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Technique Finds Gene Regulatory Sites Without Knowledge Of RegulatorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new statistical technique developed by researchers at the University of Illinois allows scientists to scan a genome for specific gene-regulatory regions without requiring prior knowledge of the relevant transcription factors. The technique has been experimentally validated in both the mouse genome and the fruit fly genome. (Source: Genetics News From Medical News Today)
Source: Genetics News From Medical News Today - November 21, 2009 Category: Genetics & Stem Cells Tags: Genetics Source Type: news

Schizophrenia Gene's Role May Be Broader, More Potent, Than ThoughtEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
UCSF scientists studying nerve cells in fruit flies have uncovered a new function for a gene whose human equivalent may play a critical role in schizophrenia. Scientists have known that the mutated form of the human gene - one of three consistently associated with schizophrenia - mildly disrupts the transmission of chemical signals between nerve cells in the brain. (Source: Genetics News From Medical News Today)
Source: Genetics News From Medical News Today - November 21, 2009 Category: Genetics & Stem Cells Tags: Schizophrenia Source Type: news

Ancestry Attracts, But Love Is BlindEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
People preferentially marry those with similar ancestry, but their decisions are not necessarily based on hair, eye or skin colour. Research, published in BioMed Central's open access journal Genome Biology, shows that Mexicans mate according to proportions of Native American to European ancestry, while Puerto Ricans are more likely to settle down with someone carrying a similar mix of African and European genes. (Source: Genetics News From Medical News Today)
Source: Genetics News From Medical News Today - November 21, 2009 Category: Genetics & Stem Cells Tags: Genetics Source Type: news

HMGA2 Is Confirmed To Be Associated with Human Adult HeightEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent genome-wide association studies have identified a novel polymorphism, rs1042725, in the HMGA2 gene for human adult height, a highly heritable complex trait. Replications in independent populations are needed to evaluate a positive finding and determine its generality. Thus, we performed a replication study to examine the associations between polymorphisms in HMGA2 and adult height in two US Caucasian populations (an unrelated sample of 998 subjects and a family-based sample of 8385 subjects) and a Chinese population (1638 unrelated Han subjects). We confirmed the association between rs1042725 in HMGA2 and adult heig...
Source: Annals of Human Genetics - November 21, 2009 Category: Genetics & Stem Cells Authors: Tie-Lin Yang, Yan Guo, Li-Shu Zhang, Qing Tian, Han Yan, Yan-Fang Guo, Hong-Wen Deng Source Type: journals

Guapa, it's your genetic ancestry I loveEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In Latino populations, love unites people with similar mix of ancestries (Source: New Scientist - Genetics)
Source: New Scientist - Genetics - November 20, 2009 Category: Genetics & Stem Cells Source Type: journals

Study Examines Challenges Of Diagnosing Neurofibromatosis Type 1-like SyndromeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An analysis of patients with a syndrome similar to the genetic disorder, neurofibromatosis type 1, indicates that diagnosis may be difficult because of shared clinical findings, such as certain pigmentary characteristics, according to a study in the November 18 issue of JAMA. (Source: Genetics News From Medical News Today)
Source: Genetics News From Medical News Today - November 20, 2009 Category: Genetics & Stem Cells Tags: Genetics Source Type: news

Novel motifs distinguish multiple homologues of Polycomb in vertebrates: expansion and diversification of the epigenetic toolkitEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our analysis shows that PC is an ancient gene dating back to pre bilaterian origin that has not only been conserved but has also expanded during the evolution of complexity. Unique motifs acquired by each homologue have been maintained for more than 500 millions years indicating their functional relevance in boosting the epigenetic 'tool kit'. We report the presence of a DNA interaction motif adjacent to chromodomain in all vertebrate PC homologues and suggest a three-way 'PC-histoneH3-DNA' interaction that can restrict nucleosome dynamics. The signature motifs of PC homologues and insect specific motif identi...
Source: BMC Genomics - Latest articles - November 20, 2009 Category: Genetics & Stem Cells Authors: Ramamoorthy SenthilkumarRakesh Mishra Source Type: journals

