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https://www.readbyqxmd.com/read/28107752/genome-nuclear-lamina-interactions-from-cell-populations-to-single-cells
#1
REVIEW
J Omar Yáñez-Cuna, Bas van Steensel
Lamina-associated domains (LADs) are large genomic regions that interact with the nuclear lamina (NL) and help to guide the spatial folding of chromosomes in the interphase nucleus. LADs have been linked to gene repression and other functions. Recent studies have begun to uncover some of the molecular players that drive LAD-NL interactions. A picture emerges in which DNA sequence, chromatin components and nuclear lamina proteins play an important role. Complementary to this, imaging and single-cell genomics approaches have revealed that some LAD-NL interactions are variable from cell to cell, while others are very stable...
January 17, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28107688/sequencing-and-de-novo-assembly-of-visceral-mass-transcriptome-of-the-critically-endangered-land-snail-satsuma-myomphala-annotation-and-ssr-discovery
#2
Se Won Kang, Bharat Bhusan Patnaik, Hee-Ju Hwang, So Young Park, Jong Min Chung, Dae Kwon Song, Hongray Howrelia Patnaik, Jae Bong Lee, Changmu Kim, Soonok Kim, Young-Su Park, Hong Seog Park, Seung-Hwan Park, Yeon Soo Han, Jun Sang Lee, Yong Seok Lee
Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis...
October 29, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28107606/dishevelled-segment-polarity-protein-3-dvl3-a-novel-and-easily-applicable-recurrence-predictor-in-localized-prostate-adenocarcinoma
#3
Pil-Jong Kim, Ji Y Park, Hong-Gee Kim, Yong Mee Cho, Heounjeong Go
OBJECTIVE: To identify new biomarkers for the biochemical recurrence (BCR) of prostate adenocarcinoma. PATIENTS AND METHODS: Clinical information of 500 prostate adenocarcinoma patients and their 152 RNA-sequencing and protein-array data from The Cancer Genome Atlas (TCGA) were separated into a discovery-set and a validation-set. Each dataset was analyzed according to the Gleason grade groups reflecting BCR. The results obtained from the analysis using TCGA dataset were confirmed by immunohistochemistry analyses of the confirmation cohort composed of 395 localized prostate adenocarcinoma patients...
January 20, 2017: BJU International
https://www.readbyqxmd.com/read/28107530/broad-scale-genetic-diversity-of-cannabis-for-forensic-applications
#4
Christophe Dufresnes, Catherine Jan, Friederike Bienert, Jérôme Goudet, Luca Fumagalli
Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs...
2017: PloS One
https://www.readbyqxmd.com/read/28107514/karyopherin-alpha-proteins-regulate-oligodendrocyte-differentiation
#5
Benjamin M Laitman, John N Mariani, Chi Zhang, Setsu Sawai, Gareth R John
Proper regulation of the coordinated transcriptional program that drives oligodendrocyte (OL) differentiation is essential for central nervous system myelin formation and repair. Nuclear import, mediated in part by a group of karyopherin alpha (Kpna) proteins, regulates transcription factor access to the genome. Understanding how canonical nuclear import functions to control genomic access in OL differentiation may aid in the creation of novel therapeutics to stimulate myelination and remyelination. Here, we show that members of the Kpna family regulate OL differentiation, and may play distinct roles downstream of different pro-myelinating stimuli...
2017: PloS One
https://www.readbyqxmd.com/read/28107502/rnai-based-functional-genomics-identifies-new-virulence-determinants-in-mucormycosis
#6
Trung Anh Trieu, María Isabel Navarro-Mendoza, Carlos Pérez-Arques, Marta Sanchis, Javier Capilla, Patricia Navarro-Rodriguez, Loida Lopez-Fernandez, Santiago Torres-Martínez, Victoriano Garre, Rosa María Ruiz-Vázquez, Francisco E Nicolás
Mucorales are an emerging group of human pathogens that are responsible for the lethal disease mucormycosis. Unfortunately, functional studies on the genetic factors behind the virulence of these organisms are hampered by their limited genetic tractability, since they are reluctant to classical genetic tools like transposable elements or gene mapping. Here, we describe an RNAi-based functional genomic platform that allows the identification of new virulence factors through a forward genetic approach firstly described in Mucorales...
