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bioRxiv2020

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

BackgroundA novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus. MethodsPutative recombination was investigated by RDP4 and Simplot v3.5.1 and discordant phylogenetic clustering in individual genomic fragments was confirmed by phylogenetic analysis using maximum likelihood and Bayesian methods. ResultsOur analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat-SARS-like coronavirus sequences. Specifically, in the 5-part spanning the first 11,498 nucleotides and the last 3-part spanning 24,341-30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat-SARS-like coronavirus sequences, whereas in the middle region spanning the 3-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch. ConclusionsThe levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention.

microbiology↗

bioRxiv2020

A global lipid map defines a network essential for Zika virus replication

Zika virus (ZIKV), an arbovirus of global concern, remodels intracellular membranes to form replication sites. How ZIKV dysregulates lipid networks to allow this, and consequences for disease, is poorly understood. Here, we performed comprehensive lipidomics to create a lipid network map during ZIKV infection. We found that ZIKV significantly alters host lipid composition, with the most striking changes seen within subclasses of sphingolipids. Ectopic expression of ZIKV NS4B protein resulted in similar changes, demonstrating a role for NS4B in modulating sphingolipid pathways. Disruption of sphingolipid biosynthesis in various cell types, including human neural progenitor cells, blocked ZIKV infection. Additionally, the sphingolipid ceramide redistributes to ZIKV replication sites and increasing ceramide levels by multiple pathways sensitizes cells to ZIKV infection. Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV infection.

microbiology↗

bioRxiv2020

A Vibrio Cholerae Core Genome Multilocus Sequence Typing Scheme to Facilitate the Epidemiological Study of Cholera

Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive dataset of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates which could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease-of-use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/). IMPORTANCEToxigenic Vibrio cholerae of the O1 and O139 serogroups are the causative agent of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing (cgMLST) scheme for V. cholerae. Using cgMLST, we established an outbreak threshold that can efficiently identify outbreak related strains and potential sources of introduction. We also defined a sublineage threshold that is similar to traditional MLST sequence type which will provide context to this new typing method by relating it to previous MLST results. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease-of-use, making this scheme the most suitable method for V. cholerae typing and surveillance worldwide.

microbiology↗

bioRxiv2020

Highly Efficient Antibiofilm and Antifungal Activity of Green Propolis against Candida species in dentistry material

BackgroundThis study evaluated the influence of green propolis extract on the adhesion and biofilm formation of Candida species on dentistry material. MethodsPhytochemical analysis of green propolis extract was performed by High Performance Liquid Chromatography. Adhesion was quantified in a Neubauer chamber, counting the number of yeast cells adhered to the fragments; Biofilm formation was determined by counting the number of colony forming units (CFU). The intensity of biofilm formation adhesion was classified as negative, weak, moderate, strong and very strong. Fifteen compounds were identified in green propolis extract, mainly flavonoids. ResultsAll strains were able to adhere and form biofilm on the surface of the orthodontic materials studied. In steel and resin, the adhesion intensity of the yeast cells was weak at all incubation times, except for C. parapsilosis and C. tropicalis which at 12hs showed moderate intensity. Regarding biofilm formation (24 and 48 hours), it was observed in the steel that C. albicans had moderate intensity at 24 and 48 hours; C. parapsilosis at 24 and 48 hours had very strong intensity; C. tropicalis at 24 hours had strong intensity and at 48 hours very strong. While in the resin, all species at 24 and 48 hours had strong intensity, except for C. tropicalis which at 48 hours had very strong intensity. Green propolis extract showed antifungal activity and was able to inhibit both adhesion and biofilm formation at 2.5 g/mL. ConclusionsThis study reinforces the idea that green propolis has antifungal activity and interferes with virulence factors of Candida species.

microbiology↗

bioRxiv2020

Antibiotic-induced DNA damage results in a controlled loss of pH homeostasis and genome instability

