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Identification of an exonic splicing silencer in exon 6A of the human VEGF geneEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: This work establishes the identity of cis sequences that regulate alternative VEGFsplicing and dictate the relative expression levels of VEGF isoforms. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - November 17, 2009 Category: Molecular Biology Authors: Rui WangRonald CrystalNeil Hackett Source Type: journals

The sterol carrier protein 2/3-oxoacyl-CoA thiolase (SCPx) is involved in cholesterol uptake in the midgut of Spodoptera litura: gene cloning, expression, localization and functional analysesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Spatial and temporal expression pattern of this SlSCPx gene during the larval developmental stages of S. litura showed its specific association with the midgut at the feeding stage. Over-expression of this gene increased cholesterol uptake and interference of its transcript decreased cholesterol uptake and delayed the larval to pupal metamorphosis. All of these results taken together suggest that this midgut-specific SlSCPx gene is important for cholesterol uptake and normal development in S. litura. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - November 13, 2009 Category: Molecular Biology Authors: Xing-Rong GuoSi-Chun ZhengLin LiuQi-Li Feng Source Type: journals

Functional characterization of two CITED3 homologs (gcCITED3a and gcCITED3b) in the hypoxia-tolerant grass carp, Ctenopharyngodon idellaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The grass carp gcCITED3a and gcCITED3b genes are differentially expressed and regulated in different fish organs in response to hypoxic stress. This is the first report demonstrating in vivo regulation of two closely-related CITED3 isogenes by HIF-1, as well as CITED3 regulation of HIF-1 transcriptional activity in fish. Overall, our findings suggest that unique molecular mechanisms operate through these two gcCITED3 isoforms that likely play an important regulatory role in the hypoxic response in the grass carp. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - November 3, 2009 Category: Molecular Biology Authors: Patrick NgSung-Kay ChiuTheresa KwongRichard YuMinnie WongRichard Kong Source Type: journals

Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: In this work, we provided a set of genes that are suitable reference genes for quantitative gene expression analysis by real-time RT-PCR in yeast biological samples covering a large panel of physiological states. In contrast, we invalidated and discourage the use of ACT1 as well as other commonly used reference genes (PDA1, TDH3, RDN18, etc) as internal controls for quantitative gene expression analysis in yeast. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - October 30, 2009 Category: Molecular Biology Authors: Marie-Ange TesteManon DuquenneJean FrancoisJean-Luc Parrou Source Type: journals

RAD51 paralogs promote homology-directed repair at diversifying immunoglobulin V regionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: These results demonstrate direct functions of RAD51D and XRCC2 in immunoglobulin gene conversion, and also suggest that modulation of levels of repair factors may be a useful strategy to promote gene correction in other cell types. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - October 28, 2009 Category: Molecular Biology Authors: Ellen OrdinarioMunehisa YabukiPriya HandaW. Jason CummingsNancy Maizels Source Type: journals

Dual effect of a single nucleotide polymorphism in the first intron of the porcine Secreted phosphoprotein 1 gene: allele-specific binding of C/EBP beta and activation of aberrant splicingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: At the 3' terminal end of the first intron of the porcine SPP1 we identified a unique, dually functional SNP g.3836A>G. This SNP affects the function of the SPP1 gene at the DNA level by affecting a C/EBP beta binding site and at the RNA level by activating aberrant splicing of the first intron, and thus represents an interesting DNA-marker to study phenotypic effects of SPP1 DNA-variation. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - October 20, 2009 Category: Molecular Biology Authors: Eduard MuraniSiriluck PonsuksiliHans-Martin SeyfertXuanming ShiKlaus Wimmers Source Type: journals

Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCREmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: None of the candidate reference genes was uniformly expressed across all experimental conditions, and the most suitable reference genes are conditional-, tissue-specific-, developmental-, and cultivar-dependent. Most of the new reference genes performed better than the conventional housekeeping genes. These results should guide the selection of reference genes for gene expression studies in soybean. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - September 27, 2009 Category: Molecular Biology Authors: Ruibo HuChengming FanHongyu LiQingzhu ZhangYong-Fu Fu Source Type: journals

