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https://www.readbyqxmd.com/read/28535266/mechanism-of-bacterial-gene-rearrangement-spra-catalyzed-precise-dna-recombination-and-its-directionality-control-by-sprb-ensure-the-gene-rearrangement-and-stable-expression-of-spsm-during-sporulation-in-bacillus-subtilis
#1
Kimihiro Abe, Takuo Takamatsu, Tsutomu Sato
A sporulation-specific gene, spsM, is disrupted by an active prophage, SPβ, in the genome of Bacillus subtilis. SPβ excision is required for two critical steps: the onset of the phage lytic cycle and the reconstitution of the spsM-coding frame during sporulation. Our in vitro study demonstrated that SprA, a serine-type integrase, catalyzed integration and excision reactions between attP of SPβ and attB within spsM, while SprB, a recombination directionality factor, was necessary only for the excision between attL and attR in the SPβ lysogenic chromosome...
May 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28535256/epigenetic-and-genetic-contributions-to-adaptation-in-chlamydomonas
#2
Ilkka Kronholm, Andrew Bassett, David Baulcombe, Sinéad Collins
Epigenetic modifications, such as DNA methylation or histone modifications, can be transmitted between cellular or organismal generations. However, there are no experiments measuring their role in adaptation, so here we use experimental evolution to investigate how epigenetic variation can contribute to adaptation. We manipulated DNA methylation and histone acetylation in the unicellular green alga Chlamydomonas reinhardtii both genetically and chemically to change the amount of epigenetic variation generated or transmitted in adapting populations in three different environments (salt stress, phosphate starvation, and high CO2) for two hundred asexual generations...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535200/the-draft-genome-of-blunt-snout-bream-megalobrama-amblycephala-reveals-the-development-of-intermuscular-bone-and-adaptation-to-herbivorous-diet
#3
Han Liu, Chunhai Chen, Zexia Gao, Jiumeng Min, Yongming Gu, Jianbo Jian, Xiewu Jiang, Huimin Cai, Ingo Ebersberger, Meng Xu, Xinhui Zhang, Jianwei Chen, Wei Luo, Boxiang Chen, Junhui Chen, Hong Liu, Jiang Li, Ruifang Lai, Mingzhou Bai, Jin Wei, Shaokui Yi, Huanling Wang, Xiaojuan Cao, Xiaoyun Zhou, Yuhua Zhao, Kaijian Wei, Ruibin Yang, Bingnan Liu, Shancen Zhao, Xiaodong Fang, Manfred Schartl, Xueqiao Qian, Weimin Wang
Background: The blunt snout bream, Megalobrama amblycephala , is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption. Results: As a first towards optimizing this aquatic livestock, we present a 1.116-Gb draft genome of M. amblycephala , with 779.54 Mb anchored on 24 linkage groups...
May 23, 2017: GigaScience
https://www.readbyqxmd.com/read/28535155/elevated-apobec3b-expression-drives-a-kataegic-like-mutation-signature-and-replication-stress-related-therapeutic-vulnerabilities-in-p53-defective-cells
#4
Jenni Nikkilä, Rahul Kumar, James Campbell, Inger Brandsma, Helen N Pemberton, Fredrik Wallberg, Kinga Nagy, Ildikó Scheer, Beata G Vertessy, Artur A Serebrenik, Valentina Monni, Reuben S Harris, Stephen J Pettitt, Alan Ashworth, Christopher J Lord
BACKGROUND: Elevated APOBEC3B expression in tumours correlates with a kataegic pattern of localised hypermutation. We assessed the cellular phenotypes associated with high-level APOBEC3B expression and the influence of p53 status on these phenotypes using an isogenic system. METHODS: We used RNA interference of p53 in cells with inducible APOBEC3B and assessed DNA damage response (DDR) biomarkers. The mutational effects of APOBEC3B were assessed using whole-genome sequencing...
May 23, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28534836/differentiation-and-structure-in-sulfolobus-islandicus-rod-shaped-virus-populations
#5
Maria A Bautista, Jesse A Black, Nicholas D Youngblut, Rachel J Whitaker
In the past decade, molecular surveys of viral diversity have revealed that viruses are the most diverse and abundant biological entities on Earth. In culture, however, most viral isolates that infect microbes are represented by a few variants isolated on type strains, limiting our ability to study how natural variation affects virus-host interactions in the laboratory. We screened a set of 137 hot spring samples for viruses that infect a geographically diverse panel of the hyperthemophilic crenarchaeon Sulfolobus islandicus...