Extracellular pH has been assumed to play little if any role in how bacteria respond to antibiotics and antibiotic resistance development. Here, we show that the intracellular pH of Escherichia coli equilibrates to the environmental pH following antibiotic treatment. We demonstrate that this allows the environmental pH to influence the transcription of various DNA damage response genes and physiological processes such as filamentation. Using purified RecA and a known pH-sensitive mutant variant RecA K250R we show how pH can affect the biochemical activity of a protein central to control of the bacterial DNA damage response system. Finally, two different mutagenesis assays indicate that environmental pH affects antibiotic resistance development. Specifically, at environmental pHs greater than six we find that mutagenesis plays a significant role in producing antibiotic resistant mutants. At pHs less than or equal to 6 the genome appears more stable but extensive filamentation is observed, a phenomenon that has previously been linked to increased survival in the presence of macrophages.

microbiology↗

bioRxiv2020

Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota

Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 {+/-} 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.

microbiology↗

bioRxiv2020

Breaking down of the healthcare system: Mathematical modelling for controlling the novel coronavirus (2019-nCoV) outbreak in Wuhan, China

A novel coronavirus pneumonia initially identified in Wuhan, China and provisionally named 2019-nCoV has surged in the public. In anticipation of substantial burdens on healthcare system following this human-to-human spread, we aim to scrutinise the currently available information and evaluate the burden of healthcare systems during this outbreak in Wuhan. We applied a modified SIR model to project the actual number of infected cases and the specific burdens on isolation wards and intensive care units, given the scenarios of different diagnosis rates as well as different public health intervention efficacy. Our estimates suggest the actual number of infected cases could be much higher than the reported, with estimated 26,701 cases (as of 28th January 2020) assuming 50% diagnosis rate if no public health interventions were implemented. The estimated burdens on healthcare system could be largely reduced if at least 70% efficacy of public health intervention is achieved.

microbiology↗

bioRxiv2020

Integrin β3, a RACK1 interacting protein, is required for porcine reproductive and respiratory syndrome virus infection and NF-κB activation in Marc-145 cells

Porcine reproductive and respiratory syndrome virus (PRRSV) is the pathogen of porcine reproductive and respiratory syndrome (PRRS), which is one of the most economically harmful diseases in modern pig production worldwide. Receptor of activated protein C kinase 1 (RACK1) was previously shown to be indispensable for the PRRSV replication and NF-{kappa}B activation in Marc-145 cells. Here we identified a membrane protein, integrin {beta}3 (ITGB3), as a RACK1-interacting protein. PRRSV infection in Marc-145 cells upregulated the ITGB3 expression. Abrogation of ITGB3 by siRNA knockdown or antibody blocking inhibited PRRSV infection and NF-{kappa}B activation, while on the other hand, overexpression of ITGB3 enhanced PRRSV infection and NF-{kappa}B activation. Furthermore, inhibition of ITGB3 alleviated the cytopathic effects and reduced the TCID50 titer in Marc-145 cells. We also showed that RACK1 and ITGB3 were NF-{kappa}B target genes during PRRSV infection, and that they regulate each other. Our data indicate that ITGB3, presumably as a co-receptor, plays an imperative role for PRRSV infection and NF-{kappa}B activation in Marc-145 cells. PRRSV infection activates a positive feedback loop involving the activation of NF-{kappa}B and upregulation of ITGB3 and RACK1 in Marc-145 cells. The findings would advance our elaborated understanding of the molecular host-pathogen interaction mechanisms underlying PRRSV infection in swine and suggest ITGB3 and NF-{kappa}B signaling pathway as potential therapeutic targets for PRRS control. IMPORTANCEPorcine reproductive and respiratory syndrome virus (PRRSV) is one of the pathogens in pig production worldwide. Several cell surface receptors, such as heparan sulphate, sialoadhesin, vimentin and CD163, were identified to be involved in PRRSV infection in porcine alveolar macrophages (PAMs). We identified a cell surface protein, integrin {beta}3 (ITGB3), as an interacting protein with receptor of activated protein C kinase 1 (RACK1) from Marc-145 cells. ITGB3 interacts with RACK1 and facilitates PRRSV infection and NF-{kappa}B activation in Marc-145 cells, presumably as a co-receptor of CD136 or vimentin. Both ITGB3 and RACK1 were NF-{kappa}B target genes, and they regulate each other. The activation of NF-{kappa}B and the transcription of its downstream genes are beneficial for PRRSV infection/replication. The novel findings would advance our elaborated understanding of the molecular host-pathogen interaction mechanisms underlying PRRSV infection in swine and suggest ITGB3-RACK1-NF-{kappa}B axis as a potential therapeutic target for PRRS control.

