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https://www.readbyqxmd.com/read/29220521/trypanosomatid-mitochondrial-rna-editing-dramatically-complex-transcript-repertoires-revealed-with-a-dedicated-mapping-tool
#1
Evgeny S Gerasimov, Anna A Gasparyan, Iosif Kaurov, Boris Tichý, Maria D Logacheva, Alexander A Kolesnikov, Julius Lukeš, Vyacheslav Yurchenko, Sara L Zimmer, Pavel Flegontov
RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3' to 5' on a transcript, resulting in a population of partially edited as well as pre-edited and completely edited molecules for each mitochondrial cryptogene of these protozoans. Often, the number of uridines inserted and deleted exceed the number of nucleotides that are genome-encoded...
December 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29220507/assessing-the-heterogeneity-of-in-silico-plasmid-predictions-based-on-whole-genome-sequenced-clinical-isolates
#2
Cedric C Laczny, Valentina Galata, Achim Plum, Andreas E Posch, Andreas Keller
High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data...
December 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29220483/prenatal-exposure-to-bisphenol-a-disrupts-naturally-occurring-bimodal-dna-methylation-at-proximal-promoter-of-fggy-an-obesity-relevant-gene-encoding-a-carbohydrate-kinase-in-gonadal-white-adipose-tissues-of-cd-1-mice
#3
Julia A Taylor, Keiko Shioda, Shino Mitsunaga, Shiomi Yawata, Brittany M Angle, Susan C Nagel, Frederick S Vom Saal, Toshi Shioda
Exposure of mammalian fetuses to endocrine disruptors can increase the risk of adult-onset diseases. For example, we previously showed that exposure of mouse fetuses to bisphenol A (BPA) caused adult-onset obesity. To obtain insights into roles of epigenetic changes in the delayed toxic effects of endocrine disruption, we determined effects of fetal mouse exposure to BPA on genome-wide DNA methylation and mRNA expression in gonadal white adipose tissues by deep sequencing (MBD-seq and RNA-seq), bisulfite pyrosequencing, and real-time qPCR...
December 6, 2017: Endocrinology
https://www.readbyqxmd.com/read/29220419/high-resolution-single-cell-sequencing-of-malaria-parasites
#4
Simon G Trevino, Standwell C Nkhoma, Shalini Nair, Benjamin J Daniel, Karla Moncada, Stanley Khoswe, Rachel L Banda, François Nosten, Ian H Cheeseman
Single-cell genomics is a powerful tool for determining the genetic architecture of complex communities of unicellular organisms. In areas of high transmission, malaria patients are often challenged by the activities of multiple Plasmodium falciparum lineages, which can potentiate pathology, spread drug resistance loci and also complicate most genetic analysis. Single-cell sequencing of P. falciparum would be key to understanding infection complexity, though efforts are hampered by the extreme nucleotide composition of its genome (∼80% AT-rich)...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29220374/a-blaoxa-181-harbouring-multi-resistant-st147-klebsiella-pneumoniae-isolate-from-pakistan-that-represent-an-intermediate-stage-towards-pan-drug-resistance
#5
Fouzia Nahid, Rabaab Zahra, Linus Sandegren
Carbapenem resistant Klebsiella pneumoniae (CR-KP) infections are an ever-increasing global issue, especially in the Indian subcontinent. Here we report genetic insight into a blaOXA-181 harbouring Klebsiella pneumoniae, belonging to the pandemic lineage ST147, that represents an intermediate stage towards pan-drug resistance. The CR-KP isolate DA48896 was isolated from a patient from Pakistan and was susceptible only to tigecycline and colistin. It harboured blaOXA-181 and was assigned to sequence type ST147...
