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https://www.readbyqxmd.com/read/29342229/a-rapid-epistatic-mixed-model-association-analysis-by-linear-retransformations-of-genomic-estimated-values
#1
Chao Ning, Dan Wang, Huimin Kang, Raphael Mrode, Lei Zhou, Shizhong Xu, Jian-Feng Liu
Motivation: Epistasis provides a feasible way for probing potential genetic mechanism of complex traits. However, time-consuming computation challenges successful detection of interaction in practice, especially when linear mixed model (LMM) is used to control type I error in the presence of population structure and cryptic relatedness. Results: A rapid epistatic mixed-model association analysis (REMMA) method was developed to overcome computational limitation. This method first estimates individuals' epistatic effects by an extended genomic best linear unbiased prediction (EG-BLUP) model with additive and epistatic kinship matrix, then pairwise interaction effects are obtained by linear retransformations of individuals' epistatic effects...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29338683/genomic-repeats-misassembly-and-reannotation-a-case-study-with-long-read-resequencing-of-porphyromonas-gingivalis-reference-strains
#2
Luis Acuña-Amador, Aline Primot, Edouard Cadieu, Alain Roulet, Frédérique Barloy-Hubler
BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29335552/a-pathway-for-biological-methane-production-using-bacterial-iron-only-nitrogenase
#3
Yanning Zheng, Derek F Harris, Zheng Yu, Yanfen Fu, Saroj Poudel, Rhesa N Ledbetter, Kathryn R Fixen, Zhi-Yong Yang, Eric S Boyd, Mary E Lidstrom, Lance C Seefeldt, Caroline S Harwood
Methane (CH4) is a potent greenhouse gas that is released from fossil fuels and is also produced by microbial activity, with at least one billion tonnes of CH4 being formed and consumed by microorganisms in a single year 1 . Complex methanogenesis pathways used by archaea are the main route for bioconversion of carbon dioxide (CO2) to CH4 in nature2-4. Here, we report that wild-type iron-iron (Fe-only) nitrogenase from the bacterium Rhodopseudomonas palustris reduces CO2 simultaneously with nitrogen gas (N2) and protons to yield CH4, ammonia (NH3) and hydrogen gas (H2) in a single enzymatic step...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29329459/using-pool-seq-to-search-for-genomic-regions-affected-by-hybrid-inviability-in-the-copepod-t-californicus
#4
Thiago G Lima, Christopher S Willett
The formation of reproductive barriers between allopatric populations involves the accumulation of incompatibilities that lead to intrinsic postzygotic isolation. The evolution of these incompatibilities is usually explained by the Dobzhansky-Muller model, where epistatic interactions that arise within the diverging populations, lead to deleterious interactions when they come together in a hybrid genome. These incompatibilities can lead to hybrid inviability, killing individuals with certain genotypic combinations, and causing the population's allele frequency to deviate from Mendelian expectations...
January 10, 2018: Journal of Heredity
https://www.readbyqxmd.com/read/29325614/ethical-issues-in-neurogenetics
#5
Wendy R Uhlmann, J Scott Roberts
Many neurogenetic conditions are inherited and therefore diagnosis of a patient will have implications for the patient's relatives and can raise ethical issues. Predictive genetic testing offers asymptomatic relatives the opportunity to determine their risk status for a neurogenetic condition, and professional guidelines emphasize patients' autonomy and informed, voluntary decision making. Beneficence and nonmaleficence both need to be considered when making decisions about disclosure and nondisclosure of genetic information and test results...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29323541/development-of-a-targeted-next-generation-sequencing-assay-to-detect-diagnostically-relevant-mutations-of-jak2-calr-and-mpl-in-myeloproliferative-neoplasms
#6
Thomas Frawley, Cathal P O'Brien, Eibhlin Conneally, Elisabeth Vandenberghe, Melanie Percy, Stephen E Langabeer, Karl Haslam
BACKGROUND: The classical Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs), consisting of polycythemia vera, essential thrombocythemia, and primary myelofibrosis, are a heterogeneous group of neoplasms that harbor driver mutations in the JAK2, CALR, and MPL genes. The detection of these mutations has been incorporated into the recent World Health Organization (WHO) diagnostic criteria for MPN. Given a pressing clinical need to screen for these mutations in a routine diagnostic setting, a targeted next-generation sequencing (NGS) assay for the detection of MPN-associated mutations located in JAK2 exon 14, JAK2 exon 12, CALR exon 9, and MPL exon 10 was developed to provide a single platform alternative to reflexive, stepwise diagnostic algorithms...
