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https://www.readbyqxmd.com/read/29466411/molecular-epidemiology-of-tuberculosis-in-tasmania-and-genomic-characterisation-of-its-first-known-multi-drug-resistant-case
#1
Sanjay S Gautam, Micheál Mac Aogáin, Louise A Cooley, Greg Haug, Janet A Fyfe, Maria Globan, Ronan F O'Toole
BACKGROUND: The origin and spread of tuberculosis (TB) in Tasmania and the types of strains of Mycobacterium tuberculosis complex (MTBC) present in the population are largely unknown. OBJECTIVE: The aim of this study was to perform the first genomic analysis of MTBC isolates from Tasmania to better understand the epidemiology of TB in the state. METHODS: Whole-genome sequencing was performed on cultured isolates of MTBC collected from 2014-2016...
2018: PloS One
https://www.readbyqxmd.com/read/29458427/the-genomic-underpinnings-of-eukaryotic-virus-taxonomy-creating-a-sequence-based-framework-for-family-level-virus-classification
#2
Pakorn Aiewsakun, Peter Simmonds
BACKGROUND: The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of viruses detected in environmental (metagenomic) studies that lack any phenotypic data...
February 20, 2018: Microbiome
https://www.readbyqxmd.com/read/29446469/clinical-trials-in-allergen-immunotherapy-current-concepts-and-future-needs
#3
REVIEW
O Pfaar, M Alvaro, V Cardona, E Hamelmann, R Mösges, J Kleine-Tebbe
Allergen immunotherapy (AIT) is a safe, effective treatment for allergic rhinoconjunctivitis and allergic asthma. However, AIT's clinical effect is still contested - primarily due to heterogeneity in clinical trial designs, study populations, therapeutic formulations and efficacy criteria. After discussing current concepts and unmet needs, an international panel of experts made several recommendations: (i) explore and validate definitions for [clinical] responders in AIT-trials; (ii) use of well-documented, standardized provocation tests prior to inclusion of subjects with relevant diseases in AIT trials; (iii) monitoring neo-sensitizations and occurrence of new allergy in extended AIT trials, and exclusion of polyallergic participants; (iv) validation of allergen exposure chambers with regard to natural exposure; (v) in studies of seasonal allergies, focus on peak exposure but also consider organising two parallel, geographically distinct but otherwise identical trials; (vi) discuss adaptive trial designs with the regulatory authorities; (vii) use e-health and m-health technologies to capture more information on individual exposure to allergens; (viii) initiate research on potential psychological, biochemical, immune, neural and even genomic markers of the placebo response; (ix) identify trial designs and primary endpoints that will give children with allergies easier, faster access to AIT formulations; and (x) promote and apply standardized methods for reporting systemic and local adverse events...
February 15, 2018: Allergy
https://www.readbyqxmd.com/read/29426945/characterization-of-the-complete-mitogenome-of-indian-mouse-deer-moschiola-indica-artiodactyla-tragulidae-and-its-evolutionary-significance
#4
Rama K Sarvani, Drashti R Parmar, Wajeeda Tabasum, Neelima Thota, Ara Sreenivas, Ajay Gaur
The mitochondrial genome of Indian mouse deer (Moschiola indica) was sequenced, assembled and characterized for the first time using 22 pairs of polymerase chain reaction (PCR) primers. The mitogenome of M. indica which is 16,444 bp in size was found very similar to most vertebrates in organisation that harbours 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and 1A + T-rich region. Its comparison with over 52 mitogenomes of the order Artiodactyla, showed a conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins except that M...
February 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29402885/transcriptional-decomposition-reveals-active-chromatin-architectures-and-cell-specific-regulatory-interactions
#5
Sarah Rennie, Maria Dalby, Lucas van Duin, Robin Andersson
Transcriptional regulation is tightly coupled with chromosomal positioning and three-dimensional chromatin architecture. However, it is unclear what proportion of transcriptional activity is reflecting such organisation, how much can be informed by RNA expression alone and how this impacts disease. Here, we develop a computational transcriptional decomposition approach separating the proportion of expression associated with genome organisation from independent effects not directly related to genomic positioning...