2017: PloS One
https://www.readbyqxmd.com/read/29220350/deep-sequencing-of-near-full-length-hiv-1-genomes-from-plasma-identifies-circulating-subtype-c-and-infrequent-occurrence-of-ac-recombinant-form-in-southern-india
#6
Shuba Varshini Alampalli, Michael M Thomson, Raghavan Sampathkumar, Karthi Sivaraman, Anto Jesuraj U K J, Chirag Dhar, George D Souza, Neil Berry, Annapurna Vyakarnam
India has the third largest number of HIV-1-infected individuals accounting for approximately 2.1 million people, with a predominance of circulating subtype C strains and a low prevalence of subtype A and A1C and BC recombinant forms, identified over the past two decades. Recovery of near full-length HIV-1 genomes from a plasma source coupled with advances in next generation sequencing (NGS) technologies and development of universal methods for amplifying whole genomes of HIV-1 circulating in a target geography or population provides the opportunity for a detailed analysis of HIV-1 strain identification, evolution and dynamics...
2017: PloS One
https://www.readbyqxmd.com/read/29218002/xenopus-laevis-as-a-model-organism-for-the-study-of-spinal-cord-formation-development-function-and-regeneration
#7
REVIEW
Laura N Borodinsky
The spinal cord is the first central nervous system structure to develop during vertebrate embryogenesis, underscoring its importance to the organism. Because of its early formation, accessibility to the developing spinal cord in amniotes is challenging, often invasive and the experimental approaches amenable to model systems like mammals are limited. In contrast, amphibians, in general and the African-clawed frog Xenopus laevis, in particular, offer model systems in which the formation of the spinal cord, the differentiation of spinal neurons and glia and the establishment of spinal neuron and neuromuscular synapses can be easily investigated with minimal perturbations to the whole organism...
2017: Frontiers in Neural Circuits
https://www.readbyqxmd.com/read/29217829/genome-wide-genotyping-uncovers-genetic-profiles-and-history-of-the-russian-cattle-breeds
#8
Andrey Yurchenko, Nikolay Yudin, Ruslan Aitnazarov, Alexandra Plyusnina, Vladimir Brukhin, Vladimir Soloshenko, Bulat Lhasaranov, Ruslan Popov, Ivan A Paronyan, Kirill V Plemyashov, Denis M Larkin
One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously...
December 8, 2017: Heredity
https://www.readbyqxmd.com/read/29217792/genome-sequence-of-listeria-monocytogenes-strain-f4244-a-4b-serotype
#9
Taylor W Bailey, Naila C do Nascimento, Arun K Bhunia
Listeria monocytogenes is an opportunistic invasive foodborne pathogen. Here, we performed whole-genome sequencing of L. monocytogenes strain F4244 (serotype 4b) using Illumina sequencing. The sequence showed 94.5% identity with strain F2365, serotype 4b, and 90.6% with EGD-e, serotype 1/2a.
December 7, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29217584/aging-and-neurodegeneration-are-associated-with-increased-mutations-in-single-human-neurons
#10
Michael A Lodato, Rachel E Rodin, Craig L Bohrson, Michael E Coulter, Alison R Barton, Minseok Kwon, Maxwell A Sherman, Carl M Vitzthum, Lovelace J Luquette, Chandri Yandava, Pengwei Yang, Thomas W Chittenden, Nicole E Hatem, Steven C Ryu, Mollie B Woodworth, Peter J Park, Christopher A Walsh
It has long been hypothesized that aging and neurodegeneration are associated with somatic mutation in neurons; however, methodological hurdles have prevented testing this hypothesis directly. We used single-cell whole-genome sequencing to perform genome-wide somatic single-nucleotide variant (sSNV) identification on DNA from 161 single neurons from the prefrontal cortex and hippocampus of fifteen normal individuals (aged 4 months to 82 years) as well as nine individuals affected by early-onset neurodegeneration due to genetic disorders of DNA repair (Cockayne syndrome and Xeroderma pigmentosum)...
