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Background: The question of whether the coronavirus genome contain as-yetununderstood genetic component. Purpose (Objective): Elucidate the novel functions of the discovered tRNA-like base sequence and lead to the development of novel therapeutic agents. Methods: A novel tRNA-like base sequence was found in the sequences complementary to the genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-CoV. By comparing mutations in the tRNA-like base sequences of these two viruses, it was found that base pairing in the cloverleaf model of SARS-CoV-2 was more robust than that of SARS-CoV. Results: The results of homology search between a short sequence of the coronavirus tRNA-like base sequence and human genes suggest that the molecule produced by this novel tRNA-like sequence may be involved in the splicing of human messenger RNA. Conclusions: Experimental molecular evidence of the tRNA-like base sequence discovered in this study is urgently needed. [ABSTRACT FROM AUTHOR]

Rotaviruses are a major cause of diarrhea in young children, causing an estimated 215,000 deaths worldwide every year (1). These viruses are nonenveloped and have a genome consisting of 11 [...]

Despite innovations in HIV prevention and treatment, HIV outbreaks do occur in the United States. Local public health staff identified >200 persons with HIV resulting from an injection drug use [...]

Denisova Cave in the Siberian Altai (Russia) is a key site for understanding the complex relationships between hominin groups that inhabited Eurasia in the Middle and Late Pleistocene epoch. DNA sequenced from human remains found at this site has revealed the presence of a hitherto unknown hominin group, the Denisovans.sup.1,2, and high-coverage genomes from both Neanderthal and Denisovan fossils provide evidence for admixture between these two populations.sup.3. Determining the age of these fossils is important if we are to understand the nature of hominin interaction, and aspects of their cultural and subsistence adaptations. Here we present 50 radiocarbon determinations from the late Middle and Upper Palaeolithic layers of the site. We also report three direct dates for hominin fragments and obtain a mitochondrial DNA sequence for one of them. We apply a Bayesian age modelling approach that combines chronometric (radiocarbon, uranium series and optical ages), stratigraphic and genetic data to calculate probabilistically the age of the human fossils at the site. Our modelled estimate for the age of the oldest Denisovan fossil suggests that this group was present at the site as early as 195,000 years ago (at 95.4% probability). All Neanderthal fossils--as well as Denisova 11, the daughter of a Neanderthal and a Denisovan.sup.4--date to between 80,000 and 140,000 years ago. The youngest Denisovan dates to 52,000-76,000 years ago. Direct radiocarbon dating of Upper Palaeolithic tooth pendants and bone points yielded the earliest evidence for the production of these artefacts in northern Eurasia, between 43,000 and 49,000 calibrated years before present (taken as ad 1950). On the basis of current archaeological evidence, it may be assumed that these artefacts are associated with the Denisovan population. It is not currently possible to determine whether anatomically modern humans were involved in their production, as modern-human fossil and genetic evidence of such antiquity has not yet been identified in the Altai region.Bayesian modelling of chronometric, stratigraphic and genetic data from Denisova Cave provides a chronological framework for understanding Neanderthal and Denisovan presence at the site, as well as interactions between these groups., Author(s): Katerina Douka [sup.1] [sup.2] , Viviane Slon [sup.3] , Zenobia Jacobs [sup.4] [sup.5] , Christopher Bronk Ramsey [sup.2] , Michael V. Shunkov [sup.6] [sup.7] , Anatoly P. Derevianko [sup.6] [...]

Chironomid flies (non-biting midges) are among the most abundant and diverse animals in Arctic regions, but detailed analyses of species distributions and biogeographical patterns are hampered by challenging taxonomy and reliance on morphology for species-level identification. Here we take advantage of available DNA barcode data of Arctic Chironomidae in BOLD to analyse similarities in species distributions across a northern Nearctic--West Palearctic gradient. Using more than 260 000 barcodes representing 4666 BINs (Barcode Index Numbers) and 826 named species (some with interim names) from a combination of public and novel data, we show that the Greenland chironomid fauna shows affinities to both the Nearctic and the West Palearctic regions. While raw taxon counts indicate a strong Greenland--North American affinity, comparisons using Chao's dissimilarity metric support a slightly higher similarity between Greenland and West Palearctic chironomid communities. Results were relatively consistent across different definitions of species taxonomic units, including morphologically determined species, BINs, and superBINs based on a ~4.5% threshold. While most taxa found in Greenland are shared with at least one other region, reflecting circum-Arctic dispersal, our results also reveal that Greenland harbours a small endemic biodiversity. Our exploratory study showcases how DNA barcoding efforts using standardized gene regions contribute to an understanding of broad-scale patterns in biogeography by enabling joint analysis of public DNA sequence data derived from diverse prior studies.Key words: Diptera, zoogeography, biogeography, Canada, Norway, Svalbard.Les chironomides (moucherons non-piqueurs) sont parmi les animaux les plus abondants et diversifies dans les regions arctiques, mais des analyses detaillees des distributions de ces especes et de leur repartition biogeographique sont entravees par une taxonomie difficile et une dependance a la morphologie pour l'identification des especes. Ici, les auteurs tirent profit des donnees disponibles en matiere de codes a barres de l'ADN pour les chironomides arctiques au sein de la base de donnees BOLD pour analyser les similarites pour ce qui est des distributions des especes au long d'un gradient nordique Nearctique-Palearctique occidental. Au moyen de plus de 260 000 codes a barres representant 4666 BIN (<< Barcode Index Numbers >>) et 826 especes nommees (dont certaines de maniere interimaire) a partir d'une combinaison de donnees publiques et inedites, les auteurs montrent que la faune des chironomides du Groenland montre des ressemblances a la fois avec celles des regions Nearctique et Palearctique occidentale. Bien que des decomptes bruts indiquent une grande affinite Groenland--Amerique du Nord, des comparaisons a l'aide de l'indice de dissimilarite de Chao suggerent une similarite legerement plus elevee entre les communautes du Groenland et du Palearctique occidental. Les resultats etaient relativement coherents en faisant appel a diverses definitions des unites taxonomiques specifiques, incluant les especes definies sur une base morphologique, des BIN et des superBIN a un seuil de 4,5%. Bien que la plupart des taxons du Groenland soient partages avec au moins une autre region, ce qui reflete une distribution circum-arctique, les resultats revelent aussi que le Groenland recele une petite biodiversite endemique. Cette etude exploratoire demontre comment les efforts en matiere de codage a barres au moyen de regions geniques standardisees contribuent a la comprehension de la biogeographie a grande echelle en rendant possible l'analyse conjointe de donnees moleculaires publiques derivees de diverses etudes anterieures. [Traduit par la Redaction]Mots-cles: Diptera, zoogeographie, biogeographie, Canada, Norvege, Svalbard., IntroductionThe Arctic is home to about 21000 described species, many of which are specifically adapted to a cold climate (CAFF 2013). As this diversity is under pressure from several sources, [...]