February 5, 2018: Nature Communications
https://www.readbyqxmd.com/read/29392493/grapevine-virus-i-a-putative-new-vitivirus-detected-in-co-infection-with-grapevine-virus-g-in-new-zealand
#6
Arnaud G Blouin, Kar Mun Chooi, Ben Warren, Kathryn R Napier, Roberto A Barrero, Robin M MacDiarmid
A novel virus, with characteristics of viruses classified within the genus Vitivirus, was identified from a sample of Vitis vinifera cv. Chardonnay in New Zealand. The virus was detected with high throughput sequencing (small RNA and total RNA) and its sequence was confirmed by Sanger sequencing. Its genome is 7507 nt long (excluding the polyA tail) with an organisation similar to that described for other classifiable members of the genus Vitivirus. The closest relative of the virus is grapevine virus E (GVE) with 65% aa identity in ORF1 (65% nt identity) and 63% aa identity in the coat protein (66% nt identity)...
February 1, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29380064/the-complete-nucleotide-sequence-and-genome-organisation-of-a-novel-member-of-the-family-betaflexiviridae-from-actinidia-chinensis
#7
Stella Veerakone, Lia W Liefting, Joe Tang, Lisa I Ward
We report the complete genome sequence of a novel virus, tentatively named "actinidia seed-borne latent virus" (ASbLV), isolated from Actinidia chinensis in Auckland, New Zealand. The complete genome of ASbLV is 8,192 nucleotides long, excluding the 3' poly(A) tail, contains four open reading frames, and is most closely related to Caucasus prunus virus (56% nucleotide sequence identity), a member of the genus Prunevirus. Based on the demarcation criteria of the family Betaflexiviridae, ASbLV is a new member of the genus Prunevirus...
January 29, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29378768/chromothripsis-and-ring-chromosome-22-a-paradigm-of-genomic-complexity-in-the-phelan-mcdermid-syndrome-22q13-deletion-syndrome
#8
Nehir Kurtas, Filippo Arrigoni, Edoardo Errichiello, Claudio Zucca, Cristina Maghini, Maria Grazia D'Angelo, Silvana Beri, Roberto Giorda, Sara Bertuzzo, Massimo Delledonne, Luciano Xumerle, Marzia Rossato, Orsetta Zuffardi, Maria Clara Bonaglia
INTRODUCTION: Phelan-McDermid syndrome (PMS) is caused by SHANK3 haploinsufficiency. Its wide phenotypic variation is attributed partly to the type and size of 22q13 genomic lesion (deletion, unbalanced translocation, ring chromosome), partly to additional undefined factors. We investigated a child with severe global neurodevelopmental delay (NDD) compatible with her distal 22q13 deletion, complicated by bilateral perisylvian polymicrogyria (BPP) and urticarial rashes, unreported in PMS...
January 29, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29366467/epidemiological-analysis-of-salmonella-clusters-identified-by-whole-genome-sequencing-england-and-wales-2014
#9
Alison Waldram, Gayle Dolan, Philip M Ashton, Claire Jenkins, Timothy J Dallman
The unprecedented level of bacterial strain discrimination provided by whole genome sequencing (WGS) presents new challenges with respect to the utility and interpretation of the data. Whole genome sequences from 1445 isolates of Salmonella belonging to the most commonly identified serotypes in England and Wales isolated between April and August 2014 were analysed. Single linkage single nucleotide polymorphism thresholds at the 10, 5 and 0 level were explored for evidence of epidemiological links between clustered cases...
