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1

Functional analysis of Toll-related genes in Drosophila  

PubMed Central

The Drosophila genome encodes a total of nine Toll and related proteins. The immune and developmental functions of Toll and 18Wheeler (18W) have been analyzed extensively, while the in vivo functions of the other Toll-related proteins require further investigation. We performed transgenic experiments and found that overexpression of Toll-related genes caused different extents of lethality and developmental defects. Moreover, 18w, Toll-6, Toll-7 and Toll-8 often caused related phenotypic changes, consistent with the idea that these four genes have more conserved molecular structure and thus may regulate similar processes in vivo. Deletion alleles of Toll-6, Toll-7 and Toll-8 were generated by targeted homologous recombination or P element excision. These mutant alleles were viable, fertile, and had no detectable defect in the inducible expression of antimicrobial peptide genes except for the Toll-8 mutant had some defects in leg development. The expression of 18w, Toll-7 and Toll-8 mRNA showed wide and overlapping patterns in imaginal discs and the 18w, Toll-8 double and Toll-7, Toll-8 double mutants showed substantially increased lethality. Overall our results suggest that some of the Toll-related proteins, such as 18W, Toll-7 and Toll-8, may have redundant functions in regulating developmental processes.

Yagi, Yoshimasa; Nishida, Yasuyoshi; Ip, Y. Tony

2014-01-01

2

Comparative and functional analysis of cardiovascular-related genes  

SciTech Connect

The ability to detect putative cis-regulatory elements in cardiovascular-related genes has been accelerated by the availability of genomic sequence data from numerous vertebrate species and the recent development of comparative genomic tools. This improvement is anticipated to lead to a better understanding of the complex regulatory architecture of cardiovascular (CV) genes and how genetic variants in these non-coding regions can potentially play a role in cardiovascular disease. This manuscript reviews a recently established database dedicated to the comparative sequence analysis of 250 human CV genes of known importance, 37 of which currently contain sequence comparison data for organisms beyond those of human, mouse and rat. These data have provided a glimpse into the variety of possible insights from deep vertebrate sequence comparisons and the identification of putative gene regulatory elements.

Cheng, Jan-Fang; Pennacchio, Len A.

2003-09-01

3

An Unsupervised Approach to Predict Functional Relations between Genes Based on Expression Data  

PubMed Central

This work presents a novel approach to predict functional relations between genes using gene expression data. Genes may have various types of relations between them, for example, regulatory relations, or they may be concerned with the same protein complex or metabolic/signaling pathways and obviously gene expression data should contain some clues to such relations. The present approach first digitizes the log-ratio type gene expression data of S. cerevisiae to a matrix consisting of 1, 0, and ?1 indicating highly expressed, no major change, and highly suppressed conditions for genes, respectively. For each gene pair, a probability density mass function table is constructed indicating nine joint probabilities. Then gene pairs were selected based on linear and probabilistic relation between their profiles indicated by the sum of probability density masses in selected points. The selected gene pairs share many Gene Ontology terms. Furthermore a network is constructed by selecting a large number of gene pairs based on FDR analysis and the clustering of the network generates many modules rich with similar function genes. Also, the promoters of the gene sets in many modules are rich with binding sites of known transcription factors indicating the effectiveness of the proposed approach in predicting regulatory relations.

Altaf-Ul-Amin, Md.; Sato, Tetsuo; Ono, Naoaki; Kanaya, Shigehiko

2014-01-01

4

Identification of Three Related Human GRO Genes Encoding Cytokine Functions  

Microsoft Academic Search

The product of the human GRO gene is a cytokine with inflammatory and growth-regulatory properties; GRO is also called MGSA for melanoma growth-stimulatory activity. We have identified two additional genes, GRObeta and GROgamma, that share 90% and 86% identity at the deduced amino acid level with the original GROalpha isolate. One amino acid substitution of proline in GROalpha by leucine

Stephen Haskill; Amy Peace; John Morris; Sarah A. Sporn; Anthony Anisowicz; Sam W. Lee; Temple Smith; George Martin; Peter Ralph; Ruth Sager

1990-01-01

5

Gene-sequence-tag expression analyses of 1,800 genes related to chloroplast functions  

Microsoft Academic Search

Quantification of the expression levels of nuclear genes encoding plastid proteins under different genetic or environmental conditions can contribute to the genetic dissection of plastid functions. To facilitate such measurements, a set of 1,827 Arabidopsis thaliana genes coding for plastid proteins was PCR-amplified from genomic DNA and spotted on nylon membranes to generate an array of chloroplast-specific gene-sequence-tags (GSTs). The

Joachim Kurth; Claudio Varotto; Paolo Pesaresi; Alexander Biehl; Erik Richly; Francesco Salamini; Dario Leister

2002-01-01

6

The Function and Interaction of Genes Related to Esophageal Squamous Cell Cancer  

Microsoft Academic Search

Objective: To study the function and interaction of genes related to esophageal squamous cell cancer and discuss esophageal cancer molecular mechanism.Methods: The gene microarray date set of esophageal was downloaded from the GEO BRB-ArrayTools and online tool was used to analysis the difference expression genes between esophageal squamous cell cancer and normal tissue, and analysis the functional and interaction of

Yu Long Chen; Su Gai Yin; Yao Song Wu

2011-01-01

7

Identification and functional analysis of differentially expressed genes related to obesity using DNA microarray.  

PubMed

We looked for differentially expressed genes at different stages of preadipocyte differentiation and examined their functions, based on DNA microarrays of preadipocytes obtained from healthy subjects undergoing cosmetic liposuction. We downloaded gene expression profile GSE25910 from the Gene Expression Omnibus database and identified the differentially expressed genes with packages in R language. The selected differentially expressed genes were further analyzed using bioinformatics methods. Comparing gene expression at different stages of preadipocytes differentiation, we found that expression of 668 and 1007 genes were altered in middle and late stages compared with the early stage, respectively. Function analysis revealed that the differentially expressed genes were mainly related to fatty acid metabolic processes in the former two stages. PMID:24446288

Du, J Y; Yang, H; Tian, D R; Wang, Q M; He, L

2014-01-01

8

Functional Features, Biological Pathways, and Protein Interaction Networks of Addiction-Related Genes  

PubMed Central

Addictions are chronic and common brain disorders affected by many genetic, environmental, and behavioral factors. Recent genome-wide linkage and association studies have revealed several promising genomic regions and multiple genes relating to addictions. To explore the underlying biological processes in the development of addictions, we used 62 genes recently reviewed by Li and Burmeister (2009) as representative addiction-related genes, and then we investigated their features in gene function, pathways, and protein interaction networks. We performed enrichment tests of their Gene Ontology (GO) annotations and of their pathways in the Ingenuity Pathways Analysis (IPA) system. The tests revealed that these addiction-related genes were highly enriched in neurodevelopment-related processes. Interestingly, we found circadian rhythm signaling in one of the enriched pathways. Moreover, these addiction-related genes tended to have higher connectivity and shorter characteristic shortest-path distances compared to control genes in the protein–protein interaction (PPI) network. This investigation is the first of such kind in addiction studies, and it is useful for further addiction candidate-gene prioritization and verification, thus helping us to better understand molecular mechanisms of addictions.

Sun, Jingchun; Zhao, Zhongming

2010-01-01

9

Identification of functionally related genes using data mining and data integration: a breast cancer case study  

PubMed Central

Background The identification of the organisation and dynamics of molecular pathways is crucial for the understanding of cell function. In order to reconstruct the molecular pathways in which a gene of interest is involved in regulating a cell, it is important to identify the set of genes to which it interacts with to determine cell function. In this context, the mining and the integration of a large amount of publicly available data, regarding the transcriptome and the proteome states of a cell, are a useful resource to complement biological research. Results We describe an approach for the identification of genes that interact with each other to regulate cell function. The strategy relies on the analysis of gene expression profile similarity, considering large datasets of expression data. During the similarity evaluation, the methodology determines the most significant subset of samples in which the evaluated genes are highly correlated. Hence, the strategy enables the exclusion of samples that are not relevant for each gene pair analysed. This feature is important when considering a large set of samples characterised by heterogeneous experimental conditions where different pools of biological processes can be active across the samples. The putative partners of the studied gene are then further characterised, analysing the distribution of the Gene Ontology terms and integrating the protein-protein interaction (PPI) data. The strategy was applied for the analysis of the functional relationships of a gene of known function, Pyruvate Kinase, and for the prediction of functional partners of the human transcription factor TBX3. In both cases the analysis was done on a dataset composed by breast primary tumour expression data derived from the literature. Integration and analysis of PPI data confirmed the prediction of the methodology, since the genes identified to be functionally related were associated to proteins close in the PPI network. Two genes among the predicted putative partners of TBX3 (GLI3 and GATA3) were confirmed by in vivo binding assays (crosslinking immunoprecipitation, X-ChIP) in which the putative DNA enhancer sequence sites of GATA3 and GLI3 were found to be bound by the Tbx3 protein. Conclusion The presented strategy is demonstrated to be an effective approach to identify genes that establish functional relationships. The methodology identifies and characterises genes with a similar expression profile, through data mining and integrating data from publicly available resources, to contribute to a better understanding of gene regulation and cell function. The prediction of the TBX3 target genes GLI3 and GATA3 was experimentally confirmed.

Mosca, Ettore; Bertoli, Gloria; Piscitelli, Eleonora; Vilardo, Laura; Reinbold, Rolland A; Zucchi, Ileana; Milanesi, Luciano

2009-01-01

10

Eukaryotic operon-like transcription of functionally related genes in Drosophila  

PubMed Central

Complex biological processes require coordinated function of many genes. One evolutionary solution to the problem of coordinately expressing functionally related genes in bacteria and nematodes is organization of genes in operons. Surprisingly, eukaryotic operons are considered rare outside the nematode lineage. In Drosophila melanogaster, we found lounge lizard (llz), which encodes a degenerin/ENaC cation channel, cotranscribed with CheB42a, a nonhomologous gene of unknown function residing <100 bp upstream. These two genes were transcribed from a single promoter as one primary transcript and were processed posttranscriptionally to generate individual mRNAs. The mechanism did not involve alternative splicing, and it differed from the trans splicing used in nematode operons. Both genes were expressed in the same tissues, and previous work suggested that both may be involved in courtship behavior. A bioinformatic approach identified numerous additional loci as potential Drosophila operons. These data reveal eukaryotic operon-like transcription of functionally related genes in Drosophila. The results also suggest that operon-based transcription may be more common in eukaryotes than previously appreciated.

Ben-Shahar, Yehuda; Nannapaneni, Kishore; Casavant, Thomas L.; Scheetz, Todd E.; Welsh, Michael J.

2007-01-01

11

Expression pattern and functions of autophagy-related gene atg5 in zebrafish organogenesis.  

PubMed

The implications of autophagy-related genes in serious neural degenerative diseases have been well documented. However, the functions and regulation of the family genes in embryonic development remain to be rigorously studied. Here, we report on for the first time the important role of atg5 gene in zebrafish neurogenesis and organogenesis as evidenced by the spatiotemporal expression pattern and functional analysis. Using morpholino oligo knockdown and mRNA overexpression, we demonstrated that zebrafish atg5 is required for normal morphogenesis of brain regionalization and body plan as well as for expression regulation of neural gene markers: gli1, huC, nkx2.2, pink1, ?-synuclein, xb51 and zic1. We further demonstrated that ATG5 protein is involved in autophagy by LC3-II/LC3I ratio and rapamycin-induction experiments, and that ATG5 is capable of regulating expression of itself gene in the manner of a feedback inhibition loop. In addition, we found that expression of another autophagy-related gene, atg12, is maintained at a higher constant level like a housekeeping gene. This indicates that the formation of the ATG12–ATG5 conjugate may be dependent on ATG5 protein generation and its splicing, rather than on ATG12 protein in zebrafish. Importantly, in the present study, we provide a mechanistic insight into the regulation and functional roles of atg5 in development of zebrafish nervous system. PMID:22082871

Hu, Zhanying; Zhang, Jingpu; Zhang, Qingyou

2011-12-01

12

Evidence for Related Functions of the RNA Genes of Saccharomyces cerevisiae  

PubMed Central

The yeast genes RNA2-RNA11 are necessary for splicing of nuclear intron-containing pre-mRNAs. We investigated the relationships among these genes by asking whether increased expression of one RNA gene leads to suppression of the temperature-sensitive lethality of a mutation in any other RNA gene. The presence of extra plasmid-borne copies of the RNA3 gene relieves the lethality of temperature-sensitive rna4 mutations. A region of the yeast genome (SRN2) is described that suppresses temperature-sensitive rna2 mutations when it is present on either medium or high-copy number plasmids. Neither suppression occurs via a bypass of RNA gene function since null alleles of rna2 and rna4 are not suppressed by elevated dosage of SRN2 and RNA3, respectively. These results suggest that the SRN2 and RNA2 gene products have related functions, as do the RNA3 and RNA4 gene products.

Last, Robert L.; Maddock, Janine R.; Woolford, John L.

1987-01-01

13

Relating gene expression data on two-component systems to functional annotations in Escherichia coli  

PubMed Central

Background Obtaining physiological insights from microarray experiments requires computational techniques that relate gene expression data to functional information. Traditionally, this has been done in two consecutive steps. The first step identifies important genes through clustering or statistical techniques, while the second step assigns biological functions to the identified groups. Recently, techniques have been developed that identify such relationships in a single step. Results We have developed an algorithm that relates patterns of gene expression in a set of microarray experiments to functional groups in one step. Our only assumption is that patterns co-occur frequently. The effectiveness of the algorithm is demonstrated as part of a study of regulation by two-component systems in Escherichia coli. The significance of the relationships between expression data and functional annotations is evaluated based on density histograms that are constructed using product similarity among expression vectors. We present a biological analysis of three of the resulting functional groups of proteins, develop hypotheses for further biological studies, and test one of these hypotheses experimentally. A comparison with other algorithms and a different data set is presented. Conclusion Our new algorithm is able to find interesting and biologically meaningful relationships, not found by other algorithms, in previously analyzed data sets. Scaling of the algorithm to large data sets can be achieved based on a theoretical model.

Denton, Anne M; Wu, Jianfei; Townsend, Megan K; Sule, Preeti; Pruss, Birgit M

2008-01-01

14

DNA Hypomethylation Affects Cancer-Related Biological Functions and Genes Relevant in Neuroblastoma Pathogenesis  

PubMed Central

Neuroblastoma (NB) pathogenesis has been reported to be closely associated with numerous genetic alterations. However, underlying DNA methylation patterns have not been extensively studied in this developmental malignancy. Here, we generated microarray-based DNA methylation profiles of primary neuroblastic tumors. Stringent supervised differential methylation analyses allowed us to identify epigenetic changes characteristic for NB tumors as well as for clinical and biological subtypes of NB. We observed that gene-specific loss of DNA methylation is more prevalent than promoter hypermethylation. Remarkably, such hypomethylation affected cancer-related biological functions and genes relevant to NB pathogenesis such as CCND1, SPRR3, BTC, EGF and FGF6. In particular, differential methylation in CCND1 affected mostly an evolutionary conserved functionally relevant 3? untranslated region, suggesting that hypomethylation outside promoter regions may play a role in NB pathogenesis. Hypermethylation targeted genes involved in cell development and proliferation such as RASSF1A, POU2F2 or HOXD3, among others. The results derived from this study provide new candidate epigenetic biomarkers associated with NB as well as insights into the molecular pathogenesis of this tumor, which involves a marked gene-specific hypomethylation.