May 19, 2017: Viruses
https://www.readbyqxmd.com/read/28534829/variation-in-the-genetic-repertoire-of-viruses-infecting-micromonas-pusilla-reflects-horizontal-gene-transfer-and-links-to-their-environmental-distribution
#6
Jan F Finke, Danielle M Winget, Amy M Chan, Curtis A Suttle
Prasinophytes, a group of eukaryotic phytoplankton, has a global distribution and is infected by large double-stranded DNA viruses (prasinoviruses) in the family Phycodnaviridae. This study examines the genetic repertoire, phylogeny, and environmental distribution of phycodnaviruses infecting Micromonas pusilla, other prasinophytes and chlorophytes. Based on comparisons among the genomes of viruses infecting M. pusilla and other phycodnaviruses, as well as the genome from a host isolate of M. pusilla, viruses infecting M...
May 19, 2017: Viruses
https://www.readbyqxmd.com/read/28534821/from-genome-to-phenotype-an-integrative-approach-to-evaluate-the-biodiversity-of-lactococcus-lactis
#7
REVIEW
Valérie Laroute, Hélène Tormo, Christel Couderc, Muriel Mercier-Bonin, Pascal Le Bourgeois, Muriel Cocaign-Bousquet, Marie-Line Daveran-Mingot
Lactococcus lactis is one of the most extensively used lactic acid bacteria for the manufacture of dairy products. Exploring the biodiversity of L. lactis is extremely promising both to acquire new knowledge and for food and health-driven applications. L. lactis is divided into four subspecies: lactis, cremoris, hordniae and tructae, but only subsp. lactis and subsp. cremoris are of industrial interest. Due to its various biotopes, Lactococcus subsp. lactis is considered the most diverse. The diversity of L...
May 19, 2017: Microorganisms
https://www.readbyqxmd.com/read/28534784/incorporation-of-solvent-effect-into-multi-objective-evolutionary-algorithm-for-improved-protein-structure-prediction
#8
Shangce Gao, Jiujun Cheng, Yuki Todo, Mengchu Zhou
The problem of predicting the three-dimensional structure of a protein from its one-dimensional sequence has been called the "holy grail of molecular biology", and it has become an important part of structural genomics projects. Despite the rapid developments in computer technology and computational intelligence, it remains challenging and fascinating. In this paper, to solve it we propose a multi-objective evolutionary algorithm. We decompose the protein energy function Chemistry at HARvard Macromolecular Mechanics force fields into bond and non-bond energies as the first and second objectives...
May 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28534660/radiation-induced-pulmonary-fibrosis-as-a-model-of-progressive-fibrosis-contributions-of-dna-damage-inflammatory-response-and-cellular-senescence-genes
#9
Tyler A Beach, Carl J Johnston, Angela M Groves, Jacqueline P Williams, Jacob N Finkelstein
Purpose/Aim of Study: Studies of pulmonary fibrosis (PF) have resulted in DNA damage, inflammatory response, and cellular senescence being widely hypothesized to play a role in the progression of the disease. Utilizing these aforementioned terms, genomics databases were interrogated along with the term, "pulmonary fibrosis," to identify genes common among all 4 search terms. Findings were compared to data derived from a model of radiation-induced progressive pulmonary fibrosis (RIPF) to verify that these genes are similarly expressed, supporting the use of radiation as a model for diseases involving PF, such as human idiopathic pulmonary fibrosis (IPF)...
May 23, 2017: Experimental Lung Research
https://www.readbyqxmd.com/read/28534505/proteomic-identification-of-erp29-as-a-key-chemoresistant-factor-activated-by-the-aggregating-p53-mutant-arg282trp
#10
Y Zhang, Y Hu, J-L Wang, H Yao, H Wang, L Liang, C Li, H Shi, Y Chen, J-Y Fang, J Xu
Mutation of the TP53 gene represents a prevalent genetic alteration in human cancers, and a subset of p53 mutants may form amyloid-like aggregates that contribute to the gain of oncogenic functions (GOFs) and chemoresistance. Here we identify the pathways that may mediate the aggregation-associated GOF by using combined proteomic analysis and genome-wide recruitment profiling. Mass spectrometry revealed activation of unfolded protein response (UPR) pathway and upregulation of endoplasmic reticulum protein 29 (ERp29) in (R282W)TP53-expressing cells that were exposed to cisplatin stress...
