samples from suspected scrub typhus cases were screened by Weil-Felix test as per institute’s diagnostic protocol after which IgM ELISA for Scrub Typhus was performed. All the IgM positive samples and 20 highly suspected but ELISA negative samples were subjected to qRT PCR, targeting 56 kDa type-specific gene of O. tsutsugamushi. Statistical analysis was done by MS-Excel for Windows v2013® and MedCalc® v17.9 for Windows (MedCalc Software, Acacialaan 22, B-8400 Ostend, Belgium). In this study, we have successfully evaluated the performance of qRT PCR kit for diagnosis of scrub typhus. Out of 54 samples tested, 24 IgM ELISA positive samples and 3 IgM ELISA negative samples have shown the presence of bacterial DNA with quantification of DNA copies. It has also been observed that 21 out of 27 PCR positive samples (77.8%) were detected within the 1st 7 days of illness. All the demographic, as well as clinical data, were also analysed. The performance of the commercial qRT PCR kit used in our study is satisfactory, which provides the extra advantage of quantification of DNA copies and increases diagnostic accuracy within the 1st week of fever.
ARTICLE | doi:10.20944/preprints202005.0374.v2
Subject: Life Sciences, Other Keywords: natural cosmetics; organic cosmetics; green cosmetics; cosmetology; certification
Online: 27 May 2020 (05:02:20 CEST)
The market of natural and organic cosmetics has been growing in last decades. The increase in interest in this type of product is a consequence of the concern that consumers have been presenting in relation to the environment and health. In addition to the appreciation the use of sustainable ingredients in cosmetic formulations, the consumers are also concerned about pollution caused by the use of plastics, which leads industries to reinvent themselves and rethink about the composition of packaging. The factor that most drives the purchase of natural and organic cosmetics is the fact that the consumer, in addition to contributing to the preservation of the environment, is also using a sustainable product. The growing demand for natural and organic cosmetics results in a concern of the brands with the organic issue, with the decreased use of animal derived ingredients and with the updating the parameters required for certification of a cosmetic as natural or organic. Due to the few studies available in this area, the importance of clarifying the definitions and concepts of natural and organic cosmetics is evident, in order to contribute with accurate information for the cosmetic sector.
ARTICLE | doi:10.20944/preprints202005.0439.v1
Subject: Life Sciences, Biochemistry Keywords: curcumin; COVID-19; nucleocapsid phosphoprotein; membrane glycoprotein; antiviral mechanism
Online: 27 May 2020 (04:54:08 CEST)
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a respiratory syndrome caused by positive RNA virus resulting in outbreak of corona virus disease 2019 (COVID-19). The SARS-CoV-2 genome and its association to SAR-CoV-1 vary from ca. 66% to 96% depending on the type of betacoronavirdeae family members. With several drugs, viz. chloroquine, hydroxychloroquine, ivermectin, quinidine, artemisinin, remdesivir, azithromycin considered for clinical trials, there has been an inherent need to find distinctive antiviral mechanisms of these drugs. On the other hand, curcumin, a natural bioactive molecule has been shown to have a therapeutic potential for various diseases, but no role of it in COVID-19 has been explored. In this work, we show the binding potential of curcumin targeted to a host of SARS-CoV-2 proteins, viz. spike glycoproteins (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), membrane glycoprotein (PDB ID: 6M17) along with nsp10 (PDB ID: 6W4H) and RNA dependent RNA polymerase (PDB ID: 6M71) structures. Our results indicate that curcumin has potential antiviral protein binding affinity towards SARS-CoV-2 proteins which is comparable with other repurposed drugs that are considered for clinical trials.
Tue, 26 May 2020
COMMUNICATION | doi:10.20944/preprints202005.0423.v1
Online: 26 May 2020 (08:14:47 CEST)
Zinc plays a crucial role in the process of virion maturation inside the host cell. The accessory Cys-rich proteins expressed in SARS-CoV-2 by genes ORF7a and ORF8 are likely involved in zinc binding and in interactions with cellular antigens activated by extensive disulfide bonds. In this report we provide a proof of concept for the feasibility of a structural study of orf7a and orf8 proteins. We make the point that lack of cellular zinc, or substitution thereof, might lead to a significant slowing down of viral maturation.
Mon, 25 May 2020
Subject: Life Sciences, Virology Keywords: human coronavirus; SARS-CoV; MERS-CoV; SARS-CoV-2; envelope protein; immunopathology
Online: 25 May 2020 (17:54:57 CEST)
Since the severe acute respiratory syndrome (SARS) outbreak in 2003, human coronaviruses (hCoVs) have been identified as causative agents of severe acute respiratory tract infections. Two more hCoV outbreaks have since occurred, the most recent being SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). The clinical presentation of SARS and MERS is remarkably similar to COVID-19, with hyperinflammation causing a severe form of the disease in some patients. Previous studies show that the expression of the SARS-CoV E protein is associated with the hyperinflammatory response that could culminate in acute respiratory distress syndrome (ARDS), a potentially fatal complication. This immune-mediated damage is largely caused by a cytokine storm, which is induced by significantly elevated levels of inflammatory cytokines interleukin (IL)-1beta and IL-6, which are partly mediated by the expression of the SARS-CoV E protein. The interaction between the SARS-CoV E protein and the host protein, syntenin, as well as the viroporin function of SARS-CoV E, are linked to this cytokine dysregulation. This review aims to compare the clinical presentation of virulent hCoVs with a specific focus on the cause of the immunopathology. The review also proposes that inhibition of IL-1beta and IL-6 in severe cases can improve patient outcome.
ARTICLE | doi:10.20944/preprints202005.0413.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; nucleocapsid (N); genomics; coronavirus; Wuhan; Pandemic
Online: 25 May 2020 (17:45:40 CEST)
Severe acute respiratory syndrome novel coronavirus 2 (SARS-CoV-2) has caused the global pandemic as COVID-19, which is the most notorious global public health crisis in the last 100 years. SARS-CoV-2 is composed of four structural proteins and several non-structured proteins. The multi-facet nucleocapsid (N) protein is the major component of structural proteins of CoVs, However, there are no dedicated genomic, sequences and structural analyses focusing on potential roles of N protein. Hence, there is an urgent requirement of a detailed study on N protein of SARS-CoV-2. Herein, we are presenting a comprehensive study on N protein from SARS-CoV-2. We have identified seven motifs conserved in the three major domains namely N-terminal domain, linker regions and the C-terminal domains. Out of seven motifs, six motifs are conserved across different members of coronaviridae, while motif4 is specific for SARS CoVs with potential amyloidogenic properties. Additionally, we report this protein has large patches of disordered regions flanking with these seven motifs. These motifs are hubs of epitopes with 67 experimentally verified epitopes from related viruses. We report the presence of three nuclear localization signals (NLS1-NLS3 mapped to 36-41, 256-26, and 363-389 residues, respectively) and two nuclear export signals (NES1-NLS2 from 151-161 and 217-230 residues, respectively) in the N protein of SARS-CoV-2. These deciphered two Q-patches as Q-patch1 and Q-patch2, mapped in the regions of 266-306, and 361-418 residues, which potentially help in the aggregation of the viral proteins along with 219LALLLLDR226 patch. Additionally, we have identified 14 antiviral drugs potentially binding to seven motifs of N-proteins using docking-based drug discovery methods.
Sun, 24 May 2020
ARTICLE | doi:10.20944/preprints202005.0407.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; spike protein; D614G mutation; genotype distribution; furin cleavage site; secondary structure; sequence analysis; homology modeling
Online: 24 May 2020 (20:31:16 CEST)
We analyzed the SARS-CoV-2 spike (S) protein amino acid sequence extracted from 11,542 viral genomic sequences submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database through April 27, 2020. Consistent with prior reports, we found a major S protein mutation, D614 to G614, that was represented in 56% of all the analyzed sequences. All other mutations combined were less than 10%. After parsing the data geographically, we found most of the Chinese patient samples showed D614 (97%). By contrast, most patient samples in many European countries showed G614 (51 to 88%). In the United States, the genotypic distribution in California and Washington was similar to Asian countries, while the distribution in other US states was comparable to Europe. We observed a dramatic increase in the frequency of G614 over time in multiple regions, surpassing D614 when both were present, suggesting G614 S protein virus outcompetes D614 S protein virus. To gain insight into the consequences of the D614G mutation, homology modeling using a multi-template threading mechanism with ab initio structural refinement was performed for a region of the S protein (S591 to N710) spanning the D614G mutation and the S1 furin cleavage site. Molecular models of this region containing D614 or G614 revealed a major difference in secondary structure at the furin domain (RRARS, R682 to S686). The D614 model predicted a random coil structure in the furin domain whereas the G614 model predicted an alpha helix. Critical residues in the cleavage domain of G614 model were found to better align with the PDB structure of a furin inhibitor. Thus, homology modeling studies suggest a potential mechanism whereby the D614G mutation may confer a competitive advantage at the furin binding domain that may contribute to the rise of the D614G SARS-CoV-2 mutant.
COMMUNICATION | doi:10.20944/preprints202005.0401.v1
Subject: Life Sciences, Other Keywords: SARS-CoV-2; Peptide Vaccine; Spike Protein; Vaccinomics; Epitope Prediction
Online: 24 May 2020 (19:11:19 CEST)
SARS-CoV-2 has been the talk of the town ever since the beginning of 2020. The pandemic has brought the complete world on a halt. Every country is trying all possible steps to combat the disease ranging from shutting the complete economy of the country to repurposing of drugs and vaccine development. The rapid data analysis and widespread tools, software and databases have made bioinformatics capable of giving new insights to the researchers to deal with the current scenario more efficiently. Vaccinomics, the new emerging field of bioinformatics uses concepts of immunogenetics and immunogenomics with in silico tools to give promising results for wet lab experiments. This approach is highly validated for the designing and development of potent vaccines. The present in-silico study was attempted to identify peptide fragments from spike surface glycoprotein that can be efficiently used for the designing and development of epitope-based vaccine designing approach. Both B-cell and T-cell epitopes are predicted using integrated computational tools. VaxiJen server was used for prediction of protective antigenicity of the protein. NetCTL was studied for analyzing most potent T cell epitopes and its subsequent MHC-I interaction through tools provided by IEDB. 3D structure prediction of peptides and MHC-I alleles (HLA-C*03:03) was further done to carry out docking studies using AutoDock4.0. Various tools from IEDB were used to predict B-cell epitopes on the basis of different essential parameters like surface accessibility, beta turns and many more. Based on results interpretation, the peptide sequence from 1138-1145 amino acid and sequence WTAGAAAYY and YDPLQPEL were obtained as a potential B-cell epitope and T-cell epitope respectively. This in-silico study will help us to identify novel epitope-based peptide vaccine target in spike protein of SARS-CoV-2. Further, in-vitro and in-vivo study needed to validate the findings.
ARTICLE | doi:10.20944/preprints202005.0397.v1
Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; Drug repurposing; N-acetyl-D-glucosamine; ORF1ab; Biodata mining; Protein modelling
Online: 24 May 2020 (18:49:41 CEST)
Causative agent of the viral pneumonia outbreak in the World identified as SARS-CoV2 leads to a severe respiratory illness like SARS and MERS. The pathogen spreading has turned into a pandemic dissemination and increased the mortality rate. Therefore, useful information is urgently necessary for effective control of the disease. Our study shows the existence of unvarying sequence with no mutation, including ORF1ab regions in 134 high-quality filtered genome sequences of SARS-CoV2 downloaded from the GISAID database. We have detected this sequence stability by using MAUVE analysis and pairwise alignment with Global Needleman Wunsch algorithm for each two different sequences, reciprocally. They also confirmed all these results were also with the Clustal W analysis. The first 6500 bp including ORF1ab region is an unvarying sequence. According to the highest TM-score of predicted protein structure analysis, the results showed it is very similar to spike protein of feline infectious peritonitis virus strain UU4 (PDB 6JX7) depending on amino acid sequences encoded by this unvarying region, and N-acetyl-D-glucosamine is the ligand of this protein. These results have confirmed that N-acetyl-D-glucosamine could play an important role in controlling of SARS-CoV-2. Also, our molecular docking analysis data supports a strong protein-ligand interaction of N-acetyl-D-glucosamine with spike receptor-binding domain bound with ACE2 (PDB 6M0J) and RNA-binding domain of nucleocapsid phosphoprotein (PDB 6WKP) from SARS CoV-2. Therefore, binding of N-acetyl-D-glucosamine to these proteins could inhibit SARS CoV-2’s replication. In the present work, we have suggested providing a repurposing compound for further in vitro and in vivo studies and new insights for ongoing clinical treatments as a new strategy to control of SARS-CoV-2 infections.
ARTICLE | doi:10.20944/preprints202005.0396.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; variant analysis; phylogenetic analysis; viral evolution
Online: 24 May 2020 (18:25:47 CEST)
The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) viral genome is an RNA virus consisting of approximately 30,000 bases. As part of testing efforts, whole genome sequencing of human isolates has resulted in over 1,600 complete genomes publicly available from GenBank. We have performed a comparative phylogenetic analysis of the sequences, in order to detect common mutations within the population. Analysis of variants occurring within the assembled genomes yields 417 variants occurring in at least 1% of the completed genomes, including 229 within the 5’ untranslated region (UTR), 152 within the 3’UTR, 2 within intergenic regions and 34 within coding sequences.
