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https://www.readbyqxmd.com/read/29651688/metschnikowia-mating-genomics
#1
Dong Kyung Lee, Tom Hsiang, Marc-André Lachance
Genes involved in mating type determination and recognition were examined in Metschnikowia and related species, to gather insights on factors affecting mating compatibility patterns among haplontic, heterothallic yeast species of the genus. We confirmed the universality of the special mating locus organisation found in Clavispora lusitaniae across and exclusive to the family Metschnikowiaceae (i.e., Metschnikowia and Clavispora). Timing of the divergence between idiomorphs was confirmed to coincide with the origin of the larger (CUG-ser) clade comprising the Debaryomycetaceae and the Metschnikowiaceae, exclusive of Cephaloascus fragrans...
April 12, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29644746/the-distinct-phopr-mediated-responses-to-phosphate-limitation-in-bacillus-subtilis-subspecies-subtilis-and-spizizenii-stem-from-differences-in-wall-teichoic-acid-composition-and-metabolism
#2
Michael P Prunty, David Noone, Kevin M Devine
The PhoPR-mediated response to phosphate limitation (PHO response) in Bacillus subtilis subsp subtilis is amplified and maintained by reducing the level of Lipid VG composed of poly(glycerol phosphate), a wall teichoic acid (WTA) biosynthetic intermediate that inhibits PhoR autokinase activity. However, the reduction in Lipid VG level is effected by activated PhoP∼P, raising the question of how the PHO response is first initiated. Furthermore, that WTA is composed of poly(ribitol phosphate) in Bacillus subtilis subsp spizizenii prompted an investigation of how the PHO response is regulated in that bacterium...
April 12, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29561903/phylogenetic-analyses-and-antimicrobial-resistance-profiles-of-campylobacter-spp-from-diarrhoeal-patients-and-chickens-in-botswana
#3
Stefan P W de Vries, Moses Vurayai, Mark Holmes, Srishti Gupta, Michael Bateman, David Goldfarb, Duncan J Maskell, Maitshwarelo Ignatius Matsheka, Andrew J Grant
Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp...
2018: PloS One
https://www.readbyqxmd.com/read/29547555/dna-supercoiling-topoisomerases-and-cohesin-partners-in-regulating-chromatin-architecture
#4
Camilla Björkegren, Laura Baranello
Although our knowledge of chromatin organization has advanced significantly in recent years, much about the relationships between different features of genome architecture is still unknown. Folding of mammalian genomes into spatial domains is thought to depend on architectural proteins, other DNA-binding proteins, and different forms of RNA. In addition, emerging evidence points towards the possibility that the three-dimensional organisation of the genome is controlled by DNA topology. In this scenario, cohesin, CCCTC-binding factor (CTCF), transcription, DNA supercoiling, and topoisomerases are integrated to dictate different layers of genome organization, and the contribution of all four to gene control is an important direction of future studies...
March 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29540241/genomic-positional-conservation-identifies-topological-anchor-point-rnas-linked-to-developmental-loci
#5
Paulo P Amaral, Tommaso Leonardi, Namshik Han, Emmanuelle Viré, Dennis K Gascoigne, Raúl Arias-Carrasco, Magdalena Büscher, Luca Pandolfini, Anda Zhang, Stefano Pluchino, Vinicius Maracaja-Coutinho, Helder I Nakaya, Martin Hemberg, Ramin Shiekhattar, Anton J Enright, Tony Kouzarides
BACKGROUND: The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider promoter conservation and positional conservation as indicators of functional commonality. RESULTS: We identify 665 conserved lncRNA promoters in mouse and human that are preserved in genomic position relative to orthologous coding genes...
March 15, 2018: Genome Biology
https://www.readbyqxmd.com/read/29540192/udp-glycosyltransferase-genes-in-trypanosomatid-genomes-have-diversified-independently-to-meet-the-distinct-developmental-needs-of-parasite-adaptations
#6
Sara Silva Pereira, Andrew P Jackson
BACKGROUND: Trypanosomatid parasites such as Trypanosoma spp. and Leishmania spp. are a major source of infectious disease in humans and domestic animals worldwide. Fundamental to the host-parasite interactions of these potent pathogens are their cell surfaces, which are highly decorated with glycosylated proteins and other macromolecules. Trypanosomatid genomes contain large multi-copy gene families encoding UDP-dependent glycosyltransferases (UGTs), the primary role of which is cell-surface decoration...
March 14, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29535103/streamlined-histone-based-fluorescence-lifetime-imaging-microscopy-flim-for-studying-chromatin-organisation
#7
Alice Sherrard, Paul Bishop, Melanie Panagi, Maria Beatriz Villagomez, Dominic Alibhai, Abderrahmane Kaidi
Changes in chromatin structure are key determinants of genomic responses. Thus, methods that enable such measurements are instrumental for investigating genome regulation and function. Here, we report further developments and validation of a streamlined method of histone-based fluorescence lifetime imaging microscopy (FLIM) that robustly detects chromatin compaction states in fixed and live cells, in 2D and 3D. We present a quality-controlled and detailed method that is simpler and faster than previous methods, and uses FLIMfit open-source software...
March 13, 2018: Biology Open
https://www.readbyqxmd.com/read/29533090/genomics-and-cure-understanding-narratives-of-patients-with-duchenne-muscular-dystrophy-in-japan
#8
Masae Kato
Globally, genomics research is expected to enhance the health of patients with intractable diseases such as Duchenne muscular dystrophy (DMD). But how do patients perceive medical and scientific attempts at creating drugs and finding cure, and why? Since the 1990s, a number of clinical trials for patients of DMD have been organized. Among them are a gene therapy and exon skipping, and they indicate the possibility of finding therapies for DMD patients. Since 2011, Japanese medical institutions have been participating in Global Clinical Trials so that Japanese DMD patients can have access to them once developed...
