Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance

COVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate, combined with high rates of transmission and fatality can cause a deadly world-wide pandemic in a matter of weeks.1 Apart from vaccines and post-infection treatment options, strategies for preparedness will be vital in responding to the current and future pandemics. Therefore, there is wide interest in approaches that allow predictions of increase in infections ('surges') before they occur. We describe here real time genomic surveillance particularly based on mutation analysis, of viral proteins as a methodology for a priori determination of surge in number of infection cases. The full results are available for SARS-CoV-2 at http://pandemics.okstate.edu/covid19/, and are updated daily as new virus sequences become available. This approach is generic and will also be applicable to other pathogens

Investigation of the Frequency of Foodborne Botulism in Patients Referred to Loghman Hospital in Tehran City, Iran, From 2008 to 2019

Background: Foodborne botulism is a fatal paralytic illness caused mainly by the neurotoxin produced by an anaerobic bacterium called Clostridium botulinum. In this study, the frequency of foodborne botulism in patients referred to a hospital in Iran has been reviewed for ten years.Methods: In this routine database study, medical records of patients with foodborne botulism referred to Loghman Hospital in Tehran City, Iran, from March 20, 2008, to March 20, 2019, were reviewed. Information on variables of age, sex, place of residence, food consumed, clinical symptoms of patients (such as dysphagia, nausea, vomiting, ataxia, etc.), toxin type, and length of hospitalization were collected with a researcher-made questionnaire. Finally, the collected data were analyzed in SPSS-24 with descriptive and analytical statistical tests.Results: In this study, 61 suspected botulism patients were clinically diagnosed in Loghman Hospital, of whom 55 patients were clinically suspected of foodborne botulism, 5 patients had iatrogenic botulism, and 1 patient had infant botulism. Of these 55 patients with the clinical diagnosis of foodborne botulism, 19 patients were confirmed by laboratory examinations, and 2 patients died. Sixteen patients confirmed by laboratory had neurotoxin botulinum type A. The mean age of the patients was 36.9 years with a standard deviation of 18.6 years. About 54.5% of the patients were male and 45.5% female. Weaknesses (58.2%), ptosis (droopy eyelid) (56.4%), and diplopia (double vision) (52.7%) were the common clinical symptoms of the patients under study. Canned foods and dairy products were the main foods consumed by the patients. The duration of admission time ranged between 1 and 41 days, with an average of 7.7 days. About 23.64% of patients were admitted to the intensive care unit.Conclusion: The prevalence of foodborne botulism is rare compared with other food poisonings but is still a major public health problem due to the consumption of traditional food products and unboiled canned foods in Iran

Building Natural Product Libraries Using Quantitative Clade-Based and Chemical Clustering Strategies

The success of natural product-based drug discovery is predicated on having chemical collections that offer broad coverage of metabolite diversity. We propose a simple set of tools combining genetic barcoding and metabolomics to help investigators build natural product libraries aimed at achieving predetermined levels of chemical coverage. It was found that such tools aided in identifying overlooked pockets of chemical diversity within taxa, which could be useful for refocusing collection strategies. We have used fungal isolates identified as Alternaria from a citizen-science-based soil collection to demonstrate the application of these tools for assessing and carrying out predictive measurements of chemical diversity in a natural product collection. Within Alternaria, different subclades were found to contain nonequivalent levels of chemical diversity. It was also determined that a surprisingly modest number of isolates (195 isolates) was sufficient to afford nearly 99% of Alternaria chemical features in the data set. However, this result must be considered in the context that 17.9% of chemical features appeared in single isolates, suggesting that fungi like Alternaria might be engaged in an ongoing process of actively exploring nature’s metabolic landscape. Our results demonstrate that combining modest investments in securing internal transcribed spacer (ITS)-based sequence information (i.e., establishing gene-based clades) with data from liquid chromatography-mass spectrometry (i.e., generating feature accumulation curves) offers a useful route to obtaining actionable insights into chemical diversity coverage trends in a natural product library. It is anticipated that these outcomes could be used to improve opportunities for accessing bioactive molecules that serve as the cornerstone of natural product-based drug discovery.Open Access fees paid for in whole or in part by the University of Oklahoma Libraries.Ye

Crc Is Involved in Catabolite Repression Control of the bkd Operons of Pseudomonas putida and Pseudomonas aeruginosa

Crc (catabolite repression control) protein of Pseudomonas aeruginosa has shown to be involved in carbon regulation of several pathways. In this study, the role of Crc in catabolite repression control has been studied in Pseudomonas putida. The bkd operons of P. putida and P. aeruginosa encode the inducible multienzyme complex branched-chain keto acid dehydrogenase, which is regulated in both species by catabolite repression. We report here that this effect is mediated in both species by Crc. A 13-kb cloned DNA fragment containing the P. putida crc gene region was sequenced. Crc regulates the expression of branched-chain keto acid dehydrogenase, glucose-6-phosphate dehydrogenase, and amidase in both species but not urocanase, although the carbon sources responsible for catabolite repression in the two species differ. Transposon mutants affected in their expression of BkdR, the transcriptional activator of the bkd operon, were isolated and identified as crc and vacB (rnr) mutants. These mutants suggested that catabolite repression in pseudomonads might, in part, involve control of BkdR levels. Originally published Journal of Bacteriology, Vol. 182, No. 4, Feb 200

