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https://www.readbyqxmd.com/read/28922869/genome-organization-of-sphingobium-indicum-b90a-an-archetypal-hexachlorocyclohexane-hch-degrading-genotype
#1
Helianthous Verma, Abhay Bajaj, Roshan Kumar, Jasvinder Kaur, Shailly Anand, Namita Nayyar, Akshita Puri, Yogendra Singh, Jitendra P Khurana, Rup Lal
Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp)...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28922794/genome-wide-variation-patterns-uncover-the-origin-and-selection-in-cultivated-ginseng-panax-ginseng-meyer
#2
Ming-Rui Li, Feng-Xue Shi, Ya-Ling Li, Peng Jiang, Lili Jiao, Bao Liu, Lin-Feng Li
Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28922793/diurnal-cycling-transcription-factors-of-pineapple-revealed-by-genome-wide-annotation-and-global-transcriptomic-analysis
#3
Anupma Sharma, Ching Man Wai, Ray Ming, Qingyi Yu
Circadian clock provides fitness advantage by coordinating internal metabolic and physiological processes to external cyclic environments. Core clock components exhibit daily rhythmic changes in gene expression, and the majority of them are transcription factors (TFs) and transcription coregulators (TCs). We annotated 1,398 TFs from 67 TF families and 80 TCs from 20 TC families in pineapple, and analyzed their tissue-specific and diurnal expression patterns. Approximately 42% of TFs and 45% of TCs displayed diel rhythmic expression, including 177 TF/TCs cycling only in the nonphotosynthetic leaf tissue, 247 cycling only in the photosynthetic leaf tissue, and 201 cycling in both...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28922777/nitrate-supply-to-grapevine-rootstocks-new-genome-wide-findings
#4
Anna Medici, Benoit Lacombe, Sandrine Ruffel
No abstract text is available yet for this article.
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922774/crop-model-assisted-phenomics-and-genome-wide-association-study-for-climate-adaptation-of-indica-rice-1-phenology
#5
Michael Dingkuhn, Richard Pasco, Julie M Pasuquin, Jean Damo, Jean-Christophe Soulié, Louis-Marie Raboin, Julie Dusserre, Abdoulaye Sow, Baboucarr Manneh, Suchit Shrestha, Alpha Balde, Tobias Kretzschmar
Phenology and time of flowering are crucial determinants of rice adaptation to climate variation. A previous study characterized flowering responses of 203 diverse indica rices (the ORYTAGE panel) to ten environments in Senegal (six sowing dates) and Madagascar (two years and two altitudes) under irrigation in the field. This study used the physiological phenology model RIDEV V2 to heuristically estimate component traits of flowering such as cardinal temperatures (base temperature (Tbase) and optimum temperature), basic vegetative phase, photoperiod sensitivity and cold acclimation, and to conduct a genome-wide association study for these traits using 16 232 anonymous single-nucleotide polymorphism (SNP) markers...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922773/crop-model-assisted-phenomics-and-genome-wide-association-study-for-climate-adaptation-of-indica-rice-2-thermal-stress-and-spikelet-sterility
#6
Michael Dingkuhn, Richard Pasco, Julie Mae Pasuquin, Jean Damo, Jean-Christophe Soulié, Louis-Marie Raboin, Julie Dusserre, Abdoulaye Sow, Baboucarr Manneh, Suchit Shrestha, Tobias Kretzschmar
Low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. Phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. Physiological models can be used to separate these effects. A 203-accession indica rice diversity panel was phenotyped for sterility in ten environments in Senegal and Madagascar and climate data were recorded. Here we report on sterility responses while a companion study reported on phenology...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922760/the-roles-of-pleiotropy-and-close-linkage-as-revealed-by-association-mapping-of-yield-and-correlated-traits-of-wheat-triticum-aestivum-l
#7
Albert W Schulthess, Jochen C Reif, Jie Ling, Jörg Plieske, Sonja Kollers, Erhard Ebmeyer, Viktor Korzun, Odile Argillier, Gunther Stiewe, Martin W Ganal, Marion S Röder, Yong Jiang
Grain yield (GY) of bread wheat (Triticum aestivum L.) is quantitatively inherited. Correlated GY-syndrome traits such as plant height (PH), heading date (HD), thousand grain weight (TGW), test weight (TW), grains per ear (GPE), and ear weight (EW) influence GY. Most quantitative genetics studies assessed the multiple-trait (MT) complex of GY-syndrome using single-trait approaches, and little is known about its underlying pleiotropic architecture. We investigated the pleiotropic architecture of wheat GY-syndrome through MT association mapping (MT-GWAS) using 372 varieties phenotyped in up to eight environments and genotyped with 18 832 single nucleotide polymorphisms plus 24 polymorphic functional markers...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922752/current-understanding-of-the-pathways-of-flavonoid-biosynthesis-in-model-and-crop-plants
#8
Takayuki Tohge, Leonardo Perez de Souza, Alisdair R Fernie
Flavonoids are a signature class of secondary metabolites formed from a relatively simple collection of scaffolds. They are extensively decorated by chemical reactions including glycosylation, methylation, and acylation. They are present in a wide variety of fruits and vegetables and as such in Western populations it is estimated that 20-50 mg of flavonoids are consumed daily per person. In planta they have demonstrated to contribute to both flower color and UV protection. Their consumption has been suggested to presenta wide range of health benefits...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922566/streptococcus-pneumoniae-and-chronic-endobronchial-infections-in-childhood
#9
Kim M Hare, Amanda J Leach, Heidi C Smith-Vaughan, Anne B Chang, Keith Grimwood
Streptococcus pneumoniae (pneumococcus) is the main cause of bacterial pneumonia worldwide and has been studied extensively in this context. However, its role in chronic endobronchial infections and accompanying lower airway neutrophilic infiltration has received little attention. Severe and recurrent pneumonia are risk factors for chronic suppurative lung disease (CSLD) and bronchiectasis; the latter causes considerable morbidity and, in some populations, premature death in children and adults. Protracted bacterial bronchitis (PBB) is another chronic endobronchial infection associated with substantial morbidity...