Mayol, Gemma; Martin-Subero, Jose I.; Rios, Jose; Queiros, Ana; Kulis, Marta; Sunol, Mariona; Esteller, Manel; Gomez, Soledad; Garcia, Idoia; de Torres, Carmen; Rodriguez, Eva; Galvan, Patricia; Mora, Jaume; Lavarino, Cinzia

2012-01-01

15

Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles  

PubMed Central

Describing at a genomic scale how mutations in different genes influence one another is essential to the understanding of how genotype correlates with phenotype and remains a major challenge in biology. Previous studies pointed out the need for accurate measurements of not only synthetic but also buffering interactions in the characterization of genetic networks and functional modules. We developed a sensitive and efficient method that allows such measurements at a genomic scale in yeast. In a pilot experiment (41 genome-wide screens), we quantified the fitness of 140,000 double deletion strains relative to the corresponding single mutants and identified many genetic interactions. In addition to synthetic growth defects (validated experimentally with factors newly identified as genetically interfering with mRNA degradation), most of the identified genetic interactions measured weak epistatic effects. These weak effects, rarely meaningful when considered individually, were crucial to defining specific signatures for many gene deletions and had a major contribution in defining clusters of functionally related genes.

Decourty, Laurence; Saveanu, Cosmin; Zemam, Kenza; Hantraye, Florence; Frachon, Emmanuel; Rousselle, Jean-Claude; Fromont-Racine, Micheline; Jacquier, Alain

2008-01-01

16

Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles.  

PubMed

Describing at a genomic scale how mutations in different genes influence one another is essential to the understanding of how genotype correlates with phenotype and remains a major challenge in biology. Previous studies pointed out the need for accurate measurements of not only synthetic but also buffering interactions in the characterization of genetic networks and functional modules. We developed a sensitive and efficient method that allows such measurements at a genomic scale in yeast. In a pilot experiment (41 genome-wide screens), we quantified the fitness of 140,000 double deletion strains relative to the corresponding single mutants and identified many genetic interactions. In addition to synthetic growth defects (validated experimentally with factors newly identified as genetically interfering with mRNA degradation), most of the identified genetic interactions measured weak epistatic effects. These weak effects, rarely meaningful when considered individually, were crucial to defining specific signatures for many gene deletions and had a major contribution in defining clusters of functionally related genes. PMID:18408161

Decourty, Laurence; Saveanu, Cosmin; Zemam, Kenza; Hantraye, Florence; Frachon, Emmanuel; Rousselle, Jean-Claude; Fromont-Racine, Micheline; Jacquier, Alain

2008-04-15

17

Dopaminergic function in relation to genes associated with risk for schizophrenia: translational mutant mouse models.  

PubMed

Mutant mice play an increasingly important role in understanding disease processes at multiple levels. In particular, they illuminate the impact of risk genes for disease on such processes. This article reviews recent advances in the application of mutant mice to study the intricacies of dopaminergic (DAergic) function in relation to the putative pathophysiology of psychotic illness, particularly schizophrenia, and antipsychotic drug action. It considers models for understanding the role(s) of risk genes, with a particular focus on DTNBP1 and NRG1, their interactions with environmental factors, and with each other (epistasis). In overview, it considers new schemas for understanding psychotic illness that integrate DAergic pathophysiology with developmental, social, and cognitive processes, and how mutant mouse models can reflect and inform on such schemas. PMID:24968777

Moran, Paula M; O'Tuathaigh, Colm M P; Papaleo, Francesco; Waddington, John L

2014-01-01

18

Expression and Function of Enamel-related Gene Products in Calvarial Development  

PubMed Central

Enamel-related gene products (ERPs) are detected in non-enamel tissues such as bone. We hypothesized that, if functional, ERP expression corresponds with distinct events during osteoblast differentiation and affects bone development and mineralization. In mouse calvariae and MC3T3 cells, expression profiles of enamel-related gene products (ERPs) correlated with key events in post-natal calvarial development and MC3T3 cell mineralization. Developing skulls from both Amel- and Ambn-deficient animals were approximately 15% shorter when compared with those of wild-type controls, and their sutures remained patent for a longer period of time. Analysis of Amel- and Ambn-deficient calvariae and calvarial osteoblast cultures revealed a dramatic reduction in mineralized nodules, a significant reduction in Runx2, Sp7, Ibsp, and Msx2 expression, and a reduction in Alx4 in Amel-deficient calvariae vs. an increase in Alx4 in Ambn-deficient calvariae. Analysis of these data indicates that ERP expression follows defined developmental profiles and affects osteoblast differentiation, mineralization, and calvarial bone development. We propose that, in parallel to their role in the developing enamel matrix, ERPs have retained an evolutionary conserved function related to the biomineralization of bones.

Atsawasuwan, P.; Lu, X.; Ito, Y.; Chen, Y.; Gopinathan, G.; Evans, C.A.; Kulkarni, A.B.; Gibson, C.W.; Luan, X.; Diekwisch, T.G.H.

2013-01-01

19

Definition of Historical Models of Gene Function and Their Relation to Students' Understanding of Genetics  

ERIC Educational Resources Information Center

Models are often used when teaching science. In this paper historical models and students' ideas about genetics are compared. The historical development of the scientific idea of the gene and its function is described and categorized into five historical models of gene function. Differences and similarities between these historical models are made…

Gericke, Niklas Markus; Hagberg, Mariana

2007-01-01

20

Functional Redundancy and Divergence within the Arabidopsis RETICULATA-RELATED Gene Family1[W][OA  

PubMed Central

A number of Arabidopsis (Arabidopsis thaliana) mutants exhibit leaf reticulation, having green veins that stand out against paler interveinal tissues, fewer cells in the interveinal mesophyll, and normal perivascular bundle sheath cells. Here, to examine the basis of leaf reticulation, we analyzed the Arabidopsis RETICULATA-RELATED (RER) gene family, several members of which cause leaf reticulation when mutated. Although transcripts of RE, RER1, and RER3 were mainly detected in the bundle sheath cells of expanded leaves, functional RER3:GREEN FLUORESCENT PROTEIN was visualized in the chloroplast membranes of all photosynthetic cells. Leaf reticulation in the re and rer3 loss-of-function mutants occurred, along with accumulation of reactive oxygen species, in a photoperiod-dependent manner. A comparison of re and rer3 leaf messenger RNA expression profiles showed more than 200 genes were similarly misexpressed in both mutants. In addition, metabolic profiles of mature leaves revealed that several biosynthetic pathways downstream of pyruvate are altered in re and rer3. Double mutant analysis showed that only re rer1 and rer5 rer6 exhibited synergistic phenotypes, indicating functional redundancy. The redundancy between RE and its closest paralog, RER1, was confirmed by overexpressing RER1 in re mutants, which partially suppressed leaf reticulation. Our results show that RER family members can be divided into four functional modules with divergent functions. Moreover, these results provide insights into the origin of the reticulated phenotype, suggesting that the RER proteins functionally interconnect photoperiodic growth, amino acid homeostasis, and reactive oxygen species metabolism during Arabidopsis leaf growth.

Perez-Perez, Jose Manuel; Esteve-Bruna, David; Gonzalez-Bayon, Rebeca; Kangasjarvi, Saijaliisa; Caldana, Camila; Hannah, Matthew A.; Willmitzer, Lothar; Ponce, Maria Rosa; Micol, Jose Luis

2013-01-01

21

Functional identification of a Leishmania gene related to the peroxin 2 gene reveals common ancestry of glycosomes and peroxisomes.  

PubMed Central

Glycosomes are membrane-bounded microbody organelles that compartmentalize glycolysis as well as other important metabolic processes in trypanosomatids. The compartmentalization of these enzymatic reactions is hypothesized to play a crucial role in parasite physiology. Although the metabolic role of glycosomes differs substantially from that of the peroxisomes that are found in other eukaryotes, similarities in signals targeting proteins to these organelles suggest that glycosomes and peroxisomes may have evolved from a common ancestor. To examine this hypothesis, as well as gain insights into the function of the glycosome, we used a positive genetic selection procedure to isolate the first Leishmania mutant (gim1-1 [glycosome import] mutant) with a defect in the import of glycosomal proteins. The mutant retains glycosomes but mislocalizes a subset glycosomal proteins to the cytoplasm. Unexpectedly, the gim1-1 mutant lacks lipid bodies, suggesting a heretofore unknown role of the glycosome. We used genetic approaches to identify a gene, GIM1, that is able to restore import and lipid bodies. A nonsense mutation was found in one allele of this gene in the mutant line. The predicted Gim1 protein is related the peroxin 2 family of integral membrane proteins, which are required for peroxisome biogenesis. The similarities in sequence and function provide strong support for the common origin model of glycosomes and peroxisomes. The novel phenotype of gim1-1 and distinctive role of Leishmania glycosomes suggest that future studies of this system will provide a new perspective on microbody biogenesis and function.

Flaspohler, J A; Rickoll, W L; Beverley, S M; Parsons, M

1997-01-01

22

Common Single Nucleotide Polymorphisms in Genes Related to Immune Function and Risk of Papillary Thyroid Cancer  

PubMed Central

Accumulating evidence suggests that alterations in immune function may be important in the etiology of papillary thyroid cancer (PTC). To identify genetic markers in immune-related pathways, we evaluated 3,985 tag single nucleotide polymorphisms (SNPs) in 230 candidate gene regions (adhesion-extravasation-migration, arachidonic acid metabolism/eicosanoid signaling, complement and coagulation cascade, cytokine signaling, innate pathogen detection and antimicrobials, leukocyte signaling, TNF/NF-kB pathway or other) in a case-control study of 344 PTC cases and 452 controls. We used logistic regression models to estimate odds ratios (OR) and calculate one degree of freedom P values of linear trend (PSNP-trend) for the association between genotype (common homozygous, heterozygous, variant homozygous) and risk of PTC. To correct for multiple comparisons, we applied the false discovery rate method (FDR). Gene region- and pathway-level associations (PRegion and PPathway) were assessed by combining individual PSNP-trend values using the adaptive rank truncated product method. Two SNPs (rs6115, rs6112) in the SERPINA5 gene were significantly associated with risk of PTC (PSNP-FDR/PSNP-trend?=?0.02/6×10?6 and PSNP-FDR/PSNP-trend?=?0.04/2×10?5, respectively). These associations were independent of a history of autoimmune thyroiditis (OR?=?6.4; 95% confidence interval: 3.0–13.4). At the gene region level, SERPINA5 was suggestively associated with risk of PTC (PRegion-FDR/PRegion?=?0.07/0.0003). Overall, the complement and coagulation cascade pathway was the most significant pathway (PPathway?=?0.02) associated with PTC risk largely due to the strong effect of SERPINA5. Our results require replication but suggest that the SERPINA5 gene, which codes for the protein C inhibitor involved in many biological processes including inflammation, may be a new susceptibility locus for PTC.

Brenner, Alina V.; Neta, Gila; Sturgis, Erich M.; Pfeiffer, Ruth M.; Hutchinson, Amy; Yeager, Meredith; Xu, Li; Zhou, Cindy; Wheeler, William; Tucker, Margaret A.; Chanock, Stephen J.; Sigurdson, Alice J.

2013-01-01

23

Virus-aided gene expression and silencing using TRV for functional analysis of floral scent-related genes.  

PubMed

Flower scent is a composite character determined by a complex mixture of low-molecular-weight volatile molecules. Despite the importance of floral fragrance, our knowledge on factors regulating these pathways remains sketchy. Virus-induced gene silencing (VIGS) and virus-aided gene expression (VAGE) are characterized by a simple inoculation procedure and rapid results as compared to transgenesis, allowing screening and characterization of scent-related genes. Here, we describe methods using TRV as a VIGS/VAGE vector for the characterization of scent-related genes, protein compartmentalization studies, and protein subcellular targeting. PMID:23386300

Spitzer-Rimon, Ben; Cna'ani, Alon; Vainstein, Alexander

2013-01-01

24

Screening and functional analysis of glioma?related genes induced by candoxin.  

PubMed

This study aimed to identify time?specific and common differential genes (CDGs) expressed in glioma cells following exposure to candoxin at three different time?points. Gene expression data from candoxin?treated human glioma (Hs 683) cells were downloaded from the Gene Expression Omnibus database (accession number, GSE1682), from a 12?time?point set of samples. Differentially expressed genes were screened between control and candoxin?treated samples at different time?points, and three time?specific gene sets and CDGs were identified. All genes were subject to pathway enrichment analysis to gain further insight into gene function. CDGs were clustered based upon their original expression between 0 and 48 h, and, from this subset, feature genes were selected. Small molecules associated with candoxin were identified by comparing the expression pattern of the most valid candidate genes with that of differential genes exposed to small molecules in the Connectivity Map. From the 12?, 24? and 48?h time?points, 746, 265 and 539 differentially expressed genes were identified, respectively. A total of 129 genes were differentially expressed and significantly enriched in focal adhesion and gap junction pathways. From these, 11 feature genes and one marker gene (EPS8L1) were identified. Four small molecules that were most relevant to candoxin action were identified. In conclusion, it is hypothesized that candoxin stimulation can cause glial inflammation through mutations in cell adhesion activity. The EPS8L1 gene may be a valid marker for glioma diagnosis, and the four small molecules identified may be relevant for future drug design. PMID:24913449

Qiu, Lei; Zhang, Xiang; Chen, Zuoquan

2014-08-01

25

Carotid plaque and candidate genes related to inflammation and endothelial function in Hispanics from northern Manhattan  

PubMed Central

BACKGROUND AND PURPOSE The genetic influence on carotid atherosclerotic plaque is mostly unknown. This study examines the association between carotid plaque and single nucleotide polymorphisms (SNPs) in selected genes implicated in inflammation and endothelial function. METHODS A total of 43 genes (197 SNPs) involved in inflammation and endothelial function were interrogated in 287 Dominicans from the Northern Manhattan Study (mean age 64±7 years, 58% women) who had undergone high-resolution B-mode ultrasound for examination of carotid plaque. Using an additive genetic model, multiple logistic regression analyses were conducted, a within gene haplotype analysis was performed and interactions between genes were examined. Results were validated in an independent set of 301 Dominicans. RESULTS Carotid plaque was present in 143(47%) participants. Nine genes had at least one SNP associated (p?0.01) with carotid plaque phenotypes: TNF, NOS2A, IL6R, TNFSF4, PPARA, IL1A, TLR4, ITGA2, HABP2. SNPs in TNFSF4, PPARA, TLR4, ITGA2, and HABP2 were also implicated with the same carotid phenotype in the validation analysis. Haplotype analysis revealed an additional gene of interest, VCAM1. CONCLUSIONS We report novel associations between variations in ten genes involved in inflammation and endothelial function and carotid plaque phenotypes in a Dominican sample, with replication for five genes in an independent Dominican sample.

Gardener, Hannah; Beecham, Ashley; Cabral, Digna; Yanuck, Danielle; Slifer, Susan; Wang, Liyong; Blanton, Susan H.; Sacco, Ralph L.; Juo, Suh-Hang Hank; Rundek, Tatjana

2011-01-01

26

TGF-? suppresses the expression of genes related to mitochondrial function in lung A549 cells.  

