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https://www.readbyqxmd.com/read/28340487/microrna-4739-regulates-osteogenic-and-adipocytic-differentiation-of-immortalized-human-bone-marrow-stromal-cells-via-targeting-lrp3
#1
Mona Elsafadi, Muthurangan Manikandan, Nehad M Alajez, Rimi Hamam, Raed Abu Dawud, Abdullah Aldahmash, Zafar Iqbal, Musaad Alfayez, Moustapha Kassem, Amer Mahmood
Understanding the regulatory networks underlying lineage differentiation and fate determination of human bone marrow stromal cells (hBMSC) is a prerequisite for their therapeutic use. The goal of the current study was to unravel the novel role of the low-density lipoprotein receptor-related protein 3 (LRP3) in regulating the osteogenic and adipogenic differentiation of immortalized hBMSCs. Gene expression profiling revealed significantly higher LRP3 levels in the highly osteogenic hBMSC clone imCL1 than in the less osteogenic clone imCL2, as well as a significant upregulation of LRP3 during the osteogenic induction of the imCL1 clone...
March 8, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28340459/transcriptional-profiling-of-porcine-granulosa-cells-exposed-to-2-3-7-8-tetrachlorodibenzo-p-dioxin
#2
Agnieszka Sadowska, Anna Nynca, Monika Ruszkowska, Lukasz Paukszto, Kamil Myszczynski, Karina Orlowska, Sylwia Swigonska, Tomasz Molcan, Jan P Jastrzebski, Renata E Ciereszko
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical compound contaminating the environment. An exposure of living organisms to TCDD may result in numerous disorders, including reproductive pathologies. The aim of the current study was to examine the effects of TCDD on the transcriptome of porcine granulosa cell line AVG-16. By employing next-generation sequencing (NGS) we aimed to identify genes potentially involved in the mechanism of TCDD action and toxicity in porcine granulosa cells...
March 16, 2017: Chemosphere
https://www.readbyqxmd.com/read/28340181/different-expression-patterns-of-sperm-motility-related-genes-in-testis-of-diploid-and-tetraploid-cyprinid-fish1
#3
Fangzhou Hu, Kang Xu, Yunfan Zhou, Chang Wu, Shi Wang, Jun Xiao, Min Wen, Rurong Zhao, Kaikun Luo, Min Tao, Wei Duan, Shaojun Liu
Sperm motility is an important standard to measure the fertility of male. In our previous study, we found that the diploid spermatozoa from allotetraploid hybrid (4nAT) had longer durations of rapid and slow progressive motility than haploid spermatozoa from common carp (COC). In this study, to explore sperm motility-related molecular mechanisms, we compared the testis tissues transcriptomes from two years old male COC and 4nAT. The RNA-seq data revealed that 2985 genes were differentially expressed between COC and 4nAT, including 2216 up-regulated and 769 down-regulated genes in 4nAT...
March 7, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28340142/multigene-signature-for-predicting-prognosis-of-patients-with-1p19q-co-deletion-diffuse-glioma
#4
Xin Hu, Emmanuel Martinez-Ledesma, Siyuan Zheng, Hoon Kim, Floris Barthel, Tao Jiang, Kenneth R Hess, Roel G W Verhaak
Background.: Co-deletion of 1p and 19q marks a diffuse glioma subtype associated with relatively favorable overall survival; however, heterogeneous clinical outcomes are observed within this category. Methods.: We assembled gene expression profiles and sample annotation of 374 glioma patients carrying the 1p/19q co-deletion. We predicted 1p/19q status using gene expression when annotation was missing. A first cohort was randomly split into training (n = 170) and a validation dataset (n = 163)...
March 8, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28340115/cellular-senescence-in-mouse-hippocampus-after-irradiation-and-the-role-of-p53-and-p21
#5
Zoey Cheng, Yan Zhen Zheng, Yu-Qing Li, C Shun Wong
Diverse stress signals including irradiation may trigger cellular senescence. We asked whether irradiation induced senescence in mouse hippocampus, and whether p53 or p21 played a role in this response. Following whole-brain irradiation, polymerase chain reaction (PCR) arrays for senescence-associated genes showed increased expression of CDKN1A (p21) and CDKN2A (p19ARF) in mouse hippocampus at 9 weeks. Upregulation of p21 and p19ARF was confirmed using real-time PCR, which also demonstrated increased CDKN2A/p16INKa expression after irradiation...
