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BMC Molecular Biology

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https://www.readbyqxmd.com/read/28298204/immunoglobulin-t-from-sea-bass-dicentrarchus-labrax-l-molecular-characterization-tissue-localization-and-expression-after-nodavirus-infection
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/28081716/heterogeneous-pattern-of-dna-methylation-in-developmentally-important-genes-correlates-with-its-chromatin-conformation
#8
Puja Sinha, Kiran Singh, Manisha Sachan
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. The aim of the present study is to investigate the establishment of chromatin marks (active or repressive) in relation to heterogeneous methylation in the promoter regions of these developmentally important genes...
January 11, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/27938330/novel-insight-into-the-composition-of-human-single-stranded-dna-binding-protein-1-hssb1-containing-protein-complexes
#9
Nicholas W Ashton, Dorothy Loo, Nicolas Paquet, Kenneth J O'Byrne, Derek J Richard
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. RESULTS: In this work, hSSB1 was immunoprecipitated from cell lysate samples that had been enriched for non-soluble nuclear proteins and those associating with hSSB1 identified by mass spectrometry...
December 9, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/27923366/3c-digital-pcr-for-quantification-of-chromatin-interactions
#10
Meijun Du, Liang Wang
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. In addition, qPCR is often limited to a certain cycle number, making it difficult to detect fragment ligations with low frequency...
December 6, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/27814680/ataxia-telangiectasia-mutated-atm-interacts-with-p400-atpase-for-an-efficient-dna-damage-response
#11
Rebecca J Smith, Matthew S Savoian, Lauren E Weber, Jeong Hyeon Park
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...
November 4, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/27090781/mice-lacking-micrornas-in-pax8-expressing-cells-develop-hypothyroidism-and-end-stage-renal-failure
#12
Malte P Bartram, Elena Amendola, Thomas Benzing, Bernhard Schermer, Gabriella de Vita, Roman-Ulrich Müller
BACKGROUND: Non-coding RNAs have gained increasing attention during the last decade. The first large group of non-coding RNAs to be characterized systematically starting at the beginning of the 21st century were small oligonucleotides--the so-called microRNAs (miRNAs). By now we have learnt that microRNAs are indispensable for most biological processes including organogenesis and maintenance of organ structure and function. The role of microRNAs has been studied extensively in the development of a number of organs, so far most studies focussed on e...
April 18, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/27074708/signal-transducer-and-activator-of-transcription-stat5-is-recruited-to-c-myc-super-enhancer
#13
Sophia Pinz, Samy Unser, Anne Rascle
BACKGROUND: c-Myc has been proposed as a putative target gene of signal transducer and activator of transcription 5 (STAT5). No functional STAT5 binding site has been identified so far within the c-Myc gene locus, therefore a direct transcriptional regulation by STAT5 remains uncertain. c-Myc super-enhancer, located 1.7 Mb downstream of the c-Myc gene locus, was recently reported as essential for the regulation of c-Myc gene expression by hematopoietic transcription factors and bromodomain and extra-terminal (BET) proteins and for leukemia maintenance...
April 14, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/27038923/immunoblot-screening-of-crispr-cas9-mediated-gene-knockouts-without-selection
#14
Jason A Estep, Erin L Sternburg, Gissell A Sanchez, Fedor V Karginov
BACKGROUND: Targeted genomic editing using the CRISPR/Cas9 methodology has opened exciting new avenues in probing gene function in virtually any model system, including cultured mammalian cells. Depending on the desired mutation, several experimental options exist in the isolation of clonal lines, such as selection with introduced markers, or screening by PCR amplification of genomic DNA. However, streamlined approaches to establishing deletion and tagging mutants with minimal genomic perturbation are of interest in applying this methodology...
April 2, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/26979160/a-reliable-method-for-quantification-of-splice-variants-using-rt-qpcr
#15
Julia Camacho Londoño, Stephan E Philipp
BACKGROUND: The majority of protein isoforms arise from alternative splicing of the encoding primary RNA transcripts. To understand the significance of single splicing events, reliable techniques are needed to determine their incidence. However, existing methods are labour-intensive, error-prone or of limited use. RESULTS: Here, we present an improved method to determine the relative incidence of transcripts that arise from alternative splicing at a single site...
