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https://www.readbyqxmd.com/read/29037147/de-novo-assembly-of-genomes-from-long-sequence-reads-reveals-uncharted-territories-of-propionibacterium-freudenreichii
#1
Paulina Deptula, Pia K Laine, Richard J Roberts, Olli-Pekka Smolander, Helena Vihinen, Vieno Piironen, Lars Paulin, Eija Jokitalo, Kirsi Savijoki, Petri Auvinen, Pekka Varmanen
BACKGROUND: Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii remained poorly characterised at the genomic level. At present, only three complete genome sequences are available for the species. RESULTS: We used the PacBio RS II sequencing platform to generate complete genomes of 20 P...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28978305/implementing-non-invasive-prenatal-testing-into-publicly-funded-antenatal-screening-services-for-down-syndrome-and-other-conditions-in-aotearoa-new-zealand
#2
Sara Filoche, Fiona Cram, Bev Lawton, Angela Beard, Peter Stone
BACKGROUND: Non-invasive prenatal testing (NIPT) is a relatively new screen for congenital conditions - specifically, common fetal aneuploidies including Down Syndrome. The test is based on isolating freely circulating fragments of fetal-placental DNA that is present in the mother's blood. NIPT has a superior clinical performance compared to current screening, and has been available privately in Aotearoa New Zealand for the last 4 years. MAIN ISSUE: The proposed implementation of NIPT as a publicly funded service may widen the inequity in access to optional antenatal screening that already exists in this country...
October 4, 2017: BMC Pregnancy and Childbirth
https://www.readbyqxmd.com/read/28902917/hsp70-j-protein-machinery-from-glossina-morsitans-morsitans-vector-of-african-trypanosomiasis
#3
Stephen J Bentley, Aileen Boshoff
Tsetse flies (Glossina spp.) are the sole vectors of the protozoan parasites of the genus Trypanosoma, the causative agents of African Trypanosomiasis. Species of Glossina differ in vector competence and Glossina morsitans morsitans is associated with transmission of Trypanosoma brucei rhodesiense, which causes an acute and often fatal form of African Trypanosomiasis. Heat shock proteins are evolutionarily conserved proteins that play critical roles in proteostasis. The activity of heat shock protein 70 (Hsp70) is regulated by interactions with its J-protein (Hsp40) co-chaperones...
2017: PloS One
https://www.readbyqxmd.com/read/28898293/the-vibrio-cholerae-var-regulon-encodes-a-metallo-%C3%AE-lactamase-and-an-antibiotic-efflux-pump-which-are-regulated-by-varr-a-lysr-type-transcription-factor
#4
Hong-Ting Victor Lin, Teresa Massam-Wu, Chen-Ping Lin, Yen-Jen Anna Wang, Yu-Chi Shen, Wen-Jung Lu, Pang-Hung Hsu, Yu-Hou Chen, Maria Ines Borges-Walmsley, Adrian Robert Walmsley
The genome sequence of V. cholerae O1 Biovar Eltor strain N16961 has revealed a putative antibiotic resistance (var) regulon that is predicted to encode a transcriptional activator (VarR), which is divergently transcribed relative to the putative resistance genes for both a metallo-β-lactamase (VarG) and an antibiotic efflux-pump (VarABCDEF). We sought to test whether these genes could confer antibiotic resistance and are organised as a regulon under the control of VarR. VarG was overexpressed and purified and shown to have β-lactamase activity against penicillins, cephalosporins and carbapenems, having the highest activity against meropenem...
2017: PloS One
https://www.readbyqxmd.com/read/28893199/comprehensive-survey-and-evolutionary-analysis-of-genome-wide-mirna-genes-from-ten-diploid-oryza-species
#5
Showkat Ahmad Ganie, Ananda Bhusan Debnath, Abubakar Mohammad Gumi, Tapan Kumar Mondal
BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. RESULT: All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species...