microbiology↗

bioRxiv2020

A mutant RNA polymerase activates the general stress response, enabling E. coli adaptation to late prolonged stationary phase

Escherichia coli populations undergo repeated replacement of parental genotypes with fitter variants deep in stationary phase. We isolated one such variant, which emerged after three weeks o of maintaining an E. coli K12 population in stationary phase. This variant displayed a small colony phenotype, slow growth and was able to outcompete its ancestor over a narrow time window in stationary phase. The variant also shows tolerance to beta-lactam antibiotics, though not previously exposed to the antibiotic. We show that an RpoC (A494V) mutation confers the slow growth and small colony phenotype to this variant. The ability of this mutation to confer a growth advantage in stationary phase depends on the availability of the stationary phase sigma factor {sigma}S. The RpoC (A494V) mutation up-regulates the {sigma}S regulon. As shown over 20 years ago, early in prolonged stationary phase, {sigma}S attenuation, but not complete loss of activity, confers a fitness advantage. Our study shows that later mutations enhance {sigma}S activity, either by mutating the gene for {sigma}S directly, or via mutations such as RpoC (A494V). The balance between the activities of the housekeeping major sigma factor and {sigma}S sets up a trade-off between growth and stress tolerance, which is tuned repeatedly during prolonged stationary phase. ImportanceAn important general mechanism of bacterial adaptation to its environment involves adjusting the balance between growing fast, and tolerating stresses. One paradigm where this plays out is in prolonged stationary phase: early studies showed that attenuation, but not complete elimination, of the general stress response enables early adaptation of the bacterium E. coli to the conditions established about 10 days into stationary phase. We show here that this balance is not static and that it is tilted back in favour of the general stress response about two weeks later. This can be established by direct mutations in the master regulator of the general stress response, or by mutations in the core RNA polymerase enzyme itself. These conditions can support the development of antibiotic tolerance though the bacterium is not exposed to the antibiotic. Further exploration of the growth-stress balance over the course of stationary phase will necessarily require a deeper understanding of the events in the extracellular milieu.

microbiology↗

bioRxiv2020

Functional characterization of clinical isolates of the opportunistic fungal pathogen Aspergillus nidulans

Aspergillus nidulans is an opportunistic fungal pathogen in patients with immunodeficiency and virulence of A. nidulans isolates has mainly been studied in the context of the chronic granulomatous disease (CGD), with characterization of clinical isolates obtained from non-CGD patients remaining elusive. This study therefore carried out a detailed biological characterization of two A. nidulans clinical isolates (CIs), obtained from a patient with breast carcinoma and pneumonia and from a patient with cystic fibrosis that underwent lung transplantation, and compared them to the reference, non-clinical A4 strain. Both CIs presented increased growth in comparison to the reference strain in the presence of physiologically-relevant carbon sources. Metabolomic analyses showed that the three strains are metabolically very different from each other in these carbon sources. Furthermore, the CIs were highly susceptible to cell wall perturbing agents but not to other physiologically-relevant stresses. Genome analyses identified several frame-shift variants in genes encoding cell wall integrity (CWI) signalling components. Significant differences in CWI signalling were confirmed by western blotting among the three strains. In vivo virulence studies using several different models revealed that strain MO80069 had significantly higher virulence in hosts with impaired neutrophil function when compared to the other strains. In summary, this study presents detailed biological characterization of two A. nidulans sensu stricto clinical isolates. Just like in A. fumigatus, strain heterogeneity exists in A. nidulans clinical strains that can define virulence traits. Further studies are required to fully characterize A. nidulans strain-specific virulence traits and pathogenicity. ImportanceImmunocompromised patients are susceptible to infections with opportunistic filamentous fungi from the genus Aspergillus. Although A. fumigatus is the main etiological agent of Aspergillus spp.-related infections, other species, such as A. nidulans are prevalent in a condition-specific manner. A. nidulans is a predominant infective agent in patients suffering from chronic granulomatous disease (CGD). A. nidulans isolates have mainly been studied in the context of CGD, although infection with A. nidulans also occurs in non-CGD patients. This study carried out a detailed biological characterization of two non-CGD A. nidulans clinical isolates and compared it to a reference strain. Phenotypic, metabolomic and genomic analyses highlight fundamental differences in carbon source utilization, stress responses and maintenance of cell wall integrity among the strains. One clinical strain had increased virulence in models with impaired neutrophil function. Just as in A. fumigatus, strain heterogeneity exists in A. nidulans clinical strains that can define virulence traits.