Three tools have transformed biotechnology over the past decade and a half. Gene reading has made it possible to quickly sequence the genome of any living creature. Gene synthesis has [...]

The increasing availability of DNA sequence data and access to sophisticated bioinformatic algorithms mean that an unbiased bioinformatics-based assessment of the predicted impact of a genomic variant is rapidly available. [...]

Histone post-translational modifications (PTMs) are associated with epigenetic states that form the basis for cell-type-specific gene expression.sup.1,2. Once established, histone PTMs can be maintained by positive feedback involving enzymes that recognize a pre-existing histone modification and catalyse the same modification on newly deposited histones. Recent studies suggest that in wild-type cells, histone PTM-based positive feedback is too weak to mediate epigenetic inheritance in the absence of other inputs.sup.3-7. RNA interference (RNAi)-mediated histone H3 lysine 9 methylation (H3K9me) and heterochromatin formation define a potential epigenetic inheritance mechanism in which positive feedback involving short interfering RNA (siRNA) amplification can be directly coupled to histone PTM positive feedback.sup.8-14. However, it is not known whether the coupling of these two feedback loops can maintain epigenetic silencing independently of DNA sequence and in the absence of enabling mutations that disrupt genome-wide chromatin structure or transcription.sup.15-17. Here, using the fission yeast Schizosaccharomyces pombe, we show that siRNA-induced H3K9me and silencing of a euchromatic gene can be epigenetically inherited in cis during multiple mitotic and meiotic cell divisions in wild-type cells. This inheritance involves the spreading of secondary siRNAs and H3K9me3 to the targeted gene and surrounding areas, and requires both RNAi and H3K9me, suggesting that the siRNA and H3K9me positive-feedback loops act synergistically to maintain silencing. By contrast, when maintained solely by histone PTM positive feedback, silencing is erased by H3K9 demethylation promoted by Epe1, or by interallelic interactions that occur after mating to cells containing an expressed allele even in the absence of Epe1. These findings demonstrate that the RNAi machinery can mediate transgenerational epigenetic inheritance independently of DNA sequence or enabling mutations, and reveal a role for the coupling of the siRNA and H3K9me positive-feedback loops in the protection of epigenetic alleles from erasure. In Schizosaccharomyces pombe, histone H3K9 methylation acts synergistically with short interfering RNA to perpetuate gene silencing during multiple mitotic and meiotic cell divisions., Author(s): Ruby Yu [sup.1] , Xiaoyi Wang [sup.1] , Danesh Moazed [sup.1] Author Affiliations: (1) Department of Cell Biology and Howard Hughes Medical Institute, Harvard Medical School, Boston, USA Main [...]

Objectives: To characterize the structure of a variant of Acinetobacter genomic island 1 (AGI1) in the Enterobacter cloacae clinical isolate EclC2185 responsible for an 8 year outbreak in Dijon University Hospital.Methods: The genome was sequenced (Miseq) and de novo assembled (Velvet). PCR and Sanger sequencing were performed to determine the sequence of the genomic island.Results: The new variant of AGI1 named AGI1-A (41.7 kb), located at the 3' end of the chromosomal trmE, was detected in an E. cloacae complex isolate identified as Enterobacter hormaechei subsp. oharae. The backbone of AGI1-A lacked A008, part of A025, A026 and the resolvase gene. Its MDR region (19.7 kb) contained two integrons followed by a hybrid transposon Tn502/Tn5053. The former integron was a typical In4-type class 1 integron carrying aadA1 and the latter integron carrying dfrA1 did not belong to a class described to date. The nucleotide sequence intI-dfrA1 was surrounded by a 78 bp imperfect repeat sequence in inverse orientation. An external circular form of AGI1-A was detected, suggesting potential mobility. AGI1-A was also detected in 15 isolates from the outbreak selected at random. They belonged to the ST114 high-risk clone.Conclusions: AGI1-A, a variant of AGI1 described in Acinetobacter baumannii, is the first genomic resistance island belonging to the Salmonella genomic island/Proteus genomic island/Acinetobacter genomic island family detected in E. cloacae. One might, therefore, fear for interspecies dissemination of genomic islands from this family. [ABSTRACT FROM AUTHOR]

Objectives: To provide detailed genetic characterization of four novel blaIMP-carrying transposons from Pseudomonas aeruginosa, Klebsiella pneumoniae and an Enterobacter sp.Methods: P. aeruginosa 60512, K. pneumoniae 447, P. aeruginosa 12939 and Enterobacter sp. A1137 were subjected to genome sequencing. The complete nucleotide sequences of two plasmids (p60512-IMP from the 60512 isolate and p447-IMP from the 447 isolate) and two chromosomes (the 12939 and A1137 isolates) were determined, then a genomic comparison of p60512-IMP, p447-IMP and four novel blaIMP-carrying transposons (Tn6394, Tn6375, Tn6411 and Tn6397) with related sequences was performed. Transferability of the blaIMP gene and bacterial antimicrobial susceptibility were tested.Results: Tn6394 and Tn6375 were located in p60512-IMP and p447-IMP, respectively, while Tn6411 and Tn6397 were integrated into the 12939 and A1137 chromosomes, respectively. Tn6394 was an ISPa17-based transposition unit that harboured the integron In992 (carrying blaIMP-1). In73 (carrying blaIMP-8), In73 and In992, together with the ISEcp1:IS1R-blaCTX-M-14-IS903D unit, the macAB-tolC region and the truncated aacC2-tmrB region, respectively, were integrated into the prototype transposons Tn1722, Tn1696 and Tn7, respectively, generating the Tn3-family unit transposons, Tn6375 and Tn6378, and the Tn7-family unit transposon Tn6411, respectively. Tn6397 was a large integrative and conjugative element carrying Tn6378.Conclusions: Complex events of transposition and homologous recombination have occurred during the original formation and further plasmid and chromosomal integration of these four transposons, promoting accumulation and spread of antimicrobial resistance genes. [ABSTRACT FROM AUTHOR]

