Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs  

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Full Text Available Abstract Background Differential coexpression analysis (DCEA is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones. Especially, the correlation-reversal is easily missed although it probably indicates remarkable biological significance. Results We developed two link-based quantitative methods, DCp and DCe, to identify differentially coexpressed genes and gene pairs (links. Bearing the uniqueness of exploiting the quantitative coexpression change of each gene pair in the coexpression networks, both methods proved to be superior to currently popular methods in simulation studies. Re-mining of a publicly available type 2 diabetes (T2D expression dataset from the perspective of differential coexpression analysis led to additional discoveries than those from differential expression analysis. Conclusions This work pointed out the critical weakness of current popular DCEA methods, and proposed two link-based DCEA algorithms that will make contribution to the development of DCEA and help extend it to a broader spectrum.

Ye Zhi-Qiang



Protein functional links in Trypanosoma brucei, identified by gene fusion analysis  

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Full Text Available Abstract Background Domain or gene fusion analysis is a bioinformatics method for detecting gene fusions in one organism by comparing its genome to that of other organisms. The occurrence of gene fusions suggests that the two original genes that participated in the fusion are functionally linked, i.e. their gene products interact either as part of a multi-subunit protein complex, or in a metabolic pathway. Gene fusion analysis has been used to identify protein functional links in prokaryotes as well as in eukaryotic model organisms, such as yeast and Drosophila. Results In this study we have extended this approach to include a number of recently sequenced protists, four of which are pathogenic, to identify fusion linked proteins in Trypanosoma brucei, the causative agent of African sleeping sickness. We have also examined the evolution of the gene fusion events identified, to determine whether they can be attributed to fusion or fission, by looking at the conservation of the fused genes and of the individual component genes across the major eukaryotic and prokaryotic lineages. We find relatively limited occurrence of gene fusions/fissions within the protist lineages examined. Our results point to two trypanosome-specific gene fissions, which have recently been experimentally confirmed, one fusion involving proteins involved in the same metabolic pathway, as well as two novel putative functional links between fusion-linked protein pairs. Conclusions This is the first study of protein functional links in T. brucei identified by gene fusion analysis. We have used strict thresholds and only discuss results which are highly likely to be genuine and which either have already been or can be experimentally verified. We discuss the possible impact of the identification of these novel putative protein-protein interactions, to the development of new trypanosome therapeutic drugs.

Trimpalis Philip



X inactivation testing for identifying a non-syndromic X-linked mental retardation gene. (United States)

The purpose of this study was to identify a gene causing non-syndromic X-linked mental retardation in an extended family, taking advantage of the X chromosome inactivation status of the females in order to determine their carrier state. X inactivation in the females was determined with the androgen receptor methylation assay; thereafter, the X chromosome was screened with evenly spaced polymorphic markers. Once initial linkage was identified, the region of interest was saturated with additional markers and the males were added to the analysis. Candidate genes were sequenced. Ten females showed skewed inactivation, while six revealed a normal inactivation pattern. A maximal lod score of 5.54 at ??=?0.00 was obtained with the marker DXS10151. Recombination events mapped the disease gene to a 17.4-Mb interval between the markers DXS10153 and DXS10157. Three candidate genes in the region were sequenced and a previously described missense mutation (P375L) was identified in the ACSL4/FACL4 gene. On the basis of the female X inactivation status, we have mapped and identified the causative mutation in a gene causing non-syndromic X-linked mental retardation. PMID:21584729

Yonath, Hagith; Marek-Yagel, Dina; Resnik-Wolf, Haike; Abu-Horvitz, Almogit; Baris, Hagit N; Shohat, Mordechai; Frydman, Moshe; Pras, Elon



Gene expression profiling after carbon ion irradiation in experimental murine tumors for identifying genes linked to its effectiveness using microarray analysis  

International Nuclear Information System (INIS)

To identify molecular mechanism of effectiveness induced by carbon-ion radiotherapy, we investigated expression profiles of murine tumors, which have various radiosensitivity for gamma irradiation, using microarrays consisting of 55k genes. Six murine tumors (squamous cell carcinoma: NR-S1, SCCVII, Fibrosarcoma: NFSa, no.8520, and Mammary carcinoma: MCano.4, MMCa) were transplanted in hind legs of C3H/Henirs mice and solid tumors were irradiated with either carbon-ion beam or gamma-ray. Growth rate of tumor, diminishing rate of tumor, recurrence rate, and cure rate were investigated as phenotype of radiosensitivity. Principal compornent analysis (PCA) was used to investigate similarity among expression profiles. Analysis of variance (ANOVA) was applied to the intensity of each tumor to evaluate significant differences. Pairwise comparisons were made by Wilcoxon test. All recurred tumors showed different profiles from non-irradiation control tumors and expression change of several hundreds genes were identified to be specific to recurred tumors. We detected several tens of genes, whose expressions were significantly up-regulated after carbon-irradiation for squamous cell carcinomas. Comparison of those expression intensity between radiosensitive (SCC-VII) and radioresistant (NR-S1) tumors revealed that carbon-irradiation caused differentially expressed genes, which were related with cell cycle arrest, Redox, or tumor necrosis factor (TNF) family, between radiosensitiveactor (TNF) family, between radiosensitive tumors and radioresistant tumors. (author)


Characterization of avrPphE, a gene for cultivar-specific avirulence from Pseudomonas syringae pv. phaseolicola which is physically linked to hrpY, a new hrp gene identified in the halo-blight bacterium. (United States)

The avirulence gene matching the R2 gene for resistance to halo-blight disease in Phaseolus was cloned and sequenced from race 4 strain 1302A of Pseudomonas syringae pv. phaseolicola. The predicted 41-kDa AvrPphE protein is hydrophilic, has no features that indicate function, and no similarity to other protein sequences. The promoter region of avrPphE contains a "harp box" motif. The gene was expressed more strongly in minimal than in nutrient-rich media. Lower concentrations of the phytoalexin phaseollin accumulated in tissue undergoing the hypersensitive reaction (HR) determined by avrPphE than by avrPphB. Homologs of avrPphE were detected in strains representing eight races of P. s. pv. phaseolicola including those virulent on cultivars with the R2 resistance gene, and in P. s. pv. tabaci but not in P. cichorii or P. s. pvs. coronafaciens, glycinea, maculicola, pisi, or syringae. Disruption of avrPphE prevented induction of the HR but did not appear to affect basic pathogenicity. Transposon mutagenesis and DNA sequencing showed that avrPphE was linked to hrpY a hrp locus identified at the left end of the hrp gene cluster. Sequence analysis showed that the region linked to avrPphE was very similar to DNA containing hrp genes from P. s. pv. syringae including hrpJ, hrpL, and hrpK. PMID:7873779

Mansfield, J; Jenner, C; Hockenhull, R; Bennett, M A; Stewart, R



Identifying links between origami and compliant mechanisms  


Origami is the art of folding paper. In the context of engineering, orimimetics is the application of folding to solve problems. Kinetic origami behavior can be modeled with the pseudo-rigid-body model since the origami are compliant mechanisms. These compliant mechanisms, when having a flat initial state and motion emerging out of the fabrication plane, are classified as lamina emergent mechanisms (LEMs). To demonstrate the feasibility of identifying links between origami and compliant mecha...

Greenberg, H. C.; Gong, M. L.; Magleby, S. P.; Howell, L. L.



Identifying links between origami and compliant mechanisms  

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Full Text Available Origami is the art of folding paper. In the context of engineering, orimimetics is the application of folding to solve problems. Kinetic origami behavior can be modeled with the pseudo-rigid-body model since the origami are compliant mechanisms. These compliant mechanisms, when having a flat initial state and motion emerging out of the fabrication plane, are classified as lamina emergent mechanisms (LEMs. To demonstrate the feasibility of identifying links between origami and compliant mechanism analysis and design methods, four flat folding paper mechanisms are presented with their corresponding kinematic and graph models. Principles from graph theory are used to abstract the mechanisms to show them as coupled, or inter-connected, mechanisms. It is anticipated that this work lays a foundation for exploring methods for LEM synthesis based on the analogy between flat-folding origami models and linkage assembly.

H. C. Greenberg



Gene expression profiling: can we identify the right target genes?  

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Full Text Available Gene expression profiling allows the simultaneous monitoring of the transcriptional behaviour of thousands of genes, which may potentially be involved in disease development. Several studies have been performed in idiopathic pulmonary fibrosis (IPF, which aim to define genetic links to the disease in an attempt to improve the current understanding of the underlying pathogenesis of the disease and target pathways for intervention. Expression profiling has shown a clear difference in gene expression between IPF and normal lung tissue, and has identified a wide range of candidate genes, including those known to encode for proteins involved in extracellular matrix formation and degradation, growth factors and chemokines. Recently, familial pulmonary fibrosis cohorts have been examined in an attempt to detect specific genetic mutations associated with IPF. To date, these studies have identified families in which IPF is associated with mutations in the gene encoding surfactant protein C, or with mutations in genes encoding components of telomerase. Although rare and clearly not responsible for the disease in all individuals, the nature of these mutations highlight the importance of the alveolar epithelium in disease pathogenesis and demonstrate the potential for gene expression profiling in helping to advance the current understanding of idiopathic pulmonary fibrosis.

J. E. Loyd



NIH Researchers Identify OCD Risk Gene (United States)

... News From NIH NIH Researchers Identify OCD Risk Gene Past Issues / Summer 2006 Table of Contents For ... and Alcoholism (NIAAA) have identified a previously unknown gene variant that doubles an individual's risk for obsessive- ...


Regulation of male fertility by X-linked genes (United States)

Infertility is a worldwide reproductive health problem, affecting men and women roughly equally. Mouse genetic studies demonstrate that more than two hundred genes specifically or predominantly regulate fertility. However, few genetic causes of infertility in humans have been identified. Here we focus on the regulation of male fertility by X-linked germ cell-specific genes. Previous genomic studies reveal that the mammalian X chromosome is enriched for genes expressed in early spermatogenesis. Recent genetic studies in mice show that X-linked germ cell-specific genes, such as Akap4, Nxf2, Taf7l, and Tex11, indeed play important roles in regulation of male fertility. Moreover, we find that the Taf7l Tex11 double mutant males exhibited much more severe defects in meiosis than either single mutant, suggesting that these two X-linked genes regulate male meiosis synergistically. The X-linked germ cell-specific genes are particularly attractive in the study of male infertility in humans. Because males are hemizygous for X-linked genes, loss-of-function mutations in the single copy X-linked genes, unlike in autosomal genes, would not be masked by a normal allele. The genetic studies of X-linked germ cell-specific genes in mice have laid a foundation for mutational analysis of their human orthologues in infertile men. PMID:19875494

Zheng, Ke; Yang, Fang; Wang, Peijing Jeremy



Linking the salt transcriptome with physiological responses of a salt-resistant Populus species as a strategy to identify genes important for stress acclimation.  


To investigate early salt acclimation mechanisms in a salt-tolerant poplar species (Populus euphratica), the kinetics of molecular, metabolic, and physiological changes during a 24-h salt exposure were measured. Three distinct phases of salt stress were identified by analyses of the osmotic pressure and the shoot water potential: dehydration, salt accumulation, and osmotic restoration associated with ionic stress. The duration and intensity of these phases differed between leaves and roots. T...

Brinker, Monika; Brosche?, Mikael; Vinocur, Basia; Abo-ogiala, Atef; Fayyaz, Payam; Janz, Dennis; Ottow, Eric A.; Cullmann, Andreas D.; Saborowski, Joachim; Kangasja?rvi, Jaakko; Altman, Arie; Polle, Andrea



Scan-statistic approach identifies clusters of rare disease variants in LRP2, a gene linked and associated with autism spectrum disorders, in three datasets. (United States)

Cluster-detection approaches, commonly used in epidemiology and astronomy, can be applied in the context of genetic sequence data for the identification of genetic regions significantly enriched with rare disease-risk variants (DRVs). Unlike existing association tests for sequence data, the goal of cluster-detection methods is to localize significant disease mutation clusters within a gene or region of interest. Here, we focus on a chromosome 2q replicated linkage region that is associated with autism spectrum disorder (ASD) and that has been sequenced in three independent datasets. We found that variants in one gene, LRP2, residing on 2q are associated with ASD in two datasets (the combined variable-threshold-test p value is 1.2 × 10(-5)). Using a cluster-detection method, we show that in the discovery and replication datasets, variants associated with ASD cluster preponderantly in 25 kb windows (adjusted p values are p(1) = 0.003 and p(2) = 0.002), and the two windows are highly overlapping. Furthermore, for the third dataset, a 25 kb region similar to those in the other two datasets shows significant evidence of enrichment of rare DRVs. The region implicated by all three studies is involved in ligand binding, suggesting that subtle alterations in either LRP2 expression or LRP2 primary sequence modulate the uptake of LRP2 ligands. BMP4 is a ligand of particular interest given its role in forebrain development, and modest changes in BMP4 binding, which binds to LRP2 near the mutation cluster, might subtly affect development and could lead to autism-associated phenotypes. PMID:22578327

Ionita-Laza, Iuliana; Makarov, Vlad; Buxbaum, Joseph D



QTLminer: identifying genes regulating quantitative traits  


Abstract Background Quantitative trait locus (QTL) mapping identifies genomic regions that likely contain genes regulating a quantitative trait. However, QTL regions may encompass tens to hundreds of genes. To find the most promising candidate genes that regulate the trait, the biologist typically collects information from multiple resources about the genes in the QTL interval. This process is very laborious and time consuming. Results QTLminer is a bioinformati...

Schughart Klaus; Alberts Rudi



QTLminer: identifying genes regulating quantitative traits  

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Full Text Available Abstract Background Quantitative trait locus (QTL mapping identifies genomic regions that likely contain genes regulating a quantitative trait. However, QTL regions may encompass tens to hundreds of genes. To find the most promising candidate genes that regulate the trait, the biologist typically collects information from multiple resources about the genes in the QTL interval. This process is very laborious and time consuming. Results QTLminer is a bioinformatics tool that automatically performs QTL region analysis. It is available in GeneNetwork and it integrates information such as gene annotation, gene expression and sequence polymorphisms for all the genes within a given genomic interval. Conclusions QTLminer substantially speeds up discovery of the most promising candidate genes within a QTL region.

Schughart Klaus



Regulation of male fertility by X-linked genes  


Infertility is a worldwide reproductive health problem, affecting men and women roughly equally. Mouse genetic studies demonstrate that more than two hundred genes specifically or predominantly regulate fertility. However, few genetic causes of infertility in humans have been identified. Here we focus on the regulation of male fertility by X-linked germ cell-specific genes. Previous genomic studies reveal that the mammalian X chromosome is enriched for genes expressed in early spermatogenesis...

Zheng, Ke; Yang, Fang; Wang, Peijing Jeremy



Scientists Spot Gene Linked to Tanning 'Addiction' (United States)

... enable JavaScript. Scientists Spot Gene Linked to Tanning 'Addiction' Understanding biology behind dependence important because of rising ... variant may be more likely to develop an "addiction" to tanning, a preliminary study suggests. The idea ...


Identifying Design Requirements for Wireless Routing Link Metrics  

CERN Document Server

In this paper, we identify and analyze the requirements to design a new routing link metric for wireless multihop networks. Considering these requirements, when a link metric is proposed, then both the design and implementation of the link metric with a routing protocol become easy. Secondly, the underlying network issues can easily be tackled. Thirdly, an appreciable performance of the network is guaranteed. Along with the existing implementation of three link metrics Expected Transmission Count (ETX), Minimum Delay (MD), and Minimum Loss (ML), we implement inverse ETX; invETX with Optimized Link State Routing (OLSR) using NS-2.34. The simulation results show that how the computational burden of a metric degrades the performance of the respective protocol and how a metric has to trade-off between different performance parameters.

Javaid, Nadeem; Djouani, Karim



Second Gene Linked to Familial Testicular Cancer (United States)

Specific variations or mutations in a particular can gene raise a man's risk of familial, or inherited, testicular germ-cell cancer, the most common form of this disease, according to new research by scientists at the National Institutes of Health. This is only the second gene to be identified that affects the risk of familial testicular cancer, and the first gene in a key biochemical pathway.


Gene expression analysis identifies global gene dosage sensitivity in cancer. (United States)

Many cancer-associated somatic copy number alterations (SCNAs) are known. Currently, one of the challenges is to identify the molecular downstream effects of these variants. Although several SCNAs are known to change gene expression levels, it is not clear whether each individual SCNA affects gene expression. We reanalyzed 77,840 expression profiles and observed a limited set of 'transcriptional components' that describe well-known biology, explain the vast majority of variation in gene expression and enable us to predict the biological function of genes. On correcting expression profiles for these components, we observed that the residual expression levels (in 'functional genomic mRNA' profiling) correlated strongly with copy number. DNA copy number correlated positively with expression levels for 99% of all abundantly expressed human genes, indicating global gene dosage sensitivity. By applying this method to 16,172 patient-derived tumor samples, we replicated many loci with aberrant copy numbers and identified recurrently disrupted genes in genomically unstable cancers. PMID:25581432

Fehrmann, Rudolf S N; Karjalainen, Juha M; Krajewska, Ma?gorzata; Westra, Harm-Jan; Maloney, David; Simeonov, Anton; Pers, Tune H; Hirschhorn, Joel N; Jansen, Ritsert C; Schultes, Erik A; van Haagen, Herman H H B M; de Vries, Elisabeth G E; Te Meerman, Gerard J; Wijmenga, Cisca; van Vugt, Marcel A T M; Franke, Lude



Identifying Gene Interaction Enrichment for Gene Expression Data  


Gene set analysis allows the inclusion of knowledge from established gene sets, such as gene pathways, and potentially improves the power of detecting differentially expressed genes. However, conventional methods of gene set analysis focus on gene marginal effects in a gene set, and ignore gene interactions which may contribute to complex human diseases. In this study, we propose a method of gene interaction enrichment analysis, which incorporates knowledge of predefined gene sets (e.g. gene ...

Zhang, Jigang; Li, Jian; Deng, Hong-wen



A Glucose-to-Gene Link (United States)

Access to the article is free, however registration and sign-in are required. Eukaryotic cell growth demands an increase in glucose uptake and metabolism to support energetic and biosynthetic needs, accompanied by changes in gene expression that control cell lineage or fate. These gene expression patterns are determined by lineage-specific or differentiation stageâÂÂspecific transcription factors, as well as by modifications of chromatin (the complex of nucleic acids and proteins that constitute chromosomes) that regulate access of transcription factors to specific DNA loci. On page 1076 of this issue, Wellen et al. propose a new mechanism to link glucose metabolism to chromatin modification and global transcriptional control via the enzyme ATP-citrate lyase and production of acetylâÂÂcoenzyme A (acetyl-CoA) (1).

Jeffrey C. Rathmell (Duke University Medical Center;); Christopher B. Newgard (Duke University Medical Center;)



Gene Mutations Linked to Colon Cancer in Black Patients (United States)

... sharing features on this page, please enable JavaScript. Gene Mutations Linked to Colon Cancer in Black Patients ... Related MedlinePlus Pages African American Health Colorectal Cancer Genes and Gene Therapy TUESDAY, Jan. 13, 2015 (HealthDay ...


Expression profiling identifies genes involved in emphysema severity  

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Full Text Available Abstract Chronic obstructive pulmonary disease (COPD is a major public health problem. The aim of this study was to identify genes involved in emphysema severity in COPD patients. Gene expression profiling was performed on total RNA extracted from non-tumor lung tissue from 30 smokers with emphysema. Class comparison analysis based on gas transfer measurement was performed to identify differentially expressed genes. Genes were then selected for technical validation by quantitative reverse transcriptase-PCR (qRT-PCR if also represented on microarray platforms used in previously published emphysema studies. Genes technically validated advanced to tests of biological replication by qRT-PCR using an independent test set of 62 lung samples. Class comparison identified 98 differentially expressed genes (p p Gene expression profiling of lung from emphysema patients identified seven candidate genes associated with emphysema severity including COL6A3, SERPINF1, ZNHIT6, NEDD4, CDKN2A, NRN1 and GSTM3.

Bowman Rayleen V



Identifying genes and gene networks involved in chromium metabolism and detoxification in Crambe abyssinica  

Energy Technology Data Exchange (ETDEWEB)

Chromium pollution is a serious environmental problem with few cost-effective remediation strategies available. Crambe abyssinica (a member of Brassicaseae), a non-food, fast growing high biomass crop, is an ideal candidate for phytoremediation of heavy metals contaminated soils. The present study used a PCR-Select Suppression Subtraction Hybridization approach in C. abyssinica to isolate differentially expressed genes in response to Cr exposure. A total of 72 differentially expressed subtracted cDNAs were sequenced and found to represent 43 genes. The subtracted cDNAs suggest that Cr stress significantly affects pathways related to stress/defense, ion transporters, sulfur assimilation, cell signaling, protein degradation, photosynthesis and cell metabolism. The regulation of these genes in response to Cr exposure was further confirmed by semi-quantitative RT-PCR. Characterization of these differentially expressed genes may enable the engineering of non-food, high-biomass plants, including C. abyssinica, for phytoremediation of Cr-contaminated soils and sediments. - Highlights: > Molecular mechanism of Cr uptake and detoxification in plants is not well known. > We identified differentially regulated genes upon Cr exposure in Crambe abyssinica. > 72 Cr-induced subtracted cDNAs were sequenced and found to represent 43 genes. > Pathways linked to stress, ion transport, and sulfur assimilation were affected. > This is the first Cr transcriptome study in a crop with phytoremediation potential. - This study describes the identification and isolation of differentially expressed genes involved in chromium metabolism and detoxification in a non-food industrial oil crop Crambe abyssinica.

Zulfiqar, Asma, E-mail: [Department of Plant, Soil, and Insect Sciences, 270 Stockbridge Road, University of Massachusetts Amherst, MA 01003 (United States); Paulose, Bibin, E-mail: [Department of Plant, Soil, and Insect Sciences, 270 Stockbridge Road, University of Massachusetts Amherst, MA 01003 (United States); Chhikara, Sudesh, E-mail: [Department of Plant, Soil, and Insect Sciences, 270 Stockbridge Road, University of Massachusetts Amherst, MA 01003 (United States); Dhankher, Om Parkash, E-mail: [Department of Plant, Soil, and Insect Sciences, 270 Stockbridge Road, University of Massachusetts Amherst, MA 01003 (United States)



Identifying leaf rust resistance genes and mapping gene Lr37 on the microsatellite map of wheat. (United States)

Based on seedling resistance tests, five resistance genes (Lr10, Lr3, Lr13, Lr14a and Lr37) against leaf rust (Puccinia triticina) were identified in 16 cultivars of European winter wheat. STS and SCAR markers were used to verify the presence of the resistance genes Lr37 and Lr10 against leaf rust in cultivars, near-isogenic lines and segregating populations. The Lr37 gene is present in a small translocation from Triticum ventricosum Ces. (Aegilops ventricosa Tausch) and is tightly linked with resistance genes Yr17 and Sr38. The Lr37 gene was identified in the cultivars Kris, Clever, Slade, Apache, Caphorn, Lorraine, Balthasar, Renan and confirmed by two PCR markers. The F3 progenies of the crosses Kris (Lr37) X Nutka (Lr37 not present) were used for map construction. Two STS/SCAR markers specific for Lr37 were mapped in relation to nine polymorphic microsatellites on chromosome 2AS. The microsatellite marker Xgwm1176 mapped relatively close to the STS and SCAR markers for Lr37 with a linkage distance of 4.1 cM. PMID:15647803

B?aszczyk, Lidia; Goyeau, Henriette; Huang, Xiu-Qiang; Röder, Marion; Stepie?, Lukasz; Che?kowski, Jerzy



Refined mapping of X-linked reticulate pigmentary disorder and sequencing of candidate genes  


X-linked reticulate pigmentary disorder with systemic manifestations in males (PDR) is very rare. Affected males are characterized by cutaneous and visceral symptoms suggestive of abnormally regulated inXammation. A genetic linkage study of a large Canadian kindred previously mapped the PDR gene to a greater than 40 Mb interval of Xp22–p21. The aim of this study was to identify the causative gene for PDR. The Canadian pedigree was expanded and additional PDR families recruited. Genetic link...

Santos, Lane J. Jaeckle; Xing, Chao; Barnes, Robert B.; Ades, Lesley C.; Megarbane, Andre; Vidal, Christopher; Xuereb, Angela; Tarpey, Patrick S.; Smith, Raffaella; Khazab, Mahmoud; Shoubridge, Cheryl; Partington, Michael; Futreal, Andrew; Stratton, Michael R.; Gecz, Jozef




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Full Text Available Search Engines are used for retrieving the information from the web. Most of the times, the importance is laid on top 10 results sometimes it may shrink as top 5, because of the time constraint and reliability on the search engines. Users believe that top 10 or 5 of total results are more relevant. Here comes the problem of spamdexing. It is a method to deceive the search result quality. Falsified metrics such as inserting enormous amount of keywords or links in website may take that website to the top 10 or 5 positions. This paper proposes a classifier based on the Reptree (Regression tree representative. As an initial step Link-based features such as neighbors, pagerank, truncated pagerank, trustrank and assortativity related attributes are inferred. Based on this features, tree is constructed. The tree uses the feature inference to differentiate spam sites from legitimate sites. WEBSPAM-UK-2007 dataset is taken as a base. It is preprocessed and converted into five datasets FEATA, FEATB, FEATC, FEATD and FEATE. Only link based features are taken for experiments. This paper focus on link spam alone. Finally a representative tree is created which will more precisely classify the web spam entries. Results are given. Regression tree classification seems to perform well as shown through experiments.

S.K. Jayanthi





Search Engines are used for retrieving the information from the web. Most of the times, the importance is laid on top 10 results sometimes it may shrink as top 5, because of the time constraint and reliability on the search engines. Users believe that top 10 or 5 of total results are more relevant. Here comes the problem of spamdexing. It is a method to deceive the search result quality. Falsified metrics such as inserting enormous amount of keywords or links in website may take that website ...

Jayanthi, S. K.; Sasikala, S.



A search for additional X-linked genes affecting sex determination in Drosophila melanogaster  


The gene Sex-lethal (Sxl) plays a pivotal role in Drosophila sexual development. Once activated in response to the X:A ratio signal in XX embryos, Sri participates in appropriate implementation of all known aspects of sexual differentiation. We have attempted to identify new X-linked genes involved in sex determination, especially those involved in the regulation of Sri. Since misregulation of Sri, or that of the genes that regulate it, leads to female-specific lethality, or synergistic femal...

Anand, Anuranjan; Das Gupta, Aindrilla; Sudha, S.; Raghavan, S.; Chandrah, Sharat H.



Identifying genes and gene networks involved in chromium metabolism and detoxification in Crambe abyssinica  

International Nuclear Information System (INIS)

Chromium pollution is a serious environmental problem with few cost-effective remediation strategies available. Crambe abyssinica (a member of Brassicaseae), a non-food, fast growing high biomass crop, is an ideal candidate for phytoremediation of heavy metals contaminated soils. The present study used a PCR-Select Suppression Subtraction Hybridization approach in C. abyssinica to isolate differentially expressed genes in response to Cr exposure. A total of 72 differentially expressed subtracted cDNAs were sequenced and found to represent 43 genes. The subtracted cDNAs suggest that Cr stress significantly affects pathways related to stress/defense, ion transporters, sulfur assimilation, cell signaling, protein degradation, photosynthesis and cell metabolism. The regulation of these genes in response to Cr exposure was further confirmed by semi-quantitative RT-PCR. Characterization of these differentially expressed genes may enable the engineering of non-food, high-biomass plants, including C. abyssinica, for phytoremediation of Cr-contaminated soils and sediments. - Highlights: ? Molecular mechanism of Cr uptake and detoxification in plants is not well known. ? We identified differentially regulated genes upon Cr exposure in Crambe abyssinica. ? 72 Cr-induced subtracted cDNAs were sequenced and found to represent 43 genes. ? Pathways linked to stress, ion transport, and sulfur assimilation were affected. ? This is the first Cr transcriptome study in a crop w transcriptome study in a crop with phytoremediation potential. - This study describes the identification and isolation of differentially expressed genes involved in chromium metabolism and detoxification in a non-food industrial oil crop Crambe abyssinica.


Identifying local co-regulation relationships in gene expression data. (United States)

Identifying interesting relationships between pairs of genes, presented over some of experimental conditions in gene expression data set, is useful for discovering novel functional gene interactions. In this paper, we introduce a new method for id entifying L ocal C o-regulation R elationships (IdLCR). These local relationships describe the behaviors of pairwise genes, which are either up- or down-regulated throughout the identified condition subset. IdLCR firstly detects the pairwise gene-gene relationships taking functional forms and the condition subsets by using a regression spline model. Then it measures the relationships using a penalized Pearson correlation and ranks the responding gene pairs by their scores. By this way, those relationships without clearly biological interpretations can be filtered out and the local co-regulation relationships can be obtained. In the simulation data sets, ten different functional relationships are embedded. Applying IdLCR to these data sets, the results show its ability to identify functional relationships and the condition subsets. For micro-array and RNA-seq gene expression data, IdLCR can identify novel biological relationships which are different from those uncovered by IFGR and MINE. PMID:25042175

Pei, Yonggang; Gao, Qinghui; Li, Juntao; Zhao, Xiting



Globicatella bacteraemia identified by 16S ribosomal RNA gene sequencing  


Background: Globicatella are streptococcus-like organisms that have been rarely isolated from clinical specimens. Their epidemiology and clinical significance remain largely unknown. Aims: To describe two cases of Globicatella bacteraemia identified by 16S ribosomal RNA (rRNA) gene sequencing. Methods: Two unidentified streptococcus-like bacteria isolated from blood cultures of patients were subject to 16S rRNA gene sequencing. Results: Two cases of Globicatella bacteraemia were identified by...

Lau, S. K. P.; Woo, P. C. Y.; Li, N. K. H.; Teng, J. L. L.; Leung, K?w; Ng, K. H. L.; Que, T?l; Yuen, K?y



Identifying genes preferentially expressed in undifferentiated embryonic stem cells  

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Full Text Available Abstract Background The mechanism involved in the maintenance and differentiation of embryonic stem (ES cells is incompletely understood. Results To address this issue, we have developed a retroviral gene trap vector that can target genes expressed in undifferentiated ES cells. This gene trap vector harbors both GFP and Neo reporter genes. G-418 drug resistance was used to select ES clones in which the vector was integrated into transcriptionally active loci. This was then followed by GFP FACS profiling to identify ES clones with reduced GFP fluorescence and, hence, reduced transcriptional activity when ES cells differentiate. Reduced expression of the GFP reporter in six of three hundred ES clones in our pilot screening was confirmed to be down-regulated by Northern blot analysis during ES cell differentiation. These six ES clones represent four different genes. Among the six integration sites, one was at Zfp-57 whose gene product is known to be enriched in undifferentiated ES cells. Three were located in an intron of a novel isoform of CSL/RBP-Jkappa which encodes the key transcription factor of the LIN-12/Notch pathway. Another was inside a gene that may encode noncoding RNA transcripts. The last integration event occurred at a locus that may harbor a novel gene. Conclusion Taken together, we demonstrate the use of a novel retroviral gene trap vector in identifying genes preferentially expressed in undifferentiated ES cells.

Leder Philip



Amplification of the X-linked Drosophila chorion gene cluster requires a region upstream from the s38 chorion gene.  


Genomic sequences controlling follicle cell-specific amplification of the X-linked Drosophila chorion gene cluster were mapped by P element-mediated transformation. Several DNA fragments containing the s38 gene and flanking sequences induced tissue-specific amplification, although replication levels were subject to position effects. Deletion analysis identified a 467-bp region upstream from the s38 transcription start site that contained sequences essential in cis for amplification. The essen...

Spradling, A. C.; Cicco, D. V.; Wakimoto, B. T.; Levine, J. F.; Kalfayan, L. J.; Cooley, L.



Gene variant linked to lung cancer risk (United States)

A variation of the gene NFKB1, called rs4648127, is associated with an estimated 44 percent reduction in lung cancer risk. When this information, derived from samples obtained as part of a large NCI-sponsored prevention clinical trial, was compared with data on a different sample collection from NCI’s genome-wide association studies (GWAS), lung cancer risk was still estimated to be lower, but only by 21 percent.


News Note: Scientists identify molecular link between BRCA1 protein levels and obesity (United States)

NCI researchers have defined a possible molecular link between breast cancer risk and obesity. New study results show that a protein called C-terminal binding protein (CtBP) acts to control a gene linked to breast cancer risk in rapidly growing cells by monitoring and responding to how the cells use and store energy (metabolic state).


A gene sets approach for identifying prognostic gene signatures for outcome prediction  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Gene expression profiling is a promising approach to better estimate patient prognosis; however, there are still unresolved problems, including little overlap among similarly developed gene sets and poor performance of a developed gene set in other datasets. Results We applied a gene sets approach to develop a prognostic gene set from multiple gene expression datasets. By analyzing 12 independent breast cancer gene expression datasets comprising 1,756 tissues with 2,411 pre-defined gene sets including gene ontology categories and pathways, we found many gene sets that were prognostic in most of the analyzed datasets. Those prognostic gene sets were related to biological processes such as cell cycle and proliferation and had additional prognostic values over conventional clinical parameters such as tumor grade, lymph node status, estrogen receptor (ER status, and tumor size. We then estimated the prediction accuracy of each gene set by performing external validation using six large datasets and identified a gene set with an average prediction accuracy of 67.55%. Conclusion A gene sets approach is an effective method to develop prognostic gene sets to predict patient outcome and to understand the underlying biology of the developed gene set. Using the gene sets approach we identified many prognostic gene sets in breast cancer.

Kim Yong Sung



Cellular senescence bypass screen identifies new putative tumor suppressor genes. (United States)

Senescence is a mechanism that limits cellular lifespan and constitutes a barrier against cellular immortalization. To identify new senescence regulatory genes that might play a role in tumorigenesis, we have designed and performed a large-scale antisense-based genetic screen in primary mouse embryo fibroblasts (MEFs). Out of this screen, we have identified five different genes through which loss of function partially bypasses senescence. These genes belong to very different biochemical families: csn2 (component of the Cop9 signalosome), aldose reductase (a metabolic enzyme) and brf1 (subunit of the RNA polymerase II complex), S-adenosyl homocysteine hydrolase and Bub1. Inactivation, at least partial, of these genes confers resistance to both p53- and p16INK4a-induced proliferation arrest. Furthermore, such inactivation inhibits p53 but not E2F1 transcriptional activity and impairs DNA-damage-induced transcription of p21. Since the aim of the screen was to identify new regulators of tumorigenesis, we have tested their inactivation in human tumors. We have found, either by northern blot or quantitative reverse transcriptase-PCR analysis, that the expression of three genes, Csn2, Aldose reductase and Brf1, is lost at different ratios in tumors of different origins. These genes are located at common positions of loss of heterogeneity (15q21.2, 7q35 and 14q32.33); therefore,we have measured genomic losses of these specific genes in different tumors. We have found that Csn2 and Brf1 also show genomic losses of one allele in different tumors. Our data suggest that the three genes identified in the genome-wide loss-of-function genetic screen are putative tumor suppressors located at 15q21.2; 7q35 and 14q32.33. PMID:17968325

Leal, J F M; Fominaya, J; Cascón, A; Guijarro, M V; Blanco-Aparicio, C; Lleonart, M; Castro, M E; Ramon Y Cajal, S; Robledo, M; Beach, D H; Carnero, A



Scientists Identify Four Candidate Obesity Genes in Mice (United States)

Press release on a recent study where researchers developed a strain of mice more likely to be obese and then, using this strain, identified four genes in mouse chromosome 7 that may relate to obesity. This study, Â?Four Out of Eight Genes in a Mouse Chromosome 7 Congenic Donor Region are Candidate Obesity Genes,Â? was conducted by Craig H. Warden, Kari A. Sarahan, and Janis S. Fisler of the University of California, Davis. The study is published in Physiologic Genomics.

APS Communications Office (American Physiological Society Communications Office)



Gene-based Association Approach Identify Genes Across Stress Traits in Fruit Flies  

DEFF Research Database (Denmark)

Identification of genes explaining variation in quantitative traits or genetic risk factors of human diseases requires both good phenotypic- and genotypic data, but also efficient statistical methods. Genome-wide association studies may reveal association between phenotypic variation and variation at nucleotide level, thus potentially identify genetic variants. However, testing million of polymorphic nucleotide positions requires conservative correction for multiple testing which lowers the probability of finding genes with small to moderate effects. To alleviate this, we apply a gene based association approach grouping variants accordingly to gene position, thus lowering the number of statistical tests performed and increasing the probability of identifying genes with small to moderate effects. Using this approach we identify numerous genes associated with different types of stresses in Drosophila melanogaster, but also identify common genes that affects the stress traits.

Rohde, Palle Duun; Edwards, Stefan McKinnon


Identifying gene regulatory modules of heat shock response in yeast  

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Full Text Available Abstract Background A gene regulatory module (GRM is a set of genes that is regulated by the same set of transcription factors (TFs. By organizing the genome into GRMs, a living cell can coordinate the activities of many genes in response to various internal and external stimuli. Therefore, identifying GRMs is helpful for understanding gene regulation. Results Integrating transcription factor binding site (TFBS, mutant, ChIP-chip, and heat shock time series gene expression data, we develop a method, called Heat-Inducible Module Identification Algorithm (HIMIA, for reconstructing GRMs of yeast heat shock response. Unlike previous module inference tools which are static statistics-based methods, HIMIA is a dynamic system model-based method that utilizes the dynamic nature of time series gene expression data. HIMIA identifies 29 GRMs, which in total contain 182 heat-inducible genes regulated by 12 heat-responsive TFs. Using various types of published data, we validate the biological relevance of the identified GRMs. Our analysis suggests that different combinations of a fairly small number of heat-responsive TFs regulate a large number of genes involved in heat shock response and that there may exist crosstalk between heat shock response and other cellular processes. Using HIMIA, we identify 68 uncharacterized genes that may be involved in heat shock response and we also identify their plausible heat-responsive regulators. Furthermore, HIMIA is capable of assigning the regulatory roles of the TFs that regulate GRMs and Cst6, Hsf1, Msn2, Msn4, and Yap1 are found to be activators of several GRMs. In addition, HIMIA refines two clusters of genes involved in heat shock response and provides a better understanding of how the complex expression program of heat shock response is regulated. Finally, we show that HIMIA outperforms four current module inference tools (GRAM, MOFA, ReMoDisvovery, and SAMBA, and we conduct two randomization tests to show that the output of HIMIA is statistically meaningful. Conclusion HIMIA is effective for reconstructing GRMs of yeast heat shock response. Indeed, many of the reconstructed GRMs are in agreement with previous studies. Further, HIMIA predicts several interesting new modules and novel TF combinations. Our study shows that integrating multiple types of data is a powerful approach to studying complex biological systems.

Li Wen-Hsiung



Identification of DNA markers linked to a blast resistance gene in rice  

International Nuclear Information System (INIS)

Identification of DNA markers closely linked to a blast (Pyricularia oryzae Cav.) resistance gene and establishment of an indirect selection method for the blast resistance gene based on linked DNA markers are reported. A pair of near isogenic lines, K80R and K79S, were developed using a local Chinese indica rice cultivar, Hong-jiao-zhan, as the resistant donor and IR24 as the recurrent parent. Ten putatitvely positive markers were identified by screening 177 mapped DNA markers. Using 143 plants composed of the F2 population of K80R/K79S, three restriction fragment length polymorphism (RFLP) markers (RG81, RG869 and RZ397) on chromosome 12 of rice were verified to be closely linked to the blast resistance gene. The resistance genotypes of each F2 resistant individual were determined by inoculation of the F3 lines. RG869 was found to be most closely linked to the resistance gene, with a genetic distance of 5.1 cM. To fine map this gene with more DNA markers, the bulk segregation analysis procedure was employed to identify the random amplified polymorphic DNA (RAPD) markers linked to the resistance gene. Six of 199 arbitrary primers were able to produce positive RAPD bands. Tight linkage between the resistance gene and the three RAPD bands, each from a different primer, was confirmed after amplification of the DNA of all the F2 individuals. The linked DNA fragments were cloned and sequenced. The results of specific amplificatienced. The results of specific amplification were in agreement with those of RAPD analysis. The half-seed RAPD analysis procedure for blast resistance detection was established. The amplified DNA patterns on the extract from the endosperm half of the mature seeds were identical to those of the total DNA from the leaves. (author). 13 refs, 3 figs


International team identifies critical genes mutated in stomach cancer (United States)

An international team of scientists, led by researchers from the Duke-NUS Graduate Medical School in Singapore and National Cancer Centre of Singapore, has identified hundreds of novel genes that are mutated in stomach cancer, the second-most lethal cancer worldwide.


Gene identified that sensitizes cancer cells to chemotherapy drugs (United States)

NCI scientists have found that a gene, Schlafen-11 (SLFN11), sensitizes cells to substances known to cause irreparable damage to DNA.  As part of their study, the researchers used a repository of 60 cell types to identify predictors of cancer cell response to classes of DNA damaging agents, widely used as chemotherapy treatments for many cancers.


Crossref an update on article level linking and digital object identifiers  

CERN Multimedia

Description of the CrossRef initiative, "an independent non-profit membership organization that was established by the publishing community to permit article linking based on digital object identifiers (DOIs)" (1 page).



PhenoLink - a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Linking phenotypes to high-throughput molecular biology information generated by ~omics technologies allows revealing cellular mechanisms underlying an organism's phenotype. ~Omics datasets are often very large and noisy with many features (e.g., genes, metabolite abundances. Thus, associating phenotypes to ~omics data requires an approach that is robust to noise and can handle large and diverse data sets. Results We developed a web-tool PhenoLink ( that links phenotype to ~omics data sets using well-established as well new techniques. PhenoLink imputes missing values and preprocesses input data (i to decrease inherent noise in the data and (ii to counterbalance pitfalls of the Random Forest algorithm, on which feature (e.g., gene selection is based. Preprocessed data is used in feature (e.g., gene selection to identify relations to phenotypes. We applied PhenoLink to identify gene-phenotype relations based on the presence/absence of 2847 genes in 42 Lactobacillus plantarum strains and phenotypic measurements of these strains in several experimental conditions, including growth on sugars and nitrogen-dioxide production. Genes were ranked based on their importance (predictive value to correctly predict the phenotype of a given strain. In addition to known gene to phenotype relations we also found novel relations. Conclusions PhenoLink is an easily accessible web-tool to facilitate identifying relations from large and often noisy phenotype and ~omics datasets. Visualization of links to phenotypes offered in PhenoLink allows prioritizing links, finding relations between features, finding relations between phenotypes, and identifying outliers in phenotype data. PhenoLink can be used to uncover phenotype links to a multitude of ~omics data, e.g., gene presence/absence (determined by e.g.: CGH or next-generation sequencing, gene expression (determined by e.g.: microarrays or RNA-seq, or metabolite abundance (determined by e.g.: GC-MS.

Bayjanov Jumamurat R



RAPD markers linked to the Vf gene for scab resistance in apple. (United States)

Scab (Venturia inaequalis) is one of the most harmful diseases of apple, significantly affecting world apple production. The identification and early selection of resistant genotypes by molecular markers would greatly improve breeding strategies. Bulked segregant analysis was chosen for the identification of RAPD markers linked to the Vf scab resistant gene. Five different RAPD markers, derived from the wild species Malus floribunda. 821, were identified, and their genetic distance from Vf gene was estimated. The markers OPAM192200 and OPAL07580 were found to be very closely linked to the Vf gene. This result was indirectly confirmed by the analysis of resistant genotypes collected from various breeding programmes. Except for cv 'Murray', which carries the Vm gene, all these resistant genotypes showed the markers OPAM192200 and OPAL07580. PMID:24166544

Tartarini, S



Leveraging Administrative Data for Program Evaluations: A Method for Linking Data Sets Without Unique Identifiers. (United States)

In community-based wellness programs, Social Security Numbers (SSNs) are rarely collected to encourage participation and protect participant privacy. One measure of program effectiveness includes changes in health care utilization. For the 65 and over population, health care utilization is captured in Medicare administrative claims data. Therefore, methods as described in this article for linking participant information to administrative data are useful for program evaluations where unique identifiers such as SSN are not available. Following fuzzy matching methodologies, participant information from the National Study of the Chronic Disease Self-Management Program was linked to Medicare administrative data. Linking variables included participant name, date of birth, gender, address, and ZIP code. Seventy-eight percent of participants were linked to their Medicare claims data. Linking program participant information to Medicare administrative data where unique identifiers are not available provides researchers with the ability to leverage claims data to better understand program effects. PMID:25139849

Lorden, Andrea L; Radcliff, Tiffany A; Jiang, Luohua; Horel, Scott A; Smith, Matthew L; Lorig, Kate; Howell, Benjamin L; Whitelaw, Nancy; Ory, Marcia



Animal models of GWAS-identified type 2 diabetes genes. (United States)

More than 65 loci, encoding up to 500 different genes, have been implicated by genome-wide association studies (GWAS) as conferring an increased risk of developing type 2 diabetes (T2D). Whilst mouse models have in the past been central to understanding the mechanisms through which more penetrant risk genes for T2D, for example, those responsible for neonatal or maturity-onset diabetes of the young, only a few of those identified by GWAS, notably TCF7L2 and ZnT8/SLC30A8, have to date been examined in mouse models. We discuss here the animal models available for the latter genes and provide perspectives for future, higher throughput approaches towards efficiently mining the information provided by human genetics. PMID:23710470

da Silva Xavier, Gabriela; Bellomo, Elisa A; McGinty, James A; French, Paul M; Rutter, Guy A



A role for migration-linked genes and genomic islands in divergence of a songbird. (United States)

Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently, there has been a debate around the role of 'genomic islands of divergence' (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson's thrush, Catharus ustulatus, is a migratory songbird with two genetically distinct subspecies that differ in a number of traits known to be involved in reproductive isolation in birds (plumage coloration, song and migratory behaviour), despite contemporary gene flow along a secondary contact zone. Here, we use RAD-PE sequencing to test emerging hypotheses about the process of divergence at the level of the genome and identify genes and gene regions involved in differentiation in this migratory songbird. Our analyses revealed distinct genomic islands on 15 of the 23 chromosomes and an accelerated rate of divergence on the Z chromosome, one of the avian sex chromosomes. Further, an analysis of loci linked to traits known to be involved in reproductive isolation in songbirds showed that genes linked to migration are significantly more differentiated than expected by chance, but that these genes lie primarily outside the genomic islands. Overall, our analysis supports the idea that genes linked to migration play an important role in divergence in migratory songbirds, but we find no compelling evidence that the observed genomic islands are facilitating adaptive divergence in migratory behaviour. PMID:24954641

Ruegg, Kristen; Anderson, Eric C; Boone, Jason; Pouls, Jazz; Smith, Thomas B



Identifying root system genes using induced mutants in barley  

International Nuclear Information System (INIS)

Root systems play an important role in plant growth and development. They absorb water and nutrients, anchor plant in the soil and affect plant tolerance to various abiotic stresses. Despite their importance, the progress in understanding the molecular processes underlying root development has been achieved only in Arabidopsis thaliana. It was accomplished through detailed analysis of root mutants with the use of advanced molecular, genomic and bioinformatic tools. Recently, similar studies performed with rice and maize root mutants have led to the identification of homologous and novel genes controlling root system formation in monocots. The collection of barley mutants with changes in root system development and morphology has been developed in our Department after mutagenic treatments of spring barley varieties with N-methyl N-nitosourea (MNU) and sodium azide. Among these mutants, the majority was characterized by seminal roots significantly shorter than roots of a parent variety throughout a whole vegetation period. Additionally, several mutants with root hairs impaired at different stages of development have been identified. These mutants have become the material of studies aimed at genetic and molecular dissection of seminal root and root hair formation in barley. The studies included the molecular mapping of genes responsible for mutant phenotype using DNA markers and root transcriptome analysis in the mutant/parent variety system. Using cDNA RDA approach, we riety system. Using cDNA RDA approach, we have identified the HvEXPB1 gene encoding root specific beta expansin related to the root hair initiation in barley. We have also initiated the database search for barley sequences homologous to the known Arabodopsis, maize and rice genes. The identified homologous ESTs are now used for isolation of the complete coding sequences and gene function will be validated through identification of mutations related to the altered phenotype. This work was supported by the IAEA Research Contracts 12611 and 12849, and Polish Ministry of Science and Higher Education grant 2 P04C 056 30. (author)


Genes Necessary for Bacterial Magnetite Biomineralization Identified by Transposon Mutagenesis (United States)

Magnetic bacteria synthesize nanoscale crystals of magnetite in intracellular, membrane-bounded organelles (magnetosomes). These crystals are preserved in the fossil record at least as far back as the late Neoproterozoic and have been tentatively identified in much older rocks (1). This fossil record may provide deep time calibration points for molecular evolution studies once the genes involved in biologically controlled magnetic mineralization (BCMM) are known. Further, a genetic and biochemical understanding of BCMM will give insight into the depositional environment and biogeochemical cycles in which magnetic bacteria play a role. The BCMM process is not well understood, though proteins have been identified from the magnetosome membrane and genetic manipulation and biochemical characterization of these proteins are underway. Most of the proteins currently thought to be involved are encoded within the mam cluster, a large cluster of genes whose products localize to the magnetosome membrane and are conserved among magnetic bacteria (2). In an effort to identify all of the genes necessary for bacterial BCMM, we undertook a transposon mutagenesis of Magnetospirillum magneticum AMB-1. Non-magnetic mutants (MNMs) were identified by growth in liquid culture followed by a magnetic assay. The insertion site of the transposon was identified two ways. First MNMs were screened with a PCR assay to determine if the transposon had inserted into the mam cluster. Second, the transposon was rescued from the mutant DNA and cloned for sequencing. The majority insertion sites are located within the mam cluster. Insertion sites also occur in operons which have not previously been suspected to be involved in magnetite biomineralization. None of the insertion sites have occurred within genes reported from previous transposon mutagenesis studies of AMB-1 (3, 4). Two of the non-mam cluster insertion sites occur in operons containing genes conserved particularly between MS-1 and MC-1. We are undertaking a complementation strategy to demonstrate the necessity of these novel genes in BCMM as well as characterizing the phenotypes of the mutants. 1. S. B. R. Chang, J. F. Stolz, J. L. Kirschvink, S. M. Awramik, Precambrian Res. 43, 305-315 (1989). 2. K. Grünberg, C. Wawer, B. M. Tebo, D. Schüler, Appl. Environ. Microbiol. 67, 4573-4582 (2001). 3. A. T. Wahyudi, H. Takeyama, T. Matsunaga, Appl. Biochem. Biotechnol. 91-3, 147-154 (2001). 4. T. Matsunaga, C. Nakamura, J. G. Burgess, K. Sode, J. Bacteriol. 174, 2748-2753 (1992).

Nash, C. Z.; Komeili, A.; Newman, D. K.; Kirschvink, J. L.



Blood pressure loci identified with a gene-centric array.  


Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated ...

Johnson, T.; Gaunt, Tr; Newhouse, Sj; Padmanabhan, S.; Tomaszewski, M.; Kumari, M.; Morris, Rw; Tzoulaki, I.; O Brien, Et; Poulter, NR; Sever, P.; Shields, Dc; Thom, S.; Wannamethee, Sg; Whincup, Ph



Identification of gene ontologies linked to prefrontal-hippocampal functional coupling in the human brain  

DEFF Research Database (Denmark)

Functional interactions between the dorsolateral prefrontal cortex and hippocampus during working memory have been studied extensively as an intermediate phenotype for schizophrenia. Coupling abnormalities have been found in patients, their unaffected siblings, and carriers of common genetic variants associated with schizophrenia, but the global genetic architecture of this imaging phenotype is unclear. To achieve genome-wide hypothesis-free identification of genes and pathways associated with prefrontal-hippocampal interactions, we combined gene set enrichment analysis with whole-genome genotyping and functional magnetic resonance imaging data from 269 healthy German volunteers. We found significant enrichment of the synapse organization and biogenesis gene set. This gene set included known schizophrenia risk genes, such as neural cell adhesion molecule (NRCAM) and calcium channel, voltage-dependent, beta 2 subunit (CACNB2), as well as genes with well-defined roles in neurodevelopmental and plasticity processes that are dysfunctional in schizophrenia and have mechanistic links to prefrontal-hippocampal functional interactions. Our results demonstrate a readily generalizable approach that can be used to identify the neurogenetic basis of systems-level phenotypes. Moreover, our findings identify gene sets in which genetic variation may contribute to disease risk through altered prefrontal-hippocampal functional interactions and suggest a link to both ongoing and developmental synaptic plasticity.

Dixson, Luanna; Walter, Henrik



Translatome analysis of CHO cells to identify key growth genes. (United States)

We report the first investigation of translational efficiency on a global scale, also known as translatome, of a Chinese hamster ovary (CHO) DG44 cell line producing monoclonal antibodies (mAb). The translatome data was generated via combined use of high resolution and streamlined polysome profiling technology and proprietary Nimblegen microarrays probing for more than 13K annotated CHO-specific genes. The distribution of ribosome loading during the exponential growth phase revealed the translational activity corresponding to the maximal growth rate, thus allowing us to identify stably and highly translated genes encoding heterogeneous nuclear ribonucleoproteins (Hnrnpc and Hnrnpa2b1), protein regulator of cytokinesis 1 (Prc1), glucose-6-phosphate dehydrogenase (G6pdh), UTP6 small subunit processome (Utp6) and RuvB-like protein 1 (Ruvbl1) as potential key players for cellular growth. Moreover, correlation analysis between transcriptome and translatome data sets showed that transcript level and translation efficiency were uncoupled for 95% of investigated genes, suggesting the implication of translational control mechanisms such as the mTOR pathway. Thus, the current translatome analysis platform offers new insights into gene expression in CHO cell cultures by bridging the gap between transcriptome and proteome data, which will enable researchers of the bioprocessing field to prioritize in high-potential candidate genes and to devise optimal strategies for cell engineering toward improving culture performance. PMID:23876478

Courtes, Franck C; Lin, Joyce; Lim, Hsueh Lee; Ng, Sze Wai; Wong, Niki S C; Koh, Geoffrey; Vardy, Leah; Yap, Miranda G S; Loo, Bernard; Lee, Dong-Yup



Homeobox genes: a molecular link between development and cancer  

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Full Text Available Homeobox genes are regulatory genes encoding nuclear proteins that act as transcription factors, regulating aspects of morphogenesis and cell differentiation during normal embryonic development of several animals. Vertebrate homeobox genes can be divided in two subfamilies: clustered, or HOX genes, and nonclustered, or divergent, homeobox genes. During the last decades, several homeobox genes, clustered and nonclustered ones, were identified in normal tissue, in malignant cells, and in different diseases and metabolic alterations. Homeobox genes are involved in the normal teeth development and in familial teeth agenesis. Normal development and cancer have a great deal in common, as both processes involve shifts between cell proliferation and differentiation. The literature is accumulating evidences that homeobox genes play an important role in oncogenesis. Many cancers exhibit expression of or alteration in homeobox genes. Those include leukemias, colon, skin, prostate, breast and ovarian cancers, among others. This review is aimed at introducing readers to some of the homeobox family functions in normal tissues and especially in cancer.