PubMed

TGF-? is a mediator of lung fibrosis and regulates the alveolar epithelial type II cell phenotype. TGF-? can induce epithelial mesenchymal transition of idiopathic pulmonary disease and cancer metastasis. Peroxisome proliferator-activated receptor gamma co-activator 1-alpha (PGC-1 ?) is a key metabolic regulator that stimulates mitochondrial biogenesis and promotes remodeling of muscle tissue to oxidative fiber-type composition. Here, we report that the induction of TGF-? decreased mRNA expression of PGC-1?, and PGC-1 target genes, such as the transcription factors NRF-2, ERR-?, and PPAR-? in lung epithelial A549 cells. In addition, TGF-? led to the reduction of super oxide dismutase 2 (anti-oxidant enzyme), cytochrome C (electron transport chain in mitochondria), and MCAD (a mitochondrial ?-oxidant enzyme) in A549 cells. Together, our results suggest that TGF-? may suppress the transcriptional activity of the genes related to mitochondrial biogenesis or function. This mechanism may provide a novel insight into the understanding of fibrosis disease. PMID:23046869

Sohn, E J; Kim, J; Hwang, Y; Im, S; Moon, Y; Kang, D M

2012-01-01

27

Gene Risk Factors for Age-Related Brain Disorders May Affect Immune System Function  

MedlinePLUS

... to environmental triggers and can respond to specific allergens and viruses. In contrast, known gene risk factors ... between disease-related genetic variations and the immune system. For the Alzheimer’s research community, the findings offer ...

28

Gene expression analysis distinguishes tissue specific and gender related functions among adult Ascaris suum tissues  

PubMed Central

Over a billion people are infected by Ascaris spp. intestinal parasites. To clarify functional differences among tissues of adult A. suum, we compared gene expression by various tissues of these worms by expression microarray methods.. The A. suum genome was sequenced and assembled to allow generation of microarray elements. Expression of over 40,000 60-mer elements was investigated in a variety of tissues from both male and female adult worms. Nearly 50 percent of the elements for which signal was detected exhibited differential expression among different tissues. The unique profile of transcripts identified for each tissue clarified functional distinctions among tissues, such as chitin binding in the ovary and peptidase activity in the intestines. Interestingly, hundreds of gender-specific elements were characterized in multiple non-reproductive tissues of female or male worms, with most prominence of gender differences in intestinal tissue. A. suum genes from the same family were frequently expressed differently among tissues. Transcript abundance for genes specific to A. suum, by comparison to Caenorhabditis elegans, varied to a greater extent among tissues than for genes conserved between A. suum and C. elegans. Analysis using C. elegans protein interaction data identified functional modules conserved between these two nematodes, resulting in identification of functional predictions of essential subnetworks of protein interactions and how these networks may vary among nematode tissues. A notable finding was very high module similarity between adult reproductive tissues and intestine. Our results provide the most comprehensive assessment of gene expression among tissues of a parasitic nematode to date.

Wang, Zhengyuan; Gao, Xin; Martin, John; Yin, Yong; Abubucker, Sahar; Rash, Amy C.; Li, Ben-Wen; Nash, Bill; Hallsworth-Pepin, Kym; Jasmer, Douglas P.; Mitreva, Makedonka

2013-01-01

29

Ovoinhibitor introns specify functional domains as in the related and linked ovomucoid gene.  

PubMed

We have isolated cDNA clones and determined the gene structure of chicken ovoinhibitor, a seven domain Kazal serine proteinase inhibitor. Using RNA blot hybridization analysis, the gene was identified initially as a region 9-23 kilobases upstream of the gene for the related inhibitor ovomucoid. Ovoinhibitor RNA appears in oviduct and liver. cDNA clones were identified by screening an oviduct cDNA library with a nick-translated DNA restriction fragment which contained an exon of the gene. The mature protein sequence derived from a cDNa clone is in excellent agreement with that which we obtained from direct sequencing of purified ovoinhibitor. The protein-sequencing strategy is reported. The P1 amino acids of the Kazal domains are consistent with the known broad inhibitory specificity of ovoinhibitor. The gene is about 10.3 kilobases in length and consists of 16 exons. Each Kazal domain is encoded by two exons. Like ovomucoid, introns fall between the coding sequences of the ovoinhibitor domains, an arrangement which may have facilitated domain duplication. The intradomain intron occurs in an identical position in all of the ovoinhibitor and ovomucoid Kazal domains, suggesting that this intron was present in the primordial inhibitor gene. We discuss the location of the intradomain intron in relation to the known structure of four Kazal inhibitors and suggest a scheme for the evolution of the ovoinhibitor gene. PMID:3571241

Scott, M J; Huckaby, C S; Kato, I; Kohr, W J; Laskowski, M; Tsai, M J; O'Malley, B W

1987-04-25

30

The stn- 1 Syntrophin Gene of C. elegans is Functionally Related to Dystrophin and Dystrobrevin  

Microsoft Academic Search

Syntrophins are a family of PDZ domain-containing adaptor proteins required for receptor localization. Syntrophins are also associated with the dystrophin complex in muscles. We report here the molecular and functional characterization of the Caenorhabditis elegans gene stn-1 (F30A10.8), which encodes a syntrophin with homology to vertebrate alpha and beta-syntrophins. stn-1 is expressed in neurons and in muscles of C.elegans. stn-1

Karine Grisoni; Kathrin Gieseler; Marie-Christine Mariol; Edwige Martin; Maité Carre-Pierrat; Gary Moulder; Robert Barstead; Laurent Ségalat

2003-01-01

31

Structural and functional characterization of the product of disease-related factor H gene conversion.  

PubMed

Numerous complement factor H (FH) mutations predispose patients to atypical hemolytic uremic syndrome (aHUS) and other disorders arising from inadequately regulated complement activation. No unifying structural or mechanistic consequences have been ascribed to these mutants beyond impaired self-cell protection. The S1191L and V1197A mutations toward the C-terminus of FH, which occur in patients singly or together, arose from gene conversion between CFH encoding FH and CFHR1 encoding FH-related 1. We show that neither single nor double mutations structurally perturbed recombinant proteins consisting of the FH C-terminal modules, 19 and 20 (FH19-20), although all three FH19-20 mutants were poor, compared to wild-type FH19-20, at promoting hemolysis of C3b-coated erythrocytes through competition with full-length FH. Indeed, our new crystal structure of the S1191L mutant of FH19-20 complexed with an activation-specific complement fragment, C3d, was nearly identical to that of the wild-type FH19-20:C3d complex, consistent with mutants binding to C3b with wild-type-like affinity. The S1191L mutation enhanced thermal stability of module 20, whereas the V1197A mutation dramatically decreased it. Thus, although mutant proteins were folded at 37 °C, they differ in conformational rigidity. Neither single substitutions nor double substitutions increased measurably the extent of FH19-20 self-association, nor did these mutations significantly affect the affinity of FH19-20 for three glycosaminoglycans, despite critical roles of module 20 in recognizing polyanionic self-surface markers. Unexpectedly, FH19-20 mutants containing Leu1191 self-associated on a heparin-coated surface to a higher degree than on surfaces coated with dermatan or chondroitin sulfates. Thus, potentially disease-related functional distinctions between mutants, and between FH and FH-related 1, may manifest in the presence of specific glycosaminoglycans. PMID:22320225

Herbert, Andrew P; Kavanagh, David; Johansson, Conny; Morgan, Hugh P; Blaum, Bärbel S; Hannan, Jonathan P; Barlow, Paul N; Uhrín, Dušan

2012-03-01

32

Immune-Related Functions of the Hivep Gene Family in East African Cichlid Fishes  

PubMed Central

Immune-related genes are often characterized by adaptive protein evolution. Selection on immune genes can be particularly strong when hosts encounter novel parasites, for instance, after the colonization of a new habitat or upon the exploitation of vacant ecological niches in an adaptive radiation. We examined a set of new candidate immune genes in East African cichlid fishes. More specifically, we studied the signatures of selection in five paralogs of the human immunodeficiency virus type I enhancer-binding protein (Hivep) gene family, tested their involvement in the immune defense, and related our results to explosive speciation and adaptive radiation events in cichlids. We found signatures of long-term positive selection in four Hivep paralogs and lineage-specific positive selection in Hivep3b in two radiating cichlid lineages. Exposure of the cichlid Astatotilapia burtoni to a vaccination with Vibrio anguillarum bacteria resulted in a positive correlation between immune response parameters and expression levels of three Hivep loci. This work provides the first evidence for a role of Hivep paralogs in teleost immune defense and links the signatures of positive selection to host–pathogen interactions within an adaptive radiation.

Diepeveen, Eveline T.; Roth, Olivia; Salzburger, Walter

2013-01-01

33

Expanding the Landscape of Chromatin Modification (CM)-Related Functional Domains and Genes in Human  

PubMed Central

Chromatin modification (CM) plays a key role in regulating transcription, DNA replication, repair and recombination. However, our knowledge of these processes in humans remains very limited. Here we use computational approaches to study proteins and functional domains involved in CM in humans. We analyze the abundance and the pair-wise domain-domain co-occurrences of 25 well-documented CM domains in 5 model organisms: yeast, worm, fly, mouse and human. Results show that domains involved in histone methylation, DNA methylation, and histone variants are remarkably expanded in metazoan, reflecting the increased demand for cell type-specific gene regulation. We find that CM domains tend to co-occur with a limited number of partner domains and are hence not promiscuous. This property is exploited to identify 47 potentially novel CM domains, including 24 DNA-binding domains, whose role in CM has received little attention so far. Lastly, we use a consensus Machine Learning approach to predict 379 novel CM genes (coding for 329 proteins) in humans based on domain compositions. Several of these predictions are supported by very recent experimental studies and others are slated for experimental verification. Identification of novel CM genes and domains in humans will aid our understanding of fundamental epigenetic processes that are important for stem cell differentiation and cancer biology. Information on all the candidate CM domains and genes reported here is publicly available.

Pu, Shuye; Turinsky, Andrei L.; Vlasblom, James; On, Tuan; Xiong, Xuejian; Emili, Andrew; Zhang, Zhaolei; Greenblatt, Jack; Parkinson, John; Wodak, Shoshana J.

2010-01-01

34

Functional Characterization of a Juvenile Hormone Esterase Related Gene in the Moth Sesamia nonagrioides through RNA Interference  

PubMed Central

Juvenile hormone esterase (JHE) is a carboxylesterase that has attracted great interest because of its critical role in regulating larval to adult transition in insects and other arthropods. Previously, we characterized an ecdysteroid sensitive and juvenile hormone non-susceptible juvenile hormone esterase related gene (SnJHER) in the corn stalk borer, Sesamia nonagrioides. SnJHER was rhythmically up-regulated close to each molt during the corn stalk borer’s larval development. In this paper we attempted to functionally characterize SnJHER using several reverse genetics techniques. To functionally characterize SnJHER, we experimented with different dsRNA administration methods, including hemolymph, bacterial or baculovirus-mediated RNA interference, (RNAi). Our findings indicate the potential implication of SnJHER in the developmental programming of Sesamia nonagrioides. It is still unclear whether SnJHER is closely related to the authentic JHE gene, with different or similar biological functions.

Kontogiannatos, Dimitrios; Swevers, Luc; Maenaka, Katsumi; Park, Enoch Y.; Iatrou, Kostas; Kourti, Anna

2013-01-01

35

A genome-wide survey and functional brain imaging study identify CTNNBL1 as a memory-related gene.  

PubMed

Unbiased genome-wide screens combined with imaging data on brain function may identify novel molecular pathways related to human cognition. Here we performed a dense genome-wide screen to identify episodic memory-related gene variants. A genomic locus encoding the brain-expressed beta-catenin-like protein 1 (CTNNBL1) was significantly (P=7 × 10(-8)) associated with verbal memory performance in a cognitively healthy cohort from Switzerland (n=1073) and was replicated in a second cohort from Serbia (n=524; P=0.003). Gene expression studies showed CTNNBL1 genotype-dependent differences in beta-catenin-like protein 1 mRNA levels in the human cortex. Functional magnetic resonance imaging in 322 subjects detected CTNNBL1 genotype-dependent differences in memory-related brain activations. Converging evidence from independent experiments and different methodological approaches suggests a role for CTNNBL1 in human memory. PMID:22105620

Papassotiropoulos, A; Stefanova, E; Vogler, C; Gschwind, L; Ackermann, S; Spalek, K; Rasch, B; Heck, A; Aerni, A; Hanser, E; Demougin, P; Huynh, K-D; Luechinger, R; Klarhöfer, M; Novakovic, I; Kostic, V; Boesiger, P; Scheffler, K; de Quervain, D J-F

2013-02-01

36

A genome-wide survey and functional brain imaging study identify CTNNBL1 as a memory-related gene  

PubMed Central

Unbiased genome-wide screens combined with imaging data on brain function may identify novel molecular pathways related to human cognition. Here we performed a dense genome-wide screen to identify episodic memory-related gene variants. A genomic locus encoding the brain-expressed beta-catenin-like protein 1 (CTNNBL1) was significantly (P=7 × 10?8) associated with verbal memory performance in a cognitively healthy cohort from Switzerland (n=1073) and was replicated in a second cohort from Serbia (n=524; P=0.003). Gene expression studies showed CTNNBL1 genotype-dependent differences in beta-catenin-like protein 1 mRNA levels in the human cortex. Functional magnetic resonance imaging in 322 subjects detected CTNNBL1 genotype-dependent differences in memory-related brain activations. Converging evidence from independent experiments and different methodological approaches suggests a role for CTNNBL1 in human memory.

Papassotiropoulos, A; Stefanova, E; Vogler, C; Gschwind, L; Ackermann, S; Spalek, K; Rasch, B; Heck, A; Aerni, A; Hanser, E; Demougin, P; Huynh, K-D; Luechinger, R; Klarhofer, M; Novakovic, I; Kostic, V; Boesiger, P; Scheffler, K; de Quervain, D J-F

2013-01-01

37

Discovery of Genes Related to Insecticide Resistance in Bactrocera dorsalis by Functional Genomic Analysis of a De Novo Assembled Transcriptome  

PubMed Central

Insecticide resistance has recently become a critical concern for control of many insect pest species. Genome sequencing and global quantization of gene expression through analysis of the transcriptome can provide useful information relevant to this challenging problem. The oriental fruit fly, Bactrocera dorsalis, is one of the world's most destructive agricultural pests, and recently it has been used as a target for studies of genetic mechanisms related to insecticide resistance. However, prior to this study, the molecular data available for this species was largely limited to genes identified through homology. To provide a broader pool of gene sequences of potential interest with regard to insecticide resistance, this study uses whole transcriptome analysis developed through de novo assembly of short reads generated by next-generation sequencing (NGS). The transcriptome of B. dorsalis was initially constructed using Illumina's Solexa sequencing technology. Qualified reads were assembled into contigs and potential splicing variants (isotigs). A total of 29,067 isotigs have putative homologues in the non-redundant (nr) protein database from NCBI, and 11,073 of these correspond to distinct D. melanogaster proteins in the RefSeq database. Approximately 5,546 isotigs contain coding sequences that are at least 80% complete and appear to represent B. dorsalis genes. We observed a strong correlation between the completeness of the assembled sequences and the expression intensity of the transcripts. The assembled sequences were also used to identify large numbers of genes potentially belonging to families related to insecticide resistance. A total of 90 P450-, 42 GST-and 37 COE-related genes, representing three major enzyme families involved in insecticide metabolism and resistance, were identified. In addition, 36 isotigs were discovered to contain target site sequences related to four classes of resistance genes. Identified sequence motifs were also analyzed to characterize putative polypeptide translational products and associate them with specific genes and protein functions.

Hsu, Ju-Chun; Wu, Wen-Jer; Feng, Hai-Tung; Haymer, David S.; Chen, Chien-Yu

2012-01-01

38

A pair of functionally redundant yeast genes (PPZ1 and PPZ2) encoding type 1-related protein phosphatases function within the PKC1-mediated pathway.  