Attributing Hardy-Weinberg Disequilibrium to Population Stratification and Genetic Association in Case-Control StudiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Loci exhibiting Hardy-Weinberg disequilibrium (HWD) are often excluded from association studies, because HWD may indicate genotyping error, population stratification or selection bias. For case-control studies, HWD can result from a genetic effect at the locus. We extend the modelling to accommodate both stratification and genetic effects. Theoretical genotype frequencies and HWD coefficients are derived under a general genetic model for a population with two strata. Maximum likelihood is used to estimate model parameters and a test for lack of fit identifies the models most consistent with the data. Simulations were used ...
Source: Annals of Human Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Vaneeta K. Grover, David E. C. Cole, David C. Hamilton Source Type: journals

Fitness Among Individuals with Early Childhood Deafness: Studies in Alumni Families from Gallaudet UniversityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The genetic fitness of an individual is influenced by their phenotype, genotype and family and social structure of the population in which they live. It is likely that the fitness of deaf individuals was quite low in the Western European population during the Middle Ages. The establishment of residential schools for deaf individuals nearly 400 years ago resulted in relaxed genetic selection against deaf individuals which contributed to the improved fitness of deaf individuals in recent times. As part of a study of deaf probands from Gallaudet University, we collected pedigree data, including the mating type and the number ...
Source: Annals of Human Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Susan H. Blanton, Walter E. Nance, Virginia W. Norris, Katherine O. Welch, Amber Burt, Arti Pandya, Kathleen S. Arnos Source Type: journals

Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by RetrotransposonsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary Centromeres tend to be the last regions to be assembled in genome projects, as their mapping is hampered by their characteristically high repeat DNA content and lack of genetic recombination. Using unique markers derived from these repeat-rich regions, we were able to generate and annotate physical maps of two maize centromeres. Functional centromeres are defined not so much by their primary DNA sequence as by the presence of CENH3, a special histone that replaces canonical histone H3 in centromeric nucleosomes. Little is known about how deposition of CENH3 is regulated, or about the interplay between centr...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Thomas K. Wolfgruber et al. Source Type: journals

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary To complement the completion of sequencing the maize B73 genome, we sequenced 27,455 full-length cDNAs (FLcDNA) from two maize B73 libraries representing the gene transcripts from most tissues and common abiotic stress conditions. The FLcDNAs are beneficial in determining the exon/intron structure of genes by aligning them to the sequenced genome; 94% of our FLcDNAs aligned to the maize genome. The 27,455 FLcDNAs were compared to gene sequences for rice, sorghum, Arabidopsis, and poplar; 22,874 were found in all four sets, and 1,737 were unique to maize. Two-thirds of the maize genome is composed of a type ...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Carol Soderlund et al. Source Type: journals

Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we have shown that a maize mutation of RDR2 causes significant changes in SAM morphology. In combination, these observations indicate the complexity of transcriptome regulation and the crucial roles of RDR2 on transcriptome regulation, chromatin modification, and SAM development. (Source: PLoS Genetics)
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Yi Jia et al. Source Type: journals

RNA-Silencing Enzymes Pol IV and Pol V in Maize: More than one Flavor?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: PLoS Genetics)
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Craig S. Pikaard et al. Source Type: journals

Caenorhabditis elegans HIM-18/SLX-4 Interacts with SLX-1 and XPF-1 and Maintains Genomic Integrity in the Germline by Processing Recombination IntermediatesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary Homologous recombination (HR) is a process that provides for the accurate and efficient repair of DNA double-strand breaks (DSBs) incurred by cells, thereby maintaining genomic integrity. Proper processing of HR intermediates is critical for biological processes ranging from replication fork restart to the accurate partitioning of chromosomes during meiotic cell divisions. This is further emphasized by the fact that impaired processing of HR intermediates in both mitotic and meiotic cells can result in tumorigenesis and congenital defects. Therefore, the identification of components involved in HR is essent...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Takamune T. Saito et al. Source Type: journals

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome ContentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary There is a growing appreciation for the role of genome structural variation in creating phenotypic variation within a species. Comparative genomic hybridization was used to compare the genome structures of two maize inbred lines, B73 and Mo17. The data reinforce the view that maize is a highly polymorphic species, but also show that there are often large genomic regions that have little or no variation. We identify several hundred sequences that, while present in both B73 and Mo17, have copy number differences in the two genomes. In addition, there are several thousand sequences, including at least 180 sequ...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Nathan M. Springer et al. Source Type: journals