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promotersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The number of regulatory sites may thus act as a versatility-producing device, in addition to serving as a source of robustness of the transcription machinery. Furthermore, our results show that the effects of TF concentration fluctuations on promoter occupancy are constrained by RNAP concentrations. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - September 21, 2009 Category: Molecular Biology Authors: Abel Gonzalez PerezVladimir Espinosa AngaricaJulio Collado-VidesAna Vasconcelos Source Type: journals

Quadruple 9-mer-based protein binding microarray with DsRed fusion proteinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our method demonstrated PBM can be conveniently performed by adopting: (1) quadruple 9-mers may increase protein-DNA binding interactions in the microarray, and (2) a one-step incubation shortens the wash and hybridization steps. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - September 17, 2009 Category: Molecular Biology Authors: Min-Jeong KimTae-Ho LeeYoon-Mok PahkYul-Ho KimHyang-Mi ParkYang Do ChoiBaek Hie NahmYeon-Ki Kim Source Type: journals

Characterization of bovine miRNAs by sequencing and bioinformatics analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The miRNA expression patterns among 11 tissues from beef cattle revealed that most miRNAs were ubiquitously expressed in all tissues, while only a few miRNAs were tissue specific. Only 60% miRNAs in this study were found to display strand bias, suggesting that there are some key factors for mature miRNA selection other than internal stability. Most bovine miRNAs are highly conserved in other three mammalian species, indicating that these miRNAs may have a role in different species that are potential molecular markers for evolution. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - September 15, 2009 Category: Molecular Biology Authors: Weiwu JinJason GrantPaul StothardStephen MooreLe Luo Guan Source Type: journals

Promoter analysis of the rabbit POU5F1 gene and its expression in preimplantation stage embryosEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: In this study we provide a comparative sequence analysis of the regulatory region of rabbit POU5F1 gene. Our data suggest that the POU5F1 gene is strictly regulated during early mammalian development. We proposed that the well conserved CR4 region containing the DE-2A enhancer is responsible for the highly conserved ESC specific gene expression. Notably, we are the first to report that the rabbit POU5F1 is not restricted to ICM cells only, but it is expressed in trophoblast cells as well. This information may be well applicable to investigate further the possible phylogenetic role and the regulation of POU5F1 ...
Source: BMC Molecular Biology - Latest articles - September 3, 2009 Category: Molecular Biology Authors: Julianna KobolakKatalin KissZsuzsanna PolgarSolomon MamoClaire Rogel-GaillardZsuzsanna TancosIstvan BockArpad BajiKrisztina TarMelinda PirityAndras Dinnyes Source Type: journals

Multigene expression of protein complexes by iterative modification of genomic Bacmid DNAEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: 1. Use of bipartite selections can significantly improve selection of modified bacterial artificial chromosomes carrying baculovirus DNA. Furthermore this approach is sufficiently robust to allow routine modification of the virus genome. 2. In addition to the commonly used p10 and polyhedrin loci, the ctx, egt, 39k, orf51, gp37, iap2 and odv-e56 loci in AcMNPV are all suitable for the high level expression of heterologous genes. 3. Two protein, four protein and eight protein complexes including virus-like particles and cellular chaperone complexes can be produced using the new approach. (Source: BMC Molecular ...
Source: BMC Molecular Biology - Latest articles - September 1, 2009 Category: Molecular Biology Authors: Rob NoadMeredith StewartMark BoyceCristina CelmaKeith WillisonPolly Roy Source Type: journals

Molecular analysis of Ku redox regulationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Together, these results suggest that the C-terminal domain and C493 of Ku80 play at most a minor role in the redox regulation of Ku, and that other cysteines are likely involved, either alone or in conjunction with these regions of Ku80. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - August 27, 2009 Category: Molecular Biology Authors: Sara BennettTracy NeherAndrea ShatillaJohn Turchi Source Type: journals

