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Ligand-specific sequential regulation of transcription factors for differentiation of MCF-7 cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our analysis indicated that a time-dependent transcriptional regulatory network including c-FOS, FRA-1, and FHL2 is vital in controlling the ERK signaling pathway through a negative feedback loop for MCF-7 cell differentiation. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 20, 2009 Category: Genetics & Stem Cells Authors: Yuko SaekiTakaho EndoKaori IdeTakeshi NagashimaNoriko YumotoTetsuro ToyodaHarukazu SuzukiYoshihide HayashizakiYoshiyuki SakakiMariko Okada-Hatakeyama Source Type: journals

Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: A comprehensive study of gene expression and associated functions during testis maturation and germ cell differentiation in the rainbow trout is presented. The study identifies new pathways involved during spermatogonia self-renewal or rapid proliferation, meiosis and gamete differentiation, in fish and potentially in all vertebrates. It also provides the necessary basis to further investigate the hormonal and molecular networks that trigger puberty and annual testicular recrudescence in seasonally breeding species. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 20, 2009 Category: Genetics & Stem Cells Authors: Antoine RollandJean-Jacques LareyreAnne-Sophie GoupilJerome MonfortMarie-Jose RicordelDiane EsquerreKarine HugotRemi HoulgatteFrederic ChalmelFlorence Le Gac Source Type: journals

A transcriptome analysis identifies molecular effectors of unconjugated bilirubin in human neuroblastoma SH-SY5Y cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These results show for the first time that UCB exposure induces ER stress response as major intracellular homeostasis in surviving neuroblastoma cells in vitro. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 19, 2009 Category: Genetics & Stem Cells Authors: Raffaella CalligarisCristina BellarosaRossana FotiPaola RoncagliaPablo GiraudiHelena KrmacClaudio TiribelliStefano Gustincich Source Type: journals

Differentially expressed genes for aggressive pecking behaviour in laying hensEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: In conclusion, our study provides new insights into which genes are involved in aggressive behaviours in chickens. Pecking and receiving hens exhibited different gene expression profiles in their brains. Following confirmation, the identification of differentially expressed genes may elucidate how the pecking order forms in laying hens at a molecular level. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 19, 2009 Category: Genetics & Stem Cells Authors: Bart BuitenhuisJakob HedgaardLuc JanssPeter Sorensen Source Type: journals

Gene network and pathway analysis of bovine mammary tissue challenged with Streptococcus uberis reveals induction of cell proliferation and inhibition of PPAR-gamma signaling as potential mechanism for the negative relationships between immune response and lipid metabolismEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Results provided novel information into the early signaling and metabolic pathways in mammary tissue that are associated with the innate immune response to S. uberis infection. Our study indicated that IMI challenge with S. uberis (strain O140J) elicited a strong transcriptomic response, leading to potent activation of pro-inflammatory pathways that were associated with a marked inhibition of lipid synthesis, stress-activated kinase signaling cascades, and PPAR signaling (most likely PPARgamma). This latter effect may provide a mechanistic explanation for the inverse relationship between immune response and mi...
Source: BMC Genomics - Latest articles - November 19, 2009 Category: Genetics & Stem Cells Authors: Kasey MoyesJames DrackleyDawn MorinMassimo BionazSandra Rodriguez-ZasRobin EvertsHarris LewinJuan Loor Source Type: journals

Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results show that previous studies of segmental collinearity between the A. thaliana, Brassica and ancestral karyotype genomes, although very useful, represent over-simplifications of their true relationships. The presence of numerous cryptic collinear genome segments and the frequent occurrence of segmental inversions mean that inference of the positions of genes in B. rapa based on the locations of orthologues in A. thaliana can be misleading. Our results will be of relevance to a wide range of plants that have polyploid genomes, many of which are being considered according to a paradigm of comprising co...
Source: BMC Genomics - Latest articles - November 18, 2009 Category: Genetics & Stem Cells Authors: Martin TrickSoo-Jin KwonSu Ryun ChoiFiona FraserEleni SoumpourouNizar DrouZhi WangSeo Yeon LeeTae-Jin YangJeong-Hwan MunAndrew PatersonChristopher TownJ PiresYong Pyo LimBeom-Seok ParkIan Bancroft Source Type: journals