December 7, 2017: Science
https://www.readbyqxmd.com/read/29217199/efficient-generation-of-transgene-and-feeder-free-induced-pluripotent-stem-cells-from-human-dental-mesenchymal-stem-cells-and-their-chemically-defined-differentiation-into-cardiomyocytes
#11
Xiaobing Tan, Qingli Dai, Tao Guo, Jingshu Xu, Qingyuan Dai
Advance in stem cell research resulted in several processes to generate induced pluripotent stem cells (iPSCs) from adult somatic cells. In our previous study, the reprogramming of iPSCs from human dental mesenchymal stem cells (MSCs) including SCAP and DPSCs, has been reported. Herein, safe iPSCs were reprogrammed from SCAP and DPSCs using non-integrating RNA virus vector, which is an RNA virus carrying no risk of altering host genome. DPSCs- and SCAP-derived iPSCs exhibited the characteristics of the classical morphology with human embryonic stem cells (hESCs) without integration of foreign genes, indicating the potential of their clinical application...
December 4, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29216901/genomic-variants-in-the-fto-gene-are-associated-with-sporadic-amyotrophic-lateral-sclerosis-in-greek-patients
#12
Konstantinos Mitropoulos, Eleni Merkouri Papadima, Georgia Xiromerisiou, Angeliki Balasopoulou, Kyriaki Charalampidou, Vasiliki Galani, Krystallia-Vassiliki Zafeiri, Efthymios Dardiotis, Styliani Ralli, Georgia Deretzi, Anne John, Kyriaki Kydonopoulou, Elpida Papadopoulou, Alba di Pardo, Fulya Akcimen, Annalisa Loizedda, Valerija Dobričić, Ivana Novaković, Vladimir S Kostić, Clint Mizzi, Brock A Peters, Nazli Basak, Sandro Orrù, Evangelos Kiskinis, David N Cooper, Spyridon Gerou, Radoje Drmanac, Marina Bartsakoulia, Evangelia-Eirini Tsermpini, Georgios M Hadjigeorgiou, Bassam R Ali, Theodora Katsila, George P Patrinos
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a devastating disease whose complex pathology has been associated with a strong genetic component in the context of both familial and sporadic disease. Herein, we adopted a next-generation sequencing approach to Greek patients suffering from sporadic ALS (together with their healthy counterparts) in order to explore further the genetic basis of sporadic ALS (sALS). RESULTS: Whole-genome sequencing analysis of Greek sALS patients revealed a positive association between FTO and TBC1D1 gene variants and sALS...
December 8, 2017: Human Genomics
https://www.readbyqxmd.com/read/29216844/comparative-analyses-of-plastid-genomes-from-fourteen-cornales-species-inferences-for-phylogenetic-relationships-and-genome-evolution
#13
Chao-Nan Fu, Hong-Tao Li, Richard Milne, Ting Zhang, Peng-Fei Ma, Jing Yang, De-Zhu Li, Lian-Ming Gao
BACKGROUND: The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. RESULTS: All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region...
December 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29216510/evolution-of-virulence-in-the-mycobacterium-tuberculosis-complex
#14
REVIEW
Mickael Orgeur, Roland Brosch
Mycobacterium tuberculosis, the causative agent of human tuberculosis is one of the most widely spread human pathogens. It has succeeded to infect a quarter of the global human population by developing most sophisticated ways to circumvent innate and adaptive immune defences. This highly specialized, major human pathogen has evolved from a pool of ancestral environmental mycobacteria, whose extant representatives are known under the name of Mycobacterium canettii. Recent whole genome analyses in combination with different phenotypic screens have provided key insights into the evolution of M...
December 4, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29216381/de-novo-gene-evolution-of-antifreeze-glycoproteins-in-codfishes-revealed-by-whole-genome-sequence-data
#15
Helle Tessand Baalsrud, Ole Kristian Tørresen, Monica Hongrø Solbakken, Walter Salzburger, Reinhold Hanel, Kjetill S Jakobsen, Sissel Jentoft
New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown...