September 18, 2017: Pediatric Pulmonology
https://www.readbyqxmd.com/read/28922368/a-tree-of-life-based-on-ninety-eight-expressed-genes-conserved-across-diverse-eukaryotic-species
#10
Pawan Kumar Jayaswal, Vivek Dogra, Asheesh Shanker, Tilak Raj Sharma, Nagendra Kumar Singh
Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed...
2017: PloS One
https://www.readbyqxmd.com/read/28922188/new-insights-into-the-role-of-glycosylation-in-lipoprotein-metabolism
#11
Marjolein A W van den Boogert, Daniel J Rader, Adriaan G Holleboom
PURPOSE OF REVIEW: Human genetics has provided new insights into the role of protein glycosylation in regulating lipoprotein metabolism. Here we review these new developments and discuss the biological insights they provide. RECENT FINDINGS: Case descriptions of patients with congenital defects in N-glycosylation (CDG-I) frequently describe a distinct hypocholesterolemia in these rare multisystem clinical syndromes. Two novel CDGs with disturbed Golgi homeostasis and trafficking defects result in mixed glycosylation disorders, hepatic steatosis and hypercholesterolemia...
September 15, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/28921852/genome-wide-cell-free-fetal-dna-screening-spots-variations-standard-screening-doesn-t-diagnostic-testing-data-needed-to-validate-results-and-prove-accuracy
#12
(no author information available yet)
No abstract text is available yet for this article.
October 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28921840/the-role-of-cadherin-genes-in-five-major-psychiatric-disorders-a-literature-update
#13
REVIEW
Ziarih Hawi, Janette Tong, Callum Dark, Hannah Yates, Beth Johnson, Mark A Bellgrove
Converging evidence from candidate gene, genome-wide linkage, and association studies support a role of cadherins in the pathophysiology of five major psychiatric disorders including attention deficit hyperactivity disorder, autism spectrum disorder (ASD), schizophrenia (SCZ), bipolar disorder (BD), and major depressive disorder (MDD). These molecules are transmembrane proteins which act as cell adhesives by forming adherens junctions (AJs) to bind cells within tissues. Members of the cadherin superfamily are also involved in biological processes such as signal transduction and plasticity that have been implicated in the etiology of major psychiatric conditions...
September 18, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28921805/cytochrome-p450-diversification-and-hostplant-utilization-patterns-in-specialist-and-generalist-moths-birth-death-and-adaptation
#14
Bernarda Calla, Katherine Noble, Reed M Johnson, Kimberly K O Walden, Mary A Schuler, Hugh M Robertson, May R Berenbaum
Across insect genomes, the size of the cytochrome P450 monooxygenase (CYP) gene superfamily varies widely. CYPome size variation has been attributed to reciprocal adaptive radiations in insect detoxification genes in response to plant biosynthetic gene radiations driven by coevolution between herbivores and their chemically defended hostplants. Alternatively, variation in CYPome size may be due to random "birth and death" processes, whereby exponential increase via gene duplications is limited by random decay via gene death or transition via divergence...
September 15, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28921760/genome-wide-association-study-of-a-nicotine-metabolism-biomarker-in-african-american-smokers-impact-of-chromosome-19-genetic-influences
#15
Meghan J Chenoweth, Jennifer J Ware, Andy Z X Zhu, Christopher B Cole, Lisa Sanderson Cox, Nikki Nollen, Jasjit S Ahluwalia, Neal L Benowitz, Robert A Schnoll, Larry W Hawk, Paul M Cinciripini, Tony P George, Caryn Lerman, Joanne Knight, Rachel F Tyndale
BACKGROUND AND AIMS: The activity of CYP2A6, the major nicotine-inactivating enzyme, is measurable in smokers using the nicotine metabolite ratio (NMR; 3'hydroxycotinine/cotinine). Due to its role in nicotine clearance, the NMR is associated with smoking behaviours and response to pharmacotherapies. The NMR is highly heritable (~80%), and on average lower in African Americans (AA) versus Whites. We previously identified several reduce and loss-of-function CYP2A6 variants common in individuals of African descent...