May 22, 2017: Oncogene
https://www.readbyqxmd.com/read/28534478/complementary-information-derived-from-crispr-cas9-mediated-gene-deletion-and-suppression
#11
Joseph Rosenbluh, Han Xu, William Harrington, Stanley Gill, Xiaoxing Wang, Francisca Vazquez, David E Root, Aviad Tsherniak, William C Hahn
CRISPR-Cas9 provides the means to perform genome editing and facilitates loss-of-function screens. However, we and others demonstrated that expression of the Cas9 endonuclease induces a gene-independent response that correlates with the number of target sequences in the genome. An alternative approach to suppressing gene expression is to block transcription using a catalytically inactive Cas9 (dCas9). Here we directly compare genome editing by CRISPR-Cas9 (cutting, CRISPRc) and gene suppression using KRAB-dCas9 (CRISPRi) in loss-of-function screens to identify cell essential genes...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28534435/genome-editing-technologies-and-patent-landscape-overview
#12
Fairouz Benahmed-Miniuk, Mat Kresz, Jitendra K Kanaujiya, Christopher D Southgate
Unlike with zinc finger nuclease and transcriptional activator-like effector nuclease DNA modification technologies that rely on lead proteins, developed through expensive and time-consuming processes, the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system has rapidly emerged as the most promising gene-editing technology to date for the modification of any selected DNA sequence. CRISPR is receiving tremendous fanfare due, in part, to its potential to provide a means to fundamentally alter medical genetics and especially cancer medicine...
May 23, 2017: Pharmaceutical Patent Analyst
https://www.readbyqxmd.com/read/28534256/crispr-cas9-mediated-correction-of-human-genetic-disease
#13
REVIEW
Ke Men, Xingmei Duan, Zhiyao He, Yang Yang, Shaohua Yao, Yuquan Wei
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) protein 9 system (CRISPR/Cas9) provides a powerful tool for targeted genetic editing. Directed by programmable sequence-specific RNAs, this system introduces cleavage and double-stranded breaks at target sites precisely. Compared to previously developed targeted nucleases, the CRISPR/Cas9 system demonstrates several promising advantages, including simplicity, high specificity, and efficiency. Several broad genome-editing studies with the CRISPR/Cas9 system in different species in vivo and ex vivo have indicated its strong potential, raising hopes for therapeutic genome editing in clinical settings...
May 3, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28534127/genetics-of-triglycerides-and-the-risk-of-atherosclerosis
#14
REVIEW
Jacqueline S Dron, Robert A Hegele
PURPOSE OF REVIEW: Plasma triglycerides are routinely measured with a lipid profile, and elevated plasma triglycerides are commonly encountered in the clinic. The confounded nature of this trait, which is correlated with numerous other metabolic perturbations, including depressed high-density lipoprotein cholesterol (HDL-C), has thwarted efforts to directly implicate triglycerides as causal in atherogenesis. Human genetic approaches involving large-scale populations and high-throughput genomic assessment under a Mendelian randomization framework have undertaken to sort out questions of causality...
July 2017: Current Atherosclerosis Reports
https://www.readbyqxmd.com/read/28534105/bacterial-diversity-of-cosmopolitan-culex-pipiens-and-invasive-aedes-japonicus-from-germany
#15
Sina Zotzmann, Antje Steinbrink, Kathrin Schleich, Felix Frantzmann, Chinhda Xoumpholphakdy, Manuela Spaeth, Claire Valiente Moro, Patrick Mavingui, Sven Klimpel
Symbiotic bacteria have gained significant attention in recent years. For example, microbiota of some mosquito species seems to influence the development and transmission of pathogens. Furthermore, several attempts using bacteria as a paratransgenetic tool have been made in order to assist the control of mosquito-borne diseases. In this study, we examined the bacterial diversity of wild-caught adult Culex (Cx.) pipiens and laboratory-reared adult Aedes japonicus (Ae. japonicus) in Germany using a culture-independent method...
