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https://www.readbyqxmd.com/read/28934485/detecting-gene-subnetworks-under-selection-in-biological-pathways
#1
Alexandre Gouy, Joséphine T Daub, Laurent Excoffier
Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, detecting selection acting on multiple genes affecting the evolution of complex traits remains challenging. In this context, gene network analysis provides a powerful framework to study the evolution of adaptive traits and facilitates the interpretation of genome-wide data...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934419/characterizing-antigenic-determinants-in-helicobacter-pylori-caga-capable-of-detecting-serum-antibodies-in-children
#2
Min-Kyoung Shin, Jin-Su Jun, Soon-Wook Kwon, Dong-Hae Lee, Jong-Hun Ha, Jin-Sik Park, Hyung Lyun Kang, Seung Chul Baik, Ji Sook Park, Ji-Hyun Seo, Hee-Shang Youn, Myung Je Cho, Woo Kon Lee
Helicobacter pylori can persistently colonize the mucosa of the human stomach, resulting in gastric disorders. Endoscopic biopsy for rapid urease test and histopathologic examination are considered as the most accurate diagnostic methods for H. pylori infection. Serological methods are recommended for children because of invasiveness of the diagnosis mentioned above. Here, the cytotoxin-associated gene A protein (Cag A), as an immunodominant antigen, was subdivided to determine which regions harbor antigenicity for humans...
November 30, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28934397/a-modifier-of-huntington-s-disease-onset-at-the-mlh1-locus
#3
Jong-Min Lee, Michael J Chao, Denise Harold, Kawther Abu Elneel, Tammy Gillis, Peter Holmans, Lesley Jones, Michael Orth, Richard H Myers, Seung Kwak, Vanessa C Wheeler, Marcy E MacDonald, James F Gusella
Huntington's disease (HD) is a dominantly inherited neurodegenerative disease caused by an expanded CAG repeat in HTT. Many clinical characteristics of HD such as age at motor onset are determined largely by the size of HTT CAG repeat. However, emerging evidence strongly supports a role for other genetic factors in modifying the disease pathogenesis driven by mutant huntingtin. A recent genome-wide association analysis to discover genetic modifiers of HD onset age provided initial evidence for modifier loci on chromosomes 8 and 15 and suggestive evidence for a locus on chromosome 3...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28933726/mollugin-has-an-anti-cancer-therapeutic-effect-by-inhibiting-tnf-%C3%AE-induced-nf-%C3%AE%C2%BAb-activation
#4
Zhe Wang, Ming Yue Li, Chunliu Mi, Ke Si Wang, Juan Ma, Xuejun Jin
The NF-κB signaling pathway plays a pivotal role in regulating the immune response and inflammation. However, it has been shown that NF-κB also has a major role in oncogenesis. Therefore, NF-κB inhibitors have been considered as potential drugs against cancer. Herein, we searched for NF-κB inhibitors from natural sources and identified mollugin from the roots of Rubia cordifolia L. as an inhibitor of NF-κB activation. We found that mollugin significantly inhibited the expression of an NF-κB reporter gene induced by tumor necrosis factor (TNF)-α in a dose-dependent manner...
July 26, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28933484/long-non-coding-rna-snhg17-is-an-unfavourable-prognostic-factor-and-promotes-cell-proliferation-by-epigenetically-silencing-p57-in-colorectal-cancer
#5
Zhonghua Ma, Shengying Gu, Min Song, Changsheng Yan, Bingqing Hui, Hao Ji, Jirong Wang, Jianping Zhang, Keming Wang, Qinghong Zhao
Recently, substantial evidence has demonstrated that long non-coding RNAs (lncRNAs) play critical roles in multiple cancers including colorectal cancer (CRC). Utilizing publicly available lncRNA-expression-profiling data from the Gene Expression Omnibus (GEO) dataset GSE21510, we screened SNHG17 as a new candidate lncRNA associated with CRC development and progression. We further demonstrated that SNHG17 was upregulated in CRC tissues, and that its overexpression was significantly correlated with tumor size, TNM stage, and lymph node metastasis in CRC patients...
