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Gene Mapping

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https://www.readbyqxmd.com/read/28097398/mapping-quantitative-trait-loci-for-root-development-under-hypoxia-conditions-in-soybean-glycine-max-l-merr
#1
Loc Van Nguyen, Ryoji Takahashi, Stephen Mwangi Githiri, Tito O Rodriguez, Nobuko Tsutsumi, Sayuri Kajihara, Takasi Sayama, Masao Ishimoto, Kyuya Harada, Keisuke Suematsu, Tomomi Abiko, Toshihiro Mochizuki
Greatest potential, QTLs for hypoxia and waterlogging tolerance in soybean roots were detected using a new phenotypic evaluation method. Waterlogging is a major environmental stress limiting soybean yield in wet parts of the world. Root development is an important indicator of hypoxia tolerance in soybean. However, little is known about the genetic control of root development under hypoxia. This study was conducted to identify quantitative trait loci (QTLs) responsible for root development under hypoxia. Recombinant inbred lines (RILs) developed from a cross between a hypoxia-sensitive cultivar, Tachinagaha, and a tolerant landrace, Iyodaizu, were used...
January 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28097321/diagnostic-yield-and-novel-candidate-genes-by-exome-sequencing-in-152-consanguineous-families-with-neurodevelopmental-disorders
#2
Miriam S Reuter, Hasan Tawamie, Rebecca Buchert, Ola Hosny Gebril, Tawfiq Froukh, Christian Thiel, Steffen Uebe, Arif B Ekici, Mandy Krumbiegel, Christiane Zweier, Juliane Hoyer, Karolin Eberlein, Judith Bauer, Ute Scheller, Tim M Strom, Sabine Hoffjan, Ehab R Abdelraouf, Nagwa A Meguid, Ahmad Abboud, Mohammed Ayman Al Khateeb, Mahmoud Fakher, Saber Hamdan, Amina Ismael, Safia Muhammad, Ebtessam Abdallah, Heinrich Sticht, Dagmar Wieczorek, André Reis, Rami Abou Jamra
Importance: Autosomal recessive inherited neurodevelopmental disorders are highly heterogeneous, and many, possibly most, of the disease genes are still unknown. Objectives: To promote the identification of disease genes through confirmation of previously described genes and presentation of novel candidates and provide an overview of the diagnostic yield of exome sequencing in consanguineous families. Design, Setting, and Participants: Autozygosity mapping in families and exome sequencing of index patients were performed in 152 consanguineous families (the parents descended from a same ancestor) with at least 1 offspring with intellectual disability (ID)...
January 11, 2017: JAMA Psychiatry
https://www.readbyqxmd.com/read/28097058/determining-virus-host-interactions-and-glycerol-metabolism-profiles-in-geographically-diverse-solar-salterns-with-metagenomics
#3
Abraham G Moller, Chun Liang
Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics...
2017: PeerJ
https://www.readbyqxmd.com/read/28096490/comprehensive-essentiality-analysis-of-the-mycobacterium-tuberculosis-genome-via-saturating-transposon-mutagenesis
#4
Michael A DeJesus, Elias R Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E Long, Cara C Boutte, Eric J Rubin, Dirk Schnappinger, Sabine Ehrt, Sarah M Fortune, Christopher M Sassetti, Thomas R Ioerger
: For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to sustain insertion. To date, these studies have analyzed subsaturated libraries, necessitating the application of statistical methods to estimate the likelihood that a gap in transposon coverage is the result of biological selection and not the stochasticity of insertion. As a result, the essentiality of many genomic features, particularly small ones, could not be reliably assessed...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096404/torc1-dependent-sumoylation-of-rpc82-promotes-rna-polymerase-iii-assembly-and-activity
#5
Pierre Chymkowitch, Aurélie Nguéa P, Håvard Aanes, Joseph Robertson, Arne Klungland, Jorrit M Enserink
Maintaining cellular homeostasis under changing nutrient conditions is essential for the growth and development of all organisms. The mechanisms that maintain homeostasis upon loss of nutrient supply are not well understood. By mapping the SUMO proteome in Saccharomyces cerevisiae, we discovered a specific set of differentially sumoylated proteins mainly involved in transcription. RNA polymerase III (RNAPIII) components, including Rpc53, Rpc82, and Ret1, are particularly prominent nutrient-dependent SUMO targets...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096075/hpprna-a-snakemake-based-handy-parameter-free-pipeline-for-rna-seq-analysis-of-numerous-samples
#6
Dapeng Wang
RNA-Seq technology has been gradually becoming a routine approach for characterizing the properties of transcriptome in terms of organisms, cell types and conditions and consequently a big burden has been put on the facet of data analysis, which calls for an easy-to-learn workflow to cope with the increased demands from a large number of laboratories across the world. We report a one-in-all solution called hppRNA, composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection, written by a series of individual Perl and R scripts, counting on well-established and preinstalled software, irrespective of single-end or paired-end, unstranded or stranded sequencing method...