ARTICLE | doi:10.20944/preprints202005.0390.v1
Subject: Life Sciences, Virology Keywords: Zika; Yellow fever; cross reactive; flavivirus; congenital infection; enhancement
Online: 24 May 2020 (17:12:58 CEST)
Zika virus (ZIKV) is a flavivirus that originated in Africa but emerged in Latin America in 2015. In this region, other flaviviruses such as Dengue (DENV), West Nile, and Yellow Fever Virus (YFV) also circulate, allowing for possible antigenic cross-reactivity to impact viral infections and immune responses. Studies have found antibody mediated enhancement between DENV and ZIKV, but the impact of YFV antibodies on ZIKV infection has not been fully explored. ZIKV infections cause congenital syndromes, such as microcephaly, necessitating further research into ZIKV vertical transmission through the placental barrier. Recent advancements in biomedical engineering have generated co-culture methods that allow for in vitro recapitulation of the maternal: fetal interface. This study utilized a transwell assay, which is a co-culture model utilizing human placental syncytiotrophoblasts, fetal umbilical cells, and a differentiating embryoid body to replicate the maternal: fetal axis. To determine if cross reactive YFV vaccine antibodies impact the pathogenesis of ZIKV across the maternal fetal axis, maternal syncytiotrophoblasts were inoculated with ZIKV or ZIKV incubated with YFV vaccine anti-sera, and viral load was measured 72 hours post inoculation. The data show that the impact of YFV on ZIKV replication is cell line dependent. In differentiating embryoids, the presence of YFV antibodies enhanced ZIKV infection. Since viral pathogenesis, and the impact of antigenic cross-reactive antibodies, is cell line specific at the maternal-fetal axis, this suggests there may be discreet mechanisms that impact congenital ZIKV infections.
ARTICLE | doi:10.20944/preprints202005.0389.v1
Subject: Life Sciences, Virology Keywords: Asian citrus psyllid; citrus greening bacterium; huanglongbing; transcriptomics; virus-vector relationship; vitellogenin; cytoskeleton; endocytotic pathway
Online: 24 May 2020 (17:03:45 CEST)
Citrus greening disease or huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus (CLas) limits the citrus production worldwide. CLas is transmitted by the Asian citrus psyllid (ACP), Diaphorina citri (Hemiptera: Psyllidae) in a persistent-propagative manner. Application of insecticides to manage the psyllid vectors and disease is the most common practice. Understanding the molecular interaction between CLas and ACP and interrupting the interrelationship can provide an alternative to insecticides for managing citrus greening disease. Transcriptome analysis of ACP in response to CLas showed differential expression of 3911 genes (2196 up-regulated, and 1715 down-regulated) including the key genes of ACP involved in cytoskeleton synthesis and nutrition-related proteins. Majority of the differentially expressed genes were categorized under molecular function followed by cellular components and biological processes. KEGG pathway analysis showed differential regulation of carbohydrate, nucleotide and energy metabolic pathways, the endocytotic pathway and the defense-related pathways. Differential regulation of genes associated with the key pathways might favors CLas to become systemic and propagate in its insect vector. The study provides an understanding of genes involved in circulation of CLas in ACP. The candidate genes involved in key physiological processes and CLas transmission by ACP would be potential targets for sustainable management of ACP and CLas.
Subject: Life Sciences, Molecular Biology Keywords: body shape index; body roundness index; metabolic risk factors; Southern China adults
Online: 24 May 2020 (16:44:12 CEST)
This purpose was to compare the ability of body shape index (ABSI) and body roundness index (BRI) with waist circumference (WC), body mass index (BMI), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) and body adiposity index (BAI) to predict metabolic risk. The cross-sectional study was conducted in 17,360 Chinese subjects (were aged 18-95 years old) who escaped cardiovascular disease (CVD) or diabetes. Biochemical and anthropometric variables were measured by trained staff. Receiver operating characteristic curve (ROC) and optimal cutoff values of obesity indices were recruited to compare the predictive ability for metabolic risk factors. The mean age of subjects was 53.7(13.1) years, 41.6 % were males. Within young group (<60 years), the areas under the curve (AUC) demonstrated that WC, BMI, WHR, WHtR and BRI were able to similarly predict high metabolic risk in males (0.74 vs. 0.74 vs. 0.73 vs. 0.73 vs. 0.73) and in females (0.73 vs. 0.73 vs. 0.71 vs. 0.73 vs. 0.73), while the approximate predictive ability were only acquired in males (0.73 vs. 0.73 vs. 0.70 vs. 0.73 vs. 0.73) within elder group (≥60 years). The optimal cut-off values of BRI for high metabolic risk were calculated in males (<60 y: 3.49 vs. ≥60 y: 3.46) and females (<60 y: 3.47 vs. ≥60 y: 3.60). Meanwhile, BRI displayed a strong prediction to elevated BP and elevated TG in males (AUC = 0.64; AUC = 0.70) and to elevated BP, elevated TG and elevated SUA in females (AUC = 0.67; AUC = 0.69; AUC =0.70). BRI was able to similarly predict high metabolic risk compared to WC, BMI, WHR, WHtR and BAI, while ABSI was not. Moreover, BRI revealed specific predictive ability for elevated BP, elevated TG and elevated SUA.
Sat, 23 May 2020
ARTICLE | doi:10.20944/preprints202005.0379.v1
Subject: Life Sciences, Virology Keywords: Coronaviruses; MERS-CoV; SARS-CoV-2; Serological assay; VSV pseudovirus
Online: 23 May 2020 (16:46:15 CEST)
Emerging highly pathogenic human coronaviruses (CoVs) represent a serious ongoing threat to the public health worldwide. The spike (S) proteins of CoVs are surface glycoproteins that facilitate viral entry into host cells via attachment to their respective cellular receptors. The S protein is believed to be a major immunogenic component of CoVs and a target for neutralizing antibodies (nAbs) and most candidate vaccines. Development of a safe and convenient assay is thus urgently needed to determine the prevalence of CoVs nAbs in the population, to study immune response in infected individuals, and to aid in vaccines and viral entry inhibitors evaluation. While live virus-based neutralization assays are used as gold standard serological methods to detect and measure nAbs, handling of highly pathogenic live CoVs requires strict bio-containment conditions in biosafety level-3 laboratories. On the other hand, use of replication-incompetent pseudoviruses bearing CoVs S proteins could represent a safe and useful method to detect nAbs in serum samples under biosafety level-2 conditions. Here, we describe a detailed protocol of a safe and convenient assay to generate vesicular stomatitis virus (VSV)-based pseudoviruses to evaluate and measure nAbs against highly pathogenic CoVs. The protocol covers methods to produce VSV pseudovirus bearing the S protein of the Middle East respiratory syndrome-CoV (MERS-CoV) and the severe acute respiratory syndrome-CoV-2 (SARS-CoV-2), pseudovirus titration, and pseudovirus neutralizing assay. Such assay could be adapted by different laboratories and researchers working on highly pathogenic CoVs without the need to handle live viruses in biosafety level-3 environment.
REVIEW | doi:10.20944/preprints202005.0376.v1
Subject: Life Sciences, Virology Keywords: virus bioinformatics; SARS-CoV-2; sequencing; epidemiology; drug design; tools
Online: 23 May 2020 (11:01:11 CEST)
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding, and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are freely available online, either through web applications or public code repositories.
ARTICLE | doi:10.20944/preprints202005.0374.v1
Subject: Life Sciences, Other Keywords: natural cosmetics; organic cosmetics; green cosmetics; cosmetology; certification
Online: 23 May 2020 (10:52:01 CEST)
The market of natural and organic cosmetics has been growing in last decades. The increase in interest in this type of product is a consequence of the concern that consumers have been presenting in relation to the environment and health. In addition to the appreciation the use of sustainable ingredients in cosmetic formulations, the consumers are also concerned about pollution caused by the use of plastics, which leads industries to reinvent themselves and rethink about the composition of packaging. The factor that most drives the purchase of natural and organic cosmetics is the fact that the consumer, in addition to contributing to the preservation of the environment, is also using a sustainable product. The growing demand for natural and organic cosmetics results in a concern of the brands with the organic issue, with the decreased use of animal derived ingredients and with the updating the parameters required for certification of a cosmetic as natural or organic.
Subject: Life Sciences, Virology Keywords: anti-viral; COVID-19; SARS-CoV-2; autophagy; chloroquine; hydroxychloroquine; immunology; infection; inflammation; lysophagy; microbiology; Plaquenil; SARS; virophagy
Online: 23 May 2020 (10:45:40 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 first proposed clinical trial has drawn worldwide hype to the 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 the articles promoting the use of CQ in the current pandemic 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 the pros, but also the cons concerning the current therapeutic options targeting this process.
ARTICLE | doi:10.20944/preprints202005.0366.v1
Subject: Life Sciences, Genetics Keywords: gene doping; gene therapy; in vivo transfection; in vivo imaging
Online: 23 May 2020 (10:11:31 CEST)
The World Anti-Doping Agency has prohibited gene doping in the context of progress in gene therapy. There is a risk that the artificial regulation of genes using plasmids could be applied for gene doping. However, no gold standard method to detect this has been established. Here, we aimed to develop a method to detect multiple transgene fragments as proof of gene doping. First, gene delivery model mice as a mimic of gene doping were created by injecting firefly luciferase plasmid with polyethylenimine (PEI) into the abdominal cavity. The results confirmed successful establishment of the model, with sufficient luminescence upon in vivo imaging. Next, multiple transgene fragments in the model were detected in plasma cell-free (cf)DNA, blood-cell-fraction DNA, and stool DNA using the TaqMan-qPCR assay, with the highest levels in plasma cfDNA. Using just a single drop of whole blood from the model, we also attempted long-term detection. The results showed that multiple transgene fragments were detected until 11 days. These findings indicate that the combination of plasma cfDNA or just one drop of whole blood with TaqMan-qPCR assay is feasible to detect plasmid-PEI-based gene doping. Our findings could accelerate the development of methods for detecting gene doping in humans.
HYPOTHESIS | doi:10.20944/preprints202005.0359.v1
Online: 23 May 2020 (05:26:13 CEST)
Severe Covid-19 disease is associated with endothelial infection, viraemia, and multi-organ dysfunction. The process through which SARS-CoV2 causes severe disease is yet to be determined. Here, we propose that in severe Covid-19 infection, SARS-CoV2 reaches the host bloodstream by infecting endothelial cells through their basal surface. This occurs, independently of ACE2, through CD147, a putative SARS-CoV2 receptor. The pathway proposed here encourages research on the mechanisms mediating endothelial cell infection in Covid-19.
Fri, 22 May 2020
REVIEW | doi:10.20944/preprints202002.0465.v2
Subject: Life Sciences, Other Keywords: vitamin D; calcium; bone mass; osteoporosis; dairy foods; fortified foods
Online: 22 May 2020 (05:18:43 CEST)
Background: Vitamin D and calcium are important dietary compounds that affect bone mass, even if other minerals (potassium, zinc, etc.) and other vitamins (A, C and K) are also involved. Vitamin D and other minerals, in fact, play an important role in calcium homeostasis and calcium absorption. Hip fractures incidence is higher in western countries, where calcium is frequently included in human diet, while the occurrence of these fractures is lower in developing countries, where diets are often poor in calcium. This situation is known as the “calcium paradox”, and may be partially explained considering phosphate toxicity, that can induce a disorder of mineral metabolism. It is important to maintain adequate dietary calcium-phosphate balance in order to perform a healthy life, reducing the risk of osteoporotic fracture in older people. Vitamin D can also act as a hormone; vitamin D2 (ergocalciferol) is derived from the UV-B radiation of ergosterol, the vitamin D precursor naturally found in plants, fungi, and invertebrates. Vitamin D3 (cholecalciferol) is originated by sunlight exposure from 7-dehydrocholesterol, a precursor of cholesterol that can also act as a provitamin D3. Dietary intake of vitamin D3 is very important when skin is exposed for short times to ultraviolet B light (UV-B) one of the three kinds of invisible light rays together with UV-A and UV-C. This can be considered the usual situation in northern latitudes and in winter season, or the typical condition for older people and/or for people with very white delicate skin. Actually, the recommended daily intake of dietary vitamin D is strictly correlated with age, ranging from 5 μg for infants, children, teen-agers and adults, including women during pregnancy and lactation, to 15 μg for people over 65 years.
Thu, 21 May 2020
ARTICLE | doi:10.20944/preprints202005.0343.v1
Subject: Life Sciences, Other Keywords: GALAXY; Assembly; Annotation; Genomic Variants Discovery; Workflow
Online: 21 May 2020 (09:57:42 CEST)
Citizen Science has come up to perform analytics over the SARS-CoV-2 genome. Public GALAXY servers provide an automated platform for genomics analysis. Study includes design of GALAXY workflows for RNASEQ assembly and annotation as well as genomic variant discovery and perform analysis across four samples of SARS-CoV-2 infected humans obtained from the local population of Wuhan, China. It provides information about transcriptomics and genomic variants across the SARS-CoV-2 genome. Study can be extended to perform evolutionary and comparative study across each species of coronaviruses. Augmented and integrated study with cheminformatics and immunoinformatics will be a way forward for drug discovery and vaccine development.
ARTICLE | doi:10.20944/preprints202005.0341.v1
Subject: Life Sciences, Endocrinology & Metabolomics Keywords: AGEs; aortic calcification; type 2 diabetes mellitus; diabetes-related complications
Online: 21 May 2020 (09:46:56 CEST)
The aim of this study was to evaluate the relationship between serum levels of advanced glycation end products (AGEs) and abdominal aortic calcification (AAC) in patients with type 2 diabetes mellitus (DM2). This was a prospective cross-sectional study conducted from January 2017 to June 2018. One-hundred and four consecutive patients with DM2 were given lateral lumbar X-rays in order to quantify aortic abdominal calcification AAC. Circulating levels of AGEs and classical cardiovascular risk factors were determined. Clinical history was also registered. Patients with higher AGEs values had higher grades of aortic calcification and higher number of diabetic related complications. Multivariate logistic regression analysis showed that being older, male and having high levels of AGEs and triglycerides were the independent risk factors associated to moderate-severe AAC when compared to no-mild AAC. Our results suggest that AGEs plays a role in the pathogenesis of aortic calcifications. In addition, the measurement of AGEs levels may be useful for assessing the severity of AAC in the setting of diabetic complications.