September 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28874668/topologically-associating-domains-are-ancient-features-that-coincide-with-metazoan-clusters-of-extreme-noncoding-conservation
#6
Nathan Harmston, Elizabeth Ing-Simmons, Ge Tan, Malcolm Perry, Matthias Merkenschlager, Boris Lenhard
Developmental genes in metazoan genomes are surrounded by dense clusters of conserved noncoding elements (CNEs). CNEs exhibit unexplained extreme levels of sequence conservation, with many acting as developmental long-range enhancers. Clusters of CNEs define the span of regulatory inputs for many important developmental regulators and have been described previously as genomic regulatory blocks (GRBs). Their function and distribution around important regulatory genes raises the question of how they relate to 3D conformation of these loci...
September 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28873470/comparative-genomics-and-phylogenomic-analyses-of-lysine-riboswitch-distributions-in-bacteria
#7
COMPARATIVE STUDY
Sumit Mukherjee, Danny Barash, Supratim Sengupta
Riboswitches are cis-regulatory elements that regulate the expression of genes involved in biosynthesis or transport of a ligand that binds to them. Among the nearly 40 classes of riboswitches discovered so far, three are known to regulate the concentration of biologically encoded amino acids glycine, lysine, and glutamine. While some comparative genomics studies of riboswitches focusing on their gross distribution across different bacterial taxa have been carried out recently, systematic functional annotation and analysis of lysine riboswitches and the genes they regulate are still lacking...
2017: PloS One
https://www.readbyqxmd.com/read/28842730/evidence-based-prioritisation-and-enrichment-of-genes-interacting-with-metformin-in-type-2-diabetes
#8
Adem Y Dawed, Ashfaq Ali, Kaixin Zhou, Ewan R Pearson, Paul W Franks
AIMS/HYPOTHESIS: There is an extensive body of literature suggesting the involvement of multiple loci in regulating the action of metformin; most findings lack replication, without which distinguishing true-positive from false-positive findings is difficult. To address this, we undertook evidence-based, multiple data integration to determine the validity of published evidence. METHODS: We (1) built a database of published data on gene-metformin interactions using an automated text-mining approach (n = 5963 publications), (2) generated evidence scores for each reported locus, (3) from which a rank-ordered gene set was generated, and (4) determined the extent to which this gene set was enriched for glycaemic response through replication analyses in a well-powered independent genome-wide association study (GWAS) dataset from the Genetics of Diabetes and Audit Research Tayside Study (GoDARTS)...
August 25, 2017: Diabetologia
https://www.readbyqxmd.com/read/28840966/the-diy-digital-medical-centre
#9
James Kenneth Timmis, Kenneth Timmis
Healthcare systems worldwide are confronted with major economic, organizational and logistical challenges. Historic evolution of health care has led to significant healthcare sector fragmentation, resulting in systemic inefficiencies and suboptimal resource exploitation. To attain a sustainable healthcare model, fundamental, system-wide improvements that effectively network, and ensure fulfilment of potential synergies between sectors, and include and facilitate coherent strategic planning and organisation of healthcare infrastructure are needed...
September 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28835372/pervasive-coexpression-of-spatially-proximal-genes-is-buffered-at-the-protein-level
#10
Georg Kustatscher, Piotr Grabowski, Juri Rappsilber
Genes are not randomly distributed in the genome. In humans, 10% of protein-coding genes are transcribed from bidirectional promoters and many more are organised in larger clusters. Intriguingly, neighbouring genes are frequently coexpressed but rarely functionally related. Here we show that coexpression of bidirectional gene pairs, and closeby genes in general, is buffered at the protein level. Taking into account the 3D architecture of the genome, we find that co-regulation of spatially close, functionally unrelated genes is pervasive at the transcriptome level, but does not extend to the proteome...
August 23, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28806822/-multiple-myeloma-current-status-in-diagnostic-testing-and-therapy
#11
Michael Kehrer, Sebastian Koob, Andreas Strauss, Dieter Christian Wirtz, Jan Schmolders
Background Multiple myeloma is a haematological blood cancer of the bone marrow and is classified by the World Health Organisation (WHO) as a plasma cell neoplasm. In multiple myeloma, normal plasma cells transform into malignant myeloma cells and produce large quantities of an abnormal immunoglobulin called monoclonal protein or M protein. This ultimately causes multiple myeloma symptoms such as bone damage or kidney problems. The annual worldwide incidence of multiple myeloma is estimated to be 6 - 7/100,000 and accounts for 1% of all cancer...