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize GenomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary Genomic insertion sites of Mu transposons were amplified and sequenced via next generation technology, revealing more than 40,000 non-redundant Mu insertion sites that are non-uniformly distributed across the maize genome and within genes. Along chromosomes, frequencies of Mu transposon insertions are strongly correlated with recombination rates. Although both Mu and recombination occur preferentially in genes, gene density does not fully explain these patterns. Instead, the finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open ch...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Sanzhen Liu et al. Source Type: journals

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize GenomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary Although TEs are a major component of all studied plant genomes, and are the most significant contributors to genome structure and evolution in almost all eukaryotes that have been investigated, their properties and reasons for existence are not well understood in any eukaryotic genome. In order to begin a comprehensive study of TE contributions to the structure, function, and evolution of both genes and genomes, we first identified all of the TEs in maize and then investigated whether there were non-random patterns in their dispersal. We used homology and TE structure criteria in an effort to discover all ...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Regina S. Baucom et al. Source Type: journals

Stage-Specific Expression Profiling of Drosophila Spermatogenesis Suggests that Meiotic Sex Chromosome Inactivation Drives Genomic Relocation of Testis-Expressed GenesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we observed meiotic expression reduction for X-linked genes in D. melanogaster through a global gene expression analysis in different phases of spermatogenesis, in agreement with MSCI. In order to test the effects of MSCI on the chromosomal distribution of testis-expressed genes, we analyzed their expression pattern throughout spermatogenesis. First, X chromosome underrepresentation was restricted to testis-biased genes over-expressed in meiosis. Second, we observed that the autosomal genes retroposed from the X chromosome more often showed complementary expression in meiosis to their X-linked parents. These...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Maria D. Vibranovski et al. Source Type: journals

Forty-Three Loci Associated with Plasma Lipoprotein Size, Concentration, and Cholesterol Content in Genome-Wide AnalysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary Genome-wide association studies (GWAS) of plasma lipoprotein fractions hold great promise for understanding lipid metabolism and its central role in cardiovascular disease and related disorders. Conventional assays for lipoprotein status determine total cholesterol content of low- or high-density lipoprotein particles (LDL-C or HDL-C, respectively) or total plasma triglyceride content (as an estimate of very-low density lipoprotein particle concentration [VLDL]). All three measures have been targets for recent GWAS. However, a more precise target for GWAS of lipoprotein metabolism would be the concentration...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Daniel I. Chasman et al. Source Type: journals

Fine-Scale Phylogenetic Discordance across the House Mouse GenomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary The phylogenetic history of individual genes can differ strongly from the species history if taxa are recently derived, making inferences of a species history from only a handful of genes especially difficult in these cases. Genome-scale data sets now allow phylogenetic histories to be reconstructed from a large number of genes. Although data sets of this size are becoming more common, few studies have characterized variation in phylogenetic history across whole genomes. We summarize fine scale variation in phylogenetic history across the genome of house mice, a recently derived group of subspecies, using a...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Michael A. White et al. Source Type: journals

Detailed Analysis of a Contiguous 22-Mb Region of the Maize GenomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary Maize is a major cereal crop and key experimental system for eukaryotic biology. Previous investigations of the maize genome at the sequence level have primarily focused on analyses of genome survey sequences and BAC contigs. Here we used a comprehensive set of resources to construct an ordered and oriented 22-Mb sequence from chromosome 4 that represents 1% of the maize genome. Genome annotation revealed the presence of 544 genes that are interspersed with transposable elements (TEs), which occupy 83.8% of the sequence. Fifty-one genes were involved in 14 tandem gene clusters and most appear to have arisen...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Fusheng Wei et al. Source Type: journals

A Dominant Mutation in mediator of paramutation2, One of Three Second-Largest Subunits of a Plant-Specific RNA Polymerase, Disrupts Multiple siRNA Silencing ProcessesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary How an individual's genes are activated or silenced is an essential question impacting all fields of biology. Usually gene expression patterns, i.e., which genes are on and which are off in different tissues and during development, are highly reproducible; and those patterns are efficiently reset in the next generation of progeny. Paramutation represents an exception to these genetic rules, in that for certain genes the silencing that is established in an individual is efficiently transmitted to their progeny. Importantly, in these subsequent generations, the silenced gene continues to silence active versio...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Lyudmila Sidorenko et al. Source Type: journals

