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Genes, Developmental (1):
Recent article
Genes, Developmental
Abstract
Thalamocortical projections convey visual, somatosensory and auditory information to the cerebral cortex. A recent report in Neural Development shows how a forward genetic screen has enabled the identification of novel mutations affecting specific decision points of thalamocortical axon pathfinding....
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PMID: 21214944
PDF is available here.
PDF is available here.
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Abstract
We previously generated an atlas of gene expression in the developing mouse kidney using microarray analysis of anatomical compartments collected via laser capture microdissection. Here, this data is further analysed to identify anchor genes via stringent bioinformatic filtering followed by high res...
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PMID: 21386911
PDF is available here.
PDF is available here.
Abstract
Our results show that TSA treatment during the peri- and postactivation period improves the development of reconstructed murine embryos, and this observation may be explained by enhanced epigenetic modification of somatic cells caused by TSA-induced hyperacetylation, demethylation and upregulation o...
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PMID: 21187677
PDF is available here.
PDF is available here.
Abstract
Abstract
We report that epigenomic landscapes in hESCs and lineage-committed cells are drastically different. By comparing the chromatin-modification profiles and DNA methylomes in hESCs and primary fibroblasts, we find that nearly one-third of the genome differs in chromatin structure. Most changes arise fr...
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PMID: 20452322
PDF is available here.
PDF is available here.
Genome Research (20)4 2010
Abstract
We report the first genome-scale study of epigenomic dynamics during normal human aging. We identify aging-associated differentially methylated regions (aDMRs) in whole blood in a discovery cohort, and then replicate these aDMRs in sorted CD4(+) T-cells and CD14(+) monocytes in an independent cohort...
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PMID: 20219945
PDF is available here.
PDF is available here.
Abstract
We review recent advances, such as comparative gene and protein expression studies, that are delineating the changes in gene and protein expression that accompany osteocyte differentiation. We also review recent studies in which time-lapse dynamic imaging approaches have been used to visualize osteo...
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PMID: 20392270
PDF is available here.
PDF is available here.
Abstract
We used a genomewide method for detecting regions of CpG methylation on the basis of the increased melting temperature of methylated DNA, termed denaturation analysis of methylation differences (DAMD). Using the DAMD assay, we find common regions of cancer-specific methylation changes in primary med...
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PMID: 19966297
PDF is available here.
PDF is available here.
Abstract
A novel gene-K23, differentially expressed in cross-subfamily cloned embryos, was isolated by RACE-PCR technique. It had 2580 base pairs (bp) in length, with a 1,425 bp open reading frame (ORF) encoding a putative protein of 474 amino acids (aa). Bioinformatic analysis indicated that K23 had 22 phos...
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PMID: 18654838
PDF is available here.
PDF is available here.
Abstract
Studies of children with developmental abnormalities of genetic origin are necessary for accurate diagnosis, prognostication, patient management, and genetic counseling. Such studies can also help to identify genes involved in normal and abnormal morphogenesis, which often act as patterning genes an...
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PMID: 20120282
PDF is available here.
PDF is available here.
Abstract
We report here that, as in zebrafish, homologues of patched and prdm1 are expressed in adaxial regions of the lamprey somite, and an eng homologue is also expressed in the somite. However, the lamprey adaxial region does not exhibit the same distinct adaxial cell morphology as in the zebrafish. In a...
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PMID: 19196331
PDF is available here.
PDF is available here.
Abstract
Abstract
We encounter in the animal kingdom. Tyrosine kinase receptors (RTKs) are transmembrane receptors present in all metazoans known to control several developmental processes. They act via the activation of various cytoplasmic signaling cascades, including the mitogen-activated protein kinase (MAPK), th...
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PMID: 19196330
PDF is available here.
PDF is available here.
Abstract
We will discuss the strengths and weaknesses of the methodologies that have been proposed to quantitatively examine developmental sequence data, and studies that have attempted to implement them in an evolutionary context....
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PMID: 19196338
PDF is available here.
PDF is available here.
Abstract
We isolated here the two homologues of Trf4/5 in Drosophila melanogaster, named DmTRF4-1 and DmTRF4-2, and investigated their biological function. DmTRF4-1 displayed poly(A) polymerase activity in vitro, whereas DmTRF4-2 did not. Gene knockdown of DmTRF4-1 by RNA interference is lethal in flies, as...
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PMID: 18765642
PDF is available here.
PDF is available here.
Abstract
We found that the Tip60-p400 acetyltransferase and histone exchange complex is necessary to maintain normal self-renewal in mouse ESCs. While Tip60-p400 has histone acetyltransferase activity, which is generally associated with transcriptional activation, it acts predominantly as a repressor of gene...