January 20, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28107481/bet-inhibitors-disrupt-rad21-dependent-conformational-control-of-kshv-latency
#7
Horng-Shen Chen, Alessandra De Leo, Zhuo Wang, Andrew Kerekovic, Robert Hills, Paul M Lieberman
Kaposi's Sarcoma-associated Herpesvirus (KSHV) establishes stable latent infection in B-lymphocytes and pleural effusion lymphomas (PELs). During latency, the viral genome persists as an epigenetically constrained episome with restricted gene expression programs. To identify epigenetic regulators of KSHV latency, we screened a focused small molecule library containing known inhibitors of epigenetic factors. We identified JQ1, a Bromodomain and Extended Terminal (BET) protein inhibitor, as a potent activator of KSHV lytic reactivation from B-cells carrying episomal KSHV...
January 20, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28107465/lead-exposure-induces-weight-gain-in-adult-rats-accompanied-by-dna-hypermethylation
#8
Honglin Sun, Ningjian Wang, Xiaomin Nie, Li Zhao, Qin Li, Zhen Cang, Chi Chen, Meng Lu, Jing Cheng, Hualing Zhai, Fangzhen Xia, Lin Ye, Yingli Lu
OBJECTIVE: Previous studies have revealed the association of lead (Pb) exposure with obesity. DNA methylation alteration has been suggested to be one of the regulatory mechanisms of obesity. We aimed to explore whether Pb exposure is related with weight gain and DNA methylation alteration. METHODS: Male adult 8 week Wistar rats were divided into 5 groups: the normal chow diet (NCD); the NCD+0.05%Pb; the NCD+0.15%Pb; the NCD+0.45%Pb and the high fat diet. Rats were exposed to different dosages of Pb through drinking water for 21 weeks...
2017: PloS One
https://www.readbyqxmd.com/read/28107443/identification-of-the-pla2g6-c-1579g-a-missense-mutation-in-papillon-dog-neuroaxonal-dystrophy-using-whole-exome-sequencing-analysis
#9
Masaya Tsuboi, Manabu Watanabe, Kazumi Nibe, Natsuko Yoshimi, Akihisa Kato, Masahiro Sakaguchi, Osamu Yamato, Miyuu Tanaka, Mitsuru Kuwamura, Kazuya Kushida, Takashi Ishikura, Tomoyuki Harada, James Kenn Chambers, Sumio Sugano, Kazuyuki Uchida, Hiroyuki Nakayama
Whole exome sequencing (WES) has become a common tool for identifying genetic causes of human inherited disorders, and it has also recently been applied to canine genome research. We conducted WES analysis of neuroaxonal dystrophy (NAD), a neurodegenerative disease that sporadically occurs worldwide in Papillon dogs. The disease is considered an autosomal recessive monogenic disease, which is histopathologically characterized by severe axonal swelling, known as "spheroids," throughout the nervous system. By sequencing all eleven DNA samples from one NAD-affected Papillon dog and her parents, two unrelated NAD-affected Papillon dogs, and six unaffected control Papillon dogs, we identified 10 candidate mutations...
2017: PloS One
https://www.readbyqxmd.com/read/28107441/fine-mapping-and-candidate-gene-analysis-of-the-tiller-suppression-gene-ts1-in-rice
#10
Lei Liu, Fen Meng, Yonggang He, Menghao Zhu, Yanhao Shen, Zhihong Zhang
Tiller number is one of the key factors that influences rice plant type and yield components. In this study, an EMS-induced rice tiller suppression mutant ts1 was characterized. Morphological and histological observations revealed that, in the ts1 plants, the tiller buds were abnormally formed and therefore cannot outgrow into tillers. With an F2 population derived from a cross between ts1 and an indica cultivar Wushansimiao, a major gene, tiller suppression 1 (ts1) was fine-mapped to a 108.5 kb genomic region between markers ID8378 and SSR6884 on the short arm of rice chromosome 2...
2017: PloS One
https://www.readbyqxmd.com/read/28107433/investigation-of-cross-contamination-and-misidentification-of-278-widely-used-tumor-cell-lines
#11
Yaqing Huang, Yuehong Liu, Congyi Zheng, Chao Shen
In recent years, biological research involving human cell lines has been rapidly developing in China. However, some of the cell lines are not authenticated before use. Therefore, misidentified and/or cross-contaminated cell lines are unfortunately commonplace. In this study, we present a comprehensive investigation of cross-contamination and misidentification for a panel of 278 cell lines from 28 institutes in China by using short tandem repeat profiling method. By comparing the DNA profiles with the cell bank databases of ATCC and DSMZ, a total of 46...
