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https://www.readbyqxmd.com/read/29684710/genomic-characterization-of-endemic-salmonella-enterica-serovar-typhimurium-and-salmonella-enterica-serovar-i-4-5-12-i-isolated-in-malaysia
#1
Soo Tein Ngoi, Kien-Pong Yap, Kwai Lin Thong
Salmonella enterica serovar Typhimurium (S. Typhimurium) and the monophasic variant Salmonella I 4,[5],12:i:- are two clinically-important non-typhoidal Salmonella serovars worldwide. However, the genomic information of these two organisms, especially the monophasic variant, is still lacking in Malaysia. The objective of the study was to compare the genomic features of a monophasic variant and two endemic S. Typhimurium strains isolated from humans. All three strains were subjected to whole genome sequencing followed by comparative genomic and phylogenetic analyses...
April 20, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29684641/methodological-considerations-for-the-identification-of-choline-and-carnitine-degrading-bacteria-in-the-gut
#2
REVIEW
Eleanor Jameson, Mussa Quareshy, Yin Chen
The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enzymes has enabled bioinformatics approaches to screen both human-associated bacterial isolate genomes and whole gut metagenomes to determine which bacteria are responsible for TMA formation in the human gut...
April 19, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29684399/a-cas9-transgenic-plasmodium-yoelii-parasite-for-efficient-gene-editing
#3
Pengge Qian, Xu Wang, Zhenke Yang, Zhenkui Li, Han Gao, Xin-Zhuan Su, Huiting Cui, Jing Yuan
The RNA-guided endonuclease Cas9 has applied as an efficient gene-editing method in malaria parasite Plasmodium. However, the size (4.2 kb) of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for genome editing in the parasites only introduced with cas9 plasmid. To establish the endogenous and constitutive expression of Cas9 protein in the rodent malaria parasite P. yoelii, we replaced the coding region of an endogenous gene sera1 with the intact SpCas9 coding sequence using the CRISPR/Cas9-mediated genome editing method, generating the cas9-knockin parasite (PyCas9ki) of the rodent malaria parasite P...
April 20, 2018: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/29684357/genome-wide-somatic-copy-number-alterations-and-mutations-in-high-grade-pancreatic-intraepithelial-neoplasia
#4
Tatsuo Hata, Masaya Suenaga, Luigi Marchionni, Anne Macgregor-Das, Jun Yu, Koji Shindo, Koji Tamura, Ralph H Hruban, Michael Goggins
To obtain a better understanding of the genetic alterations of high-grade pancreatic intraepithelial neoplasia (HG-PanIN), we performed whole-genome copy number analysis using single nucleotide polymorphism microarrays and targeted next-generation sequencing of 11 microdissected HG-PanIN and two low-grade PanIN (LG-PanIN) lesions associated with HG-PanIN. HG-PanIN mutation profiles were compared to those of their associated invasive pancreatic ductal adenocarcinoma. All PanIN lesions harbored somatic KRAS mutations...
April 20, 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/29684203/the-most-developmentally-truncated-fishes-show-extensive-hox-gene-loss-and-miniaturized-genomes
#5
Martin Malmstrøm, Ralf Britz, Michael Matschiner, Ole K Tørresen, Renny Kurnia Hadiaty, Norsham Yaakob, Heok Hui Tan, Kjetill Sigurd Jakobsen, Walter Salzburger, Lukas Rüber
The world's smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29684167/reproduction-in-domestic-ruminants-during-the-past-50-years-discovery-to-application
#6
Michael F Smith, Rodney D Geisert, John J Parrish
The study of reproductive physiology in domestic ruminants has progressed from the whole animal to the molecular level in an amazingly short period of time. The volume of information on this subject is enormous; therefore, we have focused on domestic ruminants, with an emphasis on cattle. To date, artificial insemination (AI) is perhaps the most powerful technique that reproductive physiologists and geneticists have provided the livestock industry for genetic improvement. Early efforts to establish AI as a tool were initiated in Russia around 1899 and since that time major advances in methods of semen collection, evaluation of male fertility, cryopreservation of sperm, sex-sorted semen, and estrous cycle control have occurred...
April 19, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29684163/experimental-evolution-of-yeast-for-high-temperature-tolerance
#7
Chih-Jen Huang, Mei-Yeh Lu, Ya-Wen Chang, Wen-Hsiung Li
Thermotolerance is a polygenic trait that contributes to cell survival and growth under unusually high temperatures. Although some genes associated with high temperature growth (Htg+) have been identified, how cells accumulate mutations to achieve prolonged thermotolerance is still mysterious. Here we conducted experimental evolution of a Saccharomyces cerevisiae laboratory strain with stepwise temperature increases for it to grow at 42 °C. Whole genome resequencing of 14 evolved strains and the parental strain revealed a total of 153 mutations in the evolved strains, including single nucleotide variants, small INDELs, and segmental duplication/deletion events...
