Abstract
We present the rare variant weighted aggregate statistic (RWAS), a method that groups rare variants and computes a weighted sum of differences between case and control mutation counts. We show that our method outperforms the groupwise association test of Madsen and Browning in the disease-risk model...
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PMID: 21368279
PDF is available here.
Abstract
We examine the Tree of Life (TOL) as an evolutionary hypothesis and a heuristic. The original TOL hypothesis has failed but a new "statistical TOL hypothesis" is promising. The TOL heuristic usefully organizes data without positing fundamental evolutionary truth. Reviewers: This article was reviewed...
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PMID: 21714936
PDF is available here.
Abstract
ABSTRACT: Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization....
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PMID: 21714942
PDF is available here.
Abstract
The majority of molecular processes in higher organisms are performed by various proteins and are thus determined by genes that encode these proteins. However, a significant structural component of at least half of all cellular proteins is not a polypeptide encoded by a single gene,...
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PMID: 20957246
PDF is available here.
Abstract
We then act as "anthropologists," studying what scientists do to determine which definition-theories of life they constructively hold as they design missions to seek non-terran life. We also look at how constructive beliefs about biosignatures change as observational data accumulate. And we consider...
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PMID: 21162682
PDF is available here.
Abstract
The possibility is discussed that the order of genes in chromosomes is not random but determined by natural selection, i.e., is a selectively valuable character. Cases of long-term conservation of gene linkage or synteny in evolution are presented. Examples and possible mechanisms of nonrandom gene...
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PMID: 21254548
PDF is available here.
Abstract
We hypothesized that the insulin-sensitive phenotype associated with Jnk deletion originates from loss of JNK function in skeletal muscle. Short hairpin RNA (shRNA)-mediated gene silencing was used to identify the functions of JNK subtypes in regulating energy metabolism and metabolic responses to e...
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PMID: 20094041
PDF is available here.
Abstract
Genetic variability of the caprine stearoyl-CoA desaturase 1 (SCD1) gene has been investigated by sequencing a 4.7-kb cDNA in 6 goats from the Murciano-Granadina and Malagueña breeds. Sequence alignment revealed the existence of one synonymous polymorphism at exon 5 (c.732C>T) and one nucleotide su...
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PMID: 20723706
PDF is available here.
Abstract
We report a comprehensive analysis of gck-3 function and demonstrate its requirement for several developmental processes independent of ion homeostasis, i.e., larval progression, vulva, and germ line formation. Consistent with a wide range of gck-3 function we find that endogenous GCK-3 is expressed...
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PMID: 20595048
PDF is available here.
Abstract
We examined the function of another Bar-class homeobox gene, Mbh2, and how Mbh1 and Mbh2 modulate expression of the receptors, leading to midline crossing of axons. Misexpression of Mbh1 and Mbh2 showed the same effects in the spinal cord. The competence of spinal dorsal cells to become commissural...
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PMID: 20599893
PDF is available here.
Abstract
Splice variation plays important roles in evolution and cancer. Different splice variants of a gene may be characteristic of particular cellular processes, subcellular locations or organs. Although several genomic projects have identified splice variants, there have been no large-scale computational...
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PMID: 20616384
PDF is available here.
Abstract
We detected the synthesis of two different proteins from the transcripts by two-dimensional Western blot and mass spectrometry analyses. This is the first reported occurrence of alternative splicing in M. anisopliae.
Copyright 2010 Elsevier B.V. All rights reserved....
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PMID: 20406672
PDF is available here.
Abstract
Parkinson's disease (PD) is a chronic progressive neurodegenerative movement disorder characterized by a profound and selective loss of nigrostriatal dopaminergic neurons. Another neurodegenerative disorder, Huntington's disease (HD), is characterized by striking movement abnormalities and the loss...
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PMID: 20522011
PDF is available here.
Abstract
Individuals with trisomy 21, also known as Down syndrome (DS), develop a clinical syndrome including almost identical neuropathological characteristics of Alzheimer's disease (AD) observed in non-DS individuals. The main difference is the early age of onset of AD pathology in individuals with DS, wi...
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PMID: 20522013
PDF is available here.
Abstract
We have characterized SL RNAs from Prionchulus punctatus. Surprisingly, this revealed the presence of a set of SLs that show clear sequence similarity to the SL2 family of spliced leaders, which have previously only been found within the rhabditine group (which includes C. elegans). Expression of on...
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PMID: 20566669
PDF is available here.
Abstract
We will first discuss the current knowledge about the genes and their functions underlying the biochemical pathways that determine pigmentation and then give examples where the mutations responsible for colour variation have been determined. Finally, we will discuss potential evolutionary causes for...
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PMID: 20229234
PDF is available here.