Background: Despite the clear role of the Nkx2-5 gene mutations as the trigger for Congenital Heart Disease (CHD) in different populations, the condition of these mutations in our population remains obscure. Objectives: The present study aimed to assess different Nkx2-5 gene mutations in a sample of Iranian patients with CHD. Patients and Methods: This cross-sectional study was conducted on 79 consecutive suspected non-syndromic CHD patients at Rajaie Cardiovascular Medical and Research Center between 2016 and 2017. Detailed clinical evaluations were performed and CHD was confirmed by echocardiography. The exons of the Nkx2-5 gene were sequenced. In silico analysis was done using Mutation taster, SNP nexus, and Vienna RNA package. In addition, statistical analysis was performed using the SPSS statistical software, version 16.0. P ≤ 0.05 was considered to be statistically significant. Results: The study results revealed four synonymous polymorphisms; i.e., rs2277923, rs703752, rs3729753, and c.217C > T, the last of which was novel. Regarding the frequency of different Single Nucleotide Polymorphism (SNP) genotypes, the overall frequency of wild, heterozygous, and mutant genotypes was respectively 65.8%, 31.6%, and 2.5% for rs2277923, 54.4%, 0.0%, and 45.6% for rs703752, 96.2%, 3.8%, and 0.0% for rs3729753, and 93.7%, 6.3%, and 0.0% for c.217 C > T. Bioinformatics analysis demonstrated that the detected novel variants were not pathogens. Moreover, the genotypic variants of all SNPs were independent of gender, type of heart defect, and hereditary form of the disease. Conclusions: The results could not show any major roles for different exon-related SNPs on the Nkx2-5 gene as the candidate risk profile for CHD. The results also demonstrated no significant associations between such mutations and increased likelihood of specific heart defects. [ABSTRACT FROM AUTHOR]

The virus family Filoviridae is divided into 5 genera: Cuevavirus, Marburgvirus, Ebolavirus, Striavirus, and Thamnovirus (https://talk.ictvonline.org/taxonomy). Six distinct members of Ebolavirus have been described; 4 are known to cause human [...]

High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process. In this paper, we propose an R-based RNA-Seq analysis pipeline called TRAPR, an integrated tool that facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization, transformation, statistical analysis, data visualization, and result visualization that allow researchers to build customized analysis pipelines.

Background One of the most significant public health concerns in today's world is the persistent upsurge of infections caused by multidrug resistant bacteria. As a result, clinicians are being forced to intervene with either less effective backup drugs or ones with substantial side-effects. Colistin is a last resort antimicrobial agent for the treatment of infections caused by multi-drug resistant gram-negative bacteria. Methods Escherichia coli (n = 65) isolated from street food (n = 20), hand rinse (n = 15), surface water (n = 10), and healthy human stool (n = 20) were tested for colistin resistance gene mcr-1 and response to antimicrobial agents. Antimicrobial resistance genes and virulence genes were detected by employing polymerase chain reaction. DNA fingerprinting of the strains were determined by pulsed-field gel electrophoresis. Results Screening of E. coli allowed us to confirm colistin resistance marker gene mcr-1 in 13 strains (street food, n = 4; hand rinse, n = 2; surface water, n = 4; and stool, n = 3); and two of these E. coli strains carrying mcr-1 harbored bla.sub.TEM gene encoding extended spectrum beta lactamase. Antibiotic assay results revealed all 13 E. coli strains carrying mcr-1 to be multi-drug resistant (MDR), including to colistin. The minimum inhibitory concentration (MIC) for colistin ranged from 2 to 6 [mu]g/ml. DNA sequencing confirmed homogeneity of the nucleotide sequence for mcr-1, but the E. coli strains were heterogenous, as confirmed by pulsed-field gel electrophoresis suggesting horizontal transmission of colistin resistance in Bangladesh. Conclusion Widespread dissemination of E. coli strains carrying mcr-1 encoding resistance to colistin in the present study is alarming as this is the last resort drug for the treatment of infections caused by MDR gram-negative bacteria resistant to almost all drugs used commonly. Keywords: Colistin, mcr-1, ESBL, Multi-drug resistant (MDR), Minimum inhibitory concentration (MIC), Horizontal transmission, Author(s): Fatema-Tuz Johura[sup.1], Jarin Tasnim[sup.1], Indrajeet Barman[sup.1], Sahitya Ranjan Biswas[sup.1], Fatema Tuz Jubyda[sup.1], Marzia Sultana[sup.1], Christine Marie George[sup.2], Andrew Camilli[sup.3], Kimberley D. Seed[sup.4], Niyaz Ahmed[sup.1] and Munirul Alam[sup.1] Background Antimicrobial [...]