January 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28095770/the-unique-genomic-landscape-surrounding-the-epsps-gene-in-glyphosate-resistant-amaranthus-palmeri-a-repetitive-path-to-resistance
#7
William T Molin, Alice A Wright, Amy Lawton-Rauh, Christopher A Saski
BACKGROUND: The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28095652/exosomal-trafficking-in-xenopus-development
#8
REVIEW
Michael Danilchik, Tess Tumarkin
Exosomes are small extracellular vesicles (EVs) secreted by many cell types in both normal and pathogenic circumstances. Because EVs, particularly exosomes, are known to transfer biologically active proteins, RNAs and lipids between cells, they have recently become the focus of intense interest as potential mediators of cell-cell communication, particularly in long-range and juxtacrine signaling events associated with adaptive immune function and progression of cancer. Among the EVs, exosomes appear particularly adapted for long-range delivery of cargoes between cells...
January 17, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28095469/characterization-of-dof-transcription-factors-and-their-responses-to-osmotic-stress-in-poplar-populus-trichocarpa
#9
Han Wang, Shicheng Zhao, Yuchi Gao, Jingli Yang
The DNA-binding One Zinc Finger (Dof) genes are ubiquitous in many plant species and are especial transcription regulators that participate in plant growth, development and various procedures, including biotic and abiotic stress reactions. In this study, we identified 41 PtrDof members from Populus trichocarpa genomes and classified them into four groups. The conserved motifs and gene structures of some PtrDof genes belonging to the same subgroup were almost the same. The 41 PtrDof genes were dispersed on 18 of the 19 Populus chromosomes...
2017: PloS One
https://www.readbyqxmd.com/read/28095098/reduced-penetrance-in-a-large-caucasian-pedigree-with-stickler-syndrome
#10
Stuart W Tompson, Charles Johnson, Diana Abbott, Benjamin Bakall, Vincent Soler, Tammy L Yanovitch, Kristina N Whisenhunt, Thomas Klemm, Steve Rozen, Edwin M Stone, Max Johnson, Terri L Young
BACKGROUND: In a four-generation Caucasian family variably diagnosed with autosomal dominant (AD) Stickler or Wagner disease, commercial gene screening failed to identify a mutation in COL2A1 or VCAN. We utilized linkage mapping and exome sequencing to identify the causal variant. MATERIALS AND METHODS: Genomic DNA samples collected from 40 family members were analyzed. A whole-genome linkage scan was performed using Illumina HumanLinkage-24 BeadChip followed by two-point and multipoint linkage analyses using FASTLINK and MERLIN...
January 17, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28094809/genome-wide-identification-evolution-and-expression-analysis-of-ring-finger-protein-genes-in-brassica-rapa
#11
Intikhab Alam, Yan-Qing Yang, Yong Wang, Mei-Lan Zhu, Heng-Bo Wang, Boulos Chalhoub, Yun-Hai Lu
More and more RING finger genes were found to be implicated in various important biological processes. In the present study, a total of 731 RING domains in 715 predicted proteins were identified in Brassica rapa genome (AA, 2n = 20), which were further divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47), RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5) and RING-G (1). The 715 RING finger proteins were further classified into 51 groups according to the presence of additional domains...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28094016/a-single-cell-roadmap-of-lineage-bifurcation-in-human-esc-models-of-embryonic-brain-development
#12
Zizhen Yao, John K Mich, Sherman Ku, Vilas Menon, Anne-Rachel Krostag, Refugio A Martinez, Leon Furchtgott, Heather Mulholland, Susan Bort, Margaret A Fuqua, Ben W Gregor, Rebecca D Hodge, Anu Jayabalu, Ryan C May, Samuel Melton, Angelique M Nelson, N Kiet Ngo, Nadiya V Shapovalova, Soraya I Shehata, Michael W Smith, Leah J Tait, Carol L Thompson, Elliot R Thomsen, Chaoyang Ye, Ian A Glass, Ajamete Kaykas, Shuyuan Yao, John W Phillips, Joshua S Grimley, Boaz P Levi, Yanling Wang, Sharad Ramanathan
During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development...
January 5, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28093929/characterization-of-mitochondrial-dna-polymorphisms-in-the-han-population-in-liaoning-province-northeast-china
#13
Feng-Ling Xu, Jun Yao, Mei Ding, Zhang-Sen Shi, Xue Wu, Jing-Jing Zhang, Bao-Jie Wang
This study characterized the genetic variations of mitochondrial DNA (mtDNA) to elucidate the maternal genetic structure of Liaoning Han Chinese. A total of 317 blood samples of unrelated individuals were collected for analysis in Liaoning Province. The mtDNA samples were analyzed using two distinct methods: sequencing of the hypervariable sequences I and II (HVSI and HVSII), and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the coding region. The results indicated a high gene diversity value (0...
January 17, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28093630/brassica-napus-ds-3-encoding-a-della-protein-negatively-regulates-stem-elongation-through-gibberellin-signaling-pathway
#14
Bo Zhao, Haitao Li, Juanjuan Li, Bo Wang, Cheng Dai, Jing Wang, Kede Liu
Identification and characterization of a semi-dwarfing gene ds-3 encoding a mutant DELLA protein regulating plant height through gibberellin signaling pathway. Lodging is one of the most important factors causing severe yield loss in oilseed rape. Utilization of semi-dwarf varieties has been proved the most effective way to increase lodging resistance and yield in many crops. To develop semi-dwarf germplasm in oilseed rape, we identified a semi-dwarf mutant ds-3 which showed a reduced response to phytohormones gibberellins (GAs)...