March 15, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/26944950/gene-expression-profiling-of-the-venom-gland-from-the-venezuelan-mapanare-bothrops-colombiensis-using-expressed-sequence-tags-ests
#16
Montamas Suntravat, Néstor L Uzcategui, Chairat Atphaisit, Thomas J Helmke, Sara E Lucena, Elda E Sánchez, Alexis Rodríguez Acosta
BACKGROUND: Bothrops colombiensis is a highly dangerous pit viper and responsible for over 70% of snakebites in Venezuela. Although the composition in B. colombiensis venom has been identified using a proteome analysis, the venom gland transcriptome is currently lacking. RESULTS: We constructed a cDNA library from the venom gland of B. colombiensis, and a set of 729 high quality expressed sequence tags (ESTs) was identified. A total number of 344 ESTs (47.2% of total ESTs) was related to toxins...
March 5, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/26935744/knockdown-of-sall4-inhibits-the-proliferation-and-reverses-the-resistance-of-mcf-7-adr-cells-to-doxorubicin-hydrochloride
#17
Yuan-Yuan Chen, Zhi-Zhen Li, Yuan-Yuan Ye, Feng Xu, Rui-Jie Niu, Hong-Chen Zhang, Yi-Jian Zhang, Ying-Bin Liu, Bao-San Han
BACKGROUND: Breast cancer is the most frequent malignancy in women and drug resistance is the major obstacle for its successful chemotherapy. In the present study, we analyzed the involvement of an oncofetal gene, sal-like 4 (SALL4), in the tumor proliferation and drug resistance of human breast cancer. RESULTS: Our study showed that SALL4 was up-regulated in the drug resistant breast cancer cell line, MCF-7/ADR, compared to the other five cell lines. We established the lentiviral system expressing short hairpin RNA to knockdown SALL4 in MCF-7/ADR cells...
March 2, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/26860190/what-is-normal-next-generation-sequencing-driven-analysis-of-the-human-circulating-mirnaome
#18
D P Tonge, T W Gant
BACKGROUND: MicroRNAs (miRNAs) are short non-protein-coding RNA species that have a regulatory function in modulating protein translation and degradation of specific mRNAs. MicroRNAs are estimated to target approximately 60% of all human mRNAs and are associated with the regulation of all physiological processes. Similar to many messenger RNAs (mRNA), miRNAs exhibit marked tissue specificity, and appear to be dysregulated in response to specific pathological conditions. Perhaps, one of the most significant findings is that miRNAs are detectable in various biological fluids and are stable during routine clinical processing, paving the way for their use as novel biomarkers...
February 9, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/26860083/tlk1b-mediated-phosphorylation-of-rad9-regulates-its-nuclear-cytoplasmic-localization-and-cell-cycle-checkpoint
#19
Sanket Awate, Arrigo De Benedetti
BACKGROUND: The Tousled like kinase 1B (TLK1B) is critical for DNA repair and survival of cells. Upon DNA damage, Chk1 phosphorylates TLK1B at S457 leading to its transient inhibition. Once TLK1B regains its kinase activity it phosphorylates Rad9 at S328. In this work we investigated the significance of this mechanism by overexpressing mutant TLK1B in which the inhibitory phosphorylation site was eliminated. RESULTS AND DISCUSSION: These cells expressing TLK1B resistant to DNA damage showed constitutive phosphorylation of Rad9 S328 that occurred even in the presence of hydroxyurea (HU), and this resulted in a delayed checkpoint recovery...
February 9, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/26733090/structural-and-functional-analysis-of-four-non-coding-y-rnas-from-chinese-hamster-cells-identification-molecular-dynamics-simulations-and-dna-replication-initiation-assays
#20
Quirino Alves de Lima Neto, Francisco Ferreira Duarte Junior, Paulo Sérgio Alves Bueno, Flavio Augusto Vicente Seixas, Madzia Pauline Kowalski, Eyemen Kheir, Torsten Krude, Maria Aparecida Fernandez
BACKGROUND: The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no information is available about Y RNAs in Chinese hamster cells, which have already been used to detect replication origins and alternative DNA structures around these sites. Here, we report the gene sequences and predicted structural characteristics of the Chinese hamster Y RNAs, and analyze their ability to support the initiation of chromosomal DNA replication in vitro...
January 5, 2016: BMC Molecular Biology
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