April 19, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29684056/bifidobacteria-isolated-from-vaginal-and-gut-microbiomes-are-indistinguishable-by-comparative-genomics
#8
Aline C Freitas, Janet E Hill
Bifidobacteria colonize the human gastrointestinal tract, vagina, oral cavity and breast milk. They influence human physiology and nutrition through health-promoting effects, play an important role as primary colonizers of the newborn gut, and contribute to vaginal microbiome homeostasis by producing lactic acid. Nevertheless, the mechanisms by which bifidobacteria are transmitted from mother to infant remains in discussion. Moreover, studies have suggested that Bifidobacterium spp. have specializations for gut colonization, but comparisons of strains of the same bifidobacteria species from different body sites are lacking...
2018: PloS One
https://www.readbyqxmd.com/read/29684021/laboratory-and-molecular-surveillance-of-paediatric-typhoidal-salmonella-in-nepal-antimicrobial-resistance-and-implications-for-vaccine-policy
#9
Carl D Britto, Zoe A Dyson, Sebastian Duchene, Michael J Carter, Meeru Gurung, Dominic F Kelly, David R Murdoch, Imran Ansari, Stephen Thorson, Shrijana Shrestha, Neelam Adhikari, Gordon Dougan, Kathryn E Holt, Andrew J Pollard
BACKGROUND: Children are substantially affected by enteric fever in most settings with a high burden of the disease, including Nepal. However pathogen population structure and transmission dynamics are poorly delineated in young children, the proposed target group for immunization programs. Here we present whole genome sequencing and antimicrobial susceptibility data on 198 S. Typhi and 66 S. Paratyphi A isolated from children aged 2 months to 15 years of age during blood culture surveillance at Patan Hospital, Nepal, 2008-2016...
April 23, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29683851/detection-of-numerous-hiv-1-mo-recombinants-in-france
#10
Fabienne De Oliveira, Pierre Cappy, Véronique Lemée, Alice Moisan, Charlotte Pronier, Laurence Bocket, Magali Bouvier-Alias, Marie-Laure Chaix, Elyanne Gault, Odile Morvan, Jean-Dominique Poveda, Véronique Schneider, Marc Wirden, Elodie Alessandri-Gradt, Thomas Mourez, Jean-Christophe Plantier
BACKGROUND: The broad genetic divergence of HIV-1/O relative to HIV-1/M has important implications for diagnosis, monitoring and treatment. Despite this divergence, some HIV-1/M+O dual infections and HIV-1/MO recombinant forms have been reported, mostly in Cameroon, where both groups are prevalent. Here, we describe the characteristics of such infections detected in France in 10 new patients, and discuss their implications for biological and clinical practice, owing to the presence of group O species...
April 19, 2018: AIDS
https://www.readbyqxmd.com/read/29683417/whole-genome-sequence-analysis-of-the-mycobacterium-avium-complex-and-proposal-of-the-transfer-of-mycobacterium-yongonense-to-mycobacterium-intracellulare-subsp-yongonense-subsp-nov
#11
Maria Castejon, Maria Carmen Menéndez, Iñaki Comas, Ana Vicente, Maria J Garcia
Bacterial whole-genome sequences contain informative features of their evolutionary pathways. Comparison of whole-genome sequences have become the method of choice for classification of prokaryotes, thus allowing the identification of bacteria from an evolutionary perspective, and providing data to resolve some current controversies. Currently, controversy exists about the assignment of members of the Mycobacterium avium complex, as is for the cases of Mycobacterium yongonense and 'Mycobacterium indicus pranii'...
April 23, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29683333/stability-of-global-methylation-profiles-of-whole-blood-and-extracted-dna-under-different-storage-durations-and-conditions
#12
Yingchuan Li, Xiaoqing Pan, Michelle L Roberts, Pengyuan Liu, Theodore A Kotchen, Allen W Cowley, David L Mattson, Yong Liu, Mingyu Liang, Srividya Kidambi
AIM: To test whether DNA samples stored for a prolonged period (20 years) under various storage conditions could be used for comparative methylation studies using reduced representation bisulfite sequencing. PATIENTS & METHODS: Five groups of human blood DNA samples (n = 5-6/group) were compared. The groupings were based on the anticoagulant used and storage temperature and duration. RESULTS: Methylation profiles of defined genomic regions in the DNA or blood samples archived for 20 years were similar across all storage temperatures, including 4°C...
April 23, 2018: Epigenomics
https://www.readbyqxmd.com/read/29682786/the-evaluation-of-two-genetic-polymorphisms-of-paraoxonase-1-in-patients-with-pulmonary-embolism
#13
Nursah Basol, Nevin Karakus, Asli Yasemen Savas, Kayhan Karakus, İlker Kaya, Serhat Karaman, Serbulent Yigit
BACKGROUND AND OBJECTIVE: Pulmonary embolism (PE) is caused by some genetic factors for more than half patients. Paraoxonase 1 (PON1) has significant anti-oxidative and anti-inflammatory effects. According to our knowledge, there is no study researching the relation between PON 1 gene polymorphisms and PE in the literature. Therefore, it is aimed to research possible impacts of PON 1 Q192R and L55M polymorphisms on PE, considering anti-inflammatory and anti-oxidative effects of PON 1 in Turkish population...