March 14, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28339981/transcriptome-analysis-of-comb-and-testis-from-rose-comb-silky-chicken-r1-r1-and-beijing-fatty-wild-type-chicken-r-r
#6
Y Wang, J Li, C Feng, Y Zhao, X Hu, N Li
Rose-comb was one of the chicken comb-variants first used by Bateson and Punnet in 1902 to demonstrate Mendelian inheritance in animals. Rose-comb is a monogenic trait that has been widely described in chickens. It is caused by a large structural rearrangement that leads to mis-expression of transcription factor MNR2 on chromosome 7. Rose-comb has pleiotropic effects in homozygous roosters, which is associated with poor sperm mobility. It was postulated that this is caused by the disruption of the CCDC108 gene located at the distal inversion breakpoint...
March 2, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339482/a-genome-wide-identification-and-analysis-of-the-dyw-deaminase-genes-in-the-pentatricopeptide-repeat-gene-family-in-cotton-gossypium-spp
#7
Bingbing Zhang, Guoyuan Liu, Xue Li, Liping Guo, Xuexian Zhang, Tingxiang Qi, Hailin Wang, Huini Tang, Xiuqin Qiao, Jinfa Zhang, Chaozhu Xing, Jianyong Wu
The RNA editing occurring in plant organellar genomes mainly involves the change of cytidine to uridine. This process involves a deamination reaction, with cytidine deaminase as the catalyst. Pentatricopeptide repeat (PPR) proteins with a C-terminal DYW domain are reportedly associated with cytidine deamination, similar to members of the deaminase superfamily. PPR genes are involved in many cellular functions and biological processes including fertility restoration to cytoplasmic male sterility (CMS) in plants...
2017: PloS One
https://www.readbyqxmd.com/read/28335496/quantitative-analysis-of-the-kshv-transcriptome-following-primary-infection-of-blood-and-lymphatic-endothelial-cells
#8
A Gregory Bruce, Serge Barcy, Terri DiMaio, Emilia Gan, H Jacques Garrigues, Michael Lagunoff, Timothy M Rose
The transcriptome of the Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) after primary latent infection of human blood (BEC), lymphatic (LEC) and immortalized (TIME) endothelial cells was analyzed using RNAseq, and compared to long-term latency in BCBL-1 lymphoma cells. Naturally expressed transcripts were obtained without artificial induction, and a comprehensive annotation of the KSHV genome was determined. A set of unique coding sequence (UCDS) features and a process to resolve overlapping transcripts were developed to accurately quantitate transcript levels from specific promoters...
March 19, 2017: Pathogens
https://www.readbyqxmd.com/read/28335437/effect-of-clozapine-on-dna-methylation-in-peripheral-leukocytes-from-patients-with-treatment-resistant-schizophrenia
#9
Makoto Kinoshita, Shusuke Numata, Atsushi Tajima, Hidenaga Yamamori, Yuka Yasuda, Michiko Fujimoto, Shinya Watanabe, Hidehiro Umehara, Shinji Shimodera, Takanobu Nakazawa, Masataka Kikuchi, Akihiro Nakaya, Hitoshi Hashimoto, Issei Imoto, Ryota Hashimoto, Tetsuro Ohmori
Clozapine is an atypical antipsychotic, that is established as the treatment of choice for treatment-resistant schizophrenia (SCZ). To date, no study investigating comprehensive DNA methylation changes in SCZ patients treated with chronic clozapine has been reported. The purpose of the present study is to reveal the effects of clozapine on DNA methylation in treatment-resistant SCZ. We conducted a genome-wide DNA methylation profiling in peripheral leukocytes (485,764 CpG dinucleotides) from treatment-resistant SCZ patients treated with clozapine (n = 21) in a longitudinal study...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335009/open-chromatin-profiling-of-human-postmortem-brain-infers-functional-roles-for-non-coding-schizophrenia-loci
#10
