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https://www.readbyqxmd.com/read/28209125/the-mitochondrial-genome-sequences-of-the-round-goby-and-the-sand-goby-reveal-patterns-of-recent-evolution-in-gobiid-fish
#1
Irene Adrian-Kalchhauser, Ola Svensson, Verena E Kutschera, Magnus Alm Rosenblad, Martin Pippel, Sylke Winkler, Siegfried Schloissnig, Anders Blomberg, Patricia Burkhardt-Holm
BACKGROUND: Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). RESULTS: During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28103252/comparative-and-evolutionary-analysis-of-grass-pollen-allergens-using-brachypodium-distachyon-as-a-model-system
#2
Akanksha Sharma, Niharika Sharma, Prem Bhalla, Mohan Singh
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses...
2017: PloS One
https://www.readbyqxmd.com/read/28100610/the-measles-virus-receptor-slamf1-can-mediate-particle-endocytosis
#3
Daniel Gonçalves-Carneiro, Jane A McKeating, Dalan Bailey
: The signalling lymphocyte activation molecule F1 (SLAMF1) is both a microbial sensor and entry receptor for Measles virus (MeV). Herein, we describe a new role for SLAMF1 to mediate MeV endocytosis that is in contrast with the alternative, and generally accepted, model that MeV genome enters cells only after fusion at the cell surface. We demonstrated that MeV engagement of SLAMF1 induces dramatic but transient morphological changes, most prominently in the formation of membrane blebs, which were shown to co-localise with incoming viral particles, and rearrangement of the actin cytoskeleton in infected cells...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28100306/diverse-novel-astroviruses-identified-in-wild-himalayan-marmots
#4
Yuanyun Ao, Jiemei Yu, Lili Li, Jingyuan Cao, Hongyan Deng, Yunyun Xin, Mengmeng Liu, Lin Lin, Shan Lu, Jianguo Xu, Zhaojun Duan
With advances in viral surveillance and next generation sequencing, highly diverse novel astroviruses (AstVs) and different animal hosts have been discovered in recent years. However, the existence of AstVs in marmots has yet to be shown. Here, we identified for the first time two highly divergent strains of AstVs, (tentatively named Qinghai Himalayana marmot AstV, HHMAstV1 and HHMAstV2), by viral metagenomic analysis in liver tissues isolated from wild Marmota himalayana in China. Overall, 12 of 99 (12.1%) M...
January 18, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28086752/single-genome-retrieval-of-context-dependent-variability-in-mutation-rates-for-human-germline
#5
Aleksandr B Sahakyan, Shankar Balasubramanian
BACKGROUND: Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. RESULTS: The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28074622/-holostei-versus-halecostomi-problem-insight-from-cytogenetics-of-ancient-nonteleost-actinopterygian-fish-bowfin-amia-calva
#6
Zuzana Majtánová, Radka Symonová, Lenin Arias-Rodriguez, Lauren Sallan, Petr Ráb
Bowfin belongs to an ancient lineage of nonteleost ray-finned fishes (actinopterygians) and is the only extant survivor of a once diverged group, the Halecomorphi or Amiiformes. Owing to the scarcity of extant nonteleost ray-finned lineages, also referred as "living fossils," their phylogenetic interrelationships have been the target of multiple hypotheses concerning their sister group relationships. Molecular and morphological data sets have produced controversial results; bowfin is considered as either the sister group to genome-duplicated teleosts (together forming the group of Halecostomi) or to gars (Lepisosteiformes; together forming the group of Holostei)...
January 11, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28073363/swept-away-ocean-currents-and-seascape-features-influence-genetic-structure-across-the-18-000-km-indo-pacific-distribution-of-a-marine-invertebrate-the-black-lip-pearl-oyster-pinctada-margaritifera
#7
Monal M Lal, Paul C Southgate, Dean R Jerry, Cyprien Bosserelle, Kyall R Zenger
BACKGROUND: Genetic structure in many widely-distributed broadcast spawning marine invertebrates remains poorly understood, posing substantial challenges for their fishery management, conservation and aquaculture. Under the Core-Periphery Hypothesis (CPH), genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28049722/the-linc-complex-contributes-to-heterochromatin-organisation-and-transcriptional-gene-silencing-in-plants
#8
Axel Poulet, Céline Duc, Maxime Voisin, Sophie Desset, Sylvie Tutois, Emmanuel Vanrobays, Matthias Benoit, David E Evans, Aline V Probst, Christophe Tatout
The LInker of Nucleoskeleton and Cytoskeleton (LINC) complex is an evolutionary well-conserved protein bridge connecting the cytoplasmic and nuclear compartments across the nuclear membrane. While recent data support its function in nuclear morphology and meiosis, its implication in chromatin organisation has not been studied in plants. Here 3D imaging methods have been used to investigate nuclear morphology and chromatin organisation in interphase nuclei of the model plant Arabidopsis thaliana, in which heterochromatin cluster in conspicuous chromatin domains called chromocentres...
