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https://read.qxmd.com/read/30771789/integration-of-gwas-and-brain-eqtl-identifies-flot1-as-a-risk-gene-for-major-depressive-disorder
#1
Jingmei Zhong, Shiwu Li, Wanli Zeng, Xiaoyan Li, Chunjie Gu, Jiewei Liu, Xiong-Jian Luo
Major depressive disorder (MDD) is the most prevalent mental disorder that affects more than 200 million people worldwide. Recent large-scale genome-wide association studies (GWAS) have identified multiple risk variants that show robust association with MDD. Nevertheless, how the identified risk variants confer risk of MDD remains largely unknown. To identify risk variants that are associated with gene expression in human brain and to identify genes whose expression change may contribute to the susceptibility of MDD, we systematically integrated the genetic associations from a large-scale MDD GWAS (N = 480,359) and brain expression quantitative trait loci (eQTL) data (N = 494) using a Bayesian statistical framework (Sherlock)...
February 16, 2019: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://read.qxmd.com/read/30771788/integrative-analyses-of-major-histocompatibility-complex-loci-in-the-genome-wide-association-studies-of-major-depressive-disorder
#2
Huijuan Li, Hong Chang, Xueqin Song, Weipeng Liu, Lingyi Li, Lu Wang, Yongfeng Yang, Luwen Zhang, Wenqiang Li, Yan Zhang, Dong-Sheng Zhou, Xingxing Li, Chen Zhang, Yiru Fang, Yan Sun, Jia-Pei Dai, Xiong-Jian Luo, Yong-Gang Yao, Xiao Xiao, Luxian Lv, Ming Li
Recent European genome-wide association studies (GWAS) have revealed strong statistical correlations between MDD and numerous zero-to-high linked variants in the genomic region containing major histocompatibility complex (MHC) genes (MHC region), but the underlying molecular mechanisms are still unclear. To better understand the roles of this genomic region in the neurobiology of MDD, we applied a convergent functional genomics approach to integrate GWAS data of MDD relevant biological phenotypes, gene-expression analyses results obtained from brain samples, and genetic analyses of independent Chinese MDD samples...
February 16, 2019: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://read.qxmd.com/read/30771750/vascular-smooth-muscle-mapk14-is-required-for-neointimal-hyperplasia-by-suppressing-vsmc-differentiation-and-inducing-proliferation-and-inflammation
#3
Wen Wu, Wei Zhang, Mihyun Choi, Jinjing Zhao, Ping Gao, Min Xue, Harold A Singer, David Jourd'heuil, Xiaochun Long
Injury-induced stenosis is a serious vascular complication. We previously reported that p38α (MAPK14), a redox-regulated p38MAPK family member was a negative regulator of the VSMC contractile phenotype in vitro. Here we evaluated the function of VSMC-MAPK14 in vivo in injury-induced neointima hyperplasia and the underlying mechanism using an inducible SMC-MAPK14 knockout mouse line (iSMC-MAPK14-/- ). We show that MAPK14 expression and activity were induced in VSMCs after carotid artery ligation injury in mice and ex vivo cultured human saphenous veins...
February 6, 2019: Redox Biology
https://read.qxmd.com/read/30771513/fin-whale-balaenoptera-physalus-mitogenomics-a-cautionary-tale-of-defining-sub-species-from-mitochondrial-sequence-monophyly
#4
Andrea A Cabrera, Jeroen P A Hoekendijk, Alex Aguilar, Susan G Barco, Simon Berrow, Dorete Bloch, Asunción Borrell, Haydée A Cunha, Luciano Dalla Rosa, Carolina P Dias, Pauline Gauffier, Wensi Hao, Scott Landry, Finn Larsen, Vidal Martín, Sally Mizroch, Tom Oosting, Nils Øien, Christophe Pampoulie, Simone Panigada, Rui Prieto, Christian Ramp, Vania E Rivera-Léon, Jooke Robbins, Conor Ryan, Elena Schall, Richard Sears, Mónica A Silva, Jorge Urbán, Frederick W Wenzel, Per J Palsbøll, Martine Bérubé
The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions...
February 13, 2019: Molecular Phylogenetics and Evolution
https://read.qxmd.com/read/30771506/rice-genomics-over-the-past-two-decades-and-into-the-future
#5
REVIEW
Shuhui Song, Dongmei Tian, Zhang Zhang, Songnian Hu, Jun Yu
Domestic rice (Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct field applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we briefly review its achievements over the past two decades and present the potential for its bright future...