January 11, 2018: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/29317018/outbreak-of-salmonella-bovismorbificans-associated-with-the-consumption-of-uncooked-ham-products-the-netherlands-2016-to-2017
#7
Diederik Brandwagt, Cees van den Wijngaard, Anna Dolores Tulen, Annemieke Christine Mulder, Agnetha Hofhuis, Rianne Jacobs, Max Heck, Anjo Verbruggen, Hans van den Kerkhof, Ife Slegers-Fitz-James, Lapo Mughini-Gras, Eelco Franz
In January 2017, an increase in reported Salmonellaenterica serotype Bovismorbificans cases in the Netherlands was observed since October 2016. We implemented a case-control study to identify the source, including all cases after December 2016. Adjusted odds ratios were calculated using logistic regression analysis. We traced back the distribution chain of suspected food items and sampled them for microbiological analysis. Human and food isolates were sequenced using whole genome sequencing (WGS). From October 2016 to March 2017, 54 S...
January 2018: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/29314055/legume-genetic-resources-and-transcriptome-dynamics-under-abiotic-stress-conditions
#8
REVIEW
Mostafa Abdelrahman, Sudisha Jogaiah, David J Burritt, Lam-Son Phan Tran
Grain legumes are an important source of nutrition and income for billions of consumers and farmers around the world. However, the low productivity of new legume varieties, due to the limited genetic diversity available for legume breeding programs and poor policymaker support, combined with an increasingly unpredictable global climate, is resulting in a large gap between current yields and the increasing demand for legumes as food. Hence, there is a need for novel approaches to develop new high-yielding legume cultivars that are able to cope with a range of environmental stressors...
January 4, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29310579/gene-trait-matching-across-the-bifidobacterium-longum-pan-genome-reveals-considerable-diversity-in-carbohydrate-catabolism-among-human-infant-strains
#9
Silvia Arboleya, Francesca Bottacini, Mary O'Connell-Motherway, C Anthony Ryan, R Paul Ross, Douwe van Sinderen, Catherine Stanton
BACKGROUND: Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B...
January 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29305543/genotyping-multi-drug-resistant-m-tuberculosis-from-primary-sputum-and-decontaminated-sediment-with-an-integrated-microfluidic-amplification-microarray
#10
Yvonne Linger, Christopher Knickerbocker, David Sipes, Julia Golova, Molly Franke, Roger Calderon, Leonid Lecca, Nitu Thakore, Rebecca Holmberg, Peter Qu, Alexander Kukhtin, Megan B Murray, Christopher G Cooney, Darrell P Chandler
There is a growing awareness that molecular diagnostics for detect-to-treat applications will soon need a highly multiplexed mutation detection and identification capability. In this study, we converted an open-amplicon MDR-TB microarray hybridization test into an entirely closed-amplicon consumable (an amplification microarray) and evaluated its performance on matched sputum and sediment extracts. Reproducible genotyping (LoD) was achieved with ∼25 MTB genomes (100 fg of MTB DNA) per reaction; the estimated shelf life of the test was least 18 months when stored at 4°C...
January 5, 2018: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29304850/metabolic-capability-and-in-situ-activity-of-microorganisms-in-an-oil-reservoir
#11
Yi-Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia S Zaramela, Ji-Dong Gu, Bo-Zhong Mu, Karsten Zengler
BACKGROUND: Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. RESULTS: Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach...
January 5, 2018: Microbiome
https://www.readbyqxmd.com/read/29304376/hipaa-s-individual-right-of-access-to-genomic-data-reconciling-safety-and-civil-rights
#12
Barbara J Evans
In 2014, the United States granted individuals a right of access to their own laboratory test results, including genomic data. Many observers feel that this right is in tension with regulatory and bioethical standards designed to protect the safety of people who undergo genomic testing. This commentary attributes this tension to growing pains within an expanding federal regulatory program for genetic and genomic testing. The Genetic Information Nondiscrimination Act of 2008 expanded the regulatory agenda to encompass civil rights and consumer safety...
January 4, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29297325/differential-expression-of-nbs-lrr-encoding-genes-in-the-root-transcriptomes-of-two-solanum-phureja-genotypes-with-contrasting-resistance-to-globodera-rostochiensis
#13
Alex V Kochetov, Anastasiya Y Glagoleva, Kseniya V Strygina, Elena K Khlestkina, Sophia V Gerasimova, Salmaz M Ibragimova, Natalja V Shatskaya, Gennady V Vasilyev, Dmitry A Afonnikov, Nikolay A Shmakov, Olga Y Antonova, Tatyana A Gavrilenko, Natalia V Alpatyeva, Alexander Khiutti, Olga S Afanasenko
BACKGROUND: The characterization of major resistance genes (R genes) in the potato remains an important task for molecular breeding. However, R genes are rapidly evolving and frequently occur in genomes as clusters with complex structures, and their precise mapping and identification are complicated and time consuming. RESULTS: Comparative analysis of root transcriptomes of Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis revealed a number of differentially expressed genes...
