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BMC Molecular Biology

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https://www.readbyqxmd.com/read/29933763/evaluation-of-suitable-reference-genes-for-qrt-pcr-normalization-in-strawberry-fragaria-%C3%A3-ananassa-under-different-experimental-conditions
#1
Yunting Zhang, Xiaorui Peng, Yi Liu, Yali Li, Ya Luo, Xiaorong Wang, Haoru Tang
BACKGROUND: Strawberry has received much attention due to its nutritional value, unique flavor, and attractive appearance. The availability of the whole genome sequence and multiple transcriptome databases allows the great possibility to explore gene functions, comprehensively. Gene expression profiles of a target gene can provide clues towards the understanding of its biological function. Quantitative real-time PCR (qRT-PCR) is a preferred method for rapid quantification of gene expression...
June 22, 2018: BMC Molecular Biology
https://www.readbyqxmd.com/read/29921228/laser-capture-microdissection-for-transcriptomic-profiles-in-human-skin-biopsies
#2
Silvia Santoro, Ignazio Diego Lopez, Raffaella Lombardi, Andrea Zauli, Ana Maria Osiceanu, Melissa Sorosina, Ferdinando Clarelli, Silvia Peroni, Daniele Cazzato, Margherita Marchi, Angelo Quattrini, Giancarlo Comi, Raffaele Adolfo Calogero, Giuseppe Lauria, Filippo Martinelli Boneschi
BACKGROUND: The acquisition of reliable tissue-specific RNA sequencing data from human skin biopsy represents a major advance in research. However, the complexity of the process of isolation of specific layers from fresh-frozen human specimen by laser capture microdissection, the abundant presence of skin nucleases and RNA instability remain relevant methodological challenges. We developed and optimized a protocol to extract RNA from layers of human skin biopsies and to provide satisfactory quality and amount of mRNA sequencing data...
June 19, 2018: BMC Molecular Biology
https://www.readbyqxmd.com/read/29879907/targeting-mir-9-in-gastric-cancer-cells-using-locked-nucleic-acid-oligonucleotides
#3
Joana Filipa Lima, Joana Carvalho, Inês Pinto-Ribeiro, Carina Almeida, Jesper Wengel, Laura Cerqueira, Céu Figueiredo, Carla Oliveira, Nuno Filipe Azevedo
BACKGROUND: Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recently, it has been demonstrated that gastric cancer cells display a specific miRNA expression profile, with increasing evidence of the role of miRNA-9 in this disease. miRNA-9 upregulation has been shown to influence the expression of E-cadherin-encoding gene, triggering cell motility and invasiveness. RESULTS: In this study, we designed LNA anti-miRNA oligonucleotides with a complementary sequence to miRNA-9 and tested their properties to both detect and silence the target miRNA...
June 7, 2018: BMC Molecular Biology
https://www.readbyqxmd.com/read/29587652/quantitative-profiling-of-batf-family-proteins-junb-irf-hetero-trimers-using-spec-seq
#4
Yiming K Chang, Zheng Zuo, Gary D Stormo
BACKGROUND: BATF family transcription factors (BATF, BATF2 and BATF3) form hetero-trimers with JUNB and either IRF4 or IRF8 to regulate cell fate in T cells and dendritic cells in vivo. While each combination of the hetero-trimer has a distinct role, some degree of cross-compensation was observed. The basis for the differential actions of IRF4 and IRF8 with BATF factors and JUNB is still unknown. We propose that the differences in function between these hetero-trimers may be caused by differences in their DNA binding preferences...
March 27, 2018: BMC Molecular Biology
https://www.readbyqxmd.com/read/29554889/ph-mediated-upregulation-of-aqp1-gene-expression-through-the-spi-b-transcription-factor
#5
Yihui Zhai, Hong Xu, Qian Shen, Franz Schaefer, Claus P Schmitt, Jing Chen, Haimei Liu, Jialu Liu, Jiaojiao Liu
BACKGROUND: Bicarbonate-based peritoneal dialysis (PD) fluids enhance the migratory capacity and damage-repair ability of human peritoneal mesothelial cells by upregulating AQP1. However, little is known about the underlying molecular mechanisms. RESULTS: Here we used HEK-293T cells to investigate the effect of pH on AQP1 gene transcription levels. We found that AQP1 mRNA levels increases with pH. Transfection of HEK-293T cells with luciferase reporter vectors containing different regions of the AQP1 promoter identified an upstream region in the AQP1 gene between - 2200 and - 2300 bp as an enhancer required for pH-mediated regulation of AQP1 expression...
March 20, 2018: BMC Molecular Biology
https://www.readbyqxmd.com/read/29540148/a-protocol-for-custom-crispr-cas9-donor-vector-construction-to-truncate-genes-in-mammalian-cells-using-pcdna3-backbone
#6
Neftali Vazquez, Lilia Sanchez, Rebecca Marks, Eduardo Martinez, Victor Fanniel, Alma Lopez, Andrea Salinas, Itzel Flores, Jesse Hirschmann, Robert Gilkerson, Erin Schuenzel, Robert Dearth, Reginald Halaby, Wendy Innis-Whitehouse, Megan Keniry
BACKGROUND: Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employed as genome editing tools in wide ranging organisms. Here, we provide a detailed protocol to truncate genes in mammalian cells using CRISPR Cas9 editing. We describe custom donor vector construction using Gibson assembly with the commonly utilized pcDNA3 vector as the backbone...