January 16, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28093616/rare-germline-alterations-in-cancer-related-genes-associated-with-the-risk-of-multiple-primary-tumor-development
#15
Rolando A R Villacis, Tatiane R Basso, Luisa M Canto, Maísa Pinheiro, Karina M Santiago, Juliana Giacomazzi, Cláudia A A de Paula, Dirce M Carraro, Patrícia Ashton-Prolla, Maria I Achatz, Silvia R Rogatto
: Multiple primary tumors (MPT) have been described in carriers of inherited cancer predisposition genes. However, the genetic etiology of a large proportion of MPT cases remains unclear. We reviewed 267 patients with hereditary cancer predisposition syndromes (HCPS) that underwent genetic counseling and selected 22 patients with MPT to perform genomic analysis (CytoScan HD Array, Affymetrix) aiming to identify new alterations related to a high risk of developing MPT. Twenty patients had a positive family history of cancer and 11 met phenotypic criteria for HCPS...
January 16, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28093455/genomewide-landscape-of-gene-metabolome-associations-in-escherichia-coli
#16
Tobias Fuhrer, Mattia Zampieri, Daniel C Sévin, Uwe Sauer, Nicola Zamboni
Metabolism is one of the best-understood cellular processes whose network topology of enzymatic reactions is determined by an organism's genome. The influence of genes on metabolite levels, however, remains largely unknown, particularly for the many genes encoding non-enzymatic proteins. Serendipitously, genomewide association studies explore the relationship between genetic variants and metabolite levels, but a comprehensive interaction network has remained elusive even for the simplest single-celled organisms...
January 16, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28093102/proteomic-changes-in-the-ileum-of-sheep-infected-with-mycobacterium-avium-subspecies-paratuberculosis
#17
S Pisanu, T Cubeddu, S Uzzau, S Rocca, M F Addis
Johne's disease (JD) is a chronic enteritis of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). To identify the processes activated in the sheep intestine during natural MAP infection, and to provide a panel of differential host and pathogen proteins with diagnostic and prognostic potential, a differential shotgun proteomics workflow, including mass spectrometry, label-free quantisation and pathway analysis, was applied to ileal tissues of ewes with and without JD. Out of 2889 total proteins identified, 384 were differentially expressed and 341 were expressed at a higher level in JD...
January 2017: Veterinary Journal
https://www.readbyqxmd.com/read/28092764/common-deregulated-gene-expression-profiles-and-morphological-changes-in-developing-zebrafish-larvae-exposed-to-environmental-relevant-high-to-low-concentrations-of-glucocorticoids
#18
Qiyu Chen, Caixia Li, Zhiyuan Gong, Eric Chun Yong Chan, Shane A Snyder, Siew Hong Lam
Synthetic glucocorticoids have been detected in environmental waters and their biological potency have raised concerns of their impact on aquatic vertebrates especially fish. In this study, developing zebrafish larvae exposed to representative glucocorticoids (dexamethasone, prednisolone and triamcinolone) at 50 pM to 50 nM from 3 h post-fertilisation to 5 days post-fertilisation were investigated. Microarray analysis identified 1255, 1531, and 2380 gene probes, which correspondingly mapped to 660, 882 and 1238 human/rodent homologs, as deregulated by dexamethasone, prednisolone and triamcinolone, respectively...
January 6, 2017: Chemosphere
https://www.readbyqxmd.com/read/28091870/perspectives-using-polymer-modeling-to-understand-the-formation-and-function-of-nuclear-compartments
#19
REVIEW
N Haddad, D Jost, C Vaillant
Compartmentalization is a ubiquitous feature of cellular function. In the nucleus, early observations revealed a non-random spatial organization of the genome with a large-scale segregation between transcriptionally active-euchromatin-and silenced-heterochromatin-parts of the genome. Recent advances in genome-wide mapping and imaging techniques have strikingly improved the resolution at which nuclear genome folding can be analyzed and have revealed a multiscale spatial compartmentalization with increasing evidences that such compartment may indeed result from and participate to genome function...
January 14, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28091775/developmental-and-sex-specific-differences-in-expression-of-neuropeptides-derived-from-allatotropin-gene-in-the-silkmoth-bombyx-mori
#20
Branislav Bednár, Ladislav Roller, Daniel Čižmár, Diana Mitrová, Dušan Žitňan
Allatotropin (AT) and related neuropeptides are widespread bioactive molecules that regulate development, food intake and muscle contractions in insects and other invertebrates. In moths, alternative splicing of the at gene generates three mRNA precursors encoding AT with different combinations of three structurally similar AT-like peptides (ATLI-III). We used in situ hybridization and immunohistochemistry to map the differential expression of these transcripts during the postembryonic development of Bombyx mori...
January 16, 2017: Cell and Tissue Research
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