Christopher T Johansen,
Jian Wang,
Matthew B Lanktree,
Henian Cao,
Adam D McIntyre,
Matthew R Ban,
Rebecca A Martins,
Brooke A Kennedy,
Reina G Hassell,
Maartje E Visser,
Stephen M Schwartz,
Benjamin F Voight,
Roberto Elosua,
Veikko Salomaa,
Christopher J O'Donnell,
Geesje M Dallinga-Thie,
Sonia S Anand,
Salim Yusuf,
Murray W Huff,
Sekar Kathiresan and
Robert A Hegele
Abstract
We show an accumulation of rare variants, or a mutation skew, in GWAS-identified genes in individuals with hypertriglyceridemia (HTG). Through GWAS, we identified common variants in APOA5, GCKR, LPL and APOB associated with HTG. Resequencing of these genes revealed a significant burden of 154 rare m...
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PMID: 20657596
PDF is available here.
Abstract
We used DNA microarrays to compare the mRNAs in E13.5 mouse Lmx1b mutant and wild-type limbs. We report 14 genes that require Lmx1b for their normal expression in the dorsal limb or the restriction of their expression to the ventral limb....
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PMID: 20589901
PDF is available here.
Abstract
We have described a six-generation Pakistani consanguineous family with an autosomal recessive transmission of hereditary hypotrichosis. All the five affected individuals of the family showed complete absence of scalp hair and sparse eyebrows and eyelashes. They were born with complete absence of sc...
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PMID: 20544222
PDF is available here.
Abstract
We performed a whole genome linkage analysis in a three-generation south Indian family with multiple members affected with juvenile myoclonic epilepsy (JME). The maximum two-point LOD score obtained was 3.32 at recombination fraction (theta) = 0 for D2S2248. The highest multipoint score of 3.59 was...
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PMID: 20467754
PDF is available here.
Abstract
We identified 47 previously unreported unique CNVs in 45/255 probands. We prioritized ID candidate genes using five bioinformatic gene prioritization web tools. Gene priority lists were created by comparing integral genes from each CNV from our ID cohort with sets of training genes specific either t...
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PMID: 20512354
PDF is available here.
Abstract
We sought to identify genomic factors located on chromosome 18 as well as other loci that correlate with autistic behaviors. One hundred and five individuals with 18q- were assessed by high-resolution oligo aCGH and by parental ratings of behavior on the Gilliam Autism Rating Scale. Forty-five indiv...
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PMID: 20499253
PDF is available here.
Abstract
We present mechanistic evidence that suggests DNA methylation contributes to this regulation by suppressing premature gene activation. Using the mouse Myogenin promoter as an example of the weak CpG island class of promoters, we find that it is initially methylated but becomes demethylated as develo...
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PMID: 20498275
PDF is available here.
Abstract
We show by RNAPII chromatin immunoprecipitation (ChIP) that internal operon gene 5' ends do indeed lack Ser-5(P) peaks. In contrast, Ser-2(P) peaks occur at each mRNA 3' end, where the 3'-end formation machinery binds. These results provide additional support for the idea that the serine phosphoryla...
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PMID: 20498277
PDF is available here.
Abstract
We report the first genomic mutant phenotype of Drosophila melanogaster VHL (dVHL) in the epithelial tubule network, the trachea, and show that dVHL regulates branch migration and lumen formation via its endocytic function. The endocytic function regulates the surface level of the chemotactic signal...
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PMID: 20516215
PDF is available here.
Simon E Prochnik,
James Umen,
Aurora M Nedelcu,
Armin Hallmann,
Stephen M Miller,
Ichiro Nishii,
Patrick Ferris,
Alan Kuo,
Therese Mitros,
Lillian K Fritz-Laylin,
Uffe Hellsten,
Jarrod Chapman,
Oleg Simakov,
Stefan A Rensing,
Astrid Terry,
Jasmyn Pangilinan,
Vladimir Kapitonov,
Jerzy Jurka,
Asaf Salamov,
Harris Shapiro,
Jeremy Schmutz,
Jane Grimwood,
Erika Lindquist,
Susan Lucas,
Igor V Grigoriev,
Rüdiger Schmitt,
David Kirk and
Daniel S Rokhsar
Abstract
We sequenced the 138-mega-base pair genome of V. carteri and compared its approximately 14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding pot...
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PMID: 20616280
PDF is available here.
Victoria James,
Yining Zhang,
Daniel E Foxler,
Cornelia H de Moor,
Yi Wen Kong,
Thomas M Webb,
Tim J Self,
Yungfeng Feng,
Dimitrios Lagos,
Chia-Ying Chu,
Tariq M Rana,
Simon J Morley,
Gregory D Longmore,
Martin Bushell and
Tyson V Sharp
Abstract
We reveal the identification of a family of three LIM domain-containing proteins, LIMD1, Ajuba and WTIP (Ajuba LIM proteins) as novel mammalian processing body (P-body) components, which highlight a novel mechanism of miRNA-mediated gene silencing. Furthermore, we reveal that LIMD1, Ajuba, and WTIP...
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PMID: 20616046
PDF is available here.
Abstract
We found that Ywhaz and Rpl13a, not beta-actin or Gapdh, were the most stably expressed of the internal control genes in different passages of human umbilical cord mesenchymal stem cells. Ywhaz and Rpl13a could be used as reference genes for relative gene quantification and normalization purposes in...
