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https://www.readbyqxmd.com/read/28735352/long-noncoding-rna-expression-profiles-in-chondrogenic-and-hypertrophic-differentiation-of-mouse-mesenchymal-stem-cells
#1
Zhen Cao, Song Huang, Jianmei Li, Yun Bai, Ce Dou, Chuan Liu, Fei Kang, Xiaoshan Gong, Haibin Ding, Tianyong Hou, Shiwu Dong
Long noncoding RNAs (lncRNAs) are important regulators for a variety of biological processes. Chondrogenic differentiation of mesenchymal stem cells (MSCs) is a crucial stage in chondrogenesis while chondrocyte hypertrophy is related to endochondral ossification and osteoarthritis. However, the effects of lncRNAs on chondrogenic and hypertrophic differentiation of mouse MSCs are unclear. To explore the potential mechanisms of lncRNAs during chondrogenesis and chondrocyte hypertrophy, microarray was performed to investigate the expression profiles of lncRNA and mRNA in MSCs, pre-chondrocytes, and hypertrophic chondrocytes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28735351/multiple-correlation-analyses-revealed-complex-relationship-between-dna-methylation-and-mrna-expression-in-human-peripheral-blood-mononuclear-cells
#2
Fang-Fei Xie, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Hong Zhu, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Xiao-Wei Zhu, Wei Xia, Lan Wang, Pei He, Peng-Fei Bing, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei
DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28735242/transcriptomic-analysis-of-the-larva-taenia-multiceps
#3
W H Li, N Z Zhang, L Yue, Y Yang, L Li, H B Yan, T T Li, Z G Qu, W Z Jia, B Q Fu
Taenia multiceps is an adult worm affiliated to Taeniidae family, Platyhelminthes phylum. The larvae of the parasite (Coenurus cerebralis) parasitic in the brain and spinal cord in domestic and wild ruminants or humans can led to a fatal central nervous system (CNS) disease. The aims of the present study were to define the transcriptome profiles of the larvae of T. multiceps by RNA-Seq approach, and to generate large functional gene datasets that could be used to predict the key molecular pathways linked to this cestode...
July 12, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28734934/analysis-of-rna-protein-interactions-in-vertebrate-embryos-using-uv-crosslinking-approaches
#4
Vladimir Despic, Mario Dejung, Falk Butter, Karla M Neugebauer
A decade ago, we believed that at least 300 RNA binding proteins (RBPs) were encoded in our genomes based on annotations of known or predicted RNA binding domains. Deciphering the roles of those RBPs in regulated gene expression was a vast frontier awaiting exploration. Since then, the field has developed a number of key tools that navigate the landscape of cellular RNA. These rely principally on UV crosslinking to create covalent bonds between RBPs and target RNAs in vivo, revealing not only target identities but also local binding sites upon RNA-Seq...
July 19, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28734179/computational-analysis-for-the-determination-of-deleterious-nssnps-in-human-mthfd1-gene
#5
Mansi Desai, J B Chauhan
Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol...
