819 results match your criteria BMC Molecular Biology [Journal]


MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.

BMC Mol Biol 2019 Mar 18;20(1). Epub 2019 Mar 18.

Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China.

Background: Myocyte enhancer factor 2A (MEF2A) plays an important role in cell proliferation, differentiation and survival. Functional deletion or mutation in MEF2A predisposes individuals to cardiovascular disease mainly caused by vascular endothelial dysfunction. However, the effect of the inhibition of MEF2A expression on human coronary artery endothelial cells (HCAECs) is unclear. Read More

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http://dx.doi.org/10.1186/s12867-019-0125-zDOI Listing

Transcriptomic responses to grazing reveal the metabolic pathway leading to the biosynthesis of domoic acid and highlight different defense strategies in diatoms.

BMC Mol Biol 2019 Feb 26;20(1). Epub 2019 Feb 26.

Natural History Museum of Denmark, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen K, Denmark.

Background: A major cause of phytoplankton mortality is predation by zooplankton. Strategies to avoid grazers have probably played a major role in the evolution of phytoplankton and impacted bloom dynamics and trophic energy transport. Certain species of the genus Pseudo-nitzschia produce the neurotoxin, domoic acid (DA), as a response to the presence of copepod grazers, suggesting that DA is a defense compound. Read More

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http://dx.doi.org/10.1186/s12867-019-0124-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390554PMC
February 2019

RNA sequencing, selection of reference genes and demonstration of feeding RNAi in Thrips tabaci (Lind.) (Thysanoptera: Thripidae).

BMC Mol Biol 2019 02 18;20(1). Epub 2019 Feb 18.

Department of Entomology, University of Kentucky, Lexington, KY, USA.

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. Read More

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http://dx.doi.org/10.1186/s12867-019-0123-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380046PMC
February 2019

A fragment activity assay reveals the key residues of TBC1D15 GTPase-activating protein (GAP) in Chiloscyllium plagiosum.

BMC Mol Biol 2019 02 12;20(1). Epub 2019 Feb 12.

Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.

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). Read More

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http://dx.doi.org/10.1186/s12867-019-0122-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373008PMC
February 2019
1 Read

HexA is required for growth, aflatoxin biosynthesis and virulence in Aspergillus flavus.

BMC Mol Biol 2019 02 11;20(1). Epub 2019 Feb 11.

Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

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. Read More

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http://dx.doi.org/10.1186/s12867-019-0121-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371581PMC
February 2019

Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing.

BMC Mol Biol 2019 01 15;20(1). Epub 2019 Jan 15.

College of Sports, Yantai University, Yantai, China.

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. Read More

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http://dx.doi.org/10.1186/s12867-019-0120-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334412PMC
January 2019
2 Reads

MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness.

BMC Mol Biol 2019 01 3;20(1). Epub 2019 Jan 3.

Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.

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. Read More

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https://bmcmolbiol.biomedcentral.com/articles/10.1186/s12867
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http://dx.doi.org/10.1186/s12867-018-0118-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317189PMC
January 2019
3 Reads

Graphene oxide down-regulates genes of the oxidative phosphorylation complexes in a glioblastoma.

BMC Mol Biol 2019 01 3;20(1). Epub 2019 Jan 3.

Department of Animal Nutrition and Biotechnology, Warsaw University of Life Sciences, 02-787, Warsaw, Poland.

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. Read More

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https://bmcmolbiol.biomedcentral.com/articles/10.1186/s12867
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http://dx.doi.org/10.1186/s12867-018-0119-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317254PMC
January 2019
9 Reads

The Dictyostelium discoideum homologue of Twinkle, Twm1, is a mitochondrial DNA helicase, an active primase and promotes mitochondrial DNA replication.

BMC Mol Biol 2018 12 19;19(1):12. Epub 2018 Dec 19.

Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia.

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. Read More

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https://bmcmolbiol.biomedcentral.com/articles/10.1186/s12867
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http://dx.doi.org/10.1186/s12867-018-0114-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299598PMC
December 2018
3 Reads

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.

BMC Mol Biol 2018 12 4;19(1):15. Epub 2018 Dec 4.

Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Kuala Lumpur, Malaysia.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0116-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278157PMC
December 2018
2 Reads

Molecular analysis of NPAS3 functional domains and variants.

BMC Mol Biol 2018 12 3;19(1):14. Epub 2018 Dec 3.

Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.