microbiology↗

bioRxiv2020

Composition of the North American wood frog (Rana sylvatica) skin microbiome and seasonal variation in community structure

While a number of amphibian microbiomes have been characterized, it is unclear how microbial communities might vary in response to seasonal changes in the environment and the behaviors which many amphibians exhibit. Given recent studies demonstrating the importance of the skin microbiome in frog innate immune defenses against pathogens, investigating how changes in the environment impact the microbial species present, and thus their potential contribution to skin host defense, will provide a better understanding of conditions that may alter host susceptibility to pathogens in their environment. We sampled the skin microbiome of North American wood frogs (Rana sylvatica) from two breeding ponds in the spring, along with the microbial community present in their vernal breeding pools, and frogs from the nearby forest floor in the summer and fall to determine whether the microbial composition differs by sex, vernal pond site, or temporally across season (spring, summer, fall). Taxon abundance data reveals a profile of bacterial phyla similar to those previously described on anuran skin, with Proteobacteria, Bacteroidetes, and Actinobacteria dominating the wood frog skin microbiome. Our results indicate that sex had no significant effect on skin microbiota diversity, however, this may be due to our limited female sample size. Vernal pool site had a small but significant effect on skin microbiota, but skin-associated communities were more similar to each other than to the communities observed in the frogs respective pond water. Across seasons, diversity analyses suggest there are significant differences between the skin microbiome of frogs from spring and summer/fall groups while the average -diversity per frog remained consistent. Bacterial genera known to have antifungal properties such as Pseudomonas spp. and Rhizobium spp. were prevalent, and several were considered core microbiota during at least one season. These results illustrate seasonal variation in wood frog skin microbiome structure and highlight the importance of considering temporal trends in an amphibian microbiome, particularly for species whose life history requires recurrent shifts in habitat and behavior.

microbiology↗

bioRxiv2020

Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome

Horizontal Gene Transfer, the process by which bacteria acquire new genes and functions from non-parental sources, is common in the human microbiome 1,2. If the timescale of HGT is rapid compared to the timescale of human colonization, then it could have the effect of personalizing bacterial genomes by providing incoming strains with the genes necessary to adapt to the diet or lifestyle of a new host. The extent to which HGT occurs on the timescale of human colonization, however, remains unclear. Here, we analyzed 6,188 newly isolated and sequenced gut bacteria from 34 individuals in 9 human populations, and show that HGT is more common among bacteria isolated from the same human host, indicating that the timescale of transfer is short compared to the timescale of human colonization. Comparing across 9 human populations reveals that high rates of transfer may be a recent development in human history linked to industrialization and urbanization. In addition, we find that the genes involved in transfer reflect the lifestyle of the human hosts, with elevated transfer of carbohydrate metabolism genes in hunter gatherer populations, and transfer of antibiotic resistance genes among pastoralists who live in close contact with livestock. These results suggest that host-associated bacterial genomes are not static within individuals, but continuously acquire new functionality based on host diet and lifestyle.

microbiology↗

bioRxiv2020

Polarization of microbial communities between competitive and cooperative metabolism