ARTICLE | doi:10.20944/preprints202004.0239.v5
Subject: Life Sciences, Virology Keywords: epidemic; caseload management; partial unlock; social distancing; overshoot; COVID-19; coronavirus; eco-nomic impact; ventilator utilization; SARS-CoV-2
Online: 21 May 2020 (04:13:13 CEST)
Objectives: We study partial unlock or reopening interaction with seasonal effects in a managed epidemic to quantify overshoot effects on small and large unlock steps and discover robust strategies for reducing overshoot. Methods: We simulate partial unlock of social distancing for epidemics over a range of replication factor, immunity duration and seasonality factor for strategies targeting immunity thresholds using overshoot optimization. Results: Seasonality change must be taken into account as one of the steps in an easing sequence, and a two step unlock, including seasonal effects, minimizes overshoot and deaths. It may cause undershoot, which causes rebounds and assists survival of the pathogen. Conclusions: Partial easing levels, even low levels for economic relief while waiting on a vaccine, have population immunity thresholds based on the reduced replication rates and may experience overshoot as well. We further find a two step strategy remains highly sensitive to variations in case ratio, replication factor, seasonality and timing. We demonstrate a three or more step strategy is more robust, and conclude that the best possible approach minimizes deaths under a range of likely actual conditions which include public response.
ARTICLE | doi:10.20944/preprints202005.0333.v1
Subject: Life Sciences, Biochemistry Keywords: SARS-CoV-2; COVID-19; pregnancy; trophoblasts; interactome; placenta
Online: 21 May 2020 (03:38:05 CEST)
COVID-19 is a rapidly evolving medical emergency that has drawn global attention, unprecedented in any disease of its kind in recent times. The magnitude of the health crisis emerging from this pandemic has overwhelmed health care workers worldwide and called in for extraordinary measures to contain this virus. A simple Pubmed query on “COVID-19” returned with 12214 articles (as on May 17th, 2020), published just within a few months. A detailed survey revealed around 250 clinical reports, 8 clinical trials, 9 meta-analyses, and 906 reviews that were published during this time span. Combining the strings “COVID-19 and Pregnancy” yielded a total of 132 reports while querying “COVID-19 and Placenta” returned with just 11 articles Even taking into considerations that few materials are in the PrePrint Server, we still have a gross under-representation of studies addressing the effect of this disease on pregnancy outcome and maternal & child health. An essential aspect of a successful pregnancy is proper placentation, where transiently invasive placental trophoblast cells invade the maternal endometrium to establish a functional feto-maternal communication. Based on the elegant study by David. E. Gordon, et al. published in Nature (April 30, 2020), which identified 332 human host proteins interacting with SARS-nCoV2 using an affinity-based purification, we interrogated several gene expression data sets available at NCBI-GEO related to trophoblast invasion and differentiation. Both of these processes are indispensable for placentation and fetal survival. Our analysis showed several overlaps with the interactome proteins implying that SARS-CoV-2 infection can affect several proteins, which are crucial for trophoblasts function. GeneMANIA and STRING based functional analysis further revealed that several of that SARS-CoV-2 interacting trophoblast proteins as a hub for the protein-protein interaction network. Our study thus elucidates the possible effect of SARS-CoV-2 infection on placenta formation and pregnancy outcome.
ARTICLE | doi:10.20944/preprints202005.0332.v1
Subject: Life Sciences, Genetics Keywords: coronavirus; origin; substitution rate; positive selection; demographic dynamics
Online: 21 May 2020 (03:27:52 CEST)
A new form of beta coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) causing a recent pandemic outbreak possesses a linear positive ss-RNA genome with a length of 29,903 nt. Here, the genomes of SARS-CoV-2 from 821 samples were characterised for its better understanding of the genomic and evolutionary patterns. The phylogeny of SARS-CoV-2 was reconstructed using concatenated dataset consisting of all peptide encoding sequences under Bayesian Inference (BI) and Maximum Likelihood (ML) approaches. Comparison of all peptide encoding sequences reveals high divergence of amino acid sequences proportional to divergence of nucleotides, indicating that the viral genomic evolution has not been strictly neutral. The most part of the genome was under neutral evolution, however, the specific sites for peptide encoding sequences were evolved under positive selection. As well as providing reliable evidence on transmission routes of the SARS-CoV-2 outbreak, the phylogenetics and network analyses suggest the sample reported from Guangdong province is likely ancestor of the pandemic virus form. The overall substitution rate of SARS-CoV-2 genome was estimated to be 1.65 x 10-3 per site per year, falling within the range for previously reported RNA viruses. Median estimation of tMRCA from Bayesian coalescent analyses corresponds to 10 September 2019. The exponential growth rate (r), doubling time (Td) and R0 were estimated to be 47.43 per year, 5.39 days and 2.72, respectively. These findings convincingly emphasise that the use of more comprehensive genome data improves robustness and also enhances understanding of the demographic history of the outbreak.
Wed, 20 May 2020
REVIEW | doi:10.20944/preprints202005.0329.v1
Subject: Life Sciences, Other Keywords: sustainable agriculture; carbon sequestration; crop productivity; soil acidification; soil organic matter; pyrolysis; microbial activity, biochar
Online: 20 May 2020 (11:04:28 CEST)
The sustainable production of food faces formidable challenges. Foremost is the availability of arable soils, which have been ravaged by the overuse of fertilizers and detrimental soil management techniques. As such, maintenance of soil quality, and reclamation of marginal soils, has become an increasingly important endeavor. Recently, there has been emerging interest in the use of biochar, a carbon rich, porous material thought to improve various aspects of soil performance. Biochar (BC) is produced through the thermochemical decomposition of organic matter at high temperature in an oxygen limited environment, in a process known as pyrolysis. Importantly, the source of organic material, or ‘feedstock,’ used in this process and different parameters of pyrolysis, especially temperature, determine the chemical and physical properties of biochar. Incorporation of BC impacts soil-water relations, tilth and nutrient status, pH, soil organic matter (SOM), and microbial activity. Soil amendment with BC has been shown to have an overall positive impact on soil health and crop productivity; however, initial soil properties need to be considered prior to the application of BC. There is an urgent need to understand the effects of long-term field application of BC and how it influences the soil microcosm. This knowledge will facilitate predictable enhancement of crop productivity and meaningful carbon sequestration.
CONCEPT PAPER | doi:10.20944/preprints202005.0321.v1
Subject: Life Sciences, Biochemistry Keywords: trans-species O-glycosylation; trans-species functional bridge; phenotype-specific plasma glycosylation; glycosidic exclusion; ontogenetic Tn formation
Online: 20 May 2020 (07:03:37 CEST)
The coevolution of species drives diversity in animals and plants and contributes to natural selection, while in host–parasite coevolution, a parasite may complete an incomplete evolutionary/developmental function by utilizing the host cell’s machinery. Analysis of related older data suggests that Plasmodium falciparum (P. falciparum), the pathogen of malaria tropica, cannot survive outside its human host because it is unable to perform the evolutionarily first protein glycosylation or blood group-independent (serologically A-like) O-GalNAcα1-Ser/Thr-R, Tn antigen (“T nouvelle”) formation owing to its inability for synthesizing the amino sugar N-acetyl-d-galactosamine (GalNAc). This parasite breaks the species barrier via hijacking the host's A-like/Tn formation by abundantly expressing serine residues and creating hybrid A-like/Tn structures. In the human blood group O(H), these hybrid structures are attacked by the germline-encoded nonimmune polyreactive immunoglobulin M (IgM), which physiologically regulates the expression of the syngeneic A-like/Tn antigen. In non-O blood groups, this antibody molecule has undergone the phenotypic accommodation of plasma proteins, which results in loss of blood group A- and B-corresponding anti-A and anti-B isoagglutinin activities. This loss allows the generation of human A- and B allele-connected hybrid epitopes and the development of life-threatening disease almost exclusively in non-O blood groups. Although malaria infection occurs regardless of the blood group, the synthesis of the blood group AB enables the strongest contact with the pathogen, and molecularly precluding any isoagglutinin activity makes this group the least protected and the smallest among the ABO blood groups. In contrast, blood group O(H) individuals have the least contact with the pathogen; they maintain the isoagglutinins, rarely develop severe disease, and survive this coevolution in an immunological balance with the pathogen as the largest blood group worldwide.
REVIEW | doi:10.20944/preprints202005.0316.v1
Subject: Life Sciences, Virology Keywords: RT-PCR; seroconversion; serum biomarkers; SARS-CoV2; neutralizing antibodies
Online: 20 May 2020 (04:10:24 CEST)
The progression of the recent COVID-19 pandemic surprised political authorities as well as scientists. The possibility to design powerful strategies for health care and preserving economic and social activities strongly relies on the capacity to monitor correctly the virus spreading and the immune response in the symptomatic and asymptomatic population. The available data relative to the first pandemic months indicate that the test reliability was progressively improved but also that the extremely variable methodologies used in the diagnostic studies generated data that are often not comparable. This condition prevents a simple metadata analysis for the identification of reliable diagnostics guidelines. Nevertheless, there are converging evidences that combinations of complementary approaches may enable more precise identification of virus infection. Furthermore, it appears that the similarities between SARS-CoV2 and the related types SARS-CoV1 and MERS that caused outbreaks in the last 20 years can be exploited to infer some information for which no direct evidence is still available
Tue, 19 May 2020
REVIEW | doi:10.20944/preprints202005.0315.v1
Subject: Life Sciences, Biochemistry Keywords: cancer stem cells; tumor microenvironment; metastasis; chemoresistance; epithelial to mesenchymal transition; clinical trials
Online: 19 May 2020 (14:01:27 CEST)
Despite great strides being achieved in improving cancer patients’ outcomes through better therapies and combinatorial treatment, several hurdles still remain due to therapy resistance, cancer recurrence and metastasis. Drug resistance, culminating in relapse and metastatic disease continue to be associated with fatal disease. Cancer stem cells (CSCs) are a subpopulation of cancer cells known to be resistant to therapy and cause metastasis. Whilst the debate on whether CSCs are the origins of the primary tumor rages on, CSCs have been further characterised in many cancers with data illustrating that CSCs display great abilities to self-renew, withstand therapies due to enhanced epithelial to mesenchymal (EMT) properties, enhanced expression of ABC membrane transporters, activation of several survival signaling pathways and increased immune evasion DNA repair mechanisms. CSCs also display great heterogeneity with the consequential lack of specific CSC markers presenting a great challenge to their targeting. In this updated review we re-visit CSCs within the tumor microenvironment (TME) and present novel treatment strategies targeting CSCs. These promising strategies include targeting CSCs-specific properties using small molecule inhibitors, immunotherapy, microRNA mediated inhibitors, epigenetic methods as well as targeting CSC niche-microenvironmental factors and differentiation. Lastly, we present recent clinical trials undertaken to try to turn the tide against cancer by targeting CSC-associated drug resistance and metastasis.
ARTICLE | doi:10.20944/preprints202005.0312.v1
Subject: Life Sciences, Biochemistry Keywords: marine invertebrates; glycosaminoglycans; platelets; circulating tumor cells; circulating tumor microemboli; hematogenic metastasis
Online: 19 May 2020 (07:45:44 CEST)
Although metastasis is the primary cause of death on patients with malignant solid tumors, efficient antimetastatic therapies are not clinically available thus far. Sulfated glycosaminoglycans from marine sources have shown promising pharmacological effects, acting in different steps of the metastatic process. Oversulfated dermatan sulfate from ascidians is effective in preventing metastasis by inhibition of P-selectin, a platelet surface protein involved in the platelet-tumor cell emboli formation. We report in this work that the heparan sulfate isolated from the viscera of the ascidian Phallusia nigra drastically attenuates metastasis of colon carcinoma cells in mice. Our in vitro and in vivo assessments demonstrate that the P. nigra glycan has very low anticoagulant and antithrombotic activities and a reduced hypotension potential, although efficiently preventing metastasis. Therefore, it may be a promising candidate for the development of a novel anti-metastatic drug.
Mon, 18 May 2020
ARTICLE | doi:10.20944/preprints202005.0296.v1
Subject: Life Sciences, Biophysics Keywords: W-band (75-105 GHz) MMW; H1299 human lung cancer cells; non-tumorigenic MCF-10A human epithelial cells; in vitro
Online: 18 May 2020 (04:18:39 CEST)
Therapeutically effective treatments of cancer are limited. To calibrate the efficiency of the novel technique we recently discovered to modulate cancer cell viability using tuned electromagnetic fields; H1299 human lung cancer cells were irradiated in a sweeping regime of W-band (75-105 GHz) millimeter waves (MMW) at 0.2 mW/cm2 (2 W/m2). Effects on cell morphology, cell death and senescence were examined and compared to that of non-tumorigenic MCF-10A human epithelial cells. MMW irradiation led to alterations of cell and nucleus morphology of H1299 cells, significantly increasing mortality and senescence over 14 days of observation. Extended irradiation of 10 minutes duration resulted in complete death of exposed H1299 cell population within two days, while healthy MCF-10A cells remained unaffected even after 16 minutes of irradiation under the same conditions. Irradiation effects were observed to be specific to MMW treated H1299 cells and absent in the control group of non-irradiated cells. MMW irradiation did not affect cell morphology of immortalized MCF-10A cells. Irradiation with low intensity MMW shows an antitumor effect on H1299 lung cancer cells. This method provides a novel treatment modality enabling targeted specificity for various types of cancers.
REVIEW | doi:10.20944/preprints202005.0293.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Insulin-like growth factor-1; Insulin-like growth factor-1 receptor; microgravity; osteoblasts; osteocytes; osteoclasts; IGF-1; IGF1R; rIGF-1
Online: 18 May 2020 (03:31:16 CEST)
Astronauts at are risk of losing 1.0 – 1.5% of their bone mass for every month they spend in space despite their adherence to high impact exercise training programs designed to preserve the musculoskeletal system. This article reviews the basics of bone formation and resorption and details how exposure to microgravity or simulated microgravity affects the structure and function of osteoblasts, osteocytes, osteoclasts, and their mesenchymal and hematologic stem cell precursors. It details the critical roles that insulin-like growth facor-1 and its receptor IGFR1 play in maintaining bone homeostasis and how exposure of bone cells to microgravity affects the function of these growth factors. Lastly, it discusses the potential of tumor necrosis factor-related apoptosis-inducing ligand, syncytin-A, and sclerostin inhibitors and recombinant IGF-1 as a bone-saving treatment for astronauts in space and during their colonization of the Moon.