July 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28733938/molecular-cloning-heterologous-expression-and-functional-characterization-of-a-cellulolytic-enzyme-cel-prii-from-buffalo-rumen-metagenome
#6
Ravi K Shah, Amrutlal K Patel, Deepti M Davla, Ishan K Parikh, Ramalingam B Subramanian, Kamlesh C Patel, Subhash J Jakhesara, Chaitanya G Joshi
A cellulase encoding gene, Cel PRII, was identified from Mehsani buffalo rumen metagenome, and cloned and expressed in Escherichia coli BL21(DE3)pLysS. The 1170 bp full length gene encodes a 389 residue polypeptide (Cel PRII) containing a catalytic domain belonging to glycosyl hydrolase (GH) 5 family. The fusion protein consisting of the Cel PRII, thioredoxin tag and 6x Histidine tag with predicted molecular weight of 63 kDa when recovered from inclusion bodies under denaturing conditions, exhibited cellulolytic activity against carboxymethyl cellulose (CMC)...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28733628/solute-carriers-affect-anopheles-stephensi-survival-and-plasmodium-berghei-infection-in-the-salivary-glands
#7
J Couto, S Antunes, R Pinheiro-Silva, V do Rosário, J de la Fuente, A Domingos
Malaria is caused by mosquito-borne Plasmodium spp. parasites that must infect and survive within mosquito salivary glands (SGs) prior to host transmission. Recent advances in transcriptomics and the complete genome sequencing of mosquito vectors have increased our knowledge of the SG genes and proteins involved in pathogen infection and transmission. Membrane solute carriers are key proteins involved in drug transport and are useful in the development of new interventions for transmission blocking. Herein, we applied transcriptomics analysis to compare SGs mRNA levels in Anopheles stephensi fed on non-infected and P...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733422/differences-in-dna-binding-specificity-of-floral-homeotic-protein-complexes-predict-organ-specific-target-genes
#8
Cezary Smaczniak, Jose M Muiño, Dijun Chen, Gerco C Angenent, Kerstin Kaufmann
Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors. How these factors achieve their regulatory specificities is however still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS-domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high throughput DNA sequencing (SELEX-seq) on several floral MADS-domain protein homo- and heterodimers to measure their DNA-binding specificities...
July 21, 2017: Plant Cell
https://www.readbyqxmd.com/read/28733196/proteasome-subunit-beta-type-1-p11a-polymorphism-is-a-new-prognostic-marker-in-multiple-myeloma
#9
Gergely Varga, Gábor Mikala, Katalin Piroska Kiss, Éva Kosóczki, Edit Szabó, Nóra Meggyesi, Katalin Balassa, Petra Kövy, Bálint Tegze, Gergely Szombath, Attila Tordai, Hajnalka Andrikovics, László Homolya, Tamás Masszi
BACKGROUND: Proteasome subunit beta type 1 (PSMB1) rs12717 polymorphism, a single nucleotide polymorphism with unknown functional effect, was recently reported to influence response to bortezomib-based therapy in follicular lymphoma. PATIENTS AND METHODS: We retrospectively analyzed the prognostic impact of this polymorphism in 211 consecutively diagnosed multiple myeloma cases, and performed in vitro experiments to look into its functional consequences. RESULTS: On univariate analysis, patients carrying the variant G allele showed significantly shorter progression-free survival (PFS) with a pattern suggestive of a gene-dose effect (PFS 26...
June 30, 2017: Clinical Lymphoma, Myeloma & Leukemia
https://www.readbyqxmd.com/read/28732438/investigation-of-killer-immunoglobulin-like-receptor-kir-and-hla-genotypes-to-predict-the-occurrence-of-acute-allograft-rejection-after-kidney-transplantation
#10
Davood Jafari, Mohsen Nafar, Mir Saeed Yekaninejad, Razieh Abdolvahabi, Mahboob Lesan Pezeshki, Efat Razaghi, Ali Akbar Amirzargar
After kidney transplantation, natural killer (NK) cells play a pivotal role in triggering the immune response to the allogeneic grafts primarily by their killer-cell immunoglobulin-like receptors (KIR). This process may be one mechanism that contributes to graft rejection. In this study, we have evaluated whether acute rejection after kidney transplantation was associated with predicted NK cell alloreactivity based on KIR gene and ligand along with KIR/HLA compound genotype analysis. After kidney transplantation, natural killer (NK) cells play a pivotal role in triggering the immune response to the allogeneic grafts primarily by their killer-cell immunoglobulin-like receptors (KIR)...