PubMed Central

The PKC1 gene of Saccharomyces cerevisiae encodes a homolog of mammalian protein kinase C that is required for yeast cell growth. Loss of PKC1 function results in cell lysis due to an inability to remodel the cell wall properly during growth. The PKC1 gene has been proposed to regulate a bifurcated pathway, on one branch of which function four putative protein kinases that catalyze a linear cascade of protein phosphorylation culminating in the activation of the mitogen-activated protein kinase homolog, Mpk1p. Here we describe two genes whose overexpression suppress both an mpk1 delta mutation and a pkc1 delta mutation. One of these genes is identical to the previously identified PPZ2 gene. The PPZ2 gene is predicted to encode a type 1-related protein phosphatase and is functionally redundant with a closely related gene, designated PPZ1. Deletion of both PPZ1 and PPZ2 resulted in a temperature-dependent cell lysis defect similar to that observed for bck1 delta, mkk1,2 delta, or mpk1 delta mutants. However, ppz1,2 delta mpk1 delta triple mutants displayed a cell lysis defect at all temperatures. The additivity of the ppz1,2 delta defect with the mpk1 delta defect, combined with the results of genetic epistasis experiments, suggested either that the PPZ1- and PPZ2-encoded protein phosphatases function on a branch of the PKC1-mediated pathway different from that defined by the protein kinases or that they play an auxiliary role in the pathway. The other suppressor gene, designated BCK2 (for bypass of C kinase), is predicted to encode a 92-kDa protein that is rich in serine and threonine residues. Genetic interactions between BCK2 and other pathway components suggested that BCK2 functions on a common pathway branch with PPZ1 and PPZ2. Images

Lee, K S; Hines, L K; Levin, D E

1993-01-01

39

Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites  

PubMed Central

Microsporidia of the genus Encephalitozoon are widespread pathogens of animals that harbor the smallest known nuclear genomes. Complete sequences from Encephalitozoon intestinalis (2.3 Mbp) and Encephalitozoon cuniculi (2.9 Mbp) revealed massive gene losses and reduction of intergenic regions as factors leading to their drastically reduced genome size. However, microsporidian genomes also have gained genes through horizontal gene transfers (HGT), a process that could allow the parasites to exploit their hosts more fully. Here, we describe the complete sequences of two intermediate-sized genomes (2.5 Mbp), from Encephalitozoon hellem and Encephalitozoon romaleae. Overall, the E. hellem and E. romaleae genomes are strikingly similar to those of Encephalitozoon cuniculi and Encephalitozoon intestinalis in both form and content. However, in addition to the expected expansions and contractions of known gene families in subtelomeric regions, both species also were found to harbor a number of protein-coding genes that are not found in any other microsporidian. All these genes are functionally related to the metabolism of folate and purines but appear to have originated by several independent HGT events from different eukaryotic and prokaryotic donors. Surprisingly, the genes are all intact in E. hellem, but in E. romaleae those involved in de novo synthesis of folate are all pseudogenes. Overall, these data suggest that a recent common ancestor of E. hellem and E. romaleae assembled a complete metabolic pathway from multiple independent HGT events and that one descendent already is dispensing with much of this new functionality, highlighting the transient nature of transferred genes.

Pombert, Jean-Francois; Selman, Mohammed; Burki, Fabien; Bardell, Floyd T.; Farinelli, Laurent; Solter, Leellen F.; Whitman, Douglas W.; Weiss, Louis M.; Corradi, Nicolas; Keeling, Patrick J.

2012-01-01

40

Combination Training in Aging Individuals Modifies Functional Connectivity and Cognition, and Is Potentially Affected by Dopamine-Related Genes  

PubMed Central

Background Aging is a major co-risk factor in many neurodegenerative diseases. Cognitive enrichment positively affects the structural plasticity of the aging brain. In this study, we evaluated effects of a set of structured multimodal activities (Combination Training; CT) on cognitive performances, functional connectivity, and cortical thickness of a group of healthy elderly individuals. CT lasted six months. Methodology Neuropsychological and occupational performances were evaluated before and at the end of the training period. fMRI was used to assess effects of training on resting state network (RSN) functional connectivity using Independent Component Analysis (ICA). Effects on cortical thickness were also studied. Finally, we evaluated whether specific dopamine-related genes can affect the response to training. Principal Findings Results of the study indicate that CT improves cognitive/occupational performances and reorganizes functional connectivity. Intriguingly, individuals responding to CT showed specific dopamine-related genotypes. Indeed, analysis of dopamine-related genes revealed that carriers of DRD3 ser9gly and COMT Val158Met polymorphisms had the greatest benefits from exposure to CT. Conclusions and Significance Overall, our findings support the idea that exposure to a set of structured multimodal activities can be an effective strategy to counteract aging-related cognitive decline and also indicate that significant capability of functional and structural changes are maintained in the elderly.

Pieramico, Valentina; Esposito, Roberto; Sensi, Francesca; Cilli, Franco; Mantini, Dante; Mattei, Peter A.; Frazzini, Valerio; Ciavardelli, Domenico; Gatta, Valentina; Ferretti, Antonio; Romani, Gian Luca; Sensi, Stefano L.

2012-01-01

41

Functional Variants in the Catalase and Myeloperoxidase Genes, Ambient Air Pollution, and Respiratory-related School Absences: An Example of Epistasis in Gene-Environment Interactions  

PubMed Central

The individual effect of functional single nucleotide polymorphisms within the catalase and myeloperoxidase genes (CAT and MPO) has been studied in relation to asthma; however, their interrelationship with ambient air pollution exposures has yet to be determined. The authors investigated the interrelationships between variants in CAT and MPO, ambient air pollutants, and acute respiratory illness. Health information, air pollution, and incident respiratory-related school absences were ascertained in January–June 1996 for 1,136 Hispanic and non-Hispanic white US elementary schoolchildren as part of the prospective Children's Health Study. Functional and tagging single nucleotide polymorphisms for the CAT and MPO loci were genotyped. The authors found epistasis between functional polymorphisms in the CAT/MPO loci, which differed by levels of oxidant-stress-producing air pollutants. Risk of respiratory-related school absences was elevated for children with the CAT (G/G) and MPO (G/A or A/A) genes (relative risk?=?1.35, 95% confidence interval: 1.03, 1.77; P-interaction?=?0.005). The epistatic effect of CAT and MPO variants was most evident in communities exhibiting high ambient ozone levels (P-interaction?=?0.03). The association of respiratory-illness absences with functional variants in CAT and MPO that differ by air pollution levels illustrates the need to consider genetic epistasis in assessing gene-environment interactions.

Wenten, Made; Gauderman, W. James; Berhane, Kiros; Lin, Pi-Chu; Peters, John; Gilliland, Frank D.

2009-01-01

42

Brassica GLABRA2 genes: analysis of function related to seed oil content and development of functional markers.  

PubMed

Regulation of seed oil accumulation in oilseed rape (Brassica napus) has important economic significance. However, few genes have been characterized that affect final seed oil content. Through a mutant identification, the class IV homeodomain-ZIP transcription factor GLABRA2 (GL2) has been found to regulate seed oil accumulation in Arabidopsis, in addition to its role in trichome development. In this study, we isolated four distinct orthologues of GL2 from B. napus (AC-genome), B. rapa (A) and B. oleracea (C), using an overlapping-PCR strategy. The four GL2 orthologues were very similar, with 96.10-99.69% identity in exon regions, 75.45-93.84% in intron regions, 97.34-99.87% in amino acid sequences. Alignments of the four genes revealed that the A-genome sequences of BnaA.GL2.a from B. napus and BraA.GL2.a from B. rapa are more similar than the others, and likewise the C-genome sequences of BnaC.GL2.b from B. napus and BolC.GL2.a from B. oleracea are more similar. BnaA.GL2.a and BraA.GL2.a from the A-genome are highly expressed in roots, whilst BnaC.GL2.b and BolC.GL2.a from the C-genome are preferentially expressed in seeds. Transgenic ectopic overexpression and suppression of BnaC.GL2.b in Arabidopsis allowed further investigation of the effect on seed oil content. Overexpression generated two phenotypes: the wild-type-like and the gl2-mutant-like (an Arabidopsis glabrous mutant of gl2-2), with increases in seed oil content of 3.5-5.0% in the gl2-mutant-like transgenic plants. Suppression resulted in increases of 2.5-6.1% in seed oil content, and reduced trichome number at the leaf margins. These results suggest that BnaC.GL2.b can negatively regulate oil accumulation in Arabidopsis seeds. As a result of comparing the four GL2 genes, three A/C-genome-specific primer sets were developed and a C-genome-specific EcoRV cleavage site was identified, which can be used as functional markers to distinguish these orthologues within Brassica species. The genes identified and their molecular markers developed in this study will be valuable both for oilseed rape breeding focusing on improvement of seed oil content, and for detecting gene flow between populations. PMID:20162256

Chai, Guohua; Bai, Zetao; Wei, Fang; King, Graham J; Wang, Chenggang; Shi, Lei; Dong, Caihua; Chen, Hong; Liu, Shengyi

2010-05-01

43

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes  

Microsoft Academic Search

Gene expression signatures of toxicity and clinical response benefit both safety assessment and clinical practice; however, difficulties in connecting signature genes with the predicted end points have limited their application. The Microarray Quality Control Consortium II (MAQCII) project generated 262 signatures for ten clinical and three toxicological end points from six gene expression data sets, an unprecedented collection of diverse

W Shi; M Bessarabova; D Dosymbekov; Z Dezso; T Nikolskaya; M Dudoladova; T Serebryiskaya; A Bugrim; A Guryanov; R J Brennan; R Shah; J Dopazo; M Chen; Y Deng; T Shi; G Jurman; C Furlanello; R S Thomas; J C Corton; W Tong; L Shi; Y Nikolsky

2010-01-01

44

WUSCHEL-related Homeobox genes in Populus tomentosa: diversified expression patterns and a functional similarity in adventitious root formation  

PubMed Central

Background WUSCHEL (WUS)-related homeobox (WOX) protein family members play important roles in the maintenance and proliferation of the stem cell niche in the shoot apical meristem (SAM), root apical meristem (RAM), and cambium (CAM). Although the roles of some WOXs in meristematic cell regulation have been well studied in annual plants such as Arabidopsis and rice, the expression and function of WOX members in woody plant poplars has not been systematically investigated. Here, we present the identification and comprehensive analysis of the expression and function of WOXs in Populus tomentosa. Results A genome-wide survey identified 18 WOX encoding sequences in the sequenced genome of Populus trichocarpa (PtrWOXs). Phylogenetic and gene structure analysis revealed that these 18 PtrWOXs fall into modern/WUS, intermediate, and ancient clades, but that the WOX genes in P. trichocarpa may have expanded differently from the WOX genes in Arabidopsis. In the P. trichocarpa genome, no WOX members could be closely classified as AtWOX3, AtWOX6, AtWOX7, AtWOX10, and AtWOX14, but there were two copies of WOX genes that could be classified as PtrWUS, PtrWOX2, PtrWOX4, PtrWOX5, PtrWOX8/9, and PtrWOX11/12, and three copies of WOX genes that could be classified as PtrWOX1 and PtrWOX13. The use of primers specific for each PtrWOX gene allowed the identification and cloning of 18 WOX genes from P. tomentosa (PtoWOXs), a poplar species physiologically close to P. trichocarpa. It was found that PtoWOXs and PtrWOXs shared very high amino acid sequence identity, and that PtoWOXs could be classified identically to PtrWOXs. We revealed that the expression patterns of some PtoWOXs were different to their Arabidopsis counterparts. When PtoWOX5a and PtoWOX11/12a, as well as PtoWUSa and PtoWOX4a were ectopically expressed in transgenic hybrid poplars, the regeneration of adventitious root (AR) was promoted, indicating a functional similarity of these four WOXs in AR regeneration. Conclusions This is the first attempt towards a systematical analysis of the function of WOXs in P. tomentosa. A diversified expression, yet functional similarity of PtoWOXs in AR regeneration is revealed. Our findings provide useful information for further elucidation of the functions and mechanisms of WOXs in the development of poplars.

2014-01-01

45

A novel family of TRF (DNA topoisomerase I-related function) genes required for proper nuclear segregation.  

PubMed Central

We recently reported the identification of a gene, TRF4 (for DNA topoisomerase related function), in a screen for mutations that are synthetically lethal with mutations in DNA topoisomerase I (top1). Here we describe the isolation of a second member of the TRF4 gene family, TRF5. Overexpression of TRF5 complements the inviability of top1 trf4 double mutants. The predicted Trf5 protein is 55% identical and 72% similar to Trf4p. As with Trf4p, a region of Trf5p is homologous to the catalytically dispensable N-terminus of Top1p. The TRF4/5 function is essential as trf4 trf5 double mutants are inviable. A trf4 (ts) trf5 double mutant is hypersensitive to the anti-microtubule agent thiabendazole at a semi-permissive temperature, suggesting that TRF4/5 function is required at the time of mitosis. Examination of nuclear morphology in a trf4 (ts) trf5 mutant at a restrictive temperature reveals the presence of many cells undergoing aberrant nuclear division, as well as many anucleate cells, demonstrating that the TRF4/5 function is required for proper mitosis. Database searches reveal the existence of probable Schizosaccharomyces pombe and human homologs of Trf4p, indicating that TRF4 is the canonical member of a gene family that is highly conserved evolutionarily.

Castano, I B; Heath-Pagliuso, S; Sadoff, B U; Fitzhugh, D J; Christman, M F

1996-01-01

46

Calcitonin Gene-Related Peptide Regulates Type IV Hypersensitivity through Dendritic Cell Functions  

PubMed Central

Dendritic cells (DCs) play essential roles in both innate and adaptive immune responses. In addition, mutual regulation of the nervous system and immune system is well studied. One of neuropeptides, calcitonin gene-related peptide (CGRP), is a potent regulator in immune responses; in particular, it has anti-inflammatory effects in innate immunity. For instance, a deficiency of the CGRP receptor component RAMP 1 (receptor activity-modifying protein 1) results in higher cytokine production in response to LPS (lipopolysaccharide). On the other hand, how CGRP affects DCs in adaptive immunity is largely unknown. In this study, we show that CGRP suppressed Th1 cell differentiation via inhibition of IL-12 production in DCs using an in vitro co-culture system and an in vivo ovalbumin-induced delayed-type hypersensitivity (DTH) model. CGRP also down-regulated the expressions of chemokine receptor CCR2 and its ligands CCL2 and CCL12 in DCs. Intriguingly, the frequency of migrating CCR2+ DCs in draining lymph nodes of RAMP1-deficient mice was higher after DTH immunization. Moreover, these CCR2+ DCs highly expressed IL-12 and CD80, resulting in more effective induction of Th1 differentiation compared with CCR2? DCs. These results indicate that CGRP regulates Th1 type reactions by regulating expression of cytokines, chemokines, and chemokine receptors in DCs.

Mikami, Norihisa; Sueda, Kaori; Ogitani, Yusuke; Otani, Ippei; Takatsuji, Miku; Wada, Yasuko; Watanabe, Keiko; Yoshikawa, Rintaro; Nishioka, Satoshi; Hashimoto, Nagisa; Miyagi, Yayoi; Fukada, So-ichiro; Yamamoto, Hiroshi; Tsujikawa, Kazutake

2014-01-01

47

Calcitonin gene-related peptide regulates type IV hypersensitivity through dendritic cell functions.  

