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BMC Molecular Biology

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https://www.readbyqxmd.com/read/28793862/physical-shearing-imparts-biological-activity-to-dna-and-ability-to-transmit-itself-horizontally-across-species-and-kingdom-boundaries
#1
Gorantla Venkata Raghuram, Deepika Gupta, Siddharth Subramaniam, Ashwini Gaikwad, Naveen Kumar Khare, Malcolm Nobre, Naveen Kumar Nair, Indraneel Mittra
BACKGROUND: We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage and apoptotic responses in the recipients. However, DNA is not conventionally known to spontaneously enter into cells or to have any intrinsic biological activity. We hypothesized that cellular entry and acquisition of biological properties are functions of the size of DNA...
August 9, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28774282/interaction-between-nfatc2-and-the-transcription-factor-sp1-in-pancreatic-carcinoma-cells-patu-8988t
#2
Manuela Malsy, Bernhard Graf, Katrin Almstedt
BACKGROUND: Nuclear factors of activated T-cells (NFATs) have been mainly characterized in the context of immune response regulation because, as transcription factors, they have the ability to induce gene transcription. NFAT proteins are found in several types of tumors, for instance, pancreatic carcinoma. The role of NFATs in carcinogenesis is regulating central genes in cell differentiation and cell growth. NFAT proteins are primarily located in cytoplasm and only transported to the cell nucleus after activation...
August 3, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28728573/splicing-arrays-reveal-novel-rbm10-targets-including-smn2-pre-mrna
#3
Leslie C Sutherland, Philippe Thibault, Mathieu Durand, Elvy Lapointe, Jose M Knee, Ariane Beauvais, Irina Kalatskaya, Sarah C Hunt, Julie J Loiselle, Justin G Roy, Sarah J Tessier, Gustavo Ybazeta, Lincoln Stein, Rashmi Kothary, Roscoe Klinck, Benoit Chabot
BACKGROUND: RBM10 is an RNA binding protein involved in message stabilization and alternative splicing regulation. The objective of the research described herein was to identify novel targets of RBM10-regulated splicing. To accomplish this, we downregulated RBM10 in human cell lines, using small interfering RNAs, then monitored alternative splicing, using a reverse transcription-PCR screening platform. RESULTS: RBM10 knockdown (KD) provoked alterations in splicing events in 10-20% of the pre-mRNAs, most of which had not been previously identified as RBM10 targets...
July 20, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28716034/growth-arrest-specific-gene-2-in-tilapia-oreochromis-niloticus-molecular-characterization-and-functional-analysis-under-low-temperature-stress
#4
ChangGeng Yang, Fan Wu, Xing Lu, Ming Jiang, Wei Liu, Lijuan Yu, Juan Tian, Hua Wen
BACKGROUND: Growth arrest specific 2 (gas2) gene is a component of the microfilament system that plays a major role in the cell cycle, regulation of microfilaments, and cell morphology during apoptotic processes. However, little information is available on fish gas2. In this study, the tilapia (Oreochromis niloticus) gas2 gene was cloned and characterized for the first time. RESULTS: The open reading frame was 1020 bp, encoding 340 amino acids; the 5'-untranslated region (UTR) was 140 bp and the 3'-UTR was 70 bp, with a poly (A) tail...
July 17, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28655335/identification-of-g-quadruplex-structures-that-possess-transcriptional-regulating-functions-in-the-dele-and-cdc6-cpg-islands
#5
Daniyah H Bay, Annika Busch, Fred Lisdat, Keisuke Iida, Kazunori Ikebukuro, Kazuo Nagasawa, Isao Karube, Wataru Yoshida
BACKGROUND: G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay...
June 27, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28623884/mitochondrial-rna-processing-in-absence-of-trna-punctuations-in-octocorals
#6
Gaurav G Shimpi, Sergio Vargas, Angelo Poliseno, Gert Wörheide
BACKGROUND: Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals...
June 17, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28587591/microarray-expression-profiling-in-the-denervated-hippocampus-identifies-long-noncoding-rnas-functionally-involved-in-neurogenesis
#7
Bingying Deng, Xiang Cheng, Haoming Li, Jianbing Qin, Meiling Tian, Guohua Jin
BACKGROUND: The denervated hippocampus provides a proper microenvironment for the survival and neuronal differentiation of neural progenitors. While thousands of lncRNAs were identified, only a few lncRNAs that regulate neurogenesis in the hippocampus are reported. The present study aimed to perform microarray expression profiling to identify long noncoding RNAs (lncRNAs) that might participate in the hippocampal neurogenesis, and investigate the potential roles of identified lncRNAs in the hippocampal neurogenesis...