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PMID: 18948739
PDF is available here.
PDF is available here.
Abstract
We analyzed the expression of four ZGA genes (hsp70.1, eif-1a, muerv and zscan4d) in embryos whose DNA replication was inhibited by treatment with aphidicolin, an inhibitor of DNA polymerase. Inhibiting the first round increased the expression levels of hsp70.1, eif-1a and zscan4d but decreased that...
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PMID: 18580041
PDF is available here.
PDF is available here.
Abstract
We conducted a factorial microarray analysis. Gene expression profiles were compared from wild-type and yng retinas and stage-matched whole embryos at 36 and 52 hours postfertilization (hpf). From our analysis, three categories of genes were identified: (i) Brg1-regulated retinal differentiation gen...
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PMID: 18753621
PDF is available here.
PDF is available here.
Abstract
We use a comparative genomic approach to investigate this process of gene turnover in the beta-globin gene family of placental mammals. By analyzing genomic sequence data from representatives of each of the main superordinal clades of placental mammals, we were able to reconstruct pathways of gene f...
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PMID: 18755893
PDF is available here.
PDF is available here.
Abstract
We selected a representative in Gesneriaceae, the sister to the remainder of Lamiales s.l., to isolate CYC homologues and further investigate their expression patterns using locus-specific semiquantitative reverse transcriptase polymerase chain reaction. Our results showed that four CYC homologues i...
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PMID: 18592267
PDF is available here.
PDF is available here.
Abstract
We addressed the transcription regulatory mechanism of the left-right asymmetric expression of Pitx gene in the ascidian, Ciona intestinalis. We first identified an intronic enhancer that drives Ci-Pitx left-sided expression in the epidermis and found that a single FoxH1 binding site present in this...
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PMID: 18546017
PDF is available here.
PDF is available here.
Genes & Development (22)12 2008
Abstract
We defined the genome-wide transcription dynamics that create primordial germ cells (PGCs) from the epiblast, a process that exclusively segregates them from their somatic neighbors. We also analyzed the effect of the loss of Blimp1, a key transcriptional regulator, on these dynamics. Our analysis r...
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PMID: 18559478
PDF is available here.
PDF is available here.
Development Growth & Differentiation (50 Suppl 1) 2008
Abstract
My group has long studied transcriptional gene regulation involved in cell differentiation, employing lens cell differentiation as a model. In this article, our progress over the last quarter of a century in deciphering the principles involved in developmental gene regulation is described, outlining...
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PMID: 18430167
PDF is available here.
PDF is available here.
Abstract
We isolated seven homeobox genes from the ctenophore Mnemiopsis leidyi and examined their expression through development. Phylogenetic analyses of these genes placed four in the ANTP class and three in the PRD class. These are the first reported full-length PRD class genes, although our analyses cou...
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PMID: 18504608
PDF is available here.
PDF is available here.
Abstract
We explore the degree to which the Triops limb is patterned by the same network of genes known to pattern the uniramous, multi-jointed insect appendage. Insect leg patterning proceeds through a process of subdividing the leg into proximal, intermediate, and distal regions by the activity of the tran...
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PMID: 18483814
PDF is available here.
PDF is available here.
Abstract
We have previously constructed a model for a GRN in retinal ganglion cell (RGC) differentiation in which four hierarchical tiers of transcription factors ultimately control the expression of downstream terminal genes. Math5 occupies a central node in the hierarchy because it is essential for the for...
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PMID: 18460603
PDF is available here.
PDF is available here.
Abstract
Our studies show that ablation of BAF250a in early mouse embryos results in developmental arrest (about embryonic day 6.5) and absence of the mesodermal layer, indicating its critical role in early germ-layer formation. Moreover, BAF250a deficiency compromises ES cell pluripotency, severely inhibits...
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PMID: 18448678
PDF is available here.
PDF is available here.
Developmental Cell (14)5 2008
Abstract
We assess the concordance of histone H3 lysine 4 dimethylation (H3K4me2) and trimethylation (H3K4me3) on a genome-wide scale in erythroid development by analyzing pluripotent, multipotent, and unipotent cell types. Although H3K4me2 and H3K4me3 are concordant at most genes, multipotential hematopoiet...
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PMID: 18477461
PDF is available here.
PDF is available here.
PLOS Medicine (5)3 2008
Abstract
PLOS Medicine (5)3 2008
Abstract
Abstract
We have developed an enabling technology (high-throughput magnetic resonance imaging of mouse embryos), which is used in combination with N-ethyl-N-nitrosourea/transposon mutagenesis and knockout techniques. Key future challenges now involve translating discoveries made in mouse models to human CHD...
