Read by QxMD icon Read

Comparative genomics

Anastasia K Atabekova, Anna V Pankratenko, Svetlana S Makarova, Ekaterina A Lazareva, Robert A Owens, Andrey G Solovyev, Sergey Y Morozov
Human B-cell receptor-associated protein BAP31 (HsBAP31) is the endoplasmic reticulum-resident protein involved in protein sorting and transport as well as pro-apoptotic signaling. Plant orthologs of HsBAP31 termed 'plant BAP-like proteins' (PBL proteins) have thus far remained unstudied. Recently, the PBL protein from Nicotiana tabacum (NtPBL) was identified as an interactor of Nt-4/1, a plant protein known to interact with plant virus movement proteins and affect the long-distance transport of potato spindle tuber viroid (PSTVd) via the phloem...
October 19, 2016: Biochimie
Zheng Fang, Jingxu Shao, Qingbei Weng
Cells of the P8-Se301-C1 strain are Spodoptera exigua cell clones that each harbor a partial version of the S. exigua multiple nucleopolyhedrovirus (SeMNPV) genome and which are resistant to homologous SeMNPV infections. The cells produce no viral progeny, suggesting that the infection is a latent-like viral infection. To investigate the SeMNPV genes harbored in the P8-Se301-C1 cells, the de novo transcriptomes of P8-Se301-C1 cells and S. exigua Se301 cells were analyzed and compared. A total of 54,569,296 reads were obtained from the P8-Se301-C1 cells that yielded 112,565 final unigenes with a mean length of 1,093 nt...
October 18, 2016: Virologica Sinica
Masayuki Tsuzuki, Yuichiro Watanabe
Small RNAs are key molecules in RNA silencing pathways that exert the sequence-specific regulation of gene expression and chromatin modifications in many eukaryotes. In plants, endogenous small RNAs, including microRNAs (miRNAs), trans-acting short interfering RNAs (tasiRNAs), and heterochromatic siRNAs (hc-siRNAs), play an important role in switching or orchestrating biological processes during the development and at the onset of stress responses. These endogenous and exogenous small RNAs are mainly 20-24 nucleotides in length...
2017: Methods in Molecular Biology
Fausto Petrelli, Sandro Barni, Giacomo Bregni, Filippo de Braud, Serena Di Cosimo
BACKGROUND: The interest in platinum salts in breast cancer (BC) therapy has been recently renewed as inhibition of DNA damage response may enhance the effects of DNA-damaging agents in BC tumors with high genomic instability. The present systematic review and meta-analysis of randomized trials were performed to assess the efficacy and safety of therapy with platinum salts in patients with locally advanced or metastatic (hereinafter advanced) BC. METHODS: We searched PubMed, EMBASE, SCOPUS, Web of Science, the Cochrane Library, and CINAHL for phase II/III clinical trials that assessed efficacy of platinum-based therapy in patients with advanced BC...
October 21, 2016: Breast Cancer Research and Treatment
Danielle Aberdein, John S Munday, Barbara Gandolfi, Keren E Dittmer, Richard Malik, Dorian J Garrick, Leslie A Lyons
British shorthair (BSH) kittens in multiple litters died as a result of a severe non-neoplastic lymphoproliferative disease that showed many similarities with human autoimmune lymphoproliferative syndrome (ALPS). Human ALPS is caused by inherited defects in FAS-mediated lymphocyte apoptosis and the possibility of similar defects was investigated in BSH cats. The whole genomes of two affected kittens were sequenced and compared to 82 existing cat genomes. Both BSH kittens had homozygous insertions of an adenine within exon 3 of the FAS-ligand gene...
October 21, 2016: Mammalian Genome: Official Journal of the International Mammalian Genome Society
Bartosz Roszniowski, Agnieszka Latka, Barbara Maciejewska, Dieter Vandenheuvel, Tomasz Olszak, Yves Briers, Giles S Holt, Miguel A Valvano, Rob Lavigne, Darren L Smith, Zuzanna Drulis-Kawa
Burkholderia phage AP3 (vB_BceM_AP3) is a temperate virus of the Myoviridae and the Peduovirinae subfamily (P2likevirus genus). This phage specifically infects multidrug-resistant clinical Burkholderia cenocepacia lineage IIIA strains commonly isolated from cystic fibrosis patients. AP3 exhibits high pairwise nucleotide identity (61.7 %) to Burkholderia phage KS5, specific to the same B. cenocepacia host, and has 46.7-49.5 % identity to phages infecting other species of Burkholderia. The lysis cassette of these related phages has a similar organization (putative antiholin, putative holin, endolysin, and spanins) and shows 29-98 % homology between specific lysis genes, in contrast to Enterobacteria phage P2, the hallmark phage of this genus...
