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BMC Molecular Biology

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https://read.qxmd.com/read/30777032/rna-sequencing-selection-of-reference-genes-and-demonstration-of-feeding-rnai-in-thrips-tabaci-lind-thysanoptera-thripidae
#1
Satnam Singh, Mridula Gupta, Suneet Pandher, Gurmeet Kaur, Neha Goel, Pankaj Rathore, Subba Reddy Palli
BACKGROUND: Thrips tabaci is a severe pest of onion and cotton. Due to lack of information on its genome or transcriptome, not much is known about this insect at the molecular level. To initiate molecular studies in this insect, RNA was sequenced; de novo transcriptome assembly and analysis were performed. The RNAseq data was used to identify reference and RNAi pathway genes in this insect. Additionally, feeding RNAi was demonstrated in T. tabaci for the first time. RESULTS: From the assembled transcriptome, 27,836 coding sequence (CDS) with an average size of 1236 bp per CDS were identified...
February 18, 2019: BMC Molecular Biology
https://read.qxmd.com/read/30755162/a-fragment-activity-assay-reveals-the-key-residues-of-tbc1d15-gtpase-activating-protein-gap-in-chiloscyllium-plagiosum
#2
Yangyang Jin, Guodong Lin, Yanna Chen, Yinghua Ge, Ruofeng Liang, Jia Wu, Jianqing Chen, Dan Wang, Hengbo Shi, Hui Fei, Zhengbing Lv
BACKGROUND: GTPase-activating proteins (GAPs) with a TBC (Tre-2/Bub2/Cdc16) domain architecture serve as negative regulators of Rab GTPases. The related crystal structure has been studied and reported by other members of our research group in 2017 (Chen et al. in Protein Sci 26(4):834-846, 2017). The protein crystal structure and sequencing data accession numbers in Protein structure database (PDB) are 5TUB (Shark TBC1D15 GAP) and 5TUC (Sus TBC1D15 GAP), respectively. In this paper, we analyzed the Rab-GAP specificity of TBC1D15 in the evolution and influence of key amino acid residue mutations on Rab-GAP activity...
February 12, 2019: BMC Molecular Biology
https://read.qxmd.com/read/30744561/hexa-is-required-for-growth-aflatoxin-biosynthesis-and-virulence-in-aspergillus-flavus
#3
Jun Yuan, Ding Li, Ling Qin, Jiaojiao Shen, Xiaodong Guo, Elisabeth Tumukunde, Mingzhu Li, Shihua Wang
BACKGROUND: Woronin bodies are fungal-specific organelles whose formation is derived from peroxisomes. The former are believed to be involved in the regulation of mycotoxins biosynthesis, but not in their damage repair function. The hexagonal peroxisome protein (HexA or Hex1) encoded by hexA gene in Aspergillus is the main and the essential component of the Woronin body. However, little is known about HexA in Aspergillus flavus. RESULTS: In this study, hexA knock-out mutant (ΔhexA) and complementation strain (ΔhexAC ) were produced using homologous recombination...
February 11, 2019: BMC Molecular Biology
https://read.qxmd.com/read/30646850/genome-wide-identification-of-brain-mirnas-in-response-to-high-intensity-intermittent-swimming-training-in-rattus-norvegicus-by-deep-sequencing
#4
Yanhong Zhao, Anmin Zhang, Yanfang Wang, Shuping Hu, Ruiping Zhang, Shuaiwei Qian
BACKGROUND: Physical exercise can improve brain function by altering brain gene expression. The expression mechanisms underlying the brain's response to exercise still remain unknown. miRNAs as vital regulators of gene expression may be involved in regulation of brain genes in response to exercise. However, as yet, very little is known about exercise-responsive miRNAs in brain. RESULTS: We constructed two comparative small RNA libraries of rat brain from a high-intensity intermittent swimming training (HIST) group and a normal control (NC) group...
January 15, 2019: BMC Molecular Biology
https://read.qxmd.com/read/30602381/mirnas-differentially-expressed-in-skeletal-muscle-of-animals-with-divergent-estimated-breeding-values-for-beef-tenderness
#5
Berna I G Kappeler, Luciana C A Regitano, Mirele D Poleti, Aline S M Cesar, Gabriel C M Moreira, Gustavo Gasparin, Luiz L Coutinho
BACKGROUND: MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness...