X Chromosome: Expression and EscapeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: PLoS Genetics)
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: John Parsch Source Type: journals

10 Reasons to be Tantalized by the B73 Maize GenomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: PLoS Genetics)
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Virginia Walbot Source Type: journals

A Genome-Wide Characterization of MicroRNA Genes in MaizeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary MicroRNAs are non-coding RNAs that regulate gene expression post-transcriptionally and play roles in diverse pathways including those acting on development and responses to stress. Here, we describe a genome-wide computational prediction of maize miRNA genes and their characterization with respect to expression, putative targets, evolution following whole genome duplication, and allelic diversity. The structures of unprocessed primary miRNA transcripts were determined by 5′ RACE and 3′ RACE. Expression profiles were surveyed in five tissue types by deep-sequencing of small RNA libraries. We predicted mi...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Lifang Zhang et al. Source Type: journals

The Physical and Genetic Framework of the Maize B73 GenomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we used a comprehensive physical and genetic framework map to develop a minimum tiling path (MTP) of over 16,000 BAC clones across the genome. The MTP was generated dynamically and integrated numerous data types, such as in-coming genome sequence, over 8,000 sequence-based genetic markers, and the maize optical map. This allowed us to genetically anchor, order, and orient the majority of the maize physical map and genome sequence to the genetic map. Post-genome sequencing, we constructed a golden path (AGP) of sequence-based pseudomolecules representing the ten chromosomes of the maize B73 genome (B73 RefGen...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Fusheng Wei et al. Source Type: journals

A Single Molecule Scaffold for the Maize GenomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary The maize genome contains abundant repeats interspersed by low-copy, gene-coding sequences that make it a challenge to sequence; consequently, current BAC sequence assemblies average 11 contigs per clone. The iMap deals with such complexity by the judicious integration of IBM genetic and B73 physical maps, but the B73 genome structure could differ from the IBM population because of genetic recombination and subsequent rearrangements. Accordingly, we report a genome-wide, high-resolution optical map of maize B73 genome that was constructed from the direct analysis of genomic DNA molecules without using genet...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Shiguo Zhou et al. Source Type: journals

Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 LocusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary Multicellular plants possess a unique set of DNA–dependent RNA polymerase complexes (RNAPs) that prevent certain repetitious regions of the genome from being copied into stable RNAs. Two distinct RNAPs, termed Pol IV and Pol V, are required for this type of genome-silencing behavior in the eudicot Arabidopsis thaliana, but the mechanism by which these RNAPs accomplish this function is still relatively unknown. Using genetic and molecular methodologies, we identified a Pol IV–type subunit protein as being involved in a process of meiotically-heritable gene silencing in the maize plant known as paramutati...
Source: PLoS Genetics - November 20, 2009 Category: Genetics & Stem Cells Authors: Jennifer L. Stonaker et al. Source Type: journals

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

Transcriptional regulation of tumor suppressor p53 by cAMP-responsive element-binding protein/AMP-activated protein kinase complex in response to glucose deprivationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we found that cAMP-responsive element-binding protein (CREB) collaborates with AMP-activated protein kinase [alpha] (AMPK[alpha]) to regulate the transcription of p53. Luciferase reporter assays showed that the genomic fragment spanning from [minus]531 to [minus]239 of human p53 gene is required for the transactivation of p53 in response to glucose deprivation. Within this region, we found out a putative CREB-binding site. siRNA-mediated knockdown of CREB resulted in a significant inhibition of the up-regulation of p53 and apoptosis under glucose deprivation. Consistent with these observations, glucose depri...
Source: Genes to Cells - November 20, 2009 Category: Genetics & Stem Cells Authors: Rintaro Okoshi, Kiyohiro Ando, Yusuke Suenaga, Meixiang Sang, Natsumi Kubo, Harutoshi Kizaki, Akira Nakagawara, Toshinori Ozaki Source Type: journals