Nunes Fabio Daumas



Using Drosophila melanogaster to identify chemotherapy toxicity genes. (United States)

The severity of the toxic side effects of chemotherapy shows a great deal of interindividual variability, and much of this variation is likely genetically based. Simple DNA tests predictive of toxic side effects could revolutionize the way chemotherapy is carried out. Due to the challenges in identifying polymorphisms that affect toxicity in humans, we use Drosophila fecundity following oral exposure to carboplatin, gemcitabine and mitomycin C as a model system to identify naturally occurring DNA variants predictive of toxicity. We use the Drosophila Synthetic Population Resource (DSPR), a panel of recombinant inbred lines derived from a multiparent advanced intercross, to map quantitative trait loci affecting chemotoxicity. We identify two QTL each for carboplatin and gemcitabine toxicity and none for mitomycin. One QTL is associated with fly orthologs of a priori human carboplatin candidate genes ABCC2 and MSH2, and a second QTL is associated with fly orthologs of human gemcitabine candidate genes RRM2 and RRM2B. The third, a carboplatin QTL, is associated with a posteriori human orthologs from solute carrier family 7A, INPP4A&B, and NALCN. The fourth, a gemcitabine QTL that also affects methotrexate toxicity, is associated with human ortholog GPx4. Mapped QTL each explain a significant fraction of variation in toxicity, yet individual SNPs and transposable elements in the candidate gene regions fail to singly explain QTL peaks. Furthermore, estimates of founder haplotype effects are consistent with genes harboring several segregating functional alleles. We find little evidence for nonsynonymous SNPs explaining mapped QTL; thus it seems likely that standing variation in toxicity is due to regulatory alleles. PMID:25236447

King, Elizabeth G; Kislukhin, Galina; Walters, Kelli N; Long, Anthony D



Genes to diseases (G2D) computational method to identify asthma candidate genes  


Asthma is a complex trait for which different strategies have been used to identify its environmental and genetic predisposing factors. Here, we describe a novel methodological approach to select candidate genes for asthma genetic association studies. In this regard, the Genes to Diseases (G2D) computational tool has been used in combination with a genome-wide scan performed in a sub-sample of the Saguenay?Lac-St-Jean (SLSJ) asthmatic familial collection (n?=?609) to identify candidate ...

Tremblay, K.; Lemire, M.; Potvin, C.; Tremblay, A.; Hunninghake, G. M.; Raby, B. A.; Hudson, T. J.; Perez-iratxeta, C.; Andrade-navarro, M. A.; Laprise, C.



Pleiotropy and close linkage of mutated genes. New examples of mutations of closely linked genes  

International Nuclear Information System (INIS)

The question is studied of whether the 'pleiotropic' spectrum of mutants is due to a true pleiotropic action of single genes or to mutations in closely linked genes. By means of crossings between specific, partially similar mutants of Pisum sativum, their pleiotropic spectra could be split and the single components of the spectra attributed to groups of independently functioning adjacent genes. The following results were obtained: A chlorophyll deficient, lethal cochleata mutant shows a 3:1 segregation for the whole complex. The three anomalies are, however, not due to the pleiotropic action of a single recessive gene, but to the action of at least two mutated genes, which are extremely closely linked. They show complete independence from each other with regard to their action. The dim segment of the Pisum genome was genetically analysed. It is a small chromosome region containing at least 5 genes. The segment as a whole shows an increased mutation frequency, but it is a matter of chance how many genes of the segment and which ones mutate in different irradiated embryos. In this way, different, but partially similar mutants arise giving the impression of pleiotropic gene actions. It was shown in crossing experiments that the group of diverging characters of each of these mutants is not caused by a pleiotropic gene, but by a group of closely linked mutated genes. It is assumed that the phenomenon of the mutation of closely linked or even neighbouring genes is a frequened or even neighbouring genes is a frequently occuring event in mutation experiments. Therefore, it should be considered for interpreting 'pleiotropic' effects in the widest sense of this term. (author)


Autosomal Genes of Autosomal/X-Linked Duplicated Gene Pairs and Germ-Line Proliferation in Caenorhabditis elegans  


We report molecular genetic studies of three genes involved in early germ-line proliferation in Caenorhabditis elegans that lend unexpected insight into a germ-line/soma functional separation of autosomal/X-linked duplicated gene pairs. In a genetic screen for germ-line proliferation-defective mutants, we identified mutations in rpl-11.1 (L11 protein of the large ribosomal subunit), pab-1 [a poly(A)-binding protein], and glp-3/eft-3 (an elongation factor 1-? homolog). All three are members o...

Maciejowski, John; Ahn, James Hyungsoo; Cipriani, Patricia Giselle; Killian, Darrell J.; Chaudhary, Aisha L.; Lee, Ji Inn; Voutev, Roumen; Johnsen, Robert C.; Baillie, David L.; Gunsalus, Kristin C.; Fitch, David H. A.; Hubbard, E. Jane Albert



Strategies to identify long noncoding RNAs involved in gene regulation  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Long noncoding RNAs (lncRNAs have been detected in nearly every cell type and found to be fundamentally involved in many biological processes. The characterization of lncRNAs has immense potential to advance our comprehensive understanding of cellular processes and gene regulation, along with implications for the treatment of human disease. The recent ENCODE (Encyclopedia of DNA Elements study reported 9,640 lncRNA loci in the human genome, which corresponds to around half the number of protein-coding genes. Because of this sheer number and their functional diversity, it is crucial to identify a pool of potentially relevant lncRNAs early on in a given study. In this review, we evaluate the methods for isolating lncRNAs by immunoprecipitation and review the advantages, disadvantages, and applications of three widely used approaches – microarray, tiling array, and RNA-seq – for identifying lncRNAs involved in gene regulation. We also look at ways in which data from publicly available databases such as ENCODE can support the study of lncRNAs.

Lee Catherine



Missense mutations in the adhalin gene linked to autosomal recessive muscular dystrophy  

Energy Technology Data Exchange (ETDEWEB)

Adhalin, the 50-kDa dystrophin-associated glycoprotein, is deficient in skeletal muscle of patients having severe childhood autosomal recessive muscular dystrophy (SCARMD). In several North African families, SCARMD has been linked to markers in the pericentromeric region of chromosome l3q, but SCARMD has been excluded from linkage to this locus in other families. To determine whether the adhalin gene might be involved in SCARMD, human adhalin cDNA and large portions of the adhalin gene were cloned. Adhalin is a transmembrane glycoprotein with an extracellular domain bearing limited homology to domains of entactin and nerve growth factor receptor, suggesting that adhalin may serve as a receptor for an extracellular matrix protein. The adhalin gene was mapped to chromosome 17q12-q21.33, excluding the gene from involvement in 13q-linked SCARMD. A polymorphic microsatellite was identified within intron 6 of the adhalin gene, and one allelic variant of this marker cosegregated with the disease phenotype in a large French family with a lod score of 3.61 at 0 recombination. Adhalin is undetectable in skeletal muscle from affected members of this family. Missense mutations were identified within the adhalin gene that might cause SCARMD in this family. Thus, genetic defects in at least two components, dystrophin and adhalin, of the dystrophin-glycoprotein complex can independently cause muscular dystrophies.

Roberds, S.L.; Anderson, R.D.; Lim, L.E. [Univ. of Iowa, Iowa City, IA (United States)] [and others



Gene that controls aggressiveness in breast cancer cells identified (United States)

In a discovery that sheds new light on the aggressiveness of certain breast cancers, Whitehead Institute and MIT researchers have identified a transcription factor, known as ZEB1, that is capable of converting non-aggressive basal-type cancer cells into highly malignant, tumor-forming cancer stem cells (CSCs). Intriguingly, luminal breast cancer cells, which are associated with a much better clinical prognosis, carry this gene in a state in which it seems to be permanently shut down. MIT is home to the David H. Koch Institute for Integrative Cancer Research.


Gene Mutation Linked to Type of Childhood Cancer (United States)

Researchers have identified a gene that may play a role in the growth and spread of a childhood cancer called rhabdomyosarcoma, which develops in the body's soft tissues. The finding has revealed a potential new target for the treatment of this disease.


Screening of the Bruton Tyrosine Kinase (BTK) Gene Mutations in 13 Iranian Patients with Presumed X-Linked Agammaglobulinemia  


X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the Bruton tyrosine kinase (Btk) gene. In order to identify the mutations in Btk gene in Iranian patients with antibody deficiency, 13 male patients with an XLA phenotype from 11 unrelated families were enrolled as the subjects of investigation for Btk mutation analysis using PCR-SSCP followed by sequencing. Five different mutations were identified in 5 patients from 5 unrelated families. Three mutations had been ...

Mohammad Gharagozlou; Masoud Movahedi; Zahra Pourpak; Abolhassan Farhoudi; Ali Akbar Amirzargar; Mostafa Moin; Hirokazu Kanegana; Nima Parvaneh; Asghar Aghamohammadi; Nima Rezaei; Takeshi Futatani; Toshio Miyawaki



Progression-associated genes in astrocytoma identified by novel microarray gene expression data reanalysis. (United States)

Astrocytoma is graded as pilocytic (WHO grade I), diffuse (WHO grade II), anaplastic (WHO grade III), and glioblastoma multiforme (WHO grade IV). The progression from low- to high-grade astrocytoma is associated with distinct molecular changes that vary with patient age, yet the prognosis of high-grade tumors in children and adults is equally dismal. Whether specific gene expression changes are consistently associated with all high-grade astrocytomas, independent of patient age, is not known. To address this question, we reanalyzed the microarray datasets comprising astrocytomas from children and adults, respectively. We identified nine genes consistently dysregulated in high-grade tumors, using four novel tests for identifying differentially expressed genes. Four genes encoding ribosomal proteins (RPS2, RPS8, RPS18, RPL37A) were upregulated, and five genes (APOD, SORL1, SPOCK2, PRSS11, ID3) were downregulated in high-grade by all tests. Expression results were validated using a third astrocytoma dataset. APOD, the most differentially expressed gene, has been shown to inhibit tumor cell and vascular smooth muscle cell proliferation. This suggests that dysregulation of APOD may be critical for malignant astrocytoma formation, and thus a possible novel universal target for therapeutic intervention. Further investigation is needed to evaluate the role of APOD, as well as the other genes identified, in malignant astrocytoma development. PMID:17634619

MacDonald, Tobey J; Pollack, Ian F; Okada, Hideho; Bhattacharya, Soumyaroop; Lyons-Weiler, James



ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression  


Dynamic regulation of diverse nuclear processes is intimately linked to covalent modifications of chromatin1,2. Much attention has focused on methylation at lysine 4 of histone H3 (H3K4), owing to its association with euchromatic genomic regions3,4. H3K4 can be mono-, di- or tri-methylated. Trimethylated H3K4 (H3K4me3) is preferentially detected at active genes, and is proposed to promote gene expression through recognition by transcription-activating effector molecules5. Here we identify a n...

Shi, Xiaobing; Hong, Tao; Walter, Kay L.; Ewalt, Mark; Michishita, Eriko; Hung, Tiffany; Carney, Dylan; Pen?a, Pedro; Lan, Fei; Kaadige, Mohan R.; Lacoste, Nicolas; Cayrou, Christelle; Davrazou, Foteini; Saha, Anjanabha; Cairns, Bradley R.



The congenital goiter mutation is linked to the thyroglobulin gene in the mouse.  


Rat thyroglobulin (TG) cDNA clones were used to identify DNA restriction fragment variants among inbred mouse strains. One of these variants was shown to be closely linked to the recessive mutation congenital goiter (cog), which had previously been mapped to mouse chromosome 15. These results indicate that the structural gene for thyroglobulin is on chromosome 15 and suggest that a mutation at the site of the TG gene is the basis of the cog defect. No differences were observed between cog/cog...

Taylor, B. A.; Rowe, L.



Blood Pressure Loci Identified with a Gene-Centric Array (United States)

Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10?7 study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r2 = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10?7 at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies. PMID:22100073

Johnson, Toby; Gaunt, Tom R.; Newhouse, Stephen J.; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W.; Tzoulaki, Ioanna; O'Brien, Eoin T.; Poulter, Neil R.; Sever, Peter; Shields, Denis C.; Thom, Simon; Wannamethee, Sasiwarang G.; Whincup, Peter H.; Brown, Morris J.; Connell, John M.; Dobson, Richard J.; Howard, Philip J.; Mein, Charles A.; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Smith, George Davey; Day, Ian N.M.; Lawlor, Debbie A.; Goodall, Alison H.; Fowkes, F. Gerald; Abecasis, Gonçalo R.; Elliott, Paul; Gateva, Vesela; Braund, Peter S.; Burton, Paul R.; Nelson, Christopher P.; Tobin, Martin D.; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A.; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-François; Tichet, Jean; Juhanson, Peeter; Org, Elin; Putku, Margus; Sõber, Siim; Veldre, Gudrun; Viigimaa, Margus; Levinsson, Anna; Rosengren, Annika; Thelle, Dag S.; Hastie, Claire E.; Hedner, Thomas; Lee, Wai K.; Melander, Olle; Wahlstrand, Björn; Hardy, Rebecca; Wong, Andrew; Cooper, Jackie A.; Palmen, Jutta; Chen, Li; Stewart, Alexandre F.R.; Wells, George A.; Westra, Harm-Jan; Wolfs, Marcel G.M.; Clarke, Robert; Franzosi, Maria Grazia; Goel, Anuj; Hamsten, Anders; Lathrop, Mark; Peden, John F.; Seedorf, Udo; Watkins, Hugh; Ouwehand, Willem H.; Sambrook, Jennifer; Stephens, Jonathan; Casas, Juan-Pablo; Drenos, Fotios; Holmes, Michael V.; Kivimaki, Mika; Shah, Sonia; Shah, Tina; Talmud, Philippa J.; Whittaker, John; Wallace, Chris; Delles, Christian; Laan, Maris; Kuh, Diana; Humphries, Steve E.; Nyberg, Fredrik; Cusi, Daniele; Roberts, Robert; Newton-Cheh, Christopher; Franke, Lude; Stanton, Alice V.; Dominiczak, Anna F.; Farrall, Martin; Hingorani, Aroon D.; Samani, Nilesh J.; Caulfield, Mark J.; Munroe, Patricia B.



Cross-species global and subset gene expression profiling identifies genes involved in prostate cancer response to selenium  

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Full Text Available Abstract Background Gene expression technologies have the ability to generate vast amounts of data, yet there often resides only limited resources for subsequent validation studies. This necessitates the ability to perform sorting and prioritization of the output data. Previously described methodologies have used functional pathways or transcriptional regulatory grouping to sort genes for further study. In this paper we demonstrate a comparative genomics based method to leverage data from animal models to prioritize genes for validation. This approach allows one to develop a disease-based focus for the prioritization of gene data, a process that is essential for systems that lack significant functional pathway data yet have defined animal models. This method is made possible through the use of highly controlled spotted cDNA slide production and the use of comparative bioinformatics databases without the use of cross-species slide hybridizations. Results Using gene expression profiling we have demonstrated a similar whole transcriptome gene expression patterns in prostate cancer cells from human and rat prostate cancer cell lines both at baseline expression levels and after treatment with physiologic concentrations of the proposed chemopreventive agent Selenium. Using both the human PC3 and rat PAII prostate cancer cell lines have gone on to identify a subset of one hundred and fifty-four genes that demonstrate a similar level of differential expression to Selenium treatment in both species. Further analysis and data mining for two genes, the Insulin like Growth Factor Binding protein 3, and Retinoic X Receptor alpha, demonstrates an association with prostate cancer, functional pathway links, and protein-protein interactions that make these genes prime candidates for explaining the mechanism of Selenium's chemopreventive effect in prostate cancer. These genes are subsequently validated by western blots showing Selenium based induction and using tissue microarrays to demonstrate a significant association between downregulated protein expression and tumorigenesis, a process that is the reverse of what is seen in the presence of Selenium. Conclusions Thus the outlined process demonstrates similar baseline and selenium induced gene expression profiles between rat and human prostate cancers, and provides a method for identifying testable functional pathways for the action of Selenium's chemopreventive properties in prostate cancer.

Dhir Rajiv



Gene expression profile analysis identifies metastasis and chemoresistance-associated genes in epithelial ovarian carcinoma cells. (United States)

The purpose of this study was to identify genes that associated with higher ability of metastasis and chemotherapic resistance in epithelial ovarian carcinoma (EOC) cells. An oligonucleotide microarray with probe sets complementary to 41,000(+) unique human genes and transcripts was used to determine whether gene expression profile may differentiate three epithelial ovarian cell lines (RMG-I-C, COC1 and HO8910) from their sub-lines (RMG-I-H, COCI/DDP and HO8910/PM) with higher ability of metastasis and chemotherapic resistance. Quantitative real-time PCR and immunohistochemical staining validated the microarray results. Hierarchic cluster analysis of gene expression identified 49 genes that exhibited ?2.0-fold change and P value ?0.05. Highly differential expression of GCET2, NLRP4, FOXP1 and SNX29 genes was validated by quantitative PCR in all cell line samples. Finally, FOXP1 was validated at the protein level by immunohistochemistry in paraffin embedded ovarian tissues (i.e., for metastasis, 15 primary EOC and 10 omental metastasis [OM]; for chemoresistance, 13 sensitive and 13 resistant EOC). The identification of higher ability of metastasis and chemotherapic resistance-associated genes may provide a foundation for the development of new type-specific diagnostic strategies and treatment for metastasis and chemotherapic resistance in epithelial ovarian cancer. PMID:25502083

Zhu, Liancheng; Hu, Zhenhua; Liu, Juanjuan; Gao, Jian; Lin, Bei



SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees  

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Full Text Available Abstract Background Phylogenetic trees based on sequences from a set of taxa can be incongruent due to horizontal gene transfer (HGT. By identifying the HGT events, we can reconcile the gene trees and derive a taxon tree that adequately represents the species' evolutionary history. One HGT can be represented by a rooted Subtree Prune and Regraft (RSPR operation and the number of RSPRs separating two trees corresponds to the minimum number of HGT events. Identifying the minimum number of RSPRs separating two trees is NP-hard, but the problem can be reduced to fixed parameter tractable. A number of heuristic and two exact approaches to identifying the minimum number of RSPRs have been proposed. This is the first implementation delivering an exact solution as well as the intermediate trees connecting the input trees. Results We present the SPR Identification Tool (SPRIT, a novel algorithm that solves the fixed parameter tractable minimum RSPR problem and its GPL licensed Java implementation. The algorithm can be used in two ways, exhaustive search that guarantees the minimum RSPR distance and a heuristic approach that guarantees finding a solution, but not necessarily the minimum one. We benchmarked SPRIT against other software in two different settings, small to medium sized trees i.e. five to one hundred taxa and large trees i.e. thousands of taxa. In the small to medium tree size setting with random artificial incongruence, SPRIT's heuristic mode outperforms the other software by always delivering a solution with a low overestimation of the RSPR distance. In the large tree setting SPRIT compares well to the alternatives when benchmarked on finding a minimum solution within a reasonable time. SPRIT presents both the minimum RSPR distance and the intermediate trees. Conclusions When used in exhaustive search mode, SPRIT identifies the minimum number of RSPRs needed to reconcile two incongruent rooted trees. SPRIT also performs quick approximations of the minimum RSPR distance, which are comparable to, and often better than, purely heuristic solutions. Put together, SPRIT is an excellent tool for identification of HGT events and pinpointing which taxa have been involved in HGT.

Fredriksson Robert



Gene variations linked to lung cancer susceptibility in Asian women (United States)

An international group of scientists has identified three genes that predispose Asian women who have never smoked to lung cancer. The discovery of specific genetic variations, which have not previously been associated with lung cancer risk in other populations, provides further evidence that risk of lung cancer among never-smokers, especially Asian women, may be associated with certain unique genetic characteristics that distinguishes it from lung cancer in smokers.


RFLP markers linked to the root knot nematode resistance gene Mi in tomato. (United States)

The Mi gene originating from the wild tomato species Lycopersicon peruvianum confers resistance to all major root knot nematodes (Meloidogyne spp.). This single dominant gene is located on chromosome 6 and is very closely linked to the acid phosphatase-1 (Aps-1) locus. Resistance to nematodes has been introgressed into various cultivars of the cultivated tomato (L. esculentum), in many cultivars along with the linked L. peruvianum Aps-1 (1) allele. By using a pair of nearly isogenic lines differing in a small chromosomal region containing the Mi and Aps-1 loci, we have identified two RFLP markers, GP79 and H6A2c2, which are located in the introgressed L. peruvianum region. Analysis of a test panel of 51 L. esculentum genotypes of various origins indicated that GP79 is very tightly linked to the Mi gene and allows both homozygous and heterozygous nematode-resistant genotypes to be distinguished from susceptible genotypes, irrespective of their Aps-1 alleles. Marker H6A2c2 is linked to the Aps-1 locus and is capable of discriminating between the L. peruvianum Aps-1 (1) allele and the L. esculentum Aps-1 (3) and Aps-1 (+) alleles. In combination, these RFLP markers may provide a powerful tool in breeding tomatoes for nematode resistance. PMID:24221383

Klein-Lankhorst, R; Rietveld, P; Machiels, B; Verkerk, R; Weide, R; Gebhardt, C; Koornneef, M; Zabel, P



Changes in gene expression linked to methamphetamine-induced dopaminergic neurotoxicity. (United States)

The purpose of these studies was to examine the role of gene expression in methamphetamine (METH)-induced dopamine (DA) neurotoxicity. First, the effects of the mRNA synthesis inhibitor, actinomycin-D, and the protein synthesis inhibitor, cycloheximide, were examined. Both agents afforded complete protection against METH-induced DA neurotoxicity and did so independently of effects on core temperature, DA transporter function, or METH brain levels, suggesting that gene transcription and mRNA translation play a role in METH neurotoxicity. Next, microarray technology, in combination with an experimental approach designed to facilitate recognition of relevant gene expression patterns, was used to identify gene products linked to METH-induced DA neurotoxicity. This led to the identification of several genes in the ventral midbrain associated with the neurotoxic process, including genes for energy metabolism [cytochrome c oxidase subunit 1 (COX1), reduced nicotinamide adenine dinucleotide ubiquinone oxidoreductase chain 2, and phosphoglycerate mutase B], ion regulation (members of sodium/hydrogen exchanger and sodium/bile acid cotransporter family), signal transduction (adenylyl cyclase III), and cell differentiation and degeneration (N-myc downstream-regulated gene 3 and tau protein). Of these differentially expressed genes, we elected to further examine the increase in COX1 expression, because of data implicating energy utilization in METH neurotoxicity and the known role of COX1 in energy metabolism. On the basis of time course studies, Northern blot analyses, in situ hybridization results, and temperature studies, we now report that increased COX1 expression in the ventral midbrain is linked to METH-induced DA neuronal injury. The precise role of COX1 and other genes in METH neurotoxicity remains to be elucidated. PMID:11756511

Xie, Tao; Tong, Liqiong; Barrett, Tanya; Yuan, Jie; Hatzidimitriou, George; McCann, Una D; Becker, Kevin G; Donovan, David M; Ricaurte, George A



Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos  

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Full Text Available Abstract Background Considerable progress has been made in our understanding of sex determination and dosage compensation mechanisms in model organisms such as C. elegans, Drosophila and M. musculus. Strikingly, the mechanism involved in sex determination and dosage compensation are very different among these three model organisms. Birds present yet another situation where the heterogametic sex is the female. Sex determination is still poorly understood in birds and few key determinants have so far been identified. In contrast to most other species, dosage compensation of bird sex chromosomal genes appears rather ineffective. Results By comparing microarrays from microdissected primitive streak from single chicken embryos, we identified a large number of genes differentially expressed between male and female embryos at a very early stage (Hamburger and Hamilton stage 4, long before any sexual differentiation occurs. Most of these genes are located on the Z chromosome, which indicates that dosage compensation is ineffective in early chicken embryos. Gene ontology analyses, using an enhanced annotation tool for Affymetrix probesets of the chicken genome developed in our laboratory (called Manteia, show that among these male-biased genes found on the Z chromosome, more than 20 genes play a role in sex differentiation. Conclusions These results corroborate previous studies demonstrating the rather inefficient dosage compensation for Z chromosome in birds and show that this sexual dimorphism in gene regulation is observed long before the onset of sexual differentiation. These data also suggest a potential role of non-compensated Z-linked genes in somatic sex differentiation in birds.

Mathur Sachin



Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates  


Our understanding of the molecular control of many disease pathologies requires the identification of direct substrates targeted by specific protein kinases. Here we describe an integrated proteomic strategy, termed kinase assay linked with phosphoproteomics, which combines a sensitive kinase reaction with endogenous kinase-dependent phosphoproteomics to identify direct substrates of protein kinases. The unique in vitro kinase reaction is carried out in a highly efficient manner using a pool ...

Xue, Liang; Wang, Wen-horng; Iliuk, Anton; Hu, Lianghai; Galan, Jacob A.; Yu, Shuai; Hans, Michael; Geahlen, Robert L.; Tao, W. Andy



Cloning of the Arabidopsis WIGGUM gene identifies a role for farnesylation in meristem development. (United States)

Control of cellular proliferation in plant meristems is important for maintaining the correct number and position of developing organs. One of the genes identified in the control of floral and apical meristem size and floral organ number in Arabidopsis thaliana is WIGGUM. In wiggum mutants, one of the most striking phenotypes is an increase in floral organ number, particularly in the sepals and petals, correlating with an increase in the width of young floral meristems. Additional phenotypes include reduced and delayed germination, delayed flowering, maturation, and senescence, decreased internode elongation, shortened roots, aberrant phyllotaxy of flowers, aberrant sepal development, floral buds that open precociously, and occasional apical meristem fasciation. As a first step in determining a molecular function for WIGGUM, we used positional cloning to identify the gene. DNA sequencing revealed that WIGGUM is identical to ERA1 (enhanced response to abscisic acid), a previously identified farnesyltransferase beta-subunit gene of Arabidopsis. This finding provides a link between protein modification by farnesylation and the control of meristem size. Using in situ hybridization, we examined the expression of ERA1 throughout development and found it to be nearly ubiquitous. This extensive expression domain is consistent with the pleiotropic nature of wiggum mutants and highlights a broad utility for farnesylation in plant growth and development. PMID:10840062

Ziegelhoffer, E C; Medrano, L J; Meyerowitz, E M



Gene expression patterns combined with bioinformatics analysis identify genes associated with cholangiocarcinoma. (United States)

To explore the molecular mechanisms of cholangiocarcinoma (CC), microarray technology was used to find biomarkers for early detection and diagnosis. The gene expression profiles from 6 patients with CC and 5 normal controls were downloaded from Gene Expression Omnibus and compared. As a result, 204 differentially co-expressed genes (DCGs) in CC patients compared to normal controls were identified using a computational bioinformatics analysis. These genes were mainly involved in coenzyme metabolic process, peptidase activity and oxidation reduction. A regulatory network was constructed by mapping the DCGs to known regulation data. Four transcription factors, FOXC1, ZIC2, NKX2-2 and GCGR, were hub nodes in the network. In conclusion, this study provides a set of targets useful for future investigations into molecular biomarker studies. PMID:24140882

Li, Chen; Shen, Weixing; Shen, Sheng; Ai, Zhilong



Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria  

DEFF Research Database (Denmark)

Antigenic variation of the Plasmodium falciparum multicopy var gene family enables parasite evasion of immune destruction by host antibodies. Expression of a particular var subgroup, termed upsA, is linked to the obstruction of blood vessels in the brain and to the pathogenesis of human cerebral malaria. The mechanism determining upsA activation remains unknown. Here we show that an entirely new type of gene silencing mechanism involving an exonuclease-mediated degradation of nascent RNA controls the silencing of genes linked to severe malaria. We identify a novel chromatin-associated exoribonuclease, termed PfRNase II, that controls the silencing of upsA var genes by marking their transcription start site and intron-promoter regions leading to short-lived cryptic RNA. Parasites carrying a deficient PfRNase II gene produce full-length upsA var transcripts and intron-derived antisense long non-coding RNA. The presence of stable upsA var transcripts overcomes monoallelic expression, resulting in the simultaneous expression of both upsA and upsC type PfEMP1 proteins on the surface of individual infected red blood cells. In addition, we observe an inverse relationship between transcript levels of PfRNase II and upsA-type var genes in parasites from severe malaria patients, implying a crucial role of PfRNase II in severe malaria. Our results uncover a previously unknown type of post-transcriptional gene silencing mechanism in malaria parasites with repercussions for other organisms. Additionally, the identification of RNase II as a parasite protein controlling the expression of virulence genes involved in pathogenesis in patients with severe malaria may provide new strategies for reducing malaria mortality.

Zhang, Qingfeng; Siegel, T Nicolai



A Stratified Transcriptomics Analysis of Polygenic Fat and Lean Mouse Adipose Tissues Identifies Novel Candidate Obesity Genes (United States)

Background Obesity and metabolic syndrome results from a complex interaction between genetic and environmental factors. In addition to brain-regulated processes, recent genome wide association studies have indicated that genes highly expressed in adipose tissue affect the distribution and function of fat and thus contribute to obesity. Using a stratified transcriptome gene enrichment approach we attempted to identify adipose tissue-specific obesity genes in the unique polygenic Fat (F) mouse strain generated by selective breeding over 60 generations for divergent adiposity from a comparator Lean (L) strain. Results To enrich for adipose tissue obesity genes a ‘snap-shot’ pooled-sample transcriptome comparison of key fat depots and non adipose tissues (muscle, liver, kidney) was performed. Known obesity quantitative trait loci (QTL) information for the model allowed us to further filter genes for increased likelihood of being causal or secondary for obesity. This successfully identified several genes previously linked to obesity (C1qr1, and Np3r) as positional QTL candidate genes elevated specifically in F line adipose tissue. A number of novel obesity candidate genes were also identified (Thbs1, Ppp1r3d, Tmepai, Trp53inp2, Ttc7b, Tuba1a, Fgf13, Fmr) that have inferred roles in fat cell function. Quantitative microarray analysis was then applied to the most phenotypically divergent adipose depot after exaggerating F and L strain differences with chronic high fat feeding which revealed a distinct gene expression profile of line, fat depot and diet-responsive inflammatory, angiogenic and metabolic pathways. Selected candidate genes Npr3 and Thbs1, as well as Gys2, a non-QTL gene that otherwise passed our enrichment criteria were characterised, revealing novel functional effects consistent with a contribution to obesity. Conclusions A focussed candidate gene enrichment strategy in the unique F and L model has identified novel adipose tissue-enriched genes contributing to obesity. PMID:21915269

Morton, Nicholas M.; Nelson, Yvonne B.; Michailidou, Zoi; Di Rollo, Emma M.; Ramage, Lynne; Hadoke, Patrick W. F.; Seckl, Jonathan R.; Bunger, Lutz; Horvat, Simon; Kenyon, Christopher J.; Dunbar, Donald R.



Dynamic gene expression analysis links melanocyte growth arrest with nevogenesis. (United States)

Like all primary cells in vitro, normal human melanocytes exhibit a physiologic decay in proliferative potential as it transitions to a growth-arrested state. The underlying transcriptional program(s) that regulate this phenotypic change is largely unknown. To identify molecular determinants of this process, we performed a Bayesian-based dynamic gene expression analysis on primary melanocytes undergoing proliferative arrest. This analysis revealed several related clusters whose expression behavior correlated with the melanocyte growth kinetics; we designated these clusters the melanocyte growth arrest program (MGAP). These MGAP genes were preferentially represented in benign melanocytic nevi over melanomas and selectively mapped to the hepatocyte fibrosis pathway. This transcriptional relationship between melanocyte growth stasis, nevus biology, and fibrogenic signaling was further validated in vivo by the demonstration of strong pericellular collagen deposition within benign nevi but not melanomas. Taken together, our study provides a novel view of fibroplasia in both melanocyte biology and nevogenesis. PMID:19903842

Yang, Guang; Thieu, Khanh; Tsai, Kenneth Y; Piris, Adriano; Udayakumar, Durga; Njauw, Ching-Ni Jenny; Ramoni, Marco F; Tsao, Hensin



A novel ABCD1 gene mutation in a Chinese patient with X-linked adrenoleukodystrophy. (United States)

Abstract Background: X-linked adrenoleukodystrophy (X-ALD) (OMIM: 300100) is a recessive neurodegenerative disorder caused by defects in the ABCD1 gene on chromosome Xq28. Childhood cerebral ALD (CCALD) is the most frequent phenotype. Objective: We describe an affected boy who developed normally until he was 8 years old then suffered progressive neurological deficits that ultimately led to death. Methods: Diagnosis was based on clinical symptoms, an abnormal very long chain fatty acid profile in plasma, typical CCALD MRI pattern, and molecular analysis. Results: Direct sequencing of the ABCD1 gene in this patient identified a novel splicing mutation (IVS1+1G>A) in intron 1, which is considered to be the pathogenic mutation. Conclusion: We have identified a novel ABCD1 mutation as the likely cause of CCALD in a Chinese patient. PMID:25423669

Cai, Yan-Na; Jiang, Min-Yan; Liang, Cui-Li; Peng, Min-Zhi; Cheng, Jing; Sheng, Hui-Ying; Fan, Li-Ping; Chen, Xi-Qing; Liu, Li



Scan statistic-based analysis of exome sequencing data identifies FAN1 at 15q13.3 as a susceptibility gene for schizophrenia and autism  


Schizophrenia and autism are severe, lifelong brain disorders with complex etiology and high prevalence. A strong link has been established between both disorders and de novo copy number variants, but the culprit genes remain unknown. This study uses whole-exome sequencing data and a new statistical method based on detecting clusters of rare disease-associated variants to identify the responsible gene(s) within genomic regions affected by de novo copy number variants. We discovered a new gene...

Ionita-laza, Iuliana; Xu, Bin; Makarov, Vlad; Buxbaum, Joseph D.; Roos, J. Louw; Gogos, Joseph A.; Karayiorgou, Maria



Identification of Molecular Markers Linked to a Pyrenophora teres Avirulence Gene. (United States)

ABSTRACT Genetic control of avirulence in the net blotch pathogen, Pyrenophora teres, was investigated. To establish an appropriate study system, a collection of 10 net form (P. teres f. teres) and spot form (P. teres f. maculata) isolates were evaluated on a set of eight barley lines to identify two isolates with differential virulence on an individual host line. Two net form isolates, WRS 1906, exhibiting avirulence on the cv. Heartland, and WRS 1607, exhibiting high virulence, were mated and 67 progeny were isolated and phenotyped for reaction on Heartland. The population segregated in a 1:1 ratio, 34 avirulent to 33 virulent (chi(2) = 0.0, P = 1.0), indicating single gene control of WRS 1906 avirulence on Heartland. Bulked segregant analysis was used to identify six amplified fragment length polymorphism markers closely linked to the avirulence gene (Avr(Heartland)). This work provides evidence that the P. teres-barley pathosystem conforms to the gene-for-gene model and represents an initial step toward map-based cloning of this gene. PMID:18943933

Beattie, Aaron D; Scoles, Graham J; Rossnagel, Brian G



Identifying paediatric nursing-sensitive outcomes in linked administrative health data  

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Full Text Available Abstract Background There is increasing interest in the contribution of the quality of nursing care to patient outcomes. Due to different casemix and risk profiles, algorithms for administrative health data that identify nursing-sensitive outcomes in adult hospitalised patients may not be applicable to paediatric patients. The study purpose was to test adult algorithms in a paediatric hospital population and make amendments to increase the accuracy of identification of hospital acquired events. The study also aimed to determine whether the use of linked hospital records improved the likelihood of correctly identifying patient outcomes as nursing sensitive rather than being related to their pre-morbid conditions. Methods Using algorithms developed by Needleman et al. (2001, proportions and rates of records that identified nursing-sensitive outcomes for pressure ulcers, pneumonia and surgical wound infections were determined from administrative hospitalisation data for all paediatric patients discharged from a tertiary paediatric hospital in Western Australia between July 1999 and June 2009. The effects of changes to inclusion and exclusion criteria for each algorithm on the calculated proportion or rate in the paediatric population were explored. Linked records were used to identify comorbid conditions that increased nursing-sensitive outcome risk. Rates were calculated using algorithms revised for paediatric patients. Results Linked records of 129,719 hospital separations for 79,016 children were analysed. Identification of comorbid conditions was enhanced through access to prior and/or subsequent hospitalisation records (43% of children with pressure ulcers had a form of paralysis recorded only on a previous admission. Readmissions with a surgical wound infection were identified for 103 (4.8/1,000 surgical separations using linked data. After amendment of each algorithm for paediatric patients, rates of pressure ulcers and pneumonia reduced by 53% and 15% (from 1.3 to 0.6 and from 9.1 to 7.7 per 10,000 patient days respectively, and an 84% increase in the proportion of surgical wound infection (from 5.7 to 10.4 per 1,000 separations. Conclusions Algorithms for nursing-sensitive outcomes used in adult populations have to be amended before application to paediatric populations. Using unlinked individual hospitalisation records to estimate rates of nursing-sensitive outcomes is likely to result in inaccurate rates.

Wilson Sally



Identification of candidate genes linking systemic inflammation to atherosclerosis; results of a human in vivo LPS infusion study  

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Full Text Available Abstract Background It is widely accepted that atherosclerosis and inflammation are intimately linked. Monocytes play a key role in both of these processes and we hypothesized that activation of inflammatory pathways in monocytes would lead to, among others, proatherogenic changes in the monocyte transcriptome. Such differentially expressed genes in circulating monocytes would be strong candidates for further investigation in disease association studies. Methods Endotoxin, lipopolysaccharide (LPS, or saline control was infused in healthy volunteers. Monocyte RNA was isolated, processed and hybridized to Hver 2.1.1 spotted cDNA microarrays. Differential expression of key genes was confirmed by RT-PCR and results were compared to in vitro data obtained by our group to identify candidate genes. Results All subjects who received LPS experienced the anticipated clinical response indicating successful stimulation. One hour after LPS infusion, 11 genes were identified as being differentially expressed; 1 down regulated and 10 up regulated. Four hours after LPS infusion, 28 genes were identified as being differentially expressed; 3 being down regulated and 25 up regulated. No genes were significantly differentially expressed following saline infusion. Comparison with results obtained in in vitro experiments lead to the identification of 6 strong candidate genes (BATF, BID, C3aR1, IL1RN, SEC61B and SLC43A3 Conclusion In vivo endotoxin exposure of healthy individuals resulted in the identification of several candidate genes through which systemic inflammation links to atherosclerosis.

Gusnanto Arief



Meiotic Drive Impacts Expression and Evolution of X-Linked Genes in Stalk-Eyed Flies (United States)

Although sex chromosome meiotic drive has been observed in a variety of species for over 50 years, the genes causing drive are only known in a few cases, and none of these cases cause distorted sex-ratios in nature. In stalk-eyed flies (Teleopsis dalmanni), driving X chromosomes are commonly found at frequencies approaching 30% in the wild, but the genetic basis of drive has remained elusive due to reduced recombination between driving and non-driving X chromosomes. Here, we used RNAseq to identify transcripts that are differentially expressed between males carrying either a driving X (XSR) or a standard X chromosome (XST), and found hundreds of these, the majority of which are X-linked. Drive-associated transcripts show increased levels of sequence divergence (dN/dS) compared to a control set, and are predominantly expressed either in testes or in the gonads of both sexes. Finally, we confirmed that XSR and XST are highly divergent by estimating sequence differentiation between the RNAseq pools. We found that X-linked transcripts were often strongly differentiated (whereas most autosomal transcripts were not), supporting the presence of a relatively large region of recombination suppression on XSR presumably caused by one or more inversions. We have identified a group of genes that are good candidates for further study into the causes and consequences of sex-chromosome drive, and demonstrated that meiotic drive has had a profound effect on sequence evolution and gene expression of X-linked genes in this species. PMID:24832132

Reinhardt, Josephine A.; Brand, Cara L.; Paczolt, Kimberly A.; Johns, Philip M.; Baker, Richard H.; Wilkinson, Gerald S.



Gene linked to Lou Gehrig's disease  

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Scientists have just taken a big step toward understanding the cause of Lou Gehrig's disease, one of the most devastating nerve degenerative diseases. A large team of researchers, led by Robert Brown Jr. of Harvards's Massachusetts General Hospital and Robert Horvitz, a Howard Hughes Medical Institute investigator at the Massachusetts Institute of Technology, report in the 4 March Nature that they've identified the gene that causes a hereditary form of the condition, which also goes by the name amyothophic lateral sclerosis (ALS). While most ALS cases - approximately 90% - are apparently sporadic' and not caused by an inherited gene defect, all the patients have such similar symptons that researchers are hopeful that what they learn about hereditary ALS will also apply to the sporadic form, possibly leading to new therapeutic strategies that will help both. It's a very important finding,' says neurobiologist Donald Harter of the Howard Hughes Medical Institute. It's one of the first handles we've had on the genetic basis of ALS.' The gene encodes Cu/Zn-binding superoxide dismutase and maps to the long arm of human chromosome 21.

Marx, J.



An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup. (United States)

Effective treatment of diffuse large B-cell lymphoma (DLBCL) is plagued by heterogeneous responses to standard therapy, and molecular mechanisms underlying unfavorable outcomes in lymphoma patients remain elusive. Here, we profiled 148 genomes with 91 matching transcriptomes in a DLBCL cohort treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisolone (R-CHOP) to uncover molecular subgroups linked to treatment failure. Systematic integration of high-resolution genotyping arrays and RNA sequencing data revealed novel deletions in RCOR1 to be associated with unfavorable progression-free survival (P = .001). Integration of expression data from the clinical samples with data from RCOR1 knockdowns in the lymphoma cell lines KM-H2 and Raji yielded an RCOR1 loss-associated gene signature comprising 233 genes. This signature identified a subgroup of patients with unfavorable overall survival (P = .023). The prognostic significance of the 233-gene signature for overall survival was reproduced in an independent cohort comprising 195 R-CHOP-treated patients (P = .039). Additionally, we discovered that within the International Prognostic Index low-risk group, the gene signature provides additional prognostic value that was independent of the cell-of-origin phenotype. We present a novel and reproducible molecular subgroup of DLBCL that impacts risk-stratification of R-CHOP-treated DLBCL patients and reveals a possible new avenue for therapeutic intervention strategies. PMID:25395426

Chan, Fong Chun; Telenius, Adele; Healy, Shannon; Ben-Neriah, Susana; Mottok, Anja; Lim, Raymond; Drake, Marie; Hu, Sandy; Ding, Jiarui; Ha, Gavin; Scott, David W; Kridel, Robert; Bashashati, Ali; Rogic, Sanja; Johnson, Nathalie; Morin, Ryan D; Rimsza, Lisa M; Sehn, Laurie; Connors, Joseph M; Marra, Marco A; Gascoyne, Randy D; Shah, Sohrab P; Steidl, Christian



A direct molecular link between the autism candidate gene RORa and the schizophrenia candidate MIR137 (United States)

Retinoic acid-related orphan receptor alpha gene (RORa) and the microRNA MIR137 have both recently been identified as novel candidate genes for neuropsychiatric disorders. RORa encodes a ligand-dependent orphan nuclear receptor that acts as a transcriptional regulator and miR-137 is a brain enriched small non-coding RNA that interacts with gene transcripts to control protein levels. Given the mounting evidence for RORa in autism spectrum disorders (ASD) and MIR137 in schizophrenia and ASD, we investigated if there was a functional biological relationship between these two genes. Herein, we demonstrate that miR-137 targets the 3'UTR of RORa in a site specific manner. We also provide further support for MIR137 as an autism candidate by showing that a large number of previously implicated autism genes are also putatively targeted by miR-137. This work supports the role of MIR137 as an ASD candidate and demonstrates a direct biological link between these previously unrelated autism candidate genes.

Devanna, Paolo; Vernes, Sonja C.



A large-scale overexpression screen in Saccharomyces cerevisiae identifies previously uncharacterized cell cycle genes  


We have undertaken an extensive screen to identify Saccharomyces cerevisiae genes whose products are involved in cell cycle progression. We report the identification of 113 genes, including 19 hypothetical ORFs, which confer arrest or delay in specific compartments of the cell cycle when overexpressed. The collection of genes identified by this screen overlaps with those identified in loss-of-function cdc screens but also includes genes whose products have not prev...

Stevenson, Lauren F.; Kennedy, Brian K.; Harlow, Ed



Identifying genes that contribute most to good classification in microarrays  


Abstract Background The goal of most microarray studies is either the identification of genes that are most differentially expressed or the creation of a good classification rule. The disadvantage of the former is that it ignores the importance of gene interactions; the disadvantage of the latter is that it often does not provide a sufficient focus for further investigation because many genes may be included by chance. Our strategy is to search for classification rules that p...

Kramer Barnett S; Baker Stuart G



Identifying novel genes in C. elegans using SAGE tags  

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Full Text Available Abstract Background Despite extensive efforts devoted to predicting protein-coding genes in genome sequences, many bona fide genes have not been found and many existing gene models are not accurate in all sequenced eukaryote genomes. This situation is partly explained by the fact that gene prediction programs have been developed based on our incomplete understanding of gene feature information such as splicing and promoter characteristics. Additionally, full-length cDNAs of many genes and their isoforms are hard to obtain due to their low level or rare expression. In order to obtain full-length sequences of all protein-coding genes, alternative approaches are required. Results In this project, we have developed a method of reconstructing full-length cDNA sequences based on short expressed sequence tags which is called sequence tag-based amplification of cDNA ends (STACE. Expressed tags are used as anchors for retrieving full-length transcripts in two rounds of PCR amplification. We have demonstrated the application of STACE in reconstructing full-length cDNA sequences using expressed tags mined in an array of serial analysis of gene expression (SAGE of C. elegans cDNA libraries. We have successfully applied STACE to recover sequence information for 12 genes, for two of which we found isoforms. STACE was used to successfully recover full-length cDNA sequences for seven of these genes. Conclusions The STACE method can be used to effectively reconstruct full-length cDNA sequences of genes that are under-represented in cDNA sequencing projects and have been missed by existing gene prediction methods, but their existence has been suggested by short sequence tags such as SAGE tags.

Chen Nansheng



Promotion of growth by Coenzyme Q10 is linked to gene expression in C. elegans. (United States)

Coenzyme Q (CoQ, ubiquinone) is an essential component of the respiratory chain, a cofactor of pyrimidine biosynthesis and acts as an antioxidant in extra mitochondrial membranes. More recently CoQ has been identified as a modulator of apoptosis, inflammation and gene expression. CoQ deficient Caenorhabditis elegans clk-1 mutants show several phenotypes including a delayed postembryonic growth. Using wild type and two clk-1 mutants, here we established an experimental set-up to study the consequences of endogenous CoQ deficiency or exogenous CoQ supply on gene expression and growth. We found that a deficiency of endogenous CoQ synthesis down-regulates a cluster of genes that are important for growth (i.e., RNA polymerase II, eukaryotic initiation factor) and up-regulates oxidation reactions (i.e., cytochrome P450, superoxide dismutase) and protein interactions (i.e., F-Box proteins). Exogenous CoQ supply partially restores the expression of these genes as well as the growth retardation of CoQ deficient clk-1 mutants. On the other hand exogenous CoQ supply does not alter the expression of a further sub-set of genes. These genes are involved in metabolism (i.e., succinate dehydrogenase complex), cell signalling or synthesis of lectins. Thus, our work provides a comprehensive overview of genes which can be modulated in their expression by endogenous or exogenous CoQ. As growth retardation in CoQ deficiency is linked to the gene expression profile we suggest that CoQ promotes growth via gene expression. PMID:25234594

Fischer, Alexandra; Niklowitz, Petra; Menke, Thomas; Döring, Frank



Three novel PHEX gene mutations in four Chinese families with X-linked dominant hypophosphatemic rickets  

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Highlights: Black-Right-Pointing-Pointer In our study, all of the patients were of Han Chinese ethnicity, which were rarely reported. Black-Right-Pointing-Pointer We identified three novel PHEX gene mutations in four unrelated families with XLH. Black-Right-Pointing-Pointer We found that the relationship between the phenotype and genotype of the PHEX gene was not invariant. Black-Right-Pointing-Pointer We found that two PHEX gene sites, p.534 and p.731, were conserved. -- Abstract: Background: X-linked hypophosphatemia (XLH), the most common form of inherited rickets, is a dominant disorder that is characterized by renal phosphate wasting with hypophosphatemia, abnormal bone mineralization, short stature, and rachitic manifestations. The related gene with inactivating mutations associated with XLH has been identified as PHEX, which is a phosphate-regulating gene with homologies to endopeptidases on the X chromosome. In this study, a variety of PHEX mutations were identified in four Chinese families with XLH. Methods: We investigated four unrelated Chinese families who exhibited typical features of XLH by using PCR to analyze mutations that were then sequenced. The laboratory and radiological investigations were conducted simultaneously. Results: Three novel mutations were found in these four families: one frameshift mutation, c.2033dupT in exon 20, resulting in p.T679H; one nonsense mutation, c.1294A > T in exon 11, resulting in p.K432X; and one missense mutation, c.2192T > C in exon 22, resulting in p.F731S. Conclusions: We found that the PHEX gene mutations were responsible for XLH in these Chinese families. Our findings are useful for understanding the genetic basis of Chinese patients with XLH.

Kang, Qing-lin [Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China); Xu, Jia [Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China); Metabolic Bone Disease and Genetic Research Unit, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China); Medical College of Soochow University, Suzhou, Jiangsu province 215000 (China); Zhang, Zeng [Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China); Metabolic Bone Disease and Genetic Research Unit, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China); He, Jin-wei [Metabolic Bone Disease and Genetic Research Unit, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China); Lu, Lian-song [Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China); Medical College of Soochow University, Suzhou, Jiangsu province 215000 (China); Fu, Wen-zhen [Metabolic Bone Disease and Genetic Research Unit, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China); Zhang, Zhen-lin, E-mail: [Metabolic Bone Disease and Genetic Research Unit, Department of Osteoporosis and Bone Diseases, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China)



Sleeping Beauty Plays a Significant Role in Identifying Cancer Genes (United States)

Researchers at the University of Minnesota Cancer Center and the National Cancer Institute (NCI), part of the National Institutes of Health, have discovered a new method that could accelerate the way cancer-causing genes are found and could lead to a more accurate identification of the genes


Comparative and Functional Genomics in Identifying Aflatoxin Biosynthetic Genes (United States)

Identification of genes involved in aflatoxin biosynthesis through Aspergillus flavus genomics has been actively pursued. A. flavus Expressed Sequence Tags (EST’s) and whole genome sequencing have been completed. Groups of genes that are potentially involved in aflatoxin production have been profi...


GeneFriends: An online co-expression analysis tool to identify novel gene targets for aging and complex diseases  

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Full Text Available Abstract Background Although many diseases have been well characterized at the molecular level, the underlying mechanisms are often unknown. Nearly half of all human genes remain poorly studied, yet these genes may contribute to a number of disease processes. Genes involved in common biological processes and diseases are often co-expressed. Using known disease-associated genes in a co-expression analysis may help identify and prioritize novel candidate genes for further study. Results We have created an online tool, called GeneFriends, which identifies co-expressed genes in over 1,000 mouse microarray datasets. GeneFriends can be used to assign putative functions to poorly studied genes. Using a seed list of disease-associated genes and a guilt-by-association method, GeneFriends allows users to quickly identify novel genes and transcription factors associated with a disease or process. We tested GeneFriends using seed lists for aging, cancer, and mitochondrial complex I disease. We identified several candidate genes that have previously been predicted as relevant targets. Some of the genes identified are already being tested in clinical trials, indicating the effectiveness of this approach. Co-expressed transcription factors were investigated, identifying C/ebp genes as candidate regulators of aging. Furthermore, several novel candidate genes, that may be suitable for experimental or clinical follow-up, were identified. Two of the novel candidates of unknown function that were co-expressed with cancer-associated genes were selected for experimental validation. Knock-down of their human homologs (C1ORF112 and C12ORF48 in HeLa cells slowed growth, indicating that these genes of unknown function, identified by GeneFriends, may be involved in cancer. Conclusions GeneFriends is a resource for biologists to identify and prioritize novel candidate genes involved in biological processes and complex diseases. It is an intuitive online resource that will help drive experimentation. GeneFriends is available online at:

van Dam Sipko



Cross-linked polyethylenimine–tripolyphosphate nanoparticles for gene delivery  

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Full Text Available Xianzhang Huang,1 Sujing Shen,2 Zhanfeng Zhang,1 Junhua Zhuang1 1Department of Laboratory Science, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 2Department of Laboratory Science, Guangdong Second Provincial Traditional Chinese Medicine Hospital, Guangzhou, People’s Republic of China Abstract: The high transfection efficiency of polyethylenimine (PEI makes it an attractive potential nonviral genetic vector for gene delivery and therapy. However, the highly positive charge of PEI leads to cytotoxicity and limits its application. To reduce the cytotoxicity of PEI, we prepared anion-enriched nanoparticles that combined PEI with tripolyphosphate (TPP. We then characterized the PEI-TPP nanoparticles in terms of size, zeta potential, and Fourier-transform infrared (FTIR spectra, and assessed their transfection efficiency, cytotoxicity, and ability to resist deoxyribonuclease (DNase I digestion. The cellular uptake of PEI-TPP with phosphorylated internal ribosome entry site–enhanced green fluorescent protein C1 or FAM (fluorouracil, Adriamycin [doxorubicin] and mitomycin-labeled small interfering ribonucleic acids (siRNAs was monitored by fluorescence microscopy and confocal laser microscopy. The efficiency of transfected delivery of plasmid deoxyribonucleic acid (DNA and siRNA in vitro was 1.11- to 4.20-fold higher with the PEI-TPP particles (7.6% cross-linked than with the PEI, at all N:P ratios (nitrogen in PEI to phosphorus in DNA tested. The cell viability of different cell lines was more than 90% at the chosen N:P ratios of PEI-TPP/DNA complexes. Moreover, PEI-TPP nanoparticles resisted digestion by DNase I for more than 2 hours. The time-dependent absorption experiment showed that 7.6% of cross-linked PEI-TPP particles were internalized by 293T cells within 1 hour. In summary, PEI-TPP nanoparticles effectively transfected cells while conferring little or no toxicity, and thus have potential application in gene delivery. Keywords: polyethylenimine (PEI, tripolyphosphate (TPP, nanoparticles (NPs, transfection

Huang XZ



Gene expression profiling of human adrenocortical tumors using complementary deoxyribonucleic Acid microarrays identifies several candidate genes as markers of malignancy.  


The aim of this study was to identify predictor sets of genes whose over- or underexpression in human sporadic adrenocortical tumors would help to identify malignant vs. benign tumors and to predict postsurgical metastatic recurrence. For this, we analyzed the expression of 230 candidate genes using cDNA microarrays in a series of 57 well-characterized human sporadic adrenocortical tumors (33 adenomas and 24 carcinomas). We identified two clusters of genes (the IGF-II cluster containing eight...