September 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28933076/-strategies-of-elucidation-of-biosynthetic-pathways-of-natural-products
#6
Li-Qiu Zou, Xue-Jun Kuang, Chao Sun, Shi-Lin Chen
Elucidation of the biosynthetic pathways of natural products is not only the major goal of herb genomics, but also the solid foundation of synthetic biology of natural products. Here, this paper reviewed recent advance in this field and put forward strategies to elucidate the biosynthetic pathway of natural products. Firstly, a proposed biosynthetic pathway should be set up based on well-known knowledge about chemical reactions and information on the identified compounds, as well as studies with isotope tracer...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932757/a-five-repeat-micro-dystrophin-gene-ameliorated-dystrophic-phenotype-in-the-severe-dba-2j-mdx-model-of-duchenne-muscular-dystrophy
#7
Chady H Hakim, Nalinda B Wasala, Xiufang Pan, Kasun Kodippili, Yongping Yue, Keqing Zhang, Gang Yao, Brittney Haffner, Sean X Duan, Julian Ramos, Joel S Schneider, N Nora Yang, Jeffrey S Chamberlain, Dongsheng Duan
Micro-dystrophins are highly promising candidates for treating Duchenne muscular dystrophy, a lethal muscle disease caused by dystrophin deficiency. Here, we report robust disease rescue in the severe DBA/2J-mdx model with a neuronal nitric oxide synthase (nNOS)-binding micro-dystrophin vector. 2 × 10(13) vector genome particles/mouse of the vector were delivered intravenously to 10-week-old mice and were evaluated at 6 months of age. Saturated micro-dystrophin expression was detected in all skeletal muscles and the heart and restored the dystrophin-associated glycoprotein complex and nNOS...
September 15, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28932682/stroke-associated-pattern-of-gene-expression-previously-identified-by-machine-learning-is-diagnostically-robust-in-an-independent-patient-population
#8
Grant C O'Connell, Paul D Chantler, Taura L Barr
Our group recently employed genome-wide transcriptional profiling in tandem with machine-learning based analysis to identify a ten-gene pattern of differential expression in peripheral blood which may have utility for detection of stroke. The objective of this study was to assess the diagnostic capacity and temporal stability of this stroke-associated transcriptional signature in an independent patient population. Publicly available whole blood microarray data generated from 23 ischemic stroke patients at 3, 5, and 24 h post-symptom onset, as well from 23 cardiovascular disease controls, were obtained via the National Center for Biotechnology Information Gene Expression Omnibus...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28932264/high-level-expression-and-characterization-of-a-novel-cutinase-from-malbranchea-cinnamomea-suitable-for-butyl-butyrate-production
#9
Xiaojie Duan, Yu Liu, Xin You, Zhengqiang Jiang, Shaoxiang Yang, Shaoqing Yang
BACKGROUND: Butyl butyrate has been considered as a promising fuel source because it is a kind of natural ester which can be converted from renewable and sustainable lignocellulosic biomass. Compared with the conventional chemical methods for butyl butyrate production, the enzymatic approach has been demonstrated to be more attractive, mainly owing to the mild reaction conditions, high specificity, low energy consumption, and environmental friendliness. Cutinases play an important role in the butyl butyrate production process...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28932230/high-density-linkage-map-construction-and-qtl-detection-for-three-silique-related-traits-in-orychophragmus-violaceus-derived-brassica-napus-population
#10
Yi Yang, Yusen Shen, Shunda Li, Xianhong Ge, Zaiyun Li
Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed (Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28931951/screening-of-mirna-profiles-and-construction-of-regulation-networks-in-early-and-late-lactation-of-dairy-goat-mammary-glands
#11
Zhibin Ji, Zhaohua Liu, Tianle Chao, Lei Hou, Rui Fan, Rongyan He, Guizhi Wang, Jianmin Wang
In recent years, studies related to the expression profiles of miRNAs in the dairy goat mammary gland were performed, but regulatory mechanisms in the physiological environment and the dynamic homeostasis of mammary gland development and lactation are not clear. In the present study, sequencing data analysis of early and late lactation uncovered a total of 1,487 unique miRNAs, including 45 novel miRNA candidates and 1,442 known and conserved miRNAs, of which 758 miRNAs were co-expressed and 378 differentially expressed with P < 0...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931918/association-of-hla-b-and-hla-drb1-polymorphisms-with-antithyroid-drug-induced-agranulocytosis-in-a-han-population-from-northern-china
#12
