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https://www.readbyqxmd.com/read/27928823/identification-of-differentially-expressed-genes-in-longissimus-muscle-of-pigs-with-high-and-low-intramuscular-fat-content-using-rna-sequencing
#1
K S Lim, K T Lee, J E Park, W H Chung, G W Jang, B H Choi, K C Hong, T H Kim
Intramuscular fat (IMF) content in pork is an important element of consumer preference and is positively correlated with meat quality, including tenderness and juiciness. With advances in RNA sequencing technologies, transcriptome-related differences can be associated with specific traits in animals. The objective of this study was to investigate differentially expressed genes (DEGs) closely related to IMF content in porcine longissimus muscle using RNA sequencing. A total of 107 Berkshire pigs were used for IMF content measurements, and significant differences between extremely high (H, n = 3) and low (L, n = 3) IMF content groups were found (P < 0...
December 7, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27923447/amelioration-of-non-alcoholic-fatty-liver-disease-with-npc1l1-targeted-igy-or-n-3-polyunsaturated-fatty-acids-in-mice
#2
Jin-Sik Bae, Jong-Min Park, Junghoon Lee, Byung-Chul Oh, Sang-Ho Jang, Yun Bin Lee, Young-Min Han, Chan-Young Ock, Ji-Young Cha, Ki-Baik Hahm
Patients with non-alcoholic fatty liver disease (NAFLD) have an increased risk for progression to hepatocellular carcinoma in addition to comorbidities such as cardiovascular and serious metabolic diseases; however, the current therapeutic options are limited. Based on our previous report that omega-3 polyunsaturated fatty acids (n-3 PUFAs) can significantly ameliorate high fat diet (HFD)-induced NAFLD, we explored the therapeutic efficacy of n-3 PUFAs and N-IgY, which is a chicken egg yolk-derived IgY specific for the Niemann-Pick C1-Like 1 (NPC1L1) cholesterol transporter, on NAFLD in mice...
January 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/27899990/microarray-analysis-of-differentially-expressed-genes-and-linker-genes-associated-with-the-molecular-mechanism-of-colorectal-cancer
#3
Xingjie Shen, Meng Yue, Fansheng Meng, Jingyu Zhu, Xiaoyan Zhu, Yakun Jiang
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide and remains the third leading cause of cancer-associated mortality. The present study aimed to fully elucidate the pathogenesis of CRC and identify associated genes in tumor development. Microarray GSE44076, GSE41328 and GSE44861 datasets were downloaded from the Gene Expression Omnibus database and integrated with meta-analysis. Differentially-expressed genes (DEGs) were identified from CRC samples compared with adjacent non-cancerous controls using the Limma package in R, followed by functional analysis using the Database for Annotation, Visualization, and Integrated Discovery online tool...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27895742/comparative-analysis-of-gene-expression-profiles-of-gastric-cardia-adenocarcinoma-and-gastric-non-cardia-adenocarcinoma
#4
Bin Song, Juan Du, Neng Deng, Ji-Chen Ren, Zhen-Bo Shu
In the present study, gene expression profiles were analyzed to identify the molecular mechanisms underlying gastric cardia adenocarcinoma (GCA) and gastric non-cardia adenocarcinoma (GNCA). A gene expression dataset (accession number GSE29272) was downloaded from Gene Expression Omnibus, and consisted of 62 GCA samples and 62 normal controls, as well as 72 GNCA samples and 72 normal controls. The two groups of differentially-expressed genes (DEGs) were compared to obtain common and unique DEGs. A differential analysis was performed using the Linear Models for Microarray Data package in R...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27894325/identification-of-col1a1-and-col1a2-as-candidate-prognostic-factors-in-gastric-cancer
#5
Jun Li, Yuemin Ding, Aiqing Li
BACKGROUND: The role of type I collagen, composed of collagen type I alpha 1 (COL1A1) and collagen type I alpha 2 (COL1A2), has been studied in several cancers. However, the expression of COL1A1 and COL1A2 in malignant, premalignant, and normal gastric tissues and their clinical significances in gastric cancer have not been elucidated. METHODS: Real-time quantitative PCR was performed in 55 malignant, 27 premalignant, and 19 normal tissues to measure COL1A1 and COL1A2 messenger RNA (mRNA) expression, and the correlations between COL1A1 and COL1A2 expression and clinicopathological parameters and patients' survival rate were analyzed...