Sun, 17 May 2020
Subject: Life Sciences, Molecular Biology Keywords: COVID-19; SARS-CoV-2; companion animals; cross-infection
Online: 17 May 2020 (15:27:24 CEST)
Since the COVID-19 caused by SARS-CoV-2 break out in Wuhan China from Dec. 2019, it has spread to hundreds of countries up to now. Scientists from all over the world have paid tremendous efforts to research and try to control the disease. Previous studies suggested that some of the wild animals could be intermediate hosts between humans and origination of SARS-CoV-2, and some companion animals of humans can be infected by SARS-CoV-2, which raised our curiosity about cross-infection of SARS-CoV-2 between animals and humans. Thus, we select some kinds of animals that might have contact with humans to estimate the susceptibility to SARS-CoV-2 in different animals by evolutionary analysis of their receptors for SARS-CoV-2. The results show that some companion animals of the Felidae family like the cat has a higher infection possibility while the species of the Rodent family like the rat and mouse having close contact with humans show an opposite result, which consist with recent animal experiments and researches. These should raise concerns about cross-infection between human and companion animals or animals having close contact with humans which might turn animals into depositaries of the coronavirus even after control of SARS-CoV-2 spreading and cause second or more waves of infections after social reopening. Another side of our results stands by the opinion that bioinformatic analysis can be consistent with experiments in some respects so that we can prevent unnecessary sacrifice of laboratory animals in future experiments.
Subject: Life Sciences, Virology Keywords: ACE2; Spike protein; SARS-CoV2; death rate; polymorphism; isoform variant; CD157, sankramikogenomics
Online: 17 May 2020 (14:51:39 CEST)
The 2019-Novel Coronavirus has currently gripped the world in terror, affecting 210 countries and territories. Originating from Wuhan, Hubei province, China, the virus has spread so rapidly throughout the world and has already claimed 308,927 lives and is currently afflicting 4.6 million people. The US has over 1.48 million confirmed cases of COVID-19, followed by Spain, Italy, France, UK, Germany, Turkey, Russia, Iran, and China. On careful inspection of the COVID-19 statistics, a peculiar unsettling trend becomes apparent. Western European countries and the US appear to have difficulties in overcoming the catastrophe. In contrast, countries in East Asia, Middle East and mid-Europe have sorted out the situation. Here, we will highlight this trend and propose the importance of infection-genomics (sankramikogenomics), in understanding the susceptibility to COVID-19 and the severity of disease progress. More detailed, systematic evaluation may also identify more susceptible populations. We will also highlight mere 12-fold lower affinity is insufficient to ignore CD147, as interactions occur between tens of spike proteins and equal number of cell surface ACE2 and/or CD147. Thus, both receptors are important to understand sankramikogenomics and severity of COVID-19. The observed ethnic differences in COVID severities may be due to variations in structure or tissue-specific expression (alternate splicing and accessibility) of both the target receptors. Research on both receptors may help in designing improved therapeutic strategies to fight COVID-19. Similar to pharmacogenomics to drug development and precision medicine, Sankramikogenomics will become an important field in other infectious diseases and pathogenicity.
REVIEW | doi:10.20944/preprints202005.0284.v1
Subject: Life Sciences, Other Keywords: hypoxia; HIF-1α; partial EMT; collective migration; inflammatory breast cancer; E-cadherin; metastasis
Online: 17 May 2020 (08:19:42 CEST)
Epithelial-mesenchymal transition (EMT) is a cellular biological process involved in migration of primary cancer cells to secondary sites facilitating metastasis. Besides, EMT also confers properties such as stemness, drug resistance and immune evasion which can aid a successful colonization at the distant site. EMT is not a binary process; recent evidence suggests that cells in partial EMT or hybrid E/M phenotype(s) can have enhanced stemness and drug resistance as compared to those undergoing a complete EMT. Moreover, partial EMT enables collective migration of cells as clusters of circulating tumor cells or emboli, further endorsing that cells in hybrid E/M phenotypes may be the ‘fittest’ for metastasis. Here, we review mechanisms and implications of hybrid E/M phenotypes, including their reported association with hypoxia. Hypoxia-driven activation of HIF-1α can drive EMT. In addition, cyclic hypoxia, as compared to acute or chronic hypoxia, shows the highest levels of active HIF-1α and can augment cancer aggressiveness to a greater extent, including enriching for a partial EMT phenotype. We also discuss how metastasis is influenced by hypoxia, partial EMT and collective cell migration, and call for a better understanding of interconnections among these mechanisms. We discuss the known regulators of hypoxia, hybrid EMT and collective cell migration and highlight the gaps which needs to be filled for connecting these three axes which will increase our understanding of dynamics of metastasis and help control it more effectively.
REVIEW | doi:10.20944/preprints202005.0283.v1
Subject: Life Sciences, Other Keywords: fat replacer; octenyl succinic anhydride; OSA starch; starch properties
Online: 17 May 2020 (08:14:12 CEST)
Along with the rapid development of the trend in the health sector, various studies have been conducted to find alternative healthier foods, one of which is reducing fat consumption. Currently, many researchers focus on one of modified starches that can be utilized as a fat replacer is starch modified with OSA (octenyl succinic anhydride). In the last decade, there have been quite a lot of publications related to OSA starch, further the number is still increasing. This review discusses the synthesis method of OSA starch and its optimization, functional characteristics, and its application to be a fat replacer in many kinds of products daily consumed. Various pre-treatment methods could be applied to create OSA starch which has higher degree of substitution values. The presence of conjugate bonds with the OSA group in starch polymers could produce very amphiphilic starch characteristic so as to have an emulsifying function. Emulsions shaped from OSA starch were utilized as fat replacers in foods with high level of fat content. Partial OSA starch substitution was successfully utilized as a fat replacer for several types of food products with similar sensory attributes or even slightly better than the native product. The resulting product could be defined as a healthier choice because it had relatively lower fat and calorie content. Even so, adjustments through further study are still needed so that the food produced is able to have a higher level of sensory acceptance relative to native food without fat substitution.
Sat, 16 May 2020
ARTICLE | doi:10.20944/preprints202004.0171.v2
Subject: Life Sciences, Virology Keywords: protein functional domains; short linear motifs; coronaviruses; COVID-19; severe acute respiratory syndrome-related coronavirus; 2019-nCoV; virus outbreak
Online: 16 May 2020 (18:54:17 CEST)
Although phylogenetic analysis shows coronaviruses (CoV) share similar genome sequences, CoVs encode different number of proteins (5 to 14), which has implication on viral pathogenicity and infection. Here, we aimed to identify (in-silico) the similarities between different members of coronavirus family. The analysis included 50 coronavirus proteomes, including SARS-CoV-2 (COVID-19), to find the variation of the number of protein functional motifs and domain in each coronavirus. For this role, we used the experimentally validated domain (motif) that known to be crucial for viral infection. Although human CoVs are classified within one genus, we found variations among them. SARS-CoV-1, SARS-CoV-2 and MERS-CoV encode different type of domains, which has implications on the molecular interactions triggered by each virus within human cells. Secondly, we used functional motifs to reconstruct the potential molecular pathways or interactions triggered by SARS-CoV-2 proteins within human cell.
ARTICLE | doi:10.20944/preprints202005.0273.v1
Subject: Life Sciences, Molecular Biology Keywords: COVID-19; SARS-CoV-2; pandemic; IFITM3; rs12252; rs34481144; ethnic groups; bame; cytokine storm
Online: 16 May 2020 (17:38:28 CEST)
Evidence was recently brought forward in England and the USA that Black, Asian, Latinos and Minority Ethnic people present higher mortality risk from COVID-19 than White people. While socioeconomic factors were suggested to contribute to this trend, they arguably do not explain the range of the differences observed, allowing for possible genetic implications. Almost concurrently, the analysis of a cohort in Chinese COVID-19 patients proposed an association between the severity of the disease and the presence of the minor allele of rs12252 of the IFITM3 gene. This SNP, together with rs34481144, are the two most studied polymorphisms of IFITM3 and have been associated in the past with increased severity in Influenza, Dengue, Ebola, and HIV viruses. Interferon-induced transmembrane protein 3 is an immune effector protein that is pivotal for the restriction of viral replication, but also for the regulation of cytokine production. Following up to these two developments in the SARS-CoV-2 pandemic, the present study investigates a possible connection between differences in mortality of ethnic groups in England and the haplotypes of rs12252 and rs34481144. The respective allele frequencies were collected for all 1000 Genomes Project’s populations and subgroups were pooled wherever possible to create correspondences with ethnic groups in England. A strong correlation was observed between the reported Standardized Mortality Ratios and the frequency of the combined haplotype of both reference alleles. If confirmed clinically, this finding could be pointing at possible hijacking of IFITM3 by SARS-CoV-2 virus and is expected to impact our understanding of the disease mechanisms behind COVID-19.
ARTICLE | doi:10.20944/preprints202005.0271.v1
Online: 16 May 2020 (17:07:43 CEST)
Currently, with a large number of fatality rates, coronavirus disease-2019 (COVID-19) has emerged as a potential threat to human health worldwide. It has been well-known that severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is responsible for COVID-19 and World Health Organization (WHO) proclaimed the contagious disease as a global pandemic. Researchers from different parts of the world amalgamate together inquest of remedies for this deadly virus. Recently, it has been demonstrated that the spike glycoprotein (SGP) of SARS-CoV-2 is the mediator behind the entrance into the host cells. Our group has comprehensibly analyzed the SGP of SARS-CoV-2 through multiple sequence analysis along with the phylogenetic analysis. Further, this research work predicted the most immunogenic epitopes for both B-cell and T-cell. Notably, we focused mainly on major histocompatibility complex (MHC) class I potential peptides and predicted two epitopes; WTAGAAAYY and GAAAYYVGY, that bind with the MHC class I alleles which are further validated by molecular docking analysis. Furthermore, this study also proposed that the selected epitopes were shown availability in a greater range of the population. Hence, our study comes up with a strong base for the implementation of designing novel vaccine candidates against SARS-CoV-2, however adequate laboratory works will need to be conducted for the appropriate application.
ARTICLE | doi:10.20944/preprints202004.0239.v4
Subject: Life Sciences, Virology Keywords: epidemic; caseload management; partial unlock; social distancing; overshoot; COVID-19; coronavirus; eco-nomic impact; ventilator utilization; SARS-CoV-2
Online: 16 May 2020 (16:13:16 CEST)
This paper accounts in lives-saved partial unlock strategies that may be used to facilitate reopening economies that have been shut down due to an epidemic or pandemic. For this purpose it introduces a new approach to simulation using an internal SIR engine with seasonality, and external behavior forcing calibrated with case data to account for initial human behavior under social distancing. The overall method relies on public goal setting and both professional and public feedback behavior. In this way it avoids much of the chaotic sensitivity to parameters and divergence of predictions and behavior which undermine the public image of epidemiology models and create rebounds. We study reducing the total cases by controlling threshold overshoot as economies reopen, controlling medical resource utilization, and reducing economic shutdown duration, all of these across significant scenario variation. We provide a quantitative analysis of overshoot and demonstrate a two-step manual method as well as the feedback method of avoiding it. We show goal-managed partial unlock to manage critical resources has the consequential effects of reducing economic downtime and bringing the cumulative cases down about 9%-27%, thereby saving lives with some degree of certainty. The optimization of overshoot does leave some risk of creating a residual small infection existing on birth rate and migration, and we provide some guidelines for minimizing the risk. Effectiveness is demonstrated using COVID-19 actual data and parameters for other diseases with replication factors up to 15.
ARTICLE | doi:10.20944/preprints202005.0264.v1
Subject: Life Sciences, Virology Keywords: plaque assay; neutralization; SARS; SARS-CoV-2; coronavirus; Avicel; methylcellulose; COVID
Online: 16 May 2020 (15:51:52 CEST)
When working with the novel coronavirus SARS-CoV-2 during a pandemic response, having a rapid, reproducible and reliable assay for infectious virus quantitation and utilization for evaluation of potential therapeutics is critical. Compared to traditional agarose overlay plaques visualized with neutral red, assays performed with Avicel R RC-591 semi-solid overlay provide a simplified format for rapid and easy detection and neutralization testing. The method is easily modified for higher throughput using dispensers or automated processing. Fixation using formalin provides flexibility when dealing with pathogenic agents such as SARS-CoV-2 where tissue culture plates might be removed from biocontainment for staining. Although plaque assays are considered straightforward in principle, having an easily reproducible, consistent plaque assay is an invaluable tool.
Fri, 15 May 2020
COMMUNICATION | doi:10.20944/preprints202005.0253.v1
Subject: Life Sciences, Genetics Keywords: Cas9; Cas12a; Cpf1; zebrafish; gene knockout; repair outcome
Online: 15 May 2020 (10:16:55 CEST)
CRISPR/Cas genome editing is a widely used research technology. Its simplest variant is gene knockout resulting from reparation errors after introduction of dsDNA breaks by Cas nuclease. We compared the outcomes of the break repair by two commonly used nucleases (SpCas9 and LbCas12a) in zebrafish embryos to reveal if application of one nuclease is advantageous in comparison to the other. To address this question, we injected ribonucleoprotein complexes of nucleases and corresponding guide RNAs in zebrafish zygotes and three days later sequenced the target gene regions. We found that LbCas12a breaks resulted in longer deletions and more rare inserts, in comparison to those generated by SpCas9, while the editing efficiencies of both nucleases were the same. On the other hand, overlapping protospacers were shown to lead to similarities in repair outcome, although they were cut by two different nucleases. Thus, our results indicate that the repair outcome depends both on the nuclease mode of action and on protospacer sequence.