Yayi He, Jie Zheng, Qian Zhang, Peng Hou, Feng Zhu, Jian Yang, Wenhao Li, Pu Chen, Shu Liu, Bao Zhang, Bingyin Shi
Antithyroid drug (ATD)-induced agranulocytosis is associated with human leukocyte antigen (HLA) and nearby genes in Southeast Asian and European populations. The susceptibility of the Han population from northern China to ATD-induced agranulocytosis has not been reported. We evaluated the associations of genetic variants at the HLA-B and HLA-DRB1 loci and 32 candidate single nucleotide polymorphisms (SNPs) with agranulocytosis in 29 patients with ATD-induced agranulocytosis and in 140 patients with Graves' disease (GD) as controls...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931848/integrated-analysis-of-microrna-and-mrna-expression-profiles-during-the-sex-differentiation-sensitive-period-in-oriental-river-prawn-macrobrachium-nipponense
#13
Shubo Jin, Hongtuo Fu, Shengming Sun, Sufei Jiang, Yiwei Xiong, Yongsheng Gong, Hui Qiao, Wenyi Zhang, Yan Wu
Male oriental river prawns (Macrobrachium nipponense) grow faster than females, and therefore, reach larger sizes by harvest time. Histological observations have indicated that the sex-differentiation sensitive period (which includes the formation of the androgenic gland, the testis, and the ovary) is from post-larvae (PL) developmental stage for M. nipponense. In this study, we prepared four microRNA (miRNA) and mRNA libraries using samples collected from sex-differentiation sensitive period (PL7 to PL16) to perform RNA-sequencing for identifying sex-related candidate miRNAs, genes, and metabolic pathways...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931826/microrna-profiling-study-reveals-mir-150-in-association-with-metastasis-in-nasopharyngeal-carcinoma
#14
Patrick Ying-Kit Yue, Wai-Yan Ha, Chi-Chiu Lau, Florence Man-Fung Cheung, Anne Wing-Mui Lee, Wai-Tong Ng, Roger Kai-Cheong Ngan, Chun-Chung Yau, Dora Lai-Wan Kwong, Hong-Lok Lung, Nai-Ki Mak, Maria Li Lung, Ricky Ngok-Shun Wong
MicroRNAs (miRNAs) are small non-coding RNAs that play a crucial role in pathogenesis of human cancers. Several miRNAs have been shown to involve in nasopharyngeal carcinoma (NPC) pathogenesis through alteration of gene networks. A global view of the miRNA expression profile of clinical specimens would be the best way to screen out the possible miRNA candidates that may be involved in disease pathogenesis. In this study, we investigated the expression profiles of miRNA in formalin-fixed paraffin-embedded tissues from patients with undifferentiated NPC versus non-NPC controls using a miRNA real-time PCR platform, which covered a total of 95 cancer-related miRNAs...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931629/selinene-volatiles-are-essential-precursors-for-maize-defense-promoting-fungal-pathogen-resistance
#15
Yezhang Ding, Alisa Huffaker, Tobias G Köllner, Philipp Weckwerth, Christelle A M Robert, Joseph L Spencer, Alexander E Lipka, Eric A Schmelz
To ensure food security, maize (Zea mays) is a model crop for understanding useful traits underlying stress resistance. In contrast to foliar biochemicals, root defenses limiting the spread of disease remain poorly described. To better understand below-ground defenses in the field, we performed root metabolomic profiling and uncovered unexpectedly high levels of the sesquiterpene volatile β-selinene and the corresponding non-volatile antibiotic derivative, β-costic acid. The application of metabolite-based quantitative trait loci (mQTL) mapping using bi-parental populations, genome wide association studies, and near-isogenic lines (NILs) enabled the identification of terpene synthase 21 (ZmTps21) on chromosome 9 as a β-costic acid pathway candidate gene...
September 20, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28931241/association-of-a-novel-mutation-in-the-plasmodium-falciparum-chloroquine-resistance-transporter-with-decreased-piperaquine-sensitivity
#16
Sonia Agrawal, Kara A Moser, Lindsay Morton, Michael P Cummings, Ankita Parihar, Ankit Dwivedi, Amol C Shetty, Elliott F Drabek, Christopher G Jacob, Philipp P Henrich, Christian M Parobek, Krisada Jongsakul, Rekol Huy, Michele D Spring, Charlotte A Lanteri, Suwanna Chaorattanakawee, Chanthap Lon, Mark M Fukuda, David L Saunders, David A Fidock, Jessica T Lin, Jonathan J Juliano, Christopher V Plowe, Joana C Silva, Shannon Takala-Harrison
Background: Amplified copy number in the plasmepsin II/III genes within Plasmodium falciparum has been associated with decreased sensitivity to piperaquine. To examine this association and test whether additional loci might also contribute, we performed a genome-wide association study of ex vivo P. falciparum susceptibility to piperaquine. Methods: Plasmodium falciparum DNA from 183 samples collected primarily from Cambodia was genotyped at 33716 genome-wide single nucleotide polymorphisms (SNPs)...