PubMed

Dendritic cells (DCs) play essential roles in both innate and adaptive immune responses. In addition, mutual regulation of the nervous system and immune system is well studied. One of neuropeptides, calcitonin gene-related peptide (CGRP), is a potent regulator in immune responses; in particular, it has anti-inflammatory effects in innate immunity. For instance, a deficiency of the CGRP receptor component RAMP 1 (receptor activity-modifying protein 1) results in higher cytokine production in response to LPS (lipopolysaccharide). On the other hand, how CGRP affects DCs in adaptive immunity is largely unknown. In this study, we show that CGRP suppressed Th1 cell differentiation via inhibition of IL-12 production in DCs using an in vitro co-culture system and an in vivo ovalbumin-induced delayed-type hypersensitivity (DTH) model. CGRP also down-regulated the expressions of chemokine receptor CCR2 and its ligands CCL2 and CCL12 in DCs. Intriguingly, the frequency of migrating CCR2(+) DCs in draining lymph nodes of RAMP1-deficient mice was higher after DTH immunization. Moreover, these CCR2(+) DCs highly expressed IL-12 and CD80, resulting in more effective induction of Th1 differentiation compared with CCR2(-) DCs. These results indicate that CGRP regulates Th1 type reactions by regulating expression of cytokines, chemokines, and chemokine receptors in DCs. PMID:24466057

Mikami, Norihisa; Sueda, Kaori; Ogitani, Yusuke; Otani, Ippei; Takatsuji, Miku; Wada, Yasuko; Watanabe, Keiko; Yoshikawa, Rintaro; Nishioka, Satoshi; Hashimoto, Nagisa; Miyagi, Yayoi; Fukada, So-ichiro; Yamamoto, Hiroshi; Tsujikawa, Kazutake

2014-01-01

48

Expression of Endometrial Immune-related Genes Possibly Functioning During Early Pregnancy in the Mare  

PubMed Central

Abstract Despite enormous efforts, biochemical and molecular mechanisms associated with equine reproduction, particularly processes of pregnancy establishment, have not been well characterized. Previously, PCR-selected suppression subtraction hybridization analysis was executed to identify unique molecules functioning in the equine endometrium during periods of pregnancy establishment, and granzyme B (GZMB) cDNA was found in the pregnant endometrial cDNA library. Because GZMB is produced from natural killer (NK) cells, endometrial expression of GZMB and immune-related transcripts were characterized in this study. The level of GZMB mRNA is higher in the pregnant endometrium than in non-pregnant ones. This expression was also confirmed through Western blot and immunohistochemical analyses. IL-2 mRNA declined as pregnancy progressed, while IL-15, IFNG and TGFB1 transcripts increased on day 19 and/or 25. Analyses of IL-4 and IL-12 mRNAs demonstrated the increase in these transcripts as pregnancy progressed. Increase in CCR5 and CCR4 mRNAs indicated that both Th1 and Th2 cells coexisted in the day 25 pregnant endometrium. Taken together, the endometrial expression of immune-related transcripts suggests that immunological responses are present even before the trophectoderm actually attaches to the uterine epithelial cells.

TACHIBANA, Yurika; NAKANO, Yasuko; NAGAOKA, Kentaro; KIKUCHI, Masato; NAMBO, Yasuo; HANEDA, Shingo; MATSUI, Motozumi; MIYAKE, Yo-ichi; IMAKAWA, Kazuhiko

2012-01-01

49

Structure and Expression Analyses of SVA Elements in Relation to Functional Genes  

PubMed Central

SINE-VNTR-Alu (SVA) elements are present in hominoid primates and are divided into 6 subfamilies (SVA-A to SVA-F) and active in the human population. Using a bioinformatic tool, 22 SVA element-associated genes are identified in the human genome. In an analysis of genomic structure, SVA elements are detected in the 5' untranslated region (UTR) of HGSNAT (SVA-B), MRGPRX3 (SVA-D), HYAL1 (SVA-F), TCHH (SVA-F), and ATXN2L (SVA-F) genes, while some elements are observed in the 3'UTR of SPICE1 (SVA-B), TDRKH (SVA-C), GOSR1 (SVA-D), BBS5 (SVA-D), NEK5 (SVA-D), ABHD2 (SVA-F), C1QTNF7 (SVA-F), ORC6L (SVA-F), TMEM69 (SVA-F), and CCDC137 (SVA-F) genes. They could contribute to exon extension or supplying poly A signals. LEPR (SVA-C), ALOX5 (SVA-D), PDS5B (SVA-D), and ABCA10 (SVA-F) genes also showed alternative transcripts by SVA exonization events. Dominant expression of HYAL1_SVA appeared in lung tissues, while HYAL1_noSVA showed ubiquitous expression in various human tissues. Expression of both transcripts (TDRKH_SVA and TDRKH_noSVA) of the TDRKH gene appeared to be ubiquitous. Taken together, these data suggest that SVA elements cause transcript isoforms that contribute to modulation of gene regulation in various human tissues.

Kwon, Yun-Jeong; Choi, Yuri; Eo, Jungwoo; Noh, Yu-Na; Gim, Jeong-An; Jung, Yi-Deun; Lee, Ja-Rang

2013-01-01

50

Brassica GLABRA2 genes: analysis of function related to seed oil content and development of functional markers  

Microsoft Academic Search

Regulation of seed oil accumulation in oilseed rape (Brassica napus) has important economic significance. However, few genes have been characterized that affect final seed oil content. Through\\u000a a mutant identification, the class IV homeodomain-ZIP transcription factor GLABRA2 (GL2) has been found to regulate seed oil\\u000a accumulation in Arabidopsis, in addition to its role in trichome development. In this study, we

Guohua Chai; Zetao Bai; Fang Wei; Graham J. King; Chenggang Wang; Lei Shi; Caihua Dong; Hong Chen; Shengyi Liu

2010-01-01

51

Association study of functional genetic variants of innate immunity related genes in celiac disease  

Microsoft Academic Search

BACKGROUND: Recent evidence suggest that the innate immune system is implicated in the early events of celiac disease (CD) pathogenesis. In this work for the first time we have assessed the relevance of different proinflammatory mediators typically related to innate immunity in CD predisposition. METHODS: We performed a familial study in which 105 celiac families characterized by the presence of

B Rueda; A Zhernakova; MA López-Nevot; J Martín; BPC Koeleman

2005-01-01

52

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes  

Microsoft Academic Search

EPConDB (http:\\/\\/www.cbil.upenn.edu\\/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth,

Joan M. Mazzarelli; John Brestelli; Regina K. Gorski; Junmin Liu; Elisabetta Manduchi; Deborah F. Pinney; Jonathan Schug; Peter White; Klaus H. Kaestner; Christian J. Stoeckert Jr.

2007-01-01

53

Potentially functional genetic variants in microRNA processing genes and risk of HBV-related hepatocellular carcinoma.  

PubMed

Genetic variations in miRNA processing genes may affect the biogenesis of miRNA, hence risk of HBV infection and hepatocellular carcinoma (HCC) development. In the present study, we hypothesized that potentially functional polymorphisms in 3'-untranslated region (UTR) of miRNA processing genes might contribute to susceptibility of HBV infection and HCC development. To test the hypothesis, we genotyped three selected SNPs (rs1057035 in DICER1, rs3803012 in RAN, and rs10773771 in PIWIL1) in a case-control study of 1300 HBV-positive HCC cancer cases, 1344 HBV persistent carriers, and 1344 HBV natural clearance subjects in Chinese. We observed that DICER1 rs1057035 CT/CC variant genotypes were associated with a significant decreased risk of HCC (adjusted OR = 0.79, 95% CI = 0.64-0.96) compared with wild-type TT and RAN rs3803012 AG/GG variant genotypes increased the risk of HBV persistent infection compared with AA genotype (adjusted OR = 1.35, 95% CI = 1.03-1.77). However, PIWIL1 rs10773771 CT/CC variant genotypes were associated with an approaching decreased risk of HCC (adjusted OR = 0.86, 95% CI = 0.73-1.01) and similar with RAN rs3803012 AG/GG (adjusted OR = 0.80, 95% CI = 0.61-1.06). Furthermore, reporter gene assays indicated that the three SNPs (rs1057035, rs3803012, and rs10773771) might change the binding ability of miRNAs to the 3'UTR of the three genes (DICER1, RAN, and PIWIL1), respectively. These findings indicated that DICER1 rs1057035, RAN rs3803012, and PIWIL1 rs10773771 might contribute to the risk of HBV-related HCC. PMID:23868705

Liu, Li; An, Jiaze; Liu, Jibin; Wen, Juan; Zhai, Xiangjun; Liu, Yao; Pan, Shandong; Jiang, Jie; Wen, Yang; Liu, Zheng; Zhang, Yixin; Chen, Jianguo; Xing, Jinliang; Ji, Guozhong; Shen, Hongbing; Hu, Zhibin; Fan, Zhining

2013-11-01

54

Hammondia hammondi, an avirulent relative of Toxoplasma gondii, has functional orthologs of known T. gondii virulence genes  

PubMed Central

Toxoplasma gondii is a ubiquitous protozoan parasite capable of infecting all warm-blooded animals, including humans. Its closest extant relative, Hammondia hammondi, has never been found to infect humans and, in contrast to T. gondii, is highly attenuated in mice. To better understand the genetic bases for these phenotypic differences, we sequenced the genome of a H. hammondi isolate (HhCatGer041) and found the genomic synteny between H. hammondi and T. gondii to be >95%. We used this genome to determine the H. hammondi primary sequence of two major T. gondii mouse virulence genes, TgROP5 and TgROP18. When we expressed these genes in T. gondii, we found that H. hammondi orthologs of TgROP5 and TgROP18 were functional. Similar to T. gondii, the HhROP5 locus is expanded, and two distinct HhROP5 paralogs increased the virulence of a T. gondii TgROP5 knockout strain. We also identified a 107 base pair promoter region, absent only in type III TgROP18, which is necessary for TgROP18 expression. This result indicates that the ROP18 promoter was active in the most recent common ancestor of these two species and that it was subsequently inactivated in progenitors of the type III lineage. Overall, these data suggest that the virulence differences between these species are not solely due to the functionality of these key virulence factors. This study provides evidence that other mechanisms, such as differences in gene expression or the lack of currently uncharacterized virulence factors, may underlie the phenotypic differences between these species.

Walzer, Katelyn A.; Adomako-Ankomah, Yaw; Dam, Rachel A.; Herrmann, Daland C.; Schares, Gereon; Dubey, Jitender P.; Boyle, Jon P.

2013-01-01

55

The Impact of Mitochondrial DNA and Nuclear Genes Related to Mitochondrial Functioning on the Risk of Parkinson's Disease  

PubMed Central

Mitochondrial dysfunction and oxidative stress are the major factors implicated in Parkinson’s disease (PD) pathogenesis. The maintenance of healthy mitochondria is a very complex process coordinated bi-genomically. Here, we review association studies on mitochondrial haplogroups and subhaplogroups, discussing the underlying molecular mechanisms. We also focus on variation in the nuclear genes (NDUFV2, PGC-1alpha, HSPA9, LRPPRC, MTIF3, POLG1, and TFAM encoding NADH dehydrogenase (ubiquinone) flavoprotein 2, peroxisome proliferator-activated receptor gamma coactivator 1-alpha, mortalin, leucine-rich pentatricopeptide repeat containing protein, translation initiation factor 3, mitochondrial DNA polymerase gamma, and mitochondrial transcription factor A, respectively) primarily linked to regulation of mitochondrial functioning that recently have been associated with PD risk. Possible interactions between mitochondrial and nuclear genetic variants and related proteins are discussed.

Gaweda-Walerych, Katarzyna; Zekanowski, Cezary

2013-01-01

56

The impact of mitochondrial DNA and nuclear genes related to mitochondrial functioning on the risk of Parkinson's disease.  

PubMed

Mitochondrial dysfunction and oxidative stress are the major factors implicated in Parkinson's disease (PD) pathogenesis. The maintenance of healthy mitochondria is a very complex process coordinated bi-genomically. Here, we review association studies on mitochondrial haplogroups and subhaplogroups, discussing the underlying molecular mechanisms. We also focus on variation in the nuclear genes (NDUFV2, PGC-1alpha, HSPA9, LRPPRC, MTIF3, POLG1, and TFAM encoding NADH dehydrogenase (ubiquinone) flavoprotein 2, peroxisome proliferator-activated receptor gamma coactivator 1-alpha, mortalin, leucine-rich pentatricopeptide repeat containing protein, translation initiation factor 3, mitochondrial DNA polymerase gamma, and mitochondrial transcription factor A, respectively) primarily linked to regulation of mitochondrial functioning that recently have been associated with PD risk. Possible interactions between mitochondrial and nuclear genetic variants and related proteins are discussed. PMID:24532986

Gaweda-Walerych, Katarzyna; Zekanowski, Cezary

2013-12-01

57

Single nucleotide polymorphisms in four functionally related immune response genes in the horse: CD14,TLR4, Cepsilon, andFcepsilon R1 alpha.  

PubMed

The objective of this study was to identify single nucleotide polymorphisms (SNPs) within four functionally related immune response genes in the horse, and to develop genotyping techniques that could be useful for future genomic studies of horse infectious and allergic diseases. The genes analysed were: the lipopolysaccharide (LPS) receptor gene CD14, the toll-like receptor 4 gene TLR4, the gene Cepsilon encoding the IgE heavy chain molecule and the gene FcepsilonR1 alpha coding for the alpha subunit of the IgE receptor molecule. Horse-specific primers amplifying selected gene regions were designed and SNPs were searched by selective resequencing and/or by PCR-SSCP (polymerase chain reaction-sequence specific conformational polymorphism) or PCR-RFLP (PCR-restriction fragment length polymorphism). Gene expression was analysed by RT-PCR (reverse transcriptase-PCR) of all four genes examined. For CD14, the cDNA sequence was determined and a novel sequence of the 5'UTR region was identified. The protein-coding sequence was identical to that previously deposited in GenBank. 5'UTR, intronic and both synonymous and non-synonymous exonic SNPs were identified. Three SNPs were found in the CD14 gene, four in the TLR4 gene; two SNPs were identified in the Cepsilon gene, and one SNP was found in the FcepsilonR1 alpha gene. PCR-RFLP was developed for genotyping eight of the SNPs identified. The RT-PCR assay showed that all the SNPs reported here are parts of expressed genes. The results showed that important immunity-related genes in horses are polymorphic and that even non-synonymous SNPs with potential functional impact may occur. The methods developed for genotyping and haplotyping the SNPs identified represent, along with markers described previously, a potentially useful tool for genomic analysis of the function and role of these genes in immunity and in mechanisms of disease. PMID:16164694

Vychodilova-Krenkova, L; Matiasovic, J; Horin, P

2005-10-01

58

Parallel re-modeling of EF-1? function: divergent EF-1? genes co-occur with EFL genes in diverse distantly related eukaryotes  

PubMed Central

Background Elongation factor-1? (EF-1?) and elongation factor-like (EFL) proteins are functionally homologous to one another, and are core components of the eukaryotic translation machinery. The patchy distribution of the two elongation factor types across global eukaryotic phylogeny is suggestive of a ‘differential loss’ hypothesis that assumes that EF-1? and EFL were present in the most recent common ancestor of eukaryotes followed by independent differential losses of one of the two factors in the descendant lineages. To date, however, just one diatom and one fungus have been found to have both EF-1? and EFL (dual-EF-containing species). Results In this study, we characterized 35 new EF-1?/EFL sequences from phylogenetically diverse eukaryotes. In so doing we identified 11 previously unreported dual-EF-containing species from diverse eukaryote groups including the Stramenopiles, Apusomonadida, Goniomonadida, and Fungi. Phylogenetic analyses suggested vertical inheritance of both genes in each of the dual-EF lineages. In the dual-EF-containing species we identified, the EF-1? genes appeared to be highly divergent in sequence and suppressed at the transcriptional level compared to the co-occurring EFL genes. Conclusions According to the known EF-1?/EFL distribution, the differential loss process should have occurred independently in diverse eukaryotic lineages, and more dual-EF-containing species remain unidentified. We predict that dual-EF-containing species retain the divergent EF-1? homologues only for a sub-set of the original functions. As the dual-EF-containing species are distantly related to each other, we propose that independent re-modelling of EF-1? function took place in multiple branches in the tree of eukaryotes.