YY1 is autoregulated through its own DNA-binding sitesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Taken together, the transcriptional level of YY1 is self-regulated through its internal DNA-binding sites. This study identifies YY1 as the first known autoregulating transcription factor in mammalian genomes. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - August 26, 2009 Category: Molecular Biology Authors: Jeong Do KimSungryul YuJoomyeong Kim Source Type: journals

Loss of the insulator protein CTCF during nematode evolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our findings show that CTCF and possibly chromatin insulation are present in basal nematodes. We suggest that the insulator protein CTCF has been secondarily lost in derived nematodes like C. elegans. We propose a switch in the regulation of gene expression during nematode evolution, from the common vertebrate and insect type involving distantly acting regulatory elements and chromatin insulation to a so far poorly characterised mode present in more derived nematodes. Here, all or some of these components are missing. Instead operons, polycistronic transcriptional units common in derived nematodes, seemingly a...
Source: BMC Molecular Biology - Latest articles - August 26, 2009 Category: Molecular Biology Authors: Peter HegerBirger MarinEinhard Schierenberg Source Type: journals

Selection of reference genes for expression studies with fish myogenic cell culturesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The geometric average of any three of Hprt1, Ef1alpha, Ppia and RNApolII is suitable for normalisation of gene expression data in primary myogenic cultures from Atlantic salmon. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - August 9, 2009 Category: Molecular Biology Authors: Neil BowerIan Johnston Source Type: journals

Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: It was possible to improve purity of isolated RNA by modifying protocol procedures. Further improvements, both in RNA purity and experimental cost, were achieved by using a new extraction solution, PGTX. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - August 6, 2009 Category: Molecular Biology Authors: Fernando Lopes PintoAnders ThapperWolfgang SontheimPeter Lindblad Source Type: journals

Reference gene selection for head and neck squamous cell carcinoma gene expression studiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present the first study that defines the suitability of 12 reference genes commonly used in cancer studies (ACT, ALAS, B2M, GAPDH, HMBS, HPRT, KALPHA, RPS18, RPL27, RPS29, SHAD and TBP) for the normalization of quantitative expression data in the field of head and neck squamous cell carcinoma (HNSCC). Results: Raw expression levels were measured by RT-qPCR in HNSCC and normal matched mucosa of 46 patients. We analyzed the expression stability using geNorm and NormFinder and compared the expression levels between subgroups. In HNSCC and/or normal mucosa, the four best normalization genes were ALAS, GAPDH, RPS18 and SHAD ...
Source: BMC Molecular Biology - Latest articles - August 2, 2009 Category: Molecular Biology Authors: Benjamin LallemantAlexandre EvrardChristophe CombescureHeliette ChapuisGuillaume ChambonCaroline RaynalChristophe ReynaudOmar SabraDominique JoubertFrederic HollandeJean-Gabriel LallemantSerge LumbrosoJean-Paul Brouillet Source Type: journals

Reference gene selection for head and neck squamous cell carcinoma gene expression studies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present the first study that defines the suitability of 12 housekeeping genes commonly used in cancer studies (ACT, ALAS, B2M, GAPDH, HMBS, HPRT, KALPHA, RPS18, RPL27, RPS29 , SHAD and TBP) for the normalization of quantitative expression data in the field of head and neck squamous cell carcinoma (HNSCC). Results: Raw expression levels were measured by RT-qPCR in HNSCC and normal matched mucosa of 46 patients. We analyzed the expression stabilities using geNorm and NormFinder and compared the expression levels between subgroups. In HNSCC and/or normal mucosa, the four best normalization genes were ALAS, GAPDH, RPS18 and...
Source: BMC Molecular Biology - Latest articles - August 2, 2009 Category: Molecular Biology Authors: Benjamin LallemantAlexandre EvrardChristophe CombescureHeliette ChapuisGuillaume ChambonCaroline RaynalChristophe ReynaudOmar SabraDominique JoubertFrederic HollandeJean-Gabriel LallemantSerge LumbrosoJean-Paul Brouillet Source Type: journals