ARTICLE | doi:10.20944/preprints202005.0248.v1
Subject: Life Sciences, Biophysics Keywords: cancer; differentiation commitment; acridine-orange-DNA test; pericentromere-associated domains (PADs); power law of PAD number vs. size; critical self-organisation; unravelling of PADs; silencing threshold
Online: 15 May 2020 (08:01:08 CEST)
Finding out how cells with the same genome change fates in differentiation commitment is a challenge of biology. We used MCF-7 breast cancer cells treated with the ErbB2 ligand heregulin (HRG), which induces differentiation, to address if and how the constitutive pericentromere-associated domains (PADs) may be involved in this process. PAD-specific repressive heterochromatin (H3K9me3) and active euchromatin (H3K4me3) marking, centromere (CENPA) labelling, qPCR, acridine-orange-DNA structural test, and microscopic image analysis were applied. We found a two-step DNA unfolding, at 15-20 min and 60 min after HRG treatment, coinciding with bi-phasic activation of the early response genes (c-FOS family) and two steps of critical phase transition which were revealed in transcriptome studies. In control, the distribution of PAD number and size displays a power-law scaling with a boundary at the nucleolus. PADs’ clustering correlates with centromere numbers. 15 min after HRG treatment, the unravelling of PADs occurs, coinciding with the first step of euchromatin unfolding. The second step is associated with transcription of long-non-coding-RNA from satellite III DNA. We hypothesize that splitting of the PAD clusters under the critical size threshold of the silencing domain abrupts position effect variegation. It allows the first genome transcription avalanche to occur, starting differentiation commitment.
Thu, 14 May 2020
Subject: Life Sciences, Molecular Biology Keywords: COVID-19; SARS-CoV-2; companion animal; cross-infection
Online: 14 May 2020 (11:54:31 CEST)
Since the COVID-19 caused by SARS-CoV-2 break out in Wuhan China from Dec. 2019, it has spread to hundreds of countries up to now. Scientists from all over the world have paid tremendous efforts to research and try to control the disease. Previous studies suggested that some of the wild animals could be intermediate hosts between humans and origination of SARS-CoV-2, and some companion animals of humans can be infected by SARS-CoV-2, which raised our curiosity about cross-infection of SARS-CoV-2 between animals and humans. Thus, we select some kinds of animals that might have contact with humans to estimate the susceptibility to SARS-CoV-2 in different animals by evolutionary analysis of their receptors for SARS-CoV-2. The results show that some companion animals of the Felidae family like the cat has a higher infection possibility while the species of the Rodent family like the rat and mouse having close contact with humans show an opposite result, which consist with recent animal experiments and researches. These should raise concerns about cross-infection between human and companion animals or animals to have close contact with humans which might grow into depositaries of the virus after control of SARS-CoV-2 spreading and cause second or more infection wave after social reopening. Another side of our results stands by the opinion that bioinformatic analysis can be consistent with practical experiments in some respects so that we can prevent unnecessary sacrifice of laboratory animals in future experiments.
REVIEW | doi:10.20944/preprints202005.0235.v1
Subject: Life Sciences, Other Keywords: strap muscle invasion; prognosis; differentiated thyroid carcinoma; meta-analysis; review
Online: 14 May 2020 (11:35:41 CEST)
Gross strap muscle invasion (gSMI) in patients with differentiated thyroid cancer (DTC) was defined as high-risk recurrent group in the 2015 American Thyroid Association guidelines. However, controversy persists because several studies suggested gSMI had little effect on disease outcome. Herein, a systematic review and meta-analysis was conducted to investigate impact of gSMI on outcome of DTC. Methods: A systematic search of electronic databases (PubMed, EMBASE, Cochrane Library, and MEDLINE) for studies published until February 2020 was performed. Case-control studies and randomized controlled trials that studied the impact of gSMI on outcome of DTC were included. Results: Six studies (all retrospective studies) involving 13639 patients met final inclusion criteria. Compared with no extrathyroidal extension (ETE), patients with gSMI were associated with increased risk of recurrence (P=0.0004,OR, 1.46; 95% CI: 1.18 to 1.80) and lymph node metastasis (LNM) (P<0.00001,OR 4.19;95% CI. 2.53 to 6.96). For mortality (P=0.34,OR 1.47;95% CI:0.67 to 3.25), ten-year disease-specific survival (P=0.80, OR 0.91;95% CI:0.44 to 1.88) and distant metastasis (DM) (P=0.21, OR 2.94;95% CI. 0.54 to 15.93), there was no significant difference between gSMI and no ETE group. In contrast with maximal ETE, patients with gSMI were associated with decreased risk of recurrence (P<0.0001,OR, 0.58; 95% CI: 0.44 to 0.76) , mortality (P=0.0003,OR 0.20;95% CI:0.08 to 0.48), LNM (P=0.0003,OR 0.64;95% CI. 0.50 to 0.81) and DM (P=0.0009,OR 0.28;95% CI. 0.13 to 0.59). Conclusions: DTC patients with gSMI had a higher risk of recurrence and LNM than those without ETE. However, in contrast with maximal ETE, a much better prognosis was observed in DTC patients with only gSMI. The findings of our meta-analysis provide supportive evidence for the validity of the T category changes in the 8th edition American Joint Committee on Cancer system. The actual impact of gSMI should be re-evaluated and revised in the recurrent risk stratification system in the future.
CONCEPT PAPER | doi:10.20944/preprints201910.0311.v2
Online: 14 May 2020 (08:52:09 CEST)
Technological advances made Virtual and Mixed Reality (VMR) accessible at our fingertips. However, only recently VMR has been explored for the teaching of biology. Here, we highlight how VMR applications can be useful in biology education, discuss about caveats related to VMR use that can interfere with learning, and look into the future of VMR applications in the field. We then propose that the combination of VMR with Machine Learning and Artificial Intelligence can provide unprecedented ways to visualise how species evolve in self-sustained immersive virtual worlds, thereby transforming VMR from an educational tool to the centre of biological interest.
REVIEW | doi:10.20944/preprints202005.0232.v1
Subject: Life Sciences, Microbiology Keywords: phage resistance; phage therapy; vConTACT 2.0; phage resistance ecology; bacteriophages
Online: 14 May 2020 (08:09:04 CEST)
: As antibiotic resistance undermines efforts to treat bacterial infections, phage therapy is being increasingly considered as an alternative in clinical settings and agriculture. However, a major concern in using phages is that pathogens will develop resistance to the phage. Due to the constant evolutionary pressure by phages, bacteria have evolved numerous mechanisms to block infection. If we determine the most common among them, we could use this knowledge to guide phage therapeutics. Here we compile data from 88 peer-reviewed studies where phage resistance was experimentally observed and linked to a bacterial gene, then assessed these data for patterns. In total, 141 host genes were identified to block infection against one or more of 80 phages (representing five families of the Caudovirales) across 16 microbial host genera. These data suggest that bacterial phage resistance is diverse, but even well-studied systems are understudied, and there are gaping holes in our knowledge of phage resistance across lesser-studied regions of microbial and viral sequence space. Fortunately, scalable approaches are newly available that, if broadly adopted, can provide data to power ecosystem-aware models that will guide harvesting natural variation towards designing effective, broadly applicable phage therapy cocktails as an alternative to antibiotics.
Wed, 13 May 2020
ARTICLE | doi:10.20944/preprints202005.0227.v1
Subject: Life Sciences, Genetics Keywords: meta-analysis; transcription factor; binding site; genomics; transcriptomics; chilling stress; CBF; DREB; CAMTA
Online: 13 May 2020 (15:17:16 CEST)
At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. Synergistic action of multiple pathways greatly complicates the experimental study of the molecular genetic mechanisms of the organism's reactions. As a result, a significant part of the regulatory ensemble in such complex reactions remains unidentified. We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism's response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes. Here we showed metaRE performance for identification of cold stress-responsive cis-regulatory code in Arabidopsis thaliana. MetaRE identified potential binding sites for known as well as unknown cold response regulators. Software with source files, documentation, and example data files are freely available online at the repository (https://github.com/cheburechko/MetaRE).
REVIEW | doi:10.20944/preprints202005.0222.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: myelin; myelination; development; peripheral neuropathies; protein folding; transmembrane protein; protein-membrane interaction; protein-protein interaction
Online: 13 May 2020 (04:51:20 CEST)
Myelin protein zero (P0), a type I transmembrane protein, is the most abundant protein in peripheral nervous system (PNS) myelin – the lipid-rich, periodic structure that concentrically encloses long axonal segments. Schwann cells, the myelinating glia of the PNS, express P0 throughout their development until the formation of mature myelin. In the intramyelinic compartment, the immunoglobulin-like domain of P0 bridges apposing membranes together via homophilic adhesion, forming a dense, macroscopic ultrastructure known as the intraperiod line. The C-terminal tail of P0 adheres apposing membranes together in the narrow cytoplasmic compartment of compact myelin, much like myelin basic protein (MBP). In mouse models, the absence of P0, unlike that of MBP or P2, severely disturbs the formation of myelin. Therefore, P0 is the executive molecule of PNS myelin maturation. How and when is P0 trafficked and modified to enable myelin compaction, and how disease mutations that give rise to incurable peripheral neuropathies alter the function of P0, are currently open questions. The potential mechanisms of P0 function in myelination are discussed, providing a foundation for the understanding of mature myelin development and how it derails in peripheral neuropathies.
Mon, 11 May 2020
ARTICLE | doi:10.20944/preprints202005.0198.v1
Subject: Life Sciences, Virology Keywords: de-MARylation; interferon-stimulated gene; inflammation; PARP14; ACE2; coronavirus
Online: 11 May 2020 (13:11:43 CEST)
As more cases of COVID-19 are studied and treated world-wide, it had become apparent that lethal and most severe cases of pneumonia are due to an out-of-control inflammatory response to the SARS-CoV2 virus. I explored the putative causes of this specific feature through a detailed genomic comparison with the closest SARS-CoV-2 relatives isolated from bats, as well as previous coronavirus strains responsible for the previous epidemics (SARS-CoV, and MERS-CoV). The high variability region of the nsp3 protein was confirmed to exhibit the most variations between closest strains. It was then studied in the context of physiological and molecular data available in the literature. A number of convergent findings point out de-mono-ADP-ribosylation (de-MARylation) of STAT1 by the SARS-CoV-2 nsp3 as a likely cause of the cytokine storm observed in the most severe cases of COVID-19. This may suggest new therapeutic approaches and an assay to predict the virulence of naturally circulating SARS-like animal coronaviruses.
ARTICLE | doi:10.20944/preprints202005.0195.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: Placenta; trophoblast; SARS-CoV-2; Coronaviruses; COVID-19; Single cell RNAseq; scRNA-seq; ACE2; TMPRSS2; CD147; CTSL; inflammation
Online: 11 May 2020 (12:50:48 CEST)
Infection by the Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) results in the novel coronavirus disease COVID-19, which has posed a serious threat globally. Infection of SARS-CoV-2 during pregnancy is associated with complications like preterm labor and premature rupture of membranes; a proportion of neonates born to the infected mothers are also positive for the virus. During pregnancy, the placental barrier protects the fetus from pathogens and ensures healthy development. However, whether or not SARS-CoV-2 can infect the placenta is unknown. Herein, utilizing single-cell RNA-seq data, we report that the SARS-CoV-2 binding receptor ACE2 and the S protein priming protease TMPRSS2 are co-expressed by a subset of syncytiotrophoblasts (STB) in the first trimester and extra villous trophoblasts (EVT) in the second trimester human placenta. The ACE2- and TMPRSS2-positive (ACE2+TMPRSS2+) placental subsets express mRNA for proteins involved in viral budding and replication. These cells also express mRNA for proteins that interact with SARS-CoV-2 structural and non-structural proteins in the host cells. We also discovered unique signatures of genes in ACE2+TMPRSS2+ STBs and EVTs. The ACE2+TMPRSS2+ STBs are highly differentiated cells and express genes involved mitochondrial metabolism and glucose transport. The second trimester ACE2+TMPRSS2+ EVTs are enriched for markers of endovascular trophoblasts. Further, both these subtypes abundantly expressed genes in Toll like receptor pathway, the second trimester EVTs (but not first trimester STBs) are also enriched for component of the JAK-STAT pathway that drive inflammation. To conclude, herein we uncovered the cellular targets for SARS-CoV-2 entry and show that these cells can potentially drive viremia in the developing human placenta. Our results provide a basic framework towards understanding the paraphernalia involved in SARS-CoV-2 infections in pregnancy.
Sun, 10 May 2020
CONCEPT PAPER | doi:10.20944/preprints202005.0182.v1
Subject: Life Sciences, Virology Keywords: Coronavirus Nsp proteins; ribosomal proteins homology; inhibition of ribosome turn over; rRNA methyltransferase; protein synthesis inhibition; low ATP formation; blood clotting; low blood pressure and coma
Online: 10 May 2020 (18:14:55 CEST)
Multi-Alignment method coupled with phylogenetic analysis we disclosed the Nsp9 and Nsp10 non-structural proteins of Corona Virus as rRNA RlmH/K methyltransferases with similarities with bin recombinase and int-core integrase fold. Further, Nsp9 has similarities to S8 ribosomal protein and Nap10 has similarity to S10 ribosomal protein. Previously, we showed Nsp13, Nsp14, Nsp15 and Nsp16 are also different types of rRNA RlmE/N and Cfr-like methyltransferases-ribonuclease with RNA helicase domains. Two domains of Nsp13 astonishingly have similarities to ribosomal proteins L6 and L9. Taken together, Nsp9/10 and Nsp13-16 proteins could mimic host ribosome assembly and also could methylate rRNA of mitobibosome preventing mitochondrial protein synthesis and oxidative phosphorylation. Low ATP synthesis causes lowering blood pressure following coma but very ATP concentration (1-10nM) surely induces platelets aggregation through vWA, collagen and GpIIb/IIIa proteins followed by fibrin formation and blood clotting as recently have seen in the lung of many Corona virus infected patients. We have also postulated that two polyproteins itself resemble like 28S and 38S mitoribosome subunits and compete with rRNAs inhibiting the ribosome turnover and new protein synthesis due to their similarities with many ribosomal proteins. Such finding may be valuable in computer-based novel drug design against Corona virus.