November 29, 2016: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/27881410/taz-activation-drives-fibroblast-spheroid-growth-expression-of-pro-fibrotic-paracrine-signals-and-context-dependent-ecm-gene-expression
#6
Amy J Jorgenson, Kyoung Moo Choi, Delphine Sicard, Karry M J Smith, Samantha E Hiemer, Xaralabos Varelas, Daniel J Tschumperlin
Recent studies have implicated the Hippo pathway and its transcriptional effectors YAP and TAZ as necessary for fibroblast activation and tissue fibrosis. To test the specific and sufficient roles for TAZ in driving autonomous fibroblast activation, we cultured NIH3T3 fibroblasts expressing a doxycycline-inducible nuclear-localized mutant of TAZ (TAZ4SA) in scaffold-free 3D hanging drop spheroids, or on matrices of specified mechanical rigidity. Control NIH3T3 fibroblasts formed spheroids in hanging drop culture that remained stable and neither increased nor decreased in size significantly over 15 days...
November 23, 2016: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/27881195/the-involvement-of-runx2-and-sparc-genes-in-the-bacterial-chondronecrosis-with-osteomyelitis-in-broilers
#7
E Paludo, A M G Ibelli, J O Peixoto, F C Tavernari, C A V Lima-Rosa, J R C Pandolfi, M C Ledur
Economic losses due to an increase of leg disorders in broilers have become a major concern of the poultry industry. Despite the efforts to reduce skeletal abnormalities in chickens, insufficient progress has been made. Bacterial chondronecrosis with osteomyelitis (BCO) is one of the main disorders that affect bone integrity in broilers. However, the genetic pathways and genes involved in most bone problems, including BCO, remains unclear. In this study, femoral samples from male broilers with 45 days of age affected or not with BCO were used to compare the relative expression with a reverse transcription real time PCR approach of 13 candidate genes: SPP1 (osteopontin), TNFRSF11B (osteoprotegerin), SPARC (osteonectin), CALB1 (calbidin 1), CALM (Calmodulin 2), IBSP (sialoprotein), COL1A2 (collagen, type I, α 2), BMP2 (bone morphogenetic protein 2), BMP3 (bone morphogenetic protein 3), RANKL (κ-B nuclear factor ligand), SMAD1 (SMAD family member 1), LEPR (leptin receptor) and RUNX2 (related transcription factor Runt 2)...
November 24, 2016: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/27866191/the-long-non-coding-rna-lncrna8975-1-is-upregulated-in-hypertrophic-scar-fibroblasts-and-controls-collagen-expression
#8
Jun Li, Ling Chen, Chunyu Cao, Hui Yan, Bei Zhou, Yanli Gao, Qian Li, Jingyun Li
BACKGROUND/AIMS: Long non-coding RNAs (lncRNAs) are thought to play crucial roles in human diseases. However, the function of lncRNAs in hypertrophic scar formation remains poorly understood. METHODS: In this study, we investigated the expression of lncRNA8975-1 in hypertrophic scar tissues and fibroblasts by quantitative reverse transcription PCR (qRT-PCR). To investigate its function, overexpression and knockdown of lncRNA8975-1 were performed using lentivirus infection and Stealth RNAi transfection, respectively...
2016: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/27832094/are-epigenetic-factors-implicated-in-chronic-widespread-pain
#9
Andrea Burri, Zoya Marinova, Mark D Robinson, Brigitte Kühnel, Melanie Waldenberger, Simone Wahl, Sonja Kunze, Christian Gieger, Gregory Livshits, Frances Williams
BACKGROUND: Chronic widespread musculoskeletal pain (CWP) is the cardinal symptom of fibromyalgia and affects about 12% of the general population. Familial aggregation of CWP has been repeatedly demonstrated with estimated heritabilities of around 50%, indicating a genetic susceptibility. The objective of the study was to explore genome-wide disease-differentially methylated positions (DMPs) for chronic widespread pain (CWP) in a sample of unrelated individuals and a subsample of discordant monozygotic (MZ) twins...
2016: PloS One
https://www.readbyqxmd.com/read/27831650/critical-genes-of-hepatocellular-carcinoma-revealed-by-network-and-module-analysis-of-rna-seq-data
#10
M-R Yang, Y Zhang, X-X Wu, W Chen
OBJECTIVE: RNA-seq data of hepatocellular carcinoma (HCC) was analyzed to identify critical genes related to the pathogenesis and prognosis. MATERIALS AND METHODS: Three RNA-seq datasets of HCC (GSE69164, GSE63863 and GSE55758) were downloaded from Gene Expression Omnibus (GEO), while another dataset including 54 HCC cases with survival time was obtained from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) were identified by significant analysis of microarrays (SAM) method using package samr of R...