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PMID: 20440577
PDF is available here.
Abstract
Perturbations in the cell cycle and apoptotic genes have been implicated in human malignancies. Cell cycle (MDM2 and Cyclin D1) and apoptotic (Fas) genes that are differentially expressed in urinary bladder cancer (UBC) were investigated with the susceptibility to UBC in northern India. A total of 2...
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PMID: 20380574
PDF is available here.
Abstract
An emerging literature attests to the ability of psychological stress to alter the inflammatory cytokine environment of the body. While the ability of stress to cause cytokine release is well established, the neural pathways involved in this control have yet to be identified. This study tests the hy...
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PMID: 20427720
PDF is available here.
Abstract
The present study focused on the identification of epistatic QTL pairs for body composition traits (carcass cut, lean tissue, and fat tissue weights) measured at slaughter weight (140 kg of BW) in a 3-generation full-sib population developed by crossing Pietrain sires with a crossbre...
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PMID: 20228239
PDF is available here.
Abstract
We assigned, by linkage mapping, the CTSD gene, a lysosomal proteinase, for which we previously identified an SNP in the 3'-untranslated region (AM933484, g.70G>A). We have already shown strong effects of this CTSD mutation on several production traits in Italian Large White pigs, suggesting a possi...
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PMID: 20382874
PDF is available here.
Abstract
We have sequenced the SWS1 opsin gene in a broader sample of species. We confirm that cysteine in the key amino acid position 90, characteristic of the UVS class, has been conserved throughout gull evolution but also that the terns Anous minutus, A. tenuirostris and Gygis alba, and the skimmer Rynch...
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PMID: 20015861
PDF is available here.
Abstract
We analyse the trade-off between the speed with which a gene can propagate information, the noise of its output and its metabolic cost. Our main finding is that for any given level of metabolic cost there is an optimal trade-off between noise and processing speed. Any system with a non-vanishing lea...
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PMID: 20007173
PDF is available here.
Abstract
Baculovirus is an effective vector for gene delivery into various mammalian cells, including chondrocytes and mesenchymal stem cells, and has been employed for diverse applications. By gene delivery and expression of the growth factor, recombinant baculovirus has been shown to modula...
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PMID: 20426760
PDF is available here.
Abstract
Modern drug discovery programs utilize a wide variety of technologies to aid in identification of potential drug targets, and progress them through the often long and winding path of finding novel drug-like molecules. Recombinant cell-based assays are an important tool in the drug di...
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PMID: 20392201
PDF is available here.
Abstract
We report on the modularity of the IGR IRESs and show that the ribosome-binding domain and the tRNA anticodon mimicry domain are functionally interchangeable between the Type I and the Type II IGR IRESs. Using structural probing, ribosome-binding assays, and ribosome positioning analysis by toeprint...
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PMID: 20423979
PDF is available here.
Siizkhuu Undarmaa,
Yoichi Mashimo,
Satoshi Hattori,
Naoki Shimojo,
Kimie Fujita,
Akihiko Miyatake,
Satoru Doi,
Yoichi Kohno,
Yoshitaka Okamoto,
Tomomitsu Hirota,
Mayumi Tamari,
Akira Hata and
Yoichi Suzuki
Abstract
We investigated the reproducibility of the 23 most promising asthma and asthma-related candidate genes in a moderately sized sample from the Japanese population. We compared the frequency of 33 polymorphisms in unrelated cases and controls and tested for their association with asthma, atopy and seru...
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PMID: 20395963
PDF is available here.
Abstract
We got inconsistent results with previous reports determining IkappaBalpha and C/EBPbeta mRNA expression levels. The results indicate the necessity for stability analysis of candidate reference genes in the CIH model. geNorm, NormFinder, and BestKeeper software analysis indicates that ACTB is the mo...
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PMID: 20153286
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
|
PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
|
PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
|
PMID: 19522873
PDF is available here.
Abstract
We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes....
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PMID: 19522873
PDF is available here.
Abstract
The results obtained in the present study made it possible to place selected markers responsible for development of the nervous and skeletal systems on the physical map of the donkey genome. Fluorescence in situ hybridization (FISH) was used to localize genes such as GDF5 (15q13), FRZB (4q23.1), TWI...
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PMID: 20626768
PDF is available here.
Abstract
We present model-based gene set analysis (MGSA) that analyzes all categories at once by embedding them in a Bayesian network, in which gene response is modeled as a function of the activation of biological categories. Probabilistic inference is used to identify the active categories. The Bayesian mo...
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PMID: 20172960
PDF is available here.
Abstract
Trimethyl chitosan-cysteine conjugate (TMC-Cys) was evaluated as non-viral gene carriers to combine the advantages of TMC and thiolated chitosan. TMC-Cys with various molecular weights (30, 100, and 200 kDa) and quaternization degrees (15 and 30%) was allowed to form polyelectrolyte nanocomplexes wi...
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PMID: 20093155
PDF is available here.