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T Dudley, Manuel Mattheisen, Nikolaos K Robakis, Vahram Haroutunian, Panos Roussos
Open chromatin provides access to DNA binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. To better understand the role of CREs in neuropsychiatric disorders we applied the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) to neuronal and non-neuronal nuclei isolated from frozen postmortem human brain by fluorescence-activated nuclear sorting (FANS)...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334937/dynamically-and-epigenetically-coordinated-gata-ets-sox-transcription-factor-expression-is-indispensable-for-endothelial-cell-differentiation
#11
Yasuharu Kanki, Ryo Nakaki, Teppei Shimamura, Taichi Matsunaga, Kohei Yamamizu, Shiori Katayama, Jun-Ichi Suehiro, Tsuyoshi Osawa, Hiroyuki Aburatani, Tatsuhiko Kodama, Youichiro Wada, Jun K Yamashita, Takashi Minami
Although studies of the differentiation from mouse embryonic stem (ES) cells to vascular endothelial cells (ECs) provide an excellent model for investigating the molecular mechanisms underlying vascular development, temporal dynamics of gene expression and chromatin modifications have not been well studied. Herein, using transcriptomic and epigenomic analyses based on H3K4me3 and H3K27me3 modifications at a genome-wide scale, we analysed the EC differentiation steps from ES cells and crucial epigenetic modifications unique to ECs...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334930/rcas-an-rna-centric-annotation-system-for-transcriptome-wide-regions-of-interest
#12
Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin
In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334913/tdp-43-mutations-causing-amyotrophic-lateral-sclerosis-are-associated-with-altered-expression-of-rna-binding-protein-hnrnp-k-and-affect-the-nrf2-antioxidant-pathway
#13
Diane Moujalled, Alexandra Grubman, Karla Acevedo, Shu Yang, Yazi D Ke, Donia M Moujalled, Clare Duncan, Aphrodite Caragounis, Nirma D Perera, Bradley J Turner, Mercedes Prudencio, Leonard Petrucelli, Ian Blair, Lars M Ittner, Peter J Crouch, Jeffrey R Liddell, Anthony R White
TAR DNA binding protein 43 (TDP-43) is a major disease-associated protein involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U). Our previous studies found a direct association between TDP-43 and heterogeneous nuclear ribonucleoprotein K (hnRNP K). In this study, utilizing ALS patient fibroblasts harboring a TDP-43M337V mutation and NSC-34 motor neuronal cell line expressing TDP-43Q331K mutation, we show that hnRNP K expression is impaired in urea soluble extracts from mutant TDP-43 cell models...
March 9, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334911/mertk-rs4374383-variant-predicts-incident-nonalcoholic-fatty-liver-disease-and-diabetes-role-of-mononuclear-cell-activation-and-adipokine-response-to-dietary-fat
#14
Giovanni Musso, Maurizio Cassader, Franco De Michieli, Elena Paschetta, Silvia Pinach, Francesca Saba, Daria Bongiovanni, Luciana Framarin, Mara Berrutti, Nicola Leone, Stefania Corvisieri, Renato Parente, Federica Molinaro, Antonio Sircana, Bo Simona, Roberto Gambino
The loss-of-function rs4374383 G>A variant in Myeloid-epithelial-reproductive Tyrosine Kinase (MERTK) gene has been linked to hepatic fibrosis in chronic liver diseases. MERTK is expressed by immune and non-immune cells involved in inflammation, metabolism and vascular homeostasis. We assessed the impact of MERTK rs4374383 G>A variant on nonalcoholic fatty liver disease (NAFLD) incidence and severity and on glucose and lipid metabolism.We followed-up 305 healthy nonobese nondiabetic, metabolic syndrome-free insulin sensitive participants in a population-based study, characterized for MERTK G>A polymorphism, adipokine profile and inflammatory markers...