Background Lifestyle interventions to reduce body mass index (BMI) are critical public health strategies for type 2 diabetes prevention. While weight loss interventions have shown demonstrable benefit for high-risk and prediabetic individuals, we aimed to determine whether the same benefits apply to those at lower risk. Methods and findings We performed a multi-stratum Mendelian randomization study of the effect size of BMI on diabetes odds in 287,394 unrelated individuals of self-reported white British ancestry in the UK Biobank, who were recruited from across the United Kingdom from 2006 to 2010 when they were between the ages of 40 and 69 years. Individuals were stratified on the following diabetes risk factors: BMI, diabetes family history, and genome-wide diabetes polygenic risk score. The main outcome measure was the odds ratio of diabetes per 1-kg/m.sup.2 BMI reduction, in the full cohort and in each stratum. Diabetes prevalence increased sharply with BMI, family history of diabetes, and genetic risk. Conversely, predicted risk reduction from weight loss was strikingly similar across BMI and genetic risk categories. Weight loss was predicted to substantially reduce diabetes odds even among lower-risk individuals: for instance, a 1-kg/m.sup.2 BMI reduction was associated with a 1.37-fold reduction (95% CI 1.12-1.68) in diabetes odds among non-overweight individuals (BMI < 25 kg/m.sup.2) without a family history of diabetes, similar to that in obese individuals (BMI [greater than or equal to] 30 kg/m.sup.2) with a family history (1.21-fold reduction, 95% CI 1.13-1.29). A key limitation of this analysis is that the BMI-altering DNA sequence polymorphisms it studies represent cumulative predisposition over an individual's entire lifetime, and may consequently incorrectly estimate the risk modification potential of weight loss interventions later in life. Conclusions In a population-scale cohort, lower BMI was consistently associated with reduced diabetes risk across BMI, family history, and genetic risk categories, suggesting all individuals can substantially reduce their diabetes risk through weight loss. Our results support the broad deployment of weight loss interventions to individuals at all levels of diabetes risk., Author(s): Michael Wainberg 1, Anubha Mahajan 2,3, Anshul Kundaje 1,4, Mark I. McCarthy 2,3,5, Erik Ingelsson 6,7,8,9, Nasa Sinnott-Armstrong 4,*, Manuel A. Rivas 10,* Introduction Type 2 diabetes is a [...]

مقدمه: با افزایش تعداد باکتری‌هایی که توالی‌یابی می‌شوند، نیاز به بهره‌برداری از این داده‌ها نیز بیشتر می‌شود. استفاده از این اطلاعات ژنومی از طریق به کارگیری هم‌زمان علوم بیوانفورماتیک و باکتری‌شناسی امکان‌ پذیر می‌باشد. مطالعه‌ی بیوانفورماتیک اندازه‌ی ژنوم باکتری‌های بیماری‌زا، تنوع قابل توجهی را نشان می‌دهد. فرضیات زیادی در مورد علت این تنوع و همچنین ارتباط اندازه‌ی ژنوم و فرایندهای اساسی باکتری مطرح است. هدف از انجام این مطالعه بررسی ارتباط اندازه‌ی ژنوم با تعدادی از خصوصیات ژنتیکی و رفتاری باکتری‌های بیماری‌زا بود. روش‌ها: اطلاعات توالی ژنوم 100 گونه باکتری بیماری‌زا از منابع گوناگون جمع‌آوری شد. ارتباط اندازه‌ی ژنوم با چند خصوصیت باکتری‌های بیماری‌زا مورد ارزیابی قرار گرفت. برای آنالیز داده‌ها، از نرم‌افزاری SPSS نسخه‌ی 19 استفاده شد. یافته‌ها: اندازه‌ی ژنوم در باکتری‌های بیماری‌زا، ارتباط معنی‌داری با تعدادی از خصوصیات ژنومی مانند درصد C + G، تعداد کلی ژن‌ها، پروتئین‌ها، Pseudogeneها، ژن‌های کسب شده و برخی از خصوصیات رفتاری و اکولوژیکی باکتری مانند تحرک، محدوده‌ی میزبان و تنفس نشان داد. هیچ گونه ارتباط معنی‌داری بین اندازه‌ی ژنوم، تراکم ژن در طول ژنوم و همچنین درصد DNA غیر کد کننده وجود نداشت. نتیجه‌گیری: در باکتری‌های بیماری‌زا، DNA انعطاف‌پذیری بالایی دارد و در طی تکامل، دچار کاهش اندازه می‌شود. در طی این روند، باکتری‌ها تعدادی از ژن‌های خود را از دست می‌دهند و تعداد کمتری نیز ژن کسب می‌کنند. این عوامل با کاهش تعداد پروتئین‌ها، کاهش درصد C + G و محدود ماندن زیستگاه باکتری همراه است.

Objectives: To characterize the mobile colistin resistance gene mcr-5 in Aeromonas hydrophila from backyard pigs in rural areas of China.Methods: Pig faecal samples from 194 households were directly tested for the presence of mcr-5 by PCR assay and the phenotypic antimicrobial susceptibility profiles of the mcr-5-positive isolates were determined using the broth dilution method. The genomic location and transferability of mcr-5 were analysed by S1-PFGE with Southern blotting and DNA hybridization, and natural transformation, respectively. One strain isolated from an mcr-5-positive sample was subjected to WGS and the stability of the mcr-5-harbouring plasmid over successive generations was examined by subculturing.Results: One mcr-5-positive A. hydrophila isolate showing resistance, with a colistin MIC of 4 mg/L, was isolated from a backyard pig faecal sample. mcr-5 was located on a 7915 bp plasmid designated pI064-2, which could naturally transform into a colistin-susceptible A. hydrophila strain of porcine origin and mediated colistin resistance in both the original isolate and its transformants. The plasmid backbone (3790 bp) of pI064-2 showed 81% nucleotide sequence identity to the corresponding region of the ColE2-type plasmid pAsa1 from Aeromonas salmonicida, while similar replication primases are widely distributed among aeromonads, Enterobacteriaceae and Pseudomonas species.Conclusions: To the best of our knowledge, this is the first identification of the novel colistin resistance gene mcr-5 in an A. hydrophila isolate from the faeces of a backyard pig. mcr-5 is expected to be able to disseminate among different bacterial species and genera. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) negatively regulate mRNAs at post-transcriptional level and thus can regulate different biological processes. Here we analyze the sequence characteristics and length distribution of miRNA sequences of six monocot and six dicot plants. We observe a species specific nucleotide preference of miRNAs. Although the first position of 5' end of mature miRNAs is U rich, there exists a wide variation. While the GC% of monocot mature miRNAs in general is nearly equal to the AU%, the GC% of stress induced miRNAs is significantly higher than AU%. Thus, higher content of GC% can be used as a signature of stress induced miRNAs in monocot. The length distribution of mature miRNAs shows the highest peak at 21 nucleotides with some other minor peaks at 20, 22 and 24 nucleotides. The synthesis of some miRNAs has positional preference either to 5' or to 3' arm of their precursors, but they are different in monocot and dicot. [ABSTRACT FROM AUTHOR]