October 2017: Zeitschrift Für Orthopädie und Unfallchirurgie
https://www.readbyqxmd.com/read/28792980/evolutionary-implications-of-heterochromatin-and-rdna-in-chromosome-number-and-genome-size-changes-during-dysploidy-a-case-study-in-reichardia-genus
#12
Sonja Siljak-Yakovlev, Bernard Godelle, Vlatka Zoldos, Joan Vallès, Teresa Garnatje, Oriane Hidalgo
In this study we showed that constitutive heterochromatin, GC-rich DNA and rDNA are implicated in chromosomal rearrangements during the basic chromosome number changing (dysploidy) in Reichardia genus. This small Mediterranean genus comprises 8-10 species and presents three basic chromosome numbers (x = 9, 8 and 7). To assess genome evolution and differentiation processes, studies were conducted in a dysploid series of six species: R. dichotoma, R. macrophylla and R. albanica (2n = 18), R. tingitana and R. gaditana (2n = 16), and R...
2017: PloS One
https://www.readbyqxmd.com/read/28767705/changes-in-chromosome-territory-position-within-the-nucleus-reflect-alternations-in-gene-expression-related-to-embryonic-lineage-specification
#13
Maciej Orsztynowicz, Dorota Lechniak, Piotr Pawlak, Beata Kociucka, Svatava Kubickova, Halina Cernohorska, Zofia Eliza Madeja
Loss of totipotentcy in an early embryo is directed by molecular processes responsible for cell fate decisions. Three dimensional genome organisation is an important factor linking chromatin architecture with stage specific gene expression patterns. Little is known about the role of chromosome organisation in gene expression regulation of lineage specific factors in mammalian embryos. Using bovine embryos as a model we have described these interactions at key developmental stages. Three bovine chromosomes (BTA) that differ in size, number of carried genes, and contain loci for key lineage regulators OCT4, NANOG and CDX2, were investigated...
2017: PloS One
https://www.readbyqxmd.com/read/28756001/oestrogen-receptor-distribution-related-to-functional-thymus-anatomy-of-the-european-sea-bass-dicentrarchus-labrax
#14
Matthieu Paiola, Thomas Knigge, Simona Picchietti, Aurélie Duflot, Laura Guerra, Patricia I S Pinto, Giuseppe Scapigliati, Tiphaine Monsinjon
In jawed vertebrates, the crosstalk between immune and endocrine system as well as many fundamental mechanisms of T cell development are evolutionary conserved. Oestrogens affect mammalian thymic function and plasticity, but the mechanisms of action and the oestrogen receptors involved remain unclear. To corroborate the oestrogenic regulation of thymic function in teleosts and to identify the implicated oestrogen receptor subtypes, we examined the distribution of nuclear and membrane oestrogen receptors within the thymus of the European Sea bass, Dicentrarchus labrax, in relation to its morpho-functional organisation...
July 26, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28748289/genetic-recombinational-events-in-prokaryotes-and-their-viruses-insight-into-the-study-of-evolution-and-biodiversity
#15
REVIEW
Jean-Pierre Gratia
The exact meaning of sexual reproduction and the precise evolutionary period at which recombination first took place remains the subject of intense debates. Despite some unity in biochemical organisation of genetic recombination, a plethora of mechanisms are found to exist in microbes and their viruses. Some routes used by viruses bypass barriers to genetic heterology and provide bacteria with genes conferring a selective advantage, and some contribute to genome enlargement. The present review aims at highlighting the diversity of such mechanisms with a particular focus on spontaneous zygogenesis (or Z-mating)...