August 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28931092/the-genome-wide-associated-candidate-gene-znf804a-and-psychosis-proneness-evidence-of-sex-modulated-association
#17
Marta de Castro-Catala, Aurea Mora-Solano, Thomas R Kwapil, Paula Cristóbal-Narváez, Tamara Sheinbaum, Anna Racioppi, Neus Barrantes-Vidal, Araceli Rosa
BACKGROUND: The Zinc finger protein 804A (ZNF804A) is a promising candidate gene for schizophrenia and the broader psychosis phenotype that emerged from genome-wide association studies. It is related to neurodevelopment and associated to severe symptoms of schizophrenia and alterations in brain structure, as well as positive schizotypal personality traits in non-clinical samples. Moreover, a female-specific association has been observed between ZNF804A and schizophrenia. AIM: The present study examined the association of two ZNF804A polymorphisms (rs1344706 and rs7597593) with the positive dimension of schizotypy and psychotic-like experiences in a sample of 808 non-clinical subjects...
2017: PloS One
https://www.readbyqxmd.com/read/28930984/high-fat-diet-feeding-and-high-throughput-triacylglyceride-assay-in-drosophila-melanogaster
#18
Soda Balla Diop, Ryan T Birse, Rolf Bodmer
Heart disease is the number one cause of human death worldwide. Numerous studies have shown strong connections between obesity and cardiac malfunction in humans, but more tools and research efforts are needed to better elucidate the mechanisms involved. For over a century, the genetically highly tractable model of Drosophila has been instrumental in the discovery of key genes and molecular pathways that proved to be highly conserved across species. Many biological processes and disease mechanisms are functionally conserved in the fly, such as development (e...
September 13, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930861/targeted-gene-panel-sequencing-for-early-onset-inflammatory-bowel-disease-and-chronic-diarrhea
#19
Britt-Sabina Petersen, Dietrich August, Renate Abt, Moudjahed Alddafari, Lida Atarod, Safa Baris, Hemant Bhavsar, Florian Brinkert, Mary Buchta, Alla Bulashevska, Ronnie Chee, Ana I Cordeiro, Naghi Dara, Gregor Dückers, Aisha Elmarsafy, Natalie Frede, Nermeen Galal, Patrick Gerner, Erik-Oliver Glocker, Sigune Goldacker, Jutta Hammermann, Peter Hasselblatt, Zuzana Havlicekova, Katrin Hübscher, Milos Jesenak, Neslihan E Karaca, Elif Karakoc-Aydiner, Mahboubeh M Kharaghani, Sara S Kilic, Ayca Kiykim, Christoph Klein, Christian Klemann, Robin Kobbe, Daniel Kotlarz, Martin W Laass, T Ronan Leahy, Mehrnaz Mesdaghi, Sally Mitton, João F Neves, Birol Öztürk, Luis F Pereira, Jan Rohr, Jessica L R Restrepo, Gunda Ruzaike, Nadia Saleh, Suranjith Seneviratne, Ebru Senol, Carsten Speckmann, Daniel Tegtmeyer, Paul Thankam, Jutte van der Werff Ten Bosch, Horst von Bernuth, Sebastian Zeissig, Yvonne Zeissig, Andre Franke, Bodo Grimbacher
BACKGROUND: In contrast to adult-onset inflammatory bowel disease (IBD), where many genetic loci have been shown to be involved in complex disease etiology, early-onset IBD (eoIBD) and associated syndromes can sometimes present as monogenic conditions. As a result, the clinical phenotype and ideal disease management in these patients often differ from those in adult-onset IBD. However, due to high costs and the complexity of data analysis, high-throughput screening for genetic causes has not yet become a standard part of the diagnostic work-up of eoIBD patients...
September 19, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28930843/clinical-characteristics-of-a-kif21a-mutation-in-a-chinese-family-with-congenital-fibrosis-of-the-extraocular-muscles-type-1
#20
Huiqiong Chen, Tangbing Liu, Zhenhai Zeng, Yufei Wang, Yuanyuan Lin, Lulu Cheng, Qintuo Pan, Feng Gu, Zongming Song, Zongduan Zhang
The aim of the study is to characterize the clinical ocular phenotype with congenital fibrosis of the extraocular muscles type 1 (CFEOM1) and to confirm whether the kinesin family member 21A (KIF21A) mutation was the pathogenic gene in this Chinese family.Three affected individuals and 2 asymptomatic kinsfolk from a Chinese family underwent comprehensive ophthalmic examinations, orbital computerized tomography (CT), and postoperative histological examinations were performed in the proband. All the recruited members were screened for 3 exons (8, 20, and 21) of KIF21A mutations using the polymerase chain reaction (PCR) amplification and direct sequencing of corresponding PCR products...
September 2017: Medicine (Baltimore)
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