2017: PloS One
https://www.readbyqxmd.com/read/28107422/comparison-of-hapmap-and-1000-genomes-reference-panels-in-a-large-scale-genome-wide-association-study
#12
Paul S de Vries, Maria Sabater-Lleal, Daniel I Chasman, Stella Trompet, Tarunveer S Ahluwalia, Alexander Teumer, Marcus E Kleber, Ming-Huei Chen, Jie Jin Wang, John R Attia, Riccardo E Marioni, Maristella Steri, Lu-Chen Weng, Rene Pool, Vera Grossmann, Jennifer A Brody, Cristina Venturini, Toshiko Tanaka, Lynda M Rose, Christopher Oldmeadow, Johanna Mazur, Saonli Basu, Mattias Frånberg, Qiong Yang, Symen Ligthart, Jouke J Hottenga, Ann Rumley, Antonella Mulas, Anton J M de Craen, Anne Grotevendt, Kent D Taylor, Graciela E Delgado, Annette Kifley, Lorna M Lopez, Tina L Berentzen, Massimo Mangino, Stefania Bandinelli, Alanna C Morrison, Anders Hamsten, Geoffrey Tofler, Moniek P M de Maat, Harmen H M Draisma, Gordon D Lowe, Magdalena Zoledziewska, Naveed Sattar, Karl J Lackner, Uwe Völker, Barbara McKnight, Jie Huang, Elizabeth G Holliday, Mark A McEvoy, John M Starr, Pirro G Hysi, Dena G Hernandez, Weihua Guan, Fernando Rivadeneira, Wendy L McArdle, P Eline Slagboom, Tanja Zeller, Bruce M Psaty, André G Uitterlinden, Eco J C de Geus, David J Stott, Harald Binder, Albert Hofman, Oscar H Franco, Jerome I Rotter, Luigi Ferrucci, Tim D Spector, Ian J Deary, Winfried März, Andreas Greinacher, Philipp S Wild, Francesco Cucca, Dorret I Boomsma, Hugh Watkins, Weihong Tang, Paul M Ridker, Jan W Jukema, Rodney J Scott, Paul Mitchell, Torben Hansen, Christopher J O'Donnell, Nicholas L Smith, David P Strachan, Abbas Dehghan
An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals...
2017: PloS One
https://www.readbyqxmd.com/read/28107419/a-new-israeli-tobamovirus-isolate-infects-tomato-plants-harboring-tm-22-resistance-genes
#13
Neta Luria, Elisheva Smith, Victoria Reingold, Ilana Bekelman, Moshe Lapidot, Ilan Levin, Nadav Elad, Yehudit Tam, Noa Sela, Ahmad Abu-Ras, Nadav Ezra, Ami Haberman, Liron Yitzhak, Oded Lachman, Aviv Dombrovsky
An outbreak of a new disease infecting tomatoes occurred in October-November 2014 at the Ohad village in Southern Israel. Symptomatic plants showed a mosaic pattern on leaves accompanied occasionally by narrowing of leaves and yellow spotted fruit. The disease spread mechanically and rapidly reminiscent of tobamovirus infection. Epidemiological studies showed the spread of the disease in various growing areas, in the South and towards the Southeast and Northern parts of the country within a year. Transmission electron microscope (TEM) analysis showed a single rod-like form characteristic to the Tobamovirus genus...
2017: PloS One
https://www.readbyqxmd.com/read/28107396/mixfit-methodology-for-computing-ancestry-related-genetic-scores-at-the-individual-level-and-its-application-to-the-estonian-and-finnish-population-studies
#14
Toomas Haller, Liis Leitsalu, Krista Fischer, Marja-Liisa Nuotio, Tõnu Esko, Dorothea Irene Boomsma, Kirsten Ohm Kyvik, Tim D Spector, Markus Perola, Andres Metspalu
Ancestry information at the individual level can be a valuable resource for personalized medicine, medical, demographical and history research, as well as for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data. Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition-multidimensional best fitting by MixFit...