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PMID: 18375573
PDF is available here.
PDF is available here.
Advances in Genetics (61) 2008
Abstract
Sequence conservation has traditionally been used as a means to target functional regions of complex genomes. In addition to its use in identifying coding regions of genes, the recent availability of whole genome data for a number of vertebrates has permitted high-resolution analyses of the noncodin...
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PMID: 18282512
PDF is available here.
PDF is available here.
Abstract
We devised a CGI enrichment method based on nonmethylated CpG affinity chromatography. The resulting library was sequenced to define a novel human blood CGI set that includes many that are not detected by current algorithms. Approximately half of CGIs were associated with annotated gene transcriptio...
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PMID: 18232738
PDF is available here.
PDF is available here.
Abstract
We identify direct target genes of Spt5 using fog(sk8) zebrafish mutant, which disrupts the foggy/spt5 gene. We identified that fog(sk8) and their wildtype siblings differentially express less than 5% of genes examined. These genes participate in diverse biological processes from stress response to...
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PMID: 18978947
PDF is available here.
PDF is available here.
Abstract
Abstract
Abstract
Abstract
Here we show that disruption of Nfix by Cre-recombinase mediated excision of the 2nd exon results in defects in brain development that differ from those seen in Nfia and Nfib KO mice. In particular, complete callosal agenesis is not seen in Nfix-/- mice but rather there appears to be an overabundanc...
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PMID: 18477394
PDF is available here.
PDF is available here.
Abstract
We analyzed 179 co-isogenic single P[GT1]-element insertion lines of Drosophila melanogaster to identify novel genes affecting developmental time in flies reared at 25 degrees C. Sixty percent of the lines showed a heterochronic phenotype, suggesting that a large number of genes affect this trait. M...
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PMID: 18687152
PDF is available here.
PDF is available here.
Abstract
We developed a knowledge database called "CINOBI: CionaNotochord and Brachyury-downstream gene Index" to create comprehensive catalogues of Brachyury-downstream gene sets in Ciona intestinalis. Combining genome and large-scale cDNA data, we were able to characterize 450 non-redundant Brachyury-downs...
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PMID: 18184356
PDF is available here.
PDF is available here.
Genome Biology (9)2 2008
Abstract
We describe Ancora http://ancora.genereg.net, a web resource that provides data and tools for exploring genomic organization of HCNEs for multiple genomes. Ancora includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental re...
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PMID: 18279518
PDF is available here.
PDF is available here.
Abstract
We address the question of whether a pelagic "larval" or benthic "adult" morphology originated first in metazoan lineages by testing the hypothesis that particular gene co-option patterns will be associated with the origin of feeding, indirect developing larval forms. Empirical evidence bearing on t...
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PMID: 18184359
PDF is available here.
PDF is available here.
FEBS Letters (581)30 2007
Abstract
We show, using a well-defined over-expression system, that PAX3 suppresses p53-dependent transcription from promoters of p53-responsive genes, notably BAX and HDM2-P2, and reduces p53 protein abundance by promoting its degradation. We define the functional domains of PAX3 required for this activity,...
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PMID: 18053811
PDF is available here.
PDF is available here.
Developmental Biology (312)2 2007
Abstract
We examined detailed expression of key developmental genes for the ascidian CNS, including Otx, Pax2/5/8a, En, Fgf8/17/18, Dmbx, Lhx3 and Hox genes, in the CNS around the junction of the trunk and tail of three different tailbud-stage embryos of Ciona intestinalis, employing double-fluorescence in s...
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PMID: 17996862
PDF is available here.
PDF is available here.
l Orthodontie Française (78)4 2007
Abstract
We know that cells can respond to mechanical stimuli by biochemical signaling. Thus, the link between mechanical stimuli and gene expression has become a new and important area of the morphological sciences. This field of research seems to be a revival of the old approach of developmental mechanics,...
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PMID: 18082114
PDF is available here.
PDF is available here.
Developmental Biology (312)1 2007
Abstract
We asked if they might share molecular components. We find that vegetal explants, the source of Nieuwkoop signal in recombination assays, express a number of organizer genes. The product of one of these genes, chordin, is required for signaling, suggesting that the organizer and the center share at...
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PMID: 17964564
PDF is available here.
PDF is available here.
Nature Genetics (39)12 2007
Abstract
We have carried out comprehensive Pol II chromatin immunoprecipitation microarray (ChIP-chip) assays in Drosophila embryos and identified three distinct Pol II binding behaviors: active (uniform binding across the entire transcription unit), no binding, and stalled (binding at the transcription star...