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Background: Laribacter hongkongensis is a facultative anaerobic, non-fermentative, Gram-negative bacillus associated with community-acquired gastroenteritis and traveller's diarrhoea. No clinical MDR L. hongkongensis isolate has been reported yet.Methods: We performed WGS (PacBio and Illumina) on a clinical L. hongkongensis strain HLGZ1 with an MDR phenotype.Results: HLGZ1 was resistant to eight classes of commonly used antibiotics. Its complete genome was a single circular chromosome of 3 424 272 bp with a G + C content of 62.29%. In comparison with the reference strain HLHK9, HLGZ1 had a higher abundance of genes associated with DNA metabolism and recombination. Several inserts including two acquired resistance gene clusters (RC1 and RC2) were also identified. RC1 carried two resistance gene cassette arrays, aac(6')-Ib-cr-aadA2-Δqac-Δsul1-floR-tetR-tetG and arr-3-dfrA32-ereA2-Δqac-sul1, which shared significant nucleotide sequence identities with the MDR region of Salmonella Genomic Island 1 from Salmonella enterica serovar Typhimurium DT104. There was also an integron-like structure, intl1-arr3-dfrA27-Δqac-sul1-aph(3')-Ic, and a tetR-tetA operon located on RC2. MLST analysis identified HLGZ1 as ST167, a novel ST clustered with two strains previously isolated from frogs.Conclusions: This study provides insight into the genomic characteristics of MDR L. hongkongensis and highlights the possibilities of horizontal resistance gene transfer in this bacterium with other pathogens. [ABSTRACT FROM AUTHOR]

The T cells of the immune system can be engineered to target a tumour, but why some people respond better than others to such therapy is unclear. One patient's striking response to treatment now offers some clues.The T cells of the immune system can be engineered to target a tumour, but why some people respond better than others to such therapy is unclear. One patient's striking response to treatment now offers some clues., Author(s): Marcela V. MausAuthor Affiliations:Tumour tamed by transfer of one T cell Therapies involving engineered immune cells use viral vectors based on retroviruses or lentiviruses to insert a DNA sequence, [...]

The aim of the present study was to determine characteristics of Rheb gene and protein in Raini Cashmere goat. Comparative analyses of the nucleotide sequences were performed. Open reading frames (ORFs), theoretical molecular weights of deduced polypeptides, the protein isoelectric point, protein characteristics and three-dimensional structures was predicted using online standard softwares. The full cDNA nucleotide sequence shares 99%, 99%, 99% and 94% identity with Inner Mongolia Cashmere goat, cattle, horse and human, respectively. The deduced Rheb protein of Raini Cashmere goat consist of 184 amino acid residues and its predicted molecular weight was 20478 g/mol for the unmodified protein and the estimated isoelectric point (pI) was 5.59. Results showed that Rheb has a RAS domain starting at the amino acid 4 and ending at the amino acid 170. In conclusion, our data shows the Rheb cDNA is 555 bp in length, including a complete ORF corresponding to a polypeptide of 184 amino acids. Our results in Raini Cashmere goat showed that there are 1 N-glycosylation sites, 3 protein kinase C phosphorylation sites, 2 casein kinase II phosphorylation sites, 4 microbodies C-terminal targeting signals, 2 ATP/GTP binding sites motif A (Ploop) and a prenyl group binding site for predicted Psites of Rheb. Raini Cashmere goat Rheb protein also had an interaction with other predicted proteins. Hence, can suggest that Rheb has probably role in goat cells and must detect in future investigations. [ABSTRACT FROM AUTHOR]

Panfacial bone fracture is challenging. Even experienced surgeons find restoration of original facial architecture difficult because of the severe degree of fragmentation and loss of reference segments that could guide the start of facial reconstruction. To restore the facial contour, surgeons usually follow a general sequence for panfacial bone reduction. Among the sequences, the bottom-to-top and outside-in sequence is reported to be the most widely used in recent publications. However, a single sequence cannot be applied to all cases of panfacial fractures because of the variations in panfacial bone fracture patterns. In this article, we intend to find the reference and discuss the efficacy of inside-out sequence in facial bone fracture reconstruction. [ABSTRACT FROM AUTHOR]

The study on nucleic acid retention in ion-pair reversed-phase high-performance liquid chromatography mainly focuses on size-dependence, however, other factors influencing retention behaviors have not been comprehensively clarified up to date. In this present work, the retention behaviors of oligonucleotides and double-stranded DNAs were investigated on silica-based C18 stationary phase by ion-pair reversed-phase high-performance liquid chromatography. It is found that the retention of oligonucleotides was influenced by base composition and base sequence as well as size, and oligonucleotides prone to self-dimerization have weaker retention than those not prone to self-dimerization but with the same base composition. However, homo-oligonucleotides are suitable for the size-dependent separation as a special case of oligonucleotides. For double-stranded DNAs, the retention is also influenced by base composition and base sequence, as well as size. This may be attributed to the interaction of exposed bases in major or minor grooves with the hydrophobic alky chains of stationary phase. In addition, no specific influence of guanine and cytosine content was confirmed on retention of double-stranded DNAs. Notably, the space effect resulted from the stereostructure of nucleic acids also influences the retention behavior in ion-pair reversed-phase high-performance liquid chromatography. [ABSTRACT FROM AUTHOR]