April 2018: Anthropology & Medicine
https://www.readbyqxmd.com/read/29529984/in-the-beginning-was-the-genome-genomics-and-the-bi-textuality-of-human-existence
#9
H A E Hub Zwart
This paper addresses the cultural impact of genomics and the Human Genome Project (HGP) on human self-understanding. Notably, it addresses the claim made by Francis Collins (director of the HGP) that the genome is the language of God and the claim made by Max Delbrück (founding father of molecular life sciences research) that Aristotle must be credited with having predicted DNA as the soul that organises bio-matter. From a continental philosophical perspective I will argue that human existence results from a dialectical interaction between two types of texts: the language of molecular biology and the language of civilisation; the language of the genome and the language of our socio-cultural, symbolic ambiance...
April 2018: New Bioethics: a Multidisciplinary Journal of Biotechnology and the Body
https://www.readbyqxmd.com/read/29527494/grey-matter-volume-and-cortical-structure-in-prader-willi-syndrome-compared-to-typically-developing-young-adults
#10
Katherine E Manning, Roger Tait, John Suckling, Anthony J Holland
Prader-Willi syndrome (PWS) is a neurodevelopmental disorder of genomic imprinting, presenting with a characteristic overeating disorder, mild to moderate intellectual disability, and a variable range of social and behavioral difficulties. Consequently, widespread alterations in neural structure and developmental and maturational trajectory would be expected. To date, there have been few quantitative and systematic studies of brain morphology in PWS, although alterations of volume and of cortical organisation have been reported...
2018: NeuroImage: Clinical
https://www.readbyqxmd.com/read/29526369/evidence-based-data-and-rare-cancers-the-need-for-a-new-methodological-approach-in-research-and-investigation
#11
S Mathoulin-Pélissier, K Pritchard-Jones
Rare cancers are not so rare, their incidence is increasing and, as a group, they have worse survival than the common cancers. These factors emphasise the societal need to ensure sufficient focus on research into their biological basis, aetiological factors, new more effective therapies and organisation of healthcare to improve access to best practice and innovation. Accuracy of diagnosis is one of the first hurdles to be overcome, with around one third of tumours being reclassified - by type or risk group - when subject to a centralised pathology review process...
March 2, 2018: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29515813/cloud-based-adaptive-exon-prediction-for-dna-analysis
#12
Srinivasareddy Putluri, Md Zia Ur Rahman, Shaik Yasmeen Fathima
Cloud computing offers significant research and economic benefits to healthcare organisations. Cloud services provide a safe place for storing and managing large amounts of such sensitive data. Under conventional flow of gene information, gene sequence laboratories send out raw and inferred information via Internet to several sequence libraries. DNA sequencing storage costs will be minimised by use of cloud service. In this study, the authors put forward a novel genomic informatics system using Amazon Cloud Services, where genomic sequence information is stored and accessed for processing...
February 2018: Healthcare Technology Letters
https://www.readbyqxmd.com/read/29501025/synthetic-post-translational-modification-of-histones
#13
REVIEW
Simon Nadal, Ritu Raj, Shabaz Mohammed, Benjamin G Davis
Chromatin is the physiological template of genetic information in all eukaryotic cells, a highly organised complex of DNA and histone proteins central in regulating gene expression and genome organisation. A multitude of histone post-translational modifications (PTMs) have been discovered, providing a glance into the complex interplay of these epigenetic marks in cellular processes. In the last decade, synthetic and chemical biology techniques have emerged to study these modifications, including genetic code expansion, histone semisynthesis and post-translational chemical mutagenesis...
February 28, 2018: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29497530/unravelling-the-molecular-basis-for-regulatory-t-cell-plasticity-and-loss-of-function-in-disease
#14
REVIEW
Timothy Sadlon, Cheryl Y Brown, Veronika Bandara, Christopher M Hope, John E Schjenken, Stephen M Pederson, James Breen, Alistair Forrest, Marc Beyer, Sarah Robertson, Simon C Barry
Regulatory T cells (Treg) are critical for preventing autoimmunity and curtailing responses of conventional effector T cells (Tconv). The reprogramming of T-cell fate and function to generate Treg requires switching on and off of key gene regulatory networks, which may be initiated by a subtle shift in expression levels of specific genes. This can be achieved by intermediary regulatory processes that include microRNA and long noncoding RNA-based regulation of gene expression. There are well-documented microRNA profiles in Treg and Tconv, and these can operate to either reinforce or reduce expression of a specific set of target genes, including FOXP3 itself...
2018: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/29491738/conservation-and-variation-in-strategies-for-dna-replication-of-kinetoplastid-nuclear-genomes
#15
REVIEW
Catarina A Marques, Richard McCulloch
Introduction: Understanding how the nuclear genome of kinetoplastid parasites is replicated received experimental stimulus from sequencing of the Leishmania major, Trypanosoma brucei and Trypanosoma cruzi genomes around 10 years ago. Gene annotations suggested key players in DNA replication initiation could not be found in these organisms, despite considerable conservation amongst characterised eukaryotes. Initial studies that indicated trypanosomatids might possess an archaeal-like Origin Recognition Complex (ORC), composed of only a single factor termed ORC1/CDC6, have been supplanted by the more recent identification of an ORC in T...
February 2018: Current Genomics
https://www.readbyqxmd.com/read/29466411/molecular-epidemiology-of-tuberculosis-in-tasmania-and-genomic-characterisation-of-its-first-known-multi-drug-resistant-case
#16
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
#17
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
#18
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
#19
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
#20
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
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