July 26, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28688976/genomic-analysis-of-the-marine-fish-pathogen-photobacterium-damselae-subsp-piscicida-insertion-sequences-proliferation-is-associated-with-chromosomal-reorganisations-and-rampant-gene-decay
#16
Miguel Balado, Hicham Benzekri, Alejandro M Labella, M Gonzalo Claros, Manuel Manchado, Juan J Borrego, Carlos R Osorio, Manuel L Lemos
Photobacterium damselae subsp. piscicida (Pdp) is an intracellular fish pathogen that causes photobacteriosis, a disease proven deadly in farmed fish worldwide. This work focuses on the analysis of genome sequences, chromosomes structure and gene contents of two strains from Sparus aurata (DI21) and Solea senegalensis (L091106-03H), isolated on the Spanish Atlantic coast. The comparative genomic analysis revealed that DI21 and L091106-03H share 98% of their genomes, including two virulence plasmids: pPHDP70 encoding siderophore piscibactin synthesis and pPHDP10 encoding the apoptotic toxin AIP56...
July 5, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28672223/complete-genome-sequence-of-ostreid-herpesvirus-type-1-%C3%A2%C2%B5var-isolated-during-mortality-events-in-the-pacific-oyster-crassostrea-gigas-in-france-and-ireland
#17
E A V Burioli, M Prearo, M Houssin
Infections with Ostreid herpesvirus 1 (OsHV-1) microvariants in young Pacific oysters are associated with massive mortality events and significant economic losses. Previous studies, focusing on few regions of the genome, have revealed the genomic diversity of these genotypes with respect to the reference type. We used a NGS process to sequence the whole genome of the OsHV-1 µVar in infected individuals, collected during mortality events in France and Ireland. The final genome length of OsHV-1 µVar was approximately 205kbp, shorter than the reference genotype and the overall genome organisation resembled herpes simplex viruses...
September 2017: Virology
https://www.readbyqxmd.com/read/28657425/the-regulatory-network-controlling-ethanol-induced-expression-of-alcohol-dehydrogenase-in-the-endophyte-azoarcus-sp-strain-bh72
#18
Andrea Krause, Henrike Julich, Manasee Mankar, Barbara Reinhold-Hurek
The habitat of the nitrogen-fixing endophyte Azoarcus sp. strain BH72 is grass roots grown under waterlogged conditions that produce, under these conditions, ethanol. Strain BH72 is well equipped to metabolize ethanol, with eight alcohol dehydrogenases (ADHs), of which ExaA2 and ExaA3 are the most relevant ones. exaA2 and exaA3 cluster and are surrounded by genes encoding two-component regulatory systems (TCSs) termed ExaS-ExaR and ElmS-GacA. Functional genomic analyses revealed that i) expression of the corresponding genes was induced by ethanol, ii) the genes were also expressed in the rhizoplane or even inside of rice roots, iii) both TCSs were indispensable for growth on ethanol, and iv) they were important for competitiveness during rice root colonization...
July 26, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28651000/assessing-the-impact-of-benzo-a-pyrene-on-marine-mussels-application-of-a-novel-targeted-low-density-microarray-complementing-classical-biomarker-responses
#19
Mohamed Banni, Susanna Sforzini, Volker M Arlt, Audrey Barranger, Lorna J Dallas, Caterina Oliveri, Yann Aminot, Beniamina Pacchioni, Caterina Millino, Gerolamo Lanfranchi, James W Readman, Michael N Moore, Aldo Viarengo, Awadhesh N Jha
Despite the increasing use of mussels in environmental monitoring and ecotoxicological studies, their genomes and gene functions have not been thoroughly explored. Several cDNA microarrays were recently proposed for Mytilus spp., but putatively identified partial transcripts have rendered the generation of robust transcriptional responses difficult in terms of pathway identification. We developed a new low density oligonucleotide microarray with 465 probes covering the same number of genes. Target genes were selected to cover most of the well-known biological processes in the stress response documented over the last decade in bivalve species at the cellular and tissue levels...
2017: PloS One
https://www.readbyqxmd.com/read/28640886/epigenomic-diversification-within-the-genus-lupinus
#20
Karolina Susek, Agnieszka Braszewska-Zalewska, Adam J Bewick, Robert Hasterok, Robert J Schmitz, Barbara Naganowska
Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organisation of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various plant genomes, here we present the first study for the genus Lupinus. Lupins, which are members of grain legumes (pulses), are beneficial for food security, nutrition, health and the environment...
2017: PloS One
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