Background Group A rotaviruses are the major causative agents of pediatric gastroenteritis worldwide. Several studies have reported the predominance of G4P[6] rotavirus genotypes in Korean neonates, which is uncommon in other countries. Therefore, the purposes of this study were to determine the genotype constellations of complete genomes of G4P[6] rotavirus strains isolated from Korean neonates using next-generation sequencing, to compare these sequences with other G4P[6] strains in other countries, and to determine the reason for the predominance of G4P[6] genotypes in Korean neonates. Results Twenty rotavirus G4P[6] strains, isolated from January 2013 to January 2016, were selected for whole-genome sequencing. Eleven rotavirus genes were amplified using specific primer sets, and sequencing was carried out using an Ion S5 XL next-generation sequencing platform. Genotypes of each gene were determined, and phylogenetic analyses were performed to investigate genetic distances between genes of rotaviruses in this study and those of other rotavirus G4P[6] strains whose whole-genome sequences were previously published. All 20 rotavirus strains in this study had the same genotype: G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, representing the Wa-like genotype constellation. BLAST searches of 20 G4P[6] rotavirus strains revealed that all G4 sequences in this study showed the highest nucleotide identity to G4 sequences of G4P[6] rotavirus strains isolated in Korea in 2008 (GenBank accession number: FJ603447). Additionally, P[6] gene sequences in this study showed the highest nucleotide identity to P[6] sequences of G4P[6] strains detected in Korea in 2002 (AY158093). Phylogenetic and nucleotide sequence analyses showed that G4P[6] strains in this study and previously reported G4P[6] strains in Korea were mostly detected in neonates and had similar G4 and P[6] sequences compared with other G4P[6] strains detected in other countries. Conclusions This study showed that the whole-genome constellation of rotavirus G4P[6] strains from Korean neonates resembled a Wa-like genotype constellation. Additionally, rotavirus genotypes detected in Korean neonates had unique P[6] sequences, which may be the cause of Korean neonatal rotavirus infection. Keywords: Rotavirus, Genotype, G4P[6], Korean, Neonate, Author(s): Su-Kyung Lee[sup.1] , Seoheui Choi[sup.2] , Jae-Seok Kim[sup.3] , Eun Jin Lee[sup.1] , Jungwon Hyun[sup.1] and Hyun Soo Kim[sup.1] Background Group A rotaviruses are the most important pathogens causing [...]

Domestication of a transposon (a DNA sequence that can change its position in a genome) to give rise to the RAG1-RAG2 recombinase (RAG) and V(D)J recombination, which produces the diverse repertoire of antibodies and T cell receptors, was a pivotal event in the evolution of the adaptive immune system of jawed vertebrates. The evolutionary adaptations that transformed the ancestral RAG transposase into a RAG recombinase with appropriately regulated DNA cleavage and transposition activities are not understood. Here, beginning with cryo-electron microscopy structures of the amphioxus ProtoRAG transposase (an evolutionary relative of RAG), we identify amino acid residues and domains the acquisition or loss of which underpins the propensity of RAG for coupled cleavage, its preference for asymmetric DNA substrates and its inability to perform transposition in cells. In particular, we identify two adaptations specific to jawed-vertebrates--arginine 848 in RAG1 and an acidic region in RAG2--that together suppress RAG-mediated transposition more than 1,000-fold. Our findings reveal a two-tiered mechanism for the suppression of RAG-mediated transposition, illuminate the evolution of V(D)J recombination and provide insight into the principles that govern the molecular domestication of transposons. Identification of the changes that converted a transposase to a recombinase sheds light on the evolution of the vertebrate adaptive immune system., Author(s): Yuhang Zhang [sup.1] , Tat Cheung Cheng [sup.2] , Guangrui Huang [sup.3] , Qingyi Lu [sup.3] , Marius D. Surleac [sup.4] , Jeffrey D. Mandell [sup.1] , Pierre Pontarotti [...]

The genetic compensation response (GCR) has recently been proposed as a possible explanation for the phenotypic discrepancies between gene-knockout and gene-knockdown.sup.1,2; however, the underlying molecular mechanism of the GCR remains uncharacterized. Here, using zebrafish knockdown and knockout models of the capn3a and nid1a genes, we show that mRNA bearing a premature termination codon (PTC) promptly triggers a GCR that involves Upf3a and components of the COMPASS complex. Unlike capn3a-knockdown embryos, which have small livers, and nid1a-knockdown embryos, which have short body lengths.sup.2, capn3a-null and nid1a-null mutants appear normal. These phenotypic differences have been attributed to the upregulation of other genes in the same families. By analysing six uniquely designed transgenes, we demonstrate that the GCR is dependent on both the presence of a PTC and the nucleotide sequence of the transgene mRNA, which is homologous to the compensatory endogenous genes. We show that upf3a (a member of the nonsense-mediated mRNA decay pathway) and components of the COMPASS complex including wdr5 function in GCR. Furthermore, we demonstrate that the GCR is accompanied by an enhancement of histone H3 Lys4 trimethylation (H3K4me3) at the transcription start site regions of the compensatory genes. These findings provide a potential mechanistic basis for the GCR, and may help lead to the development of therapeutic strategies that treat missense mutations associated with genetic disorders by either creating a PTC in the mutated gene or introducing a transgene containing a PTC to trigger a GCR. mRNA that contains a premature termination codon (PTC) triggers a genetic compensation response that involves both transcription of its homologous genes and degradation of the mutated transcript by the nonsense-mediated decay pathway., Author(s): Zhipeng Ma [sup.1] , Peipei Zhu [sup.1] , Hui Shi [sup.2] [sup.3] , Liwei Guo [sup.1] , Qinghe Zhang [sup.1] , Yanan Chen [sup.1] , Shuming Chen [sup.1] , [...]

The development of string theory has opened a completely new chapter and the way of thinking. A tight connection between DNA, water and strings, as well as their properties, lead to the idea that the soul is the shelter of our thoughts. Only 2% of the haploid human genome codes for proteins, while the rest consists of non-coding RNA genes, regulatory sequences, introns. The rest of the DNA, about 2.9 billion of base pairs, represents: cultural heredity of the person's family and a part being formed by the person during his/her lifetime, which gives the answer to what the use of the non-coding sequences is. Water molecules do not stay permanently united with DNA (the connection is not covalent), but they disconnect at every 0.5-1 nsec, forming and leaving the DNA molecule. It is well known that the DNA structure depends on water and that „water remembers thoughts”, and depending on the thoughts of a person it carries them to the physical structure of DNA. At the beginning of the physical organization of the water molecule there are strings. When a person dies, the DNA and water molecule are disconnected leaving only strings with an appropriate features being conditioned by three-dimensional structure of DNA shaped by water. Every person has a unique string appearance, as it is the case with the snowflakes (the DNA print in the strings).