May 2018: Food Microbiology
https://www.readbyqxmd.com/read/29352301/crystal-structure-of-a-udp-glcnac-epimerase-for-surface-polysaccharide-biosynthesis-in-acinetobacter-baumannii
#10
Bhumika S Shah, Heather E Ashwood, Stephen J Harrop, Daniel N Farrugia, Ian T Paulsen, Bridget C Mabbutt
With new strains of Acinetobacter baumannii undergoing genomic analysis, it has been possible to define regions of genomic plasticity (RGPs), encoding specific adaptive elements. For a selected RGP from a community-derived isolate of A. baumannii, we outline sequences compatible with biosynthetic machinery of surface polysaccharides, specifically enzymes utilized in the dehydration and conversion of UDP-N-acetyl-D-glucosamine (UDP-D-GlcNAc). We have determined the crystal structure of one of these, the epimerase Ab-WbjB...
2018: PloS One
https://www.readbyqxmd.com/read/29348145/fbxl13-directs-the-proteolysis-of-cep192-to-regulate-centrosome-homeostasis-and-cell-migration
#11
Ella Fung, Carmen Richter, Hong-Bin Yang, Isabell Schäffer, Roman Fischer, Benedikt M Kessler, Florian Bassermann, Vincenzo D'Angiolella
Aberrant centrosome organisation with ensuing alterations of microtubule nucleation capacity enables tumour cells to proliferate and invade despite increased genomic instability. CEP192 is a key factor in the initiation process of centrosome duplication and in the control of centrosome microtubule nucleation. However, regulatory means of CEP192 have remained unknown. Here, we report that FBXL13, a binding determinant of SCF (SKP1-CUL1-F-box)-family E3 ubiquitin ligases, is enriched at centrosomes and interacts with the centrosomal proteins Centrin-2, Centrin-3, CEP152 and CEP192...
January 18, 2018: EMBO Reports
https://www.readbyqxmd.com/read/29336158/chromosome-gene-orientations-inversion-networks-goins-of-plasmodium-proteome
#12
Viviana F Quevedo-Tumailli, Bernabe Ortega-Tenezaca, Humbert Gonzalez-Diaz
The spatial distribution of genes in chromosomes seems not to be random. For instance, only 10% of genes are transcribed from bidirectional promoters in humans and many more are organised in larger clusters. This raises intriguing questions asked by different authors before. We would like to add a few more questions in this context, related to gene orientation inversions. Does gene orientation (inversion) follow a random pattern? Is it relevant to biological activity somehow? In this paper, we define a new kind of network coined as the Gene Orientation Inversion Network (GOIN)...
January 16, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29311716/discovering-viral-genomes-in-human-metagenomic-data-by-predicting-unknown-protein-families
#13
Mauricio Barrientos-Somarribas, David N Messina, Christian Pou, Fredrik Lysholm, Annelie Bjerkner, Tobias Allander, Björn Andersson, Erik L L Sonnhammer
Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29295549/comparative-analysis-of-37-acinetobacter-bacteriophages
#14
Dann Turner, Hans-Wolfgang Ackermann, Andrew M Kropinski, Rob Lavigne, J Mark Sutton, Darren M Reynolds
Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae...
December 24, 2017: Viruses
https://www.readbyqxmd.com/read/29273645/stratification-of-knee-osteoarthritis-two-major-patient-subgroups-identified-by-genome-wide-expression-analysis-of-articular-cartilage
#15
Jamie Soul, Sara L Dunn, Sanjay Anand, Ferdinand Serracino-Inglott, Jean-Marc Schwartz, Ray P Boot-Handford, Tim E Hardingham
INTRODUCTION: Osteoarthritis (OA) is a heterogeneous and complex disease. We have used a network biology approach based on genome-wide analysis of gene expression in OA knee cartilage to seek evidence for pathogenic mechanisms that may distinguish different patient subgroups. METHODS: Results from RNA-Sequencing (RNA-Seq) were collected from intact knee cartilage at total knee replacement from 44 patients with OA, from 16 additional patients with OA and 10 control patients with non-OA...