June 6, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28532435/early-growth-response-protein-1-regulates-promoter-activity-of-%C3%AE-plasma-membrane-calcium-atpase-2-a-major-calcium-pump-in-the-brain-and-auditory-system
#8
Rebecca R Minich, Jin Li, Bruce L Tempel
BACKGROUND: Along with sodium/calcium (Ca(2+)) exchangers, plasma membrane Ca(2+) ATPases (ATP2Bs) are main regulators of intracellular Ca(2+) levels. There are four ATP2B paralogs encoded by four different genes. Atp2b2 encodes the protein pump with the fastest activation, ATP2B2. In mice, the Atp2b2 transcript has several alternate transcriptional start site variants: α, β, µ and δ. These variants are expressed in developmental and tissue specific manners. The α and β Atp2b2 transcripts are equally expressed in the brain...
May 22, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28506294/hssb1-associates-with-and-promotes-stability-of-the-blm-helicase
#9
Laura V Croft, Nicholas W Ashton, Nicolas Paquet, Emma Bolderson, Kenneth J O'Byrne, Derek J Richard
BACKGROUND: Maintenance of genome stability is critical in human cells. Mutations in or loss of genome stability pathways can lead to a number of pathologies including cancer. hSSB1 is a critical DNA repair protein functioning in the repair and signalling of stalled DNA replication forks, double strand DNA breaks and oxidised DNA lesions. The BLM helicase is central to the repair of both collapsed DNA replication forks and double strand DNA breaks by homologous recombination. RESULTS: In this study, we demonstrate that hSSB1 and BLM helicase form a complex in cells and the interaction is altered in response to ionising radiation (IR)...
May 15, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28449660/selective-measurement-of-%C3%AE-smooth-muscle-actin-why-%C3%AE-actin-can-not-be-used-as-a-housekeeping-gene-when-tissue-fibrosis-occurs
#10
Apor Veres-Székely, Domonkos Pap, Erna Sziksz, Eszter Jávorszky, Réka Rokonay, Rita Lippai, Kálmán Tory, Andrea Fekete, Tivadar Tulassay, Attila J Szabó, Ádám Vannay
BACKGROUND: Prevalence of fibroproliferative diseases, including chronic kidney disease is rapidly increasing and has become a major public health problem worldwide. Fibroproliferative diseases are characterized by increased expression of α smooth muscle actin (α-SMA) that belongs to the family of the six conserved actin isoforms showing high degree homology. The aim of the present study was to develop real-time PCRs that clearly discriminate α-SMA and ß-actin from other actin isoforms...
April 27, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28431504/erratum-to-runx1-induces-dna-replication-independent-active-dna-demethylation-at-spi1-regulatory-regions
#11
Shubham Goyal, Takahiro Suzuki, Jing-Ru Li, Shiori Maeda, Mami Kishima, Hajime Nishimura, Yuri Shimizu, Harukazu Suzuki
No abstract text is available yet for this article.
April 21, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28381210/identification-of-suitable-reference-genes-for-real-time-quantitative-pcr-analysis-of-hydrogen-peroxide-treated-human-umbilical-vein-endothelial-cells
#12
Tianyi Li, Hongying Diao, Lei Zhao, Yue Xing, Jichang Zhang, Ning Liu, Youyou Yan, Xin Tian, Wei Sun, Bin Liu
BACKGROUND: Oxidative stress can induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not received sufficient attention in related studies. The objective of this study, therefore, was to select a set of stably expressed reference genes for use in qRT-PCR normalization in oxidative stress injuries in human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (H2O2)...
April 5, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28376714/runx1-induces-dna-replication-independent-of-active-dna-demethylation-at-spi1-regulatory-regions
#13
Shubham Goyal, Takahiro Suzuki, Jing-Ru Li, Shiori Maeda, Mami Kishima, Hajime Nishimura, Yuri Shimizu, Harukazu Suzuki
BACKGROUND: SPI1 is an essential transcription factor (TF) for the hematopoietic lineage, in which its expression is tightly controlled through a -17-kb upstream regulatory region and a promoter region. Both regulatory regions are demethylated during hematopoietic development, although how the change of DNA methylation status is performed is still unknown. RESULTS: We found that the ectopic overexpression of RUNX1 (another key TF in hematopoiesis) in HEK-293T cells induces almost complete DNA demethylation at the -17-kb upstream regulatory region and partial but significant DNA demethylation at the proximal promoter region...
April 4, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28298204/immunoglobulin-t-from-sea-bass-dicentrarchus-labrax-l-molecular-characterization-tissue-localization-and-expression-after-nodavirus-infection
#14
Francesco Buonocore, Valentina Stocchi, Noelia Nunez-Ortiz, Elisa Randelli, Marco Gerdol, Alberto Pallavicini, Angelo Facchiano, Chiara Bernini, Laura Guerra, Giuseppe Scapigliati, Simona Picchietti
BACKGROUND: Immunoglobulins (Igs) are fundamental components of the adaptive immune system of vertebrates, with the IgT/IgZ isotype specific of Teleosts. In this paper we describe the identification of an IgT heavy chain from the European sea bass (Dicentrarchus labrax L.), its molecular characterization and tissue mRNA localization by in situ hybridization. RESULTS: Sea bass IgT consists of 552 aa (Accession Number KM410929) and it contains a putative 19 amino acids long signal peptide and one potential N-glycosylation site...