February 13, 2019: Genomics, Proteomics & Bioinformatics
https://read.qxmd.com/read/30771494/dna-and-chromosomal-damage-in-senegalese-sole-solea-senegalensis-as-side-effects-of-ozone-based-water-treatment-contribution-to-optimization-of-fish-farming-practices
#6
S Guilherme, R Crespo, D Azevedo, A Marques, M A Santos, R Serradeiro, M Pacheco
The progressive growth of aquaculture implicates a dependence on large water amounts, which are submitted to disinfection processes, namely ozonation. Considering the importance of genomic integrity, it is critical to improve the knowledge on ozone-related genotoxic hazard to organisms reared in recirculating aquaculture systems (RAS) applying ozonation. Therefore, genetic damage induced by ozone exposure in the Senegalese sole (Solea senegalensis) was assessed, combining the comet and the erythrocytic nuclear abnormalities (ENA) assays, reflecting different damage levels, i...
February 13, 2019: Comparative Biochemistry and Physiology. Toxicology & Pharmacology: CBP
https://read.qxmd.com/read/30771493/viral-genome-integration-of-canine-papillomavirus-16
#7
Jennifer Luff, Michelle Mader, Peter Rowland, Monica Britton, Joseph Fass, Hang Yuan
Papillomaviruses infect humans and animals, most often causing benign proliferations on skin or mucosal surfaces. Rarely, these infections persist and progress to cancer. In humans, this transformation most often occurs with high-risk papillomaviruses, where viral integration is a critical event in carcinogenesis. The first aim of this study was to sequence the viral genome of canine papillomavirus (CPV) 16 from a pigmented viral plaque that progressed to metastatic squamous cell carcinoma in a dog. The second aim was to characterize multiple viral genomic deletions and translocations as well as host integration sites...
February 13, 2019: Papillomavirus Research
https://read.qxmd.com/read/30771488/zscan10-suppresses-osteoclast-differentiation-by-regulating-expression-of-haptoglobin
#8
Yuta Yanagihara, Kazuki Inoue, Noritaka Saeki, Yuichiro Sawada, Shuhei Yoshida, Jiwon Lee, Tadahiro Iimura, Yuuki Imai
Zinc finger and SCAN domain containing 10 (Zscan10) was identified as a novel transcription factor that is involved in osteoclast differentiation in our previous report. However, the biological functions of Zscan10 are not fully understood except its roles in the maintenance of genome stability and pluripotency of embryonic stem cells. Therefore, the purpose of this study was to clarify the function of Zscan10 in somatic cells, especially during osteoclast differentiation. First, Zscan10 KO RAW264 (KO) cells were established by genome editing using CRISPR/Cas9 and single cell sorting...
February 13, 2019: Bone
https://read.qxmd.com/read/30771483/statistical-outbreak-detection-by-joining-medical-records-and-pathogen-similarity
#9
James K Miller, Jieshi Chen, Alexander Sundermann, Jane W Marsh, Melissa I Saul, Kathleen A Shutt, Marissa Pacey, Mustapha M Mustapha, Lee H Harrison, Artur Dubrawski
We present a statistical inference model for the detection and characterization of outbreaks of hospital associated infection. The approach combines patient exposures, determined from electronic medical records, and pathogen similarity, determined by whole-genome sequencing, to simultaneously identify probable outbreaks and their root-causes. We show how our model can be used to target isolates for whole-genome sequencing, improving outbreak detection and characterization even without comprehensive sequencing...
February 13, 2019: Journal of Biomedical Informatics
https://read.qxmd.com/read/30771444/expanding-the-promoter-toolbox-of-bacillus-megaterium
#10
Philip Hartz, Carsten Mattes, Martina Schad, Rita Bernhardt, Frank Hannemann
Over the past decades, Bacillus megaterium has gained significant interest in the biotechnological industry due to its high capacity for protein production. Although many proteins have been expressed efficiently using the optimized xylose inducible system so far, there is a considerable demand for novel promoters with varying activities, particularly for the adjustment of protein levels in multi-enzyme cascades. Genome-wide microarray analyses of the industrially important B. megaterium strain MS941 were applied to identify constitutive and growth phase dependent promoters for the expression of heterologous proteins from the early exponential to the early stationary phase of bacterial growth...