March 8, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334904/genome-wide-mapping-of-infection-induced-sine-rnas-reveals-a-role-in-selective-mrna-export
#15
John Karijolich, Yang Zhao, Ravi Alla, Britt Glaunsinger
Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334683/combined-metformin-and-insulin-treatment-reverses-metabolically-impaired-omental-adipogenesis-and-accumulation-of-4-hydroxynonenal-in-obese-diabetic-patients
#16
Morana Jaganjac, Shamma Almuraikhy, Fatima Al-Khelaifi, Mashael Al-Jaber, Moataz Bashah, Nayef A Mazloum, Kamelija Zarkovic, Neven Zarkovic, Georg Waeg, Wael Kafienah, Mohamed A Elrayess
OBJECTIVE: Obesity-associated impaired fat accumulation in the visceral adipose tissue can lead to ectopic fat deposition and increased risk of insulin resistance and type 2 diabetes mellitus (T2DM). This study investigated whether impaired adipogenesis of omental (OM) adipose tissues and elevated 4-hydroxynonenal (4-HNE) accumulation contribute to this process, and if combined metformin and insulin treatment in T2DM patients could rescue this phenotype. METHODS: OM adipose tissues were obtained from forty clinically well characterized obese individuals during weight reduction surgery...
March 16, 2017: Redox Biology
https://www.readbyqxmd.com/read/28334399/association-of-hiv-status-with-local-immune-response-to-anal-squamous-cell-carcinoma-implications-for-immunotherapy
#17
Elizabeth L Yanik, Genevieve J Kaunitz, Tricia R Cottrell, Farah Succaria, Tracee L McMiller, Maria L Ascierto, Jessica Esandrio, Haiying Xu, Aleksandra Ogurtsova, Toby Cornish, Evan J Lipson, Suzanne L Topalian, Eric A Engels, Janis M Taube
Importance: The programmed cell death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1) pathway play an important immunosuppressive role in cancer and chronic viral infection, and have been effectively targeted in cancer therapy. Anal squamous cell carcinoma (SCC) is associated with both human papillomavirus and HIV infection. To date, patients with HIV have been excluded from most trials of immune checkpoint blocking agents, such as anti-PD-1 and anti-PD-L1, because it was assumed that their antitumor immunity was compromised compared with immunocompetent patients...
March 23, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28334351/effects-of-antenatal-maternal-depressive-symptoms-and-socio-economic-status-on-neonatal-brain-development-are-modulated-by-genetic-risk
#18
Anqi Qiu, Mojun Shen, Claudia Buss, Yap-Seng Chong, Kenneth Kwek, Seang-Mei Saw, Peter D Gluckman, Pathik D Wadhwa, Sonja Entringer, Martin Styner, Neerja Karnani, Christine M Heim, Kieran J O'Donnell, Joanna D Holbrook, Marielle V Fortier, Michael J Meaney
This study included 168 and 85 mother-infant dyads from Asian and United States of America cohorts to examine whether a genomic profile risk score for major depressive disorder (GPRSMDD) moderates the association between antenatal maternal depressive symptoms (or socio-economic status, SES) and fetal neurodevelopment, and to identify candidate biological processes underlying such association. Both cohorts showed a significant interaction between antenatal maternal depressive symptoms and infant GPRSMDD on the right amygdala volume...
March 18, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28334262/discriminating-the-reaction-types-of-plant-type-iii-polyketide-synthases
#19
Yugo Shimizu, Hiroyuki Ogata, Susumu Goto
Motivation: Functional prediction of paralogs is challenging in bioinformatics because of rapid functional diversification after gene duplication events combined with parallel acquisitions of similar functions by different paralogs. Plant type III polyketide synthases (PKSs), producing various secondary metabolites, represent a paralogous family that has undergone gene duplication and functional alteration. Currently, there is no computational method available for the functional prediction of type III PKSs...
March 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334204/transcriptomic-and-histological-responses-of-african-rice-oryza-glaberrima-to-meloidogyne-graminicola-provide-new-insights-into-root-knot-nematode-resistance-in-monocots
#20
Anne-Sophie Petitot, Tina Kyndt, Rana Haidar, Alexis Dereeper, Myriam Collin, Janice de Almeida Engler, Godelieve Gheysen, Diana Fernandez
Background and Aims: The root-knot nematode Meloidogyne graminicola is responsible for production losses in rice ( Oryza sativa ) in Asia and Latin America. The accession TOG5681 of African rice, O. glaberrima , presents improved resistance to several biotic and abiotic factors, including nematodes. The aim of this study was to assess the cytological and molecular mechanisms underlying nematode resistance in this accession. Methods: Penetration and development in M...
February 28, 2017: Annals of Botany
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