Fraipont, Florence; El Atifi, Michelle; Cherradi, Nadia; Le Moigne, Gwennaelle; Defaye, Genevie?ve; Houlgatte, Re?mi; Bertherat, Je?ro?me; Bertagna, Xavier; Plouin, Pierre-franc?ois; Baudin, Eric; Berger, Franc?ois; Gicquel, Christine; Chabre, Olivier; Feige, Jean-jacques



Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks  

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Full Text Available Abstract Background We generalized penalized canonical correlation analysis for analyzing microarray gene-expression measurements for checking completeness of known metabolic pathways and identifying candidate genes for incorporation in the pathway. We used Wold's method for calculation of the canonical variates, and we applied ridge penalization to the regression of pathway genes on canonical variates of the non-pathway genes, and the elastic net to the regression of non-pathway genes on the canonical variates of the pathway genes. Results We performed a small simulation to illustrate the model's capability to identify new candidate genes to incorporate in the pathway: in our simulations it appeared that a gene was correctly identified if the correlation with the pathway genes was 0.3 or more. We applied the methods to a gene-expression microarray data set of 12, 209 genes measured in 45 patients with glioblastoma, and we considered genes to incorporate in the glioma-pathway: we identified more than 25 genes that correlated > 0.9 with canonical variates of the pathway genes. Conclusion We concluded that penalized canonical correlation analysis is a powerful tool to identify candidate genes in pathway analysis.

Zwinderman Aeilko H



A novel apoptosis gene identified in the pituitary gland. (United States)

Although multiple different cancers have been described, it is likely that these tumour types share a small, and common, number of newly acquired functional capabilities. Tumours that arise within the pituitary gland are no exception with respect to these new functional capabilities. Although compelling evidence for self-sufficiency in growth signals is presented, loss of functional tumour suppressor genes by classic mechanisms has not been clearly established. However, and in this context, methylation-mediated or -associated gene silencing, in particular of tumour suppressor genes, has been reported by numerous investigators in this tumour type. More recently, a search for novel genes on the basis of their inappropriate methylation has led to identification of a novel pro-apoptotic gene. Its pituitary tumour derivation and role in drug-induced apoptosis resulted in the acronym PTAG (pituitary tumour apoptosis gene) being assigned to this gene. In a model pituitary tumour cell line, AtT20, expression of PTAG per se had no discernible effects on proliferation, cell cycle profile or viability. However, enforced expression was associated with a significantly increased sensitivity to the apoptotic effects induced by bromocriptine challenge. Apoptosis was mediated through caspase activation and associated with DNA fragmentation as determined by TUNEL labelling. Similar findings are also evident in the rodent pituitary cell line, GH3 and our data shows that drugs other than bromocriptine, and that engage characterized receptors, elicit a PTAG-augmented apoptotic response. The isolation of novel genes, on the basis of their methylation status, offers a significant advantage with respect to our understanding of tumorigenesis in both the pituitary and other tumour types. The reversal of apparent gene silencing may lead to tumour cell 'sensitisation' to chemo- and radiotherapeutic treatment strategies. PMID:17135715

Farrell, W E



GeneFriends: An online co-expression analysis tool to identify novel gene targets for aging and complex diseases  


Abstract Background Although many diseases have been well characterized at the molecular level, the underlying mechanisms are often unknown. Nearly half of all human genes remain poorly studied, yet these genes may contribute to a number of disease processes. Genes involved in common biological processes and diseases are often co-expressed. Using known disease-associated genes in a co-expression analysis may help identify and prioritize novel candidate genes for further study...

van Dam Sipko; Cordeiro Rui; Craig Thomas; van Dam Jesse; Wood Shona H; de Magalhães João



New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism  

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Birth weight within the normal range is associated with a variety of adult-onset diseases, but the mechanisms behind these associations are poorly understood. Previous genome-wide association studies of birth weight identified a variant in the ADCY5 gene associated both with birth weight and type 2 diabetes and a second variant, near CCNL1, with no obvious link to adult traits. In an expanded genome-wide association meta-analysis and follow-up study of birth weight (of up to 69,308 individuals of European descent from 43 studies), we have now extended the number of loci associated at genome-wide significance to 7, accounting for a similar proportion of variance as maternal smoking. Five of the loci are known to be associated with other phenotypes: ADCY5 and CDKAL1 with type 2 diabetes, ADRB1 with adult blood pressure and HMGA2 and LCORL with adult height. Our findings highlight genetic links between fetal growth and postnatal growth and metabolism.

Horikoshi, Momoko; Yaghootkar, Hanieh



Gene Duplication Identified in an Uncommon Form of Bone Cancer (United States)

Scientists have discovered that a familial form of a rare bone cancer called chordoma is explained not by typical types of changes or mutations in the sequence of DNA in a gene, but rather by the presence of a second copy of an entire gene. Inherited large structural changes, known as copy number variations (CNVs), have been implicated in some hereditary diseases but have seldom been reported as the underlying basis for a familial cancer.


Promoter characterization and genomic organization of the gene encoding integrin-linked kinase 1. (United States)

Integrin-linked kinase (ILK)-1 is a 59-kDa serine-threonine protein kinase, which associates with the cytoplasmic domain of beta 1, beta 2 and beta 3 integrins and acts as a receptor proximal kinase regulating integrin-mediated signal transduction. We have recently identified an isoform of ILK (ILK-2), which is expressed, in a TGF-beta 1-dependent manner, in a highly invasive tumor cell line but not in normal adult tissues. In contrast, ILK-1 is ubiquitously expressed in normal tissues and is up-regulated in various tumors independent of TGF-beta 1. Here, we report the structural organization and the promoter activity of the human ILK-1 gene, contained within a 8.8-kb genomic fragment cloned from a human BAC library. The mature protein is encoded by 13 exons. The last coding exon contains the entire 3' UTR of the ILK-1 gene, which overlaps with the complementary 3' UTR sequence of the TAF2H gene, a TATA box binding protein-associated factor. A major transcriptional initiation start site was found 138 bp upstream of exon 1 in close proximity to a consensus initiator element (Inr). The ILK gene is transcribed by a TATA-less and CAAT-less promoter with typical features of housekeeping genes. The promoter activity was characterized by a luciferase reporter assay and the minimal sequence conferring promoter activity was 349 bp in size and located immediately upstream of exon 1. PMID:12020826

Melchior, Chantal; Kreis, Stephanie; Janji, Bassam; Kieffer, Nelly



Identifying genes associated with quantitative traits in pigs: integrating quantitative and molecular approaches for meat quality  

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Full Text Available Two major strategies are used to identify genes that are involved in complex traits, genome scanning and candidate gene approaches. While a quantitative trait locus (QTL strategy relies on a scan of the entire genome combined with phenotypic measurements, a candidate gene approach tries to identify genes based on their possible role in the physiology of the traits. Both strategies are based on the integration between quantitative and molecular approaches. Over the last decade, enormous effort has been applied to identify and localize QTL involved in most of the economically important traits in pigs and a number of candidate genes were suggested and further validated according to a concordant position to the detected QTL and related functions. However, lacking of information in regards to identified genes within the identified QTL, and false-positive QTL are major constraints that limit the successful of this approach. Additional approaches, including a gene expression analysis of the divergence of phenotype of interest was integrated into a candidate gene analysis, in which a putative candidate gene is the one that could be statistically detected from the genes controlling large components of inheritable gene expression variation. Furthermore, a remarkable progress of molecular approaches by newly developed technique, a study of an interaction between genes and a holistic study of biological regulation, system biology, is underway. These continuations will assist the researchers to identify direct candidate gene for quantitative traits in animal breeding.

Karl Schellander



Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesis  

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Full Text Available Abstract Background Paragangliomas of the head and neck are highly vascular and usually clinically benign tumors arising in the paraganglia of the autonomic nervous system. A significant number of cases (10–50% are proven to be familial. Multiple genes encoding subunits of the mitochondrial succinate-dehydrogenase (SDH complex are associated with hereditary paraganglioma: SDHB, SDHC and SDHD. Furthermore, a hereditary paraganglioma family has been identified with linkage to the PGL2 locus on 11q13. No SDH genes are known to be located in the 11q13 region, and the exact gene defect has not yet been identified in this family. Methods We have performed a RNA expression microarray study in sporadic, SDHD- and PGL2-linked head and neck paragangliomas in order to identify potential differences in gene expression leading to tumorigenesis in these genetically defined paraganglioma subgroups. We have focused our analysis on pathways and functional gene-groups that are known to be associated with SDH function and paraganglioma tumorigenesis, i.e. metabolism, hypoxia, and angiogenesis related pathways. We also evaluated gene clusters of interest on chromosome 11 (i.e. the PGL2 locus on 11q13 and the imprinted region 11p15. Results We found remarkable similarity in overall gene expression profiles of SDHD -linked, PGL2-linked and sporadic paraganglioma. The supervised analysis on pathways implicated in PGL tumor formation also did not reveal significant differences in gene expression between these paraganglioma subgroups. Moreover, we were not able to detect differences in gene-expression of chromosome 11 regions of interest (i.e. 11q23, 11q13, 11p15. Conclusion The similarity in gene-expression profiles suggests that PGL2, like SDHD, is involved in the functionality of the SDH complex, and that tumor formation in these subgroups involves the same pathways as in SDH linked paragangliomas. We were not able to clarify the exact identity of PGL2 on 11q13. The lack of differential gene-expression of chromosome 11 genes might indicate that chromosome 11 loss, as demonstrated in SDHD-linked paragangliomas, is an important feature in the formation of paragangliomas regardless of their genetic background.

Hogendoorn Pancras CW



Linking actin dynamics and gene transcription to drive cellular motile functions. (United States)

Numerous physiological and pathological stimuli promote the rearrangement of the actin cytoskeleton, thereby modulating cellular motile functions. Although it seems intuitively obvious that cell motility requires coordinated protein biosynthesis, until recently the linkage between cytoskeletal actin dynamics and correlated gene activities remained unknown. This knowledge gap was filled in part by the discovery that globular actin polymerization liberates myocardin-related transcription factor (MRTF) cofactors, thereby inducing the nuclear transcription factor serum response factor (SRF) to modulate the expression of genes encoding structural and regulatory effectors of actin dynamics. This insight stimulated research to better understand the actin-MRTF-SRF circuit and to identify alternative mechanisms that link cytoskeletal dynamics and genome activity. PMID:20414257

Olson, Eric N; Nordheim, Alfred



Identification of AFLP molecular linked to row- type gene in barley  

International Nuclear Information System (INIS)

Formation of the two-and six-rowed types in barley is predominantly controlled by alleles at a single locus (vrzl) which is located in long armn of chromosome 2H. This gene is a key character on the study of barley domestication and yield. Near-isogenic lines of barley were produced from crosses between Kanto Nakate Gold (tow-rowed) and Azumamugi (six-rowed). The selected lines were used for screening of AFLP polymorphic bands which are linked to vrs1 locus. After screening of a total of 1792 primer combination, five polymorphic bands were identified. A construction of high resolution map around the vrs1 locus was made using recombinant inbred lines. These markers can be used for a map-based cloning of the genes at the vrsl locus


Epigenetic genome-wide analysis identifies BEX1 as a candidate tumour suppressor gene in paediatric intracranial ependymoma. (United States)

Promoter hypermethylation and transcriptional silencing is a common epigenetic mechanism of gene inactivation in cancer. To identify targets of epigenetic silencing in paediatric intracranial ependymoma, we used a pharmacological unmasking approach through treatment of 3 ependymoma short-term cell cultures with the demethylating agent 5-Aza-2'-deoxycytidine followed by global expression microarray analysis. We identified 55 candidate epigenetically silenced genes, which are involved in the regulation of apoptosis, Wnt signalling, p53 and cell differentiation. The methylation status of 26 of these genes was further determined by combined bisulfite restriction analysis (COBRA) and genomic sequencing in a cohort of 40 ependymoma samples. The most frequently methylated genes were BEX1 (27/40 cases), BAI2 (20/40), CCND2 (18/40), and CDKN2A (14/40). A high correlation between promoter hypermethylation and decreased gene expression levels was established by real-time quantitative PCR, suggesting the involvement of these genes in ependymoma tumourigenesis. Furthermore, ectopic expression of brain-expressed X-linked 1 (BEX1) in paediatric ependymoma short-term cell cultures significantly suppressed cell proliferation and colony formation. These data suggest that promoter hypermethylation contributes to silencing of target genes in paediatric intracranial ependymoma. Epigenetic inactivation of BEX1 supports its role as a candidate tumour suppressor gene in intracranial ependymoma, and a potential target for novel therapies for ependymoma in children. PMID:24333734

Karakoula, Katherine; Jacques, Thomas S; Phipps, Kim P; Harkness, William; Thompson, Dominic; Harding, Brian N; Darling, John L; Warr, Tracy J



Gene Expression Profiling in Entamoeba histolytica Identifies Key Components in Iron Uptake and Metabolism (United States)

Entamoeba histolytica is an ameboid parasite that causes colonic dysentery and liver abscesses in humans. The parasite encounters dramatic changes in iron concentration during its invasion of the host, with relatively low levels in the intestinal lumen and then relatively high levels in the blood and liver. The liver notably contains sources of iron; therefore, the parasite's ability to use these sources might be relevant to its survival in the liver and thus the pathogenesis of liver abscesses. The objective of the present study was to identify factors involved in iron uptake, use and storage in E. histolytica. We compared the respective transcriptomes of E. histolytica trophozoites grown in normal medium (containing around 169 µM iron), low-iron medium (around 123 µM iron), iron-deficient medium (around 91 µM iron), and iron-deficient medium replenished with hemoglobin. The differentially expressed genes included those coding for the ATP-binding cassette transporters and major facilitator transporters (which share homology with bacterial siderophores and heme transporters) and genes involved in heme biosynthesis and degradation. Iron deficiency was associated with increased transcription of genes encoding a subset of cell signaling molecules, some of which have previously been linked to adaptation to the intestinal environment and virulence. The present study is the first to have assessed the transcriptome of E. histolytica grown under various iron concentrations. Our results provide insights into the pathways involved in iron uptake and metabolism in this parasite. PMID:25210888

Hernández-Cuevas, Nora Adriana; Weber, Christian; Hon, Chung-Chau; Guillen, Nancy



Distinct gene expression profiles in ovarian cancer linked to Lynch syndrome. (United States)

Ovarian cancer linked to Lynch syndrome represents a rare subset that typically presents at young age as early-stage tumors with an overrepresentation of endometrioid and clear cell histologies. We investigated the molecular profiles of Lynch syndrome-associated and sporadic ovarian cancer with the aim to identify key discriminators and central tumorigenic mechanisms in hereditary ovarian cancer. Global gene expression profiling using whole-genome c-DNA-mediated Annealing, Selection, extension, and Ligation was applied to 48 histopathologically matched Lynch syndrome-associated and sporadic ovarian cancers. Lynch syndrome-associated and sporadic ovarian cancers differed by 349 significantly deregulated genes, including PTPRH, BIRC3, SHH and TNFRSF6B. The genes involved were predominantly linked to cell growth, proliferation, and cell-to-cell signaling and interaction. When stratified for histologic subtype, hierarchical clustering confirmed distinct differences related to heredity in the endometrioid and serous subtypes. Furthermore, separate clustering was achieved in an independent, publically available data set. The distinct genetic signatures in Lynch syndrome-associated and sporadic ovarian cancers point to alternative preferred tumorigenic routes and suggest that genetic discriminators may be relevant for molecular diagnostics and targeted therapeutics. PMID:24848881

Jönsson, Jenny-Maria; Bartuma, Katarina; Dominguez-Valentin, Mev; Harbst, Katja; Ketabi, Zohreh; Malander, Susanne; Jönsson, Mats; Carneiro, Ana; Måsbäck, Anna; Jönsson, Göran; Nilbert, Mef



Linkage and candidate gene analysis of X-linked familial exudative vitreoretinopathy  

Energy Technology Data Exchange (ETDEWEB)

Familial exudative vitreoretinopathy (FEVR) is a hereditary eye disorder characterized by avascularity of the peripheral retina, retinal exudates, tractional detachment, and retinal folds. The disorder is most commonly transmitted as an autosomal dominant trait, but X-linked transmission also occurs. To initiate the process of identifying the gene responsible for the X-linked disorder, linkage analysis has been performed with three previously unreported three- or four-generation families. Two-point analysis showed linkage to MAOA (Z{sub max} = 2.1, {theta}{sub max} = 0) and DXS228 (Z{sub max} = 0.5, {theta}{sub max} = 0.11), and this was further confirmed by multipoint analysis with these same markers (Z{sub max} = 2.81 at MAOA), which both lie near the gene causing Norrie disease. Molecular genetic analysis further reveals a missense mutation (R121W) in the third exon of the Norrie`s disease gene that perfectly cosegregates with the disease through three generations in one family. This mutation was not detected in the unaffected family members and six normal unrelated controls, suggesting that it is likely to be the pathogenic mutation. Additionally, a polymorphic missense mutation (H127R) was detected in a severely affected patient. 21 refs., 3 figs., 1 tab.

Shastry, B.S.; Hartzer, M.K. [Oakland Univ., Rochester, MI (United States); Hejtmancik, J.F. [National Eye Institute, Bethesda, MD (United States)] [and others



TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation  

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Full Text Available Abstract Background The TM4SF10 gene encodes a putative four-transmembrane domains protein of unknown function termed Brain Cell Membrane Protein 1 (BCMP1, and is abundantly expressed in the brain. This gene is located on the short arm of human chromosome X at p21.1. The hypothesis that mutations in the TM4SF10 gene are associated with impaired brain function was investigated by sequencing the gene in individuals with hereditary X-linked mental retardation (XLMR. Methods The coding region (543 bp of TM4SF10, including intronic junctions, and the long 3' untranslated region (3 233 bp, that has been conserved during evolution, were sequenced in 16 male XLMR patients from 14 unrelated families with definite, or suggestive, linkage to the TM4SF10 gene locus, and in 5 normal males. Results Five sequence changes were identified but none was found to be associated with the disease. Two of these changes correspond to previously known SNPs, while three other were novel SNPs in the TM4SF10 gene. Conclusion We have investigated the majority of the known MRX families linked to the TM4SF10 gene region. In the absence of mutations detected, our study indicates that alterations of TM4SF10 are not a frequent cause of XLMR.

Holinski-Feder Elke



Identifying genes associated with quantitative traits in pigs: integrating quantitative and molecular approaches for meat quality  


Two major strategies are used to identify genes that are involved in complex traits, genome scanning and candidate gene approaches. While a quantitative trait locus (QTL) strategy relies on a scan of the entire genome combined with phenotypic measurements, a candidate gene approach tries to identify genes based on their possible role in the physiology of the traits. Both strategies are based on the integration between quantitative and molecular approaches. Over the last decade, enormous effor...

Karl Schellander



Gene sequencing project identifies abnormal gene that launches rare childhood leukemia (United States)

Research led by the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project has identified a fusion gene responsible for almost 30 percent of a rare subtype of childhood leukemia with an extremely poor prognosis. The finding offers the first evidence of a mistake that gives rise to a significant percentage of acute megakaryoblastic leukemia (AMKL) cases in children. AMKL accounts for about 10 percent of pediatric acute myeloid leukemia (AML). The discovery paves the way for desperately needed treatment advances.


Allele characterization of genes required for rpg4-mediated wheat stem rust resistance identifies Rpg5 as the R gene. (United States)

A highly virulent form of the wheat stem rust pathogen Puccinia graminis f. sp. tritici race TTKSK is virulent on both wheat and barley, presenting a major threat to world food security. The recessive and temperature-sensitive rpg4 gene is the only effective source of resistance identified in barley (Hordeum vulgare) against P. graminis f. sp. tritici race TTKSK. Efforts to position clone rpg4 localized resistance to a small interval on barley chromosome 5HL, tightly linked to the rye stem rust (P. graminis f. sp. secalis) resistance (R) gene Rpg5. High-resolution genetic analysis and post-transcriptional gene silencing of the genes at the rpg4/Rpg5 locus determined that three tightly linked genes (Rpg5, HvRga1, and HvAdf3) are required together for rpg4-mediated wheat stem rust resistance. Alleles of the three genes were analyzed from a diverse set of 14 domesticated barley lines (H. vulgare) and 8 wild barley accessions (H. vulgare subsp. spontaneum) to characterize diversity that may determine incompatibility (resistance). The analysis determined that HvAdf3 and HvRga1 code for predicted functional proteins that do not appear to contain polymorphisms determining the compatible (susceptible) interactions with the wheat stem rust pathogen and were expressed at the transcriptional level from both resistant and susceptible barley lines. The HvAdf3 alleles shared 100% amino acid identity among all 22 genotypes examined. The P. graminis f. sp. tritici race QCCJ-susceptible barley lines with HvRga1 alleles containing the limited amino acid substitutions unique to the susceptible varieties also contained predicted nonfunctional rpg5 alleles. Thus, susceptibility in these lines is likely due to the nonfunctional RPG5 proteins. The Rpg5 allele analysis determined that 9 of the 13 P. graminis f. sp. tritici race QCCJ-susceptible barley lines contain alleles that either code for predicted truncated proteins as the result of a single nucleotide substitution, resulting in a stop codon at amino acid 161, a single cytosine indel causing a frame shift, and a stop codon at amino acid 217, or an indel that deleted the entire STPK domain. The three P. graminis f. sp. tritici race QCCJ-susceptible lines (Swiss landraces Hv489, Hv492, and Hv611) and the wild barley accession WBDC160 contain rpg5 alleles predicted to encode full-length proteins containing a nonsynonomous nucleotide substitution that results in the amino acid substitution E1287A. This amino acid substitution present in the uncharacterized C-terminal domain is not found in any resistant line and may be important to elicit the resistance reaction. These data suggest that rpg4-mediated resistance against many wheat stem rust pathogen races, including P. graminis f. sp. tritici race TTKSK, rely on the Rpg5 R gene; thus, rpg4- and Rpg5-mediated resistance rely on a common R gene and should not be considered completely distinct. The data also determined that Rpg5 gene-specific molecular markers could be used to detect rpg4-mediated wheat stem rust resistance for marker-assisted selection. PMID:23841622

Arora, D; Gross, T; Brueggeman, R



Identifying and Prioritizing Genes involved in Bovine Mastitis  

DEFF Research Database (Denmark)

In the "omics" era, identification of biological entities underlying complex traits or common diseases is characterized by the integration of high-throughput experiments and knowledge that have benn published or refined in biomedical repositories. Studies in this thesis generate, collect and integrate different layers of biological data, attempting to make a systematic inference of underlying genes to bovine mastitis. Robust and flexible methods have been implemented in data summarization and integration for gene prioritization, which can be applied to study various complex traits in different species

Jiang, Li



A transcription map of the 6p22.3 reading disability locus identifying candidate genes  

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Full Text Available Abstract Background Reading disability (RD is a common syndrome with a large genetic component. Chromosome 6 has been identified in several linkage studies as playing a significant role. A more recent study identified a peak of transmission disequilibrium to marker JA04 (G72384 on chromosome 6p22.3, suggesting that a gene is located near this marker. Results In silico cloning was used to identify possible candidate genes located near the JA04 marker. The 2 million base pairs of sequence surrounding JA04 was downloaded and searched against the dbEST database to identify ESTs. In total, 623 ESTs from 80 different tissues were identified and assembled into 153 putative coding regions from 19 genes and 2 pseudogenes encoded near JA04. The identified genes were tested for their tissue specific expression by RT-PCR. Conclusions In total, five possible candidate genes for RD and other diseases mapping to this region were identified.

Gruen Jeffrey R



Pinus banksiana has at least seven expressed alcohol dehydrogenase genes in two?linked?groups  


The alcohol dehydrogenase (Adh) gene family is much more complex in Pinus banksiana than in angiosperms, with at least seven expressed genes organized as two tightly linked clusters. Intron number and position are highly conserved between P. banksiana and angiosperms. Unlike angiosperm Adh genes, numerous duplications, as large as 217 bp, were observed within the noncoding regions of P. banksiana Adh genes and may be a common feature of conifer genes. A high fr...

Perry, Daniel?J; Furnier, Glenn?R



Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production. (United States)

Immunoresponsive gene 1 (Irg1) is highly expressed in mammalian macrophages during inflammation, but its biological function has not yet been elucidated. Here, we identify Irg1 as the gene coding for an enzyme producing itaconic acid (also known as methylenesuccinic acid) through the decarboxylation of cis-aconitate, a tricarboxylic acid cycle intermediate. Using a gain-and-loss-of-function approach in both mouse and human immune cells, we found Irg1 expression levels correlating with the amounts of itaconic acid, a metabolite previously proposed to have an antimicrobial effect. We purified IRG1 protein and identified its cis-aconitate decarboxylating activity in an enzymatic assay. Itaconic acid is an organic compound that inhibits isocitrate lyase, the key enzyme of the glyoxylate shunt, a pathway essential for bacterial growth under specific conditions. Here we show that itaconic acid inhibits the growth of bacteria expressing isocitrate lyase, such as Salmonella enterica and Mycobacterium tuberculosis. Furthermore, Irg1 gene silencing in macrophages resulted in significantly decreased intracellular itaconic acid levels as well as significantly reduced antimicrobial activity during bacterial infections. Taken together, our results demonstrate that IRG1 links cellular metabolism with immune defense by catalyzing itaconic acid production. PMID:23610393

Michelucci, Alessandro; Cordes, Thekla; Ghelfi, Jenny; Pailot, Arnaud; Reiling, Norbert; Goldmann, Oliver; Binz, Tina; Wegner, André; Tallam, Aravind; Rausell, Antonio; Buttini, Manuel; Linster, Carole L; Medina, Eva; Balling, Rudi; Hiller, Karsten



Unique and recurrent WAS gene mutations in Wiskott-Aldrich syndrome and X-linked thrombocytopenia. (United States)

Wiskott-Aldrich syndrome (WAS) and X-linked thrombocytopenia (XLT) are allelic phenotypes caused by defects of the WAS gene. Fourteen distinct mutations including seven novel gene defects in 16 WAS and four XLT patients were identified by single strand conformation polymorphism analysis and DNA sequencing of the WAS gene. Eleven (79%) of these mutations are located within exons 1 to 4 with clustering in exon 2. Carrier detection in 33 at-risk females and prenatal diagnosis at 12 weeks gestation in one family with a novel WAS mutation was performed by direct mutation analysis. A remarkably high frequency (72%) of point mutations involved CpG dinucleotides. C-->T or G-->A transitions at CpG sites were identified in all isolated WAS cases (n = 7). Allele frequencies for the dinucleotide repeat at locus DXS6940 were determined in Northern European, African and Asian populations. Mutation screening alone or in combination with analysis of polymorphic loci DXS6940 and DXS255 delineated the germline origin of a unique insertion mutation and four recurrent CpG mutations, three of which arose spontaneously during maternal gametogenesis. PMID:10575547

Thompson, L J; Lalloz, M R; Layton, D M



Gene expression analysis of hematopoietic progenitor cells identifies Dlg7 as a potential stem cell gene. (United States)

Inducible hematopoietic stem/progenitor cell lines represent a model for studying genes involved in self-renewal and differentiation. Here, gene expression was studied in the inducible human CD34+ acute myelogenous leukemia cell line KG1 using oligonucleotide arrays and suppression subtractive cloning. Using this approach, we identified Dlg7, the homolog of the Drosophila Dlg1 tumor suppressor gene, as downregulated at the early stages of KG1 differentiation. Similarly, Dlg7 was expressed in normal purified umbilical cord blood CD34+CD38- progenitors but not in the more committed CD34+CD38+ population. Dlg7 expression was not detected in differentiated cells obtained from hematopoietic colonies, nor was expression detected in purified T-cells, B-cells, and monocytes. When analyzed in different types of stem cells, Dlg7 expression was detected in purified human bone marrow-derived CD133+ progenitor cells, human mesenchymal stem cells, and mouse embryonic stem (ES) cells. Overexpression of Dlg7 in mouse ES cells increased their growth rate and reduced the number of EBs emerging upon differentiation. In addition, the EBs were significantly smaller, indicating an inhibition in differentiation. This inhibition was further supported by higher expression of Bmp4, Oct4, Rex1, and Nanog in EBs overexpressing Dlg7 and lower expression of Brachyury. Finally, the Dlg7 protein was detected in liver and colon carcinoma tumors but not in normal adjacent tissues, suggesting a role for the gene in carcinogenesis. In conclusion, our results suggest that Dlg7 has a role in stem cell survival, in maintaining stem cell properties, and in carcinogenesis. Disclosure of potential conflicts of interest is found at the end of this article. PMID:17322106

Gudmundsson, Kristbjorn Orri; Thorsteinsson, Leifur; Sigurjonsson, Olafur E; Keller, Jonathan R; Olafsson, Karl; Egeland, Torstein; Gudmundsson, Sveinn; Rafnar, Thorunn



Identification of RAPD Markers Linked to the Male Sterility Gene in Sugar Beet (Beta vulgaris L.  

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Full Text Available Genetic male sterility is controlled by one pair of ressesive allele (aa in sugar beet. This trait is used in most breeding programes. The exsistance of the character in a line or population facilitates transfer of important trait to the breeding material (for example resistance to plant disease. Also, it is possible to increase genetic diversity of monogerm populations by using genetic male sterility. The time and cost of transferring of this gene will be decreased, if the character is tagged with a molecular marker. Bulked segregant analysis using 302 RAPD primers in two F2 populations (231 and 261 population was performed for the the identification of RAPD markers linked to the genetic male sterility gene. DNA preparation from 8 male fertile and male sterile plants were separately mixed. At first, the primers were tested on bulks. The primers with polymorphic bands were tested on individual plants of the bulks. Only if the polymorphism of the primers was confirmed, they were tested on the other individual plants. Finally, 10 and 6 markers were identified in 231 and 261 populations, respectively, which their distances to male sterility gene were lower than 50 cM. AB-8-18-600r marker was the nearest marker to male sterility gene. This marker showed only 3 and 1 recombination in 231 and 261 populations, respectively. The distance of this marker and genetic male sterility locus was estimated as 5.3 cM in combined F2 populations.

A. Mirzaei asl



The genomic structure of human BTK, the defective gene in X-linked agammaglobulinemia  

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It has recently been demonstrated that mutations in the gene for Bruton`s tyrosine kinase (BTK) are responsible for X-linked agammaglobulinemia. Southern blot analysis and sequencing of cDNA were used to document deletions, insertions, and single base pair substitutions. To facilitate analysis of BTK regulation and to permit the development of assays that could be used to screen genomic DNA for mutations in BTK, the authors determined the genomic organization of this gene. Subcloning of a cosmid and a yeast artificial chromosome showed that BTK is divided into 19 exons spanning 37 kilobases of genomic DNA. Analysis of the region 5{prime} to the first untranslated exon revealed no consensus TATAA or CAAT boxes; however, three retinoic acid binding sites were identified in this region. Comparison of the structure of BTK with that of other nonreceptor tyrosine kinases, including SRC, FES, and CSK, demonstrated a lack of conservation of exon borders. Information obtained in this study will contribute to understanding of the evolution of nonreceptor tyrosine kinases. It will also be useful in diagnostic studies, including carrier detection, and in studies directed towards gene therapy or gene replacement. 29 refs., 2 figs., 2 tabs.

Rohrer, J.; Parolini, O. [St. Jude Children`s Research Hospital, Memphis, TN (United States); Conley, M.E. [St. Jude Children`s Research Hospital, Memphis, TN (United States)]|[Univ. of Tennessee College of Medicine, Memphis, TN (United States); Belmont, J.W. [Baylor College of Medicine, Houston, TX (United States)



A 6-gene signature identifies four molecular subgroups of neuroblastoma  


Abstract Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB); Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA) and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK) was associated to unfavourable biology of sporadic N...

Kogner Per; Stallings Raymond; Vermeulen Joëlle; De Preter Katleen; Jörnsten Rebecka; Nethander Maria; Dalevi Daniel; Abel Frida; Maris John; Nilsson Staffan



A gene sets approach for identifying prognostic gene signatures for outcome prediction  


Abstract Background Gene expression profiling is a promising approach to better estimate patient prognosis; however, there are still unresolved problems, including little overlap among similarly developed gene sets and poor performance of a developed gene set in other datasets. Results We applied a gene sets approach to develop a prognostic gene set from multiple gene expression datasets. By analyzing 12 independent breast cancer gene expression datasets compris...

Kim Yong Sung; Kim Seon-Young



Hybridization-based resequencing of 17 X-linked intellectual disability genes in 135 patients reveals novel mutations in ATRX, SLC6A8 and PQBP1  


Abstract X-linked intellectual disability (XLID) also known as X-linked mental retardation is a highly genetically heterogeneous condition for which mutations in >90 different genes have been identified. In this study we used a custom-made sequencing array based on the Affymetrix 50k platform for mutation screening in 17 known XLID genes in patients from 135 families and found eight single nucleotide changes that were absent in controls. For four mutations affecting ATRX (p.1761M>T...

Kuss, Andreas Walter; Jensen, Lars Riff; Chen, Wei; Moser, Bettina; Lipkowitz, Bettina; Musante, Luciana; Tzschach, Andreas; Ropers, Hans Hilger; Schroeder, Christopher; Meloni, Ilaria; Raynaud, Martine; Esch, Hilde; Chelly, Jamel; Brouwer, Arjan Pm; Hackett, Anna



Identification and validation of molecular markers linked to the leaf rust resistance gene Lr19 in wheat. (United States)

A leaf rust resistance gene Lr19 on the chromosome 7DL of wheat derived from Agropyron elongatum was tagged with random amplified polymorphic DNA (RAPD) and microsatellite markers. The F(2) population of 340 plants derived from a cross between the leaf rust resistant near-isogenic line (NIL) of Thatcher (Tc + Lr19) and leaf rust susceptible line Agra Local that segregated for dominant monogenic leaf rust resistance was utilized for generating the mapping population. The molecular markers were mapped in the F(2) derived F(3) homozygous population of 140 seedlings. Sixteen RAPD markers were identified as linked to the alien gene Lr19 among which eight were in a coupling phase linkage. Twelve RAPD markers co-segregated with Lr19 locus. Nine microsatellite markers located on the long arm of chromosome 7D were also mapped as linked to the gene Lr19, including 7 markers which co-segregated with Lr19 locus, thus generating a saturated region carrying 25 molecular markers linked to the gene Lr19 within 10.2 +/- 0.062 cM on either side of the locus. Two RAPD markers S265(512) and S253(737) which flanked the locus Lr19 were converted to sequence characterized amplified region markers SCS265(512) and SCS253(736), respectively. The marker SCS265(512) was linked with Lr19 in a coupling phase and the marker SCS253(736) was linked in a repulsion phase, which when used together mimicked one co-dominant marker capable of distinguishing the heterozygous resistant seedlings from the homozygous resistant. The molecular markers were validated on NILs mostly in Thatcher background isogenic for 44 different Lr genes belonging to both native and alien origin. The validation for polymorphism in common leaf rust susceptible cultivars also confirmed the utility of these tightly linked markers to the gene Lr19 in marker-assisted selection. PMID:16896713

Gupta, Sudhir Kumar; Charpe, Ashwini; Prabhu, Kumble Vinod; Haque, Qazi Mohammad Rizwanul



A candidate gene for X-linked Ocular Albinism (OA1)  

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Ocular Albinism of the Nettleship-Fall type 1 (OA1) is the most common form of ocular albinism. It is transmitted as an X-linked recessive trait with affected males showing severe reduction of visual acuity, nystagmus, strabismus, photophobia. Ophthalmologic examination reveals foveal hypoplasia, hypopigmentation of the retina and iris translucency. Microscopic examination of melanocytes suggests that the underlying defect in OA1 is an abnormality in melanosome formation. Recently we assembled a 350 kb cosmid contig spanning the entire critical region on Xp22.3, which measures approximately 110 kb. A minimum set of cosmids was used to identify transcribed sequences using both cDNA selection and exon amplification. Two putative exons recovered by exon amplification strategy were found to be highly conserved throughout evolution and, therefore, they were used as probes for the screening of fetal and adult retina cDNA libraries. This led to the isolation of clones spanning a full-length cDNA which measures 7.6 kb. Sequence analysis revealed that the predicted protein product shows homology with syntrophines and a Xenopus laevis apical protein. The gene covers approximately 170 kb of DNA and spans the entire critical region for OA1, being deleted in two patients with contiguous gene deletion including OA1 and in one patient with isolated OA1. Therefore, this new gene represents a very strong candidate for involvement in OA1 (an alternative, but unlikely possibility to be considered is that the true OA1 gene lies within an intron of the former). Northern analysis revealed very high level of expression in retina and melanoma. Unlike most Xp22.3 genes, this gene is conserved in the mouse. We are currently performing SSCP analysis and direct sequencing of exons on DNAs from approximately 60 unrelated patients with OA1 for mutation detection.

Bassi, M.T.; Schiaffino, V.; Rugarli, E. [Baylor College of Medicine, Houston, TX (United States)



[RAPD markers linked to the stripe rust resistance gene Yr5 in the wheat variety Triticum spelta album]. (United States)

A total of 520 10-mer random primers were used to identify the RAPD markers linked to the Yr5 gene between the near-isogenic line Yr5/6 x Avocet S and recurrent parent Avocet S. Three polymorphic DNA fragments, S1496(761), S1453(880) and S1418(1950), were found linked to the Yr5 gene. In which the genetic distance between S1496(761) and Yr5 gene was 2.7 cM. The fragment S1496(761) was recovered from the gel and cloned and sequenced. A pair of specific PCR primers was designed based on the sequence. The specific primers amplified the same fragment about 761bp as the random primer S1496 did. Because the primers could amplify another non-specific fragment, the PCR products must be analyzed by electrophoresis on polyacrylamide gels. PMID:12200864

Zhong, Ming; Niu, Yong-Chun; Xu, Shi-Chang; Wu, Li-Ren



Molecular triangulation: Bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease  


A major challenge in human genetics is identifying the molecular basis of common heritable disorders. In contrast to rare single-gene diseases, multifactorial disorders are thought to arise from the combined effect of multiple gene variants, such that any single variant may have only a modest effect on disease susceptibility. We present a method to identify genes that may harbor a significant proportion of the genetic variation that predisposes individuals to a given multifactorial disorder. ...

Krauthammer, Michael; Kaufmann, Charles A.; Gilliam, T. Conrad; Rzhetsky, Andrey



In vivo genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection  


Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved in susceptibility or resistance to intestinal infection with the bacterium Serratia marcescens. We employed first whole-organism gene suppression followed by tissue-specific silencing in gut epithelium or hemocytes to identify several hundred genes involved in intestinal anti-bacterial immunity. Among the pathways identified, we showed t...

Cronin, Shane J. F.; Nehme, Nadine T.; Limmer, Stefanie; Liegeois, Samuel; Pospisilik, J. Andrew; Schramek, Daniel; Leibbrandt, Andreas; Simoes, Ricardo Matos; Gruber, Susanne; Puc, Urszula; Ebersberger, Ingo; Zoranovic, Tamara; Neely, G. Gregory; Von Haeseler, Arndt; Ferrandon, Dominique



Gene-carried chitosan-linked polyethylenimine induced high gene transfection efficiency on dendritic cells. (United States)

A dendritic cell (DC) networking system has become an attractive approach in cancer immunotherapy. Successful DC gene engineering depends on the development of transgene vectors. A cationic polymer, chitosan-linked polyethylenimine (PEI) (CP), possessing the advantages of both PEI and chitosan, has been applied in nonviral transfection of DCs. Physicochemical evaluation showed that CP/DNA complexes could form cationic nanoparticles. Compared with DCs transfected with commercial reagent, Lipofectamine2000, it showed higher transfection efficiency and lower cytotoxicity when DCs were transfected with CP/DNA complexes. A nuclear trafficking observation of CP/DNA complexes by a confocal laser scanning microscope further revealed that the CP could help DNA enter into the cytoplasm and finally into the nucleus of a DC. Finally, vaccination of DCs transfected with CP/DNA encoding gp100 slightly improved resistance to the B16BL6 melanoma challenge. This is the first report that CP polymer is used as a nonviral vector for DC gene delivery and DC vaccine. Essentially, these results might be helpful to design a promising nonviral vector for DC gene delivery. PMID:23586911

Chen, Yu-Zhe; Yao, Xing-Lei; Ruan, Gui-Xin; Zhao, Qing-Qing; Tang, Gu-Ping; Tabata, Yasuhiko; Gao, Jian-Qing



A Gene Recommender Algorithm to Identify Coexpressed Genes in C. elegans  


One of the most important uses of whole-genome expression data is for the discovery of new genes with similar function to a given list of genes (the query) already known to have closely related function. We have developed an algorithm, called the gene recommender, that ranks genes according to how strongly they correlate with a set of query genes in those experiments for which the query genes are most strongly coregulated. We used the gene recommender to find other genes coexpressed wit...

Owen, Art B.; Stuart, Josh; Mach, Kathy; Villeneuve, Anne M.; Kim, Stuart



U3 snoRNA genes are multi-copy and frequently linked to U5 snRNA genes in Euglena gracilis§  

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Full Text Available Abstract Background U3 snoRNA is a box C/D small nucleolar RNA (snoRNA involved in the processing events that liberate 18S rRNA from the ribosomal RNA precursor (pre-rRNA. Although U3 snoRNA is present in all eukaryotic organisms, most investigations of it have focused on fungi (particularly yeasts, animals and plants. Relatively little is known about U3 snoRNA and its gene(s in the phylogenetically broad assemblage of protists (mostly unicellular eukaryotes. In the euglenozoon Euglena gracilis, a distant relative of the kinetoplastid protozoa, Southern analysis had previously revealed at least 13 bands hybridizing with U3 snoRNA, suggesting the existence of multiple copies of U3 snoRNA genes. Results Through screening of a ? genomic library and PCR amplification, we recovered 14 U3 snoRNA gene variants, defined by sequence heterogeneities that are mostly located in the U3 3'-stem-loop domain. We identified three different genomic arrangements of Euglena U3 snoRNA genes: i stand-alone, ii linked to tRNAArg genes, and iii linked to a U5 snRNA gene. In arrangement ii, the U3 snoRNA gene is positioned upstream of two identical tRNAArg genes that are convergently transcribed relative to the U3 gene. This scenario is reminiscent of a U3 snoRNA-tRNA gene linkage previously described in trypanosomatids. We document here twelve different U3 snoRNA-U5 snRNA gene arrangements in Euglena; in each case, the U3 gene is linked to a downstream and convergently oriented U5 gene, with the intergenic region differing in length and sequence among the variants. Conclusion 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.

Charette J Michael



Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis  


Patient specific therapy is emerging as an important possibility for many cancer patients. However, to identify such therapies it is essential to determine the genomic and transcriptional alterations present in one tumor relative to control samples. This presents a challenge since use of a single sample precludes many standard statistical analysis techniques. We reasoned that one means of addressing this issue is by comparing transcriptional changes in one tumor with those observed in a large...

Stathias, Vasileios; Pastori, Chiara; Griffin, Tess Z.; Komotar, Ricardo; Clarke, Jennifer; Zhang, Ming; Ayad, Nagi G.



Identifying set-wise differential co-expression in gene expression microarray data  

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Full Text Available Abstract Background Previous differential coexpression analyses focused on identification of differentially coexpressed gene pairs, revealing many insightful biological hypotheses. However, this method could not detect coexpression relationships between pairs of gene sets. Considering the success of many set-wise analysis methods for microarray data, a coexpression analysis based on gene sets may elucidate underlying biological processes provoked by the conditional changes. Here, we propose a differentially coexpressed gene sets (dCoxS algorithm that identifies the differentially coexpressed gene set pairs between conditions. Results dCoxS is a two-step analysis method. In each condition, dCoxS measures the interaction score (IS, which represents the expression similarity between two gene sets using Renyi relative entropy. When estimating the relative entropy, multivariate kernel density estimation was used to model gene-gene correlation structure. Statistical tests for the conditional difference between the ISs determined the significance of differential coexpression of the gene set pair. Simulation studies supported that the IS is a representative measure of similarity between gene expression matrices. Single gene coexpression analysis of two publicly available microarray datasets detected no significant results. However, the dCoxS analysis of the datasets revealed differentially coexpressed gene set pairs related to the biological conditions of the datasets. Conclusion dCoxS identified differentially coexpressed gene set pairs not found by single gene analysis. The results indicate that set-wise differential coexpression analysis is useful for understanding biological processes induced by conditional changes.

Kim Jihun



Extragenic Suppressors of Saccharomyces Cerevisiae Prp4 Mutations Identify a Negative Regulator of Prp Genes  


The PRP4 gene encodes a protein that is a component of the U4/U6 small nuclear ribonucleoprotein particle and is necessary for both spliceosome assembly and pre-mRNA splicing. To identify genes whose products interact with the PRP4 gene or gene product, we isolated second-site suppressors of temperature-sensitive prp4 mutations. We limited ourselves to suppressors with a distinct phenotype, cold sensitivity, to facilitate analysis of mutants. Ten independent recessive suppressors were obtaine...

Maddock, J. R.; Weidenhammer, E. M.; Adams, C. C.; Lunz, R. L.; Woolford-jr, J. L.



Structure and evolution of Apetala3, a sex-linked gene in Silene latifolia  

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Full Text Available Abstract Background The evolution of sex chromosomes is often accompanied by gene or chromosome rearrangements. Recently, the gene AP3 was characterized in the dioecious plant species Silene latifolia. It was suggested that this gene had been transferred from an autosome to the Y chromosome. Results In the present study we provide evidence for the existence of an X linked copy of the AP3 gene. We further show that the Y copy is probably located in a chromosomal region where recombination restriction occurred during the first steps of sex chromosome evolution. A comparison of X and Y copies did not reveal any clear signs of degenerative processes in exon regions. Instead, both X and Y copies show evidence for relaxed selection compared to the autosomal orthologues in S. vulgaris and S. conica. We further found that promoter sequences differ significantly. Comparison of the genic region of AP3 between the X and Y alleles and the corresponding autosomal copies in the gynodioecious species S. vulgaris revealed a massive accumulation of retrotransposons within one intron of the Y copy of AP3. Analysis of the genomic distribution of these repetitive elements does not indicate that these elements played an important role in the size increase characteristic of the Y chromosome. However, in silico expression analysis shows biased expression of individual domains of the identified retroelements in male plants. Conclusions We characterized the structure and evolution of AP3, a sex linked gene with copies on the X and Y chromosomes in the dioecious plant S. latifolia. These copies showed complementary expression patterns and relaxed evolution at protein level compared to autosomal orthologues, which suggests subfunctionalization. One intron of the Y-linked allele was invaded by retrotransposons that display sex-specific expression patterns that are similar to the expression pattern of the corresponding allele, which suggests that these transposable elements may have influenced evolution of expression patterns of the Y copy. These data could help researchers decipher the role of transposable elements in degenerative processes during sex chromosome evolution.

Cegan Radim



Application of methods for identifying broiler chicken gut bacterial species linked with increased energy metabolism. (United States)

A high-throughput microbial profiling tool based on terminal restriction fragment length polymorphism was developed to monitor the poultry gut microbiota in response to dietary manipulations. Gut microbial communities from the duodena, jejuna, ilea, and ceca of 48 birds fed either a barley control diet or barley diet supplemented with exogenous enzymes for degrading nonstarch polysaccharide were characterized by using multivariate statistical methods. Analysis of samples showed that gut microbial communities varied significantly among gut sections, except between the duodenum and jejunum. Significant diet-associated differences in gut microbial communities were detected within the ileum and cecum only. The dissimilarity in bacterial community composition between diets was 73 and 66% within the ileum and cecum, respectively. Operational taxonomic units, representing bacterial species or taxonomically related groups, contributing to diet-associated differences were identified. Several bacterial species contributed to differences between diet-related gut microbial community composition, with no individual bacterial species contributing more than 1 to 5% of the total. Using canonical analysis of principal coordinates biplots, we correlated differences in gut microbial community composition within the ileum and cecum to improved performance, as measured by apparent metabolizable energy. This is the first report that directly links differences in the composition of the gut microbial community with improved performance, which implies that the presence of specific beneficial and/or absence of specific detrimental bacterial species may contribute to the improved performance in these birds. PMID:18065621

Torok, Valeria A; Ophel-Keller, Kathy; Loo, Maylene; Hughes, Robert J



Application of network properties and signal strength to identify face-to-face links in an electronic dataset  

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Understanding how people interact and socialize is important in many contexts, from disease control to urban planning. Datasets that capture this specific aspect of human life have increased in size and availability over the last few years. We have yet to understand, however, to what extent such electronic datasets may serve as a valid proxy for real life face-to-face interactions. For an observational dataset, gathered by mobile phones, we attack the problem of identifying transient and non-important links, as well as how to highlight important interactions. Using the Bluetooth signal strength parameter to distinguish between observations, we demonstrate that weak links, compared to strong links, have a lower probability of being observed at later times, while such links--on average--also have lower link-weights and a lower probability of sharing an online friendship. Further, the role of link-strength is investigated in relation to social network properties.

Sekara, Vedran



A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs  

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Full Text Available Abstract Background Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. Results We demonstrate here our first effort on the development of a three stage bacterial recombination strategy to physically link multiple genes together with their respective fluorescent protein (FP reporters in one DNA fragment. This strategy uses bacterial recombination techniques to: (1 subclone genes of interest into BAC linking vectors, (2 insert desired reporter genes into respective genes and (3 link different gene-reporters together. As proof of concept, we have generated a single DNA fragment containing the genes Trap, Dmp1, and Ibsp driving the expression of ECFP, mCherry, and Topaz FP reporter genes, respectively. Using this DNA construct, we have successfully generated transgenic reporter mice that retain two to three gene readouts. Conclusion The three stage methodology to link multiple genes with their respective fluorescent protein reporter works with reasonable efficiency. Moreover, gene linkage allows for their common chromosomal integration into a single locus. However, the testing of this multi-reporter DNA construct by transgenesis does suggest that the linkage of two different genes together, despite their large size, can still create a positional effect. We believe that gene choice, genomic DNA fragment size and the presence of endogenous insulator elements are critical variables.

Gong Shiaochin



Linkage analysis and physical mapping near the gene for x-linked agammaglobulinemia at Xq22  

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The gene for x-linked agammaglobulinemia (XLA) has been mapped to Xq22. No recombinations have been reported between the gene and the prob p212 at DXS178; however, this probe is informative in only 30-40% of women and the reported flanking markers, DXS3 and DXS94, and 10-15 cM apart. To identify additional probes that might be useful in genetic counseling, we examined 11 polymorphisms that have been mapped to the Xq21.3-q22 region in 13 families with XLA. In addition, pulsed-field gel electrophoresis and yeast artificial chromosomes (YACs) were used to further characterize the segman of DNA within which the gene for SLA must lie. The results demonstrated that DXS366 and DXS442, which share a 430-kb pulsed-field fragment, could replace DXS3 as proximal flanking markers. Probes at DXS178 and DXS265 identified the same 145-kb pulsed-field fragment, and both loci were contained within a 200-kb YAC identified with the probe p212. A highly polymorphic CA repeat (DCS178CA) was isolated from one end of this YAC and used in linkage analysis. Probes at DXS101 and DXS328 shared several pulsed-field fragments, the smallest of which was 250 kb. No recombinations were seen between XLA and the DXS178-DXS265-DXS178CA complex, DXS101, DXS328, DXS87, or the gene for proteolipid protein (PLP). Key crossovers, when combined with the linkage data from families with Alport syndrome, suggested the following order of loci: cen-DXS3-DXS366-DXS442-(PLP, DXS101, DXS328, DXS178-DXS265-DXS178CA complex, XL)-(DXS87, DXS94)-DXS327-(DXS350, DXS362)-tel. Our studies also limit the segment of DNA within which the XLA gene must lie to the 3- to 4-cM distance between DCS442 and DXS94 and they identify and orient polymorphisms that can be used in genetic counseling not only for XLA but also for Pelizaeus-Merzbacher disease (PLP deficiency), Alport syndrome (COL4A5 deficiency), and Fabry disease ([alpha]-galactosidase A difficiency). 31 refs., 5 figs., 2 tabs.

Parolini, O.; Lassiter, G.L.; Henry, M.J.; Conley, M.E. (Univ. of Tennessee College of Medicine, Memphis (United States) St. Jude Children' s Research Hospital, Memphis, TN (United States)); Hejtmancik, J.F. (National Inst. of Health, Bethesda, MD (United States)); Allen, R.C.; Belmont, J.W. (Baylor College of Medicine, Houston, TX (United States)); Barker, D.F. (Univ. of Utah, Salt Lake City (United States))



A transcription map of the 6p22.3 reading disability locus identifying candidate genes  


Abstract Background Reading disability (RD) is a common syndrome with a large genetic component. Chromosome 6 has been identified in several linkage studies as playing a significant role. A more recent study identified a peak of transmission disequilibrium to marker JA04 (G72384) on chromosome 6p22.3, suggesting that a gene is located near this marker. Results In silico cloning was used to identify possible candidate genes located near the JA04 marker. ...

Gruen Jeffrey R; Meng Haiying; Londin Eric R



Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links (United States)

Metabolic traits are molecular phenotypes that can drive clinical phenotypes and may predict disease progression. Here, we report results from a metabolome- and genome-wide association study on 1H-NMR urine metabolic profiles. The study was conducted within an untargeted approach, employing a novel method for compound identification. From our discovery cohort of 835 Caucasian individuals who participated in the CoLaus study, we identified 139 suggestively significant (P<5×10?8) and independent associations between single nucleotide polymorphisms (SNP) and metabolome features. Fifty-six of these associations replicated in the TasteSensomics cohort, comprising 601 individuals from São Paulo of vastly diverse ethnic background. They correspond to eleven gene-metabolite associations, six of which had been previously identified in the urine metabolome and three in the serum metabolome. Our key novel findings are the associations of two SNPs with NMR spectral signatures pointing to fucose (rs492602, P?=?6.9×10?44) and lysine (rs8101881, P?=?1.2×10?33), respectively. Fine-mapping of the first locus pinpointed the FUT2 gene, which encodes a fucosyltransferase enzyme and has previously been associated with Crohn's disease. This implicates fucose as a potential prognostic disease marker, for which there is already published evidence from a mouse model. The second SNP lies within the SLC7A9 gene, rare mutations of which have been linked to severe kidney damage. The replication of previous associations and our new discoveries demonstrate the potential of untargeted metabolomics GWAS to robustly identify molecular disease markers. PMID:24586186

Nicholls, Andrew W.; Salek, Reza M.; Marques-Vidal, Pedro; Morya, Edgard; Sameshima, Koichi; Montoliu, Ivan; Da Silva, Laeticia; Collino, Sebastiano; Martin, François-Pierre; Rezzi, Serge; Steinbeck, Christoph; Waterworth, Dawn M.; Waeber, Gérard; Vollenweider, Peter; Beckmann, Jacques S.; Le Coutre, Johannes; Mooser, Vincent; Bergmann, Sven; Genick, Ulrich K.; Kutalik, Zoltán



Development of two sequence-specific PCR markers linked to the le gene that reduces pod shattering in narrow-leafed Lupin (Lupinus angustifolius L.)  