Comparative transcripts profiling reveals new insight into molecular processes regulating lycopene accumulation in a sweet orange (Citrus sinensis) red-flesh mutantEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: This study provided a global picture of the gene expression changes in a sweet orange red-flesh mutant as compared to the wild type. Interpretation of the differentially expressed genes revealed new insight into the molecular processes regulating lycopene accumulation in the sweet orange red-flesh mutant. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 18, 2009 Category: Genetics & Stem Cells Authors: Qiang XuKeqin YuAndan ZhuJunli YeQing LiuJianchen ZhangXiuxin Deng Source Type: journals

Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: the repABC operonEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Horizontal gene transfer with conservation of the repABC operon structure provides a highly dynamic operon in which each member of this operon has its own evolutionary dynamics. In addition, it seems that different incompatibility groups present in the same species have different degrees of adaptation to their host genomes, in proportion to the amount of time the incompatibility group has coexisted with the host genome. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 18, 2009 Category: Genetics & Stem Cells Authors: Santiago Castillo-RamirezJorge Vazquez-CastellanosVictor GonzalezMiguel Cevallos Source Type: journals

Adaptation of the short intergenic spacers between co-directional genes to the Shine-Dalgarno motif among prokaryote genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The SD presence makes the intergenic lengths from 5 to 8 bps less frequent and causes an adaptation of the stop codon usage. Our results introduce new elements to the discussion of which factors affect the intergenic lengths, which cannot be totally explained by the pressure to compact the prokaryote genomes. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 18, 2009 Category: Genetics & Stem Cells Authors: Albert PallejaSantiago Garcia-VallveAntoni Romeu Source Type: journals

Identification of genes associated with multiple cancers via integrative analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The Mc.TGD can identify a short list of genes associated with one or multiple types of cancers. The identified genes are considerably different from those identified using meta analysis or analysis of marginal effects. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 17, 2009 Category: Genetics & Stem Cells Authors: Shuangge MaJian HuangMeena Moran Source Type: journals

Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogenyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This is the first mitogenomic study supporting the new chordate phylogeny revealed by recent phylogenomic analyses. It illustrates the beneficial effects of an increased taxon sampling coupled with the use of more realistic amino acid substitution models for the reconstruction of animal phylogeny. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 17, 2009 Category: Genetics & Stem Cells Authors: Tiratha Raj SinghGeorgia TsagkogeorgaFrederic DelsucSamuel BlanquartNoa ShenkarYossi LoyaEmmanuel DouzeryDorothee Huchon Source Type: journals

GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: GExplore is an online database for quick mining of data related to gene and protein function, providing a multi-gene display of data sets related to the domain composition of proteins as well as expression and phenotype data. GExplore is publicly available at: http://genome.sfu.ca/gexplore/ (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 16, 2009 Category: Genetics & Stem Cells Authors: Harald HutterMan-Ping NgNansheng Chen Source Type: journals

Alu repeats increase local recombination ratesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We show that the presence of a fixed AluY insertion is significantly predictive of an elevated local recombination rate within 2 kb of the insertion, independent of other known predictors. The magnitude of this effect, approximately a 6% increase, is comparable to the effects of some recombinogenic DNA sequence motifs identified via their association with recombination hot spots. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 16, 2009 Category: Genetics & Stem Cells Authors: David WitherspoonW WatkinsYuhua ZhangJinchuan XingWhitney TolpinrudDale HedgesMark BatzerLynn Jorde Source Type: journals

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome AnalyzerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: 3' tag DGE profiling with massive parallel sequencing achieved high sensitivity and reproducibility for transcriptome profiling. Although it lacks the ability of detecting alternative splicing events compared to RNA-SEQ, it is much more affordable and clearly out-performed microarrays (Affymetrix) in detecting lower abundant transcripts. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 16, 2009 Category: Genetics & Stem Cells Authors: Yan AsmannEric KleeE ThompsonEdith PerezSumit MiddhaAnn ObergTerry TherneauDavid SmithGregory PolandEric WiebenJean-Pierre Kocher Source Type: journals