Characterisation of urokinase plasminogen activator receptor variants in human airway and peripheral cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have identified multiple uPAR isoforms in the lung and immune cells and shown that expression is cell specific. These data provide a novel mechanism for uPAR regulation, as different exon splicing may determine uPAR function e.g. alternative E7b results in a soluble isoform due to the loss of the GPI anchor and exon deletions may affect uPA (ligand) and/or integrin binding and therefore influence downstream pathways. Expression of different isoforms within the lung should be taken into consideration in studies of uPAR in respiratory disease. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - July 27, 2009 Category: Molecular Biology Authors: Ceri StewartIan Sayers Source Type: journals

Selection of reference genes for normalisation of real-time RT-PCR in brain-stem death injury in Ovis ariesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Accurate normalisation is critical in obtaining reliable and reproducible results in gene expression studies. This study demonstrates tissue associated variability in the selection of these normalisation genes in BSD sheep and underlines the importance of selecting the correct reference genes for both the animal model and tissue studied. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - July 22, 2009 Category: Molecular Biology Authors: Margaret PassmoreMaria NataatmadjaJohn Fraser Source Type: journals

DNA binding by Corynebacterium glutamicum TetR-type transcription regulator AmtREmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Although the DNA binding domain of TetR-type repressors is highly conserved and a core binding motif was identified for AmtR and TetR(D), the AmtR binding domain shows individual properties compared to other TetR proteins. Besides by distinct amino acids of AmtR, DNA binding is influenced by nucleotides not only of the conserved binding motif but also by spacing nucleotides in C. glutamicum. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - July 22, 2009 Category: Molecular Biology Authors: Daniela MuhlNadja JeSZbergerKristin HasseltChristophe JardinHeinrich StichtAndreas Burkovski Source Type: journals

Selection of reliable reference genes for gene expression studies in peach using real-time PCREmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our study demonstrates that expression stability varied greatly between genes studied in peach. Based on the results from geNorm, NormFinder and BestKeeper analyses, for all the sample pools analyzed, TEF2, UBQ10 and RPII were found to be the most suitable reference genes with a very high statistical reliability, and TEF2 and RPII for the other sample series, while 18S rRNA, RPL13 and PLA2 were unsuitable as internal controls. GAPDH and ACT also performed poorly and were less stable in our analysis. To achieve accurate comparison of levels of gene expression, two or more reference genes must be used for data n...
Source: BMC Molecular Biology - Latest articles - July 19, 2009 Category: Molecular Biology Authors: Zhaoguo TongZhihong GaoFei WangJun ZhouZhen Zhang Source Type: journals

High quality RNA from multiple brain regions simultaneously acquired by laser capture microdissectionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Using this optimized method, we have consistently obtained RNA of high quality from all four simultaneously microdissected cell groups. RNA integrity numbers were all above 8, and long cDNA fragments (> 1.2 kb) were successfully amplified by reverse transcription PCR from all four samples. We conclude that RNAs isolated by this method are well suited for downstream quantitative PCR or microarray studies. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - July 5, 2009 Category: Molecular Biology Authors: Wei-Zhi WangFranziska OeschgerSheena LeeZoltan Molnar Source Type: journals

Cooperation between NRF-2 and YY-1 transcription factors is essential for triggering the expression of the PREPL-C2ORF34 bidirectional gene pairEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: This study provides new insights into the complex transcriptional mechanism of a mammalian head-to-head gene pair which requires cooperative binding of multiple transcription factors to a bidirectional minimal promoter of the shared intergenic region. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - July 2, 2009 Category: Molecular Biology Authors: Chien-Chang HuangWun-Shaing Chang Source Type: journals

Expression of HNF4alpha in the human and rat choroid plexus - Implications for drug transport across the blood-cerebrospinal-fluid (CSF) barrierEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our study evidences activity of HNF4alpha in human and rat choroid plexus. This transcription factor targets DMEs and drug transporters and may well determine availability of drugs at the blood-CSF barrier. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - July 2, 2009 Category: Molecular Biology Authors: Monika NiehofJuergen Borlak Source Type: journals