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

Abstract\ud \ud \ud \ud Background\ud \ud Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level.\ud \ud \ud \ud Results\ud \ud The microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons.\ud \ud \ud \ud Conclusions\ud \ud The sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.We acknowledge our colleagues at the University of Oklahomas Advanced Center for Genome Technology, Chunmei Qu and Ping Wang for their assistance with 454 GSFLX sequencing sample preparation and Steve Kenton for his help with deconvoluting the pooled BACs and their subsequent assembly. We also thank Eric Tang for assistance on sequencing two BACs using Sanger sequencers. This project is supported by startup funds from the University of Illinois to RM and a grant from the Energy Bioscience Institute (EBI) to SPM, MEH, RM, and DSR.We acknowledge our colleagues at the University of Oklahoma's Advanced Center for Genome Technology, Chunmei Qu and Ping Wang for their assistance with 454 GS-FLX sequencing sample preparation and Steve Kenton for his help with deconvoluting the pooled BACs and their subsequent assembly. We also thank Eric Tang for assistance on sequencing two BACs using Sanger sequencers. This project is supported by start-up funds from the University of Illinois to RM and a grant from the Energy Bioscience Institute (EBI) to SPM, MEH, RM, and DSR

The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571

<p>Abstract</p> <p>Background</p> <p>Biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. <it>Azorhizobium caulinodans </it>ORS571 has the dual capacity to fix nitrogen both as free-living organism and in a symbiotic interaction with <it>Sesbania rostrata</it>. The host is a fast-growing, submergence-tolerant tropical legume on which <it>A. caulinodans </it>can efficiently induce nodule formation on the root system and on adventitious rootlets located on the stem.</p> <p>Results</p> <p>The 5.37-Mb genome consists of a single circular chromosome with an overall average GC of 67% and numerous islands with varying GC contents. Most nodulation functions as well as a putative type-IV secretion system are found in a distinct symbiosis region. The genome contains a plethora of regulatory and transporter genes and many functions possibly involved in contacting a host. It potentially encodes 4717 proteins of which 96.3% have homologs and 3.7% are unique for <it>A. caulinodans</it>. Phylogenetic analyses show that the diazotroph <it>Xanthobacter autotrophicus </it>is the closest relative among the sequenced genomes, but the synteny between both genomes is very poor.</p> <p>Conclusion</p> <p>The genome analysis reveals that <it>A. caulinodans </it>is a diazotroph that acquired the capacity to nodulate most probably through horizontal gene transfer of a complex symbiosis island. The genome contains numerous genes that reflect a strong adaptive and metabolic potential. These combined features and the availability of the annotated genome make <it>A. caulinodans </it>an attractive organism to explore symbiotic biological nitrogen fixation beyond leguminous plants.</p

Odor stimuli: not just chemical identity

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Phylotyping and Functional Analysis of Two Ancient Human Microbiomes

Background: The Human Microbiome Project (HMP) is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas. Methodology/Principal Findings: We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases. Conclusions/Significance: We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today

Arhodomonas sp. strain Seminole and its genetic potential to degrade aromatic compounds under high-salinity conditions

Arhodomonas sp. strain Seminole was isolated from a crude oil-impacted brine soil and shown to degrade benzene, toluene, phenol, 4-hydroxybenzoic acid (4-HBA), protocatechuic acid (PCA), and phenylacetic acid (PAA) as the sole sources of carbon at high salinity. Seminole is a member of the genus Arhodomonas in the class Gammaproteobacteria, sharing 96% 16S rRNA gene sequence similarity with Arhodomonas aquaeolei HA-1. Analysis of the genome predicted a number of catabolic genes for the metabolism of benzene, toluene, 4-HBA, and PAA. The predicted pathways were corroborated by identification of enzymes present in the cytosolic proteomes of cells grown on aromatic compounds using liquid chromatography-mass spectrometry. Genome analysis predicted a cluster of 19 genes necessary for the breakdown of benzene or toluene to acetyl coenzyme A (acetyl-CoA) and pyruvate. Of these, 12 enzymes were identified in the proteome of toluene-grown cells compared to lactate-grown cells. Genomic analysis predicted 11 genes required for 4-HBA degradation to form the tricarboxylic acid (TCA) cycle intermediates. Of these, proteomic analysis of 4-HBA-grown cells identified 6 key enzymes involved in the 4-HBA degradation pathway. Similarly, 15 genes needed for the degradation of PAA to the TCA cycle intermediates were predicted. Of these, 9 enzymes of the PAA degradation pathway were identified only in PAA-grown cells and not in lactate-grown cells. Overall, we were able to reconstruct catabolic steps for the breakdown of a variety of aromatic compounds in an extreme halophile, strain Seminole. Such knowledge is important for understanding the role of Arhodomonas spp. in the natural attenuation of hydrocarbon-impacted hypersaline environments.Peer reviewedMicrobiology and Molecular GeneticsBiochemistry and Molecular Biolog

Genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader

Anaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production.Peer reviewedMicrobiology and Molecular GeneticsBiosystems and Agricultural Engineerin