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https://www.readbyqxmd.com/read/29773754/a-critical-neurodevelopmental-role-for-l-type-voltage-gated-calcium-channels-in-neurite-extension-and-radial-migration
#1
Satoshi Kamijo, Yuichiro Ishii, Shin-Ichiro Horigane, Kanzo Suzuki, Masamichi Ohkura, Junichi Nakai, Hajime Fujii, Sayaka Takemoto-Kimura, Haruhiko Bito
In spite of many association studies linking gene polymorphisms and mutations of L-type Voltage-Gated Ca2+ Channels (VGCC) in neurodevelopmental disorders, such as autism and schizophrenia, specific L-type VGCC roles during brain development remain unclear. Yet, calcium signaling has been shown to be essential for neurodevelopmental processes such as sculpting of neurites, functional wiring and fine tuning of growing networks. To bridge this gap, we performed submembraneous calcium imaging using a membrane-tethered genetically-encoded calcium indicator (GECI) Lck-G-CaMP7...
May 17, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29666371/integration-of-human-adipocyte-chromosomal-interactions-with-adipose-gene-expression-prioritizes-obesity-related-genes-from-gwas
#2
David Z Pan, Kristina M Garske, Marcus Alvarez, Yash V Bhagat, James Boocock, Elina Nikkola, Zong Miao, Chelsea K Raulerson, Rita M Cantor, Mete Civelek, Craig A Glastonbury, Kerrin S Small, Michael Boehnke, Aldons J Lusis, Janet S Sinsheimer, Karen L Mohlke, Markku Laakso, Päivi Pajukanta, Arthur Ko
Increased adiposity is a hallmark of obesity and overweight, which affect 2.2 billion people world-wide. Understanding the genetic and molecular mechanisms that underlie obesity-related phenotypes can help to improve treatment options and drug development. Here we perform promoter Capture Hi-C in human adipocytes to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We find that promoter-interacting elements in human adipocytes are enriched for adipose-related transcription factor motifs, such as PPARG and CEBPB, and contribute to heritability of cis-regulated gene expression...
April 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29393979/breaking-self-tolerance-during-autoimmunity-and-cancer-immunity-myeloid-cells-and-type-i-ifn-response-regulation
#3
REVIEW
Kristin V Tarbell, Jackson G Egen
The generation and regulation of innate immune signals are key determinants of autoimmune pathogenesis. Emerging evidence suggests that parallel processes operating in the setting of solid tumors can similarly determine the balance between tolerance and immunity and ultimately the effectiveness of the antitumor immune response. In both contexts, self-specific responses start with innate immune cell activation that leads to the initial break in self-tolerance, which can be followed by immune response amplification and maturation through innate-adaptive crosstalk, and finally immune-mediated tissue/tumor destruction that can further potentiate inflammation...
February 2, 2018: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29382897/integrative-genomic-analysis-of-methylphenidate-response-in-attention-deficit-hyperactivity-disorder
#4
Mireia Pagerols, Vanesa Richarte, Cristina Sánchez-Mora, Paula Rovira, María Soler Artigas, Iris Garcia-Martínez, Eva Calvo-Sánchez, Montse Corrales, Bruna Santos da Silva, Nina Roth Mota, Marcelo Moraes Victor, Luis Augusto Rohde, Eugenio Horacio Grevet, Claiton Henrique Dotto Bau, Bru Cormand, Miguel Casas, Josep Antoni Ramos-Quiroga, Marta Ribasés
Methylphenidate (MPH) is the most frequently used pharmacological treatment in children with attention-deficit/hyperactivity disorder (ADHD). However, a considerable interindividual variability exists in clinical outcome. Thus, we performed a genome-wide association study of MPH efficacy in 173 ADHD paediatric patients. Although no variant reached genome-wide significance, the set of genes containing single-nucleotide polymorphisms (SNPs) nominally associated with MPH response (P < 0.05) was significantly enriched for candidates previously studied in ADHD or treatment outcome...