Subject: Life Sciences, Virology Keywords: coronavirus; COVID-19; pandemic; model; partial unlock; social distancing; economic impact; ventilator utilization; SARS-CV-2; overshoot
Online: 10 May 2020 (15:14:11 CEST)
This paper analyzes the stability and usefulness of a caseload management method for COVID-19 or similar epidemics and pandemics. It reduces the total cases by controlling overshoot as groups cross the herd immunity threshold, balances medical resource utilization, and subject to those two constraints reduces economic shutdown duration across significant scenario variation. A quantitative analysis of overshoot is provided. An SIR-type model was used with clear parameters suitable for public information with tracking and predictive capabilities is used. It contains a simulation of a decision-maker for select-day partial unlock so that many scenarios can be quickly and impartially analyzed. Using certain days of the week, already practiced by some countries, is not a necessary part of the method, but was used in the simulation to give a highly quantified unlock scheme. While the model shows total cumulative cases, and therefore deaths, declining initially with flattening, when flattening begins to produce large rebounds the death rate goes back up. Partial unlock to manage critical resources had the consequential effects of reducing economic downtime and bringing the cumulative cases down about 8-12% between now and the second half of 2021, thereby saving lives with some degree of certainty. The optimization of overshoot does leave some risk of creating a residual small infection existing on birth rate and migration, and we provide some guidelines for minimizing the risk.
Sat, 9 May 2020
Subject: Life Sciences, Other Keywords: Sars-CoV-2; homology modelling; envelope membrane glycoprotein; Bat; Pangolin; Sars-CoV
Online: 9 May 2020 (08:43:08 CEST)
The Coronavirus Disease 2019 (COVID-19) is a new viral infection caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2). Genomic analyses have revealed that SARS-CoV-2 is related to Pangolin and Bat coronaviruses. In this report, a structural comparison between the Sars-CoV-2 Envelope and Membrane proteins from different human isolates with homologous proteins from closely related viruses is described. The analyses here reported show the high structural similarity of Envelope and Membrane proteins to the counterparts from Pangolin and Bat coronavirus isolates. However, the comparisons have also highlighted structural differences specific of Sars-CoV-2 proteins which may be correlated to the cross-species transmission and/or to the properties of the virus. Structural modelling has been applied to map the variant sites onto the predicted three-dimensional structure of the Envelope and Membrane proteins.
REVIEW | doi:10.20944/preprints202005.0158.v1
Subject: Life Sciences, Molecular Biology Keywords: apoptosis; cancer; phosphorylation; kinases; Bcl-2
Online: 9 May 2020 (08:40:40 CEST)
The regulation of apoptosis depends upon the Bcl-2 protein family. The process of cell death and survival is highly complicated and regulated by various types of extrinsic as well as intrinsic network of biological system. Several enzymes and regulators play crucial role in cell death and survival cycle not only in healthy but also in pathological state particularly in cancer. In cancerous cells, various proto-oncogenes and anti-apoptotic proteins are activated and responsible for the cell survival and longevity. The mechanism of activation and inactivation of various proteins in cell survival is regulated by the process of phosphorylation (kinases) and dephosphorylation (phosphatases). The current review will summarize the dynamics of Bcl-2 phosphorylation and its role in apoptosis and cell survival.
REVIEW | doi:10.20944/preprints202005.0157.v1
Subject: Life Sciences, Immunology Keywords: COVID-19; SARS-Cov-2; cytokine storm; inflammation; immunosenescence
Online: 9 May 2020 (08:35:51 CEST)
The dysregulated release of cytokines has been identified as one of the key factors behind poorer outcomes in COVID-19. This ‘cytokine storm ‘produces an excessive inflammatory and immune response, especially in the lungs, leading to acute respiratory distress (ARDS), pulmonary edema and multi-organ failure. Alleviating this inflammatory state is crucial to improve prognosis. Pro-inflammatory factors play a central role in COVID-19 severity, especially in patients with comorbidities In these situations, an overactive, untreated immune response can be deadly, suggesting that mortality in COVID-19 cases is likely due to this virally driven hyperinflammation. Administering immunomodulators has not yielded conclusive improvements in other pathologies characterized by dysregulated inflammation such as sepsis, SARS-CoV-1 and MERS. The success of these drugs at reducing COVID-19-driven inflammation is still anecdotal and comes with serious risks. It is also imperative to screen the elderly for risk factors that predispose them to severe COVID-19. Immunosenescence and comorbidities should be taken into consideration. In this review, we summarize the latest data available about the role of the cytokine storm in COVID-19 disease severity as well as potential therapeutic approaches to ameliorate it. We also examine the role of inflammation in other diseases often comorbid with COVID-19, such as aging, sepsis, and pulmonary disorders. Finally, we identify gaps in our knowledge and suggest priorities for future research aimed at stratifying patients according to risk as well as personalizing therapies in the context of COVID19-driven hyperinflammation.
ARTICLE | doi:10.20944/preprints202005.0153.v1
Subject: Life Sciences, Microbiology Keywords: Escherichia coli; antimicrobial resistance; ESBL; MDR; frozen chicken meat; Bangladesh
Online: 9 May 2020 (08:17:34 CEST)
Multidrug resistant extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is considered a serious concern to public health worldwide including Bangladesh, and chicken meat is recognized as an important reservoir of ESBL-Ec dissemination to humans. Therefore, this study aimed to determine the prevalence, and phenotypic and genotypic antimicrobial resistance pattern of ESBL-producing Escherichia coli (ESBL-Ec) in frozen chicken meat. A total of 113 frozen chicken meat samples were purchased from 40 outlets of 9 branded supershops in five megacities in Bangladesh. Isolation and identification of Escherichia coli were done based on cultural, biochemical properties and PCR assay. The resistance pattern was determined by disk diffusion method. ESBL-encoding genes were determined by multiplex PCR. The results showed that 76.1% samples were positive for Escherichia coli, of which 86% were ESBL producers. All the isolates were multidrug-resistant (MDR). Resistance to 9–11 and 12–13 antimicrobial classes was observed in 38.4% and 17.4% isolates, respectively while only 11.6% were resistant to 3–5 classes. The possible extensively drug resistance (pXDR) was found in 2.3% isolates. The high single resistance was observed for oxytetracycline (93%) and amoxicillin (91.9%), followed by ampicillin (89.5%), trimethoprim-sulphamethoxazole and pefloxacin (88.4%), and tetracycline (84.9%). Most importantly, 89.6% of isolates were resistant to carbapenems. All the isolates were positive for blaTEM gene. However, the blaSHV and blaCTX-M-2 genes were identified in two ESBL-non producer isolates. None of the isolates were carried blaCTX-M-1 gene. This study provided evidence of wide dissemination of MDR and existence of pXDR ESBL-Ec in frozen chicken meat in Bangladesh. Our data clearly indicated that frozen chicken meat is, at the present time, the most significant known food source of ESBL-Ec to which peoples are regularly exposed.
Fri, 8 May 2020
BRIEF REPORT | doi:10.20944/preprints202005.0143.v1
Subject: Life Sciences, Virology Keywords: Covid-19; Epidemiology; Chronic diseases; Serious or critical cases; Brazil; Coronavirus
Online: 8 May 2020 (12:33:24 CEST)
Chronic noncommunicable diseases (CNCDs) have been a major public health concern worldwide, especially diabetes, cardiovascular disease, chronic obstructive pulmonary disease, hypertension, in addition to obesity, which is even more worrying when the subject involves the covid-19 pandemic, because such incidences correlate with the need for intensive care units, including the possibility of death of the patient. Therefore, for countries with the highest numbers of critical cases, it is important to assess the incidence of these diseases to guide the public that most needs guidance on public policies for social isolation.
COMMUNICATION | doi:10.20944/preprints202005.0138.v1
Subject: Life Sciences, Virology Keywords: covid-19; epidemiology; epidemiological week; Brazil; coronavirus; viruses
Online: 8 May 2020 (08:08:40 CEST)
Amid the covid-19 pandemic, other diseases, including viruses, are still acting to the detriment of their seasonality and risk factors for contagion. For this reason, it is interesting to know the degree of impact of other viruses, mainly respiratory, in which they have similar symptoms, in diagnoses for contamination by the new coronavirus based on epidemiological surveys, via epidemiological weeks, in Brazil. To what extent there may be a hypothesis of confusion of contaminated data, harming the health system, with regard to the need for intensive care units and control of viruses, and negatively or positively implying in the control or uncontrolling of viruses in general.
ARTICLE | doi:10.20944/preprints202005.0136.v1
Subject: Life Sciences, Virology Keywords: deubiquitination; leukemia; ubiquitin-specific protease 2 (USP2); SARS-CoV-2 papain-like protease (PLpro); COVID-19
Online: 8 May 2020 (03:45:22 CEST)
The ubiquitin-specific protease 2 (USP) belongs to the family of deubiquitinases and plays a critical role in tumors cells’ survival and therefore signifies an important therapeutic target. Previous studies have indicated promising efficacies of potent human USP2 inhibitors including, thiopurine analogues against SARS-CoV papain-like proteases (PLpro). The PLpro have significant functional implications in the innate immune response during SARS-CoV-2 infection and considered an important antiviral target. Both proteases share strikingly similar USP fold with right-handed thumb–palm–fingers structural scaffold and conserved catalytic triad Cys-His-Asp/Asn. In this urgency situation of COVID-19 outbreak, there is a lack of in-vitro facilities readily available to test SARS-CoV-2 inhibitors in whole-cell assays. Therefore, we adopted an alternate route to identify potential USP2 inhibitor through integrated structure-based virtual screening efforts. After a subsequent virtual screening protocol, the best compounds were selected and tested. The compound Z93 showed significant IC50 value against Jurkat (9.67 µM) and MOTL-4 cells (11.8 µM). The binding mode of Z93 was extensively analyzed through molecular docking, followed by MD simulations, and molecular interactions were compared with SARS-CoV-2. The relative binding poses of Z93 fitted well in the binding site of both proteases and showed consensus π-π stacking and H-bond interactions with histidine and aspartate/asparagine residues of the catalytic triad. These results led us to speculate that compound Z93 might be the first potential chemical lead against SARS-CoV-2 PLpro, which warrants in-vitro evaluations.
Thu, 7 May 2020
ARTICLE | doi:10.20944/preprints202005.0135.v1
Subject: Life Sciences, Other Keywords: Coronavirus disease 2019 (COVID-19); Oral and maxillofacial; Urgency and emergency;
Online: 7 May 2020 (15:29:53 CEST)
The World Health Organization has defined the outbreak of the new coronavirus as a public health emergency of international concern. The average age of patients affected by the disease caused by the virus ranges from 49 to 59 years. The symptoms of coronavirus disease 2019 (COVID-19) infection include fever, cough, acute respiratory disease, and, in severe cases, the disease may progress to pneumonia and renal failure that may lead to death. Many oral and maxillofacial hospital procedures produce aerosol and droplets contaminated by blood, bacteria, and viruses. The purpose of this study is to gather recommendations from health authorities and scientific articles in order to educate surgeons regarding the procedures to assist and treat in oral and maxillofacial surgeries. The objective is to prevent the transmission of COVID-19 during the treatment of patients in urgent and emergency situations. The study’s methodology used the guidelines provided by the Brazilian College of Oral and Maxillofacial Surgery, in addition to the recommendations and epidemiologic data from national and international health authorities. The implementation of special precautions in oral and maxillofacial surgeries may elucidate questions related to the transmission of the disease by asymptomatic carriers and help control the spread of the virus.
ARTICLE | doi:10.20944/preprints202005.0134.v1
Subject: Life Sciences, Molecular Biology Keywords: Crispr-Cas9; ACE2 gene; SARS-CoV-2; new coronavirus; COVID-19
Online: 7 May 2020 (15:26:06 CEST)
The human angiotensin-converting enzyme 2 (ACE2) has a crucial role on blood pressure control; however, ACE2 is also the primary SARS-CoV-2 (S domain) virus receptor. Inhibiting or even reducing the expression of the native ACE2 might diminish the viral entry into the cells, but may cause a failure of ACE2 biological activity, primarily in patients with comorbidities, including diabetes mellitus or hypertension. Since the ACE2 catalytic site and the SARS-Cov-2 receptor are distinct, we designed a Crispr-Cas9 model system, predicting the respective sequences for a guide RNA (gRNA) and a single-stranded oligo dideoxy nucleotide (ssODN), to introduce point mutations into the exon 1 of the human ACE2 gene, which encodes the alpha-helix, implicated on the binding of the SARS-CoV-2 envelope S protein. Protein modeling predicted that the specific substitutions of residues Phe28, Lys31, and Tyr41 for Ala at the ACE2 alpha-helix do not significantly alter ACE2 native conformation. The analysis of the impact of these mutations on ACE2 receptor function predicted a weakening of the binding of the SARS-CoV-2 protein S. An experimental genome editing of cells based on these Crispr-Cas9 elements might reduce the SARS-CoV-2 ability to enter the epithelial cell, preserving the biological activity of ACE2 enzyme.
COMMUNICATION | doi:10.20944/preprints202005.0132.v1
Subject: Life Sciences, Other Keywords: risk perception; coronavirus; covid-19; risk communication; global health
Online: 7 May 2020 (15:12:32 CEST)
The ongoing COVID-19 pandemic is shaking the foundations of public health governance all over the world. Researchers are challenged by informing and supporting authorities on acquired knowledge and practical implications. This commentary applies established theories of risk perception research to COVID-19 and reflects on the role of risk perceptions in these unprecedented times. Moreover, it calls for utilizing the knowledge on risk perception to improve health risk communication, build trust and contribute to a collaborating governance.
ARTICLE | doi:10.20944/preprints202005.0119.v1
Subject: Life Sciences, Biophysics Keywords: pore-forming toxins; calcium; high-speed atomic force microscopy
Online: 7 May 2020 (10:23:54 CEST)
Pore Forming Toxins (PFTs), formed mainly by virulence factors of bacteria, belongs to Pore Forming Protein (PFP) family. Secreted as soluble monomers, they bind specific targets in membranes where their oligomerization and insertion place. Lysenin, a member of the PFTs, forms and oligomer after sphingomyelin binding, the so-called prepore, which become inserted forming a pore after a conformational change triggered by a pH decrease. In crowded conditions, oligomers tends to stay in prepore form because the prepore-to-pore transition is sterically blocked. In this study, we investigate the effect of calcium ions in those crowded conditions, finding that calcium act as a trigger for lysenin insertion. We localize the residues responsible for calcium sensitivity in a small α-helix. Our results are not only one of the few complete structural descriptions of prepore-to-pore transitions but the very first that involves a calcium triggering mechanism. The presence of glutamic or aspartic acids in the insertion domains could be an indication that calcium may be a general trigger for PFTs and more generally PFP.