2013-01-01

59

Functional analysis of pyochelin-/enantiopyochelin-related genes from a pathogenicity island of Pseudomonas aeruginosa strain PA14.  

PubMed

Genomic islands are foreign DNA blocks inserted in so-called regions of genomic plasticity (RGP). Depending on their gene content, they are classified as pathogenicity, symbiosis, metabolic, fitness or resistance islands, although a detailed functional analysis is often lacking. Here we focused on a 34-kb pathogenicity island of Pseudomonas aeruginosa PA14 (PA14GI-6), which is inserted at RGP5 and carries genes related to those for pyochelin/enantiopyochelin biosynthesis. These enantiomeric siderophores of P. aeruginosa and certain strains of Pseudomonas protegens are assembled by a thiotemplate mechanism from salicylate and two molecules of cysteine. The biochemical function of several proteins encoded by PA14GI-6 was investigated by a series of complementation analyses using mutants affected in potential homologs. We found that PA14_54940 codes for a bifunctional salicylate synthase/salicyl-AMP ligase (for generation and activation of salicylate), that PA14_54930 specifies a dihydroaeruginoic acid (Dha) synthetase (for coupling salicylate with a cysteine-derived thiazoline ring), that PA14_54910 produces a type II thioesterase (for quality control), and that PA14_54880 encodes a serine O-acetyltransferase (for increased cysteine availability). The structure of the PA14GI-6-specified metabolite was determined by mass spectrometry, thin-layer chromatography, and HPLC as (R)-Dha, an iron chelator with antibacterial, antifungal and antitumor activity. The conservation of this genomic island in many clinical and environmental P. aeruginosa isolates of different geographical origin suggests that the ability for Dha production may confer a selective advantage to its host. PMID:24682869

Maspoli, Alessandro; Wenner, Nicolas; Mislin, Gaëtan L A; Reimmann, Cornelia

2014-06-01

60

Fatty acid-dependent expression of the muscle FABP gene - comparative analysis of gene control in functionally related, but evolutionary distant animal systems.  

PubMed

The heart is the most fatty acid-dependent muscle in mammals, but flight muscles of birds and insects encounter even higher rates of fatty acid oxidation. The amount of the muscle fatty acid binding protein (H-FABP) found in these muscle reflects their metabolic activities, and increased fatty acid metabolism in endurance exercise increases FABP expression further. We have studied the mechanism of fatty acid-dependent expression of the H-FABP gene, taking advantage of the comparative analysis of gene control in functionally related, but evolutionary distant animal systems, i.e., rat heart and locust flight muscle. Luciferase reporter genes with a full-length promoter ( approximately 1 kb) from either the locust or the rat were strongly expressed in L6 myoblasts, and the expression of both constructs was markedly increased by fatty acid treatment. Because of its stronger induction by fatty acids and the absence of other vertebrate transcription factor binding sites, the locust promoter was advantageous for the identification of a fatty acid response element (FARE), an inverted repeat of a hexanucleotide half site reminiscent of steroid hormone receptor binding sites (IR-3). All mammalian H-FABP promoters contain similar sequences, however in reverse orientation (everted repeats, ER-3). Deletion of the FARE eliminated the fatty acid inducibility completely for the locust promoter, but only partly for its mammalian analogue, perhaps because of additional factors or more complex interactions. In gel shift studies, the element binds nuclear proteins from both rat cells and locust flight muscle, further attesting to the far-reaching conservation of this mechanism. Two individual proteins bind to the element, with full binding requiring the presence of free fatty acid. Antibodies to PPARs failed to induce a supershift of the protein-DNA complex, indicating that other transcription factors are responsible for the fatty acid-mediated induction of gene expression of H-FABP. PMID:17001452

Qu, H; Cui, L; Rickers-Haunerland, J; Haunerland, N H

2007-05-01

61

Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa.  

PubMed

Genes underlying environmental adaptability tend to be over-retained in polyploid plant species. Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation, but little is known about the differential expression of duplicated genes upon these stress conditions. Applying Tag-Seq technology to leaves of Brassica rapa grown under FeD, ZnD, ZnE or CdE conditions, with normal conditions as a control, we examined global gene expression changes and compared the expression patterns of multiple paralogs. We identified 812, 543, 331 and 447 differentially expressed genes under FeD, ZnD, ZnE and CdE conditions, respectively, in B. rapa leaves. Genes involved in regulatory networks centered on the transcription factors bHLH038 or bHLH100 were differentially expressed under (ZnE-induced) FeD. Further analysis revealed that genes associated with Zn, Fe and Cd responses tended to be over-retained in the B. rapa genome. Most of these multiple-copy genes showed the same direction of expression change under stress conditions. We conclude that the duplicated genes involved in trace element responses in B. rapa are functionally redundant, making the regulatory network more complex in B. rapa than in Arabidopsis thaliana. PMID:24738937

Li, Jimeng; Liu, Bo; Cheng, Feng; Wang, Xiaowu; Aarts, Mark G M; Wu, Jian

2014-07-01

62

Specific induction of cAMP in Langerhans cells by calcitonin gene-related peptide: relevance to functional effects.  

PubMed Central

Epidermal Langerhans cells (LC) are associated anatomically with epidermal nerves, and a product of these nerves, calcitonin gene-related peptide (CGRP), inhibits the antigen-presenting capacity of LC and macrophages. As the CGRP receptor appears to be coupled to Gs alpha protein, which in turn activates adenylate cyclase, the ability of CGRP to induce cAMP in LC was examined and correlated with functional effects. LC were isolated from murine epidermal cells using antibodies on magnetic microspheres. Exposure to CGRP induced a significant increase in cAMP content, which could be inhibited by coculture with a truncated form of CGRP [CGRP-(8-37)] that is a specific competitive inhibitor of CGRP. Substance P and calcitonin failed to induce cAMP in LC. Although culture in CGRP reduced the ability of murine epidermal cells enriched for LC content to present pigeon cytochrome c to a responsive clone or to present antigen for elicitation of delayed-type hypersensitivity in immune mice, culture in forskolin had little or no effect on antigen presentation despite increased cAMP content of LC as much or more than that induced by CGRP. The effect of CGRP on antigen presentation in these systems could be blocked with CGRP-(8-37). CGRP inhibited the induction of B7-2 by lipopolysaccharide on peritoneal macrophages and a LC line, whereas calcitonin did not. CGRP induces specific accumulation of cAMP in LC and inhibits LC antigen-presenting function by a receptor-mediated event. However, the induction of cAMP by itself does not account for inhibition of antigen presentation. Suppression of the expression of B7-2 may be one mechanism by which CGRP inhibits antigen presentation. Images Fig. 2

Asahina, A; Moro, O; Hosoi, J; Lerner, E A; Xu, S; Takashima, A; Granstein, R D

1995-01-01

63

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.  

PubMed

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general. PMID:22962313

Chasman, Daniel I; Fuchsberger, Christian; Pattaro, Cristian; Teumer, Alexander; Böger, Carsten A; Endlich, Karlhans; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C; O'Seaghdha, Conall M; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V; O'Connell, Jeffrey R; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D; Gierman, Hinco J; Feitosa, Mary F; Hwang, Shih-Jen; Atkinson, Elizabeth J; Lohman, Kurt; Cornelis, Marilyn C; Johansson, Asa; Tönjes, Anke; Dehghan, Abbas; Lambert, Jean-Charles; Holliday, Elizabeth G; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y; Murgia, Federico; Trompet, Stella; Imboden, Medea; Coassin, Stefan; Pistis, Giorgio; Harris, Tamara B; Launer, Lenore J; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank; Demirkan, Ayse; Oostra, Ben A; de Andrade, Mariza; Turner, Stephen T; Ding, Jingzhong; Andrews, Jeanette S; Freedman, Barry I; Giulianini, Franco; Koenig, Wolfgang; Illig, Thomas; Meisinger, Christa; Gieger, Christian; Zgaga, Lina; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H; Wright, Alan F; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G; Rivadeneira, Fernando; Aulchenko, Yurii S; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Stengel, Bénédicte; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Krämer, Bernhard K; Portas, Laura; Ford, Ian; Buckley, Brendan M; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J Wouter; Probst-Hensch, Nicole M; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S; van Duijn, Cornelia M; Borecki, Ingrid B; Kardia, Sharon L R; Liu, Yongmei; Curhan, Gary C; Rudan, Igor; Gyllensten, Ulf; Wilson, James F; Franke, Andre; Pramstaller, Peter P; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline; Hayward, Caroline; Ridker, Paul M; Parsa, Afshin; Bochud, Murielle; Heid, Iris M; Kao, W H Linda; Fox, Caroline S; Köttgen, Anna

2012-12-15

64

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function  

PubMed Central

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10?9) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10?4–2.2 × 10?7. Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

Chasman, Daniel I.; Fuchsberger, Christian; Pattaro, Cristian; Teumer, Alexander; Boger, Carsten A.; Endlich, Karlhans; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C.; O'Seaghdha, Conall M.; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V.; O'Connell, Jeffrey R.; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D.; Gierman, Hinco J.; Feitosa, Mary F.; Hwang, Shih-Jen; Atkinson, Elizabeth J.; Lohman, Kurt; Cornelis, Marilyn C.; Johansson, Asa; Tonjes, Anke; Dehghan, Abbas; Lambert, Jean-Charles; Holliday, Elizabeth G.; Sorice, Rossella; Kutalik, Zoltan; Lehtimaki, Terho; Esko, Tonu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y.; Murgia, Federico; Trompet, Stella; Imboden, Medea; Coassin, Stefan; Pistis, Giorgio; Harris, Tamara B.; Launer, Lenore J.; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D.; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank; Demirkan, Ayse; Oostra, Ben A.; de Andrade, Mariza; Turner, Stephen T.; Ding, Jingzhong; Andrews, Jeanette S.; Freedman, Barry I.; Giulianini, Franco; Koenig, Wolfgang; Illig, Thomas; Meisinger, Christa; Gieger, Christian; Zgaga, Lina; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E.; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H.; Wright, Alan F.; Campbell, Harry; Ellinghaus, David; Nothlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K.; Nauck, Matthias; Stracke, Sylvia; Volker, Uwe; Volzke, Henry; Kovacs, Peter; Stumvoll, Michael; Magi, Reedik; Hofman, Albert; Uitterlinden, Andre G.; Rivadeneira, Fernando; Aulchenko, Yurii S.; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Stengel, Benedicte; Ruggiero, Daniela; Bergmann, Sven; Kahonen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Kramer, Bernhard K.; Portas, Laura; Ford, Ian; Buckley, Brendan M.; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K.; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J. Wouter; Probst-Hensch, Nicole M.; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R.; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S.; van Duijn, Cornelia M.; Borecki, Ingrid B.; Kardia, Sharon L.R.; Liu, Yongmei; Curhan, Gary C.; Rudan, Igor; Gyllensten, Ulf; Wilson, James F.; Franke, Andre; Pramstaller, Peter P.; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline; Hayward, Caroline; Ridker, Paul M; Parsa, Afshin; Bochud, Murielle; Heid, Iris M.; Kao, W.H. Linda; Fox, Caroline S.; Kottgen, Anna

2012-01-01

65

Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues.  

PubMed

Over a billion people are infected by Ascaris spp. intestinal parasites. To clarify functional differences among tissues of adult A. suum, we compared gene expression by various tissues of these worms by expression microarray methods. The A. suum genome was sequenced and assembled to allow generation of microarray elements. Expression of over 40,000 60-mer elements was investigated in a variety of tissues from both male and female adult worms. Nearly 50 percent of the elements for which signal was detected exhibited differential expression among different tissues. The unique profile of transcripts identified for each tissue clarified functional distinctions among tissues, such as chitin binding in the ovary and peptidase activity in the intestines. Interestingly, hundreds of gender-specific elements were characterized in multiple non-reproductive tissues of female or male worms, with most prominence of gender differences in intestinal tissue. A. suum genes from the same family were frequently expressed differently among tissues. Transcript abundance for genes specific to A. suum, by comparison to Caenorhabditis elegans, varied to a greater extent among tissues than for genes conserved between A. suum and C. elegans. Analysis using C. elegans protein interaction data identified functional modules conserved between these two nematodes, resulting in identification of functional predictions of essential subnetworks of protein interactions and how these networks may vary among nematode tissues. A notable finding was very high module similarity between adult reproductive tissues and intestine. Our results provide the most comprehensive assessment of gene expression among tissues of a parasitic nematode to date. PMID:23572074

Wang, Zhengyuan; Gao, Xin; Martin, John; Yin, Yong; Abubucker, Sahar; Rash, Amy C; Li, Ben-Wen; Nash, Bill; Hallsworth-Pepin, Kym; Jasmer, Douglas P; Mitreva, Makedonka

2013-06-01

66

HA117 gene increased the multidrug resistance of K562 cells in vitro: an investigation to the function of a novel gene related to drug resistance  

Microsoft Academic Search

OBJECTIVE: A novel multi-drug resistance gene named as HA117 has been screened and cloned in multidrug resisitant leukemia cell lines in our previous research, but its function is still unknown. In this study, HA117 gene was investigated whether it could increase the drug resistance in chronic myelogenous myeloid leukemia cell line K562. METHODS: HA117 was cloned and adenovirus vectors were

Yuxia Guo; Gaihuan Zheng; Xianqing Jin; Youhua Xu; Qing Luo; Xiaomei Liu; Zhenzhen Zhao; Yong Chen

2009-01-01

67

Down syndrome critical region gene 2: expression during mouse development and in human cell lines indicates a function related to cell proliferation.  

PubMed

The isolation of the genes located in chromosome 21 and the characterisation of their function are essential steps towards the understanding of the physiopathological mechanisms involved in Down syndrome. We have used two complementary approaches to characterise the function of the novel gene DSCR2 (Down Syndrome Critical Region gene 2): the isolation and characterisation of the mouse gene homologue to the human DSCR2 gene, and the analysis of the expression of the gene in different human cell lines. We have isolated and characterised a 1012 bp of a mouse cDNA having a high homology to the human DSCR2 gene. The predicted mouse dscr2 protein has an identity of 85.4% as compared to the human protein, indicating that the DSCR2 protein has been conserved during the evolution. However, the amino acid sequence is not homologous to other known proteins, or to known protein domains. The dscr2 gene is expressed throughout all the stages of the mouse embryo development. In the adult mouse the gene is expressed in testis, kidney, liver, brain, heart, skeletal muscle, and pancreas. The expression analysis of the DSCR2 gene in different human tumour derived cell lines indicates that the gene is expressed in all proliferating cell lines tested. The levels of the DSCR2 mRNA correlate with cellular growth of T98G and Jurkat cells in response to different treatments. The expression pattern throughout the foetal development together with the correlation observed with the cell cycle indicates a possible function for the DSCR2 gene related to cell proliferation. PMID:10872820

Vidal-Taboada, J M; Lu, A; Pique, M; Pons, G; Gil, J; Oliva, R

2000-05-27

68

Effect of Lead Ion on the Function of the Human Ether-À-Go-Go-Related Gene K + Channel  

Microsoft Academic Search

Lead (Pb) is a trace metal element in the human body. In order to understand the hazard mechanism of the elevated blood lead\\u000a level on the human body, the effect of Pb2+ on the human ether-à-go-go-related gene (hERG) K+ channel in the HEK 293 cell was investigated for the first time using whole-cell patch clamp technique, molecular dynamics\\u000a simulation, and

Jiemin Zhou; Gang Hu

69

Conservation of NON-EXPRESSOR OF PATHOGENESIS-RELATED GENES1 function between Arabidopsis thaliana and Brassica napus  

Microsoft Academic Search

An Expressed Sequence Tag encoding a protein highly related to Arabidopsis NPR1 was isolated from canola quality Brassica napus. The protein, BnNPR1, interacts with the same spectrum of TGA transcription factors and NIMIN proteins as AtNPR1 in the yeast two-hybrid system. When expressed in Arabidopsis npr1 mutants, BnNPR1 restored salicylic acid-dependent expression of the marker gene PR-1 and enhanced basal

Shobha D. Potlakayala; Catherine DeLong; Andrew Sharpe; Pierre R. Fobert

2007-01-01

70

Molecular analysis of SSN6, a gene functionally related to the SNF1 protein kinase of Saccharomyces cerevisiae.  