March 14, 2018: BMC Molecular Biology
https://www.readbyqxmd.com/read/29534701/recommendations-for-mrna-analysis-of-micro-dissected-glomerular-tufts-from-paraffin-embedded-human-kidney-biopsy-samples
#7
Clemens L Bockmeyer, Juliane Wittig, Karen Säuberlich, Philipp Selhausen, Marc Eßer, Philip Zeuschner, Friedrich Modde, Kerstin Amann, Christoph Daniel
BACKGROUND: Glomeruli are excellent pre-determined natural structures for laser micro-dissection. Compartment-specific glomerular gene expression analysis of formalin-fixed paraffin-embedded renal biopsies could improve research applications. The major challenge for such studies is to obtain good-quality RNA from small amounts of starting material, as applicable for the analysis of glomerular compartments. In this work, we provide data and recommendations for an optimized workflow of glomerular mRNA analysis...
March 13, 2018: BMC Molecular Biology
https://www.readbyqxmd.com/read/29351732/nutrient-depletion-and-tor-inhibition-induce-18s-and-25s-ribosomal-rnas-resistant-to-a-5-phosphate-dependent-exonuclease-in-candida-albicans-and-other-yeasts
#8
Jacob Fleischmann, Miguel A Rocha
BACKGROUND: Messenger RNA (mRNA) represents a small percentage of RNAs in a cell, with ribosomal RNA (rRNA) making up the bulk of it. To isolate mRNA from eukaryotes, typically poly-A selection is carried out. Recently, a 5´-phosphate-dependent, 5´→3´ processive exonuclease called Terminator has become available. It will digest only RNA that has a 5´-monophosphate end and therefore it is very useful to eliminate most of rRNAs in cell. RESULTS: We have found that in the pathogenic yeast Candida albicans, while 18S and 25S components isolated from yeast in robust growth phase are easily eliminated by Terminator, those isolated from cells in the nutritionally diminished stationary phase, become resistant to digestion by this enzyme...
January 19, 2018: BMC Molecular Biology
https://www.readbyqxmd.com/read/29258436/an-optimized-rapid-bisulfite-conversion-method-with-high-recovery-of-cell-free-dna
#9
Shaohua Yi, Fei Long, Juanbo Cheng, Daixin Huang
BACKGROUND: Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DNA available in plasma. Most current methods of DNA methylation analysis are based on the difference of bisulfite-mediated deamination of cytosine between cytosine and 5-methylcytosine. However, the recovery of bisulfite-converted DNA based on current methods is very poor for the methylation analysis of cell-free DNA...
December 19, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28882106/sumoylation-in-p27kip1-via-ranbp2-promotes-cancer-cell-growth-in-cholangiocarcinoma-cell-line-qbc939
#10
Jun Yang, Yan Liu, Bing Wang, Hongzhen Lan, Ying Liu, Fei Chen, Ju Zhang, Jian Luo
BACKGROUND: Cholangiocarcinoma is one of the deadly disease with poor 5-year survival and poor response to conventional therapies. Previously, we found that p27kip1 nuclear-cytoplasmic translocation confers proliferation potential to cholangiocarcinoma cell line QBC939 and this process is mediated by crm-1. However, no other post-transcriptional regulation was found in this process including sumoylation in cholangiocarcinoma. RESULTS: In this study, we explored the role of sumoylation in the nuclear-cytoplasmic translocation of p27kip1 and its involvement of QBC939 cells' proliferation...
September 7, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28835206/an-optimised-protocol-for-isolation-of-rna-from-small-sections-of-laser-capture-microdissected-ffpe-tissue-amenable-for-next-generation-sequencing
#11
Parisa Amini, Julia Ettlin, Lennart Opitz, Elena Clementi, Alexandra Malbon, Enni Markkanen
BACKGROUND: Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA-protein crosslinking and RNA fragmentation, both of which heavily impact on RNA quantity and quality for downstream analysis. With very small sample sizes, e.g. when performing Laser-capture microdissection (LCM) to isolate specific subpopulations of cells, recovery of sufficient RNA for analysis with reverse-transcription quantitative PCR (RT-qPCR) or next-generation sequencing (NGS) becomes very cumbersome and difficult...
August 23, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28793862/physical-shearing-imparts-biological-activity-to-dna-and-ability-to-transmit-itself-horizontally-across-species-and-kingdom-boundaries
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
Rebecca R Minich, Jin Li, Bruce L Tempel
BACKGROUND: Along with sodium/calcium (Ca2+ ) exchangers, plasma membrane Ca2+ ATPases (ATP2Bs) are main regulators of intracellular Ca2+ 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
#20
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
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