ARTICLE | doi:10.20944/preprints202005.0118.v1
Subject: Life Sciences, Biochemistry Keywords: Memory; talin; mechanobiology; information-processing; MeshCODE; brain; neuroscience; integrin; learning; cytoskeleton; REM sleep
Online: 7 May 2020 (10:16:49 CEST)
The MeshCODE framework outlined here represents a unifying theory of data storage in animals, providing read/write storage of both dynamic and persistent information in a binary format. Mechanosensitive proteins, that contain force-dependent switches, can store information persistently which can be written/updated using small changes in mechanical force. These mechanosensitive proteins, such as talin, scaffold each and every synapse creating a meshwork of switches that forms a code, a MeshCODE. Synaptic transmission and action potential spike trains would operate the cytoskeletal machinery to write and update the synaptic MeshCODEs, propagating this coding throughout the brain and to the entire organism. Based on established biophysical principles, a mechanical basis for memory provides a physical location for data storage in the brain. Furthermore, the conversion and storage of sensory and temporal inputs into a binary format identifies an addressable read/write memory system supporting the view of the mind as an organic supercomputer.
HYPOTHESIS | doi:10.20944/preprints202005.0109.v1
Online: 7 May 2020 (08:18:28 CEST)
Most large fibers in central nervous system of vertebrates are decussated. The cause or the evolutionary force of this phenomenon is not convincingly described. Here we show a pattern for this nervous system property that simultaneously is found to a more basic rule in evolution.The idea here is the "function to anatomy" theorem. We claim that functions of physical, biochemical, enzymatic, etc., in lower scale of living organisms "emerge" to anatomy in larger scales. And reversely, the anatomy we see in multicelular organisms are/were functions in microscopic scales.We propose descriptions, predictions, and a probable road map to what this can implicate in biological and medical issues.
Wed, 6 May 2020
CONCEPT PAPER | doi:10.20944/preprints202005.0097.v1
Subject: Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2- human carbohydrate interaction; trans-species glycosylation; A-like/Tn formation; glycan trans-species bridge
Online: 6 May 2020 (14:41:35 CEST)
Although the angiotensin-converting-enzyme 2 (ACE2) is defined as the primary SARS-CoV-2 receptor (Severe acute respiratory syndrome-related coronavirus), the history of the amino acid serine strongly suggests that the actual or additional binding occurs via an intermediate hybrid O-glycan. The virus-encoded serine molecule, mobilized by the host’s TMPRSS2 (transmembrane protease serine subtype 2) may get access to the N-acetyl-D-galactosamine (GalNAc) host metabolism, and the resulting, hybrid A-like/Tn structure performs the adhesion of the virus to host cells. When in humans, this genetically undefined, intermediate structure will hypothetically be replaced by blood group ABO(H)-specific, mucin-type hybrid epitopes, in the blood group O(H) such hybrid epitopes become exposed to the highly anti-glycan-aggressive ABO(H) isoagglutinin activities, exerted by the germline-encoded polyreactive, nonimmune immunoglobulin M (IgM). In the non-O blood groups these activities are downregulated by phenotypic glycosylation and the formation of adaptive IgG is excluded by clonal selection. The non-O blood groups thus become a preferred target for the virus, whereas blood group O(H) individuals, lacking the AB phenotype-determining enzymes, have the least molecular contact with the pathogen; they maintain the isoagglutinins and the power of ancestral IgM, considered the humoral spearhead of innate immunity.
BRIEF REPORT | doi:10.20944/preprints202004.0433.v1
Online: 6 May 2020 (12:34:07 CEST)
The present study was designed to check the prevalence of cancer in residents of District Bannu, Khyber Pakhtunkhwa. Patients' data were collected from three consulted Institutes during the year 2005-09. The data was analyzed for different parameters; year-wise, age-wise prevalence, gender-wise, occupation wise and marital status wise prevalence, addiction status, type of cancer, site affected, diagnostic tests performed and treatment of cancer. Results revealed that during 2005, a high number of cancer patients were present. A total of 172 patients were in the age group of 51-60 years, while only 11 patients were in the age group of 80 plus years. Female patients were more as compared to males. Married people were highly affected than unmarried. Patients addicted to smoking were highly affected than non-addicted patients. Malignancy was high in patients as compared to benign cancer. The most affected site was the blood system. The most affected people occupation wise were housewives followed by the farmer. A biopsy was mostly conducted for the diagnosis of cancer. Most of the patients were treated with chemotherapeutic agents. It has been revealed that the number of cancer patients decreased per annum. Moreover, the study should be conducted on the general population of Bannu as well as of the Khyber Pakhtunkhwa to sort out the total number of patients. The government should launch preventive, diagnostic programs so that prevalence may be minimized.
Tue, 5 May 2020
BRIEF REPORT | doi:10.20944/preprints202005.0084.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; Vitamin D; Ivermectin; RNA-dependent-RNA polymerase; Spike glycoprotein; Knowledge based docking
Online: 5 May 2020 (15:18:30 CEST)
COVID-19 has emerged as deadly pandemic worldwide with no vaccine or suitable antiviral drugs to prevent or cure the disease. Because of the time-consuming process to develop new vaccines or antiviral agents, there has been a growing interest in repurposing some existing drugs to combat SARS-CoV-2. Vitamin D is known to be protective against acute respiratory distress syndrome (ARDS), pneumonia and cytokine storm. Recently it has been used as a repurposed drug for the treatment of H5N1 virus-induced lung injury. Circumstantial evidences indicate that people with low level of vitamin D are more susceptible to SARS-CoV-2. Although, vitamin D was suggested to interfere with viral replication, its interaction with any SARS-CoV-2 protein is unexplored yet. Beside this, ivermectin, a well-known anti-parasitic agent, exhibits potent anti-viral activities in vitro against viruses such as HIV-1 and dengue. Very recently, ivermectin has been found to reduce viral load of SARS-CoV-2 in vitro. We have analyzed available structures of SARS-CoV-2 proteins to identify probable binding partner(s) of vitamin D and ivermectin through knowledge-based docking studies and figured out possible implication of their binding in SARS-CoV-2 infection. Our observations suggest that the non-structural protein nsp7 possesses a potential site to house 25-hydroxyvitamin D3 (VDY) or the active form of Vitamin D, calcitrol. Binding of vitamin D with nsp7 likely to hamper the formation of nsp7-nsp8 complex which is required to bind with RNA dependent RNA polymerase (RdRP), nsp12 for optimal function. On the other hand, potential binding site of ivermectin has been identified in the S2 subunit of trimeric spike(S) glycoprotein of SARS-CoV-2. We propose that deeply inserted mode of ivermectin binding at three inter-subunit junctions may restrict large scale conformational changes of S2 helices which is necessary for efficient fusion of viral and host membrane. Our study, therefore, opens up avenues for further investigations to consider vitamin D and ivermectin as potential drugs against SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202005.0081.v1
Subject: Life Sciences, Genetics Keywords: Lung cancer; biomarker; gene ontology; protein-protein interaction networks; survival analysis
Online: 5 May 2020 (12:28:25 CEST)
Objective: The aim of study is to find key genes and enriched pathways associated with lung cancer. Participants and Methods: Differentially expressed genes (DEGs) data of 54674 genes based on stage, tumor and status of lung cancer was taken from 66 patients of African American (AAs) origin. 2392 DEGs were found based on stage, 13502 DEGs were found based on tumor, 2927 DEGs were found based on status having p value (p<0.05). Results: Total 33 common DEGs were found from stage, tumor and status of lung cancer. Gene ontology (GO) and KEGG pathway enrichment analysis was performed and 49 significant pathways were obtained, out of which 10 pathways were found to be exclusively involved in lung cancer development. Protein-protein interaction (PPI) network analysis found 69 nodes and 324 edges and identified 10 hub genes based on their highest degrees. Module analysis of PPI found that ‘Viral carcinogenesis’, ‘pathways in cancer’, ‘notch signaling pathway’, ‘AMPK signaling pathways’ had a close association with lung cancer. Conclusion: These identified DEGs regulate other genes which play important role in growth of lung cancer. The key genes and enriched pathways identified can thus help in better identification and prediction of lung cancer.
REVIEW | doi:10.20944/preprints202005.0070.v1
Subject: Life Sciences, Virology Keywords: Covid; covid-19; sars-cov-2; temperature; heat; body temperature; air temperature; viral decay; viral stability; transmission; severity
Online: 5 May 2020 (10:47:18 CEST)
Air temperature and body temperature may influence COVID-19 disease severity and transmission rates. In vitro data indicate that SARS-CoV-2 loses infectivity at normal core body temperature (37°C); however, small reductions in temperature proximate to 37°C may result in substantially increased viral stability. If these results are representative of viral decay rates in vivo, then cooler temperatures in the body may enable more rapid viral growth. Breathing cool air—even as warm as 25°C—cools upper respiratory tract (URT) surfaces to several degrees below body temperature, and these lower temperatures may make the URT exceptionally conducive to SARS-CoV-2 replication. Increased URT viral load may enable more effective transmission. Additionally, because SARS-CoV-2 infection may frequently begin in the URT before spreading through the body, an increased rate of viral replication in the URT early in the disease course may result in more rapid progression of disease, potentially causing more severe adverse outcomes. Core body temperature may also be a factor in disease severity, as lower core body temperatures may enable more rapid viral growth. The significance of air temperature and body temperature to disease severity and transmission rates may inform preventative measures and post-exposure prophylaxis treatments for COVID-19.
ARTICLE | doi:10.20944/preprints202005.0065.v1
Subject: Life Sciences, Molecular Biology Keywords: memory formation; moonlighting protein; protein-protein interaction; astrocyte-neuron lactate shuttle
Online: 5 May 2020 (06:09:47 CEST)
Long-term potentiation (LTP) is a molecular basis of memory formation. Here, we demonstrate that LTP critically depends on muscle fructose 1,6-bisphosphatase 2 (Fbp2) – a glyconeogenic enzyme and moonlighting protein protecting mitochondria against stress. We show that LTP induction regulates Fbp2 association with neuronal mitochondria and Camk2, and that the Fbp2-Camk2 interaction correlates with Camk2 autophosphorylation. Silencing of Fbp2 expression or simultaneous inhibition and tetramerization of the enzyme with a synthetic effector mimicking the action of physiological inhibitors (NAD+ and AMP) abolishes Camk2 autoactivation and blocks formation of the early phase of LTP and expression of the late phase LTP markers. Astrocyte-derived lactate reduces NAD+/NADH ratio in neurons and thus, diminishes the pool of tetrameric and increases the fraction of dimeric Fbp2. We therefore hypothesize that this NAD+-level-dependent increase of the Fbp2 dimer/tetramer ratio might be a crucial mechanism in which astrocyte-neuron lactate shuttle stimulates LTP formation.
ARTICLE | doi:10.20944/preprints202005.0063.v1
Subject: Life Sciences, Molecular Biology Keywords: p53-Mdm2; mutant p53; oncogene; stress; regulatory network; cancer dynamics
Online: 5 May 2020 (05:55:27 CEST)
We study a minimal model of the stress-driven p53 regulatory network that includes competition between active and mutant forms of the tumor-suppressor gene p53. Depending on the nature of the external stress signal, four distinct dynamical states are observed. These states can be distinguished by dierent dynamical properties and correspond to active, apoptotic, pre-malignant and cancer states. Transitions between any two of these states are found to be unidirectional and irreversible if the stress signal is either oscillatory or constant. When the signal decays exponentially, the apoptotic state vanishes, and for low stress the pre-malignant state is bounded by two critical points, allowing the system to transition reversibly from the active to the pre-malignant state. For signicantly large stress, the range of the pre-malignant state expands and the system moves to the cancerous state which is a stable attractor. This suggests that identification of the pre-malignant state may be important both for therapeutic intervention as well as for drug discovery.
REVIEW | doi:10.20944/preprints202005.0058.v1
Subject: Life Sciences, Biotechnology Keywords: synthetic biology; multi-agent modelling; individual-based modelling; agent-based modelling; systems biology; emergence; multi-scale; bioengineering; consortia; collectives
Online: 5 May 2020 (03:45:16 CEST)
Many complex behaviours in biological systems emerge from large populations of interacting molecules or cells, generating functions that go beyond the capabilities of the individual parts. Such collective phenomena are of great interest to bioengineers due to their robustness and scalability. However, engineering emergent collective functions is difficult because they arise as a consequence of complex multi-level feedback, which often spans multiple length-scales. Here, we present a perspective on how some of these challenges could be overcome by using multi-agent modelling as a design framework within synthetic biology. Using case studies covering the construction of synthetic ecologies to biological computation and synthetic cellularity, we show how multi-agent modelling can capture the core features of complex multi-scale systems and provide novel insights into the underlying mechanisms which guide emergent functionalities across scales. The ability to unravel design rules underpinning these behaviours offers a means to take synthetic biology beyond single molecules or cells and towards the creation of systems with functions that can only emerge from collectives at multiple scales.
REVIEW | doi:10.20944/preprints202004.0040.v3
Subject: Life Sciences, Virology Keywords: Dengue; COVID-19; SARS-CoV-2; epidemiology; infection; mortality; cross-protection; Dengue vaccine; ELISA; Dengvaxia
Online: 5 May 2020 (03:00:34 CEST)
Global severity maps of ongoing dengue epidemic and COVID-19 pandemic do not overlap. Countries with high dengue endemicity (>1.5 million cases/year) are observably less hit by COVID-19 in terms of infection, transmission and mortality. Based on non-overlap of dengue and COVID-19 severity maps and evidence of SARS-CoV-2 serological cross-reactions with dengue, we wonder whether immediate immunization of susceptible populations in Europe, North America and Asia (China, Iran) with available live-attenuated dengue vaccines, will cue the anti-viral immune response to thwart COVID-19 (viral interference). Risk of developing post-vaccination “Antibody-dependent Enhancement” is low as dengue is not endemic in the aforesaid regions.