Resource competition and metabolic cross-feeding are among the main drivers of microbial community assembly. Yet, the degree to which these two conflicting forces are reflected in the composition of natural communities has not been systematically investigated. Here, we use genome-scale metabolic modeling to assess resource competition and metabolic cooperation potential in large co-occurring groups, with up to 40 member species, across thousands of habitats. Our analysis revealed two distinct community types, clustering at opposite ends in a trade-off landscape between competition and cooperation. On one end lie highly cooperative communities, characterized by smaller genomes and multiple auxotrophies, reminiscent of the black queen hypothesis. At the other end lie highly competitive communities, conforming to the red queen hypothesis, featuring larger genomes and overlapping nutritional requirements. While the latter are mainly present in soils, the former are found both in free-living and host-associated habitats. Community-scale flux simulations showed that, while the competitive communities can better resist species invasion but not nutrient shift, the cooperative communities are susceptible to species invasion but resilient to nutrient change. In accord, we show, through analyzing an additional independent dataset, the colonization of the human gut by probiotic species is positively associated with the presence of cooperative species in the recipient microbiome. Together, our analysis highlights the bifurcation between competition and cooperation in the assembly of natural communities and its implications for community modulation.

microbiology↗

bioRxiv2020

Vaccination with Schistosoma mansoni cholinesterases reduces parasite burden and egg viability in a mouse model of schistosomiasis

Schistosomiasis is a neglected tropical disease which kills 300,000 people every year in developing countries and there is no vaccine. Recently, we have shown that cholinesterases (ChEs) - enzymes that regulate neurotransmission - from Schistosoma mansoni are expressed on the tegument and present in the excretory/secretory products of schistosomula and adult worms, and are essential for parasite survival in the definitive host, highlighting their utility as potential schistosomiasis vaccine targets. When treated in vitro with anti-SmChE IgG, both schistosomula and adult worms displayed significantly decreased ChE activity, which eventually resulted in parasite death. Vaccination with individual SmChEs, or a combination of all three SmChEs, significantly reduced worm burdens in two independent trials compared to controls. Liver egg burdens were significantly decreased for all vaccinated mice across both trials (13% - 46%) except for those vaccinated with SmAChE1 in trial 1. Egg viability, as determined by egg hatching from liver homogenates, was significantly reduced in the groups vaccinated with the SmChE cocktail (40%) and SmAChE2 (46%). Further, surviving worms from each vaccinated group were significantly stunted and depleted of glycogen stores, compared to controls. These results suggest that SmChEs could be incorporated into a vaccine against schistosomiasis to reduce the pathology and transmission of this debilitating disease.

microbiology↗

bioRxiv2020

Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak.

In genome evolution, genetic variants are the source of diversity, which natural selection acts upon. Treatment of human tuberculosis (TB) induces a strong selection pressure for the emergence of antibiotic resistance in the infecting Mycobacterium tuberculosis (MTB) strains. MTB evolution in response to treatment has been intensively studied and mainly attributed to point substitutions. However, the contribution of insertions and deletions (indels) to MTB genome evolution remains poorly understood. Here, we analyzed a multi-drug resistant MTB outbreak for the presence of high-quality indels and substitutions. We find that indels are significantly enriched in genes conferring antibiotic resistance. Furthermore, we show that indels are inherited during the outbreak and follow a molecular clock with an evolutionary rate of 5.37e-9 indels/site/year, which is 23x lower compared to the substitution rate. Inherited indels may co-occur with substitutions in genes along related biological pathways; examples are iron storage and resistance to second-line antibiotics. This suggests that epistatic interactions between indels and substitutions affect antibiotic resistance and compensatory evolution in MTB. Author summaryMycobacterium tuberculosis (MTB) is a human pathogen causing millions of deaths every year. Its genome evolution has been intensively characterized through point substitutions, i.e., nucleotide exchanges that are inherited. Additional mutations are short or long insertions and deletions of nucleotides, termed indels. Short indels in genes might change the reading frame and disrupt the gene product. Here we show that antibiotic treatment has a strong impact on indel evolution in an MTB outbreak. Namely, indels occur frequently in genes causing antibiotic resistance upon disruption. Furthermore, we show that the molecular clock, i.e., the temporal emergence of variants over time, holds for short indels in MTB genomes. Finally, we observe that indels may co-occur with substitutions in genes along related biological pathways. These results support the notion that indels are important contributors to MTB evolution. We anticipate that including indels in the analyses of MTB outbreaks will improve our understanding of antibiotic resistance evolution.