Identification of CENP-V as a novel microtubule-associating molecule that activates Src family kinases through SH3 domain interactionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The activation mechanisms of Src family kinases (SFKs) involve the dissociation of the intramolecular interaction between the Src homology (SH) 3 and kinase domain. This process is mediated by the intermolecular attack of outer ligands to the SH3 domain. By using a yeast two-hybrid screen, we isolated a relevant ligand involved in the activation mechanisms of SFKs. This molecule was found to be identical to a recently recognized kinetochore protein [ndash] designated as centromere protein (CENP)-V [ndash] which is required for the progression of mitosis. We show here that human CENP-V plays further roles in cell dynamics; ...
Source: Genes to Cells - November 20, 2009 Category: Genetics & Stem Cells Authors: Zen-ichiro Honda, Takeshi Suzuki, Hiroaki Honda Source Type: journals

TdT interacting factor 1 enhances TdT ubiquitylation through recruitment of BPOZ-2 into nucleus from cytoplasmEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We isolated human cDNA clone encoding Bood POZ containing gene type 2 (BPOZ-2) as a gene with a product that binds to TdT interacting factor 1 (TdIF1) using a yeast two-hybrid system. BPOZ-2 is an adaptor for E3 ligase CUL3 and participates in developmental processes. The binding between BPOZ-2 and TdIF1 was confirmed by GST pull-down and immunoprecipitation assays using specific antibodies against BPOZ-2 and TdIF1 in vitro and in vivo. Although when BPOZ-2 solely was expressed in COS7 cells, BPOZ-2 was observed mainly within the cytoplasm, co-transfection of pEGFP-BPOZ-2 and pDsRed-TdIF1 into COS7 cells resulted in co-loc...
Source: Genes to Cells - November 20, 2009 Category: Genetics & Stem Cells Authors: Takahide Hayano, Kotaro Koiwai, Hisataka Ishii, So Maezawa, Kousuke Kouda, Takuro Motoyama, Takashi Kubota, Osamu Koiwai Source Type: journals

Transcriptional regulation of human G2A in monocytes/ macrophages: involvement of c/EBPs, Runx and Pu.1Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
G2 accumulation (G2A) is a G-protein coupled receptor, activated by several ligands and stimuli, such as lysophosphatidylcholine (LPC), extracellular low pH and oxidized phospholipids including 9- and 13-hydroxyoctadecadienoic acid, and has been implicated in mediating inflammatory process under oxidative conditions. Recently, it was demonstrated that G2A in monocytes/macrophages plays critical roles in atherosclerosis deterioration, and therefore its transcriptional regulation in monocytes/macrophages is of great interest. Here, we first confirmed the expression of human G2A (hG2A) in lymph nodes, spleen and peripheral bl...
Source: Genes to Cells - November 20, 2009 Category: Genetics & Stem Cells Authors: Naoka Murakami, Tomomi Hashidate, Takeshi Harayama, Takehiko Yokomizo, Takao Shimizu, Motonao Nakamura Source Type: journals

Physical Mapping of Immune Genes in the Tammar Wallaby (Macropus eugenii)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cytogenet Genome Res (DOI:10.1159/000260372) (Source: Cytogenetic and Genome Research)
Source: Cytogenetic and Genome Research - November 19, 2009 Category: Genetics & Stem Cells Source Type: journals

Mapping quantitative trait loci (QTL) in sheep. I. A new male framework linkage map and QTL for growth rate and body weight.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A male sheep linkage map comprising 191 microsatellites was generated from a single family of 510 Awassi-Merino backcross progeny. Except for ovine chromosomes 1, 2, 10 and 17, all other chromosomes yielded a LOD score difference greater than 3.0 between the best and second-best map order. The map is on average 11% longer than the Sheep Linkage Map v4.7 male-specific map. This map was employed in quantitative trait loci (QTL) analyses on body-weight and growth-rate traits between birth and 98 weeks of age. A custom maximum likelihood program was developed to map QTL in half-sib families for non-inbred strains (QTL-MLE)...
Source: Genet Sel Evol - November 19, 2009 Category: Genetics & Stem Cells Authors: Raadsma HW, Thomson PC, Zenger KR, Cavanagh C, Lam MK, Jonas E, Jones M, Attard G, Palmer D, Nicholas FW Tags: Genet Sel Evol Source Type: journals