Mon, 4 May 2020
CONCEPT PAPER | doi:10.20944/preprints202004.0310.v2
Subject: Life Sciences, Virology Keywords: ACE2; Spike protein; SARS-CoV2; death rate; polymorphism; isoform variant; CD157, sankramikogenomics
Online: 4 May 2020 (19:12:33 CEST)
The 2019-Novel Coronavirus has currently gripped the world in terror, affecting 210 countries and territories as of April 29, 2020. Originating from Wuhan, Hubei province, China, the virus has spread so rapidly throughout the world and has already claimed 218,000 lives and is currently afflicting 3.14 million people. The US has over 1.03 million confirmed cases of COVID-19, followed by Spain, Italy, France, UK, Germany, Turkey, Russia, Iran, and China. On careful inspection of the COVID-19 statistics, a peculiar unsettling trend becomes apparent. Western European countries and the US appear to have difficulties in overcoming the catastrophe. In contrast, countries in East Asia, Middle East and mid-Europe have sorted out the situation. Here, we will highlight this trend and propose the importance of infection-genomics (sankramikogenomics), in understanding the susceptibility to COVID-19 and the severity of disease progress. More detailed evaluation may also identify more susceptible populations. Such differences are due to variations in structure or tissue-specific expression (alternate splicing and accessibility) of the target receptors. So, we will highlight mere 12-fold lower affinity is insufficient to ignore CD147, as interactions occur between tens of spike proteins and equal number of cell surface ACE2 and/or CD147. Similar to pharmacogenomics to drug development and precision medicine, Sankramikogenomics will become an important field in other infectious diseases and pathogenicity.
ARTICLE | doi:10.20944/preprints202005.0047.v1
Subject: Life Sciences, Biochemistry Keywords: tumor microenvironment; biomarkers; solid cancers; computational biology; cancer stem cells; anti-cancer stem cell therapy; chemotherapy
Online: 4 May 2020 (10:00:51 CEST)
Solid tumors display complex biology and most therapies including chemotherapy cannot prevent therapy resistance and relapse. Most therapeutics target cancer cells, but recent data suggest the presence of cancer stem cells as cells with self-renewal and tumorigenic abilities. Cancer stem cell markers have been suggested to have prognostic value and can be targeted during cancer treatment and in resistant disease. CSCs have been postulated to play significant contextual roles in tumor initiation, progression, therapy resistance and metastasis. CSCs have thus been targeted by new generation cancer drugs. The transcriptional expression of several CSC markers in different cancers was evaluated by searching publicly available The Cancer Genome Atlas (TCGA) and Gene Expression Profiling Interactive Analysis (GEPIA) databases. We report here new findings on expression and prognostic significance of CSC markers in several cancers by examining the expression of CSCs markers in tumor tissues versus the adjacent normal tissues. We found that CSC markers were mostly highly expressed various tumors such as colon, lung, pancreatic and esophageal cancers. No CSC marker is expressed in the same pattern in all cancers and individual CSC marker expression was not linked to patient survival. This analysis calls for continued research on CSCs and clinical evaluation of the CSC markers in relation to prognosis of cancers in large population samples. Novel cancer drugs ought to target CSCs, cancer cells and tumor microenvironment variations.
Sun, 3 May 2020
REVIEW | doi:10.20944/preprints202005.0041.v1
Subject: Life Sciences, Immunology Keywords: Vimentin; Cell surface vimentin; SARS-CoV; Vimentin-pathogen interactions; Anti-vimentin autoantibodies; Inflammation
Online: 3 May 2020 (09:00:43 CEST)
Vimentin is an intermediate filament protein that plays key roles in integration of cytoskeletal functions, and therefore in basic cellular processes such as cell division and migration. Consequently, vimentin has complex implications in pathophysiology. Vimentin is required for a proper immune response, but it can also act as an autoantigen in autoimmune diseases or as a damage signal. Although vimentin is a predominantly cytoplasmic protein, it can also appear at extracellular locations, either in a secreted form or at the surface of numerous cell types, often in relation to cell activation, inflammation, injury or senescence. Cell surface targeting of vimentin appears to associate with the occurrence of certain posttranslational modifications, such as phosphorylation and/or oxidative damage. At the cell surface, vimentin can act as a receptor for bacterial and viral pathogens. Indeed, vimentin has been shown to play important roles in virus attachment and entry of severe acute respiratory syndrome-related coronavirus (SARS-CoV), dengue and encephalitis viruses, among others. Moreover, the presence of vimentin in specific virus-targeted cells and its induction by proinflammatory cytokines and tissue damage contribute to its implication in viral infection. Here, we recapitulate some of the pathophysiological implications of vimentin, including the involvement of cell surface vimentin in interaction with pathogens, with a special focus on its role as a cellular receptor or co-receptor for viruses. In addition, we provide a perspective on approaches to target vimentin, including antibodies or chemical agents that could modulate these interactions to potentially interfere with viral pathogenesis, which could be useful when multi-target antiviral strategies are needed .
ARTICLE | doi:10.20944/preprints202005.0040.v1
Online: 3 May 2020 (08:49:19 CEST)
To address the expression pattern of the SARS-CoV-2 receptor ACE2 and the viral priming protease, TMPRSS2, in the respiratory tract, this study investigated RNA sequencing transcriptome profiling of samples of airway and oral mucosa. As shown, ACE2 has medium levels of expression in both small airway epithelium and masticatory mucosa, and high levels of expression in nasal epithelium. The expression of ACE2 is low in mucosal associated invariant T (MAIT) cells, and can’t be detected in alveolar macrophages. TMPRSS2 is highly expressed in small airway epithelium and nasal epithelium, and has lower expression in masticatory mucosa. Our results highlights that the nasal mucosa is the most susceptible locus in the respiratory tract for SARS-CoV-2 infection and consequently for subsequent droplet transmission and should be the focus for protection against SARS-CoV-2 infection.
Subject: Life Sciences, Immunology Keywords: COVID-19; Chronic diseases; Aging; Immune response; Public health; Healthy Aging
Online: 3 May 2020 (08:15:24 CEST)
As the novel COVID-19 disease spreads around the world, the most affected population are those who suffer from the most common chronic diseases, such as obesity, hypertension, and type 2 diabetes, which are quite associated with the so-called age-related diseases. On the other hand, since the Spanish influenza outbreak, humanity has not experienced an infectious disease that synergizes so quickly with chronic diseases, making it mortal for those individuals with comorbidities. In this context, COVID-19 is challenging for health systems all around the world due to the high prevalence of chronic diseases. Nowadays, we are facing the beginning of a new era in which health infectious and chronic diseases meet. Therefore, epidemiologic and biomedical researchers must work together to solve further contingencies, and politicians should direct science-centered decisions on public health. In the present paper, we make an urgent call to learn from the COVID-19 lessons in order to mitigate the chronic diseases prevalence and to address the influence of the infectious diseases on the aging process; since we are about to begin the Decade of Healthy Aging.
ARTICLE | doi:10.20944/preprints202005.0030.v1
Subject: Life Sciences, Biochemistry Keywords: Kamias (Averrhoa bilimbi); Ripening; Cavendish Banana (Musa acuminata); Experimental; Davao City
Online: 3 May 2020 (07:40:40 CEST)
This paper aims determine the efficacy of Kamias (Averrhoa bilimbi) fruit as a ripening agent for Cavendish banana (Musa acuminata). A quantitative experimental research design was employed in the study. Unripe Cavendish bananas and Kamias fruits were procured from the local market and the fruits were extracted to three different concentrations. Calcium carbide was used as positive control. Six bunches of unripe bananas were allowed to ripe and labeled according to the type of treatment. Ripe bananas were then subjected to sensory evaluation, titratable acidity and Benedict’s tests. Results showed that the use of Kamias fruit allowed ripening of banana for 76 hours while a 25-75% concentration of Kamias fruit extract allowed ripening for 76-96 hours. The bananas treated with Kamias Extract 75% had the highest level of acceptability and titratable acidity while the bananas treated with Kamias fruit had the highest level of reducing sugar. One-Way MANOVA reported that there is a significant difference in the duration of ripening, level of acceptability, titratable acidity and level of reducing sugar when treated with various ripening agents (p<0.05).
ARTICLE | doi:10.20944/preprints202005.0026.v1
Subject: Life Sciences, Other Keywords: coronavirus; SARS-CoV-2; Spike protein; Nucleocapsid protein; MSA
Online: 3 May 2020 (06:27:36 CEST)
SARS-CoV-2 is a novel and highly pathogenic coronavirus, which was first diagnosed in Wuhan city, China, in 2019, and spread to 185 countries and territories, and as of April 29, 2020, more than 3.11 million cases were recorded, and more than 217,000 people were killed. Despite all worldwide efforts, there is currently no vaccine, any drugs available to protect people against deadly SARS-CoV-2 coronavirus. The world urgently needs a SARS-CoV-2 coronavirus vaccine or effective antiviral drugs to relieve the human suffering associated with the pandemic that kills thousands of people every day. The SARS-CoV-2 genome encode a non-structural proteins named as ORF1a/b, and structural proteins such as spike (S) glycoprotein, nucleocapsid protein (N), small envelop protein (E) and matrix protein (M). A number of studies have been shown that CoV spike (S) glycoprotein and nucleocapsid protein (N) could be promising targets for vaccine, antibodies and therapeutic drug development to combat with deadly, pandemic SARS-CoV-2. Purposes of the present paper is the sequence analysis and amino acid variations of structural proteins deduced from novel coronavirus SARS-CoV-2 strains, isolated in different countries. Multiple sequence alignment of S, N and E proteins from four different coronavirus species, are also described. It is expected that the data from these studies will be very useful for the the designing and development of vaccines, antibodies and therapeutic agents that can be used to combat with the highly pathogenic SARS-CoV-2 coronavirus worldwide.
Sat, 2 May 2020
SHORT NOTE | doi:10.20944/preprints202005.0023.v1
Subject: Life Sciences, Other Keywords: Invasive Alien Species; Guadeloupe; Geoplanidae; Platydemus manokwari; Citizen Science
Online: 2 May 2020 (16:44:46 CEST)
The land flatworm Platydemus manokwari (Platyhelminthes, Geoplanidae) is recorded for the first time from the island of Guadeloupe (French West Indies) in the Caribbean arc. Photographs and records were obtained from citizen science and ranged from the end of 2018 to 2020; specimens were deposited in the collections of the Muséum National d'Histoire Naturelle in Paris, France. This is the first record in Guadeloupe and the second for an island in the Caribbean, after Porto Rico.
ARTICLE | doi:10.20944/preprints202005.0022.v1
Online: 2 May 2020 (16:29:38 CEST)
During December 2019, a novel coronavirus named SARS-CoV-2 has emerged in Wuhan, China. The human to human transmission of this virus has also been established. The virus has so far infected more than 2 million people and spread over 200 countries. The World Health Organization (WHO) has declared COVID-19 a global health emergency due to its spread well beyond China. It has been established that this virus originates from bats and uses an intermediate host for transfer to humans. The knowledge about the intermediate host is important to find the virus shuttle mechanism to stop future outbreaks. For this, the genetic and structural analysis of coronaviruses spike proteins was performed using a computer-assisted approach.To conduct the In silico analysis, 43 sequences of spike protein belong to different species were retrieved from the NCBI nucleotide database. Pairwise and multiple sequence alignments were performed to check the similarities and differences of the retrieved sequences. Moreover, to highlight relationships among different species, phylogenetics analysis was performed using the MEGA software tool. In the end, protein structure alignment (superimposition) was performed against the reference structure by UCSF Chimera software. The results highlighted that the maximum similarity of human protein was found against Bat and Pangolinsequences. Moreover, among Bat and Pangolin, the highest similarity was found against pangolin based on phylogenetics analysis. These results suggest that SARS-CoV-2 transfers from bats to humans through pangolins.
ARTICLE | doi:10.20944/preprints202005.0019.v1
Subject: Life Sciences, Microbiology Keywords: Barleria lupulina; cytotoxicity activity; MTT; NRU; ROS; MMP; THP-1 cell line
Online: 2 May 2020 (16:07:45 CEST)
Background: Barleria lupulina Lindl. (Hop-headed) is a small shrub, possess potent anti-inflammatory, analgesic, anti-leukemic, antitumor, anti-hyperglycemic, anti-amoebic, virucidal, diuretic, bactericidal and antibiotic properties. Methods: Cytotoxicity, bioactive assay and genetic analysis of B. lupulina were investigated in the present communication. The leaf extract was investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), Neutral red uptake (NRU), DNA fragment, reactive oxygen species (ROS) generation, mitochondrial membrane potential (MMP) assay, gene expression analysis and cDNA synthesis to evaluate anti-cancerous potency using cancerous THP-1 cell lines in vitro and in vivo. Results: HPTLC analysis reveals four spots and GC-MS analysis displayed the presence of eleven bioactive compounds among which benzofuranon, hexadecanoic acid, ethyl 9,12,15-octadecatrienoate, and 3,7,11,15-tetramethyl-2-hexadecanoic acid were the most prominent compounds. The ethanolic extract showed significant cytotoxicity (P<0.5) against THP-1 cell line at a concentration of 1mg/mL. The cells were also observed for apoptosis through DNA fragmentation in B. lupulina treated cells. Conclusions: It can be concluded that if the dose range was further refined within the range of 100-1000 µg/mL there could be dose at which the entire population of the THP-1 cell line would be apoptosis induced. The extract induced ROS in the cells after 30 minutes of exposure displaying cytotoxic effects and DNA fragmentation assay.
SHORT NOTE | doi:10.20944/preprints202005.0017.v1
Online: 2 May 2020 (15:54:19 CEST)
Maximum entropy production principle (MEPP) has been formulated in the mid-twentieth century, and today it has acquired the status of an important principle of science, which is extremely effective in considering various non-equilibrium problems. In this study, for the first time, definition of life is based on an easily measurable physical quantity that is entropy production. Life and evolution are discussed from the point of view of MEPP and the Universe, but not a human