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. Read More

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https://bmcmolbiol.biomedcentral.com/articles/10.1186/s12867
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http://dx.doi.org/10.1186/s12867-018-0117-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276216PMC
December 2018
12 Reads

Integration of transcriptome and proteome profiles in glioblastoma: looking for the missing link.

BMC Mol Biol 2018 11 21;19(1):13. Epub 2018 Nov 21.

Department of Neurosurgery, CHU Angers, University Hospital of Angers, 4, Rue Larrey, 49933, Angers Cedex 09, France.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0115-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249855PMC
November 2018
7 Reads

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.

BMC Mol Biol 2018 11 1;19(1):11. Epub 2018 Nov 1.

Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yan Jiang Xi Road, Guangzhou, 510120, China.

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. Read More

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https://bmcmolbiol.biomedcentral.com/articles/10.1186/s12867
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http://dx.doi.org/10.1186/s12867-018-0113-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211518PMC
November 2018
11 Reads

Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis.

BMC Mol Biol 2018 08 1;19(1):10. Epub 2018 Aug 1.

Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, IA, 50010, USA.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0111-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6071331PMC
August 2018
9 Reads
2.194 Impact Factor

Positive cofactor 4 (PC4) contributes to the regulation of replication-dependent canonical histone gene expression.

BMC Mol Biol 2018 07 27;19(1). Epub 2018 Jul 27.

Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Wieniawskiego 1, 61-712, Poznan, Poland.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0110-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062981PMC
July 2018
2 Reads

Evaluation of suitable reference genes for qRT-PCR normalization in strawberry (Fragaria × ananassa) under different experimental conditions.

BMC Mol Biol 2018 06 22;19(1). Epub 2018 Jun 22.

College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0109-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013875PMC
June 2018
11 Reads

Laser capture microdissection for transcriptomic profiles in human skin biopsies.

BMC Mol Biol 2018 06 19;19(1). Epub 2018 Jun 19.

Laboratory of Genetics of Complex Disorders and Department of Neurology, IRCCS Policlinico San Donato, Milan, Italy.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0108-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009967PMC
June 2018
12 Reads

Targeting miR-9 in gastric cancer cells using locked nucleic acid oligonucleotides.

BMC Mol Biol 2018 06 7;19(1). Epub 2018 Jun 7.

Department of Chemical Engineering, LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0107-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992815PMC
June 2018
4 Reads

Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq.

BMC Mol Biol 2018 03 27;19(1). Epub 2018 Mar 27.

Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0106-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869772PMC
March 2018
5 Reads

pH-mediated upregulation of AQP1 gene expression through the Spi-B transcription factor.

BMC Mol Biol 2018 03 20;19(1). Epub 2018 Mar 20.

Department of Nephrology and Rheumatology, Children's Hospital of Fudan University, No. 399 Wanyuan Road, Shanghai, 201102, China.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0104-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859780PMC
March 2018
8 Reads
2.190 Impact Factor

A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone.

BMC Mol Biol 2018 03 14;19(1). Epub 2018 Mar 14.

Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX, 78539, USA.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0105-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5853148PMC
March 2018
20 Reads

Recommendations for mRNA analysis of micro-dissected glomerular tufts from paraffin-embedded human kidney biopsy samples.

BMC Mol Biol 2018 03 13;19(1). Epub 2018 Mar 13.

Department of Nephropathology, Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstraße 8-10, 91054, Erlangen, Germany.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0103-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850911PMC
March 2018
10 Reads

Nutrient depletion and TOR inhibition induce 18S and 25S ribosomal RNAs resistant to a 5'-phosphate-dependent exonuclease in Candida albicans and other yeasts.

BMC Mol Biol 2018 01 19;19(1). Epub 2018 Jan 19.

Research Division, Greater Los Angeles VA Healthcare System, Los Angeles, CA, USA.

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. Read More

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http://dx.doi.org/10.1186/s12867-018-0102-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775620PMC
January 2018
6 Reads

An optimized rapid bisulfite conversion method with high recovery of cell-free DNA.

BMC Mol Biol 2017 Dec 19;18(1):24. Epub 2017 Dec 19.

Department of Forensic medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, China.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0101-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5735811PMC
December 2017
10 Reads

Sumoylation in p27kip1 via RanBP2 promotes cancer cell growth in cholangiocarcinoma cell line QBC939.

BMC Mol Biol 2017 09 7;18(1):23. Epub 2017 Sep 7.

Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, People's Republic of China.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0100-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590128PMC
September 2017
28 Reads

An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing.