January 30, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29339263/impact-of-organic-amendments-biochar-compost-and-peat-on-cd-and-zn-mobility-and-solubility-in-contaminated-soil-of-the-campine-region-after-three-years
#5
C E Egene, R Van Poucke, Y S Ok, E Meers, F M G Tack
To determine the long-term impact of organic amendments on metal (Cd and Zn) immobilization, soil from the Campine region was amended with holm oak-derived biochar, compost, and peat, and monitored over a 3-year period. Pot experiments were conducted by mixing the amendments independently at 2% and 4% (g/g) with the soil. The mobility and solubility of metals in the treatments were assessed by means of rhizon soil moisture samplers, sequential BCR extractions, and diffusive gradient in thin films (DGT). Over the three-year period, the 2% biochar addition resulted in an average decrease in pore water concentration of 40% for Cd and 48% for Zn whereas the 4% addition led to an average decrease of 66% for Cd and 77% for Zn...
June 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29275034/the-ability-to-predict-pregnancy-loss-in-cattle-with-elisas-that-detect-pregnancy-associated-glycoproteins-is-antibody-dependent
#6
Ahmed O Gatea, Michael F Smith, Ky G Pohler, Tina Egen, Marcos H C Pereira, José L M Vasconselos, John C Lawrence, Jonathan A Green
The concentration of circulating pregnancy associated glycoproteins (PAGs) early in pregnancy may serve as markers to predict late embryonic mortality or fetal mortality in cattle. In this study, pregnancies were established in dairy cows, by either fixed-time AI (FTAI) or fixed-time embryo transfer (FTET) with in vitro produced embryos. Circulating PAGs were measured with different combinations of antibodies in either a laboratory-based ELISA or a commercial ELISA. For the in-house ELISA, three monoclonal 'trapping' antibodies (A6, J2, and L4) and two polyclonal 'detection' antisera (antibodies F2 or 45) were used to quantify PAGs in serum from the same cows...
March 1, 2018: Theriogenology
https://www.readbyqxmd.com/read/29210733/in-reply-to-griffith
#7
Barry Egener
No abstract text is available yet for this article.
December 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/29127305/cis-snps-set-testing-and-predixcan-analysis-for-gene-expression-data-using-linear-mixed-models
#8
Ping Zeng, Ting Wang, Shuiping Huang
Understanding the functional mechanism of SNPs identified in GWAS on complex diseases is currently a challenging task. The studies of expression quantitative trait loci (eQTL) have shown that regulatory variants play a crucial role in the function of associated SNPs. Detecting significant genes (called eGenes) in eQTL studies and analyzing the effect sizes of cis-SNPs can offer important implications on the genetic architecture of associated SNPs and interpretations of the molecular basis of diseases. We applied linear mixed models (LMM) to the gene expression level and constructed likelihood ratio tests (LRT) to test for eGene in the Geuvadis data...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28881962/applying-meta-analysis-to-genotype-tissue-expression-data-from-multiple-tissues-to-identify-eqtls-and-increase-the-number-of-egenes
#9
Dat Duong, Lisa Gai, Sagi Snir, Eun Yong Kang, Buhm Han, Jae Hoon Sul, Eleazar Eskin
Motivation: There is recent interest in using gene expression data to contextualize findings from traditional genome-wide association studies (GWAS). Conditioned on a tissue, expression quantitative trait loci (eQTLs) are genetic variants associated with gene expression, and eGenes are genes whose expression levels are associated with genetic variants. eQTLs and eGenes provide great supporting evidence for GWAS hits and important insights into the regulatory pathways involved in many diseases...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28860778/improvements-in-motor-tasks-through-the-use-of-smartphone-technology-for-individuals-with-duchenne-muscular-dystrophy
#10
Camila Miliani Capelini, Talita Dias da Silva, James Tonks, Suzanna Watson, Mayra Priscila Boscolo Alvarez, Lilian Del Ciello de Menezes, Francis Meire Favero, Fátima Aparecida Caromano, Thais Massetti, Carlos Bandeira de Mello Monteiro
BACKGROUND: In individuals severely affected with Duchenne muscular dystrophy (DMD), virtual reality has recently been used as a tool to enhance community interaction. Smartphones offer the exciting potential to improve communication, access, and participation, and present the unique opportunity to directly deliver functionality to people with disabilities. OBJECTIVE: To verify whether individuals with DMD improve their motor performance when undertaking a visual motor task using a smartphone game...