Wild types of narrow-leaf lupin (Lupinus angustifolius L.) have seed pods that shatter upon maturity, leading to the loss of their seeds before or during the harvest process. Two recessive genes have been incorporated into domesticated cultivars of this species to maximize harvest-ability of the produce. One of these genes is called lentus (le). Two microsatellite - anchored fragment length polymorphism (MFLP) candidate markers were identified as closely linked to the le gene in a recombinant...

Boersma, Jeffrey G.; Buirchell, Bevan J.; Krishnapillai Sivasithamparam; Huaan Yang



GeneLink: a database to facilitate genetic studies of complex traits  

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Full Text Available Abstract Background In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data management systems are often critical to the success of these projects. To minimize the difficulties inherent in complex trait studies, we have developed GeneLink, a Web-accessible, password-protected Sybase database. Results GeneLink is a powerful tool for complex trait mapping, enabling genotypic data to be easily merged with pedigree and extensive phenotypic data. Specifically designed to facilitate large-scale (multi-center genetic linkage or association studies, GeneLink securely and efficiently handles large amounts of data and provides additional features to facilitate data analysis by existing software packages and quality control. These include the ability to download chromosome-specific data files containing marker data in map order in various formats appropriate for downstream analyses (e.g., GAS and LINKAGE. Furthermore, an unlimited number of phenotypes (either qualitative or quantitative can be stored and analyzed. Finally, GeneLink generates several quality assurance reports, including genotyping success rates of specified DNA samples or success and heterozygosity rates for specified markers. Conclusions GeneLink has already proven an invaluable tool for complex trait mapping studies and is discussed primarily in the context of our large, multi-center study of hereditary prostate cancer (HPC. GeneLink is freely available at

Wolfsberg Tyra G



RNA-Seq identifies novel myocardial gene expression signatures of heart failure. (United States)

Heart failure is a complex clinical syndrome and has become the most common reason for adult hospitalization in developed countries. Two subtypes of heart failure, ischemic heart disease (ISCH) and dilated cardiomyopathy (DCM), have been studied using microarray platforms. However, microarray has limited resolution. Here we applied RNA sequencing (RNA-Seq) to identify gene signatures for heart failure from six individuals, including three controls, one ISCH and two DCM patients. Using genes identified from this small RNA-Seq dataset, we were able to accurately classify heart failure status in a much larger set of 313 individuals. The identified genes significantly overlapped with genes identified via genome-wide association studies for cardiometabolic traits and the promoters of those genes were enriched for binding sites for transcriptions factors. Our results indicate that it is possible to use RNA-Seq to classify disease status for complex diseases such as heart failure using an extremely small training dataset. PMID:25528681

Liu, Yichuan; Morley, Michael; Brandimarto, Jeffrey; Hannenhalli, Sridhar; Hu, Yu; Ashley, Euan A; Tang, W H Wilson; Moravec, Christine S; Margulies, Kenneth B; Cappola, Thomas P; Li, Mingyao



Apoptosis-linked gene-2 connects the Raf-1 and ASK1 signalings  

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Raf-1 plays important roles in cell proliferation, differentiation, and survival. However, the unique and essential function of Raf-1 is anti-apoptotic. The molecules that mediate Raf-1's anti-apoptotic function are not known. In the course of identifying new substrates of Raf-1, we found that the Raf-1 kinase domain interacted with apoptosis-linked gene-2 (ALG-2) in yeast two-hybrid system. Our further studies showed that Raf-1 phosphorylated ALG-2 in an in vitro kinase assay. We also found that apoptosis signal-regulating kinase 1 (ASK1) strongly phosphorylated ALG-2. Importantly, Raf-1 blocks the ASK1-dependent ALG-2 phosphorylation. Since ALG-2 associates with ASK1, and both ASK1 and ALG-2 are involved in apoptosis, our observations indicate that Raf-1 may mediate its anti-apoptotic function by interrupting ASK1-dependent phosphorylation of ALG-2


ALK1 signalling analysis identifies angiogenesis related genes and reveals disparity between TGF-? and constitutively active receptor induced gene expression  

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Full Text Available Abstract Background TGF-?1 is an important angiogenic factor involved in the different aspects of angiogenesis and vessel maintenance. TGF-? signalling is mediated by the T?RII/ALK5 receptor complex activating the Smad2/Smad3 pathway. In endothelial cells TGF-? utilizes a second type I receptor, ALK1, activating the Smad1/Smad5 pathway. Consequently, a perturbance of ALK1, ALK5 or T?RII activity leads to vascular defects. Mutations in ALK1 cause the vascular disorder hereditary hemorrhagic telangiectasia (HHT. Methods The identification of ALK1 and not ALK5 regulated genes in endothelial cells, might help to better understand the development of HHT. Therefore, the human microvascular endothelial cell line HMEC-1 was infected with a recombinant constitutively active ALK1 adenovirus, and gene expression was studied by using gene arrays and quantitative real-time PCR analysis. Results After 24 hours, 34 genes were identified to be up-regulated by ALK1 signalling. Analysing ALK1 regulated gene expression after 4 hours revealed 13 genes to be up- and 2 to be down-regulated. Several of these genes, including IL-8, ET-1, ID1, HPTP? and TEAD4 are reported to be involved in angiogenesis. Evaluation of ALK1 regulated gene expression in different human endothelial cell types was not in complete agreement. Further on, disparity between constitutively active ALK1 and TGF-?1 induced gene expression in HMEC-1 cells and primary HUVECs was observed. Conclusion Gene array analysis identified 49 genes to be regulated by ALK1 signalling and at least 14 genes are reported to be involved in angiogenesis. There was substantial agreement between the gene array and quantitative real-time PCR data. The angiogenesis related genes might be potential HHT modifier genes. In addition, the results suggest endothelial cell type specific ALK1 and TGF-? signalling.

Hafner Mathias



Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies  

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Full Text Available Abstract Background With over 20 parapatric races differing in their warningly colored wing patterns, the butterfly Heliconius erato provides a fascinating example of an adaptive radiation. Together with matching races of its co-mimic Heliconius melpomene, H. erato also represents a textbook case of Müllerian mimicry, a phenomenon where common warning signals are shared amongst noxious organisms. It is of great interest to identify the specific genes that control the mimetic wing patterns of H. erato and H. melpomene. To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in Heliconius. Results Scoring AFLP polymorphisms in H. erato broods allowed us to survey loci at approximately 362 kb intervals across the genome. With this strategy we were able to identify markers tightly linked to two color pattern genes: D and Cr, which were then used to screen H. erato BAC libraries in order to identify clones for sequencing. Gene density across 600 kb of BAC sequences appeared relatively low, although the number of predicted open reading frames was typical for an insect. We focused analyses on the D- and Cr-linked H. erato BAC sequences and on the Yb-linked H. melpomene BAC sequence. A comparative analysis between homologous regions of H. erato (Cr-linked BAC and H. melpomene (Yb-linked BAC revealed high levels of sequence conservation and microsynteny between the two species. We found that repeated elements constitute 26% and 20% of BAC sequences from H. erato and H. melpomene respectively. The majority of these repetitive sequences appear to be novel, as they showed no significant similarity to any other available insect sequences. We also observed signs of fine scale conservation of gene order between Heliconius and the moth Bombyx mori, suggesting that lepidopteran genome architecture may be conserved over very long evolutionary time scales. Conclusion Here we have demonstrated the tractability of progressing from a genetic linkage map to genomic sequence data in Heliconius butterflies. We have also shown that fine-scale gene order is highly conserved between distantly related Heliconius species, and also between Heliconius and B. mori. Together, these findings suggest that genome structure in macrolepidoptera might be very conserved, and show that mapping and positional cloning efforts in different lepidopteran species can be reciprocally informative.

Halder Georg



Refinement of the localization of the X-linked ocular albinism gene  

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Although physical and genetic mapping studies assigned the X-linked ocular albinism gene to Xp22.3, the exact gene order in this region is still unclear. The authors present additional genetic mapping data concerning X-linked ocular albinism that suggests the consensus order Xpter-STS-DXS237-KAL-(OA1, DXS143)- DXS85-DXS16-Xcen. 14 refs., 1 fig.

Bergen, A.A.B.; Zijp, P.; Schuurman, E.J.M.; Bleeker-Wagemakers, E.M.; Apkarian, P. (Netherlands Ophthalmic Research Inst., Amsterdam (Netherlands)); Ommen, G.J.B. van (Univ. of Leiden (Netherlands))



GlycoFish: A Database of Zebrafish N-linked Glycoproteins Identified Using SPEG Method Coupled with LC/MS  


Zebrafish (Danio rerio) is a model organism to study the mechanisms and pathways of human disorders. Many dysfunctions in neurological, development and neuromuscular systems are due to glycosylation deficiencies, but the glycoproteins involved in zebrafish embryonic development have not been established. In this study, a mass spectrometry-based glycoproteomic characterization of zebrafish embryos was performed to identify the N-linked glycoproteins and N-linked glycosylation sites. To increas...

Baycin-hizal, Deniz; Tian, Yuan; Akan, Ilhan; Jacobson, Elena; Clark, Dean; Wu, Alexander; Jampol, Russell; Palter, Karen; Betenbaugh, Michael; Zhang, Hui



GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed  

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Full Text Available Abstract Background The amount of gene expression data in the public repositories, such as NCBI Gene Expression Omnibus (GEO has grown exponentially, and provides a gold mine for bioinformaticians, but has not been easily accessible by biologists and clinicians. Results We developed an automated approach to annotate and analyze all GEO data sets, including 1,515 GEO data sets from 231 microarray types across 42 species, and performed 12,658 group versus group comparisons of 24 GEO-specified types. We then built GeneChaser, a web server that enables biologists and clinicians without bioinformatics skills to easily identify biological and clinical conditions in which a gene or set of genes was differentially expressed. GeneChaser displays these conditions in graphs, gives statistical comparisons, allows sort/filter functions and provides access to the original studies. We performed a single gene search for Nanog and a multiple gene search for Nanog, Oct4, Sox2 and LIN28, confirmed their roles in embryonic stem cell development, identified several drugs that regulate their expression, and suggested their potential roles in sex determination, abnormal sperm morphology, malaria infection, and cancer. Conclusion We demonstrated that GeneChaser is a powerful tool to elucidate information on function, transcriptional regulation, drug-response and clinical implications for genes of interest.

Venkatasubrahmanyam Shivkumar



In vivo negative selection screen identifies genes required for Francisella virulence (United States)

Francisella tularensis subverts the immune system to rapidly grow within mammalian hosts, often causing tularemia, a fatal disease. This pathogen targets the cytosol of macrophages where it replicates by using the genes encoded in the Francisella pathogenicity island. However, the bacteria are recognized in the cytosol by the host's ASC/caspase-1 pathway, which is essential for host defense, and leads to macrophage cell death and proinflammatory cytokine production. We used a microarray-based negative selection screen to identify Francisella genes that contribute to growth and/or survival in mice. The screen identified many known virulence factors including all of the Francisella pathogenicity island genes, LPS O-antigen synthetic genes, and capsule synthetic genes. We also identified 44 previously unidentified genes that were required for Francisella virulence in vivo, indicating that this pathogen may use uncharacterized mechanisms to cause disease. Among these, we discovered a class of Francisella virulence genes that are essential for growth and survival in vivo but do not play a role in intracellular replication within macrophages. Instead, these genes modulate the host ASC/caspase-1 pathway, a previously unidentified mechanism of Francisella pathogenesis. This finding indicates that the elucidation of the molecular mechanisms used by other uncharacterized genes identified in our screen will increase our understanding of the ways in which bacterial pathogens subvert the immune system. PMID:17389372

Weiss, David S.; Brotcke, Anna; Henry, Thomas; Margolis, Jeffrey J.; Chan, Kaman; Monack, Denise M.



Adipose Co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes  

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Full Text Available Abstract Background High serum triglyceride (TG levels is an established risk factor for coronary heart disease (CHD. Fat is stored in the form of TGs in human adipose tissue. We hypothesized that gene co-expression networks in human adipose tissue may be correlated with serum TG levels and help reveal novel genes involved in TG regulation. Methods Gene co-expression networks were constructed from two Finnish and one Mexican study sample using the blockwiseModules R function in Weighted Gene Co-expression Network Analysis (WGCNA. Overlap between TG-associated networks from each of the three study samples were calculated using a Fisher’s Exact test. Gene ontology was used to determine known pathways enriched in each TG-associated network. Results We measured gene expression in adipose samples from two Finnish and one Mexican study sample. In each study sample, we observed a gene co-expression network that was significantly associated with serum TG levels. The TG modules observed in Finns and Mexicans significantly overlapped and shared 34 genes. Seven of the 34 genes (ARHGAP30, CCR1, CXCL16, FERMT3, HCST, RNASET2, SELPG were identified as the key hub genes of all three TG modules. Furthermore, two of the 34 genes (ARHGAP9, LST1 reside in previous TG GWAS regions, suggesting them as the regional candidates underlying the GWAS signals. Conclusions This study presents a novel adipose gene co-expression network with 34 genes significantly correlated with serum TG across populations.

Haas Blake E



Functional genomics identifies novel genes essential for clear cell renal cell carcinoma tumor cell proliferation and migration. (United States)

Currently there is a lack of targeted therapies that lead to long-term attenuation or regression of disease in patients with advanced clear cell renal cell carcinoma (ccRCC). Our group has implemented a high-throughput genetic analysis coupled with a high-throughput proliferative screen in order to investigate the genetic contributions of a large cohort of overexpressed genes at the functional level in an effort to better understand factors involved in tumor initiation and progression. Patient gene array analysis identified transcripts that are consistently elevated in patient ccRCC as compared to matched normal renal tissues. This was followed by a high-throughput lentivirus screen, independently targeting 195 overexpressed transcripts identified in the gene array in four ccRCC cell lines. This revealed 31 'hits' that contribute to ccRCC cell proliferation. Many of the hits identified are not only presented in the context of ccRCC for the first time, but several have not been previously linked to cancer. We further characterize the function of a group of hits in tumor cell invasion. Taken together these findings reveal pathways that may be critical in ccRCC tumorigenicity, and identifies novel candidate factors that could serve as targets for therapeutic intervention or diagnostic/prognostic biomarkers for patients with advanced ccRCC. PMID:24979721

Von Roemeling, Christina A; Marlow, Laura A; Radisky, Derek C; Rohl, Austin; Larsen, Hege Ekeberg; Wei, Johnny; Sasinowska, Heather; Zhu, Heng; Drake, Richard; Sasinowski, Maciek; Tun, Han W; Copland, John A



Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression  

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Full Text Available Abstract Background Cartilage plays a fundamental role in the development of the human skeleton. Early in embryogenesis, mesenchymal cells condense and differentiate into chondrocytes to shape the early skeleton. Subsequently, the cartilage anlagen differentiate to form the growth plates, which are responsible for linear bone growth, and the articular chondrocytes, which facilitate joint function. However, despite the multiplicity of roles of cartilage during human fetal life, surprisingly little is known about its transcriptome. To address this, a whole genome microarray expression profile was generated using RNA isolated from 18–22 week human distal femur fetal cartilage and compared with a database of control normal human tissues aggregated at UCLA, termed Celsius. Results 161 cartilage-selective genes were identified, defined as genes significantly expressed in cartilage with low expression and little variation across a panel of 34 non-cartilage tissues. Among these 161 genes were cartilage-specific genes such as cartilage collagen genes and 25 genes which have been associated with skeletal phenotypes in humans and/or mice. Many of the other cartilage-selective genes do not have established roles in cartilage or are novel, unannotated genes. Quantitative RT-PCR confirmed the unique pattern of gene expression observed by microarray analysis. Conclusion Defining the gene expression pattern for cartilage has identified new genes that may contribute to human skeletogenesis as well as provided further candidate genes for skeletal dysplasias. The data suggest that fetal cartilage is a complex and transcriptionally active tissue and demonstrate that the set of genes selectively expressed in the tissue has been greatly underestimated.

Cohn Zachary A



GeneBrowser 2: an application to explore and identify common biological traits in a set of genes  

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Full Text Available Abstract Background The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes whose interpretation requires finding relevant biological roles for the problem at hand. The required information is typically available in public databases, and usually, this information must be manually retrieved to complement the analysis. This process is a very time-consuming task that should be automated as much as possible. Results GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided include the following: a central point with the most relevant biological information for each inserted gene; a list of the most related papers in PubMed and gene expression studies in ArrayExpress; and an extended approach to functional analysis applied to Gene Ontology, homologies, gene chromosomal localisation and pathways. Conclusions GeneBrowser provides a unique entry point to several visualisation and analysis methods, providing fast and easy analysis of a set of genes. GeneBrowser fills the gap between Web portals that analyse one gene at a time and functional analysis tools that are limited in scope and usually desktop-based.

Oliveira José



Newly identified fusion genes in lung and colorectal cancer may guide treatment with 'targeted' drugs (United States)

Novel gene abnormalities discovered in a subpopulation of lung and colorectal tumors could potentially identify patients with a good chance of responding to highly specific "targeted" drugs already in use for treating other cancers, scientists report.


Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics  


Abstract Background When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names. Results A little detective work traced the problem to default date format conversions and floating-point format conversions in the very useful Excel program package. The date conversions affect at least 30 gene names; the floating-point conversions affect at least 2,000 if Riken identifiers are included. These con...

Carl, Barrett J.; Marston, Linehan W.; Uchio Edward; Bussey Kimberly J; Riss Joseph; Kane David W; Zeeberg Barry R; Weinstein John N




A major objective of both animal and plant genomics research is to identify disease resistance genes and pathways. Popular approaches to achieve this goal include candidate gene testing, genome-wide QTL screens, and DNA microarrays. We argue that the two-hybrid assay, which detects protein-protein...


ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants  

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Full Text Available Abstract Background Uncovering the key sequence elements in gene promoters that regulate the expression of plant genomes is a huge task that will require a series of complementary methods for prediction, substantial innovations in experimental validation and a much greater understanding of the role of combinatorial control in the regulation of plant gene expression. Results To add to this larger process and to provide alternatives to existing prediction methods, we have developed several tools in the statistical package R. ModuleFinder identifies sets of genes and treatments that we have found to form valuable sets for analysis of the mechanisms underlying gene co-expression. CoReg then links the hierarchical clustering of these co-expressed sets with frequency tables of promoter elements. These promoter elements can be drawn from known elements or all possible combinations of nucleotides in an element of various lengths. These sets of promoter elements represent putative cis-acting regulatory elements common to sets of co-expressed genes and can be prioritised for experimental testing. We have used these new tools to analyze the response of transcripts for nuclear genes encoding mitochondrial proteins in Arabidopsis to a range of chemical stresses. ModuleFinder provided a subset of co-expressed gene modules that are more logically related to biological functions than did subsets derived from traditional hierarchical clustering techniques. Importantly ModuleFinder linked responses in transcripts for electron transport chain components, carbon metabolism enzymes and solute transporter proteins. CoReg identified several promoter motifs that helped to explain the patterns of expression observed. Conclusion ModuleFinder identifies sets of genes and treatments that form useful sets for analysis of the mechanisms behind co-expression. CoReg links the clustering tree of expression-based relationships in these sets with frequency tables of promoter elements. These sets of promoter elements represent putative cis-acting regulatory elements for sets of genes, and can then be tested experimentally. We consider these tools, both built on an open source software product to provide valuable, alternative tools for the prioritisation of promoter elements for experimental analysis.

Whelan James



Seven mutations in the human insulin gene linked to permanent neonatal/infancy-onset diabetes mellitus  


Permanent neonatal diabetes mellitus (PNDM) is a rare disorder usually presenting within 6 months of birth. Although several genes have been linked to this disorder, in almost half the cases documented in Italy, the genetic cause remains unknown. Because the Akita mouse bearing a mutation in the Ins2 gene exhibits PNDM associated with pancreatic ? cell apoptosis, we sequenced the human insulin gene in PNDM subjects with unidentified mutations. We discovered 7 heterozygous mutations in 10 unr...

Colombo, Carlo; Porzio, Ottavia; Liu, Ming; Massa, Ornella; Vasta, Mario; Salardi, Silvana; Beccaria, Luciano; Monciotti, Carla; Toni, Sonia; Pedersen, Oluf; Hansen, Torben; Federici, Luca; Pesavento, Roberta; Cadario, Francesco; Federici, Giorgio



Fast-X on the Z: Rapid evolution of sex-linked genes in birds  


Theoretical work predicts natural selection to be more efficient in the fixation of beneficial mutations in X-linked genes than in autosomal genes. This “fast-X effect” should be evident by an increased ratio of nonsynonymous to synonymous substitutions (dN/dS) for sex-linked genes; however, recent studies have produced mixed support for this expectation. To make an independent test of the idea of fast-X evolution, we focused on birds, which have female heterogamety (males ZZ, females ZW)...

Mank, Judith E.; Axelsson, Erik; Ellegren, Hans



Bioinformatic analysis of nematode migration-associated genes identifies novel vertebrate neural crest markers. (United States)

Neural crest cells are highly motile, yet a limited number of genes governing neural crest migration have been identified by conventional studies. To test the hypothesis that cell migration genes are likely to be conserved over large evolutionary distances and from diverse tissues, we searched for vertebrate homologs of genes important for migration of various cell types in the invertebrate nematode and examined their expression during vertebrate neural crest cell migration. Our systematic analysis utilized a combination of comparative genomic scanning, functional pathway analysis and gene expression profiling to uncover previously unidentified genes expressed by premigratory, emigrating and/or migrating neural crest cells. The results demonstrate that similar gene sets are expressed in migratory cell types across distant animals and different germ layers. Bioinformatics analysis of these factors revealed relationships between these genes within signaling pathways that may be important during neural crest cell migration. PMID:25051358

Kwon, Seung-Hae; Park, Ok Kyu; Nie, Shuyi; Kwak, Jina; Hwang, Byung Joon; Bronner, Marianne E; Kee, Yun



Gene-Based Rare Allele Analysis Identified a Risk Gene of Alzheimer’s Disease  


Alzheimer’s disease (AD) has a strong propensity to run in families. However, the known risk genes excluding APOE are not clinically useful. In various complex diseases, gene studies have targeted rare alleles for unsolved heritability. Our study aims to elucidate previously unknown risk genes for AD by targeting rare alleles. We used data from five publicly available genetic studies from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the database of Genotypes and Phenotypes (...

Kim, Jong Hun; Song, Pamela; Lim, Hyunsun; Lee, Jae-hyung; Lee, Jun Hong; Park, Sun Ah



Identifying Candidate Genes for Type 2 Diabetes Mellitus and Obesity through Gene Expression Profiling in Multiple Tissues or Cells (United States)

Type 2 Diabetes Mellitus (T2DM) and obesity have become increasingly prevalent in recent years. Recent studies have focused on identifying causal variations or candidate genes for obesity and T2DM via analysis of expression quantitative trait loci (eQTL) within a single tissue. T2DM and obesity are affected by comprehensive sets of genes in multiple tissues. In the current study, gene expression levels in multiple human tissues from GEO datasets were analyzed, and 21 candidate genes displaying high percentages of differential expression were filtered out. Specifically, DENND1B, LYN, MRPL30, POC1B, PRKCB, RP4-655J12.3, HIBADH, and TMBIM4 were identified from the T2DM-control study, and BCAT1, BMP2K, CSRNP2, MYNN, NCKAP5L, SAP30BP, SLC35B4, SP1, BAP1, GRB14, HSP90AB1, ITGA5, and TOMM5 were identified from the obesity-control study. The majority of these genes are known to be involved in T2DM and obesity. Therefore, analysis of gene expression in various tissues using GEO datasets may be an effective and feasible method to determine novel or causal genes associated with T2DM and obesity. PMID:24455749

Meng, Yuhuan; Zhou, Jinghui; Zhuo, Min; Ling, Fei; Zhang, Yu; Du, Hongli; Wang, Xiaoning



Evidence that SIZN1 is a Candidate X-Linked Mental Retardation Gene  


An estimated 1-3% of individuals within the United States are diagnosed with mental retardation (MR), yet the cause is unknown in nearly 50% of the patients. While several environmental, genetic and combined teratogenetic etiologies have been identified, many causative genes remain to be identified. Furthermore, the pathogenetic mechanisms underlying MR are known for very few of these genes. Males have a much higher incidence of MR implicating genes on the X-chromosome. We have recently ident...

Cho, Ginam; Bhat, Shambhu S.; Gao, Jinsong; Collins, Julianne S.; Rogers, R. Curtis; Simensen, Richard J.; Schwartz, Charles E.; Golden, Jeffrey A.; Srivastava, Anand K.



Robust consensus clustering for identification of expressed genes linked to malignancy of human colorectal carcinoma  


Previous studies have been conducted in gene expression profiling to identify groups of genes that characterize the colorectal carcinoma disease. Despite the success of previous attempts to identify groups of genes in the progression of the colorectal carcinoma disease, their methods either require subjective interpretation of the number of clusters, or lack stability during different runs of the algorithms. All of which limits the usefulness of these methods. In this study, we propo...

Wahyudi, Gatot; Wasito, Ito; Melia, Tisha; Budi, Indra



A New Resource for Characterizing X-Linked Genes in Drosophila melanogaster: Systematic Coverage and Subdivision of the X Chromosome With Nested, Y-Linked Duplications  


Interchromosomal duplications are especially important for the study of X-linked genes. Males inheriting a mutation in a vital X-linked gene cannot survive unless there is a wild-type copy of the gene duplicated elsewhere in the genome. Rescuing the lethality of an X-linked mutation with a duplication allows the mutation to be used experimentally in complementation tests and other genetic crosses and it maps the mutated gene to a defined chromosomal region. Duplications can also be used to sc...

Cook, R. Kimberley; Deal, Megan E.; Deal, Jennifer A.; Garton, Russell D.; Brown, C. Adam; Ward, Megan E.; Andrade, Rachel S.; Spana, Eric P.; Kaufman, Thomas C.; Cook, Kevin R.



Identifying and prioritizing disease-related genes based on the network topological features. (United States)

Identifying and prioritizing disease-related genes are the most important steps for understanding the pathogenesis and discovering the therapeutic targets. The experimental examination of these genes is very expensive and laborious, and usually has a higher false positive rate. Therefore, it is highly desirable to develop computational methods for the identification and prioritization of disease-related genes. In this study, we develop a powerful method to identify and prioritize candidate disease genes. The novel network topological features with local and global information are proposed and adopted to characterize genes. The performance of these novel features is verified based on the 10-fold cross-validation test and leave-one-out cross-validation test. The proposed features are compared with the published features, and fused strategy is investigated by combining the current features with the published features. And, these combination features are also utilized to identify and prioritize Parkinson's disease-related genes. The results indicate that identified genes are highly related to some molecular process and biological function, which provides new clues for researching pathogenesis of Parkinson's disease. The source code of Matlab is freely available on request from the authors. PMID:25183318

Li, Zhan-Chao; Lai, Yan-Hua; Chen, Li-Li; Xie, Yun; Dai, Zong; Zou, Xiao-Yong



Functional Genomics Approach to Identifying Genes Required for Biofilm Development by Streptococcus mutans  


Streptococcus mutans, the primary etiological agent of human dental caries, is an obligate biofilm-forming bacterium. The goals of this study were to identify the gene(s) required for biofilm formation by this organism and to elucidate the role(s) that some of the known global regulators of gene expression play in controlling biofilm formation. In S. mutans UA159, the brpA gene (for biofilm regulatory protein) was found to encode a novel protein of 406 amino acid residues. A strain carrying a...

Wen, Zezhang T.; Burne, Robert A.



Transcriptional analysis of Gli3 mutants identifies Wnt target genes in the developing hippocampus. (United States)

Early development of the hippocampus, which is essential for spatial memory and learning, is controlled by secreted signaling molecules of the Wnt gene family and by Wnt/?-catenin signaling. Despite its importance, little is known, however, about Wnt-regulated genes during hippocampal development. Here, we used the Gli3 mutant mouse extra-toes (Xt(J)), in which Wnt gene expression in the forebrain is severely affected, as a tool in a microarray analyses to identify potential Wnt target genes. This approach revealed 53 candidate genes with restricted or graded expression patterns in the dorsomedial telencephalon. We identified conserved Tcf/Lef-binding sites in telencephalon-specific enhancers of several of these genes, including Dmrt3, Gli3, Nfia, and Wnt8b. Binding of Lef1 to these sites was confirmed using electrophoretic mobility shift assays. Mutations in these Tcf/Lef-binding sites disrupted or reduced enhancer activity in vivo. Moreover, ectopic activation of Wnt/?-catenin signaling in an ex vivo explant system led to increased telencephalic expression of these genes. Finally, conditional inactivation of Gli3 results in defective hippocampal growth. Collectively, these data strongly suggest that we have identified a set of direct Wnt target genes in the developing hippocampus and provide inside into the genetic hierarchy underlying Wnt-regulated hippocampal development. PMID:22235033

Hasenpusch-Theil, Kerstin; Magnani, Dario; Amaniti, Eleni-Maria; Han, Lin; Armstrong, Douglas; Theil, Thomas



A generally applicable translational strategy identifies S100A4 as a candidate gene in allergy  

DEFF Research Database (Denmark)

The identification of diagnostic markers and therapeutic candidate genes in common diseases is complicated by the involvement of thousands of genes. We hypothesized that genes co-regulated with a key gene in allergy, IL13, would form a module that could help to identify candidate genes. We identified a T helper 2 (TH2) cell module by small interfering RNA-mediated knockdown of 25 putative IL13-regulating transcription factors followed by expression profiling. The module contained candidate genes whose diagnostic potential was supported by clinical studies. Functional studies of human TH2 cells as well as mouse models of allergy showed that deletion of one of the genes, S100A4, resulted in decreased signs of allergy including TH2 cell activation, humoral immunity, and infiltration of effector cells. Specifically, dendritic cells required S100A4 for activating T cells. Treatment with an anti-S100A4 antibody resulted in decreased signs of allergy in the mouse model as well as in allergen-challenged T cells from allergic patients. This strategy, which may be generally applicable to complex diseases, identified and validated an important diagnostic and therapeutic candidate gene in allergy.

Bruhn, Sören; Fang, Yu



A medical record-linked biorepository to identify novel biomarkers for atherosclerotic cardiovascular disease  


Background: Atherosclerotic vascular disease (AVD), a leading cause of morbidity and mortality, is increasing in prevalence in the developing world. We describe an approach to establish a biorepository linked to medical records with the eventual goal of facilitating discovery of biomarkers for AVD.

Zi Ye; Kalloo, Fara S.; Kullo, Iftikhar J.



A medical record-linked biorepository to identify novel biomarkers for atherosclerotic cardiovascular disease  

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Full Text Available Background: Atherosclerotic vascular disease (AVD, a leading cause of morbidity and mortality, is increasing in prevalence in the developing world. We describe an approach to establish a biorepository linked to medical records with the eventual goal of facilitating discovery of biomarkers for AVD.

Zi Ye



Screening of 38 genes identifies mutations in 62% of families with nonsyndromic deafness in Turkey. (United States)

More than 60% of prelingual deafness is genetic in origin, and of these up to 95% are monogenic autosomal recessive traits. Causal mutations have been identified in 1 of 38 different genes in a subset of patients with nonsyndromic autosomal recessive deafness. In this study, we screened 49 unrelated Turkish families with at least three affected children born to consanguineous parents. Probands from all families were negative for mutations in the GJB2 gene, two large deletions in the GJB6 gene, and the 1555A>G substitution in the mitochondrial DNA MTRNR1 gene. Each family was subsequently screened via autozygosity mapping with genomewide single-nucleotide polymorphism arrays. If the phenotype cosegregated with a haplotype flanking one of the 38 genes, mutation analysis of the gene was performed. We identified 22 different autozygous mutations in 11 genes, other than GJB2, in 26 of 49 families, which overall explains deafness in 62% of families. Relative frequencies of genes following GJB2 were MYO15A (9.9%), TMIE (6.6%), TMC1 (6.6%), OTOF (5.0%), CDH23 (3.3%), MYO7A (3.3%), SLC26A4 (1.7%), PCDH15 (1.7%), LRTOMT (1.7%), SERPINB6 (1.7%), and TMPRSS3 (1.7%). Nineteen of 22 mutations are reported for the first time in this study. Unknown rare genes for deafness appear to be present in the remaining 23 families. PMID:21117948

Duman, Duygu; Sirmaci, Asli; Cengiz, F Basak; Ozdag, Hilal; Tekin, Mustafa



Identificação de marcadores RAPD ligados a um gene de resistência ao cancro da haste da soja Identification of RAPD markers linked to a soybean stem canker resistance gene  

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Full Text Available O cancro da haste da soja (Glycine max é uma importante doença causada pelo fungo Diaporthe phaseolorum f. sp. meridionalis/Phomopsis phaseoli f. sp. meridionalis. Visando identificar marcadores RAPD associados a genes de resistência ao cancro da haste, causado pelo isolado CH8, presentes na linhagem UFV 91-61, foi realizado, inicialmente, um estudo sobre a herança da resistência, por meio do cruzamento desta linhagem com a variedade suscetível Paranaíba. Os resultados indicaram que um gene dominante controla a resistência a este isolado. Através de análises com marcadores moleculares na população F2 foram identificados dois marcadores RAPD produzidos pela amplificação do primer OPAB19. Os dois fragmentos de DNA de aproximadamente 1.150 e 1.320 pb produzidos por este primer estão ligadas em fases de repulsão e acoplamento, respectivamente, a uma distância de 4,7 cM do gene de resistência da linhagem UFV 91-61. Estes marcadores poderão ser usados para monitorar a introgressão deste gene em cultivares de soja adaptados e abre a possibilidade de uma sistemática procura de marcadores ligados a outros genes de resistência para o cancro da haste da soja, os quais poderiam ser posteriormente piramidados num único background genético.Soybean stem canker is a serious soybean (Glycine max disease caused by the fungi Diaporthe phaseolorum f. sp. meridionalis/Phomopsis phaseoli f. sp. meridionalis. We have crossed the soybean resistant line UFV 91-61 with the susceptible cultivar Paranaiba, and analyze the F2 population in order to understand the genetics underlying resistance to this pathogen (isolate CH8 and to identify molecular markers linked to it. The results indicate that a single dominant gene controls resistance to this isolate. RAPD analysis in the F2 population identified two DNA fragments of approximately 1,150 and 1,320 bp of primer OPAB19 linked in the repulsion and coupling phase at 4.7 cM of the resistance gene of line UFV 91-61. These markers will be very useful for monitoring the introgression of this gene into soybean adapted cultivars, and open up the possibility for a systematic search for markers linked to other resistance genes for stem canker that could be pyramided into the same genetic background.




Identificação de marcadores RAPD ligados a um gene de resistência ao cancro da haste da soja / Identification of RAPD markers linked to a soybean stem canker resistance gene  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: Portuguese Abstract in portuguese O cancro da haste da soja (Glycine max) é uma importante doença causada pelo fungo Diaporthe phaseolorum f. sp. meridionalis/Phomopsis phaseoli f. sp. meridionalis. Visando identificar marcadores RAPD associados a genes de resistência ao cancro da haste, causado pelo isolado CH8, presentes na linhag [...] em UFV 91-61, foi realizado, inicialmente, um estudo sobre a herança da resistência, por meio do cruzamento desta linhagem com a variedade suscetível Paranaíba. Os resultados indicaram que um gene dominante controla a resistência a este isolado. Através de análises com marcadores moleculares na população F2 foram identificados dois marcadores RAPD produzidos pela amplificação do primer OPAB19. Os dois fragmentos de DNA de aproximadamente 1.150 e 1.320 pb produzidos por este primer estão ligadas em fases de repulsão e acoplamento, respectivamente, a uma distância de 4,7 cM do gene de resistência da linhagem UFV 91-61. Estes marcadores poderão ser usados para monitorar a introgressão deste gene em cultivares de soja adaptados e abre a possibilidade de uma sistemática procura de marcadores ligados a outros genes de resistência para o cancro da haste da soja, os quais poderiam ser posteriormente piramidados num único background genético. Abstract in english Soybean stem canker is a serious soybean (Glycine max) disease caused by the fungi Diaporthe phaseolorum f. sp. meridionalis/Phomopsis phaseoli f. sp. meridionalis. We have crossed the soybean resistant line UFV 91-61 with the susceptible cultivar Paranaiba, and analyze the F2 population in order to [...] understand the genetics underlying resistance to this pathogen (isolate CH8) and to identify molecular markers linked to it. The results indicate that a single dominant gene controls resistance to this isolate. RAPD analysis in the F2 population identified two DNA fragments of approximately 1,150 and 1,320 bp of primer OPAB19 linked in the repulsion and coupling phase at 4.7 cM of the resistance gene of line UFV 91-61. These markers will be very useful for monitoring the introgression of this gene into soybean adapted cultivars, and open up the possibility for a systematic search for markers linked to other resistance genes for stem canker that could be pyramided into the same genetic background.




The phenotypic patterns of essential hypertension are the key to identifying "high blood pressure" genes. (United States)

The genes that cause or increase susceptibility to essential hypertension (EH) and related animal models remain unknown. Their identification is unlikely to be realized with current genetic approaches, because of ambiguities in the genotype-phenotype relationships in these polygenic disorders. In turn, the phenotype is not just an aggregate of traits, but needs to be related to specific components of the circulatory control system at different stages of EH. Hence, clues about important genes must come through the phenotype, reversing the order of current approaches. A recent systems analysis has highlighted major differences in circulatory control in the two main syndromes of EH: (1) stress-and-salt-related EH (SSR-EH)--a constrictor hypertension with low blood volume; (2) hypertensive obesity--SSR-EH plus obesity. Each is initiated through sensitization of central synapses linking the cerebral cortex to the hypothalamic defense area. Several mechanisms are probably involved, including cerebellar effects on baroreflexes. The result is a sustained increase in sympathetic neural activity at stimulus levels that have no effect in normal subjects. Subsequent progression of EH is largely through interactions with non-neural mechanisms, including changes in concentration of vascular autacoids (e.g., nitric oxide) and the amplifying effect of structural changes in large resistance vessels. The rising vasoconstriction increases heterogeneity of blood flow, causing rarefaction (decreased microvascular density) and deterioration of vital organs. SSR-EH also increases food intake in response to stress, but only 40% of these individuals develop hypertensive obesity. Their brain ignores the adiposity signals that normally reduce eating. Hyperinsulinemia masks the sympathetic vasoconstriction through its dilator action, raises blood volume, whilst renal nephropathy and other diabetic complications are common. In each syndrome the neural and non-neural determinants of hypertension provide targets for identifying high BP genes. Reading the genome from the phenotype will require new approaches, such as those used in developmental genetics. In addition, transgenic technology may help verify hypotheses and examine whether an observed effect is through single or multiple mechanisms. To obtain answers will require substantial collaborative efforts between physiologists and geneticists. PMID:21208016

Korner, P I



DArT markers tightly linked with the Rfc1 gene controlling restoration of male fertility in the CMS-C system in cultivated rye (Secale cereale L.)  


The Rfc1 gene controls restoration of male fertility in rye (Secale cereale L.) with sterility-inducing cytoplasm CMS-C. Two populations of recombinant inbred lines (RIL) were used in this study to identify DArT markers located on the 4RL chromosome, in the close vicinity of the Rfc1 gene. In the population developed from the 541×2020LM intercross, numerous markers tightly linked with the restorer gene were identified. This group contained 91 DArT markers and three SCARs additionally analyze...

Stoja?owski, Stefan Andrzej; Milczarski, Pawe?; Hanek, Monika; Bolibok-bra?goszewska, Hanna; Mys?ko?w, Beata; Kilian, Andrzej; Rakoczy-trojanowska, Monika



Whole genome transcriptional profiling identifies novel differentiation regulated genes in keratinocytes. (United States)

Keratinocyte differentiation plays a pivotal role in the epidermal barrier. Single keratinocyte differentiation genes have already been studied, but many important constituents of this process may have been missed so far. Gene expression profiling by microarray was carried out in cultured normal human epidermal keratinocytes undergoing confluence-induced differentiation to find novel differentiation genes. Candidate gene lists were established and genes of potential dermatological interest were validated by quantitative reverse transcription polymerase chain reaction and immunohistochemical analysis. Some of these points lead to the identification of counter-regulation of heme oxygenase and biliverdin reductase as well as glutaredoxin and glutathione reductase indicative of potential novel redox signaling in differentiating human keratinocytes. Others indicate a strong concert down-regulation of interleukin-1 signaling at previously unidentified levels during keratinocyte differentiation. We believe that identified genes contribute to a more comprehensive understanding of the complicated epidermal differentiation process and lead to better understanding of dermatological diseases. PMID:19961536

Paragh, György; Ugocsai, Peter; Vogt, Thomas; Schling, Petra; Kel, Alexander E; Tarabin, Victoria; Liebisch, Gerhard; Orsó, Evelyn; Markó, Loránt; Balogh, Attila; Köbling, Tamás; Remenyik, Eva; Wikonkál, Norbert M; Mandl, József; Farwick, Mike; Schmitz, Gerd



Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics  

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Full Text Available Abstract Background When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names. Results A little detective work traced the problem to default date format conversions and floating-point format conversions in the very useful Excel program package. The date conversions affect at least 30 gene names; the floating-point conversions affect at least 2,000 if Riken identifiers are included. These conversions are irreversible; the original gene names cannot be recovered. Conclusions Users of Excel for analyses involving gene names should be aware of this problem, which can cause genes, including medically important ones, to be lost from view and which has contaminated even carefully curated public databases. We provide work-arounds and scripts for circumventing the problem.

Barrett J Carl



Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans  

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Full Text Available Abstract Background Physiologically based modelling using DEBtox (dynamic energy budget in toxicology and transcriptional profiling were used in Caenorhabditis elegans to identify how physiological modes of action, as indicated by effects on system level resource allocation were associated with changes in gene expression following exposure to three toxic chemicals: cadmium, fluoranthene (FA and atrazine (AZ. Results For Cd, the physiological mode of action as indicated by DEBtox model fitting was an effect on energy assimilation from food, suggesting that the transcriptional response to exposure should be dominated by changes in the expression of transcripts associated with energy metabolism and the mitochondria. While evidence for effect on genes associated with energy production were seen, an ontological analysis also indicated an effect of Cd exposure on DNA integrity and transcriptional activity. DEBtox modelling showed an effect of FA on costs for growth and reproduction (i.e. for production of new and differentiated biomass. The microarray analysis supported this effect, showing an effect of FA on protein integrity and turnover that would be expected to have consequences for rates of somatic growth. For AZ, the physiological mode of action predicted by DEBtox was increased cost for maintenance. The transcriptional analysis demonstrated that this increase resulted from effects on DNA integrity as indicated by changes in the expression of genes chromosomal repair. Conclusions Our results have established that outputs from process based models and transcriptomics analyses can help to link mechanisms of action of toxic chemicals with resulting demographic effects. Such complimentary analyses can assist in the categorisation of chemicals for risk assessment purposes.

Svendsen Claus



A Novel Ant Colony Optimization Based Algorithm for Identifying Gene Regulatory Elements  


It is one of the most important tasks in bioinformatics to identify the regulatory elements in gene sequences.  Most of the current algorithms for identifying regulatory elements are easily to converge into a local optimum, and have high time complexity. Therefore, we propose a novel optimization algorithm named ACRI(ant-colony-regulatory-identification) for identifying regulatory elements. Based on powerful optimization ability of ant-colony algorithm, the algorithm ...

Wei Liu; Hanwu Chen; Ling Chen; Yixin Chen



DArT markers tightly linked with the Rfc1 gene controlling restoration of male fertility in the CMS-C system in cultivated rye (Secale cereale L.). (United States)

The Rfc1 gene controls restoration of male fertility in rye (Secale cereale L.) with sterility-inducing cytoplasm CMS-C. Two populations of recombinant inbred lines (RIL) were used in this study to identify DArT markers located on the 4RL chromosome, in the close vicinity of the Rfc1 gene. In the population developed from the 541×2020LM intercross, numerous markers tightly linked with the restorer gene were identified. This group contained 91 DArT markers and three SCARs additionally analyzed in the study. All these markers were mapped in the distance not exceeding 6 cM from the gene of interest. In the second mapping population (541×Ot1-3 intercross), only 9 DArT markers located closely to the Rfc1 gene were identified. Five of these DArT markers were polymorphic in both populations. PMID:21559995

Stoja?owski, Stefan Andrzej; Milczarski, Pawe?; Hanek, Monika; Bolibok-Br?goszewska, Hanna; My?ków, Beata; Kilian, Andrzej; Rakoczy-Trojanowska, Monika



Suppression subtractive hybridization identified differentially expressed genes in lung adenocarcinoma: ERGIC3 as a novel lung cancer-related gene  

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Full Text Available Abstract Background To understand the carcinogenesis caused by accumulated genetic and epigenetic alterations and seek novel biomarkers for various cancers, studying differentially expressed genes between cancerous and normal tissues is crucial. In the study, two cDNA libraries of lung cancer were constructed and screened for identification of differentially expressed genes. Methods Two cDNA libraries of differentially expressed genes were constructed using lung adenocarcinoma tissue and adjacent nonmalignant lung tissue by suppression subtractive hybridization. The data of the cDNA libraries were then analyzed and compared using bioinformatics analysis. Levels of mRNA and protein were measured by quantitative real-time polymerase chain reaction (q-RT-PCR and western blot respectively, as well as expression and localization of proteins were determined by immunostaining. Gene functions were investigated using proliferation and migration assays after gene silencing and gene over-expression. Results Two libraries of differentially expressed genes were obtained. The forward-subtracted library (FSL and the reverse-subtracted library (RSL contained 177 and 59 genes, respectively. Bioinformatic analysis demonstrated that these genes were involved in a wide range of cellular functions. The vast majority of these genes were newly identified to be abnormally expressed in lung cancer. In the first stage of the screening for 16 genes, we compared lung cancer tissues with their adjacent non-malignant tissues at the mRNA level, and found six genes (ERGIC3, DDR1, HSP90B1, SDC1, RPSA, and LPCAT1 from the FSL were significantly up-regulated while two genes (GPX3 and TIMP3 from the RSL were significantly down-regulated (P? Conclusions The two libraries of differentially expressed genes may provide the basis for new insights or clues for finding novel lung cancer-related genes; several genes were newly found in lung cancer with ERGIC3 seeming a novel lung cancer-related gene. ERGIC3 may play an active role in the development and progression of lung cancer.

Wu Mingsong



Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins  

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Full Text Available Abstract Background While occurring enzymatically in biological systems, O-linked glycosylation affects protein folding, localization and trafficking, protein solubility, antigenicity, biological activity, as well as cell-cell interactions on membrane proteins. Catalytic enzymes involve glycotransferases, sugar-transferring enzymes and glycosidases which trim specific monosaccharides from precursors to form intermediate structures. Due to the difficulty of experimental identification, several works have used computational methods to identify glycosylation sites. Results By investigating glycosylated sites that contain various motifs between Transmembrane (TM and non-Transmembrane (non-TM proteins, this work presents a novel method, GlycoRBF, that implements radial basis function (RBF networks with significant amino acid pairs (SAAPs for identifying O-linked glycosylated serine and threonine on TM proteins and non-TM proteins. Additionally, a membrane topology is considered for reducing the false positives on glycosylated TM proteins. Based on an evaluation using five-fold cross-validation, the consideration of a membrane topology can reduce 31.4% of the false positives when identifying O-linked glycosylation sites on TM proteins. Via an independent test, GlycoRBF outperforms previous O-linked glycosylation site prediction schemes. Conclusion A case study of Cyclic AMP-dependent transcription factor ATF-6 alpha was presented to demonstrate the effectiveness of GlycoRBF. Web-based GlycoRBF, which can be accessed at, can identify O-linked glycosylated serine and threonine effectively and efficiently. Moreover, the structural topology of Transmembrane (TM proteins with glycosylation sites is provided to users. The stand-alone version of GlycoRBF is also available for high throughput data analysis.

Lee Tzong-Yi



Rho GEFs and Cancer: Linking Gene Expression and Metastatic Dissemination (United States)

Guanine nucleotide exchange factors (GEFs) that promote GTP loading onto the guanosine triphosphatases (GTPases) Rho and Rac are prominent players in cancer progression. Recent studies have highlighted the relevance of several GEFs, including the phosphatidylinositol 3,4,5-trisphosphate Rac exchangers P-Rex1 and P-Rex2a, in breast tumorigenesis. New evidence suggests that the exchange factors Vav2 and Vav3 play synergistic roles in breast cancer by sustaining tumor growth, neoangiogenesis, and metastasis. The identification of a Vav-regulated transcriptome and Vav-related genes that control specific steps of metastatic dissemination of breast cancer cells to the lungs highlights the complexities of the signaling networks regulated by Rho/Rac GTPases and may lead to novel therapeutic targets.

Laura Barrio-Real (University of Pennsylvania;Perelman School of Medicine REV); Marcelo G. Kazanietz (University of Pennsylvania;Perelman School of Medicine REV)



Changes in gene expression linked with adult reproductive diapause in a northern malt fly species: a candidate gene microarray study  

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Full Text Available Abstract Background Insect diapause is an important biological process which involves many life-history parameters important for survival and reproductive fitness at both individual and population level. Drosophila montana, a species of D. virilis group, has a profound photoperiodic reproductive diapause that enables the adult flies to survive through the harsh winter conditions of high latitudes and altitudes. We created a custom-made microarray for D. montana with 101 genes known to affect traits important in diapause, photoperiodism, reproductive behaviour, circadian clock and stress tolerance in model Drosophila species. This array gave us a chance to filter out genes showing expression changes during photoperiodic reproductive diapause in a species adapted to live in northern latitudes with high seasonal changes in environmental conditions. Results Comparisons among diapausing, reproducing and young D. montana females revealed expression changes in 24 genes on microarray; for example in comparison between diapausing and reproducing females one gene (Drosophila cold acclimation gene, Dca showed up-regulation and 15 genes showed down-regulation in diapausing females. Down-regulation of seven of these genes was specific to diapause state while in five genes the expression changes were linked with the age of the females rather than with their reproductive status. Also, qRT-PCR experiments confirmed couch potato (cpo gene to be involved in diapause of D. montana. Conclusions A candidate gene microarray proved to offer a practical and cost-effective way to trace genes that are likely to play an important role in photoperiodic reproductive diapause and further in adaptation to seasonally varying environmental conditions. The present study revealed two genes, Dca and cpo, whose role in photoperiodic diapause in D. montana is worth of studying in more details. Also, further studies using the candidate gene microarray with more specific experimental designs and target tissues may reveal additional genes with more restricted expression patterns.

Hoikkala Anneli



The search for identifying links of the territory guarantees an improvement of current urban landscape planning  


Since the second half of the 20th century an uncontrolled and generalized growth of historic urban centres takes place, based on anarchic town-planning that causes a break with the natural evolutionary process of these cities. Our proposal aims to make a commitment with the new contemporary urban development models, in search for characteristic links that reestablish the natural growth and transformation of the landscape. Therefore, we have designed the investigation project on the specific ...

Carmen Carcel; Francisco Juan Vidal



Identifying directed links in large scale functional networks: application to brain fMRI  


Abstract Background Biological experiments increasingly yield data representing large ensembles of interacting variables, making the application of advanced analytical tools a forbidding task. We present a method to extract networks of correlated activity, specifically from functional MRI data, such that: (a) network nodes represent voxels, and (b) the network links can be directed or undirected, representing temporal relationships between the nodes. The method provides a sna...

Vania, Apkarian A.; Baliki Marwan; Centeno Maria V; Ravishankar, Rao A.; Cecchi Guillermo A; Chialvo Dante R



A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets  

DEFF Research Database (Denmark)

Close to 50 genetic loci have been associated with type 2 diabetes (T2D), but they explain only 15% of the heritability. In an attempt to identify additional T2D genes, we analyzed global gene expression in human islets from 63 donors. Using 48 genes located near T2D risk variants, we identified gene coexpression and protein-protein interaction networks that were strongly associated with islet insulin secretion and HbA(1c). We integrated our data to form a rank list of putative T2D genes, of which CHL1, LRFN2, RASGRP1, and PPM1K were validated in INS-1 cells to influence insulin secretion, whereas GPR120 affected apoptosis in islets. Expression variation of the top 20 genes explained 24% of the variance in HbA(1c) with no claim of the direction. The data present a global map of genes associated with islet dysfunction and demonstrate the value of systems genetics for the identification of genes potentially involved in T2D.