February 13, 2019: Journal of Biotechnology
https://read.qxmd.com/read/30771437/uvb-drives-different-stages-of-epigenome-alterations-during-progression-of-skin-cancer
#11
Yuqing Yang, Renyi Wu, Davit Sargsyan, Ran Yin, Hsiao-Chen Kuo, Irene Yang, Lujing Wang, David Cheng, Chao Wang, Shanyi Li, Rasika Hudlikar, Yaoping Lu, Ah-Ng Kong
Exposure to ultraviolet B (UVB) irradiation results in multitude of cellular responses including generation of reactive oxygen species and DNA damage and is responsible for non-melanoma skin cancers (NMSCs). Although genetic mutation is well documented, the epi-mutation, the alteration in epigenetics, remains elusive. In this study, we utilized CpG Methyl-seq to identify a genome-wide DNA CpG methylation, to profile the DNA methylation in UVB-irradiated SKH-1 mouse skin epidermis and non-melanoma skin papillomas at various stages...
February 13, 2019: Cancer Letters
https://read.qxmd.com/read/30771401/interactions-between-plasmids-and-other-mobile-genetic-elements-affect-their-transmission-and-persistence
#12
REVIEW
Francisco Dionisio, Rita Zilhão, João Alves Gama
Plasmids are genetic elements that play a role in bacterial evolution by providing new genes that promote adaptation to diverse conditions. Plasmids are also known to reduce bacterial competitiveness in the absence of selection for plasmid-encoded traits. It is easier to understand plasmid persistence when considering the evidence that plasmid maintenance can improve during co-evolution with the bacterial host, i.e. the chromosome. However, bacteria isolated from nature often harbor diverse mobile elements: phages, transposons, genomic islands and even other plasmids...
February 13, 2019: Plasmid
https://read.qxmd.com/read/30771385/in-situ-hybridization-for-the-localization-of-two-pepino-mosaic-virus-isolates-in-mixed-infections
#13
C Gómez-Aix, C Alcaide, P Gómez, M A Aranda, M A Sánchez-Pina
In situ hybridization (ISH) is an informative and relatively accessible technique for the localization of viral genomes in plant tissue and cells. However, simultaneous visualization of related plant viruses in mixed infections may be limited by the nucleotide similarity in the genomes and the single chromogenic detection over the same sample preparation. To address this issue, we used two Pepino mosaic virus isolates and performed ISH over consecutive serial cross-sections of paraffin-embedded leaf samples of single and mixed infected Nicotiana benthamiana plants...
February 13, 2019: Journal of Virological Methods
https://read.qxmd.com/read/30771384/localized-surface-plasmon-resonance-biosensing-of-tomato-yellow-leaf-curl-virus
#14
Arash Razmi, Arezoo Golestanipour, Maryam Nikkhah, Abdolreza Bagheri, Masoud Shamsbakhsh, Saeed Malekzadeh-Shafaroudi
Current techniques for plant virus detection, such as RT- PCR and ELISA, require multistep procedures and rely on sophisticated equipment. Due to the global spread of plant viruses, the development of simpler, faster and cheaper assay methods is inevitable. Gold nanoparticles (AuNPs) had raised much interest during recent years due to their novel optical properties or diagnostic purposes. The localized surface plasmon resonance (LSPR1 ) of AuNPs had been used in the development of novel colorimetric nano-biosensing systems...
February 13, 2019: Journal of Virological Methods
https://read.qxmd.com/read/30771369/evaluation-of-an-all-in-one-seven-day-wgs-solution-in-the-investigation-of-a-staphylococcus-aureus-outbreak-in-a-neonatal-intensive-care-unit
#15
Caroline Rouard, Nadège Bourgeois-Nicolaos, Lalaina Rahajamanana, Olivier Romain, Lydia Pouga, Véronique Derouin, Daniele De Luca, Florence Doucet-Populaire
BACKGROUND: Meticillin-susceptible and resistant Staphylococcus aureus (MSSA and MRSA) are responsible for outbreaks in intensive care units. MSSA infections have the same morbidity and mortality rate as MRSA infections but are less often studied. Whole genome sequencing (WGS) is increasingly used for outbreak monitoring but still requires specific installation and trained personnel to obtain and analyse the data. AIM: To evaluate the workflow and the benefits of the bioMerieux Episeq® (bioMerieux, France) solution in exploring an increased incidence of S...