April 22, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29682782/a-hierarchical-clustering-method-for-dimension-reduction-in-joint-analysis-of-multiple-phenotypes
#14
Xiaoyu Liang, Qiuying Sha, Yeonwoo Rho, Shuanglin Zhang
Genome-wide association studies (GWAS) have become a very effective research tool to identify genetic variants of underlying various complex diseases. In spite of the success of GWAS in identifying thousands of reproducible associations between genetic variants and complex disease, in general, the association between genetic variants and a single phenotype is usually weak. It is increasingly recognized that joint analysis of multiple phenotypes can be potentially more powerful than the univariate analysis, and can shed new light on underlying biological mechanisms of complex diseases...
April 22, 2018: Genetic Epidemiology
https://www.readbyqxmd.com/read/29682607/the-role-of-hsp40-conserved-motifs-in-the-response-to-cytotoxic-stress
#15
Samantha J Sojourner, Willie M Graham, Aurellia M Whitmore, Jana S Miles, Devon Freeny, Hernan Flores-Rozas
Doxorubicin, a highly effective therapeutic agent against several types of cancer, is associated with serious side-effects, particularly cardiotoxicity. In addition, drug resistance leads to unsuccessful outcomes in many patients. There are no current biomarkers to indicate doxorubicin treatment response in patients. To understand the mechanisms of toxicity of doxorubicin, a whole-genome sensitivity screen was performed in the yeast S. cerevisiae . A deletion mutant of the yeast DNAJ (YDJ1), a J-domain heat-shock protein 40 (HSP40) was among the most sensitive strains...
2018: Journal of Nature and Science
https://www.readbyqxmd.com/read/29682505/overview-on-clinical-relevance-of-intra-tumor-heterogeneity
#16
REVIEW
Giorgio Stanta, Serena Bonin
Today, clinical evaluation of tumor heterogeneity is an emergent issue to improve clinical oncology. In particular, intra-tumor heterogeneity (ITH) is closely related to cancer progression, resistance to therapy, and recurrences. It is interconnected with complex molecular mechanisms including spatial and temporal phenomena, which are often peculiar for every single patient. This review tries to describe all the types of ITH including morphohistological ITH, and at the molecular level clonal ITH derived from genomic instability and nonclonal ITH derived from microenvironment interaction...
2018: Frontiers in Medicine
https://www.readbyqxmd.com/read/29682127/de-novo-sequencing-of-a-sparassis-latifolia-genome-and-its-associated-comparative-analyses
#17
Donglai Xiao, Lu Ma, Chi Yang, Zhenghe Ying, Xiaoling Jiang, Yan-Quan Lin
Known to be rich in β- glucan, Sparassis latifolia ( S. latifolia ) is a valuable edible fungus cultivated in East Asia. A few studies have suggested that S. latifolia is effective on antidiabetic, antihypertension, antitumor, and antiallergen medications. However, it is still unclear genetically why the fungus has these medical effects, which has become a key bottleneck for its further applications. To provide a better understanding of this fungus, we sequenced its whole genome, which has a total size of 48...
2018: Canadian Journal of Infectious Diseases & Medical Microbiology
https://www.readbyqxmd.com/read/29681898/the-versatile-mutational-resistome-of-pseudomonas-aeruginosa
#18
REVIEW
Carla López-Causapé, Gabriel Cabot, Ester Del Barrio-Tofiño, Antonio Oliver
One of the most striking features of Pseudomonas aeruginosa is its outstanding capacity for developing antimicrobial resistance to nearly all available antipseudomonal agents through the selection of chromosomal mutations, leading to the failure of the treatment of severe hospital-acquired or chronic infections. Recent whole-genome sequencing (WGS) data obtained from in vitro assays on the evolution of antibiotic resistance, in vivo monitoring of antimicrobial resistance development, analysis of sequential cystic fibrosis isolates, and characterization of widespread epidemic high-risk clones have provided new insights into the evolutionary dynamics and mechanisms of P...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29681755/recent-advances-in-flower-color-variation-and-patterning-of-japanese-morning-glory-and-petunia
#19
REVIEW
Yasumasa Morita, Atsushi Hoshino
The Japanese morning glory ( Ipomoea nil ) and petunia ( Petunia hybrida ), locally called "Asagao" and "Tsukubane-asagao", respectively, are popular garden plants. They have been utilized as model plants for studying the genetic basis of floricultural traits, especially anthocyanin pigmentation in flower petals. In their long history of genetic studies, many mutations affecting flower pigmentation have been characterized, and both structural and regulatory genes for the anthocyanin biosynthesis pathway have been identified...
January 2018: Breeding Science
https://www.readbyqxmd.com/read/29681748/recent-progress-in-whole-genome-sequencing-high-density-linkage-maps-and-genomic-databases-of-ornamental-plants
#20
REVIEW
Masafumi Yagi
Genome information is useful for functional analysis of genes, comparative genomic analysis, breeding of new varieties by marker-assisted selection, and map-based gene isolation. Genome-related research in ornamentals plants has been relatively slow to develop because of their heterozygosity or polyploidy. Advances in analytical instruments, such as next-generation sequencers and information processing technologies have revolutionized biology, and have been applied in a large number and variety of species, including ornamental plants...
January 2018: Breeding Science
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