microbiology↗

bioRxiv2020

Rethinking the role of lipids in lager yeast cell during beer fermentation from a transcriptome and systems biology perspective

Brewing lager yeast (Saccharomyces pastorianus) is exposed to stressful conditions during beer fermentation, including ethanol toxicity. In response to ethanol toxicity, various biological mechanisms are modulated, including lipid biosynthesis. It is well known that during beer fermentation, the composition of yeast membranes changes in response to ethanol toxicity, making it less fluid and permeable. Additionally, neutral lipids and lipid droplets (LDs) are produced in response to ethanol toxicity. LDs are membranous organelles that transport lipids and proteins, acting as hubs for inter-organellar communication and modulating the activity of mechanisms necessary for ethanol tolerance, such as proteostasis and autophagy. Unfortunately, little is known about the interplay between autophagy, lipid metabolism, and proteostasis (ALP) in lager cells during beer fermentation. Therefore, transcriptome analyses using publicly available DNA microarray data obtained from lager yeast cells were used to identify all the ALP-associated genes that were upregulated during beer fermentation compared to yeast biomass propagation. Thereafter, a top-down systems biology analysis was applied, involving constructing an ALP-associated shortest-pathway protein-protein interaction network (ALP network), identifying important nodes and communities within the ALP network, and identifying the overrepresented biological processes and cellular components using a Gene Ontology (GO) analysis. The transcriptome analyses indicated the upregulation of 204 non-redundant ALP-associated genes during beer fermentation, whose respective proteins interact in the shortest-pathway ALP network. Thirteen communities were selected from the ALP network, and they were associated with multiple overrepresented GO biological processes and cellular components, such as mitophagy, cytoplasm-to-vacuole transport, piecemeal microautophagy of the nucleus, endoplasmic reticulum (ER) stress, ergosterol and lipid biosynthesis, LDs, ER membrane, and phagophore assembly. These results indicate that ethanol tolerance in lager yeasts could be due to the modulation of proteostasis and various forms of autophagy by lipid biosynthesis and LDs, thus highlighting the importance of lipids for beer fermentation.

microbiology↗

bioRxiv2020

Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody

The newly identified 2019 novel coronavirus (2019-nCoV) has caused more than 800 laboratory-confirmed human infections, including 25 deaths, posing a serious threat to human health. Currently, however, there is no specific antiviral treatment or vaccine. Considering the relatively high identity of receptor binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS-CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Here, we report for the first time that a SARS-CoV-specific human monoclonal antibody, CR3022, could bind potently with 2019-nCoV RBD (KD of 6.3 nM). The epitope of CR3022 does not overlap with the ACE2 binding site within 2019-nCoV RBD. Therefore, CR3022 has the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-nCoV infections. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g., m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, indicating that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD.

microbiology↗

bioRxiv2020

Beware of asymptomatic transmission: Study on 2019-nCoV prevention and control measures based on extended SEIR model

BackgroundThe 2019 new coronavirus, "2019-nCoV", was discovered from Wuhan Viral Pneumonia cases in December 2019, and was named by the World Health Organization on January 12, 2020. In the early stage, people knows little about the 2019-nCoV virus was not clear, and the spread period was encountering Chinas annual spring migration, which made the epidemic spread rapidly from Wuhan to almost all provinces in China. MethodsThis study builds a SEIRD model that considers the movement of people across regions, revealing the effects of three measures on controlling the spread of the epidemic.Based on MATLAB R2017a, computational experiments were performed to simulate the epidemic prevention and control measures. FindingsThe research results show that current prevention and control measures in China are very necessary. This study further validates the concerns of international and domestic experts regarding asymptomatic transmission (E-status). InterpretationThe results of this study are applicable to explore the impact of the implementation of relevant measures on the prevention and control of epidemic spread, and to identify key individuals that may exist during the spread of the epidemic.

microbiology↗