2017: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/28609879/a-revision-of-the-new-zealand-weevil-genus-irenimus-pascoe-1876-coleoptera-curculionidae-entiminae
#11
Samuel D J Brown
The taxonomy of the New Zealand weevil genus Irenimus Pascoe, 1876 is revised, resulting in a narrower concept of the genus than has been considered in recent decades. In total, the genus now contains only seven species. In addition to the type species, I. parilis Pascoe, 1876, the genus contains I. duplex (Broun, 1904) and five newly described species: I. aniptus new species (type locality, Oamaru, DN), I. crinitus new species (type locality, Hakataramea Valley, SC), I. minimus new species (type locality, Alexandra, CO), I...
May 8, 2017: Zootaxa
https://www.readbyqxmd.com/read/28591901/-determinants-for-the-access-to-follow-up-rehabilitation-concerning-cardiological-patients-after-surgery
#12
R Lohss, M Blumenthal, A Gottschling-Lang, C Egen, C Gutenbrunner, C Sturm
Objective The aim was to analyze individual and environmental factors influencing the access to follow-up rehabilitation of cardiological patients after surgery. Methods An exploratory, cross-sectional study without intervention was conducted. A standardized questionnaire was used for data collection in two acute care clinics at cardiological and cardiosurgical wards. Multivariate logistic regression was used to measure the influence of different factors on the access to follow-up rehabilitation. In 61.0% of the patients a follow-up rehabilitation was granted...
June 7, 2017: Die Rehabilitation
https://www.readbyqxmd.com/read/28453768/%C3%AE-e%C3%AE-7-integrin-identifies-subsets-of-pro-inflammatory-colonic-cd4-t-lymphocytes-in-ulcerative-colitis
#13
Christopher A Lamb, John C Mansfield, Gaik W Tew, Deena Gibbons, Anna K Long, Peter Irving, Lauri Diehl, Jeff Eastham-Anderson, Maria B Price, Graeme O'Boyle, David E J Jones, Sharon O'Byrne, Adrian Hayday, Mary E Keir, Jackson G Egen, John A Kirby
Background and Aims: The αEβ7 integrin is crucial for retention of T lymphocytes at mucosal surfaces through its interaction with E-cadherin. Pathogenic or protective functions of these cells during human intestinal inflammation, such as ulcerative colitis [UC], have not previously been defined, with understanding largely derived from animal model data. Defining this phenotype in human samples is important for understanding UC pathogenesis and is of translational importance for therapeutic targeting of αEβ7-E-cadherin interactions...
May 1, 2017: Journal of Crohn's & Colitis
https://www.readbyqxmd.com/read/28434998/use-of-two-photon-microscopy-to-study-leishmania-major-infection-of-the-skin
#14
REVIEW
Matheus Batista Carneiro, Leah Shan Hohman, Jackson G Egen, Nathan C Peters
Intra-vital two-photon microscopy (2P-IVM) allows for in-situ investigation of tissue organization, cell behavior and the dynamic interactions between different cell types in their natural environment. This methodology has also expanded our understanding of the immune response against pathogens. Leishmania are protozoan intracellular parasites that have adapted to successfully establish infection within the context of an inflammatory response in the skin following transmission by the bite of an infected sand fly...
April 19, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28406900/gene-co-expression-network-connectivity-is-an-important-determinant-of-selective-constraint
#15
Niklas Mähler, Jing Wang, Barbara K Terebieniec, Pär K Ingvarsson, Nathaniel R Street, Torgeir R Hvidsten
While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28388432/large-diverse-population-cohorts-of-hipscs-and-derived-hepatocyte-like-cells-reveal-functional-genetic-variation-at-blood-lipid-associated-loci
#16
Evanthia E Pashos, YoSon Park, Xiao Wang, Avanthi Raghavan, Wenli Yang, Deepti Abbey, Derek T Peters, Juan Arbelaez, Mayda Hernandez, Nicolas Kuperwasser, Wenjun Li, Zhaorui Lian, Ying Liu, Wenjian Lv, Stacey L Lytle-Gabbin, Dawn H Marchadier, Peter Rogov, Jianting Shi, Katherine J Slovik, Ioannis M Stylianou, Li Wang, Ruilan Yan, Xiaolan Zhang, Sekar Kathiresan, Stephen A Duncan, Tarjei S Mikkelsen, Edward E Morrisey, Daniel J Rader, Christopher D Brown, Kiran Musunuru
Genome-wide association studies have struggled to identify functional genes and variants underlying complex phenotypes. We recruited a multi-ethnic cohort of healthy volunteers (n = 91) and used their tissue to generate induced pluripotent stem cells (iPSCs) and hepatocyte-like cells (HLCs) for genome-wide mapping of expression quantitative trait loci (eQTLs) and allele-specific expression (ASE). We identified many eQTL genes (eGenes) not observed in the comparably sized Genotype-Tissue Expression project's human liver cohort (n = 96)...