Synthesis of N-substituted iminosugars from 2'-carbonyl-C-glycofuranosides.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Under basic conditions 2'-carbonyl 5-N-substituted-C-glycofuranosides undergo a tandem beta-elimination and intramolecular hetero-Michael addition to form N-substituted iminosugar derivatives in good to excellent yields. PMID: 19917320 [PubMed - in process] (Source: Carbohydrate Research)
Source: Carbohydrate Research - November 19, 2009 Category: Genetics & Stem Cells Authors: Luo H, Zou W, Shao H Tags: Carbohydr Res Source Type: journals

Multiple Roles for Heterochromatin Protein 1 Genes in Drosophila.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Heterochromatin is the gene-poor, transposon-rich, late-replicating chromatin compartment that was first cytologically defined more than 70 years ago. The identification of heterochromatin protein 1 (HP1) paved the way for a molecular dissection of this important component of complex eukaryotic genomes. Although initial studies revealed HP1's key role in heterochromatin maintenance and function, more recent studies have discovered a role for HP1 in numerous processes including, surprisingly, euchromatic gene expression. Drosophila genomes possess at least five HP1 paralogs that have significantly different roles, rangi...
Source: Annual Review of Genetics - November 19, 2009 Category: Genetics & Stem Cells Authors: Vermaak D, Malik HS Tags: Annu Rev Genet Source Type: journals

ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses [RESOURCES]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ProPhylER (Protein Phylogeny and Evolutionary Rates) is a next-generation curated proteome resource that uses comparative sequence analysis to predict constraint and mutation impact for eukaryotic proteins. Its purpose is to inform any research program for which protein function and structure are relevant, by the predictive power of evolutionary constraint analyses. ProPhylER currently has nearly 9000 clusters of related proteins, including more than 200,000 sequences. It serves data via two interfaces. The "ProPhylER Interface" displays predictive analyses in sequence space; the "CrystalPainter" maps evolutionary constrai...
Source: Genome Research - November 19, 2009 Category: Genetics & Stem Cells Authors: Binkley, J., Karra, K., Kirby, A., Hosobuchi, M., Stone, E. A., Sidow, A. Tags: RESOURCES Source Type: journals

Genome-wide mapping of SMAD target genes reveals the role of BMP signaling in embryonic stem cell fate determination [LETTERS]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Embryonic stem (ES) cells are under precise control of both intrinsic self-renewal gene regulatory network and extrinsic growth factor-triggered signaling cascades. How external signaling pathways connect to core self-renewal transcriptional circuits is largely unknown. To probe this, we chose BMP signaling, which is previously recognized as a master control for both self-renewal and lineage commitment of murine ES cells. Here, we mapped target gene promoter occupancy of SMAD1/5 and SMAD4 on a genome-wide scale and found that they associate with a large group of developmental regulators that are enriched for H3K27 trimethy...
Source: Genome Research - November 19, 2009 Category: Genetics & Stem Cells Authors: Fei, T., Xia, K., Li, Z., Zhou, B., Zhu, S., Chen, H., Zhang, J., Chen, Z., Xiao, H., Han, J.-D. J., Chen, Y.-G. Tags: LETTERS Source Type: journals

Gene change in cannibals reveals evolution in actionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Devastating brain disease caused by human cannibalism promoted protective gene mutation to emerge just 200 years ago (Source: New Scientist - Genetics)
Source: New Scientist - Genetics - November 19, 2009 Category: Genetics & Stem Cells Source Type: journals

Cognitive Dysfunction Reversed In Mouse Model Of Down's SyndromeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A study by neuroscientist William C. Mobley, MD, PhD, chair of the Department of Neurosciences at the University of California, San Diego School of Medicine, and colleagues at Stanford University Medical School has demonstrated a possible new approach to slowing the inevitable progression of cognitive decline found in Down's syndrome. (Source: Genetics News From Medical News Today)
Source: Genetics News From Medical News Today - November 19, 2009 Category: Genetics & Stem Cells Tags: Neurology / Neuroscience Source Type: news