ABSTRACT Stacking interaction between the aromatic heterocyclic bases plays an important role in the double helical structures of nucleic acids. Considering the base as rigid body, there are total of 18 degrees of freedom of a dinucleotide step. Some of these parameters show sequence preferences, indicating that the detailed atomic interactions are important in the stacking. Large variants of non-canonical base pairs have been seen in the crystallographic structures of RNA. However, their stacking preferences are not thoroughly deciphered yet from experimental results. The current theoretical approaches use either the rigid body degrees of freedom where the atomic information are lost or computationally expensive all atom simulations. We have used a hybrid simulation approach incorporating Monte-Carlo Metropolis sampling in the hyperspace of 18 stacking parameters where the interaction energies using AMBER-parm99bsc0 and CHARMM-36 force-fields were calculated from atomic positions. We have also performed stacking energy calculations for structures from Monte-Carlo ensemble by Dispersion corrected density functional theory. The available experimental data with Watson-Crick base pairs are compared to establish the validity of the method. Stacking interaction involving A:U and G:C base pairs with non-canonical G:U base pairs also were calculated and showed that these structures were also sequence dependent. This approach could be useful to generate multiscale modeling of nucleic acids in terms of coarse-grained parameters where the atomic interactions are preserved. This method would also be useful to predict structure and dynamics of different base pair steps containing non Watson-Crick base pairs, as found often in the non-coding RNA structures. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 212-226, 2016. [ABSTRACT FROM AUTHOR]

Lophophora williamsii (peyote) is a small, spineless, greenish-blue cactus found in Mexico and the southwestern United States. Ingestion of the cactus can result in hallucinations due to its content of mescaline. In the United States, L. williamsii is classified as a Schedule I controlled substance. In this study, we use DNA analysis of the chloroplast trnL/ trnF region and chloroplast rbcL gene to identify the individuals of Lophophora. Using the rbcL gene, Lophophora specimens could be distinguished from outgroups, but species within the genus could not be distinguished. The trnL/ trnF region split the Lophophora genus into several groups based on the length and substructure of an AT-rich segment of the sequence. Our results indicate that the genetic variability at the trnL/ trnF locus is greater than previously recognized. Although DNA structures at the trnL/ trnF region and rbcL gene do not align with the classification of Lophophora species, they can be used to aid in forensic analysis. [ABSTRACT FROM AUTHOR]

The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the Saccharomyces cerevisiae ORC bound to a 72-base-pair origin DNA sequence that contains the ARS consensus sequence (ACS) and the B1 element. The ORC encircles DNA through extensive interactions with both phosphate backbone and bases, and bends DNA at the ACS and B1 sites. Specific recognition of thymine residues in the ACS is carried out by a conserved basic amino acid motif of Orc1 in the minor groove, and by a species-specific helical insertion motif of Orc4 in the major groove. Moreover, similar insertions into major and minor grooves are also embedded in the B1 site by basic patch motifs from Orc2 and Orc5, respectively, to contact bases and to bend DNA. This work pinpoints a conserved role of ORC in modulating DNA structure to facilitate origin selection and helicase loading in eukaryotes. The cryo-EM structure of the yeast origin recognition complex (ORC) bound to a 72-base-pair origin DNA sequence provides insights into the basis of the origin selection mechanism., Author(s): Ningning Li [sup.1] , Wai Hei Lam [sup.2] , Yuanliang Zhai [sup.2] [sup.3] [sup.6] , Jiaxuan Cheng [sup.4] , Erchao Cheng [sup.4] , Yongqian Zhao [sup.2] [sup.3] , Ning [...]

Vibrio cholerae in O-group 139 was first isolated in 1992 and by 1993 had been found throughout the Indian subcontinent. This epidemic expansion probably resulted from a single source after a lateral gene transfer (LGT) event that changed the serotype of an epidemic V. cholerae O1 El Tor strain to O139. However, some studies found substantial genetic diversity, perhaps caused by multiple origins. To further explore the relatedness of O139 strains, we analyzed nine sequenced loci from 96 isolates from patients at the Infectious Diseases Hospital, Calcutta, from 1992 to 2000. We found 64 novel alleles distributed among 51 sequence types. LGT events produced three times the number of nucleotide changes compared to mutation. In contrast to the traditional concept of epidemic spread of a homogeneous clone, the establishment of variant alleles generated by LGT during the rapid expansion of a clonal bacterial population may be a paradigm in infections and epidemics.

The sequencing of the genome of Plasmodium falciparum promises to revolutionize the way in which malaria research will be carried out. Beyond simple gene discovery, the genome sequence will facilitate the comprehensive determination of the parasite?s gene expression during its developmental phases, pathology, and in response to environmental variables, such as drug treatment and host genetic background. This article reviews the current status of the P. falciparum genome sequencing project and the unique insights it has generated. We also summarize the application of bioinformatics and analytical tools that have been developed for functional genomics. The aim of these activities is the rational, information-based identification of new therapeutic strategies and targets, based on a thorough insight into the biology of Plasmodium spp.

We describe two serogroup O157 Escherichia coli strains from Brazilian infants with diarrhea. A variety of assays indicate that these strains belong to the enteropathogenic, not the enterohemorrhagic, pathotype. These strains possess a novel bfpA allele encoding the type IV pilin characteristic of typical enteropathogenic E. coli strains. Our results emphasize the pitfalls of classifying pathogenic E. coli by serogroup.

Despite substantial eff orts, the cause of a signifi cant proportion of mendelian disorders is still unknown. Recently, signifi cant advances in determination of nucleotide sequence present an opportunity to investigate the genetic material down to a single nucleotide resolution on the whole exome or genome scale. This opens complete possibilities for deciphering genetic etiology of genetic disorders and, most importantly, expanding the fi eld of genetic studies from limited cases of diseases occurring in large families to smaller familial confi gurations, making detection of causative genes possible even in trios of parents with a single aff ected proband. Despite the development in both the technology of next generation sequencing and increases in computational power for complex data analysis, the interpretation of results, making sense of genome-scale information in medical setting and conveying this information to the patient, have been lagging behind. In addition, novel ethical questions have opened, especially those related to reporting of incidental fi ndings. These issues are the key points for discussion prior to setting the protocols and guidelines for implementing the whole exome and genome sequencing into clinical practice. This overview will initially give a brief introduction to the technical background behind the next generation sequencing and methodological steps involved. Basic introduction to some of the key steps in data analysis of the next generation sequencing data and challenges encountered thereby will also be given, based on our experiences at the Centre for Mendelian Genomics in Slovenia. [ABSTRACT FROM AUTHOR]