January 3, 2019: BMC Molecular Biology
https://read.qxmd.com/read/30602369/graphene-oxide-down-regulates-genes-of-the-oxidative-phosphorylation-complexes-in-a-glioblastoma
#6
Maciej Szmidt, Adrian Stankiewicz, Kaja Urbańska, Sławomir Jaworski, Marta Kutwin, Mateusz Wierzbicki, Marta Grodzik, Beata Burzyńska, Monika Góra, André Chwalibog, Ewa Sawosz
BACKGROUND: Recently different forms of nanographene were proposed as the material with high anticancer potential. However, the mechanism of the suppressive activity of the graphene on cancer development remains unclear. We examined the effect of oxygenated, reduced and pristine graphene on the gene expression in glioblastoma U87 cell line. RESULTS: Conducting microarrays and RT-qPCR analysis we explored that graphene oxide (rather than reduced graphene oxide and pristine graphene) down-regulates the mRNA expression of mitochondrial oxidative phosphorylation (OXPHOS) nuclear genes of complexes I, III, IV and V...
January 3, 2019: BMC Molecular Biology
https://read.qxmd.com/read/30563453/the-dictyostelium-discoideum-homologue-of-twinkle-twm1-is-a-mitochondrial-dna-helicase-an-active-primase-and-promotes-mitochondrial-dna-replication
#7
Ashley Harman, Christian Barth
BACKGROUND: DNA replication requires contributions from various proteins, such as DNA helicases; in mitochondria Twinkle is important for maintaining and replicating mitochondrial DNA. Twinkle helicases are predicted to also possess primase activity, as has been shown in plants; however this activity appears to have been lost in metazoans. Given this, the study of Twinkle in other organisms is required to better understand the evolution of this family and the roles it performs within mitochondria...
December 19, 2018: BMC Molecular Biology
https://read.qxmd.com/read/30514321/matrix-association-region-scaffold-attachment-region-mar-sar-sequence-its-vital-role-in-mediating-chromosome-breakages-in-nasopharyngeal-epithelial-cells-via-oxidative-stress-induced-apoptosis
#8
Sang-Nee Tan, Sai-Peng Sim, Alan S B Khoo
BACKGROUND: Oxidative stress is known to be involved in most of the aetiological factors of nasopharyngeal carcinoma (NPC). Cells that are under oxidative stress may undergo apoptosis. We have previously demonstrated that oxidative stress-induced apoptosis could be a potential mechanism mediating chromosome breakages in nasopharyngeal epithelial cells. Additionally, caspase-activated DNase (CAD) may be the vital player in mediating the chromosomal breakages during oxidative stress-induced apoptosis...
December 4, 2018: BMC Molecular Biology
https://read.qxmd.com/read/30509165/molecular-analysis-of-npas3-functional-domains-and-variants
#9
Leiah M Luoma, Fred B Berry
BACKGROUND: NPAS3 encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of Npas3 was found to cause alterations in neurodevelopment, as well as a marked reduction in neurogenesis in the adult mouse hippocampus. This neurogenic deficit, alongside the reduction in cortical interneuron number, likely contributes to the behavioral and cognitive alterations observed in Npas3 knockout mice. Although loss of Npas3 has been found to affect proliferation and apoptosis, the molecular function of NPAS3 is largely uncharacterized outside of predictions based on its high homology to bHLH-PAS transcription factors...
December 3, 2018: BMC Molecular Biology
https://read.qxmd.com/read/30463513/integration-of-transcriptome-and-proteome-profiles-in-glioblastoma-looking-for-the-missing-link
#10
Jean-Michel Lemée, Anne Clavreul, Marc Aubry, Emmanuelle Com, Marie de Tayrac, Jean Mosser, Philippe Menei
BACKGROUND: Glioblastoma (GB) is the most common and aggressive tumor of the brain. Genotype-based approaches and independent analyses of the transcriptome or the proteome have led to progress in understanding the underlying biology of GB. Joint transcriptome and proteome profiling may reveal new biological insights, and identify pathogenic mechanisms or therapeutic targets for GB therapy. We present a comparison of transcriptome and proteome data from five GB biopsies (TZ) vs their corresponding peritumoral brain zone (PBZ)...