The vasa regulatory region mediates germline expression and maternal transmission of proteins in the malaria mosquito Anopheles gambiae: a versatile tool for genetic control strategiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: : We have characterized vasa regulatory regions that are not only suited to drive transgenes in the early germline of both sexes but could also be utilized to manipulate the zygotic genome of developing embryos via maternal deposition of active molecules. We have used computational models to show that a homing endonuclease-based gene drive system can function in the presence of maternal deposition and describe a novel non-invasive control strategy based on early vasa driven homing endonuclease expression. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - July 1, 2009 Category: Molecular Biology Authors: Philippos PapathanosNikolai WindbichlerMiriam MenichelliAustin BurtAndrea Crisanti Source Type: journals

Identification of valid reference genes during the differentiation of human myoblastsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: RNA expression analyses including three independent softwares revealed that RPLPO, TBP as reference genes or NF calculated by geNorm software, are suitable to normalize the mRNA expression in myoblast after culture under differentiation conditions. Significant correlations can be identified between the differentiations markers ACTA1, MYOG, MYH3 and creatine phosphokinase (CK) activity, when the expression is normalized with the NF calculated with RPLPO and TBP. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - July 1, 2009 Category: Molecular Biology Authors: Jens Stern-StraeterGabriel BonaterraKarl HormannRalf KinscherfUlrich Goessler Source Type: journals

Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This investigation provides a validated set of reference genes for studying A. ferrooxidans gene expression under typical biological conditions and an initial point of departure for exploring new experimental setups in this microorganism and eventually in other closely related Acidithiobacilli. The information could also be of value for future transcriptomic experiments in other bacterial systems. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - June 24, 2009 Category: Molecular Biology Authors: Pamela NietoPaulo CovarrubiasEugenia JedlickiDavid HolmesRaquel Quatrini Source Type: journals

Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The collection of B. amphitrite ESTs and their annotation has been made publically available representing an important resource for both basic and applied research on this species. We developed a qRT-PCR assay to determine the most reliable reference genes. Transcripts encoding cytochrome b and NADH dehydrogenase subunit 1 were expressed most stably, although other genes also performed well and could prove useful to normalize gene expression studies. In order to minimize sample variability, we recommend that future molecular genetic studies of B. amphitrite that utilise RNA should pay particular attention to t...
Source: BMC Molecular Biology - Latest articles - June 23, 2009 Category: Molecular Biology Authors: Tristano Bacchetti De GregorisMarco BorraElio BiffaliThomas BekelJ BurgessRichard KirbyAnthony Clare Source Type: journals

Elongation factor eEF1B modulates functions of the release factors eRF1 and eRF3 and the efficiency of translation termination in yeastEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The data obtained demonstrate involvement of the translation elongation factor eEF1B in modulating the functions of translation termination factors and suggest its possible role in GDP for GTP exchange on eRF3. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - June 21, 2009 Category: Molecular Biology Authors: Igor ValouevGleb FominovElizaveta SokolovaVladimir SmirnovMichael Ter-Avanesyan Source Type: journals

A strategy for enrichment of claudins based on their affinity to Clostridium perfringens enterotoxinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: CPE116-319 provides an efficient tool for single step enrichment of different claudins from cell lysates. Numerous proteins were shown to be co-enriched with the CPE-binding claudins, but there are no indications (except for claudins -1 and -5) for an association with tight junctions. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - June 21, 2009 Category: Molecular Biology Authors: Dorte LohrbergEberhard KrauseMichael SchumannJorg PiontekLars WinklerIngolf BlasigReiner Haseloff Source Type: journals

Identification, characterization and expression of novel Sex Hormone Binding Globulin alternative first exons in the human prostateEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The identification of multiple transcription start sites (TSS) upstream of the annotated first exon of human SHBG, and the detection of the alternative transcripts in human prostate, concur with the prediction of the ENCODE (ENCyclopedia of DNA Elements) project, and suggest that the regulation of SHBG is much more complex than previously reported. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - June 16, 2009 Category: Molecular Biology Authors: Tomas PinosAnna Barbosa-DesonglesAntoni HurtadoAlbert Santamaria-MartinezInes de TorresJoan MoroteJaume ReventosFrancina Munell Source Type: journals