Taneera, Jalal; Lang, Stefan



Contiguous gene deletion involving L1CAM and AVPR2 causes X-linked hydrocephalus with nephrogenic diabetes insipidus. (United States)

X-linked hydrocephalus with aqueductal stenosis (HSAS) is caused by mutation or deletion of the L1 cell adhesion molecule gene (L1CAM) at Xq28. Central diabetes insipidus (CDI) can arise as a consequence of resultant hypothalamic dysfunction from hydrocephalus and must be distinguished from nephrogenic diabetes insipidus (NDI) by exogenous vasopressin response. Causes of NDI are heterogeneous and include mutation or deletion of the arginine vasopressin receptor 2 gene (AVPR2), which is located approximately 29 kb telomeric to L1CAM. We identified a patient with both HSAS and NDI where DNA sequencing failure suggested the possibility of a contiguous gene deletion. A 32.7 kb deletion mapping from L1CAM intron1 to AVPR2 exon2 was confirmed. A 90 bp junctional insertion fragment sharing short direct repeat homology with flanking sequences was identified. To our knowledge this is the first reported case of an Xq28 microdeletion involving both L1CAM and AVPR2, defining a new contiguous gene syndrome comprised of HSAS and NDI. Contiguous gene deletion should be considered as a mechanism for all patients presenting with hydrocephalus and NDI. PMID:17318848

Tegay, David H; Lane, Andrew H; Roohi, Jasmin; Hatchwell, Eli



GlycoFish: A Database of Zebrafish N-linked Glycoproteins Identified Using SPEG Method Coupled with LC/MS (United States)

Zebrafish (Danio rerio) is a model organism to study the mechanisms and pathways of human disorders. Many dysfunctions in neurological, development and neuromuscular systems are due to glycosylation deficiencies, but the glycoproteins involved in zebrafish embryonic development have not been established. In this study, a mass spectrometry-based glycoproteomic characterization of zebrafish embryos was performed to identify the N-linked glycoproteins and N-linked glycosylation sites. To increase the number of glycopeptides, proteins from zebrafish were digested with two different proteases, chymotrypsin and trypsin, into peptides of different length. The N-glycosylated peptides of zebrafish were then captured by the solid phase extraction of N-linked glycopeptides (SPEG) method and the peptides were identified with an LTQ OrbiTrap Velos mass spectrometer. From 265 unique glycopeptides, including 269 consensus NXT/S glycosites, we identified 169 different N-glycosylated proteins. The identified glycoproteins were highly abundant in proteins belonging to the transporter, cell adhesion, and ion channel/ion binding categories which are important to embryonic, organ, and central nervous system development. This proteomics data will expand our knowledge about glycoproteins in zebrafish and may be used to elucidate the role glycosylation plays in cellular processes and disease. The glycoprotein data are available through the GlycoFish database ( introduced in this paper. PMID:21591763

Baycin-Hizal, Deniz; Tian, Yuan; Akan, Ilhan; Jacobson, Elena; Clark, Dean; Wu, Alexander; Jampol, Russell; Palter, Karen; Betenbaugh, Michael; Zhang, Hui



Analysis of global gene expression profiles to identify differentially expressed genes critical for embryo development in Brassica rapa. (United States)

Embryo development represents a crucial developmental period in the life cycle of flowering plants. To gain insights into the genetic programs that control embryo development in Brassica rapa L., RNA sequencing technology was used to perform transcriptome profiling analysis of B. rapa developing embryos. The results generated 42,906,229 sequence reads aligned with 32,941 genes. In total, 27,760, 28,871, 28,384, and 25,653 genes were identified from embryos at globular, heart, early cotyledon, and mature developmental stages, respectively, and analysis between stages revealed a subset of stage-specific genes. We next investigated 9,884 differentially expressed genes with more than fivefold changes in expression and false discovery rate ? 0.001 from three adjacent-stage comparisons; 1,514, 3,831, and 6,633 genes were detected between globular and heart stage embryo libraries, heart stage and early cotyledon stage, and early cotyledon and mature stage, respectively. Large numbers of genes related to cellular process, metabolism process, response to stimulus, and biological process were expressed during the early and middle stages of embryo development. Fatty acid biosynthesis, biosynthesis of secondary metabolites, and photosynthesis-related genes were expressed predominantly in embryos at the middle stage. Genes for lipid metabolism and storage proteins were highly expressed in the middle and late stages of embryo development. We also identified 911 transcription factor genes that show differential expression across embryo developmental stages. These results increase our understanding of the complex molecular and cellular events during embryo development in B. rapa and provide a foundation for future studies on other oilseed crops. PMID:25214014

Zhang, Yu; Peng, Lifang; Wu, Ya; Shen, Yanyue; Wu, Xiaoming; Wang, Jianbo



Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. (United States)

Microbial community metagenomes and individual microbial genomes are becoming increasingly accessible by means of high-throughput sequencing. Assessing organismal membership within a community is typically performed using one or a few taxonomic marker genes such as the 16S rDNA, and these same genes are also employed to reconstruct molecular phylogenies. There is thus a growing need to bioinformatically catalog strongly conserved core genes that can serve as effective taxonomic markers, to assess the agreement among phylogenies generated from different core gene, and to characterize the biological functions enriched within core genes and thus conserved throughout large microbial clades. We present a method to recursively identify core genes (i.e. genes ubiquitous within a microbial clade) in high-throughput from a large number of complete input genomes. We analyzed over 1,100 genomes to produce core gene sets spanning 2,861 bacterial and archaeal clades, ranging in size from one to >2,000 genes in inverse correlation with the ?-diversity (total phylogenetic branch length) spanned by each clade. These cores are enriched as expected for housekeeping functions including translation, transcription, and replication, in addition to significant representations of regulatory, chaperone, and conserved uncharacterized proteins. In agreement with previous manually curated core gene sets, phylogenies constructed from one or more of these core genes agree with those built using 16S rDNA sequence similarity, suggesting that systematic core gene selection can be used to optimize both comparative genomics and determination of microbial community structure. Finally, we examine functional phylogenies constructed by clustering genomes by the presence or absence of orthologous gene families and show that they provide an informative complement to standard sequence-based molecular phylogenies. PMID:21931822

Segata, Nicola; Huttenhower, Curtis



Use of RFLPs to identify genes for aluminium tolerance in maize  

International Nuclear Information System (INIS)

The objective of this study was to identify restriction fragment length polymorphism (RFLP) markers linked to quantitative trait loci that control Al tolerance in maize. The strategy used was bulked segregant analysis, which is based on selecting for bulk bred true F2 individuals. The genetic material used consisted of an F2 population derived from a cross between Al susceptible (L53) and Al tolerant (L1327) maize inbred lines. Both lines were developed in the maize breeding programme of the Centro Nacional de Pesquisa de Milho e Sorgo. The relative seminal root length (RSRL) index was used as the phenotypic measure of tolerance. The frequency distribution of RSRL showed continuous distribution, which is typical of a quantitatively inherited character, with a tendency towards Al susceptible individuals. The estimated heritability [(?2F2 - ?2E)/?2F2] was found to be 60%. This moderately high heritability value suggests that, although the character has a quantitative nature, it may be controlled by a small number of genes. Those seedlings of the F2 population that scored the highest and lowest values for RSRL were subsequently selfed to obtain the F3 families. These families were evaluated in nutrient solution to identify those that were not segregating. On the basis of the results, five individuals were chosen for each bulk. Sixty-five probes were selected abulk. Sixty-five probes were selected at an average interval of 30 cM, covering all ten maize chromosomes. For the hybridization work, a non-radioactive labelling system, using dig-dUTP and alkaline phosphatase, proved to be quite efficient and reliable, resulting in Southern blots with good resolution and allowing the membranes to be stripped and reprobed at least three times. Twenty-three markers showed a co-drominant effect, identifying 40 RFLP loci that could distinguish the parental inbred lines. These 23 probes are now being hybridized with DNA from the two contrasting bulks. Also, a search for other informative markers is being carried out to increase genome coverage. (author). 29 refs, 2 figs, 1 tab


Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program  


Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression – early w...

Knapp, D.; Schulz, H.; Rascon, C. A.; Volkmer, M.; Scholz, J.; Nacu, E.; Le, M.; Novozhilov, S.; Tazaki, A.; Protze, S.; Jacob, T.; Hubner, N.; Habermann, B.; Tanaka, E. M.



A proposal of a novel experimental procedure to genetically identify disease gene loci in humans  


Forward genetics in humans is beneficial in terms of diagnosis and treatment of genetic diseases, and discovery of gene functions. However, experimental mating is not possible among humans. In order to overcome this problem, I propose a novel experimental procedure to genetically identify human disease gene loci. To accomplish this, somatic cells from patients or their parents are reprogrammed to the pluripotent state, oogenesis is induced, the oocytes are parthenogenetically activated in the...

Muto, Taro



Links between core promoter and basic gene features influence gene expression  


Abstract Background Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression systems. Here we analyzed the relationship between general features of genes and their contribution to expression levels. Results Genes were di...

Sinvani Hadar; Golan-Mashiach Michal; Elfakess Rofa; Moshonov Sandra; Dikstein Rivka



Forward chemical genetic screens in Arabidopsis identify genes that influence sensitivity to the phytotoxic compound sulfamethoxazole  

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Full Text Available Background The sulfanilamide family comprises a clinically important group of antimicrobial compounds which also display bioactivity in plants. While there is evidence that sulfanilamides inhibit folate biosynthesis in both bacteria and plants, the complete network of plant responses to these compounds remains to be characterized. As such, we initiated two forward genetic screens in Arabidopsis in order to identify mutants that exhibit altered sensitivity to sulfanilamide compounds. These screens were based on the growth phenotype of seedlings germinated in the presence of the compound sulfamethoxazole (Smex. Results We identified a mutant with reduced sensitivity to Smex, and subsequent mapping indicated that a gene encoding 5-oxoprolinase was responsible for this phenotype. A mutation causing enhanced sensitivity to Smex was mapped to a gene lacking any functional annotation. Conclusions The genes identified through our forward genetic screens represent novel mediators of Arabidopsis responses to sulfanilamides and suggest that these responses extend beyond the perturbation of folate biosynthesis.

Schreiber Karl J



Identifying the most suitable endogenous control for determining gene expression in hearts from organ donors  

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Full Text Available Abstract Background Quantitative real-time reverse transcription PCR (qRT-PCR is a useful tool for assessing gene expression in different tissues, but the choice of adequate controls is critical to normalise the results, thereby avoiding differences and maximizing sensitivity and accuracy. So far, many genes have been used as a single reference gene, without having previously verified their value as controls. This practice can lead to incorrect conclusions and recent evidence indicates a need to use the geometric mean of data from several control genes. Here, we identified an appropriate set of genes to be used as an endogenous reference for quantifying gene expression in human heart tissue. Results Our findings indicate that out of ten commonly used reference genes (GADPH, PPIA, ACTB, YWHAZ, RRN18S, B2M, UBC, TBP, RPLP and HPRT, PPIA, RPLP and GADPH show the most stable gene transcription levels in left ventricle specimens obtained from organ donors, as assessed using geNorm and Normfinder software. The expression of TBP was found to be highly regulated. Conclusion We propose the use of PPIA, RPLP and GADPH as reference genes for the accurate normalisation of qRT-PCR performed on heart tissue. TBP should not be used as a control in this type of tissue.

Gómez Enrique



Flux variability scanning based on enforced objective flux for identifying gene amplification targets  

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Full Text Available Abstract Background In order to reduce time and efforts to develop microbial strains with better capability of producing desired bioproducts, genome-scale metabolic simulations have proven useful in identifying gene knockout and amplification targets. Constraints-based flux analysis has successfully been employed for such simulation, but is limited in its ability to properly describe the complex nature of biological systems. Gene knockout simulations are relatively straightforward to implement, simply by constraining the flux values of the target reaction to zero, but the identification of reliable gene amplification targets is rather difficult. Here, we report a new algorithm which incorporates physiological data into a model to improve the model’s prediction capabilities and to capitalize on the relationships between genes and metabolic fluxes. Results We developed an algorithm, flux variability scanning based on enforced objective flux (FVSEOF with grouping reaction (GR constraints, in an effort to identify gene amplification targets by considering reactions that co-carry flux values based on physiological omics data via “GR constraints”. This method scans changes in the variabilities of metabolic fluxes in response to an artificially enforced objective flux of product formation. The gene amplification targets predicted using this method were validated by comparing the predicted effects with the previous experimental results obtained for the production of shikimic acid and putrescine in Escherichia coli. Moreover, new gene amplification targets for further enhancing putrescine production were validated through experiments involving the overexpression of each identified targeted gene under condition-controlled batch cultivation. Conclusions FVSEOF with GR constraints allows identification of gene amplification targets for metabolic engineering of microbial strains in order to enhance the production of desired bioproducts. The algorithm was validated through the experiments on the enhanced production of putrescine in E. coli, in addition to the comparison with the previously reported experimental data. The FVSEOF strategy with GR constraints will be generally useful for developing industrially important microbial strains having enhanced capabilities of producing chemicals of interest.

Park Jong



UV cross-linking identifies four polypeptides that require the TATA box to bind to the Drosophila hsp70 promoter  

International Nuclear Information System (INIS)

A protein fraction that requires the TATA sequence to bind to the hsp70 promoter has been partially purified from nuclear extracts of Drosophila embryos. This TATA factor produces a large DNase I footprint that extends from -44 to +35 on the promoter. A mutation that changes TATA to TATG interferes both with the binding of this complex and with the transcription of the hsp70 promoter in vitro, indicating that this interaction is important for transcriptional activity. Using a highly specific protein-DNA cross-linking assay, we have identified four polypeptides that require the TATA sequence to bind to the hsp70 promoter. Polypeptides of 26 and 42 kilodaltons are in intimate contact with the TATA sequence. Polypeptides of 150 and 60 kilodaltons interact within the region from +24 to +47 in a TATA-dependent manner. Both the extended footprint and the polypeptides identified by UV cross-linking indicate that the Drosophila TATA factor is a multicomponent complex


Identification of microsatellite markers (SSR linked to a new bacterial blight resistance gene xa33(t in rice cultivar ‘Ba7’  

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Full Text Available This study attempts to identify a new source of bacterial blight (BB resistance gene and microsatellite makers (SSR linked to it. A total number of 139 F2 progenies generated from a cross between the resistant donor ‘Ba7’and ‘Pin Kaset’ were developed and used for this study. A Thai Xoo isolate, TXO16, collected from Phitsanulok province, was used to evaluate the resistance reaction in the F2 population. The segregation ratio of resistance (R and susceptibility (S was statistically fitted to 1R:3S model indicating single recessive gene segregation. Twenty F2 individuals consisting of 10 resistant and 10 susceptible plants were chosen for DNA analysis. Sixty-two polymorphic markers covering all rice chromosomes were used to identify the location and linked markers of the resistance gene. Four SSR markers, viz. RM30, RM7243, RM5509 and RM400, located on the long arm of rice chromosome 6, could clearly discriminate between resistant and susceptible phenotypes, and 161 BC2F2:3 individuals carrying BB resistance gene were developed through MAS using these SSR markers. This population was inoculated with TXO16 to validate and confirm the location of the gene and linked markers. The segregation ratio was statistically fitted to 1R:3S model confirming a recessive nature of the gene action in this germplasm. Phenotypic-genotypic association including five additional markers suggested that RM20590 was tightly linked to this resistance gene (R2=59.12 %. The BB phenotype was controlled by a recessive gene with incomplete dominance of susceptible allele providing intermediate resistance to Xoo pathogen in heterozygotes. The location of the gene was in the vicinity of a dominant gene, Xa7, which was previously reported. However, the resistance gene identified here was different from Xa7 because of the different nature of gene action. Consequently, this gene was tentatively designated as xa33(t. The resistance gene from rice cultivar ‘Ba7’ and the closely linked markers found in this study will be useful for rice breeders as a source to improve BB resistance through MAS in rice breeding programs.

Theerayut Toojinda



Functional characterization of two newly identified Human Endogenous Retrovirus coding envelope genes  

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Full Text Available Abstract A recent in silico search for coding sequences of retroviral origin present in the human genome has unraveled two new envelope genes that add to the 16 genes previously identified. A systematic search among the latter for a fusogenic activity had led to the identification of two bona fide genes, named syncytin-1 and syncytin-2, most probably co-opted by primate genomes for a placental function related to the formation of the syncytiotrophoblast by cell-cell fusion. Here, we show that one of the newly identified envelope gene, named envP(b, is fusogenic in an ex vivo assay, but that its expression – as quantified by real-time RT-PCR on a large panel of human tissues – is ubiquitous, albeit with a rather low value in most tissues. Conversely, the second envelope gene, named envV, discloses a placenta-specific expression, but is not fusogenic in any of the cells tested. Altogether, these results suggest that at least one of these env genes may play a role in placentation, but most probably through a process different from that of the two previously identified syncytins.

Heidmann Thierry



VCP gene analyses in Japanese patients with sporadic amyotrophic lateral sclerosis identify a new mutation. (United States)

Accumulating evidence has proven that mutations in the VCP gene encoding valosin-containing protein (VCP) cause inclusion body myopathy with Paget disease of the bone and frontotemporal dementia. This gene was later found to be causative for amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease, occurring typically in elderly persons. We thus sequenced the VCP gene in 75 Japanese patients with sporadic ALS negative for mutations in other genes causative for ALS and found a novel mutation, p.Arg487His, in 1 patient. The newly identified mutant as well as known mutants rendered neuronal cells susceptible to oxidative stress. The presence of the mutation in the Japanese population extends the geographic region for involvement of the VCP gene in sporadic ALS to East Asia. PMID:25457024

Hirano, Makito; Nakamura, Yusaku; Saigoh, Kazumasa; Sakamoto, Hikaru; Ueno, Shuichi; Isono, Chiharu; Mitsui, Yoshiyuki; Kusunoki, Susumu



Expression and cloning of the human X-linked hypophosphatemia gene cDNA.  


X-linked hypophosphatemia (XLH), which is a heritable metabolic bone disease characterized biochemically by selective renal phosphate (Pi) wasting, is associated with mutations in the PEX (Phosphate-regulating gene with homologies to Endopeptidases on the X-chromosome) gene. To further explore the physiologic role of PEX and define its effect in XLH we have determined the expression and tissue distribution. Northern analysis found abundant PEX mRNA in a restricted pattern, predominantly in ad...

Grieff, M.; Mumm, S.; Waeltz, P.; Mazzarella, R.; Whyte, Mp; Thakker, Rv; Schlessinger, D.



Fatal hemophagocytic lymphohistiocytosis in X-linked chronic granulomatous disease associated with a perforin gene variant  


A patient with previously unrecognized X-linked chronic granulomatous disease (X-CGD) died of multi-organ failure, secondary to ongoing infection and hemophagocytic lymphohistiocytosis (HLH). Post mortem histological investigations were compatible with X-CGD, and a CYBB gene mutation was confirmed. No homozygous mutations in the genes encoding perforin (PRF1), MUNC 13-4 or syntaxin-11 (STX11) were found; however, there was a heterozygous alteration c.1471G>A in the PRF1 g...

Montfrans, J. M.; Rudd, E.; Corput, L.; Henter, J. I.; Nikkels, P. G. J.; Wulffraat, N. M.; Boelens, J. J.



Faced with inequality: chicken do not have a general dosage compensation of sex-linked genes  

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Full Text Available Abstract Background The contrasting dose of sex chromosomes in males and females potentially introduces a large-scale imbalance in levels of gene expression between sexes, and between sex chromosomes and autosomes. In many organisms, dosage compensation has thus evolved to equalize sex-linked gene expression in males and females. In mammals this is achieved by X chromosome inactivation and in flies and worms by up- or down-regulation of X-linked expression, respectively. While otherwise widespread in systems with heteromorphic sex chromosomes, the case of dosage compensation in birds (males ZZ, females ZW remains an unsolved enigma. Results Here, we use a microarray approach to show that male chicken embryos generally express higher levels of Z-linked genes than female birds, both in soma and in gonads. The distribution of male-to-female fold-change values for Z chromosome genes is wide and has a mean of 1.4–1.6, which is consistent with absence of dosage compensation and sex-specific feedback regulation of gene expression at individual loci. Intriguingly, without global dosage compensation, the female chicken has significantly lower expression levels of Z-linked compared to autosomal genes, which is not the case in male birds. Conclusion The pronounced sex difference in gene expression is likely to contribute to sexual dimorphism among birds, and potentially has implication to avian sex determination. Importantly, this report, together with a recent study of sex-biased expression in somatic tissue of chicken, demonstrates the first example of an organism with a lack of global dosage compensation, providing an unexpected case of a viable system with large-scale imbalance in gene expression between sexes.

Kultima Kim



Genes for and molecular markers linked with resistance to Phytophthora fragariae in strawberry  


A gene-for-gene model is presented which explains interactions between cultivars of strawberry and races of Phytophthora fragariae var. fragariae, the causal agent of red core (red stele) root rot. The model allows the constitution of a universal differential set of strawberry genotypes and the characterizing of fungal isolates into races, the genotyping of strawberry cultivars and selections in a breeding programme, and facilitates the search for linked molecular markers for more efficient s...

Weg, W. E.; Henken, B.; Haymes, K. M.; Den Nijs, A. P. M.



Cellular imaging demonstrates genetic mosaicism in heterozygous carriers of an X-linked ciliopathy gene  


X-linked retinitis pigmentosa (XLRP) is the least common genetic type of retinitis pigmentosa; however, it has extremely devastating consequences to patients' activities of daily living. RPGR and RP2 genes expressed in the photoreceptor sensory cilia are predominantly implicated in XLRP; however, the interpretation of genetic mutations and their correlation with clinical phenotypes remain unknown, and the role of these genes in photoreceptor cilia function is not completely elucidated. Theref...

Pyo Park, Sung; Hwan Hong, In; Tsang, Stephen H.; Chang, Stanley



Gene expression differences between Noccaea caerulescens ecotypes help to identify candidate genes for metal phytoremediation. (United States)

Populations of Noccaea caerulescens show tremendous differences in their capacity to hyperaccumulate and hypertolerate metals. To explore the differences that could contribute to these traits, we undertook SOLiD high-throughput sequencing of the root transcriptomes of three phenotypically well-characterized N. caerulescens accessions, i.e., Ganges, La Calamine, and Monte Prinzera. Genes with possible contribution to zinc, cadmium, and nickel hyperaccumulation and hypertolerance were predicted. The most significant differences between the accessions were related to metal ion (di-, trivalent inorganic cation) transmembrane transporter activity, iron and calcium ion binding, (inorganic) anion transmembrane transporter activity, and antioxidant activity. Analysis of correlation between the expression profile of each gene and the metal-related characteristics of the accessions disclosed both previously characterized (HMA4, HMA3) and new candidate genes (e.g., for nickel IRT1, ZIP10, and PDF2.3) as possible contributors to the hyperaccumulation/tolerance phenotype. A number of unknown Noccaea-specific transcripts also showed correlation with Zn(2+), Cd(2+), or Ni(2+) hyperaccumulation/tolerance. This study shows that N. caerulescens populations have evolved great diversity in the expression of metal-related genes, facilitating adaptation to various metalliferous soils. The information will be helpful in the development of improved plants for metal phytoremediation. PMID:24559272

Halimaa, Pauliina; Lin, Ya-Fen; Ahonen, Viivi H; Blande, Daniel; Clemens, Stephan; Gyenesei, Attila; Häikiö, Elina; Kärenlampi, Sirpa O; Laiho, Asta; Aarts, Mark G M; Pursiheimo, Juha-Pekka; Schat, Henk; Schmidt, Holger; Tuomainen, Marjo H; Tervahauta, Arja I



Identifying genes and gene networks involved in chromium metabolism and detoxification in Crambe abyssinica. (United States)

Chromium pollution is a serious environmental problem with few cost-effective remediation strategies available. Crambe abyssinica (a member of Brassicaseae), a non-food, fast growing high biomass crop, is an ideal candidate for phytoremediation of heavy metals contaminated soils. The present study used a PCR-Select Suppression Subtraction Hybridization approach in C. abyssinica to isolate differentially expressed genes in response to Cr exposure. A total of 72 differentially expressed subtracted cDNAs were sequenced and found to represent 43 genes. The subtracted cDNAs suggest that Cr stress significantly affects pathways related to stress/defense, ion transporters, sulfur assimilation, cell signaling, protein degradation, photosynthesis and cell metabolism. The regulation of these genes in response to Cr exposure was further confirmed by semi-quantitative RT-PCR. Characterization of these differentially expressed genes may enable the engineering of non-food, high-biomass plants, including C. abyssinica, for phytoremediation of Cr-contaminated soils and sediments. PMID:21784565

Zulfiqar, Asma; Paulose, Bibin; Chhikara, Sudesh; Dhankher, Om Parkash



Candidate gene linkage approach to identify DNA variants that predispose to preterm birth  

DEFF Research Database (Denmark)

BACKGROUND: The aim of this study was to identify genetic variants contributing to preterm birth (PTB) using a linkage candidate gene approach. METHODS: We studied 99 single-nucleotide polymorphisms (SNPs) for 33 genes in 257 families with PTBs segregating. Nonparametric and parametric analyses were used. Premature infants and mothers of premature infants were defined as affected cases in independent analyses. RESULTS: Analyses with the infant as the case identified two genes with evidence of linkage: CRHR1 (P = 0.0012) and CYP2E1 (P = 0.0011). Analyses with the mother as the case identified four genes with evidence of linkage: ENPP1 (P = 0.003), IGFBP3 (P = 0.006), DHCR7 (P = 0.009), and TRAF2 (P = 0.01). DNA sequence analysis of the coding exons and splice sites for CRHR1 and TRAF2 identified no new likely etiologic variants. CONCLUSION: These findings suggest the involvement of six genes acting through the infant and/or the mother in the etiology of PTB.

Bream, Elise N A; Leppellere, Cara R



A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA. (United States)

Salmonella enterica serovar blegdam has a restriction and modification system encoded by genes linked to serB. We have cloned these genes, putative alleles of the hsd locus of Escherichia coli K-12, and confirmed by the sequence similarities of flanking DNA that the hsd genes of S. enterica serovar blegdam have the same chromosomal location as those of E. coli K-12 and Salmonella enterica serovar typhimurium LT2. There is, however, no obvious similarity in their nucleotide sequences, and while the gene order in S. enterica serovar blegdam is serB hsdM, S and R, that in E. coli K-12 and S. enterica serovar typhimurium LT2 is serB hsdR, M and S. The hsd genes of S. enterica serovar blegdam identify a third family of serB-linked hsd genes (type ID). The polypeptide sequence predicted from the three hsd genes show some similarities (18-50% identity) with the polypeptides of known and putative type I restriction and modification systems; the highest levels of identity are with sequences of Haemophilus influenzae Rd. The HsdM polypeptide has the motifs characteristic of adenine methyltransferases. Comparisons of the HsdR sequence with those for three other families of type I systems and three putative HsdR polypeptides identify two highly conserved regions in addition to the seven proposed DEAD-box motifs. PMID:8939428

Titheradge, A J; Ternent, D; Murray, N E



Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling. (United States)

Breast cancers (BCs) of the luminal B subtype are estrogen receptor-positive (ER+), highly proliferative, resistant to standard therapies and have a poor prognosis. To better understand this subtype we compared DNA copy number aberrations (CNAs), DNA promoter methylation, gene expression profiles, and somatic mutations in nine selected genes, in 32 luminal B tumors with those observed in 156 BCs of the other molecular subtypes. Frequent CNAs included 8p11-p12 and 11q13.1-q13.2 amplifications, 7q11.22-q34, 8q21.12-q24.23, 12p12.3-p13.1, 12q13.11-q24.11, 14q21.1-q23.1, 17q11.1-q25.1, 20q11.23-q13.33 gains and 6q14.1-q24.2, 9p21.3-p24,3, 9q21.2, 18p11.31-p11.32 losses. A total of 237 and 101 luminal B-specific candidate oncogenes and tumor suppressor genes (TSGs) presented a deregulated expression in relation with their CNAs, including 11 genes previously reported associated with endocrine resistance. Interestingly, 88% of the potential TSGs are located within chromosome arm 6q, and seven candidate oncogenes are potential therapeutic targets. A total of 100 candidate oncogenes were validated in a public series of 5,765 BCs and the overexpression of 67 of these was associated with poor survival in luminal tumors. Twenty-four genes presented a deregulated expression in relation with a high DNA methylation level. FOXO3, PIK3CA and TP53 were the most frequent mutated genes among the nine tested. In a meta-analysis of next-generation sequencing data in 875 BCs, KCNB2 mutations were associated with luminal B cases while candidate TSGs MDN1 (6q15) and UTRN (6q24), were mutated in this subtype. In conclusion, we have reported luminal B candidate genes that may play a role in the development and/or hormone resistance of this aggressive subtype. PMID:24416132

Cornen, Stéphanie; Guille, Arnaud; Adélaïde, José; Addou-Klouche, Lynda; Finetti, Pascal; Saade, Marie-Rose; Manai, Marwa; Carbuccia, Nadine; Bekhouche, Ismahane; Letessier, Anne; Raynaud, Stéphane; Charafe-Jauffret, Emmanuelle; Jacquemier, Jocelyne; Spicuglia, Salvatore; de The, Hugues; Viens, Patrice; Bertucci, François; Birnbaum, Daniel; Chaffanet, Max



Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes.  

DEFF Research Database (Denmark)

BACKGROUND: Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of sequences that have signals concordant with conserved RNA secondary structures have been discovered in the human genome. Moreover, genome wide transcription profiling with tiling arrays indicate that the majority of the genome is transcribed. RESULTS: We have combined tiling array data with genome wide structural RNA predictions to search for novel noncoding and structural RNA genes that are expressed in the human neuroblastoma cell line SK-N-AS. Using this strategy, we identify thousands of human candidate RNA genes. To further verify the expression of these genes, we focused on candidate genes that had a stable hairpin structures or a high level of covariance. Using northern blotting, we verify the expression of 2 out of 3 of the hairpin structures and 3 out of 9 high covariance structures in SK-N-AS cells. CONCLUSION: Our results demonstrate that many human noncoding, structured and conserved RNA genes remain to be discovered and that tissue specific tiling array data can be used in combination with computational predictions of sequences encoding structural RNAs to improve the search for such genes. Udgivelsesdato: 2007-null

Weile, Christian; Gardner, Paul P



Microarray and differential display identify genes involved in jasmonate-dependent anther development. (United States)

Jasmonate (JA) is a signaling compound essential for anther development and pollen fertility in Arabidopsis. Mutations that block the pathway of JA synthesis result into male sterility. To understand the processes of anther and pollen maturation, we used microarray and differential display approaches to compare gene expression pattern in anthers of wild-type Arabidopsis and the male-sterile mutant, opr3. Microarray experiment revealed 25 genes that were up-regulated more than 1.8-fold in wild-type anthers as compared to mutant anthers. Experiments based on differential display identified 13 additional genes up-regulated in wild-type anthers compared to opr3 for a total of 38 differentially expressed genes. Searches of the Arabidopsis and non-redundant databases disclosed known or likely functions for 28 of the 38 genes identified, while 10 genes encode proteins of unknown function. Northern blot analysis of eight representative clones as probes confirmed low expression in opr3 anthers compared with wild-type anthers. JA responsiveness of these same genes was also investigated by northern blot analysis of anther RNA isolated from wild-type and opr3 plants, In these experiments, four genes were induced in opr3 anthers within 0.5-1 h of JA treatment while the remaining genes were up-regulated only 1-8 h after JA application. None of these genes was induced by JA in anthers of the coil mutant that is deficient in JA responsiveness. The four early-induced genes in opr3 encode lipoxygenase, a putative bHLH transcription factor, epithiospecifier protein and an unknown protein. We propose that these and other early components may be involved in JA signaling and in the initiation of developmental processes. The four late genes encode an extensin-like protein, a peptide transporter and two unknown proteins, which may represent components required later in anther and pollen maturation. Transcript profiling has provided a successful approach to identify genes involved in anther and pollen maturation in Arabidopsis. PMID:13677466

Mandaokar, Ajin; Kumar, V Dinesh; Amway, Matt; Browse, John



Hybridisation-based resequencing of 17 X-linked intellectual disability genes in 135 patients reveals novel mutations in ATRX, SLC6A8 and PQBP1  


X-linked intellectual disability (XLID), also known as X-linked mental retardation, is a highly genetically heterogeneous condition for which mutations in >90 different genes have been identified. In this study, we used a custom-made sequencing array based on the Affymetrix 50k platform for mutation screening in 17 known XLID genes in patients from 135 families and found eight single-nucleotide changes that were absent in controls. For four mutations affecting ATRX (p.1761M>T), PQBP1 (p.155R>...

Jensen, Lars R.; Chen, Wei; Moser, Bettina; Lipkowitz, Bettina; Schroeder, Christopher; Musante, Luciana; Tzschach, Andreas; Kalscheuer, Vera M.; Meloni, Ilaria; Raynaud, Martine; Esch, Hilde; Chelly, Jamel; Brouwer, Arjan P. M.; Hackett, Anna; Haar, Sigrun



Gene Expression Analyses Identify Narp Contribution in the Development of l-DOPA-Induced Dyskinesia. (United States)

In Parkinson's disease, long-term dopamine replacement therapy is complicated by the appearance of l-DOPA-induced dyskinesia (LID). One major hypothesis is that LID results from an aberrant transcriptional program in striatal neurons induced by l-DOPA and triggered by the activation of ERK. To identify these genes, we performed transcriptome analyses in the striatum in 6-hydroxydopamine-lesioned mice. A time course analysis (0-6 h after treatment with l-DOPA) identified an acute signature of 709 genes, among which genes involved in protein phosphatase activity were overrepresented, suggesting a negative feedback on ERK activation by l-DOPA. l-DOPA-dependent deregulation of 28 genes was blocked by pretreatment with SL327, an inhibitor of ERK activation, and 26 genes were found differentially expressed between highly and weakly dyskinetic animals after treatment with l-DOPA. The intersection list identified five genes: FosB, Th, Nptx2, Nedd4l, and Ccrn4l. Nptx2 encodes neuronal pentraxin II (or neuronal activity-regulated pentraxin, Narp), which is involved in the clustering of glutamate receptors. We confirmed increased Nptx2 expression after l-DOPA and its blockade by SL327 using quantitative RT-PCR in independent experiments. Using an escalating l-DOPA dose protocol, LID severity was decreased in Narp knock-out mice compared with their wild-type littermates or after overexpression of a dominant-negative form of Narp in the striatum. In conclusion, we have identified a molecular signature induced by l-DOPA in the dopamine-denervated striatum that is dependent on ERK and associated with LID. Here, we demonstrate the implication of one of these genes, Nptx2, in the development of LID. PMID:25568106

Charbonnier-Beaupel, Fanny; Malerbi, Marion; Alcacer, Cristina; Tahiri, Khadija; Carpentier, Wassila; Wang, Chuansong; During, Matthew; Xu, Desheng; Worley, Paul F; Girault, Jean-Antoine; Hervé, Denis; Corvol, Jean-Christophe



Transcriptome analysis identifies genes with enriched expression in the mouse central Extended Amygdala (United States)

The central Extended Amygdala (EAc) is an ensemble of highly interconnected limbic structures of the anterior brain, and forms a cellular continuum including the Bed Nucleus of the Stria Terminalis (BNST), the central nucleus of the Amygdala (CeA) and the Nucleus Accumbens shell (AcbSh). This neural network is a key site for interactions between brain reward and stress systems, and has been implicated in several aspects of drug abuse. In order to increase our understanding of EAc function at the molecular level, we undertook a genome-wide screen (Affymetrix) to identify genes whose expression is enriched in the EAc. We focused on the less-well known BNST-CeA areas of the EAc, and identified 121 genes that exhibit more than 2-fold higher expression level in the EAc compared to whole brain. Among these, forty-three genes have never been described to be expressed in the EAc. We mapped these genes throughout the brain, using non-radioactive in situ hybridization, and identified eight genes with a unique and distinct rostro-caudal expression pattern along AcbSh, BNST and CeA. Q-PCR analysis performed in brain and peripheral organ tissues indicated that, with the exception of one (Spata13), all these genes are predominantly expressed in brain. These genes encode signaling proteins (Adora2, GPR88, Arpp21 and Rem2), a transcription factor (Limh6) or proteins of unknown function (Rik130, Spata13 and Wfs1). The identification of genes with enriched expression expands our knowledge of EAc at a molecular level, and provides useful information to towards genetic manipulations within the EAc. PMID:18786617

Becker, Jérôme A. J.; Befort, Katia; Blad, Clara; Filliol, Dominique; Ghate, Aditee; Dembele, Doulaye; Thibault, Christelle; Koch, Muriel; Muller, Jean; Lardenois, Aurélie; Poch, Olivier; Kieffer, Brigitte L.



Transcriptome analysis identifies genes with enriched expression in the mouse central extended amygdala. (United States)

The central extended amygdala (EAc) is an ensemble of highly interconnected limbic structures of the anterior brain, and forms a cellular continuum including the bed nucleus of the stria terminalis (BNST), the central nucleus of the amygdala (CeA) and the nucleus accumbens shell (AcbSh). This neural network is a key site for interactions between brain reward and stress systems, and has been implicated in several aspects of drug abuse. In order to increase our understanding of EAc function at the molecular level, we undertook a genome-wide screen (Affymetrix) to identify genes whose expression is enriched in the mouse EAc. We focused on the less-well known BNST-CeA areas of the EAc, and identified 121 genes that exhibit more than twofold higher expression level in the EAc compared with whole brain. Among these, 43 genes have never been described to be expressed in the EAc. We mapped these genes throughout the brain, using non-radioactive in situ hybridization, and identified eight genes with a unique and distinct rostro-caudal expression pattern along AcbSh, BNST and CeA. Q-PCR analysis performed in brain and peripheral organ tissues indicated that, with the exception of one (Spata13), all these genes are predominantly expressed in brain. These genes encode signaling proteins (Adora2, GPR88, Arpp21 and Rem2), a transcription factor (Limh6) or proteins of unknown function (Rik130, Spata13 and Wfs1). The identification of genes with enriched expression expands our knowledge of EAc at a molecular level, and provides useful information to toward genetic manipulations within the EAc. PMID:18786617

Becker, J A J; Befort, K; Blad, C; Filliol, D; Ghate, A; Dembele, D; Thibault, C; Koch, M; Muller, J; Lardenois, A; Poch, O; Kieffer, B L



Gene expression in bovine rumen epithelium during weaning identifies molecular regulators of rumen development and growth. (United States)

During weaning, epithelial cell function in the rumen transitions in response to conversion from a pre-ruminant to a true ruminant environment to ensure efficient nutrient absorption and metabolism. To identify gene networks affected by weaning in bovine rumen, Holstein bull calves were fed commercial milk replacer only (MRO) until 42 days of age, then were provided diets of either milk + orchardgrass hay (MH) or milk + grain-based calf starter (MG). Rumen epithelial RNA was extracted from calves sacrificed at four time points: day 14 (n?=?3) and day 42 (n?=?3) of age while fed the MRO diet and day 56 (n?=?3/diet) and day 70 (n?=?3/diet) while fed the MH and MG diets for transcript profiling by microarray hybridization. Five two-group comparisons were made using Permutation Analysis of Differential Expression® to identify differentially expressed genes over time and developmental stage between days 14 and 42 within the MRO diet, between day 42 on the MRO diet and day 56 on the MG or MH diets, and between the MG and MH diets at days 56 and 70. Ingenuity Pathway Analysis (IPA) of differentially expressed genes during weaning indicated the top 5 gene networks involving molecules participating in lipid metabolism, cell morphology and death, cellular growth and proliferation, molecular transport, and the cell cycle. Putative genes functioning in the establishment of the rumen microbial population and associated rumen epithelial inflammation during weaning were identified. Activation of transcription factor PPAR-? was identified by IPA software as an important regulator of molecular changes in rumen epithelium that function in papillary development and fatty acid oxidation during the transition from pre-rumination to rumination. Thus, molecular markers of rumen development and gene networks regulating differentiation and growth of rumen epithelium were identified for selecting targets and methods for improving and assessing rumen development and function, particularly in the growing calf. PMID:23314861

Connor, Erin E; Baldwin, Ransom L; Li, Cong-jun; Li, Robert W; Chung, Hoyoung



Dissecting the Gene Network of Dietary Restriction to Identify Evolutionarily Conserved Pathways and New Functional Genes  


Dietary restriction (DR), limiting nutrient intake from diet without causing malnutrition, delays the aging process and extends lifespan in multiple organisms. The conserved life-extending effect of DR suggests the involvement of fundamental mechanisms, although these remain a subject of debate. To help decipher the life-extending mechanisms of DR, we first compiled a list of genes that if genetically altered disrupt or prevent the life-extending effects of DR. We called these DR–essential ...

Wuttke, Daniel; Connor, Richard; Vora, Chintan; Craig, Thomas; Li, Yang; Wood, Shona; Vasieva, Olga; Shmookler Reis, Robert; Tang, Fusheng; Magalha?es, Joa?o Pedro



A voting approach to identify a small number of highly predictive genes using multiple classifiers (United States)

Background Microarray gene expression profiling has provided extensive datasets that can describe characteristics of cancer patients. An important challenge for this type of data is the discovery of gene sets which can be used as the basis of developing a clinical predictor for cancer. It is desirable that such gene sets be compact, give accurate predictions across many classifiers, be biologically relevant and have good biological process coverage. Results By using a new type of multiple classifier voting approach, we have identified gene sets that can predict breast cancer prognosis accurately, for a range of classification algorithms. Unlike a wrapper approach, our method is not specialised towards a single classification technique. Experimental analysis demonstrates higher prediction accuracies for our sets of genes compared to previous work in the area. Moreover, our sets of genes are generally more compact than those previously proposed. Taking a biological viewpoint, from the literature, most of the genes in our sets are known to be strongly related to cancer. Conclusion We show that it is possible to obtain superior classification accuracy with our approach and obtain a compact gene set that is also biologically relevant and has good coverage of different biological processes. PMID:19208118

Hassan, Md Rafiul; Hossain, M Maruf; Bailey, James; Macintyre, Geoff; Ho, Joshua WK; Ramamohanarao, Kotagiri



Identifying estrogen receptor ? target genes using integrated computational genomics and chromatin immunoprecipitation microarray  


The estrogen receptor ? (ER?) regulates gene expression by either direct binding to estrogen response elements or indirect tethering to other transcription factors on promoter targets. To identify these promoter sequences, we conducted a genome-wide screening with a novel microarray technique called ChIP-on-chip. A set of 70 candidate ER? loci were identified and the corresponding promoter sequences were analyzed by statistical pattern recognition and comparative genomics approaches. We fo...

Jin, Victor X.; Leu, Yu-wei; Liyanarachchi, Sandya; Sun, Hao; Fan, Meiyun; Nephew, Kenneth P.; Huang, Tim H. -m; Davuluri, Ramana V.



Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy  


Forward genetic screens with ENU (N-ethyl-N-nitrosourea) mutagenesis can facilitate gene discovery, but mutation identification is often difficult. We present the first study in which an ENU- induced mutation was identified by massively parallel DNA sequencing. This mutation causes heterotaxy and complex congenital heart defects and was mapped to a 2.2-Mb interval on mouse chromosome 7. Massively parallel sequencing of the entire 2.2-Mb interval identified 2 single-base substitutions, one in ...

Zhang, Zhen; Alpert, Deanne; Francis, Richard; Chatterjee, Bishwanath; Yu, Qing; Tansey, Terry; Sabol, Steven L.; Cui, Cheng; Bai, Yongli; Koriabine, Maxim; Yoshinaga, Yuko; Cheng, Jan-fang; Chen, Feng; Martin, Joel; Schackwitz, Wendy



Global Gene Expression Analysis Identifies PDEF Transcriptional Networks Regulating Cell Migration during Cancer Progression  


Prostate derived ETS factor (PDEF) is an ETS (epithelial-specific E26 transforming sequence) family member that has been identified as a potential tumor suppressor. In multiple invasive breast cancer cells, PDEF expression inhibits cell migration by preventing the acquisition of directional morphological polarity conferred by changes in cytoskeleton organization. In this study, microarray analysis was used to identify >200 human genes that displayed a common differential expression pattern in...

Turner, David P.; Findlay, Victoria J.; Kirven, A. Darby; Moussa, Omar; Watson, Dennis K.



A modified entropy-based approach for identifying gene-gene interactions in case-control study. (United States)

Gene-gene interactions may play an important role in the genetics of a complex disease. Detection and characterization of gene-gene interactions is a challenging issue that has stimulated the development of various statistical methods to address it. In this study, we introduce a method to measure gene interactions using entropy-based statistics from a contingency table of trait and genotype combinations. We also developed an exploration procedure by using graphs. We propose a standardized relative information gain (RIG) measure to evaluate the interactions between single nucleotide polymorphism (SNP) combinations. To identify the k (th) order interactions, contingency tables of trait and genotype combinations of k SNPs are constructed, with which RIGs are calculated. The RIGs are standardized using the mean and standard deviation from the permuted datasets. SNP combinations yielding high standardized RIG are chosen for gene-gene interactions. Detection of high-order interactions and comparison of interaction strengths between different orders are made possible by using standardized RIG. We have applied the proposed standardized entropy-based method to two types of data sets from a simulation study and a real genetic association study. We have compared our method and the multifactor dimensionality reduction (MDR) method through power analysis of eight different genetic models with varying penetrance rates, number of SNPs, and sample sizes. Our method shows successful identification of genetic associations and gene-gene interactions both in simulation and real genetic data. Simulation results suggest that the proposed entropy-based method is better able to detect high-order interactions and is superior to the MDR method in most cases. The proposed method is well suited for detecting interactions without main effects as well as for models including main effects. PMID:23874943

Yee, Jaeyong; Kwon, Min-Seok; Park, Taesung; Park, Mira



Progress in the identification of DNA markers linked to the Yd2 gene in barley  

International Nuclear Information System (INIS)

Barley yellow dwarf (BYD) is the most damaging virus disease in wheat and other cereal crops worldwide and the yield loss inflicted by the virus (BYDV) and be quite severe. While some protection against the disease can be realized by crop management practices, resistant varieties clearly offer the greatest opportunity for reducing yield losses. Possible sources of BYD resistance have been found in wheat, barely, rye and wheatgrass species. Among them, the Yd2 gene from chromosome 3H of barley currently shows the best genetic resistance in any cereal species and it has been widely deployed in many leading barley varieties. We have developed 94 F2 derived families from the cross between Betzes, a susceptible barley variety that does not carry Yd2, and Atlas 68, a resistant variety that has Yd2. These families were evaluated in two and three replicate tests for BYD symptom expression in field nurseries at Davis, California, and at Aberdeen, Idaho, respectively. To minimize the mapping effort at this early stage, we used 18 and 23 homozygous resistant and susceptible F2 derived families, respectively, and have identified RFLP markers that are closely linked to Yd2. We are now moving to the next phase of this work, which is to extend the RFLP mapping population size to include all the F2 derived families and to saturate the region carrying Yd2 with marker loci available to us from genome mapping programmes in barley, wheat and other relatedgrammes in barley, wheat and other related species


GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Rapid progress in high-throughput biotechnologies (e.g. microarrays and exponential accumulation of gene functional knowledge make it promising for systematic understanding of complex human diseases at functional modules level. Based on Gene Ontology, a large number of automatic tools have been developed for the functional analysis and biological interpretation of the high-throughput microarray data. Results Different from the existing tools such as Onto-Express and FatiGO, we develop a tool named GO-2D for identifying 2-dimensional functional modules based on combined GO categories. For example, it refines biological process categories by sorting their genes into different cellular component categories, and then extracts those combined categories enriched with the interesting genes (e.g., the differentially expressed genes for identifying the cellular-localized functional modules. Applications of GO-2D to the analyses of two human cancer datasets show that very specific disease-relevant processes can be identified by using cellular location information. Conclusion For studying complex human diseases, GO-2D can extract functionally compact and detailed modules such as the cellular-localized ones, characterizing disease-relevant modules in terms of both biological processes and cellular locations. The application results clearly demonstrate that 2-dimensional approach complementary to current 1-dimensional approach is powerful for finding modules highly relevant to diseases.

Yang Da



Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The hierarchical clustering tree (HCT with a dendrogram 1 and the singular value decomposition (SVD with a dimension-reduced representative map 2 are popular methods for two-way sorting the gene-by-array matrix map employed in gene expression profiling. While HCT dendrograms tend to optimize local coherent clustering patterns, SVD leading eigenvectors usually identify better global grouping and transitional structures. Results This study proposes a flipping mechanism for a conventional agglomerative HCT using a rank-two ellipse (R2E, an improved SVD algorithm for sorting purpose seriation by Chen 3 as an external reference. While HCTs always produce permutations with good local behaviour, the rank-two ellipse seriation gives the best global grouping patterns and smooth transitional trends. The resulting algorithm automatically integrates the desirable properties of each method so that users have access to a clustering and visualization environment for gene expression profiles that preserves coherent local clusters and identifies global grouping trends. Conclusion We demonstrate, through four examples, that the proposed method not only possesses better numerical and statistical properties, it also provides more meaningful biomedical insights than other sorting algorithms. We suggest that sorted proximity matrices for genes and arrays, in addition to the gene-by-array expression matrix, can greatly aid in the search for comprehensive understanding of gene expression structures. Software for the proposed methods can be obtained at

Lee Yun-Shien



Transcriptional profiling identifies upregulated genes following induction of epithelial-mesenchymal transition in squamous carcinoma cells. (United States)

During the progression of head and neck squamous cell carcinoma (HNSCC), the induction of an epithelial-mesenchymal transition (EMT) program may play a critical role in the dissemination of cells from the primary tumor to distant metastatic foci. The process of EMT involves the activation of several important genes and pathways to help maintain survival and growth and evolve into highly invasive and metastatic variants. In this study, expression microarray analysis identified a set of 145 upregulated genes in EMT-like HNSCC cells. Some of the strongly upregulated transcripts include genes that are reportedly involved in invasion and metastasis, such as DOCK10, LOX, ROBO1 and SRGN. Importantly, the Tbx3 gene, a member of the T-box transcription factor, was strongly upregulated in SCC cells displaying an EMT-like phenotype compared to cells with an epitheloid, non-EMT behavior. Tbx3 was also found to be strongly upregulated at the protein and gene expression level in an experimental model of snail-induced EMT cells. In addition, siRNA-induced Tbx3 depletion modestly suppressed cell invasion while enhancing Tbx3-mediated resistance to anoikis. Our findings provide evidence that Tbx3 overexpression promotes SCC cell survival displaying an EMT phenotype. This set of newly identified genes that are modulated during EMT-like conversion may be important diagnostic biomarkers during the process of HNSCC progression. PMID:22154512

Humtsoe, Joseph O; Koya, Eriko; Pham, Eric; Aramoto, Takayoshi; Zuo, Jian; Ishikawa, Tohru; Kramer, Randall H



Chromatin structure analysis of single gene molecules by psoralen cross-linking and electron microscopy. (United States)

Nucleosomes occupy a central role in regulating eukaryotic gene expression by blocking access of transcription factors to their target sites on chromosomal DNA. Analysis of chromatin structure and function has mostly been performed by probing DNA accessibility with endonucleases. Such experiments average over large numbers of molecules of the same gene, and more recently, over entire genomes. However, both digestion and averaging erase the structural variation between molecules indicative of dynamic behavior, which must be reconstructed for any theory of regulation. Solution of this problem requires the structural analysis of single gene molecules. In this chapter, we describe a method by which single gene molecules are purified from the yeast Saccharomyces cerevisiae and cross-linked with psoralen, allowing the determination of nucleosome configurations by transmission electron microscopy. We also provide custom analysis software that semi-automates the analysis of micrograph data. This single-gene technique enables detailed examination of chromatin structure at any genomic locus in yeast. PMID:25311125

Brown, Christopher R; Eskin, Julian A; Hamperl, Stephan; Griesenbeck, Joachim; Jurica, Melissa S; Boeger, Hinrich



A silent mutation, C924T (G308G), in the L1CAM gene results in X linked hydrocephalus (HSAS).  


The L1 cell adhesion molecule (L1CAM) is a neuronal gene involved in the development of the nervous system. Mutations in L1CAM are known to cause several clinically overlapping X linked mental retardation conditions: X linked hydrocephalus (HSAS), MASA syndrome (mental retardation, aphasia, shuffling gait, adducted thumbs), spastic paraplegia type I (SPG1), and X linked agenesis of the corpus callosum (ACC). In an analysis of a family with HSAS, we identified a C-->T transition (C924T) in exo...

Du, Y. Z.; Dickerson, C.; Aylsworth, A. S.; Schwartz, C. E.



Two novel mutations identified in the Wiskott-Aldrich syndrome protein gene cause Wiskott-Aldrich syndrome and thrombocytopenia. (United States)

Wiskott-Aldrich syndrome (WAS) and X-linked thrombocytopenia (XLT) are rare X-linked genetic disorders caused by mutations of the Wiskott-Aldrich syndrome protein (WASP) gene. Both disorders are clinically characterized by chronic thrombocytopenia of small platelets. WAS is a more severe form of the disorder and also courses with eczema, and immune dysfunction. In the present study, we investigated two novel mutations of the WASP gene in two Spanish families with patients clinically diagnosed as having XLT and WAS, respectively. In one of the families a missense mutation in exon 12 (1488A>G), resulting in the highly conserved glutamic residue changing to glycine at position 485 (D485G), was identified in several members. Notably, a female of this family, with clinical signs of XLT, was determined as the carrier of the mutation and showed a skewed pattern of X-inactivation, preferentially inactivating the X-chromosome carrying the wild-type allele. In the case of the second family, we describe a WAS patient with a single base deletion in exon 2 (266-267delA), resulting in a frameshift (at codon 78) that creates a stop codon at amino acid 127. As a consequence, there was no WASP expression. PMID:17390083

Andreu, Nuria; Matamoros, Núria; Escudero, Antonio; Fillat, Cristina



Manipulation of nonsense mediated decay identifies gene mutations in colon cancer Cells with microsatellite instability. (United States)

Cancer cells showing microsatellite instability (MSI) demonstrate a high frequency of acquired frameshift mutations that result in the generation of nonsense mutations. RNA transcripts carrying these nonsense mutations are usually targeted for degradation through the nonsense mediated decay (NMD) pathway. Blocking this pathway with drugs such as emitine, results in the 'stabilization' of these mutant transcripts, which can now be detected on cDNA arrays. Unfortunately, emetine also induces a stress response that results in upregulation of additional transcripts which contribute to the analysis of the array. As a result, identifying which genes truly carry nonsense mutations is made more difficult. To overcome this, we have combined the emetine treatment with actinomycin D, which effectively prevents the upregulation of stress response genes while still stabilizing mutant transcripts. When we applied this modified approach to the analysis of MSI-positive colon cancer cells, we identified mutations in the UVRAG and p300 genes. PMID:14737099

Ionov, Yurij; Nowak, Norma; Perucho, Manuel; Markowitz, Sanford; Cowell, John K



An insight into the phylogenetic history of HOX linked gene families in vertebrates  

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Full Text Available Abstract Background The human chromosomes 2q, 7, 12q and 17q show extensive intra-genomic homology, containing duplicate, triplicate and quadruplicate paralogous regions centered on the HOX gene clusters. The fact that two or more representatives of different gene families are linked with HOX clusters is taken as evidence that these paralogous gene sets might have arisen from a single chromosomal segment through block or whole chromosome duplication events. This would imply that the constituent genes including the HOX clusters reflect the architecture of a single ancestral block (before vertebrate origin where all of these genes were linked in a single copy. Results In the present study we have employed the currently available set of protein data for a wide variety of vertebrate and invertebrate genomes to analyze the phylogenetic history of 11 multigene families with three or more of their representatives linked to human HOX clusters. A topology comparison approach revealed four discrete co-duplicated groups: group 1 involves the genes from GLI, HH, INHB, IGFBP (cluster-1, and SLC4A families; group 2 involves ERBB, ZNFN1A, and IGFBP (cluster-2 gene families; group 3 involves the HOX clusters and the SP gene family; group 4 involves the integrin beta chain and myosine light chain families. The distinct genes within each co-duplicated group share the same evolutionary history and are duplicated in concert with each other, while the constituent genes of two different co-duplicated groups may not share their evolutionary history and may not have duplicated simultaneously. Conclusion We conclude that co-duplicated groups may themselves be remnants of ancient small-scale duplications (involving chromosomal segments or gene-clusters which occurred at different time points during chordate evolution. Whereas the recent combination of genes from distinct co-duplicated groups on different chromosomal regions (human chromosomes 2q, 7, 12q, and 17q is probably the outcome of subsequent rearrangement of genomic segments, including syntenic groups of genes.