December 22, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29261138/was-the-watchmaker-blind-or-was-she-one-eyed
#16
REVIEW
Raymond Noble, Denis Noble
The question whether evolution is blind is usually presented as a choice between no goals at all ('the blind watchmaker') and long-term goals which would be external to the organism, for example in the form of special creation or intelligent design. The arguments either way do not address the question whether there are short-term goals within rather than external to organisms. Organisms and their interacting populations have evolved mechanisms by which they can harness blind stochasticity and so generate rapid functional responses to environmental challenges...
December 20, 2017: Biology
https://www.readbyqxmd.com/read/29250906/opportunities-for-training-for-nutritional-professionals-in-nutritional-genomics-what-is-out-there
#17
Jorja Collins, Melissa M Adamski, Cliona Twohig, Chiara Murgia
AIM: To identify and profile training courses available to dietitians and nutritionists in the area of nutritional genomics. Genetic technology is progressing quickly, leading to increased public interest and requests from the public for personalised nutrition advice based on genetic background. Tertiary courses often lack specific curriculum in nutritional genomics, preventing graduates from discussing confidently with their clients the relationships between genetics, nutrition and health...
December 18, 2017: Nutrition & Dietetics: the Journal of the Dietitians Association of Australia
https://www.readbyqxmd.com/read/29248294/phenotyping-of-per3-variants-reveals-widespread-effects-on-circadian-preference-sleep-regulation-and-health
#18
REVIEW
Simon N Archer, Christina Schmidt, Gilles Vandewalle, Derk-Jan Dijk
Period3 (Per3) is one of the most robustly rhythmic genes in humans and animals. It plays a significant role in temporal organisation in peripheral tissues. The effects of PER3 variants on many phenotypes have been investigated in targeted and genome-wide studies. PER3 variants, especially the human variable number tandem repeat (VNTR), associate with diurnal preference, mental disorders, non-visual responses to light, brain and cognitive responses to sleep loss/circadian misalignment. Introducing the VNTR into mice alters responses to sleep loss and expression of sleep homeostasis-related genes...
November 6, 2017: Sleep Medicine Reviews
https://www.readbyqxmd.com/read/29241134/effects-of-the-herbicides-linuron-and-s-metolachlor-on-perez-s-frog-embryos
#19
Carla Quintaneiro, Amadeu M V M Soares, Marta S Monteiro
Presence of pesticides in the environment and their possible effects on aquatic organisms are of great concern worldwide. The extensive use of herbicides in agricultural areas are one of the factors contributing to the known decline of amphibian populations. Thus, as non-target species, amphibians can be exposed in early life stages to herbicides in aquatic systems. In this context, this study aims to evaluate effects of increasing concentrations of two maize herbicides, linuron and S-metolachlor on embryos of the Perez' frog (Pelophylax perezi) during 192 h...
November 29, 2017: Chemosphere
https://www.readbyqxmd.com/read/29233255/burkholderia-stabilis-outbreak-associated-with-contaminated-commercially-available-washing-gloves-switzerland-may-2015-to-august-2016
#20
Rami Sommerstein, Urs Führer, Elia Lo Priore, Carlo Casanova, Dominik M Meinel, Helena Mb Seth-Smith, Andreas Kronenberg, On Behalf Of Anresis, Daniel Koch, Laurence Senn, Andreas F Widmer, Adrian Egli, Jonas Marschall, On Behalf Of Swissnoso
We describe an outbreak of Burkholderia stabilis associated with contaminated washing gloves, a commercially available Class I medical device. Triggered by an increase in Burkholderia cepacia complex (BCC) bacteremias and the detection of BCC in unopened packages of washing gloves, an ad hoc national outbreak committee comprising representatives of a public health organisation, a regulatory agency, and an expert association convened and commissioned an outbreak investigation. The investigation included retrospective case finding across Switzerland and whole genome sequencing (WGS) of isolates from cases and gloves...
December 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
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