December 5, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29216330/genome-wide-analysis-of-the-brachypodium-distachyon-l-p-beauv-hsp90-gene-family-reveals-molecular-evolution-and-expression-profiling-under-drought-and-salt-stresses
#16
Ming Zhang, Zhiwei Shen, Guoqing Meng, Yu Lu, Yilei Wang
The structure, evolution, and function of heat shock proteins 90 (Hsp90s) have been investigated in great detail in fungi and animals. However, studies on the Hsp90 genes in plants are generally limited. Brachypodium distachyon (L.) P. Beauv., as a model plant for cereal crops, has become a potential biofuel grass. During its long evolution, the Hsp90 gene family in Brachypodium has developed some strategies to cope with adverse environments. How the Hsp90 gene family in Brachypodium evolved in different plant lineages and what its role is in plant responses to drought and salt stresses remains to be elucidated...
2017: PloS One
https://www.readbyqxmd.com/read/29216271/genomic-and-phenotypic-characteristics-of-swedish-c-jejuni-water-isolates
#17
Anna Nilsson, Cecilia Johansson, Astrid Skarp, René Kaden, Lars Engstrand, Hilpi Rautelin
Campylobacter jejuni is the most common cause of bacterial gastroenteritis. Major reservoirs are warm-blooded animals, poultry in particular, but Campylobacter can also be transmitted via water. In this paper, we have taken a closer look at the biology and potential virulence of C. jejuni water isolates. Seven C. jejuni isolates from incoming surface water at water plants in Sweden were characterized with whole genome sequencing and phenotypical testing. Multi locus sequence typing analysis revealed that these isolates belonged to groups known to include both common (ST48CC) and uncommon (ST1275CC, ST683, ST793 and ST8853) human pathogens...
2017: PloS One
https://www.readbyqxmd.com/read/29216251/molecular-characterization-of-hepatitis-b-virus-in-bangladesh-reveals-a-highly-recombinant-population
#18
Saif Ullah Munshi, Thanh Thi Thanh Tran, Truc Nhu Thanh Vo, Shahina Tabassum, Nahida Sultana, Trang Hoa Nguyen, Munira Jahan, Chau Ngoc Le, Stephen Baker, Motiur Rahman
The natural history and treatment outcome of hepatitis B viruses (HBV) infection is largely dependent on genotype, subgenotype, and the presence or absence of virulence associated mutations. We have studied the prevalence of genotype and subgenotype as well as virulence and drug resistance associated mutations and prevalence of recombinant among HBV from Bangladesh. A prospective cross-sectional study was conducted among treatment naïve chronic HBV patients attending at Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh for HBV viral load assessment between June and August 2015...
2017: PloS One
https://www.readbyqxmd.com/read/29215763/breast-cancer-the-translation-of-big-genomic-data-to-cancer-precision-medicine
#19
REVIEW
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Cancer is a complex genetic disease that consequence from the accumulation of genomic alterations, in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past two decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study (GWAS) and next generation sequencing (NGS) that contributing to big genomic data. International collaborative efforts have contributed in curating these data to identify clinically significant alterations that could be used in the clinical settings...
December 7, 2017: Cancer Science
https://www.readbyqxmd.com/read/29215633/measuring-mutation-accumulation-in-single-human-adult-stem-cells-by-whole-genome-sequencing-of-organoid-cultures
#20
Myrthe Jager, Francis Blokzijl, Valentina Sasselli, Sander Boymans, Roel Janssen, Nicolle Besselink, Hans Clevers, Ruben van Boxtel, Edwin Cuppen
Characterization of mutational processes in adult stem cells (ASCs) will improve our understanding of aging-related diseases, such as cancer and organ failure, and may ultimately help prevent the development of these diseases. Here, we present a method for cataloging mutations in individual human ASCs without the necessity of using error-prone whole-genome amplification. Single ASCs are expanded in vitro into clonal organoid cultures to generate sufficient DNA for accurate whole-genome sequencing (WGS) analysis...
January 2018: Nature Protocols
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