April 6, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28369161/enhanced-methods-to-detect-haplotypic-effects-on-gene-expression
#17
Robert Brown, Gleb Kichaev, Nicholas Mancuso, James Boocock, Bogdan Pasaniuc
Motivation: Expression quantitative trait loci (eQTLs), genetic variants associated with gene expression levels, are identified in eQTL mapping studies. Such studies typically test for an association between single nucleotide polymorphisms (SNPs) and expression under an additive model, which ignores interaction and haplotypic effects. Mismatches between the model tested and the underlying genetic architecture can lead to a loss of association power. Here we introduce a new haplotype-based test for eQTL studies that looks for haplotypic effects on expression levels...
August 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28285768/dynamic-role-of-trans-regulation-of-gene-expression-in-relation-to-complex-traits
#18
Chen Yao, Roby Joehanes, Andrew D Johnson, Tianxiao Huan, Chunyu Liu, Jane E Freedman, Peter J Munson, David E Hill, Marc Vidal, Daniel Levy
Identifying causal genetic variants and understanding their mechanisms of effect on traits remains a challenge in genome-wide association studies (GWASs). In particular, how genetic variants (i.e., trans-eQTLs) affect expression of remote genes (i.e., trans-eGenes) remains unknown. We hypothesized that some trans-eQTLs regulate expression of distant genes by altering the expression of nearby genes (cis-eGenes). Using published GWAS datasets with 39,165 single-nucleotide polymorphisms (SNPs) associated with 1,960 traits, we explored whole blood gene expression associations of trait-associated SNPs in 5,257 individuals from the Framingham Heart Study...
April 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28250200/cxcl14-is-a-candidate-biomarker-for-hedgehog-signalling-in-idiopathic-pulmonary-fibrosis
#19
MULTICENTER STUDY
Guiquan Jia, Sanjay Chandriani, Alexander R Abbas, Daryle J DePianto, Elsa N N'Diaye, Murat B Yaylaoglu, Heather M Moore, Ivan Peng, Jason DeVoss, Harold R Collard, Paul J Wolters, Jackson G Egen, Joseph R Arron
BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is associated with aberrant expression of developmental pathways, including Hedgehog (Hh). As Hh signalling contributes to multiple pro-fibrotic processes, Hh inhibition may represent a therapeutic option for IPF. However, no non-invasive biomarkers are available to monitor lung Hh activity. METHODS: We assessed gene and protein expression in IPF and control lung biopsies, mouse lung, fibroblasts stimulated in vitro with sonic hedgehog (SHh), and plasma in IPF patients versus controls, and cancer patients before and after treatment with vismodegib, a Hh inhibitor...
September 2017: Thorax
https://www.readbyqxmd.com/read/28122634/integrated-genome-wide-analysis-of-expression-quantitative-trait-loci-aids-interpretation-of-genomic-association-studies
#20
Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Sai-Xia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael L Feolo, Nataliya R Sharopova, Anne Sturcke, Alejandro A Schäffer, Nancy Heard-Costa, Han Chen, Po-Ching Liu, Richard Wang, Kimberly A Woodhouse, Kahraman Tanriverdi, Jane E Freedman, Nalini Raghavachari, Josée Dupuis, Andrew D Johnson, Christopher J O'Donnell, Daniel Levy, Peter J Munson
BACKGROUND: Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenotype-associated SNPs in genome-wide association studies (GWAS). The small sample sizes of some previous eQTL studies have limited their statistical power. We conducted an eQTL investigation of microarray-based gene and exon expression levels in whole blood in a cohort of 5257 individuals, exceeding the single cohort size of previous studies by more than a factor of 2...
January 25, 2017: Genome Biology
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