February 13, 2019: Journal of Hospital Infection
https://read.qxmd.com/read/30771258/genome-wide-analysis-of-dna-methylation-in-relation-to-socioeconomic-status-during-development-and-early-adulthood
#16
Thomas W McDade, Calen P Ryan, Meaghan J Jones, Morgan K Hoke, Judith Borja, Gregory E Miller, Christopher W Kuzawa, Michael S Kobor
OBJECTIVES: Socioeconomic status (SES) is a powerful determinant of health, but the underlying biological mechanisms are poorly understood. This study investigates whether levels of DNA methylation at CpG sites across the genome are associated with SES in a cohort of young adults in the Philippines. METHODS: DNA methylation was assayed with the Illumina HumanMethylation450 Bead Chip, in leukocytes from 489 participants in the Cebu Longitudinal Health and Nutrition Survey (mean age = 20...
February 16, 2019: American Journal of Physical Anthropology
https://read.qxmd.com/read/30771224/subtraction-of-epstein-barr-virus-and-microsatellite-instability-genotypes-from-the-lauren-histotypes-combined-molecular-and-histologic-subtyping-with-clinicopathological-and-prognostic-significance-validated-in-a-cohort-of-1-248-cases
#17
Shih-Chiang Huang, Kwai-Fong Ng, Ta-Sen Yeh, Chi-Tung Cheng, Jie-Sian Lin, Yu-Jen Liu, Huei-Chieh Chuang, Tse-Ching Chen
Limited studies investigated clinicopathological and prognostic significance of histologic and molecular subgroups of gastric cancer concurrently. We retrospectively enrolled 1,248 patients with gastric cancer who received radical gastrectomy with lymphadenectomy and classified these cases into the Epstein-Barr virus (EBV)-associated and microsatellite instability (MSI)-associated subtypes by EBV-encoded small RNA in situ hybridization and immunohistochemical stains for DNA mismatch repair proteins, respectively...
February 16, 2019: International Journal of Cancer. Journal International du Cancer
https://read.qxmd.com/read/30771135/proteomic-and-genomic-profiling-of-pancreatic-cancer
#18
REVIEW
Daniel Ansari, William Torén, Qimin Zhou, Dingyuan Hu, Roland Andersson
Pancreatic cancer remains the most fatal human tumor type. The aggressive tumor biology coupled with the lack of early detection strategies and effective treatment are major reasons for the poor survival rate. Collaborative research efforts have been devoted to understand pancreatic cancer at the molecular level. Large-scale genomic studies have generated important insights into the genetic drivers of pancreatic cancer. In the post-genomic era, protein sequencing of tumor tissue, cell lines, pancreatic juice, and blood from patients with pancreatic cancer has provided a fundament for the development of new diagnostic and prognostic biomarkers...
February 15, 2019: Cell Biology and Toxicology
https://read.qxmd.com/read/30771074/just-choice-a-danielsian-analysis-of-the-aims-and-scope-of-prenatal-screening-for-fetal-abnormalities
#19
Greg Stapleton, Wybo Dondorp, Peter Schröder-Bäck, Guido de Wert
Developments in Non-Invasive Prenatal Testing (NIPT) and cell-free fetal DNA analysis raise the possibility that antenatal services may soon be able to support couples in non-invasively testing for, and diagnosing, an unprecedented range of genetic disorders and traits coded within their unborn child's genome. Inevitably, this has prompted debate within the bioethics literature about what screening options should be offered to couples for the purpose of reproductive choice. In relation to this problem, the European Society of Human Genetics (ESHG) and American Society of Human Genetics (ASHG) tentatively recommend that any expansion of this type of screening, as facilitated by NIPT, should be limited to serious congenital and childhood disorders...
February 15, 2019: Medicine, Health Care, and Philosophy
https://read.qxmd.com/read/30771045/comparative-transcriptomics-analysis-uncovers-alternative-splicing-events-and-molecular-markers-in-cabbage-brassica-oleracea-l
#20
Yuanyuan Xu, Aisong Zeng, Lixiao Song, Jiaqing Li, Jiyong Yan
Alternative splicing (AS) events were identified and verified in cabbage by comparative transcriptome analysis. The corresponding markers were developed and the germplasm resources were identified. Alternative splicing (AS) is a central regulatory mechanism that greatly contributes to plant gene expression and transcriptome diversity. A large body of evidence has shown that AS complexity is relevant for plant development, evolution, complexity, and adaptation. Both insertion/deletion (InDel) and single nucleotide polymorphism (SNP) are typically co-dominant inheritance markers and have abundant polymorphisms...
February 15, 2019: Planta
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