October 21, 2016: Applied Microbiology and Biotechnology
Guoqin Yu, Steve Phillips, Mitchell H Gail, James J Goedert, Michael Humphrys, Jacques Ravel, Yanfang Ren, Neil E Caporaso
BACKGROUND: The human microbiota is postulated to affect cancer risk, but collecting microbiota specimens with prospective follow-up for diseases will take time. Buccal cell samples have been obtained from mouthwash for the study of human genomic DNA in many cohort studies. Here we evaluate the feasibility of using buccal cell samples to examine associations of human microbiota and disease risk. METHODS: We obtained buccal cells from mouthwash in 41 healthy participants using a protocol that is widely employed to obtain buccal cells for the study of human DNA...
October 21, 2016: Cancer Epidemiology, Biomarkers & Prevention
Katherine A Guthrie, Hilary S Gammill, Mads Kamper-Jørgensen, Anne Tjønneland, Vijayakrishna K Gadi, J Lee Nelson, Wendy Leisenring
Natural acquisition of small amounts of foreign cells or DNA, referred to as microchimerism, occurs primarily through maternal-fetal exchange during pregnancy. Microchimerism can persist long-term and has been associated with both beneficial and adverse human health outcomes. Quantitative microchimerism data present challenges for statistical analysis, including a skewed distribution, excess zero values, and occasional large values. Methods for comparing microchimerism levels across groups while controlling for covariates are not well established...
October 21, 2016: American Journal of Epidemiology
Fernando Vargas-Romero, Guillermo Mendoza-Hernández, Francisco Suarez-Güemes, Rogelio Hernández-Pando, Mauricio Castañón-Arreola
Mycobacterium bovis is the causative agent of tuberculosis in farms, wildlife and causes sporadic disease in humans. Despite the high similitude in genome sequence between M. bovis strains, some strains like the wild boar 04-303 isolate show a highly virulent phenotype in animal models. Comparative studies will contribute to link protein expression with the virulence phenotype. In vitro, the 04-303 strain was more phagocytized by J774A.1 macrophages in comparison with 444 strain (a cow isolate with the same genotype) and BCG...
October 18, 2016: Microbial Pathogenesis
Kattina Zavala, Michael W Vandewege, Federico G Hoffmann, Juan C Opazo
The study of the evolutionary history of genes related to human disease lies at the interface of evolution and medicine. These studies provide the evolutionary context on which medical researchers should work, and are also useful in providing information to suggest further genetic experiments, especially in model species where genetic manipulations can be made. Here we studied the evolution of the β-adrenoreceptor gene family in vertebrates with the aim of adding an evolutionary framework to the already abundant physiological information...
October 18, 2016: General and Comparative Endocrinology
Chaoyun Hao, Zhiqiang Xia, Rui Fan, Lehe Tan, Lisong Hu, Baoduo Wu, Huasong Wu
BACKGROUND: Piper nigrum L., or "black pepper", is an economically important spice crop in tropical regions. Black pepper production is markedly affected by foot rot disease caused by Phytophthora capsici, and genetic improvement of black pepper is essential for combating foot rot diseases. However, little is known about the mechanism of anti- P. capsici in black pepper. The molecular mechanisms underlying foot rot susceptibility were studied by comparing transcriptome analysis between resistant (Piper flaviflorum) and susceptible (Piper nigrum cv...
October 21, 2016: BMC Genomics
Pierre Dehoux, Jean Christophe Marvaud, Amr Abouelleil, Ashlee M Earl, Thierry Lambert, Catherine Dauga
BACKGROUND: Clostridium bolteae and Clostridium clostridioforme, previously included in the complex C. clostridioforme in the group Clostridium XIVa, remain difficult to distinguish by phenotypic methods. These bacteria, prevailing in the human intestinal microbiota, are opportunistic pathogens with various drug susceptibility patterns. In order to better characterize the two species and to obtain information on their antibiotic resistance genes, we analyzed the genomes of six strains of C...