October 2016: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/27821779/decreasing-maternal-myostatin-programs-adult-offspring-bone-strength-in-a-mouse-model-of-osteogenesis-imperfecta
#11
Arin K Oestreich, William M Kamp, Marcus G McCray, Stephanie M Carleton, Natalia Karasseva, Kristin L Lenz, Youngjae Jeong, Salah A Daghlas, Xiaomei Yao, Yong Wang, Ferris M Pfeiffer, Mark R Ellersieck, Laura C Schulz, Charlotte L Phillips
During fetal development, the uterine environment can have effects on offspring bone architecture and integrity that persist into adulthood; however, the biochemical and molecular mechanisms remain unknown. Myostatin is a negative regulator of muscle mass. Parental myostatin deficiency (Mstn(tm1Sjl/+)) increases muscle mass in wild-type offspring, suggesting an intrauterine programming effect. Here, we hypothesized that Mstn(tm1Sjl/+) dams would also confer increased bone strength. In wild-type offspring, maternal myostatin deficiency altered fetal growth and calvarial collagen content of newborn mice and conferred a lasting impact on bone geometry and biomechanical integrity of offspring at 4 mo of age, the age of peak bone mass...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27813341/pharmacological-and-biological-therapeutic-strategies-for-osteogenesis-imperfecta
#12
Ronit Marom, Yi-Chien Lee, Ingo Grafe, Brendan Lee
Osteogenesis imperfecta (OI) is a connective tissue disorder characterized by bone fragility, low bone mass, and bone deformities. The majority of cases are caused by autosomal dominant pathogenic variants in the COL1A1 and COL1A2 genes that encode type I collagen, the major component of the bone matrix. The remaining cases are caused by autosomal recessively or dominantly inherited mutations in genes that are involved in the post-translational modification of type I collagen, act as type I collagen chaperones, or are members of the signaling pathways that regulate bone homeostasis...
November 3, 2016: American Journal of Medical Genetics. Part C, Seminars in Medical Genetics
https://www.readbyqxmd.com/read/27805295/juxtaposed-genes-in-7q21-22-amplicon-contribute-for-two-major-gastric-cancer-sub-types-by-mutual-exclusive-expression
#13
Sembulingam Tamilzhalagan, Muthulakshmi Muthuswami, Kumaresan Ganesan
Genomic Copy Number Variations (CNV) and the associated gene signatures are useful for cancer prognosis, diagnosis, and targeted therapeutics. Earlier, 7q21-22 region was reported for frequent amplification in gastric cancer and potential candidate genes were identified. An analysis of the expression pattern of the 159 genes located in this amplicon revealed the consistent elevated expression of 21 genes in gastric tumors. These genes are closely arranged within the 20 Mb region, and they showed a bimodal expression pattern...
November 2, 2016: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/27798868/gene-expression-analysis-identifies-specific-patterns-of-dysregulated-molecular-pathways-and-genetic-subgroups-of-human-hepatocellular-carcinoma
#14
Holger G Hass, Ulrich Vogel, Michael Scheurlen, Jürgen Jobst
BACKGROUND: Hepatocellular carcinoma comprises of a group of heterogeneous tumors of different etiologies. The multistep process of liver carcinogenesis involves various genetic and phenotypic alterations. The molecular pathways and driver mutations involved are still under investigation. MATERIALS AND METHODS: DNA micorarray technology was used to identify differentially expressed genes between human hepatocarcinoma and non-tumorous liver tissues to establish a unique specific gene-expression profile independent of the underlying liver disease...
October 2016: Anticancer Research
https://www.readbyqxmd.com/read/27761249/asymptomatic-parental-mosaicism-for-osteogenesis-imperfecta-associated-with-a-new-splice-site-mutation-in-col1a2
#15
Anja Lisbeth Frederiksen, Morten Duno, Iben B G Johnsen, Morten Frost Nielsen, Anne Bruun Krøigård
Recurrent lethal perinatal osteogenesis imperfecta may result from asymptomatic parental mosaicism. A previously unreported mutation in COL1A2 leads to recurrent cases of fetal osteogenesis imperfecta Sillence type IIA, which emphasizes the importance of clinical and genetic evaluation of mosaicism in asymptomatic parents as verified mosaicism highly increases recurrence risk.