September 16, 2017: Addiction
https://www.readbyqxmd.com/read/28921602/human-leukocyte-antigen-variants-and-risk-of-hepatocellular-carcinoma-modified-by-hcv-genotypes-a-genome-wide-association-study
#16
Mei-Hsuan Lee, Yu-Han Huang, Hsuan-Yu Chen, Charles Seik-Soon Khor, Ya-Hsuan Chang, Yu-Ju Lin, Chin-Lan Jen, Sheng-Nan Lu, Hwai-I Yang, Nao Nishida, Masaya Sugiyama, Masashi Mizokami, Yong Yuan, Gibert L'Italien, Katsushi Tokunaga, Chien-Jen Chen
BACKGROUND & AIMS: We conducted a genome-wide association study (GWAS) to discover genetic variants associated with hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC). METHODS: We genotyped 502 HCC cases and 749 non-HCC controls by using the Axiom(TM) -CHB genome-wide array. After identifying single nucleotide polymorphism (SNP) cluster located in the human leukocyte antigen region which were potentially associated with HCC, HLA-DQB1 genotyping was performed to analyze 994 anti-HCV seropositives collected in the period of 1991-2013 in a community-based cohort for evaluating long-term predictability of HLA variants for identifying the risk of HCC...
September 16, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28921535/genome-wide-host-rna-signatures-of-infectious-diseases-discovery-and-clinical-translation
#17
REVIEW
Harriet D Gliddon, Jethro A Herberg, Michael Levin, Myrsini Kaforou
The use of whole blood gene expression to derive diagnostic biomarkers capable of distinguishing between phenotypically similar diseases holds great promise but remains a challenge. Differential gene expression analysis is used to identify the key genes that undergo changes in expression relative to healthy individuals, as well as to patients with other diseases. These key genes can act as diagnostic, prognostic and predictive markers of disease. Gene expression 'signatures' in the blood hold potential to be used for the diagnosis of infectious diseases, where current diagnostics are unreliable, ineffective or of limited potential...
September 16, 2017: Immunology
https://www.readbyqxmd.com/read/28921524/karyotype-variation-of-cho-host-cell-lines-over-time-in-culture-characterized-by-chromosome-counting-and-chromosome-painting
#18
Sabine Vcelar, Vaibhav Jadhav, Michael Melcher, Norbert Auer, Astrid Hrdina, Rebecca Sagmeister, Kelley Heffner, Anja Puklowski, Michael Betenbaugh, Till Wenger, Friedrich Leisch, Martina Baumann, Nicole Borth
Genomic rearrangements are a common phenomenon in rapidly growing cell lines such as Chinese hamster ovary (CHO) cells, a feature that in the context of production of biologics may lead to cell line and product instability. Few methods exist to assess such genome wide instability. Here we use the population distribution of chromosome numbers per cell as well as chromosome painting to quantify the karyotypic variation in several CHO host cell lines. CHO-S, CHO-K1 8mM glutamine and CHO-K1 cells adapted to grow in media containing no glutamine were analyzed over up to 6 months in culture...
September 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28921505/nfatc1-activation-by-dna-hypomethylation-in-chronic-lymphocytic-leukemia-correlates-with-clinical-staging-and-can-be-inhibited-by-ibrutinib
#19
Christine Wolf, Angela Garding, Katharina Filarsky, Jasmin Bahlo, Sandra Robrecht, Natalia Becker, Manuela Zucknick, Arefeh Rouhi, Anja Weigel, Rainer Claus, Dieter Weichenhan, Barbara Eichhorst, Kirsten Fischer, Michael Hallek, Florian Kuchenbauer, Christoph Plass, Hartmut Döhner, Stephan Stilgenbauer, Peter Lichter, Daniel Mertens
B cell receptor (BCR) signaling is key for survival of chronic lymphocytic leukemia (CLL) cells, and BCR signaling inhibitors are clinically active. However, relapse and resistance to treatment require novel treatment options. In order to detect novel candidate therapeutic targets, we performed a genome-wide DNA methylation screen with custom arrays and identified aberrant promoter DNA methylation in 2192 genes. The transcription factor NFATC1 that is a downstream effector of BCR signaling was among the top hypomethylated genes and was concomitantly transcriptionally upregulated in CLL...
September 18, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28921393/genome-wide-compound-heterozygote-analysis-highlights-alleles-associated-with-adult-height-in-europeans
#20
Kaiyin Zhong, Gu Zhu, Xiaoxi Jing, A Emile J Hendriks, Sten L S Drop, M Arfan Ikram, Scott Gordon, Changqing Zeng, Andre G Uitterlinden, Nicholas G Martin, Fan Liu, Manfred Kayser
Adult height is the most widely genetically studied common trait in humans; however, the trait variance explainable by currently known height-associated single nucleotide polymorphisms (SNPs) identified from the previous genome-wide association studies (GWAS) is yet far from complete given the high heritability of this complex trait. To exam if compound heterozygotes (CH) may explain extra height variance, we conducted a genome-wide analysis to screen for CH in association with adult height in 10,631 Dutch Europeans enriched with extremely tall people, using our recently developed method implemented in the software package CollapsABEL...
September 18, 2017: Human Genetics
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