May 22, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28534088/the-ppar-gamma-binding-sequence-pal3-is-necessary-for-basal-but-dispensable-for-high-fat-diet-regulated-human-renin-expression-in-the-kidney
#16
Peter Lachmann, Jenny Selbmann, Linda Hickmann, Bernd Hohenstein, Christian Hugo, Vladimir T Todorov
We reported earlier that PPAR-gamma regulates renin transcription through a human-specific atypical binding sequence termed hRen-Pal3. Here we developed a mouse model to investigate the functional relevance of the hRen-Pal3 sequence in vivo since it might be responsible for the increased renin production in obesity and thus for the development of accompanying arterial hypertension. We used bacterial artificial chromosome construct and co-placement strategy to generate two transgenic mouse lines expressing the human renin gene from identical genomic locus without affecting the intrinsic mouse renin expression...
May 22, 2017: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/28534081/power-of-pedigree-likelihood-analysis-in-extended-pedigrees-to-classify-rare-variants-of-uncertain-significance-in-cancer-risk-genes
#17
Elisabeth A Rosenthal, John Michael O Ranola, Brian H Shirts
Rare and private variants of uncertain significance (VUS) are routinely identified in clinical panel, exome, and genome sequencing. We investigated the power of single family co-segregation analysis to aid classification of VUS. We simulated thousands of pedigrees using demographics in China and the United States, segregating benign and pathogenic variants. Genotypes and phenotypes were simulated using penetrance models for Lynch syndrome and breast/ovarian cancer. We calculated LOD scores adjusted for proband ascertainment (LODadj), to determine power to yield quantitative evidence for, or against, pathogenicity of the VUS...
May 22, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28534065/tailoring-high-density-oligonucleotide-arrays-for-transcript-profiling-of-different-arabidopsis-thaliana-accessions-using-a-sequence-based-approach
#18
Anastassia Boudichevskaia, Hieu Xuan Cao, Renate Schmidt
Excluding polymorphic probes from GeneChip (®) transcript profiling experiments via a sequence-based approach results in improved detection of differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24. GeneChip(®) arrays represent a powerful tool for transcript profiling experiments. The ATH1 GeneChip(®) has been designed based on the sequence of the Arabidopsis thaliana reference genome Col-0, hence the features on the array exactly match the sequences of Col-0 transcripts...
May 22, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28534044/hsp-and-deafness-neurocristopathy-caused-by-a-novel-mosaic-sox10-mutation
#19
Sandra Donkervoort, Diana Bharucha-Goebel, Pomi Yun, Ying Hu, Payam Mohassel, Ahmet Hoke, Wadih M Zein, Daniel Ezzo, Andrea M Atherton, Ann C Modrcin, Majed Dasouki, A Reghan Foley, Carsten G Bönnemann
OBJECTIVE: To identify the underlying genetic cause in 2 sisters affected with progressive lower extremity spasticity, neuropathy, and early-onset deafness. METHODS: Whole-exome sequencing was performed, and segregation testing of variants was investigated using targeted Sanger sequencing. An inherited paternal mosaic mutation was further evaluated through quantitative analysis of the ratio of mutant vs wild-type allele in genomic DNA from various tissues, including blood, dermal fibroblasts, and saliva...
June 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28534009/genomic-insight-into-mechanisms-of-reversion-of-antibiotic-resistance-in-multidrug-resistant-mycobacterium-tuberculosis-induced-by-a-nanomolecular-iodine-containing-complex-fs-1
#20
Aleksandr I Ilin, Murat E Kulmanov, Ilya S Korotetskiy, Rinat A Islamov, Gulshara K Akhmetova, Marina V Lankina, Oleg N Reva
Drug induced reversion of antibiotic resistance is a promising way to combat multidrug resistant infections. However, lacking knowledge of mechanisms of drug resistance reversion impedes employing this approach in medicinal therapies. Induction of antibiotic resistance reversion by a new anti-tuberculosis drug FS-1 has been reported. FS-1 was used in this work in combination with standard anti-tuberculosis antibiotics in an experiment on laboratory guinea pigs infected with an extensively drug resistant (XDR) strain Mycobacterium tuberculosis SCAID 187...
2017: Frontiers in Cellular and Infection Microbiology
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