Grzeschik Karl-Heinz



STAT1-induced ASPP2 transcription identifies a link between neuroinflammation, cell polarity, and tumor suppression. (United States)

Inflammation and loss of cell polarity play pivotal roles in neurodegeneration and cancer. A central question in both diseases is how the loss of cell polarity is sensed by cell death machinery. Here, we identify apoptosis-stimulating protein of p53 with signature sequences of ankyrin repeat-, SH3 domain-, and proline-rich region-containing protein 2 (ASPP2), a haploinsufficient tumor suppressor, activator of p53, and regulator of cell polarity, as a transcriptional target of signal transducer and activator of transcription 1 (STAT1). LPS induces ASPP2 expression in murine macrophage and microglial cell lines, a human monocyte cell line, and primary human astrocytes in vitro. LPS and IFNs induce ASPP2 transcription through an NF-?B RELA/p65-independent but STAT1-dependent pathway. In an LPS-induced maternal inflammation mouse model, LPS induces nuclear ASPP2 in vivo at the blood-cerebral spinal fluid barrier (the brain's barrier to inflammation), and ASPP2 mediates LPS-induced apoptosis. Consistent with the role of ASPP2 as a gatekeeper to inflammation, ASPP2-deficient brains possess enhanced neuroinflammation. Elevated ASPP2 expression is also observed in mouse models and human neuroinflammatory disease tissue, where ASPP2 was detected in GFAP-expressing reactive astrocytes that coexpress STAT1. Because the ability of ASPP2 to maintain cellular polarity is vital to CNS development, our findings suggest that the identified STAT1/ASPP2 pathway may connect tumor suppression and cell polarity to neuroinflammation. PMID:24958857

Turnquist, Casmir; Wang, Yihua; Severson, David T; Zhong, Shan; Sun, Bin; Ma, Jingyi; Constaninescu, Stefan N; Ansorge, Olaf; Stolp, Helen B; Molnár, Zoltán; Szele, Francis G; Lu, Xin



Robust consensus clustering for identification of expressed genes linked to malignancy of human colorectal carcinoma. (United States)

Previous studies have been conducted in gene expression profiling to identify groups of genes that characterize the colorectal carcinoma disease. Despite the success of previous attempts to identify groups of genes in the progression of the colorectal carcinoma disease, their methods either require subjective interpretation of the number of clusters, or lack stability during different runs of the algorithms. All of which limits the usefulness of these methods. In this study, we propose an enhanced algorithm that provides stability and robustness in identifying differentially expressed genes in an expression profile analysis. Our proposed algorithm uses multiple clustering algorithms under the consensus clustering framework. The results of the experiment show that the robustness of our method provides a consistent structure of clusters, similar to the structure found in the previous study. Furthermore, our algorithm outperforms any single clustering algorithms in terms of the cluster quality score. PMID:21738330

Wahyudi, Gatot; Wasito, Ito; Melia, Tisha; Budi, Indra



Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes  

DEFF Research Database (Denmark)

Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 x raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.

Xu, Xun; Liu, Xin



Mutations of the WASP gene in 10 Japanese patients with Wiskott-Aldrich syndrome and X-linked thrombocytopenia. (United States)

Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disorder characterized by thrombocytopenia, immunodeficiency, and eczema. X-linked thrombocytopenia (XLT) is a mild form of WAS with isolated thrombocytopenia. Both phenotypes are caused by mutation of the Wiskott-Aldrich syndrome protein (WASP) gene. In this study, we identified mutations of the WASP gene in 10 Japanese patients from 9 unrelated families with WAS/XLT. All XLT patients (n = 3) and one WAS patient had a missense mutation at the PH domain of WASP. Two WAS patients had nonsense mutations. One WAS patient had exon 8 skipping caused by one nucleotide deletion at the acceptor site of intron 7. Three WAS patients had genomic deletions; one of the three had a large genomic deletion involving exons 3 to 7. Codons 45 and 86 seem to be the hot spots of the WASP mutation, because missense mutations in these codons have been reported previously in several WAS/XLT patients in addition to the patients in this report, and patients with the same mutation show a similar clinical phenotype. All other mutations are novel, indicating that the mutations of WASP are heterogeneous. EB virus-transformed cell lines from XLT patients expressed nearly normal amounts of WASP, whereas those from typical WAS patients expressed almost undetectable amounts of WASP. We conclude that the analysis of gene mutation and protein expression of WASP are useful together in assessing the severity of WAS. PMID:10729999

Itoh, S; Nonoyama, S; Morio, T; Imai, K; Okawa, H; Ochs, H D; Shimadzu, M; Yata, J



Functional coupling analysis suggests link between the obesity gene FTO and the BDNF-NTRK2 signaling pathway  

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Full Text Available Abstract Background The Fat mass and obesity gene (FTO has been identified through genome wide association studies as an important genetic factor contributing to a higher body mass index (BMI. However, the molecular context in which this effect is mediated has yet to be determined. We investigated the potential molecular network for FTO by analyzing co-expression and protein-protein interaction databases, Coxpresdb and IntAct, as well as the functional coupling predicting multi-source database, FunCoup. Hypothalamic expression of FTO-linked genes defined with this bioinformatics approach was subsequently studied using quantitative real time-PCR in mouse feeding models known to affect FTO expression. Results We identified several candidate genes for functional coupling to FTO through database studies and selected nine for further study in animal models. We observed hypothalamic expression of Profilin 2 (Pfn2, cAMP-dependent protein kinase catalytic subunit beta (Prkacb, Brain derived neurotrophic factor (Bdnf, neurotrophic tyrosine kinase, receptor, type 2 (Ntrk2, Signal transducer and activator of transcription 3 (Stat3, and Btbd12 to be co-regulated in concert with Fto. Pfn2 and Prkacb have previously not been linked to feeding regulation. Conclusions Gene expression studies validate several candidates generated through database studies of possible FTO-interactors. We speculate about a wider functional role for FTO in the context of current and recent findings, such as in extracellular ligand-induced neuronal plasticity via NTRK2/BDNF, possibly via interaction with the transcription factor CCAAT/enhancer binding protein ? (C/EBP?.

Rask-Andersen Mathias



Expression of X-linked Genes in Deceased Neonates and Surviving Cloned Female Piglets (United States)

Animal cloning through somatic cell nuclear transfer is very inefficient, probably due to insufficient reprogramming of the donor nuclei, which in turn would cause the dysregulation of gene expression. X-Chromosome inactivation (XCI) is a multi-step epigenetic process utilized by mammals to achieve dosage compensation in females. Our aim was to determine if any dysregulation of X-linked genes, which would be indicative of unfaithful reprogramming of donor nuclei, was present in cloned pigs. Real time reverse transcription polymerase chain reaction (RT-PCR) was performed to quantify the transcript levels of five X-linked genes, XIST, TSIX, HPRT1, G6PD, ARAF1 and one autosomal gene, COL4A1 in major organs of neonatal deceased and surviving female cloned pigs and age-matched control pigs from conventional breeding. Aberrant expression level of these genes was prevalent in the neonatal deceased clones, while it was only moderate in cloned pigs that survived after birth. These results suggest a correlation between the viability of the clones and the normality of their gene expression and provide a possible explanation for the death of a large portion of cloned animals around birth. PMID:17474099

Jiang, Le; Jobst, Pete; Lai, Liangxue; Samuel, Melissa; Prather, Randall S.; Ayares, David; Yang, Xiangzhong; Tian, X. Cindy



Mutation pattern in the Bruton's tyrosine kinase gene in 26 unrelated patients with X-linked agammaglobulinemia  

DEFF Research Database (Denmark)

Mutation pattern was characterized in the Bruton's tyrosine kinase gene (BTK) in 26 patients with X-linked agammaglobulinemia, the first described immunoglobulin deficiency, and was related to BTK expression. A total of 24 different mutations were identified. Most BTK mutations were found to result in premature termination of the translation product. Mutations were detected in most BTK exons with a predominance of frameshift and nonsense mutations in the 5' end of the gene and missense mutations in its 3' part, corresponding to the catalytic domain of the enzyme. Nonsense and frameshift mutations were associated with diminished levels of BTK mRNA expression, except for a frameshift mutation in exon 17 and two nonsense mutations in exon 2, indicating that these cases are not confined to penultimate exons. One amino acid substitution (R28H) was found in the pleckstrin homology domain's residue, which is mutated in mice bearing the X-linked immunodeficiency phenotype; another substitution (R307G) was identified in the src homology domain 2. All remaining amino acid substitutions were found in the catalytic domain of Btk.

Vorechovský, I; Luo, L



An attempt to identify the likely sources of Escherichia coli harboring toxin genes in rainwater tanks. (United States)

In this study, 200 Escherichia coli isolates from 22 rainwater tank samples in Southeast Queensland, Australia were tested for the presence of 10 toxin genes (i.e., stx(1), stx(2), hlyA, ehxA, LT1, ST1, cdtB, east1, cnf1, and cvaC) associated with intestinal and extraintestinal pathotypes. Among the 22 rainwater tanks tested, 5 (28%), 7 (32%), 7 (32%), and 1 (5%) tanks contained E. coli harboring ST1, east1, cdtB, and cvaC genes, respectively. Of the 200 E. coli isolates from the 22 tanks, 43 (22%) strains from 13 (59%) tanks were harboring toxin gene. An attempt was made to establish a link between bird and possum fecal contamination and the presence of these potential clinically significant E. coli strains harboring toxin genes in rainwater tanks. Among the 214 E. coli isolates tested from birds, 30 (14%), 11 (5%) and 18 (8%) strains contained east1, cdtB, and cvaC toxin genes, respectively. Similarly, among the 214 possum E. coli isolates, 74 (35%) contained only the east1 toxin gene. All E. coli strains from rainwater tanks, bird and possum fecal samples harboring toxin genes were biochemically fingerprinted. Biochemical phenotypes (BPTs) of 14 (33%) E. coli strains from 7 rainwater tanks and 9 (21%) E. coli strains from 6 rainwater tanks were identical to a number of BPTs of E. coli strains isolated from bird and possum feces suggesting that these animals may be the sources of these E. coli in rainwater tanks. as a precautionary measure, it is recommended that rainwater should be treated prior to drinking. In addition, proper maintenance of roof and gutter hygiene and elimination of overhanging tree branches and other structures where possible to prevent the movement of possums are highly recommended. PMID:22489653

Ahmed, W; Sidhu, J P S; Toze, S



Modulation of polyglutamine-induced cell death by genes identified by expression profiling. (United States)

The majority of triplet-repeat diseases are caused by mutated genes with an extended polyglutamine tract, exemplified by Huntington's disease (HD). In order to model HD pathogenesis in a controlled system, we developed stable PC12 cell lines that express exon 1 fragments of the huntingtin gene with 23 or 74 polyglutamines driven by an inducible doxycycline (dox)-sensitive promoter (HD-23Q or HD-74Q). We aimed to identify early perturbations induced by the mutation by studying expression levels of 1824 genes at 0, 5, 10 and 18 hours after induction, using adaptor-tagged competitive PCR (ATAC-PCR). At these time points, the cells show no appreciable death or mitochondrial impairment and very low inclusion levels. A total of 126 genes, including 69 known genes, exhibited statistically significant alterations in the HD-74Q cell lines but no changes in the HD-23Q lines. We tested 11 of these genes for their abilities to modulate polyglutamine-induced cell death in transiently transfected cell models. Five genes [glucose transporter 1 (Glut1), phosphofructokinase muscle isozyme (Pfkm), prostate glutathione-S -transferase 2 (Gstm2), RNA-binding motif protein 3 (Rbm3) and KRAB-A interacting protein 1 (Krip-1)] significantly suppressed cell death in both neuronal precursor and non-neuronal cell lines, suggesting that these transcriptional changes were relevant to polyglutamine pathology. The efficient recovery of functionally relevant genes supports the utility of gene expression profiling for discovering pathways related to pathogenesis, and the importance of analyzing molecular events in the early stages of disease. PMID:12217956

Kita, Hiroko; Carmichael, Jenny; Swartz, Jina; Muro, Shizuko; Wyttenbach, Andreas; Matsubara, Kenichi; Rubinsztein, David C; Kato, Kikuya



Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes  

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Full Text Available Abstract Background The basidiomycete fungus Microbotryum violaceum is responsible for the anther-smut disease in many plants of the Caryophyllaceae family and is a model in genetics and evolutionary biology. Infection is initiated by dikaryotic hyphae produced after the conjugation of two haploid sporidia of opposite mating type. This study describes M. violaceum ESTs corresponding to nuclear genes expressed during conjugation and early hyphal production. Results A normalized cDNA library generated 24,128 sequences, which were assembled into 7,765 unique genes; 25.2% of them displayed significant similarity to annotated proteins from other organisms, 74.3% a weak similarity to the same set of known proteins, and 0.5% were orphans. We identified putative pheromone receptors and genes that in other fungi are involved in the mating process. We also identified many sequences similar to genes known to be involved in pathogenicity in other fungi. The M. violaceum EST database, MICROBASE, is available on the Web and provides access to the sequences, assembled contigs, annotations and programs to compare similarities against MICROBASE. Conclusion This study provides a basis for cloning the mating type locus, for further investigation of pathogenicity genes in the anther smut fungi, and for comparative genomics.

Devier Benjamin



Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP. (United States)

Important insights into nuclear function would arise if gene loci physically interacting with particular subnuclear domains could be readily identified. Immunofluorescence microscopy combined with fluorescence in situ hybridization (immuno-FISH), the method that would typically be used in such a study, is limited by spatial resolution and requires prior assumptions for selecting genes to probe. Our new technique, immuno-TRAP, overcomes these limitations. Using promyelocytic leukemia nuclear bodies (PML NBs) as a model, we used immuno-TRAP to determine if specific genes localize within molecular dimensions with these bodies. Although we confirmed a TP53 gene-PML NB association, immuno-TRAP allowed us to uncover novel locus-PML NB associations, including the ABCA7 and TFF1 loci and, most surprisingly, the PML locus itself. These associations were cell type specific and reflected the cell's physiological state. Combined with microarrays or deep sequencing, immuno-TRAP provides powerful opportunities for identifying gene locus associations with potentially any nuclear subcompartment. PMID:23589495

Ching, Reagan W; Ahmed, Kashif; Boutros, Paul C; Penn, Linda Z; Bazett-Jones, David P



High cortisol responses identify propensity for obesity that is linked to thermogenesis in skeletal muscle. (United States)

Subjects characterized as cortisol high responders (HRs) consume more calories after stress, but it is unknown whether cortisol responsiveness predicts a propensity for obesity. Female sheep with either high or low cortisol responses to adrenocorticotropin (ACTH) were identified. Body composition was similar in HRs and cortisol low responders (LRs), but the HRs had greater (P<0.01) adiposity than did the LRs (40.5±0.7 vs. 35.8±1.4%) after high-energy feeding, despite comparable food intake. Postprandial thermogenesis in muscle temperature was 0.8 ± 0.08°C higher in the LRs than in the HRs (P<0.01), whereas feeding-induced changes in fat temperature were similar. Leptin and insulin sensitivity were similar in the HRs and LRs. Feeding lowered (P<0.001) the respiratory control ratio in muscle (HRs 9.2±0.8-5.2±1.2; LRs 8.4±0.5-5.2±0.7), indicative of increased uncoupled respiration. Also in muscle, the feeding-induced increases in uncoupling protein (UCP)-3 (fold increase: HRs, 2.4; LRs, 2.0), ryanodine 1 receptor (RyR1; fold increase: HRs 3.1; LRs 2.1), and sarcoendoplasmic reticulum Ca(2+)-dependent ATPase (fold increase: HRs 1.5; LRs 1.6) were equivalent in the HRs and LRs. Sequencing of mitochondrial DNA revealed no haplotypic differences between the 2 groups. We conclude that predisposition to obesity can be predicted by cortisol responsiveness to an ACTH challenge and that the response is due to innate differences in muscle thermogenesis. PMID:24022403

Lee, T Kevin; Clarke, Iain J; St John, Justin; Young, I Ross; Leury, Brian L; Rao, Alexandra; Andrews, Zane B; Henry, Belinda A



NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell lines  

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Full Text Available Abstract Background Gastric cancers frequently show chromosomal alterations which can cause activation of oncogenes, and/or inactivation of tumour suppressor genes. In gastric cancer several chromosomal regions are described to be frequently lost, but for most of the regions, no tumour suppressor genes have been identified yet. The present study aimed to identify tumour suppressor genes inactivated by nonsense mutation and deletion in gastric cancer by means of GINI (gene identification by nonsense mediated decay inhibition and whole genome copy number analysis. Methods Two non-commercial gastric cancer cell lines, GP202 and IPA220, were transfected with siRNA directed against UPF1, to specifically inhibit the nonsense mediated decay (NMD pathway, and with siRNA directed against non-specific siRNA duplexes (CVII as a control. Microarray expression experiments were performed in triplicate on 4 × 44 K Agilent arrays by hybridizing RNA from UPF1-transfected cells against non-specific CVII-transfected cells. In addition, array CGH of the two cell lines was performed on 4 × 44K agilent arrays to obtain the DNA copy number profiles. Mutation analysis of GINI candidates was performed by sequencing. Results UPF1 expression was reduced for >70% and >80% in the GP202 and IPA220 gastric cancer cell lines, respectively. Integration of array CGH and microarray expression data provided a list of 134 and 50 candidate genes inactivated by nonsense mutation and deletion for GP202 and IPA220, respectively. We selected 12 candidate genes for mutation analysis. Of these, sequence analysis was performed on 11 genes. One gene, PLA2G4A, showed a silent mutation, and in two genes, CTSA and PTPRJ, missense mutations were detected. No nonsense mutations were detected in any of the 11 genes tested. Conclusion Although UPF1 was substantially repressed, thus resulting in the inhibition of the NMD system, we did not find genes inactivated by nonsense mutations. Our results show that the GINI strategy leads to a high number of false positives.

Ylstra Bauke



Lentiviral Vector-based Insertional Mutagenesis Identifies Genes Involved in the Resistance to Targeted Anticancer Therapies. (United States)

The high transduction efficiency of lentiviral vectors in a wide variety of cells makes them an ideal tool for forward genetics screenings addressing issues of cancer research. Although molecular targeted therapies have provided significant advances in tumor treatment, relapses often occur by the expansion of tumor cell clones carrying mutations that confer resistance. Identification of the culprits of anticancer drug resistance is fundamental for the achievement of long-term response. Here, we developed a new lentiviral vector-based insertional mutagenesis screening to identify genes that confer resistance to clinically relevant targeted anticancer therapies. By applying this genome-wide approach to cell lines representing two subtypes of HER2(+) breast cancer, we identified 62 candidate lapatinib resistance genes. We validated the top ranking genes, i.e., PIK3CA and PIK3CB, by showing that their forced expression confers resistance to lapatinib in vitro and found that their mutation/overexpression is associated to poor prognosis in human breast tumors. Then, we successfully applied this approach to the identification of erlotinib resistance genes in pancreatic cancer, thus showing the intrinsic versatility of the approach. The acquired knowledge can help identifying combinations of targeted drugs to overcome the occurrence of resistance, thus opening new horizons for more effective treatment of tumors. PMID:25195596

Ranzani, Marco; Annunziato, Stefano; Calabria, Andrea; Brasca, Stefano; Benedicenti, Fabrizio; Gallina, Pierangela; Naldini, Luigi; Montini, Eugenio



Genome wide association analysis of a founder population identified TAF3 as a gene for MCHC in humans. (United States)

The red blood cell related traits are highly heritable but their genetics are poorly defined. Only 5-10% of the total observed variance is explained by the genetic loci found to date, suggesting that additional loci should be searched using approaches alternative to large meta analysis. GWAS (Genome Wide Association Study) for red blood cell traits in a founder population cohort from Northern Italy identified a new locus for mean corpuscular hemoglobin concentration (MCHC) in the TAF3 gene. The association was replicated in two cohorts (rs1887582, P?=?4.25E-09). TAF3 encodes a transcription cofactor that participates in core promoter recognition complex, and is involved in zebrafish and mouse erythropoiesis. We show here that TAF3 is required for transcription of the SPTA1 gene, encoding alpha spectrin, one of the proteins that link the plasma membrane to the actin cytoskeleton. Mutations in SPTA1 are responsible for hereditary spherocytosis, a monogenic disorder of MCHC, as well as for the normal MCHC level. Based on our results, we propose that TAF3 is required for normal erythropoiesis in human and that it might have a role in controlling the ratio between hemoglobin (Hb) and cell volume and in the dynamics of RBC maturation in healthy individuals. Finally, TAF3 represents a potential candidate or a modifier gene for disorders of red cell membrane. PMID:23935956

Pistis, Giorgio; Okonkwo, Shawntel U; Traglia, Michela; Sala, Cinzia; Shin, So-Youn; Masciullo, Corrado; Buetti, Iwan; Massacane, Roberto; Mangino, Massimo; Thein, Swee-Lay; Spector, Timothy D; Ganesh, Santhi; Pirastu, Nicola; Gasparini, Paolo; Soranzo, Nicole; Camaschella, Clara; Hart, Daniel; Green, Michael R; Toniolo, Daniela



Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene. (United States)

The chromosome 16p13 region has been associated with several autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). CLEC16A has been reported as the most likely candidate gene in the region, since it contains the most disease-associated single-nucleotide polymorphisms (SNPs), as well as an imunoreceptor tyrosine-based activation motif. However, here we report that intron 19 of CLEC16A, containing the most autoimmune disease-associated SNPs, appears to behave as a regulatory sequence, affecting the expression of a neighbouring gene, DEXI. The CLEC16A alleles that are protective from T1D and MS are associated with increased expression of DEXI, and no other genes in the region, in two independent monocyte gene expression data sets. Critically, using chromosome conformation capture (3C), we identified physical proximity between the DEXI promoter region and intron 19 of CLEC16A, separated by a loop of >150 kb. In reciprocal experiments, a 20 kb fragment of intron 19 of CLEC16A, containing SNPs associated with T1D and MS, as well as with DEXI expression, interacted with the promotor region of DEXI but not with candidate DNA fragments containing other potential causal genes in the region, including CLEC16A. Intron 19 of CLEC16A is highly enriched for transcription-factor-binding events and markers associated with enhancer activity. Taken together, these data indicate that although the causal variants in the 16p13 region lie within CLEC16A, DEXI is an unappreciated autoimmune disease candidate gene, and illustrate the power of the 3C approach in progressing from genome-wide association studies results to candidate causal genes. PMID:21989056

Davison, Lucy J; Wallace, Chris; Cooper, Jason D; Cope, Nathan F; Wilson, Nicola K; Smyth, Deborah J; Howson, Joanna M M; Saleh, Nada; Al-Jeffery, Abdullah; Angus, Karen L; Stevens, Helen E; Nutland, Sarah; Duley, Simon; Coulson, Richard M R; Walker, Neil M; Burren, Oliver S; Rice, Catherine M; Cambien, Francois; Zeller, Tanja; Munzel, Thomas; Lackner, Karl; Blakenberg, Stefan; Fraser, Peter; Gottgens, Berthold; Todd, John A; Attwood, Tony; Belz, Stephanie; Braund, Peter; Cambien, François; Cooper, Jason; Crisp-Hihn, Abi; Diemert, Patrick; Deloukas, Panos; Foad, Nicola; Erdmann, Jeanette; Goodall, Alison H; Gracey, Jay; Gray, Emma; Williams, Rhian G; Heimerl, Susanne; Hengstenberg, Christian; Jolley, Jennifer; Krishnan, Unni; Lloyd-Jones, Heather; Lugauer, Ingrid; Lundmark, Per; Maouche, Seraya; Moore, Jasbir S; Muir, David; Murray, Elizabeth; Nelson, Chris P; Neudert, Jessica; Niblett, David; O'Leary, Karen; Ouwehand, Willem H; Pollard, Helen; Rankin, Angela; Rice, Catherine M; Sager, Hendrik; Samani, Nilesh J; Sambrook, Jennifer; Schmitz, Gerd; Scholz, Michael; Schroeder, Laura; Schunkert, Heribert; Syvannen, Ann-Christine; Tennstedt, Stefanie; Wallace, Chris



Homeobox genes: a molecular link between development and cancer / Genes homeobox: uma relação molecular entre o desenvolvimento e o câncer  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in portuguese Os genes homeobox são genes reguladores que codificam proteínas nucleares as quais atuam como fatores de transcrição, regulando vários aspectos da morfogênese e da diferenciação celular durante o desenvolvimento embrionário normal de diversos animais. Os genes homeobox de vertebrados podem ser subdi [...] vididos em duas famílias: os agrupados, ou HOX, e os não agrupados, ou divergentes. Durante as últimas décadas, vários genes homeobox, agrupados e não agrupados, foram identificados em tecidos normais, em células malignas e em diferentes doenças e condições metabólicas. Os genes homeobox estão envolvidos, por exemplo, no desenvolvimento normal do dente e em agenesias dentárias de ocorrência familiar. O desenvolvimento normal e o câncer têm muito em comum, já que ambos envolvem proliferação celular e diferenciação. A literatura tem mostrado um número cada vez maior de trabalhos relacionando os genes homeobox à oncogênese. Muitos tipos de câncer exibem expressão ou alteração nos genes homeobox. Eles incluem leucemias, câncer de cólon, pele, próstata, mama e ovário, entre outros. Esta revisão objetiva levar os leitores a conhecer algumas das funções da família homeobox nos tecidos normais e especialmente no câncer. Abstract in english Homeobox genes are regulatory genes encoding nuclear proteins that act as transcription factors, regulating aspects of morphogenesis and cell differentiation during normal embryonic development of several animals. Vertebrate homeobox genes can be divided in two subfamilies: clustered, or HOX genes, [...] and nonclustered, or divergent, homeobox genes. During the last decades, several homeobox genes, clustered and nonclustered ones, were identified in normal tissue, in malignant cells, and in different diseases and metabolic alterations. Homeobox genes are involved in the normal teeth development and in familial teeth agenesis. Normal development and cancer have a great deal in common, as both processes involve shifts between cell proliferation and differentiation. The literature is accumulating evidences that homeobox genes play an important role in oncogenesis. Many cancers exhibit expression of or alteration in homeobox genes. Those include leukemias, colon, skin, prostate, breast and ovarian cancers, among others. This review is aimed at introducing readers to some of the homeobox family functions in normal tissues and especially in cancer.

Fabio Daumas, Nunes; Fernanda Campos Souza de, Almeida; Renata, Tucci; Suzana Cantanhede Orsini Machado de, Sousa.



Large-Scale Evaluation of Candidate Genes Identifies Associations between VEGF Polymorphisms and Bladder Cancer Risk  


Common genetic variation could alter the risk for developing bladder cancer. We conducted a large-scale evaluation of single nucleotide polymorphisms (SNPs) in candidate genes for cancer to identify common variants that influence bladder cancer risk. An Illumina GoldenGate assay was used to genotype 1,433 SNPs within or near 386 genes in 1,086 cases and 1,033 controls in Spain. The most significant finding was in the 5? UTR of VEGF (rs25648, p for likelihood ratio test, 2 degrees of freedom...

Garci?a-closas, Montserrat; Malats, Nu?ria; Real, Francisco X.; Yeager, Meredith; Welch, Robert; Silverman, Debra; Kogevinas, Manolis; Dosemeci, Mustafa; Figueroa, Jonine; Chatterjee, Nilanjan; Tardo?n, Adonina; Serra, Consol; Carrato, Alfredo; Garci?a-closas, Reina; Murta-nascimento, Cristiane



Gene expression of TLR homologues identified by genome-wide screening of the earthworm Dendrobaena veneta. (United States)

TLRs represent one of the most important components of innate immunity. Currently, these receptors have been extensively studied in vertebrates and insects, but our knowledge for annelids is very limited. Therefore, the aim of our study was to identify earthworm TLR homologs by genome-wide screening, and to determine the expression of candidate genes as a response to Gram-positive and Gram-negative bacteria. Using a combination of deep pyrosequencing and quantitative PCR we found six candidate genes, for which all were expressed in Dentrobaena veneta. Two of the candidates showed significant response to bacterial exposure. In conclusion, TLRs seem to have a role in earthworm immunology. PMID:24574024

Fjøsne, Trine F; Stenseth, Else-Berit; Myromslien, Frøydis; Rudi, Knut



Mayo Clinic study identifies optimal gene targets for new colon cancer test (United States)

A study presented today by Mayo Clinic researchers at the American Association for Cancer Research(AACR) Annual Meeting 2012 in Chicago identified two genes that are optimal targets to be analyzed in a new noninvasive test for colorectal cancer developed by Mayo Clinic, in collaboration with Exact Sciences Corporation. The test uses a small sample of a patient's stool to check for specific DNA changes, known as gene methylation, that occur as cancer develops. The test can quickly detect both early stage cancer and precancerous polyps.


Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications  

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Full Text Available Abstract Background The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several large-throughput datasets. Understanding the underlying evolutionary dynamics is crucial for discerning random parts of the network from biologically important properties shaped by natural selection. Results We present a detailed statistical analysis of the protein interactions in Saccharomyces cerevisiae based on several large-throughput datasets. Protein pairs resulting from gene duplications are used as tracers into the evolutionary past of the network. From this analysis, we infer rate estimates for two key evolutionary processes shaping the network: (i gene duplications and (ii gain and loss of interactions through mutations in existing proteins, which are referred to as link dynamics. Importantly, the link dynamics is asymmetric, i.e., the evolutionary steps are mutations in just one of the binding parters. The link turnover is shown to be much faster than gene duplications. Both processes are assembled into an empirically grounded, quantitative model for the evolution of protein interaction networks. Conclusions According to this model, the link dynamics is the dominant evolutionary force shaping the statistical structure of the network, while the slower gene duplication dynamics mainly affects its size. Specifically, the model predicts (i a broad distribution of the connectivities (i.e., the number of binding partners of a protein and (ii correlations between the connectivities of interacting proteins, a specific consequence of the asymmetry of the link dynamics. Both features have been observed in the protein interaction network of S. cerevisiae.

Wagner Andreas



Search for a Microsatellite Marker Linked with Resistance Gene to Xanthomonas axonopodis pv. malvacearum in Brazilian Cotton  

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Full Text Available The cotton cultivar DELTAOPAL is resistant under field as well as under glasshouse conditions to the Brazilian isolates of Xanthomonas axonopodis pv. malvacearum (Xam. Segregating populations derived from the cross between this cultivar and one susceptible cv. BRS ITA 90, were utilized to identify molecular marker linked with the resistance gene to Xam by “Bulk Segregant Analysis (BSA”. Two hundred and twenty microsatellite (Single Sequence Repeat—SSR primers were tested. The amplification products were visualized in polyacrylamide gels stained with silver nitrate. Only one primer was informative and showed polymorphism between the DNA of the parents and their respective bulks of homozygous F2 populations contrasting for resistance and susceptibility, and hence was used to analyze DNA of 120 F2 populations. The microsatellite primer yielded one band of 80 bp linked with the resistance locus, which was absent in the susceptible parent as well as in the bulk of the homozygous susceptible plants of the cross. The segregation ratio as determined by phenotypic analysis was 3R:1S. It is believed that the microsatellite marker was linked with the resistance locus and hence may offer new perspectives for marker assisted selection against the angular leaf spot disease of cotton. It is however, felt necessary to repeat the microsatellite analysis and make sure that the primer is tightly linked with the resistance locus and at the same time verify the genetic distance between the marker and the resistance locus.

Mariana Marangoni



Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing. (United States)

Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development and seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed, and renewable resources. Little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. As a first step toward understanding these networks, we profiled all mRNAs in the maize kernel and endosperm at eight successive stages during the first 12 d after pollination. Analysis of these gene sets identified temporal programs of gene expression, including hundreds of transcription-factor genes. We found a close correlation of the sequentially expressed gene sets with distinct cellular and metabolic programs in distinct compartments of the developing endosperm. The results constitute a preliminary atlas of spatiotemporal patterns of endosperm gene expression in support of future efforts for understanding the underlying mechanisms that control seed yield and quality. PMID:24821765

Li, Guosheng; Wang, Dongfang; Yang, Ruolin; Logan, Kyle; Chen, Hao; Zhang, Shanshan; Skaggs, Megan I; Lloyd, Alan; Burnett, William J; Laurie, John D; Hunter, Brenda G; Dannenhoffer, Joanne M; Larkins, Brian A; Drews, Gary N; Wang, Xiangfeng; Yadegari, Ramin



Quantitative analysis of bristle number in Drosophila mutants identifies genes involved in neural development (United States)

BACKGROUND: The identification of the function of all genes that contribute to specific biological processes and complex traits is one of the major challenges in the postgenomic era. One approach is to employ forward genetic screens in genetically tractable model organisms. In Drosophila melanogaster, P element-mediated insertional mutagenesis is a versatile tool for the dissection of molecular pathways, and there is an ongoing effort to tag every gene with a P element insertion. However, the vast majority of P element insertion lines are viable and fertile as homozygotes and do not exhibit obvious phenotypic defects, perhaps because of the tendency for P elements to insert 5' of transcription units. Quantitative genetic analysis of subtle effects of P element mutations that have been induced in an isogenic background may be a highly efficient method for functional genome annotation. RESULTS: Here, we have tested the efficacy of this strategy by assessing the extent to which screening for quantitative effects of P elements on sensory bristle number can identify genes affecting neural development. We find that such quantitative screens uncover an unusually large number of genes that are known to function in neural development, as well as genes with yet uncharacterized effects on neural development, and novel loci. CONCLUSIONS: Our findings establish the use of quantitative trait analysis for functional genome annotation through forward genetics. Similar analyses of quantitative effects of P element insertions will facilitate our understanding of the genes affecting many other complex traits in Drosophila.

Norga, Koenraad K.; Gurganus, Marjorie C.; Dilda, Christy L.; Yamamoto, Akihiko; Lyman, Richard F.; Patel, Prajal H.; Rubin, Gerald M.; Hoskins, Roger A.; Mackay, Trudy F.; Bellen, Hugo J.



Whole-exome sequencing identifies rare pathogenic variants in new predisposition genes for familial colorectal cancer. (United States)

Purpose:Colorectal cancer is an important cause of mortality in the developed world. Hereditary forms are due to germ-line mutations in APC, MUTYH, and the mismatch repair genes, but many cases present familial aggregation but an unknown inherited cause. The hypothesis of rare high-penetrance mutations in new genes is a likely explanation for the underlying predisposition in some of these familial cases.Methods:Exome sequencing was performed in 43 patients with colorectal cancer from 29 families with strong disease aggregation without mutations in known hereditary colorectal cancer genes. Data analysis selected only very rare variants (0-0.1%), producing a putative loss of function and located in genes with a role compatible with cancer. Variants in genes previously involved in hereditary colorectal cancer or nearby previous colorectal cancer genome-wide association study hits were also chosen.Results:Twenty-eight final candidate variants were selected and validated by Sanger sequencing. Correct family segregation and somatic studies were used to categorize the most interesting variants in CDKN1B, XRCC4, EPHX1, NFKBIZ, SMARCA4, and BARD1.Conclusion:We identified new potential colorectal cancer predisposition variants in genes that have a role in cancer predisposition and are involved in DNA repair and the cell cycle, which supports their putative involvement in germ-line predisposition to this neoplasm.Genet Med advance online publication 24 July 2014Genetics in Medicine (2014); doi:10.1038/gim.2014.89. PMID:25058500

Esteban-Jurado, Clara; Vila-Casadesús, Maria; Garre, Pilar; Lozano, Juan José; Pristoupilova, Anna; Beltran, Sergi; Muñoz, Jenifer; Ocaña, Teresa; Balaguer, Francesc; López-Cerón, Maria; Cuatrecasas, Miriam; Franch-Expósito, Sebastià; Piqué, Josep M; Castells, Antoni; Carracedo, Angel; Ruiz-Ponte, Clara; Abulí, Anna; Bessa, Xavier; Andreu, Montserrat; Bujanda, Luis; Caldés, Trinidad; Castellví-Bel, Sergi



hCTR1: a human gene for copper uptake identified by complementation in yeast. (United States)

The molecular mechanisms responsible for the cellular uptake of copper in mammalian cells are unknown. We describe isolation of a human gene involved in this process by complementation of the yeast high-affinity copper uptake mutant, ctr1. Besides complementing ctr1 growth defect on nonfermentable media, the human gene also rescues iron transport and SOD1 defects in ctr1 yeast. Overexpression of the gene in yeast leads to vulnerability to the toxicity of copper overload. In addition, its expression in ctr1 yeast significantly increases the level of cellular copper, as demonstrated by atomic absorption. We propose this gene as a candidate for high-affinity copper uptake in humans and by analogy have named it hCTR1. The hCTR1 and yeast CTR1 predicted transmembrane proteins are 29% identical, but the human protein is substantially smaller in both the extracellular metal-binding and intracellular domains. An additional human gene similar to hCTR1, here named hCTR2, was identified in a database search. Both hCTR1 and hCTR2 are expressed in all human tissues examined, and both genes are located in 9q31/32. These studies, together with the previously recognized functional and sequence similarity between the Menkes/Wilson copper export proteins and CCC2 in yeast, demonstrate that similar copper homeostatic mechanisms are used in these evolutionarily divergent organisms. PMID:9207117

Zhou, B; Gitschier, J



Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life  

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Full Text Available Abstract Background Seagrasses are a polyphyletic group of monocotyledonous angiosperms that have adapted to a completely submerged lifestyle in marine waters. Here, we exploit two collections of expressed sequence tags (ESTs of two wide-spread and ecologically important seagrass species, the Mediterranean seagrass Posidonia oceanica (L. Delile and the eelgrass Zostera marina L., which have independently evolved from aquatic ancestors. This replicated, yet independent evolutionary history facilitates the identification of traits that may have evolved in parallel and are possible instrumental candidates for adaptation to a marine habitat. Results In our study, we provide the first quantitative perspective on molecular adaptations in two seagrass species. By constructing orthologous gene clusters shared between two seagrasses (Z. marina and P. oceanica and eight distantly related terrestrial angiosperm species, 51 genes could be identified with detection of positive selection along the seagrass branches of the phylogenetic tree. Characterization of these positively selected genes using KEGG pathways and the Gene Ontology uncovered that these genes are mostly involved in translation, metabolism, and photosynthesis. Conclusions These results provide first insights into which seagrass genes have diverged from their terrestrial counterparts via an initial aquatic stage characteristic of the order and to the derived fully-marine stage characteristic of seagrasses. We discuss how adaptive changes in these processes may have contributed to the evolution towards an aquatic and marine existence.

Reusch Thorsten BH



Identifying candidate genes affecting developmental time in Drosophila melanogaster: pervasive pleiotropy and gene-by-environment interaction  

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Full Text Available Abstract Background Understanding the genetic architecture of ecologically relevant adaptive traits requires the contribution of developmental and evolutionary biology. The time to reach the age of reproduction is a complex life history trait commonly known as developmental time. In particular, in holometabolous insects that occupy ephemeral habitats, like fruit flies, the impact of developmental time on fitness is further exaggerated. The present work is one of the first systematic studies of the genetic basis of developmental time, in which we also evaluate the impact of environmental variation on the expression of the trait. Results 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°C. Sixty percent of the lines showed a heterochronic phenotype, suggesting that a large number of genes affect this trait. Mutant lines for the genes Merlin and Karl showed the most extreme phenotypes exhibiting a developmental time reduction and increase, respectively, of over 2 days and 4 days relative to the control (a co-isogenic P-element insertion free line. In addition, a subset of 42 lines selected at random from the initial set of 179 lines was screened at 17°C. Interestingly, the gene-by-environment interaction accounted for 52% of total phenotypic variance. Plastic reaction norms were found for a large number of developmental time candidate genes. Conclusion We identified components of several integrated time-dependent pathways affecting egg-to-adult developmental time in Drosophila. At the same time, we also show that many heterochronic phenotypes may arise from changes in genes involved in several developmental mechanisms that do not explicitly control the timing of specific events. We also demonstrate that many developmental time genes have pleiotropic effects on several adult traits and that the action of most of them is sensitive to temperature during development. Taken together, our results stress the need to take into account the effect of environmental variation and the dynamics of gene interactions on the genetic architecture of this complex life-history trait.

Hasson Esteban



Identifying genes related to choriogenesis in insect panoistic ovaries by Suppression Subtractive Hybridization  

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Full Text Available Abstract Background Insect ovarioles are classified into two categories: panoistic and meroistic, the later having apparently evolved from an ancestral panoistic type. Molecular data on oogenesis is practically restricted to meroistic ovaries. If we aim at studying the evolutionary transition from panoistic to meroistic, data on panoistic ovaries should be gathered. To this end, we planned the construction of a Suppression Subtractive Hybridization (SSH library to identify genes involved in panoistic choriogenesis, using the cockroach Blattella germanica as model. Results We constructed a post-vitellogenic ovary library by SSH to isolate genes involved in choriogenesis in B. germanica. The tester library was prepared with an ovary pool from 6- to 7-day-old females, whereas the driver library was prepared with an ovary pool from 3- to 4-day-old females. From the SSH library, we obtained 258 high quality sequences which clustered into 34 unique sequences grouped in 19 contigs and 15 singlets. The sequences were compared against non-redundant NCBI databases using BLAST. We found that 44% of the unique sequences had homologous sequences in known genes of other organisms, whereas 56% had no significant similarity to any of the databases entries. A Gene Ontology analysis was carried out, classifying the 34 sequences into different functional categories. Seven of these gene sequences, representative of different categories and processes, were chosen to perform expression studies during the first gonadotrophic cycle by real-time PCR. Results showed that they were mainly expressed during post-vitellogenesis, which validates the SSH technique. In two of them corresponding to novel genes, we demonstrated that they are specifically expressed in the cytoplasm of follicular cells in basal oocytes at the time of choriogenesis. Conclusion The SSH approach has proven to be useful in identifying ovarian genes expressed after vitellogenesis in B. germanica. For most of the genes, functions related to choriogenesis are postulated. The relatively high percentage of novel genes obtained and the practical absence of chorion genes typical of meroistic ovaries suggest that mechanisms regulating chorion formation in panoistic ovaries are significantly different from those of meroistic ones.

Bellés Xavier



A microarray approach to identify genes known only by their mutant phenotype  

International Nuclear Information System (INIS)

The Scandinavian barley (Hordeum vulgare L.) mutant collection contains 357 mutants representing 105 loci deficient in chloroplast development and chlorophyll biosynthesis. A few of the mutants are spontaneous, but the majority has been induced by various irradiation and chemical treatments. Less than ten of the loci (corresponding to 30 mutations) have been connected to a gene at the DNA level. In order to identify other genes deficient in the collection we have developed a cDNA microarray approach. Three barley mutant strains, xantha-h.57, xantha-f.27 and xantha-g.28, with known mutations in the genes encoding the three subunits of the chlorophyll biosynthetic enzyme magnesium chelatase, were used for the development of the microarray method. The mutation xantha-h.57 prevents transcription of Xantha-h mRNA. Microarrays were prepared by robotic spotting of PCR products from 968 clones at 1760 positions. Most material was from cloned ESTs (expressed sequence tags). The barley Xantha-h gene was printed at six positions in duplicate. cDNA from the three mutant strains were differentially labeled with fluorescent nucleotides. Labeled cDNA from one mutant was mixed in equal amounts with labeled cDNA of another mutant and competitively hybridized to the microarrayed clones. The combination of labeled cDNA from xantha-h.57 with that of xantha-f.27 or xantha-g.28 specifically highlighted the positions representing the Xantha-h gene on the microarrays. We regard these experimn the microarrays. We regard these experiments as a demonstration that microarrays provide a very promising method for screening large DNA libraries in order to clone genes known only through their mutant phenotype. This opens up a new way of using the microarray technology for cloning genes from eukaryotes with complex genomes for which genome sequencing is unlikely to proceed. Our results also put the many available plant mutant collections in focus as treasuries for gene hunters. (author)


Library screen identifies Enterococcus faecalis CcpA, the catabolite control protein A, as an effector of Ace, a collagen adhesion protein linked to virulence. (United States)

The Enterococcus faecalis cell wall-anchored protein Ace is an important virulence factor involved in cell adhesion and infection. Expression of Ace on the cell surface is affected by many factors, including stage of growth, culture temperature, and environmental components, such as serum, urine, and collagen. However, the mechanisms that regulate or modulate Ace display are not well understood. With interest in identifying genes associated with Ace expression, we utilized a whole-cell enzyme-linked immunosorbent assay (ELISA)-based screening method to identify mutants from a transposon insertion mutant library which exhibited distinct Ace surface expression profiles. We identified a ccpA insertion mutant which showed significantly decreased levels of Ace surface expression at early growth phase versus those of wild-type OG1RF. Confirmation of the observation was achieved through flow cytometry and complementation analysis. Compared to the wild type, the E. faecalis ccpA mutant had an impaired ability to adhere to collagen when grown to early exponential phase, consistent with the lack of Ace expression in the early growth phase. As a key component of carbon catabolite regulation, CcpA has been previously reported to play a critical role in regulating expression of proteins involved in E. faecalis carbohydrate uptake and utilization. Our discovery is the first to associate CcpA with the production of a major E. faecalis virulence factor, providing new insights into the regulation of E. faecalis pathogenesis. PMID:23974022

Gao, Peng; Pinkston, Kenneth L; Bourgogne, Agathe; Cruz, Melissa R; Garsin, Danielle A; Murray, Barbara E; Harvey, Barrett R



Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes. (United States)

We genotyped a Chinese and an Indian-origin rhesus macaque using the Affymetrix Genome-Wide Human SNP Array 6.0 and cataloged 85,473 uniquely mapping heterospecific SNPs. These SNPs were assigned to rhesus chromosomes according to their probe sequence alignments as displayed in the human and rhesus reference sequences. The conserved gene order (synteny) revealed by heterospecific SNP maps is in concordance with that of the published human and rhesus macaque genomes. Using these SNPs' original human rs numbers, we identified 12,328 genes annotated in humans that are associated with these SNPs, 3674 of which were found in at least one of the two rhesus macaques studied. Due to their density, the heterospecific SNPs allow fine-grained comparisons, including approximate boundaries of intra- and extra-chromosomal rearrangements involving gene orthologs, which can be used to distinguish rhesus macaque chromosomes from human chromosomes. PMID:22982528

Kanthaswamy, Sree; Ng, Jillian; Ross, Cody T; Trask, Jessica Satkoski; Smith, David Glenn; Buffalo, Vince S; Fass, Joseph N; Lin, Dawei



Localisation of the MRX3 gene for non-specific X linked mental retardation.  


A family is described with five affected males segregating a new gene for non-specific X linked mental retardation (MRX). Linkage analysis localised the gene at Xq28-qter. The maximum lod score was 2.89 with DXS52 (St14) at theta = 0.0. A recombinant was observed with DXS304 (U6.2) defining the proximal limit to the localisation. No evidence for linkage was determined using markers at several points along the remainder of the X chromosome, including the regions known to contain MRX1 and MRX2....

Gedeon, A.; Kerr, B.; Mulley, J.; Turner, G.



Mis-splicing of the ABCC2 gene linked with Bt toxin resistance in Helicoverpa armigera  


Toxins from the bacterium Bacillus thuringiensis (Bt) are used widely for insect control in sprays and transgenic plants, but their efficacy is reduced when pests evolve resistance. Previous work showed that mutations in a gene encoding the transporter protein ABCC2 are linked with resistance to Bt toxins Cry1Ab, Cry1Ac or both in four species of Lepidoptera. Here we compared the ABCC2 gene of Helicoverpa armigera (HaABCC2) between susceptible strains and a laboratory-selected strain with >1,...

Xiao, Yutao; Zhang, Tao; Liu, Chenxi; Heckel, David G.; Li, Xianchun; Tabashnik, Bruce E.; Wu, Kongming



Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds  

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Full Text Available Abstract Background DNA barcoding of life using a standardized COI sequence was proposed as a species identification system, and as a method for detecting putative new species. Previous tests in birds showed that individuals can be correctly assigned to species in ~94% of the cases and suggested a threshold of 10× mean intraspecific difference to detect potential new species. However, these tests were criticized because they were based on a single maternally inherited gene rather than multiple nuclear genes, did not compare phylogenetically identified sister species, and thus likely overestimated the efficacy of DNA barcodes in identifying species. Results To test the efficacy of DNA barcodes we compared ~650 bp of COI in 60 sister-species pairs identified in multigene phylogenies from 10 orders of birds. In all pairs, individuals of each species were monophyletic in a neighbor-joining (NJ tree, and each species possessed fixed mutational differences distinguishing them from their sister species. Consequently, individuals were correctly assigned to species using a statistical coalescent framework. A coalescent test of taxonomic distinctiveness based on chance occurrence of reciprocal monophyly in two lineages was verified in known sister species, and used to identify recently separated lineages that represent putative species. This approach avoids the use of a universal distance cutoff which is invalidated by variation in times to common ancestry of sister species and in rates of evolution. Conclusion Closely related sister species of birds can be identified reliably by barcodes of fixed diagnostic substitutions in COI sequences, verifying coalescent-based statistical tests of reciprocal monophyly for taxonomic distinctiveness. Contrary to recent criticisms, a single DNA barcode is a rapid way to discover monophyletic lineages within a metapopulation that might represent undiscovered cryptic species, as envisaged in the unified species concept. This identifies a smaller set of lineages that can also be tested independently for species status with multiple nuclear gene approaches and other phenotypic characters.

Baker Allan J



Genome-wide screen identifies drug-induced regulation of the gene giant axonal neuropathy (Gan) in a mouse model of antiretroviral-induced painful peripheral neuropathy. (United States)

Painful peripheral neuropathy is a debilitating complication of the treatment of HIV with nucleoside reverse transcriptase inhibitors (NRTIs). Patients are living longer with these drugs; however many develop excruciating, unremitting, and often treatment-limiting neuropathy that is resistant to conventional pain management therapies. Improving patient comfort and quality of life is paramount and depends on a clearer understanding of this devastating side effect. The mechanisms underlying the development of NRTI-induced neuropathy, however, remain unclear. Using a mouse model of NRTI-induced neuropathy, the authors conducted an unbiased whole-genome microarray screen to identify molecular targets in the spinal dorsal horn, which is the location where integration of ascending sensory transmission and descending modulatory effects occur. Analysis of the microarray data identified a change in the gene giant axonal neuropathy 1 (Gan1). Mutation of this gene has been linked to the development of giant axonal neuropathy (GAN), a rare autosomal recessive condition characterized by a progressive sensorimotor neuropathy. Gan1 has not been previously linked to nerve pathologies in other populations. In this study, downregulation of the Gan1 gene and the gene protein product, gigaxonin, was validated via quantitative polymerase chain reaction ([qPCR] gene expression) and Western blot analyses (protein level). Our report is the first to suggest that Gan1 might be a novel molecular target in the development of NRTI-induced peripheral neuropathy with implications for new therapeutic approaches to preventing or reducing a significant side effect of HIV treatment. PMID:19398414

Dorsey, Susan G; Leitch, Carmen C; Renn, Cynthia L; Lessans, Sherrie; Smith, Barbara A; Wang, Xiao M; Dionne, Raymond A



Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci. (United States)

Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ?50,000 SNP genotyping array (the ITMAT-Broad-CARe array) covering ?2,000 candidate genes. SNP-lipid associations were replicated either in a cohort comprising an additional 24,736 samples or within the Global Lipid Genetic Consortium. We identified four, six, ten, and four unreported SNPs in established lipid genes for HDL-C, LDL-C, TC, and TGs, respectively. We also identified several lipid-related SNPs in previously unreported genes: DGAT2, HCAR2, GPIHBP1, PPARG, and FTO for HDL-C; SOCS3, APOH, SPTY2D1, BRCA2, and VLDLR for LDL-C; SOCS3, UGT1A1, BRCA2, UBE3B, FCGR2A, CHUK, and INSIG2 for TC; and SERPINF2, C4B, GCK, GATA4, INSR, and LPAL2 for TGs. The proportion of explained phenotypic variance in the subset of studies providing individual-level data was 9.9% for HDL-C, 9.5% for LDL-C, 10.3% for TC, and 8.0% for TGs. This large meta-analysis of lipid phenotypes with the use of a dense gene-centric approach identified multiple SNPs not previously described in established lipid genes and several previously unknown loci. The explained phenotypic variance from this approach was comparable to that from a meta-analysis of GWAS data, suggesting that a focused genotyping approach can further increase the understanding of heritability of plasma lipids. PMID:23063622

Asselbergs, Folkert W; Guo, Yiran; van Iperen, Erik P A; Sivapalaratnam, Suthesh; Tragante, Vinicius; Lanktree, Matthew B; Lange, Leslie A; Almoguera, Berta; Appelman, Yolande E; Barnard, John; Baumert, Jens; Beitelshees, Amber L; Bhangale, Tushar R; Chen, Yii-Der Ida; Gaunt, Tom R; Gong, Yan; Hopewell, Jemma C; Johnson, Toby; Kleber, Marcus E; Langaee, Taimour Y; Li, Mingyao; Li, Yun R; Liu, Kiang; McDonough, Caitrin W; Meijs, Matthijs F L; Middelberg, Rita P S; Musunuru, Kiran; Nelson, Christopher P; O'Connell, Jeffery R; Padmanabhan, Sandosh; Pankow, James S; Pankratz, Nathan; Rafelt, Suzanne; Rajagopalan, Ramakrishnan; Romaine, Simon P R; Schork, Nicholas J; Shaffer, Jonathan; Shen, Haiqing; Smith, Erin N; Tischfield, Sam E; van der Most, Peter J; van Vliet-Ostaptchouk, Jana V; Verweij, Niek; Volcik, Kelly A; Zhang, Li; Bailey, Kent R; Bailey, Kristian M; Bauer, Florianne; Boer, Jolanda M A; Braund, Peter S; Burt, Amber; Burton, Paul R; Buxbaum, Sarah G; Chen, Wei; Cooper-Dehoff, Rhonda M; Cupples, L Adrienne; deJong, Jonas S; Delles, Christian; Duggan, David; Fornage, Myriam; Furlong, Clement E; Glazer, Nicole; Gums, John G; Hastie, Claire; Holmes, Michael V; Illig, Thomas; Kirkland, Susan A; Kivimaki, Mika; Klein, Ronald; Klein, Barbara E; Kooperberg, Charles; Kottke-Marchant, Kandice; Kumari, Meena; LaCroix, Andrea Z; Mallela, Laya; Murugesan, Gurunathan; Ordovas, Jose; Ouwehand, Willem H; Post, Wendy S; Saxena, Richa; Scharnagl, Hubert; Schreiner, Pamela J; Shah, Tina; Shields, Denis C; Shimbo, Daichi; Srinivasan, Sathanur R; Stolk, Ronald P; Swerdlow, Daniel I; Taylor, Herman A; Topol, Eric J; Toskala, Elina; van Pelt, Joost L; van Setten, Jessica; Yusuf, Salim; Whittaker, John C; Zwinderman, A H; Anand, Sonia S; Balmforth, Anthony J; Berenson, Gerald S; Bezzina, Connie R; Boehm, Bernhard O; Boerwinkle, Eric; Casas, Juan P; Caulfield, Mark J; Clarke, Robert; Connell, John M; Cruickshanks, Karen J; Davidson, Karina W; Day, Ian N M; de Bakker, Paul I W; Doevendans, Pieter A; Dominiczak, Anna F; Hall, Alistair S; Hartman, Catharina A; Hengstenberg, Christian; Hillege, Hans L; Hofker, Marten H; Humphries, Steve E; Jarvik, Gail P; Johnson, Julie A; Kaess, Bernhard M; Kathiresan, Sekar; Koenig, Wolfgang; Lawlor, Debbie A; März, Winfried; Melander, Olle; Mitchell, Braxton D; Montgomery, Grant W; Munroe, Patricia B; Murray, Sarah S; Newhouse, Stephen J; Onland-Moret, N Charlotte; Poulter, Neil; Psaty, Bruce; Redline, Susan; Rich, Stephen S; Rotter, Jerome I; Schunkert, Heribert; Sever, Peter; Shuldiner, Alan R; Silverstein, Roy L; Stanton, Alice; Thorand, Barbara; Trip, Mieke D; Tsai, Michael Y; van der Harst, Pim; van der Schoot, Ellen; van der Schouw, Yvonne T; Verschuren, W M Monique; Watkins, Hugh; Wilde, Arthur A M; Wolffenbuttel, Bruce H R; Whitfield, John B; Hovingh, G Kees; Ballantyne, Christie M; Wijmenga, Cisca; Reilly, Muredach P; Martin, Nicholas G; Wilson, James G; Rader, Daniel J; Samani, Nilesh J; Reiner, Alex P; Hegele, Robert A; Kastelein, John J P; Hingorani, Aroon D; Talmud, Philippa J; Hakonarson, Hakon; Elbers, Clara C; Keating, Brendan J; Drenos, Fotios



Identifying protein complexes based on the integration of PPI network and gene expression data. (United States)

Identification of protein complexes is crucial to understand principles of cellular organisation and predict protein functions. In this paper, a novel protein complex discovery algorithm IPCIPG is proposed based on the integration of Protein-Protein Interaction network (PPI network) and gene expression data. IPCIPG is a local search algorithm which has two versions: IPCIPG-n for identifying non-overlapping clusters and IPCIPG-o for detecting overlapping clusters. The experimental results on the yeast PPI network show that IPCIPG can identify protein complexes with specific biological meaning more effectively, precisely and comprehensively than six other algorithms: HUNTER, HC-PIN, CMC, SPICi, MOCDE and MCL. PMID:25667384

Chen, Weijie; Li, Min; Wu, Xuehong; Wang, Jianxin



Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci.  


Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ?50,000 ...

Asselbergs, Fw; Guo, Y.; Iperen, Ep; Sivapalaratnam, S.; Tragante, V.; Lanktree, Mb; Lange, La; Almoguera, B.; Appelman, Ye; Barnard, J.; Baumert, J.; Beitelshees, Al; Bhangale, Tr; Chen, Yd; Gaunt, Tr



Large-Scale Gene-Centric Meta-analysis across 32 Studies Identifies Multiple Lipid Loci  


Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ?50,000 ...

Asselbergs, Folkert w; Guo, Yiran; Van iperen, Erik p A.; Sivapalaratnam, Suthesh; Tragante, Vinicius; Lanktree, Matthew b; Lange, Leslie a; Almoguera, Berta; Appelman, Yolande e; Barnard, John; Baumert, Jens; Beitelshees, Amber l; Bhangale, Tushar r; Chen, Yii-der ida; Gaunt, Tom r



An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora  

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Full Text Available Abstract Background Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. Results Assembling the expressed sequence tags (ESTs of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. Conclusion We present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.

Colombo Carlos A



Weighted gene co-expression network analysis identifies biomarkers in glycerol kinase deficient mice. (United States)

Symptomatic glycerol kinase deficiency (GKD) is associated with episodic metabolic and central nervous system deterioration. We report here the first application of weighted gene co-expression network analysis (WGCNA) to investigate a knockout (KO) murine model of a human genetic disease. WGCNA identified networks and key hub transcripts from liver mRNA of glycerol kinase (Gyk) KO and wild-type (WT) mice. Day of life 1 (dol1) samples from KO mice contained a network module enriched for organic acid metabolism before Gyk KO mice develop organic acidemia and die on dol3-4. Furthermore, the module containing Gyk was enriched with apoptotic genes. We used causal testing to elucidate the causal relationships between intramodular hub genes Acot, Psat and Plk3. Important causal relationships are confirmed in cell cultures. We provide evidence that GK may have an apoptotic moonlighting role that is lost in GKD. This first application of WGCNA to mouse knockout data provides insights into the molecular mechanisms of GKD pathogenesis. The resulting systems-genetic gene screening method identifies candidate biomarkers for GKD. PMID:19546021

MacLennan, Nicole K; Dong, Jun; Aten, Jason E; Horvath, Steve; Rahib, Lola; Ornelas, Loren; Dipple, Katrina M; McCabe, Edward R B



Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing.  

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OAK-B135 In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3 kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection, but also highlight that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.

Hong, R. L., Hamaguchi, L., Busch, M. A., and Weigel, D.



Phylogenomic analysis identifies red algal genes of endosymbiotic origin in the chromalveolates. (United States)

Endosymbiosis has spread photosynthesis to many branches of the eukaryotic tree; however, the history of photosynthetic organelle (plastid) gain and loss remains controversial. Fortuitously, endosymbiosis may leave a genomic footprint through the transfer of endosymbiont genes to the "host" nucleus (endosymbiotic gene transfer, EGT). EGT can be detected through comparison of host genomes to uncover the history of past plastid acquisitions. Here we focus on a lineage of chlorophyll c-containing algae and protists ("chromalveolates") that are postulated to share a common red algal secondary endosymbiont. This plastid is originally of cyanobacterial origin through primary endosymbiosis and is closely related among the Plantae (i.e., red, green, and glaucophyte algae). To test these ideas, an automated phylogenomics pipeline was used with a novel unigene data set of 5,081 expressed sequence tags (ESTs) from the haptophyte alga Emiliania huxleyi and genome or EST data from other chromalveolates, red algae, plants, animals, fungi, and bacteria. We focused on nuclear-encoded proteins that are targeted to the plastid to express their function because this group of genes is expected to have phylogenies that are relatively easy to interpret. A total of 708 genes were identified in E. huxleyi that had a significant Blast hit to at least one other taxon in our data set. Forty-six of the alignments that were derived from the 708 genes contained at least one other chromalveolate (i.e., besides E. huxleyi), red and/or green algae (or land plants), and one or more cyanobacteria, whereas 15 alignments contained E. huxleyi, one or more other chromalveolates, and only cyanobacteria. Detailed phylogenetic analyses of these data sets turned up 19 cases of EGT that did not contain significant paralogy and had strong bootstrap support at the internal nodes, allowing us to confidently identify the source of the plastid-targeted gene in E. huxleyi. A total of 17 genes originated from the red algal lineage, whereas 2 genes were of green algal origin. Our data demonstrate the existence of multiple red algal genes that are shared among different chromalveolates, suggesting that at least a subset of this group may share a common origin. PMID:16357039

Li, Shenglan; Nosenko, Tetyana; Hackett, Jeremiah D; Bhattacharya, Debashish



Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments  

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Full Text Available Abstract Background Comparative genomics has put additional demands on the assessment of similarity between sequences and their clustering as means for classification. However, defining the optimal number of clusters, cluster density and boundaries for sets of potentially related sequences of genes with variable degrees of polymorphism remains a significant challenge. The aim of this study was to develop a method that would identify the cluster centroids and the optimal number of clusters for a given sensitivity level and could work equally well for the different sequence datasets. Results A novel method that combines the linear mapping hash function and multiple sequence alignment (MSA was developed. This method takes advantage of the already sorted by similarity sequences from the MSA output, and identifies the optimal number of clusters, clusters cut-offs, and clusters centroids that can represent reference gene vouchers for the different species. The linear mapping hash function can map an already ordered by similarity distance matrix to indices to reveal gaps in the values around which the optimal cut-offs of the different clusters can be identified. The method was evaluated using sets of closely related (16S rRNA gene sequences of Nocardia species and highly variable (VP1 genomic region of Enterovirus 71 sequences and outperformed existing unsupervised machine learning clustering methods and dimensionality reduction methods. This method does not require prior knowledge of the number of clusters or the distance between clusters, handles clusters of different sizes and shapes, and scales linearly with the dataset. Conclusions The combination of MSA with the linear mapping hash function is a computationally efficient way of gene sequence clustering and can be a valuable tool for the assessment of similarity, clustering of different microbial genomes, identifying reference sequences, and for the study of evolution of bacteria and viruses.

Helal Manal



Cloning of the Arabidopsis WIGGUM gene identifies a role for farnesylation in meristem development  


Control of cellular proliferation in plant meristems is important for maintaining the correct number and position of developing organs. One of the genes identified in the control of floral and apical meristem size and floral organ number in Arabidopsis thaliana is WIGGUM. In wiggum mutants, one of the most striking phenotypes is an increase in floral organ number, particularly in the sepals and petals, correlating with an increase in the width of young floral meristems. Additional phenotypes ...

Ziegelhoffer, Eva C.; Medrano, Leonard J.; Meyerowitz, Elliot M.



Genetic interactions affecting human gene expression identified by variance association mapping  


Non-additive interaction between genetic variants, or epistasis, is a possible explanation for the gap between heritability of complex traits and the variation explained by identified genetic loci. Interactions give rise to genotype dependent variance, and therefore the identification of variance quantitative trait loci can be an intermediate step to discover both epistasis and gene by environment effects (GxE). Using RNA-sequence data from lymphoblastoid cell lines (LCLs) from the TwinsUK co...

Brown, Andrew Anand; Buil, Alfonso; Vin?uela, Ana; Lappalainen, Tuuli; Zheng, Hou-feng; Richards, J. Brent; Small, Kerrin S.; Spector, Timothy D.; Dermitzakis, Emmanouil T.; Durbin, Richard



Novel Genes Identified in a High Density Genome Wide Association Study for Nicotine Dependence  


Tobacco use is a leading contributor to disability and death worldwide, and genetic factors contribute in part to the development of nicotine dependence. To identify novel genes for which natural variation contributes to the development of nicotine dependence, we performed a comprehensive genome wide association study using nicotine dependent smokers as cases and non-dependent smokers as controls. To allow the efficient, rapid, and cost effective screen of the genome, the study was carried ou...

Bierut, Laura Jean; Madden, Pamela A. F.; Breslau, Naomi; Johnson, Eric O.; Hatsukami, Dorothy; Pomerleau, Ovide F.; Swan, Gary E.; Rutter, Joni; Bertelsen, Sarah; Fox, Louis; Fugman, Douglas; Goate, Alison M.; Hinrichs, Anthony L.; Konvicka, Karel; Martin, Nicholas G.



Microsatellite Scan Identifies New Candidate Genes for Susceptibility to Alcoholic Chronic Pancreatitis in Japanese Patients  


Alcohol abuse is one of the most common risk factor for chronic pancreatitis, but the underlying pathophysiological mechanisms remain unclear. The aim of this study was to identify genes that contribute to susceptibility or resistance for alcoholic chronic pancreatitis by screening the whole genome. Sixty-five patients with alcoholic chronic pancreatitis (63 men and 2 women, mean age 55.2 years) and 99 healthy Japanese controls were enrolled in this study. This was an association study using ...

Kei Kitahara; Shigeyuki Kawa; Yoshihiko Katsuyama; Takeji Umemura; Yayoi Ozaki; Mari Takayama; Norikazu Arakura; Masao Ota



Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model  


The most common risk factor for developing hepatocellular carcinoma (HCC) is chronic infection with hepatitis B virus (HBV). To better understand the evolutionary forces driving HCC we performed a near saturating transposon mutagenesis screen in a mouse HBV model of HCC. This screen identified 21 candidate early stage drivers, and a bewildering number (2860) of candidate later stage drivers, that were enriched for genes mutated, deregulated, or that function in signaling pathways important fo...

Bard-chapeau, Emilie A.; Nguyen, Anh-tuan; Rust, Alistair G.; Sayadi, Ahmed; Lee, Philip; Chua, Belinda Q.; New, Lee-sun; Jong, Johann; Ward, Jerrold M.; Chin, Christopher Ky; Chew, Valerie; Toh, Han Chong; Abastado, Jean-pierre; Benoukraf, Touati; Soong, Richie



Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes  


Abstract Background Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of sequences that have signals concordant with conserved RNA secondary structures have been discovered in the human genome. Moreover, genome wide transcription profiling with tiling arrays indicate that the majority of the genome is transcribed. Results We have combined tilin...

Vinther Jeppe; Hedegaard Mads M; Gardner Paul P; Weile Christian



Vanderbilt-led team identifies new breast cancer gene expression pattern (United States)

A study led by Vanderbilt-Ingram Cancer Center investigators has identified a gene expression pattern that may explain why chemotherapy prior to surgery isn’t effective against some tumors and suggests new therapy options for patients with specific subtypes of breast cancer. Other investigators in the study include researchers from the Royal Marsden Hospital in London, UK; the MD Anderson Cancer Center in Houston, Texas; and the Instituto Nacional de Enfermedades Neoplásicas (INEN) in Lima, Perú.


Differentially expressed genes identified by cross-species microarray in the blind cavefish Astyanax  


Changes in gene expression were examined by microarray analysis during development of the eyed surface dwelling (surface fish) and blind cave-dwelling (cavefish) forms of the teleost Astyanax mexicanus De Filippi, 1853. The cross-species microarray used surface and cavefish RNA hybridized to a DNA chip prepared from a closely related species, the zebrafish Danio rerio Hamilton, 1822. We identified a total of 67 differentially expressed probe sets at three days post-fertilization: six upregula...

Strickler, Allen G.; Jeffery, William R.



ADA5/SPT20 links the ADA and SPT genes, which are involved in yeast transcription.  


In this report we described the cloning and characterization of ADA5, a gene identified by resistance to GAL4-VP16-mediated toxicity. ADA5 binds directly to the VP16 activation domain but not to a transcriptionally defective VP16 double point mutant. Double mutants with mutations in ada5 and other genes (ada2 or ada3) isolated by resistance to GAL4-VP16 grow like ada5 single mutants, suggesting that ADA5 is in the same pathway as the other ADA genes. Further, ADA5 cofractionates and coprecipi...

Marcus, G. A.; Horiuchi, J.; Silverman, N.; Guarente, L.



Penn study finds cancer suppressor gene links metabolism with cellular aging (United States)

It is perhaps impossible to overstate the importance of the tumor suppressor gene p53. It is the single most frequently mutated gene in human tumors. p53 keeps pre-cancerous cells in check by causing cells, among other things, to become senescent – aging at the cellular level. Loss of p53 causes cells to ignore the cellular signals that would normally make mutant or damaged cells die or stop growing. Now, a team of researchers from the Perelman School of Medicine, University of Pennsylvania (home of the Abramson Cancer Center), has identified a class of p53 target genes and regulatory molecules that represent more promising therapeutic candidates.


Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways  

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Full Text Available Abstract Background Cell lines have been used to study cancer for decades, but truly quantitative assessment of their performance as models is often lacking. We used gene expression profiling to quantitatively assess the gene expression of nine cell line models of cervical cancer. Results We find a wide variation in the extent to which different cell culture models mimic late-stage invasive cervical cancer biopsies. The lowest agreement was from monolayer HeLa cells, a common cervical cancer model; the highest agreement was from primary epithelial cells, C4-I, and C4-II cell lines. In addition, HeLa and SiHa cell lines cultured in an organotypic environment increased their correlation to cervical cancer significantly. We also find wide variation in agreement when we considered how well individual biological pathways model cervical cancer. Cell lines with an anti-correlation to cervical cancer were also identified and should be avoided. Conclusion Using gene expression profiling and quantitative analysis, we have characterized nine cell lines with respect to how well they serve as models of cervical cancer. Applying this method to individual pathways, we identified the appropriateness of particular cell lines for studying specific pathways in cervical cancer. This study will allow researchers to choose a cell line with the highest correlation to cervical cancer at a pathway level. This method is applicable to other cancers and could be used to identify the appropriate cell line and growth condition to employ when studying other cancers.

Iyer Vishwanath R



Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals  

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Full Text Available Abstract Background The usefulness of log2 transformation for cDNA microarray data has led to its widespread application to Affymetrix data. For Affymetrix data, where absolute intensities are indicative of number of transcripts, there is a systematic relationship between variance and magnitude of measurements. Application of the log2 transformation expands the scale of genes with low intensities while compressing the scale of genes with higher intensities thus reversing the mean by variance relationship. The usefulness of these transformations needs to be examined. Results Using an Affymetrix GeneChip® dataset, problems associated with applying the log2 transformation to absolute intensity data are demonstrated. Use of the spread-versus-level plot to identify an appropriate variance stabilizing transformation is presented. For the data presented, the spread-versus-level plot identified a power transformation that successfully stabilized the variance of probe set summaries. Conclusion The spread-versus-level plot is helpful to identify transformations for variance stabilization. This is robust against outliers and avoids assumption of models and maximizations.

Dumur Catherine I



Differential display identifies overexpression of the USP36 gene, encoding a deubiquitinating enzyme, in ovarian cancer  

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Full Text Available Objectives. To find potential diagnostic markers or therapeutic targets, we used differential display technique to identify genes that are over or under expressed in human ovarian cancer. Methods. Genes were initially identified by differential display between two human ovarian surface epithelium cultures and two ovarian cancer cell lines, A2780 and Caov-3. Genes were validated by relative quantitative RT-PCR and RNA in situ hybridization. Results. Twenty-eight non-redundant sequences were expressed differentially in the normal ovarian epithelium and ovarian cancer cell lines. Seven of the 28 sequences showed differential expression between normal ovary and ovarian cancer tissue by RT-PCR. USP36 was over-expressed in ovarian cancer cell lines and tissues by RT-PCR and RNA in situ hybridization. Northern blot analysis and RT-PCR revealed two transcripts for USP36 in ovarian tissue. The major transcript was more specific for ovarian cancer and was detected by RT-PCR in 9/9 ovarian cancer tissues, 3/3 cancerous ascites, 5/14 (36% sera from patients with ovarian cancer, and 0/7 sera from women without ovarian cancer. Conclusion. USP36 is overexpressed in ovarian cancer compared to normal ovary and its transcripts were identified in ascites and serum of ovarian cancer patients.

Jianduan Li, Lisa M. Olson, Zhengyan Zhang, Lina Li, Miri Bidder, Loan Nguyen, John Pfeifer, Janet S. Rader



Inactivating mutations in an SH2 domain-encoding gene in X-linked lymphoproliferative syndrome  


X-linked lymphoproliferative syndrome (XLP) is an inherited immunodeficiency characterized by increased susceptibility to Epstein–Barr virus (EBV). In affected males, primary EBV infection leads to the uncontrolled proliferation of virus-containing B cells and reactive cytotoxic T cells, often culminating in the development of high-grade lymphoma. The XLP gene has been mapped to chromosome band Xq25 through linkage analysis and the discovery of patients harboring large constitutional genomi...

Nichols, Kim E.; Harkin, D. Paul; Levitz, Seth; Krainer, Michael; Kolquist, Kathryn Ann; Genovese, Cameo; Bernard, Amy; Ferguson, Martin; Zuo, Lin; Snyder, Eric; Buckler, Alan J.; Wise, Carol; Ashley, Jennifer; Lovett, Michael; Valentine, Marcus B.



On estimation and identifiability issues of sex-linked inheritance with a case study of pigmentation in Swiss barn owl (Tyto alba). (United States)

Genetic evaluation using animal models or pedigree-based models generally assume only autosomal inheritance. Bayesian animal models provide a flexible framework for genetic evaluation, and we show how the model readily can accommodate situations where the trait of interest is influenced by both autosomal and sex-linked inheritance. This allows for simultaneous calculation of autosomal and sex-chromosomal additive genetic effects. Inferences were performed using integrated nested Laplace approximations (INLA), a nonsampling-based Bayesian inference methodology. We provide a detailed description of how to calculate the inverse of the X- or Z-chromosomal additive genetic relationship matrix, needed for inference. The case study of eumelanic spot diameter in a Swiss barn owl (Tyto alba) population shows that this trait is substantially influenced by variation in genes on the Z-chromosome ([Formula: see text] and [Formula: see text]). Further, a simulation study for this study system shows that the animal model accounting for both autosomal and sex-chromosome-linked inheritance is identifiable, that is, the two effects can be distinguished, and provides accurate inference on the variance components. PMID:24967075

Larsen, Camilla T; Holand, Anna M; Jensen, Henrik; Steinsland, Ingelin; Roulin, Alexandre



Screening of the Bruton Tyrosine Kinase (BTK Gene Mutations in 13 Iranian Patients with Presumed X-Linked Agammaglobulinemia  

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Full Text Available X-linked agammaglobulinemia (XLA is an immunodeficiency caused by mutations in the Bruton tyrosine kinase (Btk gene. In order to identify the mutations in Btk gene in Iranian patients with antibody deficiency, 13 male patients with an XLA phenotype from 11 unrelated families were enrolled as the subjects of investigation for Btk mutation analysis using PCR-SSCP followed by sequencing. Five different mutations were identified in 5 patients from 5 unrelated families. Three mutations had been reported previously including TTTG deletion in intron 15 (4 bps upstream of exon 16 boundary, nonsense point mutation (1896G>A that resulted in a premature stop codon (W588X in kinase domain, and nucleotide alteration in invariant splice donor site of exon12 (IVS12+1G>A. While 2 novel missense mutations (2084A>G, 1783T>C were identified leading to amino acid changes (I651T, Y551H. The results of this study further support the notion that molecular genetic testing represents an important tool for definitive and early diagnosis of XLA and may allow accurate carrier detection and prenatal diagnosis.

Mohammad Gharagozlou



Expression and replication studies to identify new candidate genes involved in normal hearing function. (United States)

Considerable progress has been made in identifying deafness genes, but still little is known about the genetic basis of normal variation in hearing function. We recently carried out a Genome Wide Association Study (GWAS) of quantitative hearing traits in southern European populations and found several SNPs with suggestive but none with significant association. In the current study, we followed up these SNPs to investigate which of them might show a genuine association with auditory function using alternative approaches. Firstly, we generated a shortlist of 19 genes from the published GWAS results. Secondly, we carried out immunocytochemistry to examine expression of these 19 genes in the mouse inner ear. Twelve of them showed distinctive cochlear expression patterns. Four showed expression restricted to sensory hair cells (Csmd1, Arsg, Slc16a6 and Gabrg3), one only in marginal cells of the stria vascularis (Dclk1) while the others (Ptprd, Grm8, GlyBP, Evi5, Rimbp2, Ank2, Cdh13) in multiple cochlear cell types. In the third step, we tested these 12 genes for replication of association in an independent set of samples from the Caucasus and Central Asia. Nine out of them showed nominally significant association (p<0.05). In particular, 4 were replicated at the same SNP and with the same effect direction while the remaining 5 showed a significant association in a gene-based test. Finally, to look for genotype-phenotype relationship, the audiometric profiles of the three genotypes of the most strongly associated gene variants were analyzed. Seven out of the 9 replicated genes (CDH13, GRM8, ANK2, SLC16A6, ARSG, RIMBP2 and DCLK1) showed an audiometric pattern with differences between different genotypes further supporting their role in hearing function. These data demonstrate the usefulness of this multistep approach in providing new insights into the molecular basis of hearing and may suggest new targets for treatment and prevention of hearing impairment. PMID:24454846

Girotto, Giorgia; Vuckovic, Dragana; Buniello, Annalisa; Lorente-Cánovas, Beatriz; Lewis, Morag; Gasparini, Paolo; Steel, Karen P



An evolutionary genomic approach to identify genes involved in human birth timing. (United States)

Coordination of fetal maturation with birth timing is essential for mammalian reproduction. In humans, preterm birth is a disorder of profound global health significance. The signals initiating parturition in humans have remained elusive, due to divergence in physiological mechanisms between humans and model organisms typically studied. Because of relatively large human head size and narrow birth canal cross-sectional area compared to other primates, we hypothesized that genes involved in parturition would display accelerated evolution along the human and/or higher primate phylogenetic lineages to decrease the length of gestation and promote delivery of a smaller fetus that transits the birth canal more readily. Further, we tested whether current variation in such accelerated genes contributes to preterm birth risk. Evidence from allometric scaling of gestational age suggests human gestation has been shortened relative to other primates. Consistent with our hypothesis, many genes involved in reproduction show human acceleration in their coding or adjacent noncoding regions. We screened >8,400 SNPs in 150 human accelerated genes in 165 Finnish preterm and 163 control mothers for association with preterm birth. In this cohort, the most significant association was in FSHR, and 8 of the 10 most significant SNPs were in this gene. Further evidence for association of a linkage disequilibrium block of SNPs in FSHR, rs11686474, rs11680730, rs12473870, and rs1247381 was found in African Americans. By considering human acceleration, we identified a novel gene that may be associated with preterm birth, FSHR. We anticipate other human accelerated genes will similarly be associated with preterm birth risk and elucidate essential pathways for human parturition. PMID:21533219

Plunkett, Jevon; Doniger, Scott; Orabona, Guilherme; Morgan, Thomas; Haataja, Ritva; Hallman, Mikko; Puttonen, Hilkka; Menon, Ramkumar; Kuczynski, Edward; Norwitz, Errol; Snegovskikh, Victoria; Palotie, Aarno; Peltonen, Leena; Fellman, Vineta; DeFranco, Emily A; Chaudhari, Bimal P; McGregor, Tracy L; McElroy, Jude J; Oetjens, Matthew T; Teramo, Kari; Borecki, Ingrid; Fay, Justin; Muglia, Louis



Exome sequencing identifies FANCM as a susceptibility gene for triple-negative breast cancer (United States)

Inherited predisposition to breast cancer is known to be caused by loss-of-function mutations in BRCA1, BRCA2, PALB2, CHEK2, and other genes involved in DNA repair. However, most families severely affected by breast cancer do not harbor mutations in any of these genes. In Finland, founder mutations have been observed in each of these genes, suggesting that the Finnish population may be an excellent resource for the identification of other such genes. To this end, we carried out exome sequencing of constitutional genomic DNA from 24 breast cancer patients from 11 Finnish breast cancer families. From all rare damaging variants, 22 variants in 21 DNA repair genes were genotyped in 3,166 breast cancer patients, 569 ovarian cancer patients, and 2,090 controls, all from the Helsinki or Tampere regions of Finland. In Fanconi anemia complementation gene M (FANCM), nonsense mutation c.5101C>T (p.Q1701X) was significantly more frequent among breast cancer patients than among controls [odds ratio (OR) = 1.86, 95% CI = 1.26–2.75; P = 0.0018], with particular enrichment among patients with triple-negative breast cancer (TNBC; OR = 3.56, 95% CI = 1.81–6.98, P = 0.0002). In the Helsinki and Tampere regions, respectively, carrier frequencies of FANCM p.Q1701X were 2.9% and 4.0% of breast cancer patients, 5.6% and 6.6% of TNBC patients, 2.2% of ovarian cancer patients (from Helsinki), and 1.4% and 2.5% of controls. These findings identify FANCM as a breast cancer susceptibility gene, mutations in which confer a particularly strong predisposition for TNBC. PMID:25288723

Kiiski, Johanna I.; Pelttari, Liisa M.; Khan, Sofia; Freysteinsdottir, Edda S.; Reynisdottir, Inga; Hart, Steven N.; Shimelis, Hermela; Vilske, Sara; Kallioniemi, Anne; Schleutker, Johanna; Leminen, Arto; Bützow, Ralf; Blomqvist, Carl; Barkardottir, Rosa B.; Couch, Fergus J.; Aittomäki, Kristiina; Nevanlinna, Heli



Identification of genes involved in the acetamidino group modification of the flagellin N-linked glycan of Methanococcus maripaludis. (United States)

N-linked glycosylation of protein is a posttranslational modification found in all three domains of life. The flagellin proteins of the archaeon Methanococcus maripaludis are known to be modified with an N-linked tetrasaccharide consisting of N-acetylgalactosamine (GalNAc), a diacetylated glucuronic acid (GlcNAc3NAc), an acetylated and acetamidino-modified mannuronic acid with a substituted threonine group (ManNAc3NAmA6Thr), and a novel terminal sugar residue [(5S)-2-acetamido-2,4-dideoxy-5-O-methyl-?-L-erythro-hexos-5-ulo-1,5-pyranose]. To identify genes involved in biosynthesis of the component sugars of this glycan, three genes, mmp1081, mmp1082, and mmp1083, were targeted for in-frame deletion, based on their annotation and proximity to glycosyltransferase genes known to be involved in assembly of the glycan. Mutants carrying a deletion in any of these three genes remained flagellated and motile. A strain with a deletion of mmp1081 had lower-molecular-mass flagellins in Western blots. Mass spectrometry of purified flagella revealed a truncated glycan with the terminal sugar absent and the threonine residue and the acetamidino group missing from the third sugar. No glycan modification was seen in either the ?mmp1082 or ?mmp1083 mutant grown in complex Balch III medium. However, a glycan identical to the ?mmp1081 glycan was observed when the ?mmp1082 or ?mmp1083 mutant was grown under ammonia-limited conditions. We hypothesize that MMP1082 generates ammonia and tunnels it through MMP1083 to MMP1081, which acts as the amidotransferase, modifying the third sugar residue of the M. maripaludis glycan with the acetamidino group. PMID:22408155

Jones, Gareth M; Wu, John; Ding, Yan; Uchida, Kaoru; Aizawa, Shin-Ichi; Robotham, Anna; Logan, Susan M; Kelly, John; Jarrell, Ken F



Novel mutations in the connexin 32 gene associated with X-linked Charcot-Marie-Tooth disease  

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Charcot-Marie-Tooth disease is a pathologically and genetically hetergenous group of disorders that cause a progressive neuropathy, defined pathologically by degeneration of the myelin (CMT 1) of the axon (CMT 2) of the peripheral nerves. An X-linked type of the demyelinating form of this disorder (CMT X) has recently been linked to mutations in the connexin 32 (Cx32) gene, which codes for a 284 amino acid gap junction protein found in myelinated peripheral nerve. To date some 7 different mutations in this gene have been identified as being responsible for CMT X. The majority of these predict nonconservative amino acid substitutions, while one is a frameshift mutation which predicts a premature stop at codon 21. We report the results of molecular studies on three further local CMT X kindreds. The Cx32 gene was amplified by PCR in three overlapping fragments 300-450 bp in length using leukocyte-derived DNA as template. These were either sequenced directly using a deaza dGTP sequencing protocol, or were cloned and sequenced using a TA vector. In two of the kindreds the affected members carried a point mutation which was predicted to effect a non-conservative amino acid change within the first transmembrane domain. Both of these mutations caused a restriction site alteration (the loss of an Nla III and the creation of a Pvu II, respectively), and the former mutation was observed to segregate with the clinicial phenotype in affected family members. Affected members of the third kindred, which was a very large multigenerational family that had been extensively studied previously, were shown to carry a point mutation predicted to cause a premature truncation of the Cx32 gene product in the intracellular carboxy terminus. This mutation obliterated an Rsa I site which allowed a rapid screen of several other family members.

Tan, C.; Ainsworth, P. [Victoria Hospital, Ontario (Canada)]|[Childrens Hospital of Western Ontario (Canada)



Microarray analysis identifies a common set of cellular genes modulated by different HCV replicon clones  

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Full Text Available Abstract Background Hepatitis C virus (HCV RNA synthesis and protein expression affect cell homeostasis by modulation of gene expression. The impact of HCV replication on global cell transcription has not been fully evaluated. Thus, we analysed the expression profiles of different clones of human hepatoma-derived Huh-7 cells carrying a self-replicating HCV RNA which express all viral proteins (HCV replicon system. Results First, we compared the expression profile of HCV replicon clone 21-5 with both the Huh-7 parental cells and the 21-5 cured (21-5c cells. In these latter, the HCV RNA has been eliminated by IFN-? treatment. To confirm data, we also analyzed microarray results from both the 21-5 and two other HCV replicon clones, 22-6 and 21-7, compared to the Huh-7 cells. The study was carried out by using the Applied Biosystems (AB Human Genome Survey Microarray v1.0 which provides 31,700 probes that correspond to 27,868 human genes. Microarray analysis revealed a specific transcriptional program induced by HCV in replicon cells respect to both IFN-?-cured and Huh-7 cells. From the original datasets of differentially expressed genes, we selected by Venn diagrams a final list of 38 genes modulated by HCV in all clones. Most of the 38 genes have never been described before and showed high fold-change associated with significant p-value, strongly supporting data reliability. Classification of the 38 genes by Panther System identified functional categories that were significantly enriched in this gene set, such as histones and ribosomal proteins as well as extracellular matrix and intracellular protein traffic. The dataset also included new genes involved in lipid metabolism, extracellular matrix and cytoskeletal network, which may be critical for HCV replication and pathogenesis. Conclusion Our data provide a comprehensive analysis of alterations in gene expression induced by HCV replication and reveal modulation of new genes potentially useful for selection of antiviral targets.

Gerosolimo Germano



Molecular Cloning of a Bacteroides caccae TonB-Linked Outer Membrane Protein Identified by an Inflammatory Bowel Disease Marker Antibody (United States)

Commensal enteric bacteria are a required pathogenic factor in inflammatory bowel disease (IBD), but the identity of the pertinent bacterial species is unresolved. Using an IBD-associated pANCA monoclonal antibody, a 100-kDa protein was recently characterized from an IBD clinical isolate of Bacteroides caccae (p2Lc3). In this study, consensus oligonucleotides were designed from 100-kDa peptides and used to identify a single-copy gene from the p2Lc3 genome. Sequence analysis of the genomic clone revealed a 2,844-bp (948 amino acid) open reading frame encoding features typical of the TonB-linked outer membrane protein family. This gene, termed ompW, was detected by Southern analysis only in B. caccae and was absent in other species of Bacteroides and gram-negative coliforms. The closest homologues of OmpW included the outer membrane proteins SusC of Bacteroides thetaiotaomicron and RagA of Porphyromonas gingivalis. Recombinant OmpW protein was immunoreactive with the monoclonal antibody, and serum anti-OmpW immunoglobulin A levels were elevated in a Crohn's disease patient subset. These findings suggest that OmpW may be a target of the IBD-associated immune response and reveal its structural relationship to a bacterial virulence factor of P. gingivalis and periodontal disease. PMID:11553542

Wei, Bo; Dalwadi, Harnisha; Gordon, Lynn K.; Landers, Carol; Bruckner, David; Targan, Stephan R.; Braun, Jonathan



Heterogeneous activation of the TGF? pathway in glioblastomas identified by gene expression-based classification using TGF?-responsive genes  

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Full Text Available Abstract Background TGF? has emerged as an attractive target for the therapeutic intervention of glioblastomas. Aberrant TGF? overproduction in glioblastoma and other high-grade gliomas has been reported, however, to date, none of these reports has systematically examined the components of TGF? signaling to gain a comprehensive view of TGF? activation in large cohorts of human glioma patients. Methods TGF? activation in mammalian cells leads to a transcriptional program that typically affects 5–10% of the genes in the genome. To systematically examine the status of TGF? activation in high-grade glial tumors, we compiled a gene set of transcriptional response to TGF? stimulation from tissue culture and in vivo animal studies. These genes were used to examine the status of TGF? activation in high-grade gliomas including a large cohort of glioblastomas. Unsupervised and supervised classification analysis was performed in two independent, publicly available glioma microarray datasets. Results Unsupervised and supervised classification using the TGF?-responsive gene list in two independent glial tumor gene expression data sets revealed various levels of TGF? activation in these tumors. Among glioblastomas, one of the most devastating human cancers, two subgroups were identified that showed distinct TGF? activation patterns as measured from transcriptional responses. Approximately 62% of glioblastoma samples analyzed showed strong TGF? activation, while the rest showed a weak TGF? transcriptional response. Conclusion Our findings suggest heterogeneous TGF? activation in glioblastomas, which may cause potential differences in responses to anti-TGF? therapies in these two distinct subgroups of glioblastomas patients.

Xu Xie L



Winge's sex-linked color patterns and SDL in the guppy: genes or gene complexes?  


In Poecilia reticulata, different phenotypes appear due to dominance, codominance, poligeny, or some demonstrated interallelic interactions. Recent(both molecular and classical) investigations suggest a mechanism of expression of several different loci in a single color pattern, resulting in high numbers of possible color pattern phenotypes. The color pattern seems to be determined by complex interactions of many genes (at the same locus or not, located on the same chromosome or not), ...

Valentin Petrescu-mag, I.



Linking genes to diseases with a SNPedia-Gene Wiki mashup  


Abstract Background A variety of topic-focused wikis are used in the biomedical sciences to enable the mass-collaborative synthesis and distribution of diverse bodies of knowledge. To address complex problems such as defining the relationships between genes and disease, it is important to bring the knowledge from many different domains together. Here we show how advances in wiki technology and natural language processing can be used to automatically assemble ‘meta-wikis’ ...

Good Benjamin M; Clarke Erik L; Loguercio Salvatore; Su Andrew I



Winge's sex-linked color patterns and SDL in the guppy: genes or gene complexes?  

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Full Text Available In Poecilia reticulata, different phenotypes appear due to dominance, codominance, poligeny, or some demonstrated interallelic interactions. Recent(both molecular and classical investigations suggest a mechanism of expression of several different loci in a single color pattern, resulting in high numbers of possible color pattern phenotypes. The color pattern seems to be determined by complex interactions of many genes (at the same locus or not, located on the same chromosome or not, under variable environmental conditions. For example, the Maculatus color pattern is due to the presence of  both Maculatus red and Maculatus black elements. On their turn, having in view the latest definitions of  the gene, both Maculatus red and Maculatus black could have a composite nature, too. Sexdetermination in the guppy is studied since the 1920s. The deepest mechanism of sex determination is not clear yet, but classical studies of Winge early in the past century and recent molecular studies revealed a possible composite nature of the so called master sex determining gene, located at SDL of the Y chromosome.

I. Valentin Petrescu-Mag



Stability of expression-linked surface antigen gene in Trypanosoma equiperdum. (United States)

African trypanosomes evade clearance in immune-competent hosts by periodically replacing their major surface glycoprotein with an antigenically different glycoprotein. Expression of many of these variant surface glycoproteins (VSGs) is associated with the duplication and transposition of silent basic copy genes (BCs) into unlinked genomic expression sites. The new expression-linked VSG gene copies (ELCs) are oriented with their 3' ends proximal to chromosome telomeres. Other VSG genes are activated without the production of an ELC. The 3' ends of these VSG genes are near chromosome telomeres both when they are active and when they are inactive. Recently, we have shown that activation of the VSG-1 gene in the BoTaR (Bordeaux trypanozoon antigen repertoire) serodeme of Trypanosoma equiperdum involves the duplication and transposition of a telomeric BC gene into one of at least three unlinked telomeric sites. Here we show that the VSG-1 ELC is inactivated but not eliminated in some antigenic variants derived from a VSG-1 expressor. In addition, a subsequent variant that again expresses VSG-1 has not reactivated the residual VSG-1 ELC (R-ELC), but instead contains a new, active VSG-1 ELC in an unlinked telomeric site. These results show that the simple presence of an ELC in a potential expression site is not sufficient for its expression. PMID:6320015

Buck, G A; Longacre, S; Raibaud, A; Hibner, U; Giroud, C; Baltz, T; Baltz, D; Eisen, H


Gene Expression Profiling in Hereditary, BRCA1-linked Breast Cancer: Preliminary Report  

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Full Text Available Abstract Global analysis of gene expression by DNA microarrays is nowadays a widely used tool, especially relevant for cancer research. It helps the understanding of complex biology of cancer tissue, allows identification of novel molecular markers, reveals previously unknown molecular subtypes of cancer that differ by clinical features like drug susceptibility or general prognosis. Our aim was to compare gene expression profiles in breast cancer that develop against a background of inherited predisposing mutations versus sporadic breast cancer. In this preliminary study we analysed seven hereditary, BRCA1 mutation-linked breast cancer tissues and seven sporadic cases that were carefully matched by histopathology and ER status. Additionally, we analysed 6 samples of normal breast tissue. We found that while the difference in gene expression profiles between tumour tissue and normal breast can be easily recognized by unsupervised algorithms, the difference between those two types of tumours is more discrete. However, by supervised methods of data analysis, we were able to select a set of genes that may differentiate between hereditary and sporadic tumours. The most significant difference concerns genes that code for proteins engaged in regulation of transcription, cellular metabolism, signalling, proliferation and cell death. Microarray results for chosen genes (TOB1, SEPHS2 were validated by real-time RT-PCR.

Dudaladava Volha



Transcriptional profiling of whole blood identifies a unique 5-gene signature for myelofibrosis and imminent myelofibrosis transformation  

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Identifying a distinct gene signature for myelofibrosis may yield novel information of the genes, which are responsible for progression of essential thrombocythemia and polycythemia vera towards myelofibrosis. We aimed at identifying a simple gene signature - composed of a few genes - which were selectively and highly deregulated in myelofibrosis patients. Gene expression microarray studies have been performed on whole blood from 69 patients with myeloproliferative neoplasms. Amongst the top-20 of the most upregulated genes in PMF compared to controls, we identified 5 genes (DEFA4, ELA2, OLFM4, CTSG, and AZU1), which were highly significantly deregulated in PMF only. None of these genes were significantly regulated in ET and PV patients. However, hierarchical cluster analysis showed that these genes were also highly expressed in a subset of patients with ET (n?=?1) and PV (n?=?4) transforming towards myelofibrosis and/or being featured by an aggressive phenotype. We have identified a simple 5-gene signature, which is uniquely and highly significantly deregulated in patients in transitional stages of ET and PV towards myelofibrosis and in patients with PMF only. Some of these genes are considered to be responsible for the derangement of bone marrow stroma in myelofibrosis. Accordingly, this gene-signature may reflect key processes in the pathogenesis and pathophysiology of myelofibrosis development.

Hasselbalch, Hans Carl; Skov, Vibe



Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data  

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Three-dimensional gene expression PointCloud data generated by the Berkeley Drosophila Transcription Network Project (BDTNP) provides quantitative information about the spatial and temporal expression of genes in early Drosophila embryos at cellular resolution. The BDTNP team visualizes and analyzes Point-Cloud data using the software application PointCloudXplore (PCX). To maximize the impact of novel, complex data sets, such as PointClouds, the data needs to be accessible to biologists and comprehensible to developers of analysis functions. We address this challenge by linking PCX and Matlab via a dedicated interface, thereby providing biologists seamless access to advanced data analysis functions and giving bioinformatics researchers the opportunity to integrate their analysis directly into the visualization application. To demonstrate the usefulness of this approach, we computationally model parts of the expression pattern of the gene even skipped using a genetic algorithm implemented in Matlab and integrated into PCX via our Matlab interface.

Ruebel, Oliver; Keranen, Soile V.E.; Biggin, Mark; Knowles, David W.; Weber, Gunther H.; Hagen, Hans; Hamann, Bernd; Bethel, E. Wes



A case of familial X-linked thrombocytopenia with a novel WAS gene mutation  

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Full Text Available Wiskott-Aldrich syndrome (WAS is an inherited X-linked disorder. The WAS gene is located on the X chromosome and undergoes mutations, which affect various domains of the WAS protein, resulting in recurrent infection, eczema, and thrombocytopenia. However, the clinical features and severity of the disease vary according to the type of mutations in the WAS gene. Here, we describe the case of a 4-year-old boy with a history of marked thrombocytopenia since birth, who presented with recurrent herpes simplex infection and late onset of eczema. Examination of his family history revealed that older brother, who died from intracranial hemorrhage, had chronic idiopathic thrombocytopenia. Therefore, we proceeded with genetic analysis and found a new deletion mutation in the WAS gene: c.858delC (p.ser287Leufs*21 as a hemizygous form.

Eu Kyoung Lee



GATA4 knockdown in MA-10 Leydig cells identifies multiple target genes in the steroidogenic pathway. (United States)

GATA4 is an essential transcription factor required for the initiation of genital ridge formation, for normal testicular and ovarian differentiation at the time of sex determination, and for male and female fertility in adulthood. In spite of its crucial roles, the genes and/or gene networks that are ultimately regulated by GATA4 in gonadal tissues remain to be fully understood. This is particularly true for the steroidogenic lineages such as Leydig cells of the testis where many in vitro (promoter) studies have provided good circumstantial evidence that GATA4 is a key regulator of Leydig cell gene expression and steroidogenesis, but formal proof is still lacking. We therefore performed a microarray screening analysis of MA-10 Leydig cells in which Gata4 expression was knocked down using an siRNA strategy. Analysis identified several GATA4-regulated pathways including cholesterol synthesis, cholesterol transport, and especially steroidogenesis. A decrease in GATA4 protein was associated with decreased expression of steroidogenic genes previously suspected to be GATA4 targets such as Cyp11a1 and Star. Gata4 knockdown also led to an important decrease in other novel steroidogenic targets including Srd5a1, Gsta3, Hsd3b1, and Hsd3b6, as well as genes known to participate in cholesterol metabolism such as Scarb1, Ldlr, Soat1, Scap, and Cyp51. Consistent with the decreased expression of these genes, a reduction in GATA4 protein compromised the ability of MA-10 cells to produce steroids both basally and under hormone stimulation. These data therefore provide strong evidence that GATA4 is an essential transcription factor that sits atop of the Leydig cell steroidogenic program. PMID:25504870

Bergeron, Francis; Nadeau, Gabriel; S Viger, Robert



The medicinal leech genome encodes 21 innexin genes: different combinations are expressed by identified central neurons. (United States)

Gap junctional proteins are important components of signaling pathways required for the development and ongoing functions of all animal tissues, particularly the nervous system, where they function in the intracellular and extracellular exchange of small signaling factors and ions. In animals whose genomes have been sufficiently sequenced, large families of these proteins, connexins, pannexins, and innexins, have been found, with 25 innexins in the nematode Caenorhabditis elegans Starich et al. (Cell Commun Adhes 8: 311-314, 2001) and at least 37 connexins in the zebrafish Danio rerio Cruciani and Mikalsen (Biol Chem 388:253-264, 2009). Having recently sequenced the medicinal leech Hirudo verbana genome, we now report the presence of 21 innexin genes in this species, nine more than we had previously reported from the analysis of an EST-derived transcriptomic database Dykes and Macagno (Dev Genes Evol 216: 185-97, 2006); Macagno et al. (BMC Genomics 25:407, 2010). Gene structure analyses show that, depending on the leech innexin gene, they can contain from 0 to 6 introns, with closely related paralogs showing the same number of introns. Phylogenetic trees comparing Hirudo to another distantly related leech species, Helobdella robusta, shows a high degree of orthology, whereas comparison to other annelids shows a relatively low level. Comparisons with other Lophotrochozoans, Ecdyzozoans and with vertebrate pannexins suggest a low number (one to two) of ancestral innexin/pannexins at the protostome/deuterostome split. Whole-mount in situ hybridization for individual genes in early embryos shows that ?50% of the expressed innexins are detectable in multiple tissues. Expression analyses using quantitative PCR show that ?70% of the Hirudo innexins are expressed in the nervous system, with most of these detected in early development. Finally, quantitative PCR analysis of several identified adult neurons detects the presence of different combinations of innexin genes, a property that may underlie the participation of these neurons in different adult coupling circuits. PMID:22358128

Kandarian, Brandon; Sethi, Jasmine; Wu, Allan; Baker, Michael; Yazdani, Neema; Kym, Eunice; Sanchez, Alejandro; Edsall, Lee; Gaasterland, Terry; Macagno, Eduardo



Dorsal horn-enriched genes identified by DNA microarray, in situ hybridization and immunohistochemistry  

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Full Text Available Abstract Background Neurons in the dorsal spinal cord play important roles in nociception and pain. These neurons receive input from peripheral sensory neurons and then transmit the signals to the brain, as well as receive and integrate descending control signals from the brain. Many molecules important for pain transmission have been demonstrated to be localized to the dorsal horn of the spinal cord. Further understanding of the molecular interactions and signaling pathways in the dorsal horn neurons will require a better knowledge of the molecular neuroanatomy in the dorsal spinal cord. Results A large scale screening was conducted for genes with enriched expression in the dorsal spinal cord using DNA microarray and quantitative real-time PCR. In addition to genes known to be specifically expressed in the dorsal spinal cord, other neuropeptides, receptors, ion channels, and signaling molecules were also found enriched in the dorsal spinal cord. In situ hybridization and immunohistochemistry revealed the cellular expression of a subset of these genes. The regulation of a subset of the genes was also studied in the spinal nerve ligation (SNL neuropathic pain model. In general, we found that the genes that are enriched in the dorsal spinal cord were not among those found to be up-regulated in the spinal nerve ligation model of neuropathic pain. This study also provides a level of validation of the use of DNA microarrays in conjunction with our novel analysis algorithm (SAFER for the identification of differences in gene expression. Conclusion This study identified molecules that are enriched in the dorsal horn of the spinal cord and provided a molecular neuroanatomy in the spinal cord, which will aid in the understanding of the molecular mechanisms important in nociception and pain.

Koblan Kenneth S



Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis  

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Full Text Available Abstract Background Spermatogenesis is a late developmental process that involves a coordinated expression program in germ cells and a permanent communication between the testicular somatic cells and the germ-line. Current knowledge regarding molecular factors driving male germ cell proliferation and differentiation in vertebrates is still limited and mainly based on existing data from rodents and human. Fish with a marked reproductive cycle and a germ cell development in synchronous cysts have proven to be choice models to study precise stages of the spermatogenetic development and the germ cell-somatic cell communication network. In this study we used 9K cDNA microarrays to investigate the expression profiles underlying testis maturation during the male reproductive cycle of the trout, Oncorhynchus mykiss. Results Using total testis samples at various developmental stages and isolated spermatogonia, spermatocytes and spermatids, 3379 differentially expressed trout cDNAs were identified and their gene activation or repression patterns throughout the reproductive cycle were reported. We also performed a tissue-profiling analysis and highlighted many genes for which expression signals were restricted to the testes or gonads from both sexes. The search for orthologous genes in genome-sequenced fish species and the use of their mammalian orthologs allowed us to provide accurate annotations for trout cDNAs. The analysis of the GeneOntology terms therefore validated and broadened our interpretation of expression clusters by highlighting enriched functions that are consistent with known sequential events during male gametogenesis. Furthermore, we compared expression profiles of trout and mouse orthologs and identified a complement of genes for which expression during spermatogenesis was maintained throughout evolution. 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.

Esquerré Diane



A genetic pedigree analysis to identify gene mutations involved in femoral head necrosis. (United States)

The present study presents results from a linkage and mutation screening analysis aiming to identify the causative gene of femoral head necrosis, also known as osteonecrosis of femoral head (ONFH), in a Chinese pedigree. We collected clinical data on the osteonecrosis pedigree, and extracted blood and genomic DNA from the family members. Polymerase chain reaction (PCR) and direct sequencing allowed to identify a mutation in the COL2A1 gene of the proband; the clinical manifestations of the proband meet the criteria for osteonecrosis. The exons of COL2A1 were amplified by polymerase chain reaction and mutation screening was conducted by direct sequencing in all the family members. The locus was also sequenced in 50 unrelated healthy controls. The c.3665G>A heterozygous mutation was detected in patients of the pedigree, but not in healthy individuals. We conclude that a mutation in the COL2A1 gene is the causative agent of ONFH in this family. Therefore, this mutation may be associated with osteonecrosis in Chinese populations. PMID:25050885

Wang, Lin; Pan, Hehai; Zhu, Zhen-An



An elm EST database for identifying leaf beetle egg-induced defense genes  

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Full Text Available Abstract Background Plants can defend themselves against herbivorous insects prior to the onset of larval feeding by responding to the eggs laid on their leaves. In the European field elm (Ulmus minor, egg laying by the elm leaf beetle ( Xanthogaleruca luteola activates the emission of volatiles that attract specialised egg parasitoids, which in turn kill the eggs. Little is known about the transcriptional changes that insect eggs trigger in plants and how such indirect defense mechanisms are orchestrated in the context of other biological processes. Results Here we present the first large scale study of egg-induced changes in the transcriptional profile of a tree. Five cDNA libraries were generated from leaves of (i untreated control elms, and elms treated with (ii egg laying and feeding by elm leaf beetles, (iii feeding, (iv artificial transfer of egg clutches, and (v methyl jasmonate. A total of 361,196 ESTs expressed sequence tags (ESTs were identified which clustered into 52,823 unique transcripts (Unitrans and were stored in a database with a public web interface. Among the analyzed Unitrans, 73% could be annotated by homology to known genes in the UniProt (Plant database, particularly to those from Vitis, Ricinus, Populus and Arabidopsis. Comparative in silico analysis among the different treatments revealed differences in Gene Ontology term abundances. Defense- and stress-related gene transcripts were present in high abundance in leaves after herbivore egg laying, but transcripts involved in photosynthesis showed decreased abundance. Many pathogen-related genes and genes involved in phytohormone signaling were expressed, indicative of jasmonic acid biosynthesis and activation of jasmonic acid responsive genes. Cross-comparisons between different libraries based on expression profiles allowed the identification of genes with a potential relevance in egg-induced defenses, as well as other biological processes, including signal transduction, transport and primary metabolism. Conclusion Here we present a dataset for a large-scale study of the mechanisms of plant defense against insect eggs in a co-evolved, natural ecological plant–insect system. The EST database analysis provided here is a first step in elucidating the transcriptional responses of elm to elm leaf beetle infestation, and adds further to our knowledge on insect egg-induced transcriptomic changes in plants. The sequences identified in our comparative analysis give many hints about novel defense mechanisms directed towards eggs.

Büchel Kerstin



A genome-wide shRNA screen identifies GAS1 as a novel melanoma metastasis suppressor gene  


Metastasis suppressor genes inhibit one or more steps required for metastasis without affecting primary tumor formation. Due to the complexity of the metastatic process, the development of experimental approaches for identifying genes involved in metastasis prevention has been challenging. Here we describe a genome-wide RNAi screening strategy to identify candidate metastasis suppressor genes. Following expression in weakly metastatic B16-F0 mouse melanoma cells, shRNAs were selected based up...

Gobeil, Stephane; Zhu, Xiaochun; Doillon, Charles J.; Green, Michael R.



Johns Hopkins scientists link gene to tamoxifen-resistant breast cancers (United States)

After mining the genetic records of thousands of breast cancer patients, researchers from the Johns Hopkins Kimmel Cancer Center have identified a gene whose presence may explain why some breast cancers are resistant to tamoxifen, a widely used hormone treatment generally used after surgery, radiation and other chemotherapy.


Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing. (United States)

AFLP-based genome scans are widely used to study the genetics of adaptation and to identify genomic regions potentially under selection. However, this approach usually fails to detect the actual genes or mutations targeted by selection owing to the difficulties of obtaining DNA sequences from AFLP fragments. Here, we combine classical AFLP outlier detection with 454 sequencing of AFLP fragments to obtain sequences from outlier loci. We applied this approach to the study of resistance to Bacillus thuringiensis israelensis (Bti) toxins in the dengue vector Aedes aegypti. A genome scan of Bti-resistant and Bti-susceptible A. aegypti laboratory strains was performed based on 432 AFLP markers. Fourteen outliers were detected using two different population genetic algorithms. Out of these, 11 were successfully sequenced. Three contained transposable elements (TEs) sequences, and the 10 outliers that could be mapped at a unique location in the reference genome were located on different supercontigs. One outlier was in the vicinity of a gene coding for an aminopeptidase potentially involved in Bti toxin-binding. Patterns of sequence variability of this gene showed significant deviation from neutrality in the resistant strain but not in the susceptible strain, even after taking into account the known demographic history of the selected strain. This gene is a promising candidate for future functional analysis. PMID:22348648

Paris, Margot; Despres, Laurence



Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations.  