We perform the conventional band structure and local density of states (LDOS) calculations in the vicinity of the Fermi level at ab initio molecular orbital level with 6-31G base set for one DNA duplex with repeated mononucleotide sequences and four DNA duplexes with repeated dinucleotide sequences in B form neutralized by Na+. The LDOS of six other DNA duplexes with repeated trinucleotide sequences in the same states are analyzed. The obtained results are compared with those by the band calculations based on periodic boundary condition using screw axis symmetry. The investigations focused on the influence of the base composition and base sequence on the DNA conductivity. The band structure and LDOS calculation results indicated that base guanine is more important for DNA conductivity than the other bases, and DNA conductivity varies with base sequence of DNA. Moreover, poly (dG) • poly (dC) shows the best conductor in our DNA duplex models. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Abstract: Salvia divinorum (diviner''s sage) is a plant in the mint family that produces an hallucinogenic compound, salvinorin A. The plant is used, often by chewing or smoking, as a “recreational” drug source and is regulated or banned in several states and countries. We describe a simple DNA technique, polymerase chain reaction of the ribulose bisphosphate carboxylase large subunit (rbcL) gene, that can distinguish S. divinorum leaf pieces from pieces of tobacco or cannabis. We have also found DNA sequences adjacent to the chloroplast leucine transfer RNA (trnL) gene that are specific to S. divinorum and distinguish it from other horticulturally popular Salvia species. We report some significant differences between the S. divinorum trnL sequences we determined and those now published in GenBank. [Copyright &y& Elsevier]

This article presents a case of tick infestation of the lower eyelid by a previously unreported species. A 71-year-old male presented with a tick attached to the lower eyelid. The tick was identified morphologically, and then molecularly via polymerase chain reaction (PCR) and sequencing of its DNA. In addition, a review of the literature relevant to the genera of ticks associated with infestation of the human eye is provided. The tick, which was in the nymphal developmental stage, was first identified according to taxonomic keys as Dermacentor sp. For complete species identification, 16s rDNA gene PCR and sequencing were performed, which showed that the tick was D. marginatus. Systematizing tick species could assist physicians in determining the potential for transmission of tick-borne human diseases. [ABSTRACT FROM AUTHOR]

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When rope is found at a crime scene, the type of fiber is currently identified through its microscopic characteristics. However, these characteristics may not always unambiguously distinguish some types of rope from others. If rope samples contain cells from the plants of origin, then DNA analysis may prove to be a better way to identify the type of rope obtained from a crime scene. The objective of this project was to develop techniques of DNA analysis that can be used to differentiate between ropes made from Cannabis sativa L. (hemp), Agave sisalana Perrine (sisal), Musa textilis Née (abaca, “Manila hemp”), Linum usitatissimum L. (flax), and Corchorus olitorus L. (jute). The procedures included extracting the DNA from the rope, performing polymerase chain reaction (PCR) using the extracted DNA as a template, and analyzing the DNA products. A primer pair for PCR, chosen from within a chloroplast gene for the large subunit of ribulose bisphosphate carboxylase/oxygenase, was designed to be specific for plant DNA and complementary to the genes from all five plants. The resulting PCR fragments were approximately 771 base pairs long. The PCR fragments, distinguished through base sequence analysis or restriction enzyme analysis, could be used to identify the five different rope types. The procedure provides a useful addition to visual methods of comparing rope samples. [ABSTRACT FROM AUTHOR]

Based on non-homogeneous model, a modified model is proposed. The new model deals with codon preference in protein-coding regions, reflects more accurately the key biological features of the regions. In addition, it is demonstrated, via an example, the modified model offers better solutions than previous model does. [ABSTRACT FROM AUTHOR]

Bulldogs, French bulldogs, and Boston terriers aren't the only dogs with short, wide heads, but they do share another feature not found in other breeds: a short, kinked tail. These [...]

A multi-copy plasmid containing the SNQ3 gene confers hyper-resistance to 4-nitroquinoline-N-oxide (4NQO), Trenimon, MNNG, cycloheximide, and to sulfometuron methyl in yeast transformants. Restriction analysis, subcloning, and DNA sequencing revealed an open reading frame of 1950 bp on the SNQ3-containing insert DNA. Gene disruption and transplacement into chromosomal DNA yielded 4NQO-sensitive null mutants which were also more sensitive than the wild-type to Trenimon, cycloheximide, sulfometuron methyl, and MNNG. Hydropathic analysis showed that the SNQ3-encoded protein is most likely not membrane-bound, while the codon bias index points to low expression of the gene. [ABSTRACT FROM AUTHOR]

Gonadotropin-releasing hormone (GnRH) has been shown to play a role in the regulation of human chorionic gonadotropin (hCG) secretion by the human placenta. Molecular studies have demonstrated that human placental trophoblast cells synthesize a progonadotropin-releasing hormone (pro-GnRH) identical to its human hypothalamic counterpart. However, far less is known about nonhuman primates. To determine whether pro-GnRH exists in the rhesus placenta, pro-GnRH mRNA was cloned, sequenced, and shown to be 97.6% homologous to its human placental counterpart. A single base difference (base 1167) in the domain encoding GnRH results in the same amino acid, arginine, in position 8, whereas four base differences (bases 1200, 1253, 1268, 1292) in the domain encoding GnRH-associated peptide (GAP) result in four different amino acids in positions 19, 37, 42, and 50. The absence of a basic amino acid in position 50 suggests the rhesus sequence may be cleaved to yield GAP peptides different from the human placenta. Thus, these data justify the use of mammalian GnRH in studies of rhesus placental function, but indicate the need to investigate the roles unique GAP peptides may play in placental/uterine function. [ABSTRACT FROM AUTHOR]

The composition of nuclear DNA in 3 Vicia species are compared. The species V. eriocarpa, V. johannis and V. melanops are from three separate subgeneric sections of Vicia and show a fourfold variation in their amounts of nuclear DNA. DNA melting experiments, buoyant density gradient analysis and Cot reassociation experiments show that the quantitiative change in nuclear DNA between the three species is achieved by changes in the amounts of both repetitive and nonrepetitive DNA sequences. It is suggested that while the increase in the repetitive fraction is achieved by the proliferation of repetitive base sequences the increase in the nonrepetitive fraction is due to the steady accretion of highly diverged base sequences resulting from mutations, deletions, insertions and base sequence rearrangements among families of repetitive sequences. [ABSTRACT FROM AUTHOR]