June 2017: Iranian Journal of Allergy, Asthma, and Immunology
https://www.readbyqxmd.com/read/28732366/rassf6-downregulation-promotes-the-epithelial-mesenchymal-transition-and-predicts-poor-prognosis-in-colorectal-cancer
#11
Rui Zhou, Lin Qiu, Xiaolong Liu, Lijuan Ling, Ninglei Li, Kun Zhou, Jingbo Sun, Jian Yan, Canliang Tan, Xiaoping Huang, Luzhe Han, Liangchun Yin, Gang Xiao, Lixin Liu
Distant metastasis is the primary barrier for the successful treatment of patients with colorectal cancer, and thus, searching for new therapeutic targets by further exploring the molecular mechanisms of colorectal cancer metastasis is important. In this study, we investigated the biological and clinical significance of RASSF6 in colorectal cancer as well as the underlying molecular mechanisms. We found that low RASSF6 expression corresponds to a poor prognosis in colorectal cancer patients, and low RASSF6 expression is distinctly associated with tumour progression...
July 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732175/genome-wide-identification-functional-prediction-and-evolutionary-analysis-of-r2r3-myb-superfamily-in-brassica-napus
#12
Ali Hajiebrahimi, Hajar Owji, Shiva Hemmati
R2R3-MYBs are important transcription factors (TFs) in planta, involved in development and various stress conditions. Phylogenetic analysis showed the presence of 249 R2R3-MYB TFs in Brassica napus called BnaR2R3-MYBs, clustered into 38 clades. BnaR2R3-MYBs were distributed on 19 chromosomes of B. napus. Sixteen gene clusters were identified. BnaR2R3-MYBs were characterized by motif prediction, gene structure analysis and gene ontology. Evolutionary analysis revealed that BnaR2R3-MYBs are mainly formed as a result of whole genome duplication...
July 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28732143/ifnl4-rs368234815-and-rs117648444-variants-predict-off-treatment-hbsag-seroclearance-in-ifn-treated-hbeag-negative-chronic-hepatitis-b-patients
#13
Enrico Galmozzi, Floriana Facchetti, Glenda Grossi, Alessandro Loglio, Mauro Vigano, Giovanna Lunghi, Massimo Colombo, Pietro Lampertico
BACKGROUND AND AIM: Robust baseline predictors of interferon (IFN) response in HBeAg negative chronic hepatitis B (CHB) patients are not currently available. The recently described rs368234815 TT/ΔG dinucleotide and rs117648444 nonsynonymous P70S polymorphisms in IFN lambda 4 (IFNL4) gene, which are strongly associated with response to IFN in hepatitis C virus (HCV) infection, could be also useful in IFN treated CHB patients. Here we assessed whether IFNL4 rs368234815 and rs117648444 polymorphisms predict IFN induced HBsAg clearance in CHB patients...
July 21, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28732013/the-kp1_4563-gene-is-regulated-by-the-camp-receptor-protein-and-controls-type-3-fimbrial-function-in-klebsiella-pneumoniae-ntuh-k2044
#14
Mei Luo, Shiya Yang, Xuan Li, Pin Liu, Jian Xue, Xipeng Zhou, Kewen Su, Xuan Xu, Ying Qing, Jingfu Qiu, Yingli Li
Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen that can adhere to host cells or extracellular matrix via type 1 and type 3 fimbriae. KP1_4563 is a gene encoding a hypothetical protein in K. pneumoniae NTUH-K2044. KP1_4563 is located between the type 1 and type 3 fimbrial gene clusters and is likely associated with fimbrial function given its putative conserved domains of unknown function (DUF1471). Cyclic AMP receptor protein (CRP) regulates virulence-related gene expression and is a crucial transcriptional regulator in many bacteria...
2017: PloS One
https://www.readbyqxmd.com/read/28731922/a-novel-g-55040074delt-in-alas2-gene-resulting-in-a-monomeric-protein-and-severe-sideroblastic-anemia-phenotype
#15
Prateek Bhatia, Aditya Singh, Avani Hedge
Sideroblastic anemias are a rare group of disorders resulting from defective iron incorporation during heme synthesis and hence characterized by anemia and presence of ringed sideroblasts in bone marrow. The most common form is an X-linked disorder caused by mutations in ALAS2 gene. In the current paper, a case of X-linked sideroblastic anemia caused by a novel homozygous deletional mutation in exon 10 of ALAS2 gene is presented. The female infant developed moderately severe anemia at 6 months of age, which did not improve despite adequate nutritional support...