December 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29287446/a-simple-microsatellite-based-method-for-hazelnut-oil-dna-analysis
#14
Sabrina Lucchetti, Gianni Pastore, Guido Leoni, Serena Arima, Nicolò Merendino, Simona Baima, Roberto Ambra
Molecular food traceability requires continuous updates to identify more robust, efficient and affordable methodologies to guarantee food quality and safety and especially consumers' health. Available commercial kits are often unsatisfactory and require modifications to successfully detect single components on complex and transformed food matrices. Here we report a simple method for molecular traceability of cold-pressed hazelnut oil based on microsatellite DNA markers. Different genomic extraction methodologies were tested and a total genome pre-amplification step was applied on PCR-negative samples...
April 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29286473/a-simple-fluorescence-based-reporter-assay-to-identify-cellular-components-required-for-ricin-toxin-a-chain-rta-trafficking-in-yeast
#15
Björn Becker, Manfred J Schmitt
Bacterial and plant A/B toxins exploit the natural trafficking pathways in eukaryotic cells to reach their intracellular target(s) in the cytosol and to ultimately kill. Such A/B toxins generally consist of an enzymatically active Asubunit (e.g., ricin toxin A (RTA)) and one or more cell binding Bsubunit(s), which are responsible for toxin binding to specific cell surface receptors. Our current knowledge of how A/B toxins are capable of efficiently intoxicating cells helped scientists to understand fundamental cellular mechanisms, like endocytosis and intracellular protein sorting in higher eukaryotic cells...
December 15, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29286433/methodology-for-sputum-induction-and-laboratory-processing
#16
Julien Guiot, Sophie Demarche, Monique Henket, Virginie Paulus, Sophie Graff, Florence Schleich, Jean-Louis Corhay, Renaud Louis, Catherine Moermans
The technique of sputum induction and processing is a recognized non-invasive method allowing the collection and analysis of cells from the airways, which is interesting in various respiratory diseases like asthma, chronic obstructive pulmonary disease (COPD), chronic cough, or idiopathic pulmonary fibrosis. This technique is well tolerated, safe and non-invasive, but is currently limited to research services and specialized centers in clinical practice because it is technically demanding, time-consuming, and requires trained staff...
December 17, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29259947/prevalence-of-trichinella-spp-infections-in-hunted-wild-boars-in-northern-iran
#17
Ali Rostami, Hooshang Khazan, Bahram Kazemi, Eshrat Beigom Kia, Mojgan Bandepour, Niloofar Taghipour, Gholamreza Mowlavi
Background: Trichinellosis is an important and neglected foodborne zoonotic infectious disease in worldwide. The most human outbreaks in recent years have been related to consumption of wild boar meat. This cross-sectional study determined the prevalence of Trichinella spp. infections in hunted wild boars in northern Iran. Methods: Thirty-five hunted wild boars were subjected in this study in 2015. All samples were examined by conventional artificial digestion method to detect of muscle larvae...
December 2017: Iranian Journal of Public Health
https://www.readbyqxmd.com/read/29259772/genetics-in-the-21st-century-implications-for-patients-consumers-and-citizens
#18
Jonathan Roberts, Anna Middleton
The first human genome project, completed in 2003, uncovered the genetic building blocks of humankind. Painstakingly cataloguing the basic constituents of our DNA ('genome sequencing') took ten years, over three billion dollars and was a multinational collaboration. Since then, our ability to sequence genomes has been finessed so much that by 2017 it is possible to explore the 20,000 or so human genes for under £1000, in a matter of days. Such testing offers clues to our past, present and future health, as well as information about how we respond to medications so that truly 'personalised medicine' is now a reality...
2017: F1000Research
https://www.readbyqxmd.com/read/29258987/the-application-of-mutmap-in-forward-genetic-studies-based-on-whole-genome-sequencing
#19
Jin Hong Yuan, Jun Hua Li, Jiao Jiao Yuan, Ke Li Jia, Shu Fen Li, Chuan Liang Deng, Wu Jun Gao
Classical forward genetic analysis relies on construction of complicated progeny populations and development of many molecular markers for linkage analysis in genetic mapping, which is both time- and cost-consuming. The recently developed MutMap is a new forward genetic approach based on high-throughput next-generation sequencing technologies. It is more efficient and affordable than traditional methods. Moreover, new extended methods based on MutMap have been developed: MutMap+, which is based on self-crossing; MutMap-Gap, which is used to recognize the causative variations occurring in genome gap regions; QTL-seq, a method similar to MutMap for mapping quantitative trait loci...
December 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29238598/breeding-next-generation-tree-fruits-technical-and-legal-challenges
#20
REVIEW
Lorenza Dalla Costa, Mickael Malnoy, Ivana Gribaudo
The new plant breeding technologies (NPBTs) have recently emerged as powerful tools in the context of 'green' biotechnologies. They have wide potential compared to classical genetic engineering and they are attracting the interest of politicians, stakeholders and citizens due to the revolutionary impact they may have on agriculture. Cisgenesis and genome editing potentially allow to obtain pathogen-resistant plants or plants with enhanced qualitative traits by introducing or disrupting specific genes in shorter times compared to traditional breeding programs and by means of minimal modifications in the plant genome...
2017: Horticulture Research
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