October 2016: Clinical Case Reports
https://www.readbyqxmd.com/read/27754873/dynamic-remodeling-of-endometrial-extracellular-matrix-regulates-embryo-receptivity-in-cattle
#16
Saara Carollina Scolari, Guilherme Pugliesi, Ricardo de Francisco Strefezzi, Sónia Cristina Andrade, Luiz Lehmann Coutinho, Mario Binelli
We aimed to evaluate in the bovine endometrium whether (1) key genes involved in endometrial extracellular matrix (ECM) remodeling are regulated by the endocrine peri-ovulatory milieu; and (2) specific endometrial ECM-related transcriptome can be linked to pregnancy outcome. In Experiment 1, pre-ovulatory follicle growth of cows was manipulated to obtain two groups with specific endocrine peri-ovulatory profiles: the Large Follicle-Large CL group (LF-LCL) served as a paradigm for greater receptivity and fertility and showed greater plasma pre-ovulatory estradiol and post-ovulatory progesterone concentrations when compared to the Small Follicle-Small CL group (SF-SCL)...
October 17, 2016: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/27748872/clinical-characteristics-and-the-identification-of-novel-mutations-of-col1a1-and-col1a2-in-61%C3%A2-chinese-patients-with-osteogenesis-imperfecta
#17
Hao Zhang, Hua Yue, Chun Wang, Weiwei Hu, Jiemei Gu, Jinwei He, Wenzhen Fu, Yunqiu Hu, Miao Li, Zhenlin Zhang
Osteogenesis imperfecta (OI) is an inherited connective tissue disorder characterized by brittle bone fractures. The aim of the present study was to investigate the pathogenic gene mutation spectrum and clinical manifestations of mutations in collagen type I, alpha 1 (COL1A1) and collagen type I, alpha 2 (COL1A2) genes in Chinese patients with OI. A total of 61 unrelated Chinese OI patients with COL1A1 and COL1A2 mutations were recruited. All the exons and the exon-intron boundaries of the COL1A1 and COL1A2 genes were amplified and directly sequenced and lumbar spine bone mineral density was measured by dual‑energy X‑ray absorptiometry...
October 12, 2016: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27711115/potency-biomarker-signature-genes-from-multiparametric-osteogenesis-assays-will-cgmp-human-bone-marrow-mesenchymal-stromal-cells-make-bone
#18
Alba Murgia, Elena Veronesi, Olivia Candini, Anna Caselli, Naomi D'souza, Valeria Rasini, Andrea Giorgini, Fabio Catani, Lorenzo Iughetti, Massimo Dominici, Jorge S Burns
In skeletal regeneration approaches using human bone marrow derived mesenchymal stromal cells (hBM-MSC), functional evaluation before implantation has traditionally used biomarkers identified using fetal bovine serum-based osteogenic induction media and time courses of at least two weeks. However, emerging pre-clinical evidence indicates donor-dependent discrepancies between these ex vivo measurements and the ability to form bone, calling for improved tests. Therefore, we adopted a multiparametric approach aiming to generate an osteogenic potency assay with improved correlation...
2016: PloS One
https://www.readbyqxmd.com/read/27681326/genetic-and-biochemical-biomarkers-in-canine-glaucoma
#19
K L Graham, C McCowan, A White
In many health-related fields, there is great interest in the identification of biomarkers that distinguish diseased from healthy individuals. In addition to identifying the diseased state, biomarkers have potential use in predicting disease risk, monitoring disease progression, evaluating treatment efficacy, and informing pathogenesis. This review details the genetic and biochemical markers associated with canine primary glaucoma. While there are numerous molecular markers (biochemical and genetic) associated with glaucoma in dogs, there is no ideal biomarker that allows early diagnosis and/or identification of disease progression...
September 28, 2016: Veterinary Pathology
https://www.readbyqxmd.com/read/27677223/a-novel-homozygous-variant-in-serpinh1-associated-with-a-severe-lethal-presentation-of-osteogenesis-imperfecta-with-hydranencephaly
#20
Charlotte Marshall, Jaime Lopez, Laura Crookes, Rebecca C Pollitt, Meena Balasubramanian
Osteogenesis imperfecta (OI) is a genetic disorder characterised by low bone mineral density resulting in fractures. 85-90% of patients with OI carry a variant in the type 1 collagen genes, COL1A1 and COL1A2, which follows an autosomal dominant pattern of inheritance. However, within the last two decades, there have been growing number of variants identified in genes that follow an autosomal recessive pattern of inheritance. Our proband is a child born in Mexico with multiple fractures of ribs, minimal calvarial mineralisation, platyspondyly, marked compression and deformed long bones...
December 20, 2016: Gene
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