July 20, 2017: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/28731196/microrna-106a-promotes-cell-migration-and-invasion-by-targeting-tissue-inhibitor-of-matrix-metalloproteinase-2-in-cervical-cancer
#16
Xia Li, Qi Zhou, Ling Tao, Chunxia Yu
Increasing evidence has demonstrated that miRNAs play a critical role in tumor development and progression. Previous studies have revealed that miR-106a is abnormally expressed in various cancers. However, its function and underlying mechanism in cervical cancer (CC) remains unknown. In this study, we confirmed that the expression of miR-106a was significantly upregulated in both CC cell lines and tissues by qRT-PCR. The increased expression of miR-106a was obviously associated with adverse prognostic features...
July 18, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28731158/the-long-non-coding-rna-snhg3-functions-as-a-competing-endogenous-rna-to-promote-malignant-development-of-colorectal-cancer
#17
Weizhen Huang, Yunming Tian, Shaoting Dong, Yinlian Cha, Jun Li, Xiaohong Guo, Xia Yuan
Accumulating evidence has revealed that aberrantly expressed long non-coding transcripts are involved in the development and progression of colorectal cancer (CRC). Small nucleolar RNA host gene 3 (SNHG3) is a newly identified lncRNA, and little is known about its clinical significance and biological functions in the development of CRC. In the present study, we found that the expression of SNHG3 was significantly upregulated in CRC, and upregulation of SNHG3 predicted poor prognosis for patients with CRC as determined through analysis of the data obtained from TCGA database...
July 18, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28730144/molecular-characterization-of-the-human-stomach-microbiota-in-gastric-cancer-patients
#18
Guoqin Yu, Javier Torres, Nan Hu, Rafael Medrano-Guzman, Roberto Herrera-Goepfert, Michael S Humphrys, Lemin Wang, Chaoyu Wang, Ti Ding, Jacques Ravel, Philip R Taylor, Christian C Abnet, Alisa M Goldstein
Helicobacter pylori (Hp) is the primary cause of gastric cancer but we know little of its relative abundance and other microbes in the stomach, especially at the time of gastric cancer diagnosis. Here we characterized the taxonomic and derived functional profiles of gastric microbiota in two different sets of gastric cancer patients, and compared them with microbial profiles in other body sites. Paired non-malignant and tumor tissues were sampled from 160 gastric cancer patients with 80 from China and 80 from Mexico...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28729899/evolutionary-loss-of-melanogenesis-in-the-tunicate-molgula-occulta
#19
Claudia Racioppi, Maria Carmen Valoroso, Ugo Coppola, Elijah K Lowe, C Titus Brown, Billie J Swalla, Lionel Christiaen, Alberto Stolfi, Filomena Ristoratore
BACKGROUND: Analyzing close species with diverse developmental modes is instrumental for investigating the evolutionary significance of physiological, anatomical and behavioral features at a molecular level. Many examples of trait loss are known in metazoan populations living in dark environments. Tunicates are the closest living relatives of vertebrates and typically present a lifecycle with distinct motile larval and sessile adult stages. The nervous system of the motile larva contains melanized cells associated with geotactic and light-sensing organs...
2017: EvoDevo
https://www.readbyqxmd.com/read/28729861/comparative-omics-and-trait-analyses-of-marine-pseudoalteromonas-phages-advance-the-phage-otu-concept
#20
Melissa B Duhaime, Natalie Solonenko, Simon Roux, Nathan C Verberkmoes, Antje Wichels, Matthew B Sullivan
Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition...
2017: Frontiers in Microbiology
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