Analysis of expressed sequence tags and identification of genes encoding cell-wall-degrading enzymes from the fungivorous nematode Aphelenchus avenaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We have described at least 2214 putative genes in A. avenae and identified a set of genes encoding a range of cell wall degrading enzymes. This EST dataset represents a starting point for studies in a number of different fundamental and applied areas. The presence of genes encoding a battery of cell-wall-degrading enzymes in A. avenae and their similarities with the genes from other plant parasitic nematodes suggest that this nematode can act not only as a fungal feeder but also a plant parasite. Further studies on genes encoding cell-wall-degrading enzymes in A. avenae will accelerate our understanding of the ...
Source: BMC Genomics - Latest articles - November 16, 2009 Category: Genetics & Stem Cells Authors: Nurul KarimJohn JonesHiroaki OkadaTaisei Kikuchi Source Type: journals

Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500K SNP array genomic hybridizationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Affymetrix GeneChip(R) 500K array genomic hybridization detected pathogenic genomic imbalance in 10 of 10 patients with idiopathic developmental disability in whom 100K GeneChip(R) array genomic hybridization had found genomic imbalance, 1 of 44 patients in whom 100K GeneChip(R) array genomic hybridization had found no abnormality, and 16 of 100 patients who had not previously been tested. Effective clinical interpretation of these studies requires considerable skill and experience. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 16, 2009 Category: Genetics & Stem Cells Authors: J FriedmanShelin AdamLaura ArbourLinlea ArmstrongAgnes BarossPatricia BirchCornelius BoerkoelSusanna ChanDavid ChaiAllen DelaneyStephane FlibotteWilliam GibsonSylvie LangloisEmmanuelle LemyreH LiPatrick MacLeodJoan MathersJacques MichaudBarbara McGillivra Source Type: journals

Target gene approaches: Gene expression in Daphnia magna exposed to predator-borne kairomones or to microcystin-producing and microcystin-free Microcystis aeruginosaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Gene expression analysis using a normalisation factor based on three reference genes showed that transcription levels of actin and alpha-tubulin were not substantially changed by predator-borne chemical cues from fishes or invertebrates, although changes in expression on the protein level were shown elsewhere. These changes in protein level could be caused by others than the investigated paralogs, showing the importance of the construction of phylogenetic trees for candidate gene approaches. However, fish kairomones caused an up-regulation, and Chaoborus kairomone caused a down-regulation of cyclophylin, which...
Source: BMC Genomics - Latest articles - November 16, 2009 Category: Genetics & Stem Cells Authors: Anke SchwarzenbergerCornelius CourtsEric Von Elert Source Type: journals

U3 snoRNA genes are multi-copy and frequently linked to U5 snRNA genes in Euglena gracilisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The multiple U3 snoRNA-U5 snRNA gene linkages, which cluster into distinct families based on sequence similarities within the intergenic spacer, presumably arose by genome, chromosome, and/or locus duplications. We discuss possible reasons for the existence of the unusually large number of U3 snoRNA genes in the Euglena genome. Variability in the signal intensities of the multiple Southern hybridization bands raises the possibility that Euglena contains a naturally aneuploid chromosome complement. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 16, 2009 Category: Genetics & Stem Cells Authors: J. CharetteMichael Gray Source Type: journals

A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have undertaken a whole genome approach in order to further understand the mechanism(s) regulating the cell's toxicity to nickel compounds. We have used computational methods to integrate the data and generate global models of the yeast's cellular response to NiSO4. The results of our study shed light on molecular pathways associated with the cellular response of eukaryotic cells to nickel compounds and provide potential implications for further understanding the toxic effects of nickel compounds to human cells. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 15, 2009 Category: Genetics & Stem Cells Authors: Adriana AritaXue ZhouThomas EllenXin LiuJingxiang BaiJohn RooneyAdrienne KurtzCatherine KleinWei DaiThomas BegleyMax Costa Source Type: journals

A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Generated set of chickpea ESTs serves as a resource of high quality transcripts for gene discovery and development of functional markers associated with abiotic stress tolerance that will be helpful to facilitate chickpea breeding. Mapping of gene-based markers in chickpea will also add more anchoring points to align genomes of chickpea and other legume species. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 15, 2009 Category: Genetics & Stem Cells Authors: Rajeev VarshneyPavana HiremathPazhamala LekhaJunichi KashiwagiJayashree BalajiAmit DeokarVincent VadezYongli XiaoRamamurthy SrinivasanPooran GaurKadambot SiddiqueChristopher TownDavid Hoisington Source Type: journals