Validation of housekeeping genes for quantitative real-time PCR in in-vivo and in-vitro models of cerebral ischaemiaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have validated endogenous control genes for qRT-PCR analysis of gene expression in in-vitro and in-vivo cerebral ischaemia models. For normalization purposes, Rpl13a and Sdha are found to be the most suitable genes for the in-vitro model and Sdha and Ywhaz for the in-vivo model. Genes previously used as housekeeping genes for the in-vivo model in the literature were not validated as good control genes in the present study, showing the need for careful evaluation for each new experimental setup. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - June 15, 2009 Category: Molecular Biology Authors: Carme GubernOlivia HurtadoRocio RodriguezJesus MoralesVictor RomeraMaria MoroIgnacio LizasoainJoaquin SerenaJudith Mallolas Source Type: journals

RNF168, a new RING finger, MIU-containing protein that modifies chromatin by ubiquitination of histones H2A and H2AXEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The RING finger protein RNF168 is a new ubiquitin ligase that functions as chromatin modifier, through histone ubiquitination. We hypothesize a dual function for RNF168. In normal condition RNF168 regulates gene expression by modulating ubiquitination of histone H2A. Upon DNA lesions, RNF168 is recruited to DNA damage response foci where it contributes to increase the amount of ubiquitinated proteins, thereby facilitating the downstream signalling cascade. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - June 5, 2009 Category: Molecular Biology Authors: Sabrina PinatoCristina ScandiuzziNadia ArnaudoElisabetta CitterioGiovanni GaudinoLorenza Penengo Source Type: journals

Reference genes for QRT-PCR tested under various stress conditions in Folsomia candida and Orchesella cincta (Insecta, Collembola)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We present a panel of reference genes for two emerging ecological genomic species tested under a variety of treatments. Within each species, different treatments resulted in differences in the top stable reference genes. Moreover, the two species differed in suitable reference genes even when exposed to similar stresses. This might be attributed to dissimilarity of physiology. It is vital to rigorously test a panel of reference genes for each species and treatment, in advance of relative quantification of QRT-PCR gene expression measurements. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - June 1, 2009 Category: Molecular Biology Authors: Muriel de BoerTjalf de BoerJanine MarienMartijn TimmermansBenjamin NotaNico van StraalenJacintha EllersDick Roelofs Source Type: journals

DNA methylation-histone modification relationships across the desmin locus in human primary cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Overall, our results constitute the first study correlating patterns of histone modifications and underlying DNA methylation of a muscle-specific LCR and its associated downstream gene region whilst additionally placing this within a much broader genomic context. Our results clearly show that there are distinct patterns of histone H3 and H4 acetylation and H3 methylation at the DES LCR, promoter and intragenic region. In addition, the presence of H3K27me3 at the DES methylation-free CpG only in non-expressing PBMCs may serve to silence this gene in non-muscle tissues. Generally, our work demonstrate the importa...
Source: BMC Molecular Biology - Latest articles - May 27, 2009 Category: Molecular Biology Authors: Marianne Lindahl AllenChristoph KochGayle ClellandIan DunhamMichael Antoniou Source Type: journals

Systematic cloning and analysis of autophagy-related genes from the silkworm Bombyx moriEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Bioinformatics in combination with RT-PCR enable us to remodel a preliminary pathway of autophagy in the silkworm. Amplification and cloning of most autophagy-related genes from the silkgland indicated autophagy is indeed an activated process. Furthermore, the time-course transcriptional profiles of BmATG8 and BmATG12 revealed that both genes are up-regulated along the maturation of the silkgland during the fifth instar. These findings suggest that the autophagy should play an important role in Bombyx mori silkgland. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - May 27, 2009 Category: Molecular Biology Authors: Xuan ZhangZhan-Ying HuWei-Fang LiQing-Rong LiXiao-Juan DengWan-Ying YangYang CaoCong-Zhao Zhou Source Type: journals