We developed bulked segregant analysis as a method for rapidly identifying markers linked to any specific gene or genomic region. Two bulked DNA samples are generated from a segregating population from a single cross. Each pool, or bulk, contains individuals that are identical for a particular trait or genomic region but arbitrary at all unlinked regions. The two bulks are therefore genetically dissimilar in the selected region but seemingly heterozygous at all other regions. The two bulks ca...

Michelmore, R. W.; Paran, I.; Kesseli, R. V.



Identification of microsatellite markers (SSR) linked to a new bacterial blight resistance gene xa33(t) in rice cultivar ‘Ba7’  


This study attempts to identify a new source of bacterial blight (BB) resistance gene and microsatellite makers (SSR) linked to it. A total number of 139 F2 progenies generated from a cross between the resistant donor ‘Ba7’and ‘Pin Kaset’ were developed and used for this study. A Thai Xoo isolate, TXO16, collected from Phitsanulok province, was used to evaluate the resistance reaction in the F2 population. The segregation ratio of resistance (R) and susceptibility (S) was statisticall...

Theerayut Toojinda



Mutations in the JARID1C Gene, Which Is Involved in Transcriptional Regulation and Chromatin Remodeling, Cause X-Linked Mental Retardation  


In families with nonsyndromic X-linked mental retardation (NS-XLMR), >30% of mutations seem to cluster on proximal Xp and in the pericentric region. In a systematic screen of brain-expressed genes from this region in 210 families with XLMR, we identified seven different mutations in JARID1C, including one frameshift mutation and two nonsense mutations that introduce premature stop codons, as well as four missense mutations that alter evolutionarily conserved amino acids. In two of these famil...

Jensen, Lars Riff; Amende, Marion; Gurok, Ulf; Moser, Bettina; Gimmel, Verena; Tzschach, Andreas; Janecke, Andreas R.; Tariverdian, Gholamali; Chelly, Jamel; Fryns, Jean-pierre; Van esch, Hilde; Kleefstra, Tjitske; Hamel, Ben; Moraine, Claude; Ge?cz, Jozef



Mutations in the small GTPase gene RAB39B are responsible for X-linked mental retardation associated with autism, epilepsy, and macrocephaly  


Human Mental Retardation (MR) is a common and highly heterogeneous pediatric disorder affecting around 3% of the general population; at least 215 X-linked MR (XLMR) conditions have been described, and mutations have been identified in 83 different genes, encoding proteins with a variety of function, such as chromatin remodeling, synaptic function, and intracellular trafficking. The small GTPases of the RAB family, which play an essential role in intracellular vesicular trafficking, have been ...

Larizza, Lidia



HindIII identifies a two allele DNA polymorphism of the human cannabinoid receptor gene (CNR)  

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HCNR p5, a 0.9 kb BamHI/EcoRI fragment from the human cannabinoid receptor gene inserted into pUC19, was used as probe. The fragment is located in an intron approximately 14 kb 5{prime} of the initiation codon. This fragment is a clean single copy sequence by genomic blotting. Hybridization of human genomic DNA digested with HindIII identified a two allele RFLP with bands at 5.5 (A1) and 3.3 kb (A2). The human cannabinoid receptor gene has been genetically mapped in CEPH reference pedigrees to the centromeric/q region of chromosome 6. In situ hybridization localizes it to 6q14-q15. Codominant segregation has been observed in 26 informative two- and three-generation CEPH pedigrees and in 14 medium-sized disease families.

Caenazzo, L.; Hoehe, M.R.; Hsieh, W.T.; Berrettini, W.H.; Bonner, T.I.; Gershon, E.S. (National Inst. of Health, Bethesda, MD (United States))



An ant colony optimization based algorithm for identifying gene regulatory elements. (United States)

It is one of the most important tasks in bioinformatics to identify the regulatory elements in gene sequences. Most of the existing algorithms for identifying regulatory elements are inclined to converge into a local optimum, and have high time complexity. Ant Colony Optimization (ACO) is a meta-heuristic method based on swarm intelligence and is derived from a model inspired by the collective foraging behavior of real ants. Taking advantage of the ACO in traits such as self-organization and robustness, this paper designs and implements an ACO based algorithm named ACRI (ant-colony-regulatory-identification) for identifying all possible binding sites of transcription factor from the upstream of co-expressed genes. To accelerate the ants' searching process, a strategy of local optimization is presented to adjust the ants' start positions on the searched sequences. By exploiting the powerful optimization ability of ACO, the algorithm ACRI can not only improve precision of the results, but also achieve a very high speed. Experimental results on real world datasets show that ACRI can outperform other traditional algorithms in the respects of speed and quality of solutions. PMID:23746735

Liu, Wei; Chen, Hanwu; Chen, Ling



An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes. (United States)

Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; and (2) small interfering RNAs (siRNAs), the latter derived in plants by a process typically requiring an RNA-dependent RNA polymerase. We constructed and analyzed an expression atlas of soybean (Glycine max) small RNAs, identifying over 500 loci generating 21-nucleotide phased siRNAs (phasiRNAs; from PHAS loci), of which 483 overlapped annotated protein-coding genes. Via the integration of miRNAs with parallel analysis of RNA end (PARE) data, 20 miRNA triggers of 127 PHAS loci were detected. The primary class of PHAS loci (208 or 41% of the total) corresponded to NB-LRR genes; some of these small RNAs preferentially accumulate in nodules. Among the PHAS loci, novel representatives of TAS3 and noncanonical phasing patterns were also observed. A noncoding PHAS locus, triggered by miR4392, accumulated preferentially in anthers; the phasiRNAs are predicted to target transposable elements, with their peak abundance during soybean reproductive development. Thus, phasiRNAs show tremendous diversity in dicots. We identified novel miRNAs and assessed the veracity of soybean miRNAs registered in miRBase, substantially improving the soybean miRNA annotation, facilitating an improvement of miRBase annotations and identifying at high stringency novel miRNAs and their targets. PMID:25465409

Arikit, Siwaret; Xia, Rui; Kakrana, Atul; Huang, Kun; Zhai, Jixian; Yan, Zhe; Valdés-López, Oswaldo; Prince, Silvas; Musket, Theresa A; Nguyen, Henry T; Stacey, Gary; Meyers, Blake C



Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon  

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Full Text Available Abstract Background Transcript profiling of closely related species provides a means for identifying genes potentially important in species diversification. However, the predictive value of transcript profiling for inferring downstream-physiological processes has been unclear. In the present study we use shotgun proteomics to validate inferences from microarray studies regarding physiological differences in three Pachycladon species. We compare transcript and protein profiling and evaluate their predictive value for inferring glucosinolate chemotypes characteristic of these species. Results Evidence from heterologous microarrays and shotgun proteomics revealed differential expression of genes involved in glucosinolate hydrolysis (myrosinase-associated proteins and biosynthesis (methylthioalkylmalate isomerase and dehydrogenase, the interconversion of carbon dioxide and bicarbonate (carbonic anhydrases, water use efficiency (ascorbate peroxidase, 2 cys peroxiredoxin, 20 kDa chloroplastic chaperonin, mitochondrial succinyl CoA ligase and others (glutathione-S-transferase, serine racemase, vegetative storage proteins, genes related to translation and photosynthesis. Differences in glucosinolate hydrolysis products were directly confirmed. Overall, prediction of protein abundances from transcript profiles was stronger than prediction of transcript abundance from protein profiles. Protein profiles also proved to be more accurate predictors of glucosinolate profiles than transcript profiles. The similarity of species profiles for both transcripts and proteins reflected previously inferred phylogenetic relationships while glucosinolate chemotypes did not. Conclusions We have used transcript and protein profiling to predict physiological processes that evolved differently during diversification of three Pachycladon species. This approach has also identified candidate genes potentially important in adaptation, which are now the focus of ongoing study. Our results indicate that protein profiling provides a valuable tool for validating transcript profiles in studies of adaptive divergence.

Schmidt Silvia



A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis  

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Full Text Available Abstract Background Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches - the examination of similarities to known disease genes and/or the evaluation of functional annotation of genes. Each of these approaches has its own caveats. Here we employ a previously described method of candidate gene prioritization based mainly on gene annotation, in accompaniment with a technique based on the evaluation of pertinent sequence motifs or signatures, in an attempt to refine the gene prioritization approach. We apply this approach to X-linked mental retardation (XLMR, a group of heterogeneous disorders for which some of the underlying genetics is known. Results The gene annotation-based binary filtering method yielded a ranked list of putative XLMR candidate genes with good plausibility of being associated with the development of mental retardation. In parallel, a motif finding approach based on linear discriminatory analysis (LDA was employed to identify short sequence patterns that may discriminate XLMR from non-XLMR genes. High rates (>80% of correct classification was achieved, suggesting that the identification of these motifs effectively captures genomic signals associated with XLMR vs. non-XLMR genes. The computational tools developed for the motif-based LDA is integrated into the freely available genomic analysis portal Galaxy ( Nine genes (APLN, ZC4H2, MAGED4, MAGED4B, RAP2C, FAM156A, FAM156B, TBL1X, and UXT were highlighted as highly-ranked XLMR methods. Conclusions The combination of gene annotation information and sequence motif-orientated computational candidate gene prediction methods highlight an added benefit in generating a list of plausible candidate genes, as has been demonstrated for XLMR. Reviewers: This article was reviewed by Dr Barbara Bardoni (nominated by Prof Juergen Brosius; Prof Neil Smalheiser and Dr Dustin Holloway (nominated by Prof Charles DeLisi.

Lombard Zané



Three CCT domain-containing genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice  


CCT domain-containing genes generally control flowering in plants. Currently, only six of the 41 CCT family genes have been confirmed to control flowering in rice. To efficiently identify more heading date-related genes from the CCT family, we compared the positions of heading date QTLs and CCT genes and found that 25 CCT family genes were located in the QTL regions. Association mapping showed that a total of 19 CCT family genes were associated with the heading date. Five of the seven associa...

Zhang, Li; Li, Qiuping; Dong, Haijiao; He, Qin; Liang, Liwen; Tan, Cong; Han, Zhongmin; Yao, Wen; Li, Guangwei; Zhao, Hu; Xie, Weibo; Xing, Yongzhong



Combined expression patterns of QTL-linked candidate genes best predict thermotolerance in Drosophila melanogaster. (United States)

Knockdown resistance to high temperature (KRHT) is a thermal adaptation trait in Drosophila melanogaster. Here we used quantitative real-time PCR (qRT-PCR) to test for possible associations between KRHT and the expression of candidate genes within quantitative trait loci (QTL) in eight recombinant inbred lines (RIL). hsp60 and hsc70-3 map within an X-linked QTL, while CG10383, catsup, ddc, trap1, and cyp6a13 are linked in a KRHT-QTL on chromosome 2. hsc70-3 expression increased by heat-hardening. Principal Components analysis revealed that catsup, ddc and trap1 were either co-expressed or combined in their expression levels. This composite expression variable (e-PC1) was positively associated to KRHT in non-hardened RIL. In heat-hardened flies, hsp60 was negatively related to hsc70-3 on e-PC2, with effects on KRHT. These results are consistent with the notion that QTL can be shaped by expression variation in combined candidate loci. We found composite variables of gene expression (e-PCs) that best correlated to KRHT. Network effects with other untested linked loci are apparent because, in spite of their associations with KRHT phenotypes, e-PCs were sometimes uncorrelated with their QTL genotype. PMID:19651134

Norry, Fabian M; Larsen, Peter F; Liu, Yongjie; Loeschcke, Volker



The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services  

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Full Text Available Abstract Background Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. Results Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications. Conclusion By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at

Hanspers Kristina



Oil palm (Elaeis guineensis Jacq. tissue culture ESTs: Identifying genes associated with callogenesis and embryogenesis  

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Full Text Available Abstract Background Oil palm (Elaeis guineensis Jacq. is one of the most important oil bearing crops in the world. However, genetic improvement of oil palm through conventional breeding is extremely slow and costly, as the breeding cycle can take up to 10 years. This has brought about interest in vegetative propagation of oil palm. Since the introduction of oil palm tissue culture in the 1970s, clonal propagation has proven to be useful, not only in producing uniform planting materials, but also in the development of the genetic engineering programme. Despite considerable progress in improving the tissue culture techniques, the callusing and embryogenesis rates from proliferating callus cultures remain very low. Thus, understanding the gene diversity and expression profiles in oil palm tissue culture is critical in increasing the efficiency of these processes. Results A total of 12 standard cDNA libraries, representing three main developmental stages in oil palm tissue culture, were generated in this study. Random sequencing of clones from these cDNA libraries generated 17,599 expressed sequence tags (ESTs. The ESTs were analysed, annotated and assembled to generate 9,584 putative unigenes distributed in 3,268 consensi and 6,316 singletons. These unigenes were assigned putative functions based on similarity and gene ontology annotations. Cluster analysis, which surveyed the relatedness of each library based on the abundance of ESTs in each consensus, revealed that lipid transfer proteins were highly expressed in embryogenic tissues. A glutathione S-transferase was found to be highly expressed in non-embryogenic callus. Further analysis of the unigenes identified 648 non-redundant simple sequence repeats and 211 putative full-length open reading frames. Conclusion This study has provided an overview of genes expressed during oil palm tissue culture. Candidate genes with expression that are modulated during tissue culture were identified. However, in order to confirm whether these genes are suitable as early markers for embryogenesis, the genes need to be tested on earlier stages of tissue culture and a wider range of genotypes. This collection of ESTs is an important resource for genetic and genome analyses of the oil palm, particularly during tissue culture development.

Ooi Leslie CL



A missense mutation, p.V132G, in the X-linked spermine synthase gene (SMS) causes Snyder-Robinson syndrome  


Snyder-Robinson syndrome (SRS, OMIM 309583) is a rare X-linked syndrome characterized by mental retardation, marfanoid habitus, skeletal defects, osteoporosis and facial asymmetry. Linkage analysis localized the related gene to Xp21.3-p22.12, and a G-to-A transition at point +5 of intron 4 of the spermine synthase gene, which caused truncation of the SMS protein and loss of enzyme activity, was identified in the original family. Here we describe another family with Snyder-Robinson syndrome in...

Becerra-solano, L. E.; Butler, J.; Castan?eda-cisneros, G.; Mccloskey, D. E.; Wang, X.; Pegg, A. E.; Schwartz, C. E.; Sa?nchez-corona, J.; Garci?a-ortiz, J. E.



Disulfide cross-linked low generation dendrimers with high gene transfection efficacy, low cytotoxicity, and low cost. (United States)

Cationic poly(amidoamine) (PAMAM) dendrimers were widely used as nonviral gene carriers. PAMAM dendrimer-based products such as Superfect and Priofect were already commercially available gene transfection reagents. However, these products are based on high generation dendrimers with high cost and serious cytotoxicity. In this study, we prepared high efficient gene carriers using disulfide cross-linked low generation (generation 2, G2) PAMAM dendrimers. These synthesized materials can effectively condense DNA into ~200 nm polyplexes and degrade into G2 dendrimers after cellular uptake. Confocal laser scanning microscope studies revealed high cellular uptake behavior of disulfide cross-linked G2 PAMAM dendrimers. Compared to G2 and G5 PAMAM dendrimers, disulfide cross-linked G2 PAMAM dendrimers showed much improved gene transfection efficacy (both EGFP and luciferase gene) and low cytotoxicity on both HEK293 and HeLa cell lines. The disulfide cross-linked G2 dendrimer prepared at a linker/dendrimer molar ratio of 1:1 showed the highest gene transfection efficacy and exhibited comparable efficacy to branched PEI with a molecular weight of 25 kD, a commercially available nonviral gene vector. Our study demonstrated that disulfide cross-linked low generation PAMAM dendrimers with high transfection efficacy, low cytotoxicity, and low cost are efficient alternatives to high generation PAMAM dendrimers in gene delivery. PMID:23050493

Liu, Hongmei; Wang, Hui; Yang, Wenjun; Cheng, Yiyun



Globicatella sanguinis bacteraemia identified by partial 16S rRNA gene sequencing. (United States)

Globicatella sanguinis is a gram-positive coccus, resembling non-haemolytic streptococci. The organism has been isolated infrequently from normally sterile sites of humans. Three isolates obtained by blood culture could not be identified by Rapid 32 ID Strep, but partial sequencing of the 16S rRNA gene revealed the identity of the isolated bacteria, and supplementary biochemical tests confirmed the species identification. The cases histories illustrate the dilemma of finding relevant, newly recognized, opportunistic pathogens and the identification achievement (s) that can be obtained by using new molecular diagnostics. PMID:17654358

Abdul-Redha, Rawaa Jalil; Balslew, Ulla; Christensen, Jens Jørgen; Kemp, Michael



Globicatella sanguinis bacteraemia identified by partial 16S rRNA gene sequencing.  

DEFF Research Database (Denmark)

Globicatella sanguinis is a gram-positive coccus, resembling non-haemolytic streptococci. The organism has been isolated infrequently from normally sterile sites of humans. Three isolates obtained by blood culture could not be identified by Rapid 32 ID Strep, but partial sequencing of the 16S rRNA gene revealed the identity of the isolated bacteria, and supplementary biochemical tests confirmed the species identification. The cases histories illustrate the dilemma of finding relevant, newly recognized, opportunistic pathogens and the identification achievement (s) that can be obtained by using new molecular diagnostics.

Abdul-Redha, Rawaa Jalil; Balslew, Ulla



B.E.A.R. GeneInfo: A tool for identifying gene-related biomedical publications through user modifiable queries  

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Full Text Available Abstract Background Once specific genes are identified through high throughput genomics technologies there is a need to sort the final gene list to a manageable size for validation studies. The triaging and sorting of genes often relies on the use of supplemental information related to gene structure, metabolic pathways, and chromosomal location. Yet in disease states where the genes may not have identifiable structural elements, poorly defined metabolic pathways, or limited chromosomal data, flexible systems for obtaining additional data are necessary. In these situations having a tool for searching the biomedical literature using the list of identified genes while simultaneously defining additional search terms would be useful. Results We have built a tool, BEAR GeneInfo, that allows flexible searches based on the investigators knowledge of the biological process, thus allowing for data mining that is specific to the scientist's strengths and interests. This tool allows a user to upload a series of GenBank accession numbers, Unigene Ids, Locuslink Ids, or gene names. BEAR GeneInfo takes these IDs and identifies the associated gene names, and uses the lists of gene names to query PubMed. The investigator can add additional modifying search terms to the query. The subsequent output provides a list of publications, along with the associated reference hyperlinks, for reviewing the identified articles for relevance and interest. An example of the use of this tool in the study of human prostate cancer cells treated with Selenium is presented. Conclusions This tool can be used to further define a list of genes that have been identified through genomic or genetic studies. Through the use of targeted searches with additional search terms the investigator can limit the list to genes that match their specific research interests or needs. The tool is freely available on the web at http://prostategenomics.org1, and the authors will provide scripts and database components if requested

Zhou Guohui



Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey  

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Full Text Available Abstract Background Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as Arabidopsis thaliana do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied. Results Several molecular biology tools were used to isolate flower-specific gene promoters from Oncidium 'Gower Ramsey' (Onc. GR. A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in Onc. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (TI genes (OnTI1, OnTI2 and OnTI3, which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable A. thaliana transformation analyses. Conclusions By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.

Tung Shu-Yun



A biochemical genomics approach for identifying genes by the activity of their products. (United States)

For the identification of yeast genes specifying biochemical activities, a genomic strategy that is rapid, sensitive, and widely applicable was developed with an array of 6144 individual yeast strains, each containing a different yeast open reading frame (ORF) fused to glutathione S-transferase (GST). For the identification of ORF-associated activities, strains were grown in defined pools, and GST-ORFs were purified. Then, pools were assayed for activities, and active pools were deconvoluted to identify the source strains. Three previously unknown ORF-associated activities were identified with this strategy: a cyclic phosphodiesterase that acts on adenosine diphosphate-ribose 1"-2" cyclic phosphate (Appr>p), an Appr-1"-p-processing activity, and a cytochrome c methyltransferase. PMID:10550052

Martzen, M R; McCraith, S M; Spinelli, S L; Torres, F M; Fields, S; Grayhack, E J; Phizicky, E M



Identification of dosage sensitive genes involved in physiopathology of aneuploidy linked to chromosome 21  


A copy number variation of genes from human chromosome 21 (HSA21) leads to morphological and physiological anomalies of a great number of organs among patients. Trisomy 21 or Down's syndrome, and partial monosomy of the HSA21 lead to complex and variable phenotypes. In order to identify dosage sensitive genes, we developed a model of monosomy for the Prmt2-Col6a1 region of the murine chromosome 10 (MMU10). The analysis of this model showed that the Ms1Yah mice develop an alteration af the inf...

Dalloneau, Emilie



X chromosome cDNA microarray screening identifies a functional PLP2 promoter polymorphism enriched in patients with X-linked mental retardation  


X-linked Mental Retardation (XLMR) occurs in 1 in 600 males and is highly genetically heterogeneous. We used a novel human X chromosome cDNA microarray (XCA) to survey the expression profile of X-linked genes in lymphoblasts of XLMR males. Genes with altered expression verified by Northern blot and/or quantitative PCR were considered candidates. To validate this approach, we documented the expected changes of expression in samples from a patient with a known X chromosome microdeletion and fro...

Zhang, Lilei; Jie, Chunfa; Obie, Cassandra; Abidi, Fatima; Schwartz, Charles E.; Stevenson, Roger E.; Valle, David; Wang, Tao



Expression profiling of Crambe abyssinica under arsenate stress identifies genes and gene networks involved in arsenic metabolism and detoxification  

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Full Text Available Abstract Background Arsenic contamination is widespread throughout the world and this toxic metalloid is known to cause cancers of organs such as liver, kidney, skin, and lung in human. In spite of a recent surge in arsenic related studies, we are still far from a comprehensive understanding of arsenic uptake, detoxification, and sequestration in plants. Crambe abyssinica, commonly known as 'abyssinian mustard', is a non-food, high biomass oil seed crop that is naturally tolerant to heavy metals. Moreover, it accumulates significantly higher levels of arsenic as compared to other species of the Brassicaceae family. Thus, C. abyssinica has great potential to be utilized as an ideal inedible crop for phytoremediation of heavy metals and metalloids. However, the mechanism of arsenic metabolism in higher plants, including C. abyssinica, remains elusive. Results To identify the differentially expressed transcripts and the pathways involved in arsenic metabolism and detoxification, C. abyssinica plants were subjected to arsenate stress and a PCR-Select Suppression Subtraction Hybridization (SSH approach was employed. A total of 105 differentially expressed subtracted cDNAs were sequenced which were found to represent 38 genes. Those genes encode proteins functioning as antioxidants, metal transporters, reductases, enzymes involved in the protein degradation pathway, and several novel uncharacterized proteins. The transcripts corresponding to the subtracted cDNAs showed strong upregulation by arsenate stress as confirmed by the semi-quantitative RT-PCR. Conclusions Our study revealed novel insights into the plant defense mechanisms and the regulation of genes and gene networks in response to arsenate toxicity. The differential expression of transcripts encoding glutathione-S-transferases, antioxidants, sulfur metabolism, heat-shock proteins, metal transporters, and enzymes in the ubiquitination pathway of protein degradation as well as several unknown novel proteins serve as molecular evidence for the physiological responses to arsenate stress in plants. Additionally, many of these cDNA clones showing strong upregulation due to arsenate stress could be used as valuable markers. Further characterization of these differentially expressed genes would be useful to develop novel strategies for efficient phytoremediation as well as for engineering arsenic tolerant crops with reduced arsenic translocation to the edible parts of plants.

Kandasamy Suganthi



ADA5/SPT20 links the ADA and SPT genes, which are involved in yeast transcription. (United States)

In this report we described the cloning and characterization of ADA5, a gene identified by resistance to GAL4-VP16-mediated toxicity. ADA5 binds directly to the VP16 activation domain but not to a transcriptionally defective VP16 double point mutant. Double mutants with mutations in ada5 and other genes (ada2 or ada3) isolated by resistance to GAL4-VP16 grow like ada5 single mutants, suggesting that ADA5 is in the same pathway as the other ADA genes. Further, ADA5 cofractionates and coprecipitates with ADA3. However, an ada5 deletion mutant exhibits a broader spectrum of phenotypes than mutants with null mutations in the other ADA genes. Most interestingly, ADA5 is identical to SPT20 (S.M. Roberts and F. Winston, Mol. Cell. Biol. 16: 3206-3213, 1996), showing that it shares phenotypes with the ADA and SPT family of genes. Of the other SPT genes tested, mutants with mutations in SPT7 and, strikingly, SPT15 (encoding the TATA-binding protein) show resistance to GAL4-VP16. We present a speculative pathway of transcriptional activation involving the ADA2-ADA3-GCN5-ADA5 complex and the TATA-binding protein. PMID:8649430

Marcus, G A; Horiuchi, J; Silverman, N; Guarente, L



Genes mapping to boron tolerance QTL in barley identified by suppression subtractive hybridization. (United States)

Boron tolerance is a quantitative trait controlled by multiple genes. Suppression subtractive hybridization was carried out on root cDNA from bulked boron tolerant and intolerant doubled haploid barley lines grown under moderate boron stress to identify genes associated with boron tolerance. One hundred and eleven clones representing known proteins were found to be up-regulated in the tolerant bulk upon boron stress. Nine clones were genetically mapped to previously reported boron tolerance QTL. These include a clone identical to the boron transporter gene Bot1 and a clone coding for a bromo-adjacent homology domain-containing protein, mapping to the 6H boron tolerance locus and co-segregating with reduced boron intake in a Clipper x Sahara-3771 mapping population. A third clone mapping to the 2H QTL region encoding an S-adenosylmethionine decarboxylase precursor was found to provide tolerance to high boron by heterologous expression. Yeast cells expressing Sahara SAMDC were able to grow on 15 mm boron solid media and maintained cellular boron concentrations at 13% lower than control cells expressing empty vector. The data suggest that an antioxidative response mechanism involving polyamines and the ascorbate-glutathione pathway in Sahara barley may provide an advantage in tolerating high soil concentrations of boron. PMID:19906153

Hassan, Mahmood; Oldach, Klaus; Baumann, Ute; Langridge, Peter; Sutton, Tim



Polymorphisms of COTL1 gene identified by proteomic approach and their association with autoimmune disorders (United States)

To select candidate genes, we attempted to comparative analysis of protein levels between rheumatoid arthritis (RA) patients and healthy controls by two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF-MS). We identified 17 proteins that showed up- or down-regulated spots in RA patients. We found that coactosin-like1 (COTL1) were highly expressed in RA patients compared with healthy controls. We performed a case-control study to determine whether the COTL1 gene polymorphisms were associated with RA and systemic lupus erythematosus (SLE). The genotype frequency of c.-1124G>T and the allelic frequency of c.484G>A in RA patients, and the genotype frequency of c.484G>A in SLE patients were significantly different from healthy controls (P = 0.009, 0.027, and 0.025, respectively). We also investigated the correlation with the levels of rheumatoid factor (RF) and anti-cyclic citrullinated peptide (CCP) antibody in RA patients, and anti-nuclear antibodies (ANA) in SLE patients. The c.484G>A polymorphism in RA patients has significant association with the levels of anti-CCP antibody (P = 0.03). Our findings demonstrated that c.-1124G>T and c.484G>A polymorphisms of the COTL1 gene might be associated with the genetic susceptibility of autoimmune disorders. PMID:19307756

Jin, Eun-Heui; Shim, Seung-Cheol; Kim, Hwan-Gyu



Identificação e validação de marcadores microssatélites ligados ao gene Rpp5 de resistência à ferrugem-asiática-da-soja / Identification and validation of microsatellite markers linked to the Rpp5 gene conferring resistance to Asian soybean rust  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: Portuguese Abstract in portuguese O objetivo deste trabalho foi identificar novos marcadores microssatélites, ligados ao gene Rpp5 de resistência à ferrugem-da-soja, e validar os marcadores previamente mapeados, para que possam ser utilizados em programas de seleção assistida por marcadores moleculares (SAM). Para tanto, uma populaç [...] ão F2 com 100 indivíduos, derivada do cruzamento entre a PI 200526 e a cultivar Coodetec 208, suscetível à ferrugem, foi artificialmente infectada e avaliada quanto à sua reação de resistência à ferrugem. Marcadores microssatélites foram testados nos genitores e em dois "bulks" contrastantes, para a identificação de marcadores ligados. Dois novos marcadores, potencialmente associados à resistência, foram testados em plantas individuais, e se constatou que eles estão ligados ao gene Rpp5 e estão presentes no grupo de ligação N da soja. A eficiência de seleção foi determinada em relação a todos os marcadores ligados ao gene Rpp5, e a combinação entre os marcadores Sat_275+Sat_280 foi de 100%. Abstract in english The main objective of this work was to identify new microsatellite markers, linked to the Rpp5 resistance gene to Asian soybean rust, and to validate previously mapped markers for use in marker-assisted selection (MAS) programs. To this end, a F2 population with 100 individuals, derived from crossin [...] g between PI 200526 and cultivar Coodetec 208, susceptible to rust, was artificially infected and evaluated for its reaction of resistance to rust. Microsatellite markers were tested on parents and in the two contrasting bulks to identifying linked markers. Two new markers, potentially associated with resistance, were tested in individual plants, and they were found to be linked to gene Rpp5 and to be present in the N linkage group of soybean. The selection efficiencies were determined for all markers linked to gene Rpp5, and the combination of the markers Sat_275+Sat_280 was 100%.

Thaiza Galhardo Silva, Morceli; Sandra Helena Unêda, Trevisoli; Antonio Ayrton, Morceli Junior; Romeu Afonso de Souza, Kiihl; Eberson Sanches, Calvo; Antonio Orlando, Di Mauro; Alexandre, Garcia.



Mutations of Bruton's tyrosine kinase gene in Brazilian patients with X-linked agammaglobulinemia  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english Mutations in Bruton's tyrosine kinase (BTK) gene are responsible for X-linked agammaglobulinemia (XLA), which is characterized by recurrent bacterial infections, profound hypogammaglobulinemia, and decreased numbers of mature B cells in peripheral blood. We evaluated 5 male Brazilian patients, rangi [...] ng from 3 to 10 years of age, from unrelated families, whose diagnosis was based on recurrent infections, markedly reduced levels of IgM, IgG and IgA, and circulating B cell numbers

V.D., Ramalho; E.B., Oliveira Júnior; S.M., Tani; P., Roxo Júnior; M.M.S., Vilela.



Intermittent X-linked thrombocytopenia with a novel WAS gene mutation. (United States)

X-linked thrombocytopenia (XLT) is caused by mutations in the WAS gene and characterized by thrombocytopenia with minimal or no immunodeficiency. Patients with XLT usually exhibit persistent thrombocytopenia, and intermittent thrombocytopenia has been described only in two families. Here, we report a patient with intermittent XLT carrying a novel missense mutation (Ala56Thr). He showed residual expression of Wiskott-Aldrich syndrome protein in the lymphocytes and platelets. There appeared to be an association between normal platelet numbers and a post infectious state. Our findings further support the importance of analysis of Wiskott-Aldrich syndrome protein in male patients who exhibit fluctuating courses of thrombocytopenia. PMID:24115682

Wada, Taizo; Itoh, Masatsune; Maeba, Hideaki; Toma, Tomoko; Niida, Yo; Saikawa, Yutaka; Yachie, Akihiro



A mechanistic link between gene regulation and genome architecture in mammalian development. (United States)

The organization of chromatin within the nucleus and the regulation of transcription are tightly linked. Recently, mechanisms underlying this relationship have been uncovered. By defining the organizational hierarchy of the genome, determining changes in chromatin organization associated with changes in cell identity, and describing chromatin organization within the context of linear genomic features (such as chromatin modifications and transcription factor binding) and architectural proteins (including Cohesin, CTCF, and Mediator), a new paradigm in genome biology was established wherein genomes are organized around gene regulatory factors that govern cell identity. As such, chromatin organization plays a central role in establishing and maintaining cell state during development, with gene regulation and genome organization being mutually dependent effectors of cell identity. PMID:24998386

Bonora, Giancarlo; Plath, Kathrin; Denholtz, Matthew



Mutations of Bruton's tyrosine kinase gene in Brazilian patients with X-linked agammaglobulinemia  

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Full Text Available Mutations in Bruton's tyrosine kinase (BTK gene are responsible for X-linked agammaglobulinemia (XLA, which is characterized by recurrent bacterial infections, profound hypogammaglobulinemia, and decreased numbers of mature B cells in peripheral blood. We evaluated 5 male Brazilian patients, ranging from 3 to 10 years of age, from unrelated families, whose diagnosis was based on recurrent infections, markedly reduced levels of IgM, IgG and IgA, and circulating B cell numbers <2%. BTK gene analysis was carried out using PCR-SSCP followed by sequencing. We detected three novel (Ala347fsX55, I355T, and Thr324fsX24 and two previously reported mutations (Q196X and E441X. Flow cytometry revealed a reduced expression of BTK protein in patients and a mosaic pattern of BTK expression was obtained from mothers, indicating that they were XLA carriers.

V.D. Ramalho



Use of RNA fingerprinting to identify fungal genes specifically expressed during ectomycorrhizal interaction. (United States)

The ecosystem soil is characterized by interactions between microorganisms and plants including mycorrhiza--mutualistic interactions between fungi and plant roots. Species of the basidiomycete genus Tricholoma form ectomycorrhiza with tree roots which is characterized by morphological and metabolic changes of both partners, yet molecular mechanisms of the interaction are poorly understood. We performed differential display with arbitrarily primed RT-PCR using ectomycorrhiza between the basidiomycete Tricholoma vaccinum and its compatible host spruce (Picea abies) to isolate mycorrhiza-specific fungal gene fragments. 76 differentially expressed PCR fragments were verified and checked for plant or fungal origin and expression pattern. Of 20 fungal fragments with mycorrhiza-specific expression, sequence analyses were performed to identify homologs with known function of the encoded protein. Among the genes identified were orthologs to an aldehyde dehydrogenase, an alcohol dehydrogenase and a protein of the MATE transporter family, all with possible function in plant pathogen response. A phospholipase B, a beta-glucosidase and a binding protein of basic amino acids might play a role in nutrient exchange and growth in planta. A protein similar to inactive E2 compounds of ubiquitin-conjugating enzymes like CROC-1 and MMS2, a Ras protein and an APS kinase were placed in signal transduction and two retrotransposons of the Ty3-gypsy and the Ty1-copia family are expressed most likely due to stress. PMID:17009294

Krause, Katrin; Kothe, Erika



Identifying and Targeting ROS1 Gene Fusions in Non-Small Cell Lung Cancer (United States)

Purpose Oncogenic gene fusions involving the 3’ region of ROS1 kinase have been identified in various human cancers. In this study, we sought to characterize ROS1 fusion genes in non-small cell lung cancer (NSCLC) and establish the fusion proteins as drug targets. Experimental Design A NSCLC tissue microarray (TMA) panel containing 447 samples was screened for ROS1 rearrangement by fluorescence in-situ hybridization (FISH). This assay was also used to screen NSCLC patients. In positive samples, the identity of the fusion partner was determined through inverse-PCR and RT-PCR. In addition, the clinical utility of ROS1 inhibition was assessed by treating a ROS1-positive patient with crizotinib. The HCC78 cell line, which expresses the SLC34A2-ROS1 fusion, was treated with kinase inhibitors that have activity against ROS1. The effects of ROS1 inhibition on proliferation, cell-cycle progression, and cell signaling pathways were analyzed by MTS assay, flow cytometry, and western blotting. Results In the TMA panel, 5/428 (1.2%) evaluable samples were found to be positive for ROS1 rearrangement. Additionally, 1/48 patients tested positive for rearrangement, and this patient demonstrated tumor shrinkage upon treatment with crizotinib. The patient and one TMA sample displayed expression of the recently identified SDC4-ROS1 fusion, while two TMA samples expressed the CD74-ROS1 fusion and two others expressed the SLC34A2-ROS1 fusion. In HCC78 cells, treatment with ROS1 inhibitors was anti-proliferative and down-regulated signaling pathways that are critical for growth and survival. Conclusions ROS1 inhibition may be an effective treatment strategy for the subset of NSCLC patients whose tumors express ROS1 fusion genes. PMID:22919003

Davies, Kurtis D.; Le, Anh T.; Theodoro, Mariana F.; Skokan, Margaret C.; Aisner, Dara L.; Berge, Eamon M.; Terracciano, Luigi M.; Incarbone, Matteo; Roncalli, Massimo; Cappuzzo, Federico; Camidge, D. Ross; Varella-Garcia, Marileila; Doebele, Robert C.



Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa  

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Full Text Available Abstract Background Phylostratigraphy is a method used to correlate the evolutionary origin of founder genes (that is, functional founder protein domains of gene families with particular macroevolutionary transitions. It is based on a model of genome evolution that suggests that the origin of complex phenotypic innovations will be accompanied by the emergence of such founder genes, the descendants of which can still be traced in extant organisms. The origin of multicellularity can be considered to be a macroevolutionary transition, for which new gene functions would have been required. Cancer should be tightly connected to multicellular life since it can be viewed as a malfunction of interaction between cells in a multicellular organism. A phylostratigraphic tracking of the origin of cancer genes should, therefore, also provide insights into the origin of multicellularity. Results We find two strong peaks of the emergence of cancer related protein domains, one at the time of the origin of the first cell and the other around the time of the evolution of the multicellular metazoan organisms. These peaks correlate with two major classes of cancer genes, the 'caretakers', which are involved in general functions that support genome stability and the 'gatekeepers', which are involved in cellular signalling and growth processes. Interestingly, this phylogenetic succession mirrors the ontogenetic succession of tumour progression, where mutations in caretakers are thought to precede mutations in gatekeepers. Conclusions A link between multicellularity and formation of cancer has often been predicted. However, this has not so far been explicitly tested. Although we find that a significant number of protein domains involved in cancer predate the origin of multicellularity, the second peak of cancer protein domain emergence is, indeed, connected to a phylogenetic level where multicellular animals have emerged. The fact that we can find a strong and consistent signal for this second peak in the phylostratigraphic map implies that a complex multi-level selection process has driven the transition to multicellularity.

Domazet-Lošo Tomislav



PATE, a gene expressed in prostate cancer, normal prostate, and testis, identified by a functional genomic approach  


To identify target antigens for prostate cancer therapy, we have combined computer-based screening of the human expressed sequence tag database and experimental expression analysis to identify genes that are expressed in normal prostate and prostate cancer but not in essential human tissues. Using this approach, we identified a gene that is expressed specifically in prostate cancer, normal prostate, and testis. The gene has a 1.5-kb transcript that encodes a protein of 14 kDa. We named this g...

Bera, Tapan K.; Maitra, Rangan; Iavarone, Carlo; Salvatore, Giuliana; Kumar, Vasantha; Vincent, James J.; Sathyanarayana, B. K.; Duray, Paul; Lee, B. K.; Pastan, Ira



Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry  

Energy Technology Data Exchange (ETDEWEB)

Chemical cross-linking combined with mass spectrometry provides a powerful method for identifying protein-protein interactions and probing the structure of protein complexes. Cross-linking is the process of covalently joining two proteins using cross-linking reagents. After proteolytic cleavage, the cross-linked peptides can be identified using tandem mass spectrometry. A number of strategies have been reported that take advantage of the high sensitivity and high resolution of modern mass spectrometers. Approaches typically include synthesis of novel cross-linking compounds and/or isotopic labelling of the cross-linkering reagent and/or protein to aid both identification and quantitation. However, these approaches have various limitations. These limitations can be overcome with a label-free approach and application of associated data analysis algorithms described in this work.

Du, Xiuxia; Chowdhury, Saiful M.; Manes, Nathan P.; Wu, Si; Mayer, M. Uljana; Adkins, Joshua N.; Anderson, Gordon A.; Smith, Richard D.



A gene expression signature identifies two prognostic subgroups of basal breast cancer. (United States)

Prognosis of basal breast cancers is poor but heterogeneous. Medullary breast cancers (MBC) display a basal profile, but a favorable prognosis. We hypothesized that a previously published 368-gene expression signature associated with MBC might serve to define a prognostic classifier in basal cancers. We collected public gene expression and histoclinical data of 2145 invasive early breast adenocarcinomas. We developed a Support Vector Machine (SVM) classifier based on this 368-gene list in a learning set, and tested its predictive performances in an independent validation set. Then, we assessed its prognostic value and that of six prognostic signatures for disease-free survival (DFS) in the remaining 2034 samples. The SVM model accurately classified all MBC samples in the learning and validation sets. A total of 466 cases were basal across other sets. The SVM classifier separated them into two subgroups, subgroup 1 (resembling MBC) and subgroup 2 (not resembling MBC). Subgroup 1 exhibited 71% 5-year DFS, whereas subgroup 2 exhibited 50% (P = 9.93E-05). The classifier outperformed the classical prognostic variables in multivariate analysis, conferring lesser risk for relapse in subgroup 1 (HR = 0.52, P = 3.9E-04). This prognostic value was specific to the basal subtype, in which none of the other prognostic signatures was informative. Ontology analysis revealed effective immune response (IR), enhanced tumor cell apoptosis, elevated levels of metastasis-inhibiting factors and low levels of metastasis-promoting factors in the good-prognosis subgroup, and a more developed cell migration system in the poor-prognosis subgroup. In conclusion, based on this 368-gene SVM model derived from an MBC signature, basal breast cancers were classified in two prognostic subgroups, suggesting that MBC and basal breast cancers share similar molecular alterations associated with aggressiveness. This signature could help define the prognosis, adapt the systemic treatment, and identify new therapeutic targets. PMID:20490655

Sabatier, Renaud; Finetti, Pascal; Cervera, Nathalie; Lambaudie, Eric; Esterni, Benjamin; Mamessier, Emilie; Tallet, Agnès; Chabannon, Christian; Extra, Jean-Marc; Jacquemier, Jocelyne; Viens, Patrice; Birnbaum, Daniel; Bertucci, François



Human hair growth deficiency is linked to a genetic defect in the phospholipase gene LIPH. (United States)

The molecular mechanisms controlling human hair growth and scalp hair loss are poorly understood. By screening about 350,000 individuals in two populations from the Volga-Ural region of Russia, we identified a gene mutation in families who show an inherited form of hair loss and a hair growth defect. Affected individuals were homozygous for a deletion in the LIPH gene on chromosome 3q27, caused by short interspersed nuclear element-retrotransposon-mediated recombination. The LIPH gene is expressed in hair follicles and encodes a phospholipase called lipase H (alternatively known as membrane-associated phosphatidic acid-selective phospholipase A1alpha), an enzyme that regulates the production of bioactive lipids. These results suggest that lipase H participates in hair growth and development. PMID:17095700

Kazantseva, Anastasiya; Goltsov, Andrey; Zinchenko, Rena; Grigorenko, Anastasia P; Abrukova, Anna V; Moliaka, Yuri K; Kirillov, Alexander G; Guo, Zhiru; Lyle, Stephen; Ginter, Evgeny K; Rogaev, Evgeny I



Diapause specific gene expression in the eggs of multivoltine silkworm Bombyx mori, identified by suppressive subtractive hybridization. (United States)

Molecular mechanism controlling egg diapause remains obscure in silkworm, Bombyx mori. An attempt is made to decipher various molecular events occurring during embryonic diapause in multivoltine silkworm, B. mori. Using suppressive subtractive hybridization (SSH), 186 cDNA clones isolated from both diapause and nondiapause eggs were sequenced. Of the sequenced clones, 29 matched with silkbase entries and these identified putative genes were classified into six functional groups such as regulatory, food utilization, stress response, metabolic, ribosomal and transposable elements. Among these genes, twelve belonged to regulatory group while, one taste receptor type 2 member 117 gene was related to food utilization. One heat shock cognate 70 kDa protein and 3 of the ubiquitin family were identified under stress response category. Similarly, four genes were identified as metabolic genes, 3 belonging to chitin family and one propanediol utilization protein. Of the seven genes identified in ribosomal groups, most of them were 60s ribosomal protein subunits. However, one negative regulation of transcription gene identified was a transposable element. The qPCR analysis confirmed the expression of 21 of the above genes, wherein, 6 were upregulated during diapause, 12 during non-diapause, while, 3 remained unchanged. PMID:22248932

Sasibhushan, Sirigineedi; Ponnuvel, Kangayam M; Vijayaprakash, Nanjappa B



Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD (United States)

Chronic Obstructive Pulmonary Disease (COPD) is a complex disease. Genetic, epigenetic, and environmental factors are known to contribute to COPD risk and disease progression. Therefore we developed a systematic approach to identify key regulators of COPD that integrates genome-wide DNA methylation, gene expression, and phenotype data in lung tissue from COPD and control samples. Our integrative analysis identified 126 key regulators of COPD. We identified EPAS1 as the only key regulator whose downstream genes significantly overlapped with multiple genes sets associated with COPD disease severity. EPAS1 is distinct in comparison with other key regulators in terms of methylation profile and downstream target genes. Genes predicted to be regulated by EPAS1 were enriched for biological processes including signaling, cell communications, and system development. We confirmed that EPAS1 protein levels are lower in human COPD lung tissue compared to non-disease controls and that Epas1 gene expression is reduced in mice chronically exposed to cigarette smoke. As EPAS1 downstream genes were significantly enriched for hypoxia responsive genes in endothelial cells, we tested EPAS1 function in human endothelial cells. EPAS1 knockdown by siRNA in endothelial cells impacted genes that significantly overlapped with EPAS1 downstream genes in lung tissue including hypoxia responsive genes, and genes associated with emphysema severity. Our first integrative analysis of genome-wide DNA methylation and gene expression profiles illustrates that not only does DNA methylation play a ‘causal’ role in the molecular pathophysiology of COPD, but it can be leveraged to directly identify novel key mediators of this pathophysiology. PMID:25569234

Yoo, Seungyeul; Takikawa, Sachiko; Geraghty, Patrick; Argmann, Carmen; Campbell, Joshua; Lin, Luan; Huang, Tao; Tu, Zhidong; Feronjy, Robert; Spira, Avrum; Schadt, Eric E.; Powell, Charles A.; Zhu, Jun



Whole exome sequencing in dominant cataract identifies a new causative factor, CRYBA2, and a variety of novel alleles in known genes. (United States)

Pediatric cataracts are observed in 1-15 per 10,000 births with 10-25 % of cases attributed to genetic causes; autosomal dominant inheritance is the most commonly observed pattern. Since the specific cataract phenotype is not sufficient to predict which gene is mutated, whole exome sequencing (WES) was utilized to concurrently screen all known cataract genes and to examine novel candidate factors for a disease-causing mutation in probands from 23 pedigrees affected with familial dominant cataract. Review of WES data for 36 known cataract genes identified causative mutations in nine pedigrees (39 %) in CRYAA, CRYBB1, CRYBB3, CRYGC (2), CRYGD, GJA8 (2), and MIP and an additional likely causative mutation in EYA1; the CRYBB3 mutation represents the first dominant allele in this gene and demonstrates incomplete penetrance. Examination of crystallin genes not yet linked to human disease identified a novel cataract gene, CRYBA2, a member of the ??-crystallin superfamily. The p.(Val50Met) mutation in CRYBA2 cosegregated with disease phenotype in a four-generation pedigree with autosomal dominant congenital cataracts with incomplete penetrance. Expression studies detected cryba2 transcripts during early lens development in zebrafish, supporting its role in congenital disease. Our data highlight the extreme genetic heterogeneity of dominant cataract as the eleven causative/likely causative mutations affected nine different genes, and the majority of mutant alleles were novel. Furthermore, these data suggest that less than half of dominant cataract can be explained by mutations in currently known genes. PMID:23508780

Reis, Linda M; Tyler, Rebecca C; Muheisen, Sanaa; Raggio, Victor; Salviati, Leonardo; Han, Dennis P; Costakos, Deborah; Yonath, Hagith; Hall, Sarah; Power, Patricia; Semina, Elena V



RNA-Sequencing Analysis of 5' Capped RNAs Identifies Many New Differentially Expressed Genes in Acute Hepatitis C Virus Infection  

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Full Text Available We describe the first report of RNA sequencing of 5' capped (Pol II RNAs isolated from acutely hepatitis C virus (HCV infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. We identified 100, 684, and 1,844 significantly differentially expressed annotated genes in acutely infected proliferative Huh 7.5 cells at 6, 48, and 72 hours, respectively (fold change ? 1.5 and Bonferroni adjusted p-values < 0.05. Most of the differentially expressed genes (>80% and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling were not identified by previous gene array studies. These genes are critical components of host immune, inflammatory and oncogenic pathways and provide new information regarding changes that may benefit the virus or mediate HCV induced pathology. RNAi knockdown studies of newly identified highly upregulated FUT1 and KLHDC7B genes provide evidence that their gene products regulate and facilitate HCV replication in hepatocytes. Our approach also identified novel Pol II unannotated transcripts that were upregulated. Results further identify new pathways that regulate HCV replication in hepatocytes and suggest that our approach will have general applications in studying viral-host interactions in model systems and clinical biospecimens.

Bret S. E. Heale



Three CCT domain-containing genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice. (United States)

CCT domain-containing genes generally control flowering in plants. Currently, only six of the 41 CCT family genes have been confirmed to control flowering in rice. To efficiently identify more heading date-related genes from the CCT family, we compared the positions of heading date QTLs and CCT genes and found that 25 CCT family genes were located in the QTL regions. Association mapping showed that a total of 19 CCT family genes were associated with the heading date. Five of the seven associated genes within QTL regions and two of four associated genes outside of the QTL regions were confirmed to regulate heading date by transformation. None of the seven non-associated genes outside of the QTL regions regulates heading date. Obviously, combination of candidate gene-based association mapping with linkage analysis could improve the identification of functional genes. Three novel CCT family genes, including one non-associated (OsCCT01) and two associated genes (OsCCT11 and OsCCT19) regulated the heading date. The overexpression of OsCCT01 delayed flowering through suppressing the expression of Ehd1, Hd3a and RFT1 under both long day and short day conditions. Potential functions in regulating heading date of some untested CCT family genes were discussed. PMID:25563494

Zhang, Li; Li, Qiuping; Dong, Haijiao; He, Qin; Liang, Liwen; Tan, Cong; Han, Zhongmin; Yao, Wen; Li, Guangwei; Zhao, Hu; Xie, Weibo; Xing, Yongzhong



Pathway-driven gene stability selection of two rheumatoid arthritis GWAS identifies and validates new susceptibility genes in receptor mediated signalling pathways. (United States)

Rheumatoid arthritis (RA) is the commonest chronic, systemic, inflammatory disorder affecting ?1% of the world population. It has a strong genetic component and a growing number of associated genes have been discovered in genome-wide association studies (GWAS), which nevertheless only account for 23% of the total genetic risk. We aimed to identify additional susceptibility loci through the analysis of GWAS in the context of biological function. We bridge the gap between pathway and gene-oriented analyses of GWAS, by introducing a pathway-driven gene stability-selection methodology that identifies potential causal genes in the top-associated disease pathways that may be driving the pathway association signals. We analysed the WTCCC and the NARAC studies of ?5000 and ?2000 subjects, respectively. We examined 700 pathways comprising ?8000 genes. Ranking pathways by significance revealed that the NARAC top-ranked ?6% laid within the top 10% of WTCCC. Gene selection on those pathways identified 58 genes in WTCCC and 61 in NARAC; 21 of those were common (P(overlap)< 10(-21)), of which 16 were novel discoveries. Among the identified genes, we validated 10 known RA associations in WTCCC and 13 in NARAC, not discovered using single-SNP approaches on the same data. Gene ontology functional enrichment analysis on the identified genes showed significant over-representation of signalling activity (P< 10(-29)) in both studies. Our findings suggest a novel model of RA genetic predisposition, which involves cell-membrane receptors and genes in second messenger signalling systems, in addition to genes that regulate immune responses, which have been the focus of interest previously. PMID:21653640

Eleftherohorinou, Hariklia; Hoggart, Clive J; Wright, Victoria J; Levin, Michael; Coin, Lachlan J M



Targeted deep resequencing identifies MID2 mutation for X-linked intellectual disability with varied disease severity in a large kindred from India. (United States)

We report a novel missense mutation (c.1040G>A, p.Arg347Gln) in MID2, which encodes ubiquitin ligase E3, as the likely cause of X-linked mental retardation in a large kindred. The mutation was observed in all affected and obligate carriers but not in any unaffected males of the family or in population controls (n = 200). When transiently expressed in HEK293T cell line, the mutation was found to abolish the function of the COS domain in the protein. The GFP-tagged mutant protein accumulated in the cytoplasm instead of binding to the cytoskeleton resulting in its altered subcellular localization. Screening of coding exons of this gene in additional 480 unrelated individuals with idiopathic intellectual disability identified another novel variation p.Asn343Ser. This study highlights the growing role of the ubiquitin pathway in intellectual disability and also, the difference in MID2 determined phenotype observed in this study compared with that of its paralogue MID1 reported in literature. PMID:24115387

Geetha, Thenral S; Michealraj, Kulandaimanuvel Antony; Kabra, Madhulika; Kaur, Gurjit; Juyal, Ramesh C; Thelma, B K



Relative power of linkage and transmission disequilibrium test strategies to detect non-HLA linked coeliac disease susceptibility genes  


BACKGROUND—Susceptibility to coeliac disease is genetically determined by possession of specific HLA DQ alleles, acting in concert with one or more non-HLA linked genes. The pattern of familial risk is most parsimonious with a multiplicative model for the interaction between these two classes of genes. Haplotype sharing probabilities across the HLA region in affected sibling pairs suggest that genes within the MHC complex contribute no more than 40% of the sibling familial risk of coeliac d...

Bevan, S.; Popat, S.; Houlston, R.



Response of NBS encoding resistance genes linked to both heat and fungal stress in Brassica oleracea. (United States)

Environmental stresses, including both abiotic and biotic stresses, cause considerable yield loss in crops and can significantly affect their development. Under field conditions, crops are exposed to a variety of concurrent stresses. Among abiotic and biotic stresses, heat and Fusarium oxysporum, are the most important factors affecting development and yield productivity of Brassica oleracea. Genes encoding the nucleotide-binding site (NBS) motif are known to be related to responses to abiotic and biotic stresses in many plants. Hence, this study was conducted to characterize the NBS encoding genes obtained from transcriptome profiles of two cabbage genotypes with contrasting responses to heat stress, and to test expression levels of selected NBS- leucine reich repeat (LRR) genes in F. oxysporum infected plants. We selected 80 up-regulated genes from a total of 264 loci, among which 17 were confirmed to be complete and incomplete members of the TIR-NBS-LRR (TNL) class families, and another identified as an NFYA-HAP2 family member. Expression analysis using qRT-PCR revealed that eight genes showed significant responses to heat shock treatment and F. oxysporum infection. Additionally, in the commercial B. oleracea cultivars with resistance to F. oxysporum, the Bol007132, Bol016084, and Bol030522 genes showed dramatically higher expression in the F. oxysporum resistant line than in the intermediate and susceptible lines. The results of this study will facilitate the identification and the development of molecular markers based on multiple stress resistance genes related to heat and fungal stress under field conditions in B. oleracea. PMID:25461701

Kim, Young-Wook; Jung, Hee-Jeong; Park, Jong-In; Hur, Yoonkang; Nou, Ill-Sup