New methods to analyse microarray data that partially lack a reference signalEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: A definition of gene presence based on signal at least twice as high as the background and higher than the reference signal (method 4) had the best test characteristics, allowing the analysis of 6-17% more of the genes not present in the reference strain. This method is recommended to analyse microarray data that partially lack a reference signal. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 13, 2009 Category: Genetics & Stem Cells Authors: Neeltje CarpaijAd FluitJodi LindsayMarc BontenRob Willems Source Type: journals

Correlation of microsynteny conservation and disease gene distribution in mammalian genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The correlation between microsynteny conservation and disease gene locations indicates that regions of the mouse genome with high microsynteny conservation may contain undiscovered human disease genes. This study not only demonstrates that gene function constrains mammalian genome organization, but also identifies regions of the mouse genome that can be experimentally examined to produce mouse models of human disease. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 12, 2009 Category: Genetics & Stem Cells Authors: Simon LovellXiting LiNimmi WeerasingheKathryn Hentges Source Type: journals

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation siteEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results provide evidence for novel transcript variants with intronic poly(A) sites. The expression of these novel variants was confirmed with computational and experimental tools. Our data provide a genome-wide resource for identification of novel human transcript variants with intronic polyadenylation sites, and offer a new view into the mystery of the human transcriptome. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 12, 2009 Category: Genetics & Stem Cells Authors: Pingzhang WangPeng YuPeng GaoTaiping ShiDalong Ma Source Type: journals

Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The Gene Array is an effective expression profiling tool at gene and exon expression level, the latter made possible by probe set annotation modifications. We demonstrate that the Gene Array is capable of detecting alternative splicing and isoform variation. As expected, in comparison to the Exon Array, it is limited by reduced gene content coverage and is not able to detect as wide a range of alternative splicing events. However, for the events that can be monitored by both platforms, we estimate that the selectivity and sensitivity levels are comparable. We hope our findings will shed light on the potential ...
Source: BMC Genomics - Latest articles - November 12, 2009 Category: Genetics & Stem Cells Authors: Kevin HaJasmin Coulombe-HuntingtonJacek Majewski Source Type: journals

An expression database for roots of the model legume Medicago truncatula under salt stressEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 11, 2009 Category: Genetics & Stem Cells Authors: Daofeng LiZhen SuJiangli DongTao Wang Source Type: journals

Endogenous control genes in complex vascular tissue samplesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have found that for real-time PCR in heterogeneous tissue samples, it may be a better choice to normalize real-time PCR Ct values to the carefully measured mass of total RNA than to use endogenous control genes. We base this conclusion on the fact that total RNA mass normalization of real-time PCR data shows better correlation to microarray data. Because microarray data use a different normalization approach based on a larger part of the transcriptome, we conclude that omitting endogenous control genes will give measurements more in accordance with actual concentrations. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 10, 2009 Category: Genetics & Stem Cells Authors: Lasse FolkersenSanela KurtovicAnton RazuvaevHanna AgardhAnders GabrielsenGabrielle Paulsson-Berne Source Type: journals

Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: To our knowledge, this is the first study on miRNA gene expression in AIV infected chickens using a deep sequencing approach. During AIV infection, many host miRNAs were differentially regulated, supporting the hypothesis that certain miRNAs might be essential in the host-pathogen interactions. Elucidation of the mechanism of these miRNAs on the regulation of host-AIV interaction will lead to the development of new control strategies to prevent or treat AIV infections in poultry. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 5, 2009 Category: Genetics & Stem Cells Authors: Ying WangVinayak BrahmakshatriyaHuifeng ZhuBlanca LupianiSanjay ReddyByung-Jun YoonPreethi GunaratneJong KimRui ChenJunjun WangHuaijun Zhou Source Type: journals

Evolution of genomic sequence inhomogeneity at mid-range scalesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: MRI regions have comparable levels of de novo mutations to the control genomic sequences with average base composition. De novo substitutions rapidly erode MRI regions, bringing their nucleotide composition toward genome-average levels. However, those substitutions that favor the maintenance of MRI properties have a higher chance to spread through the entire population. Indels have a clear tendency to maintain MRI features yet they have a smaller impact than substitutions. All in all, the observed fixation bias for mutations helps to preserve MRI regions during evolution. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 5, 2009 Category: Genetics & Stem Cells Authors: Ashwin PrakashSamuel ShepardJie HeBenjamin HartMiao ChenSurya AmarachinthaOlga Mileyeva-BiebesheimerJason BechtelAlexei Fedorov Source Type: journals

Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal deathEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These results suggest that MUC contribute to fetal malformations, preterm birth and low birth weight due to underlying molecular defects that result in hypoplastic umbilical arteries and/or placental insufficiency. The results of the current study demonstrate the effects of MUC on fetal growth and organ development in scNT-derived pigs, and provide important insight into the molecular mechanisms underlying angiogenesis during umbilical cord development. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 5, 2009 Category: Genetics & Stem Cells Authors: Jong-Yi ParkJae-Hwan KimYun-Jung ChoiKyu-Chan HwangSeong-Keun ChoHo-Hyun ParkSeung-Sam PaikTeoan KimChanKyu ParkHoon Taek LeeHan Geuk SeoSoo-Bong ParkSeongsoo HwangJin-Hoi Kim Source Type: journals

Information-theoretic gene-gene and gene-environment interaction analysis of quantitative traitsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The KWII and PAI are promising metrics for analyzing the GEI of QT. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 4, 2009 Category: Genetics & Stem Cells Authors: Pritam ChandaLara SuchestonSong LiuAidong ZhangMurali Ramanathan Source Type: journals

Comparative analysis of plant genomes allows the definition of the Phytolongins: a novel non-SNARE longin domain protein family.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: "Longins" have been defined as R-SNAREs composed of both a longin domain and a SNARE motif. However, expressed gene isoforms and splice variants of longins are examples of non-SNARE motif containing longins. The discovery of Phytolongins, a family of non-SNARE longin domain proteins, together with recent evidence on the conservation of the longin-like fold in proteins involved in both vesicle fusion (e.g. the Trs20 tether) and vesicle formation (e.g. sigma and mu adaptin) highlight the importance of the longin-like domain in protein trafficking and suggest that it was one of the primordial building blocks of t...
Source: BMC Genomics - Latest articles - November 4, 2009 Category: Genetics & Stem Cells Authors: Marco VedovatoValeria RossiJoel DacksFrancesco Filippini Source Type: journals

Computational prediction of splicing regulatory elements shared by Tetrapoda organismsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Difference in intronic enhancers supporting 5' and 3' splice sites suggests an independent splicing commitment for neighboring exons. Increased evolutionary conservation for ISEs/ISSs within intronic flanks and effect of modulation of predicted elements on splicing suggest functional significance of found elements in splicing regulation. Most of the elements identified were shown to have direct implications in human splicing and therefore could be useful for building computational splicing models in biomedical research. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - November 4, 2009 Category: Genetics & Stem Cells Authors: Alexander ChurbanovIgor VorechovskyChindo Hicks Source Type: journals

Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Members of known multigenic families involved in cell wall biogenesis, and new genes that might participate in cell elongation were identified. Significant differences were shown in the expression of such genes in half- and fully-grown hypocotyls. No clear correlation was found between the abundance of transcripts (transcriptomic data) and the presence of the proteins (proteomic data) demonstrating (i) the importance of post-transcriptional events for the regulation of genes during cell elongation and (ii) that transcriptomic and proteomic data are complementary. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 31, 2009 Category: Genetics & Stem Cells Authors: Elisabeth JametDavid RoujolHelene San ClementeMuhammad IrshadLudivine Soubigou-TaconnatJean-Pierre RenouRafael Pont-Lezica Source Type: journals

EST and microarray analysis of horn development in Onthophagus beetlesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have laid the foundation for a systematic analysis of the genetic basis of horned beetle development and diversification with the potential to contribute significantly to several major frontiers in evolutionary developmental biology. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 30, 2009 Category: Genetics & Stem Cells Authors: Teiya KijimotoJames CostelloZuojian TangArmin MoczekJusten Andrews Source Type: journals

Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining cDNA libraries generated by SGP represent a valuable cCDS FLIc source. The conservation of 7-mers in 3'UTRs indicates that these motifs are functionally important. Identity between some of these 7-mers and miRNA target sequences suggests that they are miRNA targets in Salmo salar transcripts as well. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 30, 2009 Category: Genetics & Stem Cells Authors: Rune AndreassenSigbjorn LunnnerBjorn Hoyheim Source Type: journals

Hepatic gene expression profiling reveals protective responses in Atlantic salmon vaccinated against furunculosisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Efficiency of vaccination against furunculosis depends largely on the ability of host to neutralize the negative impacts of immune responses combined with efficient clearance and prevention of tissue damages. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 30, 2009 Category: Genetics & Stem Cells Authors: Stanko SkugorSven-Martin JorgensenBjarne GjerdeAleksei Krasnov Source Type: journals

Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogensEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This work demonstrates a strategy for the identification of potential virulence factors that are conserved across a number of human pathogenic bacterial species, confirming the usefulness of this tool. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 29, 2009 Category: Genetics & Stem Cells Authors: Chris StubbenMelanie DuffieldIan CooperDonna FordJason GansAndrey KarlyshevBryan LingardPetra OystonAnna de RochefortJian SongBrendan WrenRick TitballMurray Wolinsky Source Type: journals

Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulexEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Nuclear receptors are ancient proteins with highly conserved DNA-binding domains. The DNA-binding domains of the nuclear receptors of D. pulex contain the same degree of conservation that is typically found within nuclear receptors of other species. Most of the receptors identified in D. pulex have orthologs within the vertebrate and invertebrate lineages examined with the exception of the novel HR97 group and the DpHR10 and potentially the DpHR11 receptors found in D. pulex. These groups of receptors may harbour functions that are intrinsic to crustacean physiology. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 28, 2009 Category: Genetics & Stem Cells Authors: Susanne ThomsonWilliam BaldwinYing WangGwijun KwonGerald LeBlanc Source Type: journals

Anti-proliferative action of vitamin D in MCF7 is still active after siRNA-VDR knock-downEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: In conclusion, siRNA and genome wide studies both suggest that the anti-proliferative effects of 1,25D in MCF7 breast tumor cell lines do not rely on classical Vitamin D pathway per se. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 28, 2009 Category: Genetics & Stem Cells Authors: Jose CostaPaul EijkMark van de WielDerk ten BergFernando SchmittCarmen NarvaezJoEllen WelshBauke Ylstra Source Type: journals

A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheatEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The construction of the Brachypodium physical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion of Brachypodium genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at http://phymap.ucdavis.edu/brachypodium/. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 27, 2009 Category: Genetics & Stem Cells Authors: Yong GuYaqin MaNaxin HuoJohn VogelFrank YouGerard LazoWilliam NelsonCarol SoderlundJan DvorakOlin AndersonMing-Cheng Luo Source Type: journals

A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These data suggest for the first time that TORC1 provides directional information when CREB is bound at bidirectional promoters and possible pausing of the CREB protein after initial transcriptional activation. Also, this combined approach demonstrates the ability to more broadly characterize CREB protein-DNA interactions wherein not only DNA binding sites are discovered, but also the potential of the promoter sequence to respond to CREB is evaluated. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 27, 2009 Category: Genetics & Stem Cells Authors: Danette HartzellNathan TrinkleinJacqui MendezNancy MurphyShelley AldredKeith WoodMarjeta Urh Source Type: journals

Inherent promoter bidirectionality facilitates maintenance of sequence integrity and transcription of parasitic DNA in mammalian genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These data strongly suggest that the selective force that shields endogenous CpG containing promoter from epigenetic silencing can extend to exogenous foreign DNA elements inserted in close proximity in the opposite orientation, with resulting transcription and maintenance of sequence integrity of such elements in the host genome. Over time this may result in 'domestication' of such elements to provide novel cellular and developmental functions. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 27, 2009 Category: Genetics & Stem Cells Authors: Paul KalitsisRichard Saffery Source Type: journals

Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulonsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Trypanosome genes form post-transcriptional regulons in which mRNAs with functions in particular pathways, or encoding components of protein complexes, show almost identical patterns of regulation. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 26, 2009 Category: Genetics & Stem Cells Authors: Rafael QueirozCorinna BenzKurt FellenbergJorg HoheiselChristine Clayton Source Type: journals

Exploring the molecular basis of insecticide resistance in the dengue vector Aedes aegypti: a case study in Martinique Island (French West Indies)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: These results suggest that the high level of insecticide resistance found in Ae. aegypti mosquitoes from Martinique island is the consequence of both target-site and metabolic based resistance mechanisms. Insecticide resistance levels and associated mechanisms are discussed in relation with the environmental context of Martinique Island. These finding have important implications for dengue vector control in Martinique and emphasizes the need to develop new tools and strategies for maintaining an effective control of Aedes mosquito populations worldwide. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 26, 2009 Category: Genetics & Stem Cells Authors: Sebastien MarcombeRodolphe PoupardinFrederic DarrietStephane ReynaudJulien BonnetClare StrodeCecile BrenguesAndre YebakimaHilary RansonVincent CorbelJean-Philippe David Source Type: journals