PubMed

Mutations in the SSN6 gene suppress the invertase derepression defect caused by a lesion in the SNF1 protein kinase gene. We cloned the SSN6 gene of Saccharomyces cerevisiae and identified its 3.3-kilobase poly(A)-containing RNA. Disruption of the gene caused phenotypes similar to, but more severe than, those caused by missense mutations: high-level constitutivity for invertase, clumpiness, temperature-sensitive growth, alpha-specific mating defects, and failure to homozygous diploids to sporulate. In contrast, the presence of multiple copies of SSN6 interfered with derepression of invertase. An ssn6 mutation was also shown to cause glucose-insensitive expression of a GAL10-lacZ fusion and maltase. The mating defects of MAT alpha ssn6 strains were associated with production of two a-specific products, a-factor and barrier, and reduced levels of alpha-factor; no deficiency of MAT alpha 2 RNA was detected. We showed that ssn6 partially restored invertase expression in a cyr1-2 mutant, although ssn6 was clearly not epistatic to cyr1-2. We also determined the nucleotide sequence of SSN6, which is predicted to encode a 107-kilodalton protein with stretches of polyglutamine and poly(glutamine-alanine). Possible functions of the SSN6 product are discussed. PMID:3316983

Schultz, J; Carlson, M

1987-10-01

71

Senescence-related functional nuclear barrier by down-regulation of nucleo-cytoplasmic trafficking gene expression  

SciTech Connect

One of the characteristic natures of senescent cells is the hypo- or irresponsiveness not only to growth factors but also to apoptotic stress. In the present study, we confirmed the inhibition of nuclear translocation of activated p-ERK1/2 and NF-kB p50 in response to growth stimuli or LPS in the senescent human diploid fibroblasts. In order to elucidate the underlying mechanism for the senescence-associated hypo-responsiveness, we carried out the comparison study for gene expression profiles through microarray analysis. In consequence, we observed the vast reduction in expression of nucleo-cytoplasmic trafficking genes in senescent cells, when compared with those in young cells. Expression levels of several nucleoporins, karyopherin {alpha}, karyopherin {beta}, Ran, and Ran-regulating factors were confirmed to be down-regulated in senescent HDFs by using RT-PCR and Western blot methods. Taken together, these data suggest the operation of certain senescence-associated functional nuclear barriers by down-regulation of the nucleo-cytoplasmic trafficking genes in the senescent cells.

Kim, Sung Young; Ryu, Sung Jin; Ahn, Hong Ju; Choi, Hae Ri; Kang, Hyun Tae [Department of Biochemistry and Molecular Biology, Aging and Apoptosis Research Center, Institute on Aging, Seoul National University College of Medicine, Seoul 110-799 (Korea, Republic of)] [Department of Biochemistry and Molecular Biology, Aging and Apoptosis Research Center, Institute on Aging, Seoul National University College of Medicine, Seoul 110-799 (Korea, Republic of); Park, Sang Chul, E-mail: scpark@snu.ac.kr [Department of Biochemistry and Molecular Biology, Aging and Apoptosis Research Center, Institute on Aging, Seoul National University College of Medicine, Seoul 110-799 (Korea, Republic of)

2010-01-01

72

The Maize tha4 Gene Functions in Sec-Independent Protein Transport in Chloroplasts and Is Related to hcf106, tatA, and tatB  

PubMed Central

Proteins are translocated across the chloroplast thylakoid membrane by a variety of mechanisms. Some proteins engage a translocation machinery that is derived from the bacterial Sec export system and require an interaction with a chloroplast-localized SecA homologue. Other proteins engage a machinery that is SecA-independent, but requires a transmembrane pH gradient. Recently, a counterpart to this ? pH mechanism was discovered in bacteria. Genetic studies revealed that one maize protein involved in this mechanism, HCF106, is related in both structure and function to the bacterial tatA and tatB gene products. We describe here the mutant phenotype and molecular cloning of a second maize gene that functions in the ? pH mechanism. This gene, thylakoid assembly 4 (tha4), is required specifically for the translocation of proteins that engage the ? pH pathway. The sequence of the tha4 gene product resembles those of the maize hcf106 gene and the bacterial tatA and tatB genes. Sequence comparisons suggest that tha4 more closely resembles tatA, and hcf106 more closely resembles tatB. These findings support the notion that this sec-independent translocation mechanism has been highly conserved during the evolution of eucaryotic organelles from bacterial endosymbionts.

Walker, Macie B.; Roy, Laura M.; Coleman, Eric; Voelker, Rodger; Barkan, Alice

1999-01-01

73

DEFOG: Discrete Enrichment of Functionally Organized Genes  

PubMed Central

High-throughput biological experiments commonly result in a list of genes or proteins of interest. In order to understand the observed changes of the genes and to generate new hypotheses, one needs to understand the functions and roles of the genes and how those functions relate to the experimental conditions. Typically, statistical tests are performed in order to detect enriched Gene Ontology categories or Pathways, i.e. the categories are observed in the genes of interest more often than is expected by chance. Depending on the number of genes and the complexity and quantity of functions in which they are involved, such an analysis can easily result in hundreds of enriched terms. To this end we developed DEFOG, a web-based application that facilitates the functional analysis of gene sets by hierarchically organizing the genes into functionally related modules. Our computational pipeline utilizes three powerful tools to achieve this goal: (1) GeneMANIA creates a functional consensus network of the genes of interest based on gene-list-specific data fusion of hundreds of genomic networks from publicly available sources; (2) Transitivity Clustering organizes those genes into a clear hierarchy of functionally related groups, and (3) Ontologizer performs a Gene Ontology enrichment analysis on the resulting gene clusters. DEFOG integrates this computational pipeline within an easy-to-use web interface, thus allowing for a novel visual analysis of gene sets that aids in the discovery of potentially important biological mechanisms and facilitates the creation of new hypotheses. DEFOG is available at http://www.mooneygroup.org/defog.

Wittkop, Tobias; Berman, Ari E.; Fleisch, K. Mathew; Mooney, Sean D.

2012-01-01

74

Renal gene expression profiling using kinin B1 and B2 receptor knockout mice reveals comparable modulation of functionally related genes.  

PubMed

The kinin B2 receptor, which is constitutively expressed in a large number of tissues, mediates most of the known effects of bradykinin (BK). Normally undetectable in healthy tissues, the B1 receptor is strongly over-expressed under pathological conditions. BK is an important mediator in renal homeostasis and is mainly known for its natriuretic and vasodilatory effects. Recent data evidenced a role for BK in many other biological processes, such as apoptosis, development, extracellular matrix regulation and angiogenesis. In a first step to better understand how BK and its receptors could be involved in such a large variety of biological effects, we used microarray analysis to identify, under physiological conditions, the global renal gene expression profile in mice lacking either the kinin B1 or B2 receptor. Microarray experiments were performed using Agilent Mouse Oligonucleotide Microarrays (21,000 genes/microarray). Interestingly, there was a considerable number of mostly downregulated genes in both BK null mouse models compared with wild-type mice. Furthermore, a number of genes that are known to be implicated in renal physiology and/or pathology were differentially expressed in the BK null mice, which is indicative of the important role of both BK receptors in renal function. PMID:16497160

Bachvarov, Dimcho; Bachvarova, Magdalena; Koumangaye, Rainelli; Klein, Julie; Pesquero, João Bosco; Neau, Eric; Bader, Michael; Schanstra, Joost P; Bascands, Jean Loup

2006-01-01

75

Interaction of dopamine system genes and cognitive functions in patients with schizophrenia and their relatives and in healthy subjects from the general population  

Microsoft Academic Search

Linkage between the DRD4 and COMT genes and cognitive measures characterizing verbal memory, executive functions, and associative\\u000a processes was studied in 150 patients with schizophrenia, 83 of their relatives, and 118 mentally healthy subjects without\\u000a any family history of psychoses, with the aim of detecting the main effects of the polymorphic markers ?809G\\/A and ?521C\\/T\\u000a (DRD4) and Val158Met (COMT) when

M. V. Alfimova; V. E. Golimbet; I. K. Gritsenko; T. V. Lezheiko; L. I. Abramova; M. A. Strel’tsova; I. V. Khlopina; R. Ebstein

2007-01-01

76

Functional Conservation of Clock-Related Genes in Flowering Plants: Overexpression and RNA Interference Analyses of the Circadian Rhythm in the Monocotyledon Lemna gibba1[W  

PubMed Central

Circadian rhythms are found in organisms from cyanobacteria to plants and animals. In flowering plants, the circadian clock is involved in the regulation of various physiological phenomena, including growth, leaf movement, stomata opening, and floral transitions. Molecular mechanisms underlying the circadian clock have been identified using Arabidopsis (Arabidopsis thaliana); the functions and genetic networks of a number of clock-related genes, including CIRCADIAN CLOCK ASSOCIATED1, LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION1, GIGANTEA (GI), and EARLY FLOWERING3 (ELF3), have been analyzed. The degree to which clock systems are conserved among flowering plants, however, is still unclear. We previously isolated homologs for Arabidopsis clock-related genes from monocotyledon Lemna plants. Here, we report the physiological roles of these Lemna gibba genes (LgLHYH1, LgLHYH2, LgGIH1, and LgELF3H1) in the circadian system. We studied the effects of overexpression and RNA interference (RNAi) of these genes on the rhythmic expression of morning- and evening-specific reporters. Overexpression of each gene disrupted the rhythmicity of either or both reporters, suggesting that these four homologs can be involved in the circadian system. RNAi of each of the genes except LgLHYH2 affected the bioluminescence rhythms of both reporters. These results indicated that these homologs are involved in the circadian system of Lemna plants and that the structure of the circadian clock is likely to be conserved between monocotyledons and dicotyledons. Interestingly, RNAi of LgGIH1 almost completely abolished the circadian rhythm; because this effect appeared to be much stronger than the phenotype observed in an Arabidopsis gi loss-of-function mutant, the precise role of each clock gene may have diverged in the clock systems of Lemna and Arabidopsis.

Serikawa, Masayuki; Miwa, Kumiko; Kondo, Takao; Oyama, Tokitaka

2008-01-01

77

The low density lipoprotein receptor-related protein 1: Unique tissue-specific functions revealed by selective gene knockout studies  

PubMed Central

The low-density lipoprotein (LDL) receptor-related protein (originally called LRP, but now referred to as LRP1) is a large endocytic receptor that is widely expressed in several tissues. LRP1 is a member of the LDL receptor family that plays diverse roles in various biological processes including lipoprotein metabolism, degradation of proteases, activation of lysosomal enzymes and cellular entry of bacterial toxins and viruses. Deletion of the LRP1 gene leads to lethality in mice, revealing a critical, but as of yet, undefined role in development. Tissue-specific gene deletion studies reveal an important contribution of LRP1 in the vasculature, central nervous system, in macrophages and in adipocytes. Three important properties of LRP1 dictate its diverse role in physiology: first, its ability to recognize more than thirty distinct ligands; second, its ability to bind a large number of cytoplasmic adaptor proteins via determinants located on its cytoplasmic domain in a phosphorylation-specific manner; and third, its ability to associate with and modulate the activity of other transmembrane receptors such as integrins and receptor tyrosine kinases.

Lillis, Anna P.; Van Duyn, Lauren B.; Murphy-Ullrich, Joanne E.; Strickland, Dudley K.

2008-01-01

78

Fuzzy clustering analysis of osteosarcoma related genes.  

PubMed

Osteosarcoma is the most common malignant bone-tumor with a peak manifestation during the second and third decade of life. In order to explore the influence of genetic factors on the mechanism of osteosarcoma by analyzing the inter relationship between osteosarcoma and its related genes, and then provide potential genetic references for the prevention, diagnosis and treatment of osteosarcoma, we collected osteosarcoma related gene sequences in Genebank of National Center for Biotechnology Information (NCBI) and local alignment analysis for a pair of sequences was carried out to identify the measurement association among related sequences. Then fuzzy clustering method was used for clustering analysis so as to contact the unknown genes through the consistent osteosarcoma related genes in one class. From the result of fuzzy clustering analysis, we could classify the osteosarcoma related genes into two groups and deduced that the genes clustered into one group had similar function. Based on this knowledge, we found more genes related to the pathogenesis of osteosarcoma and these genes could exert similar function as Runx2, a risk factor confirmed in osteosarcoma, this study may help better understand the genetic mechanism and provide new molecular markers and therapies for osteosarcoma. PMID:24293382

Chen, Kai; Wu, Dajiang; Bai, Yushu; Zhu, Xiaodong; Chen, Ziqiang; Wang, Chuanfeng; Zhao, Yingchuan; Li, Ming

2014-07-01

79

Lack of association between a functional variant of the BRCA-1 related associated protein (BRAP) gene and ischemic stroke  

PubMed Central

Background Atherosclerosis shares common pathogenic features with myocardial infarction (MI) and ischemic stroke. BRCA-1 associated protein (BRAP), a newly identified risk gene for MI, aggravates the inflammatory response in atherosclerosis. The aim of this study was to test the association between the BRAP gene and stroke in a Taiwanese population. Methods A total of 1,074 stroke patients and 1,936 controls were genotyped for the functional SNP rs11066001. In our previous studies, the rare allele of this SNP has been repeatedly shown to exert a recessive effect. Therefore, in the current study, we tested for the same recessive model. First, the genotype distributions between all the controls and all the stroke cases were compared. Then to reduce heterogeneity, we explored several population subsets by selecting young stroke subjects (using 45 years of age as the cutoff point), age- and sex-comparable controls, plaque-free controls, and stroke subtypes. Results We did not find any significant association for the entire data set (OR = 0.94, p = 0.74) or for the subset analyses using age- and sex-comparable controls (p = 0.70) and plaque-free controls (p = 0.91). Analyses of the four stroke subtypes also failed to show any significant associations (p = 0.42 – 0.98). For both young and old subjects, the GG genotype of rs11066001 was similar in the stroke cases and unmatched controls (8.1% vs. 9.4% in young subjects and 8.0% vs. 7.8% in old subjects). Comparing stroke cases with plaque-free controls also failed to find any significant association. Conclusions The BRAP polymorphism may not play an important role in ischemic stroke in the studied population.

2013-01-01

80

Genome-wide inventory of metal homeostasis-related gene products including a functional phytochelatin synthase in the hypogeous mycorrhizal fungus Tuber melanosporum.  