January 3, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28049421/placental-transcriptome-co-expression-analysis-reveals-conserved-regulatory-programs-across-gestation
#9
Sam Buckberry, Tina Bianco-Miotto, Stephen J Bent, Vicki Clifton, Cheryl Shoubridge, Kartik Shankar, Claire T Roberts
BACKGROUND: Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exploring the underlying organisation of the placental transcriptome through a systematic analysis of gene-wise co-expression relationships. RESULTS: In this study, we performed a comprehensive analysis of human placental co-expression using RNA sequencing and intergrated multiple transcriptome datasets spanning human gestation...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28028815/metabolic-systems-biology-a-brief-primer
#10
REVIEW
Lindsay M Edwards
In the early to mid 20(th) Century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig Von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome...
December 28, 2016: Journal of Physiology
https://www.readbyqxmd.com/read/27943584/cytogenetic-features-of-rrna-genes-across-land-plants-analysis-of-the-plant-rdna-database
#11
Sònia Garcia, Ales Kovařík, Andrew R Leitch, Teresa Garnatje
The online resource www.plantrdnadatabase.com stores information on number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2,949 karyotypes, from 1,791 species and 86 plant families and performed ancestral character state reconstructions...
December 10, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27927215/functional-characterisation-of-long-intergenic-non-coding-rnas-through-genetic-interaction-profiling-in-saccharomyces-cerevisiae
#12
Dimitris Kyriakou, Emmanouil Stavrou, Panayiota Demosthenous, Georgia Angelidou, Bryan-Joseph San Luis, Charles Boone, Vasilis J Promponas, Antonis Kirmizis
BACKGROUND: Transcriptome studies have revealed that many eukaryotic genomes are pervasively transcribed producing numerous long non-coding RNAs (lncRNAs). However, only a few lncRNAs have been ascribed a cellular role thus far, with most regulating the expression of adjacent genes. Even less lncRNAs have been annotated as essential hence implying that the majority may be functionally redundant. Therefore, the function of lncRNAs could be illuminated through systematic analysis of their synthetic genetic interactions (GIs)...
December 7, 2016: BMC Biology
https://www.readbyqxmd.com/read/27914912/identification-of-foxj1-effectors-during-ciliogenesis-in-the-foetal-respiratory-epithelium-and-embryonic-left-right-organiser-of-the-mouse
#13
Michael Stauber, Marina Weidemann, Oliver Dittrich-Breiholz, Katharina Lobschat, Leonie Alten, Michaela Mai, Anja Beckers, Michael Kracht, Achim Gossler
Formation of motile cilia in vertebrate embryos is essential for proper development and tissue function. Key regulators of motile ciliogenesis are the transcription factors FOXJ1 and NOTO, which are conserved throughout vertebrates. Downstream target genes of FOXJ1 have been identified in a variety of species, organs and cultured cell lines; in murine embryonic and foetal tissues, however, FOXJ1 and NOTO effectors have not been comprehensively analysed and our knowledge of the downstream genetic programme driving motile ciliogenesis in the mammalian lung and ventral node is fragmentary...
November 30, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27910910/genome-wide-characterisation-and-expression-profile-of-the-grapevine-atl-ubiquitin-ligase-family-reveal-biotic-and-abiotic-stress-responsive-and-development-related-members
#14
Pietro Ariani, Alice Regaiolo, Arianna Lovato, Alejandro Giorgetti, Andrea Porceddu, Salvatore Camiolo, Darren Wong, Simone Castellarin, Elodie Vandelle, Annalisa Polverari
The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903804/structural-protein-vp2-of-african-horse-sickness-virus-is-not-essential-for-virus-replication-in-vitro
#15
René G P van Gennip, Sandra G P van de Water, Christiaan A Potgieter, Piet A van Rijn
: The Reoviridae family consists of nonenveloped multilayered viruses with a double-stranded RNA genome consisting of 9 to 12 genome segments. The Orbivirus genus of the Reoviridae family contains African horse sickness virus (AHSV), bluetongue virus, and epizootic hemorrhagic disease virus, which cause notifiable diseases and are spread by biting Culicoides species. Here, we used reverse genetics for AHSV to study the role of outer capsid protein VP2, encoded by genome segment 2 (Seg-2)...