Breeding response of transcript profiling in developing seeds of Brassica napusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This paper illustrates the response of the transcription levels of 32 genes to breeding in developing rapeseed seeds. Both cultivars showed similar transcription profiles, with the Napin gene predominantly transcribed. Selective pressure for zero erucic acid, low glucosinolate, high oleic acid and high oil content, as well as high yield, resulted in higher FAD3, ACCase, FAE1, GKTP, Caleosin, GAPDH, and PEPC expression levels and lower KAS3, beta-CT, BcRK6, P450, FatA, Oleosin, FAD6, FatB, alpha-CT and SUC1 expression levels. It also resulted in altered relationships between these genes during storage accumulat...
Source: BMC Molecular Biology - Latest articles - May 24, 2009 Category: Molecular Biology Authors: Yaping HuGang WuYinglong CaoYuhua WuLing XiaoXiaodan LiChangming Lu Source Type: journals

Key role of the 3' untranslated region in the cell cycle regulated expression of the Leishmania infantum histone H2A genes: minor synergistic effect of the 5' untranslated region.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our findings indicate that both, the 5' and the 3' UTRs contain sequence elements that contribute to the cell cycle expression of L. infantum H2A. The 3' UTR region is essential for cell cycle dependent translation of the L. infantum H2A transcripts whereas the 5' UTR has a minor contribution in their S phase dependent translation. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - May 21, 2009 Category: Molecular Biology Authors: Daniel AbanadesLaura RamirezSalvador IborraKetty SoteriadouVictor GonzalezPedro BonayCarlos AlonsoManuel Soto Source Type: journals

Identification of ColR binding consensus and prediction of regulon of ColRS two-component systemEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Combined usage of experimental and computational approach enabled us to define the binding consensus for response regulator ColR and to discover several new ColR-regulated genes. For instance, genes of outer membrane lipid A 3-O-deacylase PagL and cytoplasmic membrane diacylglycerol kinase DgkA are the members of ColR regulon. Furthermore, over 40 genes were predicted to be putatively controlled by ColRS two-component system in P. putida. It is notable that many of ColR-regulated genes encode membrane-related products thus confirming the previously proposed role of ColRS system in regulation of membrane functi...
Source: BMC Molecular Biology - Latest articles - May 16, 2009 Category: Molecular Biology Authors: Paula A Kivistik, Rait Kivi, Maia Kivisaar and Rita Horak Source Type: journals

Validation of commonly used reference genes for sleep-related gene expression studiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study demonstrated that sleep deprivation does not alter the expression stability of commonly used reference genes in brain and blood. Nonetheless, the use of multiple reference genes in quantitative RT-PCR is required for the accurate results. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - May 15, 2009 Category: Molecular Biology Authors: Kil S Lee, Tathiana A Alvarenga, Camila Guindalini, Monica L Andersen, Rosa M.R.P.S. Castro and Sergio Tufik Source Type: journals

Parental origin of chromosomes influences crossover activity within the Kcnq1 transcriptionally imprinted domain of Mus musculusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Background: Among the three functions of DNA, mammalian replication and transcription can be subject to epigenetic imprinting specified by the parental origin of chromosomes, and although there is suggestive indication that this is also true for meiotic recombination, no definitive evidence has yet been reported. Results: We have now obtained such evidence on mouse chromosome 7 by assaying meiotic recombination as it occurs in reciprocal F1 mice arising in crosses between C57BL/6J and CAST/EiJ. A 166Kb region near the Kcnq1 transcriptionally imprinted domain showed significantly higher recombination activity in the CASTxB...
Source: BMC Molecular Biology - Latest articles - May 13, 2009 Category: Molecular Biology Authors: Siemon H Ng, Rose Madeira, Emil D Parvanov, Lorin M Petros, Petko M Petkov and Kenneth Paigen Source Type: journals