BMC Mol Biol 2017 08 23;18(1):22. Epub 2017 Aug 23.

Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Winterthurerstr. 260, 8057, Zurich, Switzerland.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0099-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569520PMC
August 2017
20 Reads

Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries.

BMC Mol Biol 2017 08 9;18(1):21. Epub 2017 Aug 9.

Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0098-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5550992PMC
August 2017
10 Reads

Interaction between NFATc2 and the transcription factor Sp1 in pancreatic carcinoma cells PaTu 8988t.

BMC Mol Biol 2017 08 3;18(1):20. Epub 2017 Aug 3.

Department of Obstetrics and Gynecology, University Hospital Mainz, Mainz, Germany.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0097-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543739PMC
August 2017
6 Reads

Splicing arrays reveal novel RBM10 targets, including SMN2 pre-mRNA.

BMC Mol Biol 2017 07 20;18(1):19. Epub 2017 Jul 20.

Département de Microbiologie et d'infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.

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. Read More

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http://bmcmolbiol.biomedcentral.com/articles/10.1186/s12867-
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http://dx.doi.org/10.1186/s12867-017-0096-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5520337PMC
July 2017
26 Reads

Growth arrest specific gene 2 in tilapia (Oreochromis niloticus): molecular characterization and functional analysis under low-temperature stress.

BMC Mol Biol 2017 07 17;18(1):18. Epub 2017 Jul 17.

Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0095-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5514492PMC
July 2017
28 Reads

Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands.

BMC Mol Biol 2017 06 27;18(1):17. Epub 2017 Jun 27.

School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0094-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5488298PMC
June 2017
21 Reads

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals.

BMC Mol Biol 2017 06 17;18(1):16. Epub 2017 Jun 17.

Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333, Munich, Germany.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0093-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474008PMC
June 2017
9 Reads

Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis.

BMC Mol Biol 2017 06 6;18(1):15. Epub 2017 Jun 6.

Department of Anatomy and Neurobiology, The Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, Jiangsu, People's Republic of China.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0091-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461768PMC
June 2017
13 Reads

Early growth response protein 1 regulates promoter activity of α-plasma membrane calcium ATPase 2, a major calcium pump in the brain and auditory system.

BMC Mol Biol 2017 05 22;18(1):14. Epub 2017 May 22.

Department of Pharmacology, School of Medicine, University of Washington, Seattle, WA, 98195, USA.

Background: Along with sodium/calcium (Ca) exchangers, plasma membrane Ca ATPases (ATP2Bs) are main regulators of intracellular Ca levels. There are four ATP2B paralogs encoded by four different genes. Atp2b2 encodes the protein pump with the fastest activation, ATP2B2. Read More

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http://dx.doi.org/10.1186/s12867-017-0092-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441030PMC
May 2017
25 Reads

hSSB1 associates with and promotes stability of the BLM helicase.

BMC Mol Biol 2017 05 15;18(1):13. Epub 2017 May 15.

School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0090-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5433028PMC
May 2017
11 Reads

Selective measurement of α smooth muscle actin: why β-actin can not be used as a housekeeping gene when tissue fibrosis occurs.

BMC Mol Biol 2017 04 27;18(1):12. Epub 2017 Apr 27.

MTA-SE Pediatrics and Nephrology Research Group, Budapest, Hungary.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0089-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408491PMC
April 2017
23 Reads

Erratum to: RUNX1 induces DNA replication independent active DNA demethylation at SPI1 regulatory regions.

BMC Mol Biol 2017 04 21;18(1):11. Epub 2017 Apr 21.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1186/s12867-017-0088-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5399531PMC
April 2017
10 Reads

Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells.

BMC Mol Biol 2017 04 5;18(1):10. Epub 2017 Apr 5.

Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China.

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 (HO). Read More

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http://bmcmolbiol.biomedcentral.com/articles/10.1186/s12867-
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http://dx.doi.org/10.1186/s12867-017-0086-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381023PMC
April 2017
13 Reads

RUNX1 induces DNA replication independent active DNA demethylation at SPI1 regulatory regions.

BMC Mol Biol 2017 04 4;18(1). Epub 2017 Apr 4.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0087-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381148PMC
April 2017
12 Reads

Immunoglobulin T from sea bass (Dicentrarchus labrax L.): molecular characterization, tissue localization and expression after nodavirus infection.

BMC Mol Biol 2017 03 15;18(1). Epub 2017 Mar 15.

Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100, Viterbo, VT, Italy.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0085-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5353873PMC
March 2017
10 Reads

Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

BMC Mol Biol 2017 03 9;18(1). Epub 2017 Mar 9.

Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0083-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345256PMC
March 2017
8 Reads

Properties of STAT1 and IRF1 enhancers and the influence of SNPs.

BMC Mol Biol 2017 03 9;18(1). Epub 2017 Mar 9.

Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0084-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343312PMC
March 2017
19 Reads

Identification of microRNAs and their response to the stress of plant allelochemicals in Aphis gossypii (Hemiptera: Aphididae).

BMC Mol Biol 2017 02 16;18(1). Epub 2017 Feb 16.

China Agricultural University, Beijing, China.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0080-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311835PMC
February 2017
12 Reads

Binding affinity of five PBPs to Ostrinia sex pheromones.

BMC Mol Biol 2017 02 7;18(1). Epub 2017 Feb 7.

State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing, 100193, China.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0079-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5296967PMC
February 2017
8 Reads

Positive selection and functional divergence of farnesyl pyrophosphate synthase genes in plants.

BMC Mol Biol 2017 02 4;18(1). Epub 2017 Feb 4.

Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, Guangxi Medical University, Nanning, Guangxi, People's Republic of China.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0081-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5292144PMC
February 2017
9 Reads

Transcriptional regulation of human sperm-associated antigen 16 gene by S-SOX5.

BMC Mol Biol 2017 01 31;18(1). Epub 2017 Jan 31.

Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, 23298, USA.

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. Read More

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http://dx.doi.org/10.1186/s12867-017-0082-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282894PMC
January 2017
13 Reads

Heterogeneous pattern of DNA methylation in developmentally important genes correlates with its chromatin conformation.

BMC Mol Biol 2017 01 11;18(1). Epub 2017 Jan 11.

Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004, India.

Background: DNA methylation is a major epigenetic modification, playing a crucial role in the development and differentiation of higher organisms. DNA methylation is also known to regulate transcription by gene repression. Various developmental genes such as c-mos, HoxB5, Sox11, and Sry show tissue-specific gene expression that was shown to be regulated by promoter DNA methylation. Read More

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http://dx.doi.org/10.1186/s12867-016-0078-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234095PMC
January 2017
7 Reads

Novel insight into the composition of human single-stranded DNA-binding protein 1 (hSSB1)-containing protein complexes.

BMC Mol Biol 2016 12 9;17(1):24. Epub 2016 Dec 9.

School of Biomedical Research, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.

Background: Single-stranded DNA-binding proteins are essential cellular components required for the protection, metabolism and processing of single-stranded DNA. Human single-stranded DNA-binding protein 1 (hSSB1) is one such protein, with described roles in genome stability maintenance and transcriptional regulation. As yet, however, the mechanisms through which hSSB1 functions and the binding partners with which it interacts remain poorly understood. Read More

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http://dx.doi.org/10.1186/s12867-016-0077-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5148904PMC
December 2016
7 Reads

3C-digital PCR for quantification of chromatin interactions.

BMC Mol Biol 2016 12 6;17(1):23. Epub 2016 Dec 6.

Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.

Background: Chromosome conformation capture (3C) is a powerful and widely used technique for detecting the physical interactions between chromatin regions in vivo. The principle of 3C is to convert physical chromatin interactions into specific DNA ligation products, which are then detected by quantitative polymerase chain reaction (qPCR). However, 3C-qPCR assays are often complicated by the necessity of normalization controls to correct for amplification biases. Read More

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http://dx.doi.org/10.1186/s12867-016-0076-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5139078PMC
December 2016
13 Reads

Ataxia telangiectasia mutated (ATM) interacts with p400 ATPase for an efficient DNA damage response.

BMC Mol Biol 2016 11 4;17(1):22. Epub 2016 Nov 4.

Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

Background: Ataxia telangiectasia mutated (ATM) and TRRAP proteins belong to the phosphatidylinositol 3-kinase-related kinase family and are involved in DNA damage repair and chromatin remodeling. ATM is a checkpoint kinase that is recruited to sites of DNA double-strand breaks where it phosphorylates a diverse range of proteins that are part of the chromatin and DNA repair machinery. As an integral subunit of the TRRAP-TIP60 complexes, p400 ATPase is a chromatin remodeler that is also targeted to DNA double-strand break sites. Read More

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http://dx.doi.org/10.1186/s12867-016-0075-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097431PMC
November 2016
14 Reads