March 15, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28279161/methylated-site-display-msd-aflp-a-sensitive-and-affordable-method-for-analysis-of-cpg-methylation-profiles
#15
Toshiki Aiba, Toshiyuki Saito, Akiko Hayashi, Shinji Sato, Harunobu Yunokawa, Toru Maruyama, Wataru Fujibuchi, Hisaka Kurita, Chiharu Tohyama, Seiichiroh Ohsako
BACKGROUND: It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP...
March 9, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28274199/properties-of-stat1-and-irf1-enhancers-and-the-influence-of-snps
#16
Mohamed Abou El Hassan, Katherine Huang, Manoja B K Eswara, Zhaodong Xu, Tao Yu, Arthur Aubry, Zuyao Ni, Izzy Livne-Bar, Monika Sangwan, Mohamad Ahmad, Rod Bremner
BACKGROUND: STAT1 and IRF1 collaborate to induce interferon-γ (IFNγ) stimulated genes (ISGs), but the extent to which they act alone or together is unclear. The effect of single nucleotide polymorphisms (SNPs) on in vivo binding is also largely unknown. RESULTS: We show that IRF1 binds at proximal or distant ISG sites twice as often as STAT1, increasing to sixfold at the MHC class I locus. STAT1 almost always bound with IRF1, while most IRF1 binding events were isolated...
March 9, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28202045/identification-of-micrornas-and-their-response-to-the-stress-of-plant-allelochemicals-in-aphis-gossypii-hemiptera-aphididae
#17
Kang-Sheng Ma, Fen Li, Ying Liu, Ping-Zhuo Liang, Xue-Wei Chen, Xi-Wu Gao
BACKGROUND: MicroRNAs (miRNAs) are a group of short non-coding RNAs involved in the inhibition of protein translation or in mRNA degradation. Although the regulatory roles of miRNAs in various biological processes have been investigated, there is as yet an absence of studies about the regulatory roles of miRNAs involved in the metabolism of plant allelochemicals in insects. RESULTS: We constructed five small RNA libraries from apterous Aphis gossypii adults that had fed on an artificial diet containing various allelochemicals...
February 16, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28173762/binding-affinity-of-five-pbps-to-ostrinia-sex-pheromones
#18
Tiantao Zhang, Yaqi Sun, Kevin W Wanner, Brad S Coates, Kanglai He, Zhenying Wang
BACKGROUND: Pheromone binding proteins (PBPs) of male Lepidoptera function in chemical communication, mate attraction and recognition. Directional selection was previously predicted between PBP3 orthologs of Ostrinia furnacalis and Ostrinia nubilalis were interpreted as being involved in sexual isolation. RESULTS: In vitro assays show that recombinant male OfurPBP3 bound O. furnacalis sex pheromones, Z-12-tetradecenyl acetate (Z12-14:OAc) and E-12-tetradecenyl acetate (E12-14:OAc), as well as to ECB pheromones Z11- and E11-14:OAc...
February 7, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28160774/positive-selection-and-functional-divergence-of-farnesyl-pyrophosphate-synthase-genes-in-plants
#19
Jieying Qian, Yong Liu, Naixia Chao, Chengtong Ma, Qicong Chen, Jian Sun, Yaosheng Wu
BACKGROUND: Farnesyl pyrophosphate synthase (FPS) belongs to the short-chain prenyltransferase family, and it performs a conserved and essential role in the terpenoid biosynthesis pathway. However, its classification, evolutionary history, and the forces driving the evolution of FPS genes in plants remain poorly understood. RESULTS: Phylogeny and positive selection analysis was used to identify the evolutionary forces that led to the functional divergence of FPS in plants, and recombinant detection was undertaken using the Genetic Algorithm for Recombination Detection (GARD) method...
February 4, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28137312/transcriptional-regulation-of-human-sperm-associated-antigen-16-gene-by-s-sox5
#20
Ling Zhang, Yunhao Liu, Wei Li, Qiaoling Zhang, Yanwei Li, Junpin Liu, Jie Min, Chaofan Shuang, Shizheng Song, Zhibing Zhang
BACKGROUND: The mammalian sperm-associated antigen 16 gene (Spag16) uses alternative promoters to produce two major transcript isoforms (Spag16L and Spag16S) and encode proteins that are involved in the cilia/flagella formation and motility. In silico analysis of both mouse and human SPAG16L promoters reveals the existence of multiple putative SOX5 binding sites. Given that the SOX5 gene encodes a 48-kDa transcription factor (S-SOX5) and the presence of putative SOX5 binding sites at the SPAG16L promoter, regulation of SPAG16L expression by S-SOX5 was studied in the present work...
January 31, 2017: BMC Molecular Biology
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