October 21, 2016: BMC Genomics
Michał Książkiewicz, Sandra Rychel, Matthew N Nelson, Katarzyna Wyrwa, Barbara Naganowska, Bogdan Wolko
BACKGROUND: The Arabidopsis FLOWERING LOCUS T (FT) gene, a member of the phosphatidylethanolamine binding protein (PEBP) family, is a major controller of flowering in response to photoperiod, vernalization and light quality. In legumes, FT evolved into three, functionally diversified clades, FTa, FTb and FTc. A milestone achievement in narrow-leafed lupin (Lupinus angustifolius L.) domestication was the loss of vernalization responsiveness at the Ku locus. Recently, one of two existing L...
October 21, 2016: BMC Genomics
Arvind Y M Sundaram, Timothy Hughes, Shea Biondi, Nathalie Bolduc, Sarah K Bowman, Andrew Camilli, Yap C Chew, Catherine Couture, Andrew Farmer, John P Jerome, David W Lazinski, Andrew McUsic, Xu Peng, Kamran Shazand, Feng Xu, Robert Lyle, Gregor D Gilfillan
BACKGROUND: ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures...
October 21, 2016: BMC Genomics
Chunwen Tan, Wangxiong Hu, Yanqin Huang, Jiaojiao Zhou, Shu Zheng
BACKGROUND: Recent genome-wide association studies (GWAS) identified eighteen single-nucleotide polymorphisms (SNPs) to be significantly associated with the risk of colorectal cancer (CRC). However, overall results of the following replications are inconsistent and little is known about whether these associations also exit in colorectal adenomas (CRA). METHODS: The SNP genotyping was performed using a Sequenom MassARRAY to investigate the association of these eighteen SNPs with colorectal neoplasm in a case-control study consisted of 1049 colorectal cancers, 283 adenomas, and 1030 controls...
October 19, 2016: Oncotarget
Si Chen, Xiaoting Wen, Jing Li, Yuan Li, Liubing Li, Xinping Tian, Hui Yuan, Fengchun Zhang, Yongzhe Li
Takayasu arteritis (TA) is a chronic large-vessel vasculitis of unclear pathogenesis. A recent genome-wide association study (GWAS) has revealed that the FCGR2A/FCGR3A, EEFSEC, RPS9/LILRB3, RIPPLY2 and MLX genes confer susceptibility to TA. We investigated the linkage between presumptive TA-related genes (FCGR2A/FCGR3A, EEFSEC, RPS9/LILRB3, RIPPLY2 and MLX) and TA in the Han Chinese population. We performed a large case-control multi-center study of 412 Han Chinese TA patients and 597 ethnically matched healthy controls...
October 18, 2016: Oncotarget
Carlos Molina-Santiago, Zulema Udaondo, María Gómez-Lozano, Soren Molin, Juan Luis Ramos
Pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. Pan-genome analysis has revealed that 30% of genes belong to the core-genome of Pseudomonas. Accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. For the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic differences. In this study, RNA-seq analysis compared the short- and long-term responses of the toluene-sensitive KT2440 strain and the highly-tolerant DOT-T1E strain...
October 21, 2016: Environmental Microbiology
Marie-Catherine Drigeard Desgarnier, Corinne Zinflou, Justin D Mallet, Sébastien P Gendron, Sébastien J Méthot, Patrick J Rochette
Purpose: Human chromosomes are protected at their end by a long portion of hexameric tandem repeats, the telomere. In somatic cells, telomere attrition caused by endogenous and exogenous oxidative stress as well as DNA replication can threaten genomic integrity and lead to the deterioration of tissue functions and an age-related physiological decline. The human eye is a complex organ in which cells of different ocular tissues are exposed to photo-oxidation, high mitochondrial metabolic activity, and/or replicative pressure...
October 1, 2016: Investigative Ophthalmology & Visual Science
James Starrett, Shahan Derkarabetian, Marshal Hedin, Robert W Bryson, John E McCormack, Brant C Faircloth
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress...
October 21, 2016: Molecular Ecology Resources
Jean-Rene Arseneau, Royce Steeves, Mark Laflamme
The increasing use of high-throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that co-precipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often co-precipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low-salt CTAB (MoLSC) extraction protocol to accommodate contaminant rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle...
October 21, 2016: Molecular Ecology Resources
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"