An integrative genomic analysis identifies Bhmt2 as a diet-dependent genetic factor protecting against acetaminophen-induced liver toxicity [LETTERS]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Acetaminophen-induced liver toxicity is the most frequent precipitating cause of acute liver failure and liver transplant, but contemporary medical practice has mainly focused on patient management after a liver injury has been induced. An integrative genetic, transcriptional, and two-dimensional NMR-based metabolomic analysis performed using multiple inbred mouse strains, along with knowledge-based filtering of these data, identified betaine-homocysteine methyltransferase 2 (Bhmt2) as a diet-dependent genetic factor that affected susceptibility to acetaminophen-induced liver toxicity in mice. Through an effect on methioni...
Source: Genome Research - November 19, 2009 Category: Genetics & Stem Cells Authors: Liu, H.-H., Lu, P., Guo, Y., Farrell, E., Zhang, X., Zheng, M., Bosano, B., Zhang, Z., Allard, J., Liao, G., Fu, S., Chen, J., Dolim, K., Kuroda, A., Usuka, J., Cheng, J., Tao, W., Welch, K., Liu, Y., Pease, J., de Keczer, S. A., Masjedizadeh, M., Hu, J.- Tags: LETTERS Source Type: journals

A novel study of Copy Number Variations in Hirschsprung disease using the Multiple Ligation-dependent Probe Amplification (MLPA) technique.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results indicate that CNVs of the gene coding regions analyzed here are not a common molecular cause of Hirschsprung disease. However, further studies are required to determine the presence of CNVs affecting non-coding regulatory regions, as well as other candidate genes. (Source: BMC Medical Genetics - Latest articles)
Source: BMC Medical Genetics - Latest articles - November 19, 2009 Category: Genetics & Stem Cells Authors: Rocio Nunez-TorresRaquel FernandezManuel Lopez-AlonsoGuillermo AntinoloSalud Borrego 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

Psychiatric syndromes in individuals with chromosome 18 abnormalitiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study focuses on the presentations of psychiatric syndromes as they relate to specific chromosomal abnormalities of chromosome 18. Twenty-five subjects (13 with an 18q deletion, 9 with 18p tetrasomy, and 3 with an 18p deletion), were interviewed by psychiatrists (blind to specific chromosomal abnormality) using the DIGS (subjects 18 and older) or KSADS-PL (subjects under 18). A consensus best estimation diagnostic process was employed to determine psychiatric syndromes. Oligonucleotide Array Comparative Genomic Hybridization (Agilent Technologies) was utilized to define specific regions of chromosome 18 that were dele...
Source: American Journal of Medical Genetics Part B: Neuropsychiatric Genetics - November 19, 2009 Category: Genetics & Stem Cells Authors: Juan Zavala, Mercedes Ramirez, Rolando Medina, Patricia Heard, Erika Carter, AnaLisa Crandall, Daniel Hale, Jannine Cody, Michael Escamilla Source Type: journals

A systematic association mapping on chromosome 6q in bipolar affective disorder - evidence for the melanin-concentrating-hormone-receptor-2 gene as a risk factor for bipolar affective disorderEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Strong evidence of linkage between chromosomal region 6q16-q22 and bipolar affective disorder (BPAD) has previously been reported. We conducted a systematic association mapping of the 6q-linkage interval using 617 SNP markers in a BPAD case-control sample of German descent (cases = 330, controls = 325). In this screening step, 46 SNPs showed nominally significant BPAD-association (P-values between 0.0007 and 0.0484). Although none of the 46 SNPs survived correction for multiple testing, they were genotyped in a second and ethnically matched BPAD sample (cases = 328, controls = 397). At the melanin-concentrating-hormone-rec...
Source: American Journal of Medical Genetics Part B: Neuropsychiatric Genetics - November 19, 2009 Category: Genetics & Stem Cells Authors: Rami Abou Jamra, Thomas G. Schulze, Tim Becker, Felix F. Brockschmidt, Elaine Green, Margrieta A. Alblas, Jens R. Wendland, Mazda Adli, Detelina Grozeva, Jana Strohmeier, Alexander Georgi, Nick Craddock, Peter Propping, Marcella Rietschel, Markus M. Nöth Source Type: journals

Biology inspires engineeringEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A report of the Cold Spring Harbor Laboratory/Wellcome Trust Meeting on Engineering Principles in Biology, Cambridge, UK, 14-16 October 2009. (Source: Genome Biology)
Source: Genome Biology - November 19, 2009 Category: Genetics & Stem Cells 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