February 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/27899279/wormbase-parasite-a-comprehensive-resource-for-helminth-genomics
#16
Kevin L Howe, Bruce J Bolt, Myriam Shafie, Paul Kersey, Matthew Berriman
The number of publicly available parasitic worm genome sequences has increased dramatically in the past three years, and research interest in helminth functional genomics is now quickly gathering pace in response to the foundation that has been laid by these collective efforts. A systematic approach to the organisation, curation, analysis and presentation of these data is clearly vital for maximising the utility of these data to researchers. We have developed a portal called WormBase ParaSite (http://parasite...
November 27, 2016: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/27889532/characterisation-of-zbtb46-and-dc-script-znf366-in-rainbow-trout-transcription-factors-potentially-involved-in-dendritic-cell-maturation-and-activation-in-fish
#17
Jun Wang, Tiehui Wang, Ottavia Benedicenti, Catherine Collins, Kaiyu Wang, Christopher J Secombes, Jun Zou
ZBTB46 and DC-SCRIPT/ZNF366 are two zinc finger transcription factors that play important roles in regulating differentiation of dendritic cells in mammals. In this study, the ZBTB46 and DC-SCRIPT/ZNF366 homologues were identified in rainbow trout Oncorhynchus mykiss and their expression analysed in vivo and in vitro. As transcription factors, they are well conserved in sequence, genomic organisation and gene synteny. Their expression was differentially modulated by bacterial and viral PAMPs in the monocyte/macrophage like cell line RTS-11, in primary head kidney (HK) macrophages, and in HK macrophages cultured with IL-4/13A...
November 23, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27883255/genome-wide-association-of-functional-traits-linked-with-campylobacter-jejuni-survival-from-farm-to-fork
#18
Koji Yahara, Guillaume Méric, Aidan J Taylor, Stefan P W de Vries, Susan Murray, Ben Pascoe, Leonardos Mageiros, Alicia Torralbo, Ana Vidal, Anne Ridley, Sho Komukai, Helen Wimalarathna, Alison J Cody, Frances M Colles, Noel McCarthy, David Harris, James E Bray, Keith A Jolley, Martin C J Maiden, Stephen D Bentley, Julian Parkhill, Christopher D Bayliss, Andrew Grant, Duncan Maskell, Xavier Didelot, David J Kelly, Samuel K Sheppard
Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7,343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain...
November 24, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27861577/identifying-causal-genes-at-the-multiple-sclerosis-associated-region-6q23-using-capture-hi-c
#19
Paul Martin, Amanda McGovern, Jonathan Massey, Stefan Schoenfelder, Kate Duffus, Annie Yarwood, Anne Barton, Jane Worthington, Peter Fraser, Stephen Eyre, Gisela Orozco
BACKGROUND: The chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms (SNPs) associated with MS in this region, which spans around 2.5 Mb. Most GWAS variants associated with complex traits, including these four MS associated SNPs, are non-coding and their function is currently unknown. However, GWAS variants have been found to be enriched in enhancers and there is evidence that they may be involved in transcriptional regulation of their distant target genes through long range chromatin looping...
2016: PloS One
https://www.readbyqxmd.com/read/27859262/functional-and-prognostic-significance-of-the-genomic-amplification-of-frizzled-6-fzd6-in-breast-cancer
#20
Gabriele Corda, Gianluca Sala, Rossano Lattanzio, Manuela Iezzi, Michele Sallese, Giorgia Fragassi, Alessia Lamolinara, Hasan Mirza, Daniela Barcaroli, Sibylle Ermler, Elisabete Silva, Hemad Yasaei, Robert F Newbold, Paola Vagnarelli, Marcella Mottolese, Pier Giorgio Natali, Letizia Perracchio, Jelmar Quist, Anita Grigoriadis, Pierfrancesco Marra, Andrew N Tutt, Mauro Piantelli, Stefano Iacobelli, Vincenzo De Laurenzi, Arturo Sala
Frizzled receptors mediate Wnt ligand signalling, which is crucially involved in regulating tissue development and differentiation, and is often deregulated in cancer. In this study, we found that the gene encoding the Wnt receptor frizzled 6 (FZD6) is frequently amplified in breast cancer, with an increased incidence in the triple-negative breast cancer (TNBC) subtype. Ablation of FZD6 expression in mammary cancer cell lines: (1) inhibited motility and invasion; (2) induced a more symmetrical shape of organoid three-dimensional cultures; and (3) inhibited bone and liver metastasis in vivo...
February 2017: Journal of Pathology
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