November 21, 2018: BMC Molecular Biology
https://read.qxmd.com/read/30384838/analyses-of-changes-in-myocardial-long-non-coding-rna-and-mrna-profiles-after-severe-hemorrhagic-shock-and-resuscitation-via-rna-sequencing-in-a-rat-model
#11
Lin Lin, Zhengfei Yang, Guanghui Zheng, Yongxun Zhuansun, Yue Wang, Jianguo Li, Rui Chen, Wanchun Tang
BACKGROUND: Ischemia-reperfusion injury has been proven to induce organ dysfunction and death, although the mechanism is not fully understood. Long non-coding RNAs (lncRNAs) have drawn wide attention with their important roles in the gene expression of some biological processes and diseases, including myocardial ischemia-reperfusion (I/R) injury. In this paper, a total of 26 Sprague-Dawley (SD) rats were randomized into two groups: sham and ischemia-reperfusion (I/R) injury. Hemorrhagic shock was induced by removing 45% of the estimated total blood volume followed by reinfusion of shed blood...
November 1, 2018: BMC Molecular Biology
https://read.qxmd.com/read/30068312/coincidence-cloning-recovery-of-brucella-melitensis-rna-from-goat-tissues-advancing-the-in-vivo-analysis-of-pathogen-gene-expression-in-brucellosis
#12
Paola M Boggiatto, Daniel Fitzsimmons, Darrell O Bayles, David Alt, Catherine E Vrentas, Steven C Olsen
BACKGROUND: Brucella melitensis bacteria cause persistent, intracellular infections in small ruminants as well as in humans, leading to significant morbidity and economic loss worldwide. The majority of experiments on the transcriptional responses of Brucella to conditions inside the host have been performed following invasion of cultured mammalian cells, and do not address gene expression patterns during long-term infection. RESULTS: Here, we examine the application of the previously developed coincidence cloning methodology to recover and characterize B...
August 1, 2018: BMC Molecular Biology
https://read.qxmd.com/read/30053800/positive-cofactor-4-pc4-contributes-to-the-regulation-of-replication-dependent-canonical-histone-gene-expression
#13
Aleksandra Brzek, Marlena Cichocka, Jakub Dolata, Wojciech Juzwa, Daniel Schümperli, Katarzyna Dorota Raczynska
BACKGROUND: Core canonical histones are required in the S phase of the cell cycle to pack newly synthetized DNA, therefore the expression of their genes is highly activated during DNA replication. In mammalian cells, this increment is achieved by both enhanced transcription and 3' end processing. In this paper, we described positive cofactor 4 (PC4) as a protein that contributes to the regulation of replication-dependent histone gene expression. RESULTS: We showed that PC4 influences RNA polymerase II recruitment to histone gene loci in a cell cycle-dependent manner...
July 27, 2018: BMC Molecular Biology
https://read.qxmd.com/read/29933763/evaluation-of-suitable-reference-genes-for-qrt-pcr-normalization-in-strawberry-fragaria-%C3%A3-ananassa-under-different-experimental-conditions
#14
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://read.qxmd.com/read/29921228/laser-capture-microdissection-for-transcriptomic-profiles-in-human-skin-biopsies
#15
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://read.qxmd.com/read/29879907/targeting-mir-9-in-gastric-cancer-cells-using-locked-nucleic-acid-oligonucleotides
#16
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://read.qxmd.com/read/29587652/quantitative-profiling-of-batf-family-proteins-junb-irf-hetero-trimers-using-spec-seq
#17
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://read.qxmd.com/read/29554889/ph-mediated-upregulation-of-aqp1-gene-expression-through-the-spi-b-transcription-factor
#18
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://read.qxmd.com/read/29540148/a-protocol-for-custom-crispr-cas9-donor-vector-construction-to-truncate-genes-in-mammalian-cells-using-pcdna3-backbone
#19
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://read.qxmd.com/read/29534701/recommendations-for-mrna-analysis-of-micro-dissected-glomerular-tufts-from-paraffin-embedded-human-kidney-biopsy-samples
#20
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
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