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PMID: 17994019
PDF is available here.
PDF is available here.
Abstract
We demonstrate that Hox11 paralogous proteins form a complex with Pax2 and Eya1 to directly activate expression of Six2 and Gdnf in the metanephric mesenchyme. We have identified the binding site within the Six2 enhancer necessary for Hox11-Eya1-Pax2-mediated activation and demonstrate that this sit...
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PMID: 17785448
PDF is available here.
PDF is available here.
Theriogenology (68 Suppl 1) 2007
Abstract
Messenger RNA (mRNA) expression techniques have become a powerful tool to analyze the relative abundance of transcripts related to oocyte and/or embryo quality. Numerous efforts to identify candidate genes for the developmental competence of bovine oocytes and embryos have been made employing differ...
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PMID: 17524469
PDF is available here.
PDF is available here.
Theriogenology (68 Suppl 1) 2007
Abstract
We compared oocytes derived from large follicles (>or=5mm) to those from small follicles (
PDF is available here.
PDF is available here.
Abstract
The loss of Nfic did not interfere with the formation of HERS, but it caused disrupted odontoblast differentiation, which resulted in the formation of short and abnormal roots, and decreased cementum. This finding suggests that root dentin is required for normal cementum formation. Therefore, Nfic m...
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PMID: 17760551
PDF is available here.
PDF is available here.
Abstract
Our study showed that IFRG is expressed from oocytes- through to the preimplantation embryo in rabbits. This finding provides some clues for better understanding the role of IFNs in the development of the embryo. The full length of rabbit IFRG cDNA (Accession No. AJ584672), with a 2794bp encoding 13...
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PMID: 17902267
PDF is available here.
PDF is available here.
Aging Cell (6)4 2007
Abstract
We examined the genes previously known to be essential for development. From a pool of 57 genes that cause developmental arrest after inhibition using RNA interference, we have identified 24 genes that extend lifespan in Caenorhabditis elegans when inactivated during adulthood. Many of these genes a...
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PMID: 17521386
PDF is available here.
PDF is available here.
Abstract
We present a widely applicable computational approach, integrating developmental time-course microarray data with annotated in situ hybridisation studies, that facilitates the de novo prediction of tissue-specific expression for genes that have no in vivo gene expression localisation data available....
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PMID: 17658945
PDF is available here.
PDF is available here.
Mammalian Genome (18)6-7 2007
Abstract
Systems developmental biology is an approach to the study of embryogenesis that attempts to analyze complex developmental processes through integrating the roles of their molecular, cellular, and tissue participants within a computational framework. This article discusses ways of annotating these pa...
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PMID: 17566825
PDF is available here.
PDF is available here.
Ostomy/wound management (53)6 2007
Abstract
In mature skin, wound repair typically begins with hemostasis and inflammation. This is followed by a proliferative phase with reepithelialization, angiogenesis, and collagen production, and ends with the generation of a permanent scar. However, animal studies and clinical observations have shown th...
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PMID: 17586870
PDF is available here.
PDF is available here.
Acta Biologica Hungarica (58)2 2007
Abstract
In mammals, testis development is initiated by the expression of the sex-determining gene, SRY whereas the genetic trigger for sex determination in birds remains unknown. In the present study, the expression of seven genes implicated in vertebrate sex determination and differentiation were studied i...
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PMID: 17585506
PDF is available here.
PDF is available here.
Stem Cells (25)6 2007
Abstract
We describe a rapid large-scale screening strategy for the identification of genes that influence the pluripotency and differentiation of embryonic stem cells to specific fates, and we use this approach to identify genes that induce neuron formation. The power of the strategy is validated by the fac...
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PMID: 17379767
PDF is available here.
PDF is available here.
Exposure to retinoic acid at the onset of hindbrain segmentation induces episodic breathing in mice.
Abstract
We now provide a developmental mouse model of neonatal HEB. We used retinoic acid (RA) (0.5-10 mg/kg of maternal weight) to alter embryonic development of the respiratory neuronal network at the onset of hindbrain segmentation (7.5 days post-coitum). HEB was observed in vivo after RA treatment durin...
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PMID: 17610572
PDF is available here.
PDF is available here.
Abstract
We present a genome-wide survey of 10,402 constrained nonexonic elements in the human genome that have all been deposited by characterized mobile elements. These repeat instances have been under strong purifying selection since at least the boreoeutherian ancestor (100 Mya). They are most often loca...
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PMID: 17463089
PDF is available here.
PDF is available here.