2017: PloS One
https://www.readbyqxmd.com/read/28107392/upon-accounting-for-the-impact-of-isoenzyme-loss-gene-deletion-costs-anticorrelate-with-their-evolutionary-rates
#15
Christopher Jacobs, Luke Lambourne, Yu Xia, Daniel Segrè
System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism's genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene's fitness contribution to an organism "here and now" and the same gene's historical importance as evidenced by its accumulated mutations over millions of years of evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28107386/regulation-of-pi-2b-pilus-expression-in-hypervirulent-streptococcus-agalactiae-st-17-bm110
#16
Bruno Périchon, Noémi Szili, Laurence du Merle, Isabelle Rosinski-Chupin, Myriam Gominet, Samuel Bellais, Claire Poyart, Patrick Trieu-Cuot, Shaynoor Dramsi
The widely spread Streptococcus agalactiae (also known as Group B Streptococcus, GBS) "hypervirulent" ST17 clone is strongly associated with neonatal meningitis. The PI-2b locus is mainly found in ST17 strains but is also present in a few non ST17 human isolates such as the ST-7 prototype strain A909. Here, we analysed the expression of the PI-2b pilus in the ST17 strain BM110 as compared to the non ST17 A909. Comparative genome analyses revealed the presence of a 43-base pair (bp) hairpin-like structure in the upstream region of PI-2b operon in all 26 ST17 genomes, which was absent in the 8 non-ST17 strains carrying the PI-2b locus...
2017: PloS One
https://www.readbyqxmd.com/read/28107364/genetic-attributes-of-e-coli-isolates-from-chlorinated-drinking-water
#17
Michaela D J Blyton, David M Gordon
Escherichia coli, is intimately associated with both human health and water sanitation. E. coli isolates from water can either be (i) host associated commensals, indicating recent faecal contamination; (ii) diarrheal pathogens or (iii) extra-intestinal pathogens that pose a direct health risk; or (iv) free-living. In this study we genetically characterised 28 E. coli isolates obtained from treated drinking water in south eastern Australia to ascertain their likely source. We used full genome sequencing to assign the isolates to their phylogenetic group and multi-locus sequence type...
2017: PloS One
https://www.readbyqxmd.com/read/28107356/integrity-of-induced-pluripotent-stem-cell-ipsc-derived-megakaryocytes-as-assessed-by-genetic-and-transcriptomic-analysis
#18
Kai Kammers, Margaret A Taub, Ingo Ruczinski, Joshua Martin, Lisa R Yanek, Alyssa Frazee, Yongxing Gao, Dixie Hoyle, Nauder Faraday, Diane M Becker, Linzhao Cheng, Zack Z Wang, Jeff T Leek, Lewis C Becker, Rasika A Mathias
Previously, we have described our feeder-free, xeno-free approach to generate megakaryocytes (MKs) in culture from human induced pluripotent stem cells (iPSCs). Here, we focus specifically on the integrity of these MKs using: (1) genotype discordance between parent cell DNA to iPSC cell DNA and onward to the differentiated MK DNA; (2) genomic structural integrity using copy number variation (CNV); and (3) transcriptomic signatures of the derived MK lines compared to the iPSC lines. We detected a very low rate of genotype discordance; estimates were 0...
2017: PloS One
https://www.readbyqxmd.com/read/28107347/whole-genome-amplification-and-reduced-representation-genome-sequencing-of-schistosoma-japonicum-miracidia
#19
Jonathan A Shortt, Daren C Card, Drew R Schield, Yang Liu, Bo Zhong, Todd A Castoe, Elizabeth J Carlton, David D Pollock
BACKGROUND: In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans...
January 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28107343/mutations-in-the-non-catalytic-subunit-dpb2-of-dna-polymerase-epsilon-affect-the-nrm1-branch-of-the-dna-replication-checkpoint
#20
Michał Dmowski, Justyna Rudzka, Judith L Campbell, Piotr Jonczyk, Iwona J Fijałkowska
To preserve genome integrity, the S-phase checkpoint senses damaged DNA or nucleotide depletion and when necessary, arrests replication progression and delays cell division. Previous studies, based on two pol2 mutants have suggested the involvement of DNA polymerase epsilon (Pol ε) in sensing DNA replication accuracy in Saccharomyces cerevisiae. Here we have studied the involvement of Pol ε in sensing proper progression of DNA replication, using a mutant in DPB2, the gene coding for a non-catalytic subunit of Pol ε...
January 20, 2017: PLoS Genetics
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