Expulsion of Trichuris muris is associated with increased expression of Angiogenin 4 in the gut and increased acidity of mucins within the goblet cell.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Differences in gene expression levels identified between the S and E-infected mice early during infection have furthered our knowledge of how the S isolate persists for longer than the E isolate in the C57BL/6 mouse. Potential new targets for manipulation in order to aid expulsion have been identified. Further we provide evidence for a potential new marker involving the acidity of the mucins within the goblet cell which may predict outcome of infection within days of parasite exposure. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 23, 2009 Category: Genetics & Stem Cells Authors: Riccardo D'EliaMatthew deSchoolmeesterLeo ZeefSteven WrightAlan PembertonKathryn Else Source Type: journals

A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carpEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We show that CSRBH functional homologs relationships and re-analyses of gene expression data can be combined in a non-model species to predict genes of biological interest before a genome sequence is fully available. Programs to run these analyses locally are available from http://www.cbrg.ox.ac.uk/~jherbert/. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 22, 2009 Category: Genetics & Stem Cells Authors: John HerbertFrancesca BuffaHenrik VorschmittStuart EggintonRoy Bicknell Source Type: journals

Whole-genome analysis of pseudorabies virus gene expression by real-time quantitative RT-PCR assayEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Most (if not all) PRV genes begin to be expressed from the onset of viral expression. No sharp boundary was found between the groups of early and late genes classified on the basis of their requirement for viral DNA synthesis. The expressions of the PRV genes were analyzed, categorized and compared by RT2-PCR assay, with the average of the minimum cycle threshold used as a control for the calculation of a particular R value. In principle, this new calculation technique is applicable for the analysis of gene expression in all temporally changing genetic systems. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 22, 2009 Category: Genetics & Stem Cells Authors: Dora TombaczJudit TothPal PetrovszkiZsolt Boldogkoi Source Type: journals

Identification and analysis of serpin-family genes by homology and synteny across the 12 sequenced Drosophilid genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: In general, inhibitory serpins rarely change their range of proteinase targets, except by a duplication/divergence mechanism. Non-inhibitory serpins appear to derive from inhibitory serpins, but not the reverse. The conservation of different family members varied widely across the 12 sequenced Drosophilid genomes. An approach considering synteny as well as homology was important to find the largest set of orthologues. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 21, 2009 Category: Genetics & Stem Cells Authors: Matthew GarrettAne FullaondoLaurent TroxlerGos MicklemDavid Gubb Source Type: journals

KAIKObase: An integrated silkworm genome database and data mining toolsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: For efficient usage of genome information for functional studies, genomic sequences, physical and genetic map information and EST data were compiled into KAIKObase, an integrated silkworm genome database which consists of 4 map viewers, a gene viewer, and sequence, keyword and position search systems to display results and data at the level of nucleotide sequence, gene, scaffold and chromosome. Integration of the silkworm proteome database and the Bombyx trap database with KAIKObase led to a high-grade, user-friendly, and comprehensive silkworm genome database which is now available from URL: http://sgp.dna.aff...
Source: BMC Genomics - Latest articles - October 20, 2009 Category: Genetics & Stem Cells Authors: Michihiko ShimomuraHiroshi MinamiYoshitake SuetsuguHajime OhyanagiChikatada SatohBaltazar AntonioYoshiaki NagamuraKeiko Kadono-OkudaHideyuki KajiwaraHideki SezutsuJavaregowda NagarajuMarian GoldsmithQingyou XiaKimiko YamamotoKazuei Mita Source Type: journals

Analysis of regulatory protease sequences identified through bioinformatic data mining of the Schistosoma mansoni genomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Numerous proteases are identified for the first time in S. mansoni. We characterized important regulatory proteases and focus analysis on these proteases to complement the growing knowledge base of digestive proteases. This work provides a foundation for expanding knowledge of proteases in Schistosoma species and examining their diverse function and potential as targets for new chemotherapies. (Source: BMC Genomics - Latest articles)
Source: BMC Genomics - Latest articles - October 20, 2009 Category: Genetics & Stem Cells Authors: David BosChris MayfieldDennis Minchella Source Type: journals