A trypsin-like protease with apparent dual function in early Lepeophtheirus salmonis (Kroyer) development.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Based on present data and previous studies of peptidases in oocytes and embryos, we hypothesize that maternally deposited LsTryp10 protein is involved in regulation of the yolk degradome. The function of LsTryp10 produced by the embryonic cells remains unknown. To our knowledge a similar expression pattern has not previously been reported for any protease. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - May 13, 2009 Category: Molecular Biology Authors: Rasmus Skern-Mauritzen, Petter Frost, Sussie Dalvin, Bjorn Olav Kvamme, Ingunn Sommerset and Frank Nilsen Source Type: journals

Chibby forms a homodimer through a heptad repeat of leucine residues in its C-terminal coiled-coil motifEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our comprehensive mutational analysis of the Cby coiled-coil domain reveals that the four heptad leucine residues play an essential role in mediating Cby homodimerization. Although monomeric Cby is sufficient to bind to beta-catenin and block beta-catenin-mediated transcriptional activation, homodimer formation of Cby is indispensable for its efficient nuclear import. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - May 12, 2009 Category: Molecular Biology Authors: Adaobi Mofunanya, Feng-Qian Li, Jen-Chih Hsieh and Ken-Ichi Takemaru Source Type: journals

TCF/beta-catenin plays an important role in HCCR-1 oncogene expressionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: These findings suggest that the Tcf1 site on the HCCR-1 promoter is a major element regulating HCCR-1 expression and abnormal stimulation of this site may induce various human cancers. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - May 12, 2009 Category: Molecular Biology Authors: Gwang-won Cho, Mi Kim, Seung Kim, Seon Ha, Hyun Kim, Sanghee Kim and Jin W Kim Source Type: journals

Revised Mimivirus major capsid protein sequence reveals intron-containing gene structure and extra domainEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The characterisation of the full length L425 Capsid coding gene of Acanthamoebae polyphaga Mimivirus provides new insights into the structure of the main Capsid protein. The production of a full length recombinant protein will be useful for further structural studies. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - May 11, 2009 Category: Molecular Biology Authors: Said Azza, Christian Cambillau, Didier Raoult and Marie Suzan-Monti Source Type: journals

Thrombin induces Egr-1 expression in fibroblasts involving elevation of the intracellular Ca2+ concentration, phosphorylation of ERK and activation of ternary complex factorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study shows that stimulus-transcription coupling in thrombin-treated lung fibroblasts relies on the elevation of the intracellular Ca2+-concentration and the activation of PKC and ERK. In the nucleus, ternary complex factors function as key proteins linking the intracellular signaling cascade with enhanced transcription of the Egr-1 gene. This study further shows that the dominant-negative Elk-1 mutant is a valuable tool to study Elk-1-mediated gene transcription. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - May 11, 2009 Category: Molecular Biology Authors: Oliver G Rossler and Gerald Thiel Source Type: journals

Human sex hormone-binding globulin gene expression- multiple promoters and complex alternative splicingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These results extend our understanding of human SHBG gene transcription, and raise new and important questions regarding the role of novel alternatively spliced transcripts, their function in hormonally responsive tissues including the breast and prostate, and the role that aberrant SHBG gene expression may play in cancer. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - May 5, 2009 Category: Molecular Biology Authors: Atif M Nakhla, Daniel J Hryb, William Rosner, Nicholas A Romas, Zhaoying Xiang and Scott M Kahn Source Type: journals

Use of the lambda Red-recombineering method for genetic engineering of Pantoea ananatis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The lambda Red-recombineering technology was successfully used for rapid generation of chromosomal modifications in the specially selected P. ananatis recipient strain. The procedure of electro-transformation with chromosomal DNA has been developed for transfer of the marked mutation between different P. ananatis strains. Combination of these techniques with lambda Int/Xis-dependent excision of selective markers significantly accelerates basic research and construction of producing strains. (Source: BMC Molecular Biology - Latest articles)
Source: BMC Molecular Biology - Latest articles - April 23, 2009 Category: Molecular Biology Authors: Joanna I Katashkina, Yoshihiko Hara, Lyubov I Golubeva, Irina G Andreeva, Tatiana M Kuvaeva and Sergey V Mashko Source Type: journals