PubMed

Ectomycorrhizal fungi are thought to enhance mineral nutrition of their host plants and to confer increased tolerance toward toxic metals. However, a global view of metal homeostasis-related genes and pathways in these organisms is still lacking. Building upon the genome sequence of Tuber melanosporum and on transcriptome analyses, we set out to systematically identify metal homeostasis-related genes in this plant-symbiotic ascomycete. Candidate gene products (101) were subdivided into three major functional classes: (i) metal transport (58); (ii) oxidative stress defence (32); (iii) metal detoxification (11). The latter class includes a small-size metallothionein (TmelMT) that was functionally validated in yeast, and phytochelatin synthase (TmelPCS), the first enzyme of this kind to be described in filamentous ascomycetes. Recombinant TmelPCS was shown to support GSH-dependent, metal-activated phytochelatin synthesis in vitro and to afford increased Cd/Cu tolerance to metal hypersensitive yeast strains. Metal transporters, especially those related to Cu and Zn trafficking, displayed the highest expression levels in mycorrhizae, suggesting extensive translocation of both metals to root cells as well as to fungal metalloenzymes (e.g., laccase) that are strongly upregulated in symbiotic hyphae. PMID:21094264

Bolchi, Angelo; Ruotolo, Roberta; Marchini, Gessica; Vurro, Emanuela; di Toppi, Luigi Sanità; Kohler, Annegret; Tisserant, Emilie; Martin, Francis; Ottonello, Simone

2011-06-01

81

Nucleotide sequence of the repressor gene of the RA1 tetracycline resistance determinant: structural and functional comparison with three related Tet repressor genes.  

PubMed Central

The tetracycline resistance determinant of RA1 was cloned. It consists of at least two genes oriented with opposite polarity, tetA for resistance and tetR for regulation. The transcriptional control sequence was identified and analyzed. It consists of overlapping promotors with divergent orientation and a tandem arrangement of operators. Nucleotide sequencing revealed two open reading frames. One codes for a protein which was identified as a Tet repressor by comparing its primary structure with those of other Tet repressors. The RA1 tetR gene codes for 218 amino acids with a calculated molecular weight of 24.4 kDa. In the primary sequence of the RA1-, pSC101-, Tn10-, and RP1/Tn1721-encoded Tet repressors, 36% of the amino acids are identical. This homology is clustered within the first 150 amino acids, 49% of which are identical among all four proteins. These results are discussed with respect to their structure and function in comparison to other DNA binding proteins. Images

Unger, B; Klock, G; Hillen, W

1984-01-01

82

FunGene: the functional gene pipeline and repository.  

PubMed

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes. PMID:24101916

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

83

Molecular Clock and Gene Function  

Microsoft Academic Search

Molecular phylogenies based on the molecular clock require the comparison of orthologous genes. Orthologous and paralogous genes usually have very different evolutionary fates. In general, orthologs keep the same functions in species, whereas, particularly over a long time span, paralogs diverge functionally and may become pseudogenes or get lost. In eukaryotic genomes, because of the degree of redundancy of genetic

Cecilia Saccone; Corrado Caggese; Anna Maria D’Erchia; Cecilia Lanave; Marta Oliva; Graziano Pesole

2003-01-01

84

Expression in Lactococcus lactis of functional genes related to amino acid catabolism and cheese aroma formation is influenced by branched chain amino acids.  

PubMed

Formation of cheese aroma compounds by Lactococcus lactis from amino acid catabolism depends on a complex network of reactions, which involve enzymes such as aminotransferases, dehydrogenases, lyases, and decarboxylases, among others. Based on the ability of some L. lactis strains to grow with low requirements of amino acids, we have studied in L. lactis IFPL730 the effect of the branched chain amino acid (BCAA) content on the expression of functional genes related to amino acid catabolism and aroma compound formation (araT, bcaT, kivD, ytjE and panE). L. lactis IFPL730 growth rate decreased under leucine, valine or isoleucine starvation but the strain reached similar viable counts at the stationary phase in all culture conditions studied. The level of expression of some genes encoding enzymes involved in amino acid catabolism changed significantly (P<0.05) when those conditions were compared. Specially, ?-ketoisovalerate decarboxylase (kivD), BCAA-specific aminotransferase (bcaT) and C-S lyase (yjtE) gene expressions increased markedly by both isoleucine and valine starvation. In addition to gene expression, formation of volatile compounds was determined in all growth conditions. The results showed that BCAA starvation conditions caused a significant increase (P<0.05) in the formation of metabolic end products related to cheese aroma, such as 3-methylbutanal and 3-methylbutanol. PMID:23107499

García-Cayuela, Tomás; Gómez de Cadiñanos, Luz P; Peláez, Carmen; Requena, Teresa

2012-10-15

85

Identification and functional characterization of the human ether-a-go-go-related gene Q738X mutant associated with hereditary long QT syndrome type 2.  

PubMed

QT interval prolongation, a risk factor for arrhythmias, may be associated with genetic variants in genes governing cardiac repolarization. Long QT syndrome type 2 (LQT2) is caused by mutations in the human ether-a-go?go-related gene (hERG). This gene encodes a voltage-gated potassium channel comprised of 4 subunits, and the formation of functional channels requires the proper assembly of these 4 subunits. In the present study, we investigated the role of the LQT2 mutation, Q738X, which causes truncation of the C-terminus of hERG channels, in the assembly and function of hERG channels. When expressed in HEK293 cells, Q738X did not generate an hERG current. The co-expression of Q738X with wild-type (WT)-hERG did not cause the dominant-negative suppression of the WT-hERG current. Western blot analysis and confocal microscopy revealed that the Q738X mutation caused defective trafficking of hERG channel proteins. Co-immunoprecipitation demonstrated that Q738X did not exhibit dominant-negative effects due to the failure of the mutant and WT subunits to co-assemble. In conclusion, the functional loss caused by the Q738X mutation in hERG K+ channels may be attributed to the disruption of tetrameric assembly. PMID:24993425

Han, Sheng-Na; Yang, Song-Hua; Zhang, Yu; Sun, Xiao-Yan; Duan, Yan-Yan; Hu, Xiang-Jie; Fan, Tian-Li; Huang, Chen-Zheng; Yang, Ge; Zhang, Zhao; Zhang, Lirong

2014-09-01

86

Functional loss of all ndh genes in an otherwise relatively unaltered plastid genome of the holoparasitic flowering plant Cuscuta reflexa  

Microsoft Academic Search

We have cloned and sequenced an area of about 9.0 kb of the plastid DNA (ptDNA) from the holoparasitic flowering plant Cuscuta reflexa to investigate the evolutionary response of plastid genes to a reduced selective pressure. The region contains genes for the 16S rRNA, a subunit of a plastid NAD(P)H dehydrogenase (ndhB), three transfer RNAs (trnA, trnI, trnV) as well

Gerd Haberhausen; Klaus Zetsche

1994-01-01

87

Associations of Filaggrin Gene Loss-of-Function Variants and Human Papillomavirus-Related Cancer and Pre-Cancer in Danish Adults  

PubMed Central

Purpose Filaggrin proteins are expressed in the skin, oral cavity, oesophagus, and cervical mucose. Loss-of-function mutations in the filaggrin gene (FLG) reduce filaggrin expression and cause an impaired skin barrier function. We hypothesized that FLG mutation carriers would be more susceptible to human papillomavirus (HPV) infection and thus a higher risk of HPV-related cancer and pre-cancer. We investigated the association of the FLG genotype with incidence of HPV-related cancer of cervix, vagina, vulva, penis, anus and head and neck, and pre-cancer of the cervix. Methods We included 13,376 persons from four population-based studies conducted in the same background population in Copenhagen, Denmark. Participants were genotyped for the most common FLG mutations in Europeans. Information on cancer was obtained from The Danish Cancer Registry until 11 July 2011. Results There were 489 cases of prevalent and 97 cases of incident HPV-related cancer and pre-cancer (median follow-up 11.5 years). There was a statistically significant association between FLG genotype and incident HPV-related cancer and pre-cancer with a hazard ratio, HR?=?2.1 (95% confidence intervals, CI: 1.2, 3.7) for FLG mutation carriers vs. wild types. Conclusions FLG loss-of-function mutations were associated with higher incidence of HPV-related cancers and pre-cancers that are potentially screening and vaccine preventable.

Skaaby, Tea; Husemoen, Lise Lotte N.; J?rgensen, Torben; Johansen, Jeanne D.; Menne, Torkil; Szecsi, Pal B.; Stender, Steen; Bager, Peter; Thyssen, Jacob P.; Linneberg, Allan

2014-01-01

88

Exposure in utero to 2,2',3,3',4,6'-hexachlorobiphenyl (PCB 132) impairs sperm function and alters testicular apoptosis-related gene expression in rat offspring  

SciTech Connect

Toxicity of the polychlorinated biphenyls (PCBs) depends on their molecular structure. Mechanisms by prenatal exposure to a non-dioxin-like PCB, 2,2',3,4',5',6-hexachlorobiphenyl (PCB 132) that may act on reproductive pathways in male offspring are relatively unknown. The purpose was to determine whether epididymal sperm function and expression of apoptosis-related genes were induced or inhibited by prenatal exposure to PCB 132. Pregnant rats were treated with a single dose of PCB 132 at 1 or 10 mg/kg on gestational day 15. Male offspring were killed and the epididymal sperm counts, motility, velocity, reactive oxygen species (ROS) generation, sperm-oocyte penetration rate (SOPR), testicular histopathology, apoptosis-related gene expression and caspase activation were assessed on postnatal day 84. Prenatal exposure to PCB 132 with a single dose of 1 or 10 mg/kg decreased cauda epididymal weight, epididymal sperm count and motile epididymal sperm count in adult offspring. The spermatozoa of PCB 132-exposed offspring produced significantly higher levels of ROS than the controls; ROS induction and SOPR reduction were dose-related. In the low-dose PCB 132 group, p53 was significantly induced and caspase-3 was inhibited. In the high-dose group, activation of caspase-3 and -9 was significantly increased, while the expressions of Fas, Bax, bcl-2, and p53 genes were significantly decreased. Gene expression and caspase activation data may provide insight into the mechanisms by which exposure to low-dose or high-dose PCB 132 affects reproduction in male offspring in rats. Because the doses of PCB 132 administered to the dams were approximately 625-fold in low-dose group and 6250-fold higher in high-dose group than the concentration in human tissue levels, the concentrations are not biologically or environmentally relevant. Further studies using environmentally relevant doses are needed for hazard identification.

Hsu, P.-C. [Department of Safety, Health and Environmental Engineering, National Kaohsiung First University of Science and Technology, Kaohsiung, Taiwan (China); Pan, M.-H. [Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan (China); Li, L.-A. [Division of Environmental Health and Occupational Medicine, National Health Research Institutes, Zhunan, Taiwan (China); Chen, C.-J. [Department of Safety, Health and Environmental Engineering, National Kaohsiung First University of Science and Technology, Kaohsiung, Taiwan (China); Tsai, S.-S. [Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan (China); Guo, Y.L. [No. 1, Section 1, Jen-Ai Road, Department of Environmental and Occupational Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan (China)]. E-mail: leonguo@ha.mc.ntu.edu.tw

2007-05-15

89

SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors  

PubMed Central

SFMBT1 (Scm [Sex comb on midleg] with four MBT [malignant brain tumor] domains 1) is a poorly characterized mammalian MBT domain-containing protein homologous to Drosophila SFMBT, a Polycomb group protein involved in epigenetic regulation of gene expression. Here, we show that SFMBT1 regulates transcription in somatic cells and during spermatogenesis through the formation of a stable complex with LSD1 and CoREST. When bound to its gene targets, SFMBT1 recruits its associated proteins and causes chromatin compaction and transcriptional repression. SFMBT1, LSD1, and CoREST share a large fraction of target genes, including those encoding replication-dependent histones. Simultaneous occupancy of histone genes by SFMBT1, LSD1, and CoREST is regulated during the cell cycle and correlates with the loss of RNA polymerase II at these promoters during G2, M, and G1. The interplay between the repressive SFMBT1–LSD1–CoREST complex and RNA polymerase II contributes to the timely transcriptional regulation of histone genes in human cells. SFMBT1, LSD1, and CoREST also form a stable complex in germ cells, and their chromatin binding activity is regulated during spermatogenesis.

Zhang, Jin; Bonasio, Roberto; Strino, Francesco; Kluger, Yuval; Holloway, J. Kim; Modzelewski, Andrew J.; Cohen, Paula E.; Reinberg, Danny

2013-01-01

90

Text mining functional keywords associated with genes.  

PubMed

Modern experimental techniques provide the ability to gather vast amounts of biological data in a single experiment (e.g. DNA microarray experiment), making it extremely difficult for the researcher to interpret the data and form conclusions about the functions of the genes. Current approaches provide useful information that organizes or relates genes, but a major shortcoming is they either do not address specific functions of the genes or are constrained by functions predefined in other databases, which can be biased, incomplete, or out-of-date. We extended Andrade and Valencia's method [1] to statistically mine functional keywords associated with genes from MEDLINE abstracts. The MEDLINE abstracts are analyzed statistically to score and rank keywords for each gene using a background set of words for baseline frequencies. We generally got very good functional keyword information about the genes we tested, which was confirmed by searching for the individual keywords in context. The keywords extracted by our algorithm reveal a wealth of potential functional concepts, which were not represented in existing public databases. We feel that this approach is general enough to apply to medical and biological literature to find other relationships: drugs vs. genes, risk-factors vs. genes, etc. PMID:15360821

Liu, Ying; Brandon, Martin; Navathe, Shamkant; Dingledine, Ray; Ciliax, Brian J

2004-01-01

91

The function of porcine PPAR? and dietary fish oil effect on the expression of lipid and glucose metabolism related genes  

Microsoft Academic Search

Peroxisome-proliferator-activated receptor ? (PPAR?) plays a critical role in regulation of adipocyte differentiation and insulin sensitivity. To become functional, PPAR? must be activated by binding an appropriate ligand. Polyunsaturated fatty acids (PUFA) are potential ligands for PPAR?. The current experiment was designed to determine the potential for PUFA, particularly eicosapentaenoic acid and docosahexaenoic acid, to activate the function of porcine

Yu-Hsiang Yu; Shinn-Chih Wu; Winston Teng-Kuei Cheng; Harry J. Mersmann; Tang-Long Shen; Shih-Torng Ding

2011-01-01

92

Loss of functional K+ channels encoded by ether-à-go-go-related genes in mouse myometrium prior to labour onset  

PubMed Central

There is a growing appreciation that ion channels encoded by the ether-à-go-go-related gene family have a functional impact in smooth muscle in addition to their accepted role in cardiac myocytes and neurones. This study aimed to assess the expression of ERG1–3 (KCNH1–3) genes in the murine myometrium (smooth muscle layer of the uterus) and determine the functional impact of the ion channels encoded by these genes in pregnant and non-pregnant animals. Quantitative RT-PCR did not detect message for ERG2 and 3 in whole myometrial tissue extracts. In contrast, message for two isoforms of mERG1 were readily detected with mERG1a more abundant than mERG1b. In isometric tension studies of non-pregnant myometrium, the ERG channel blockers dofetilide (1 ?m), E4031 (1 ?m) and Be-KM1 (100 nm) increased spontaneous contractility and ERG activators (PD118057 and NS1643) inhibited spontaneous contractility. In contrast, neither ERG blockade nor activation had any effect on the inherent contractility in myometrium from late pregnant (19 days gestation) animals. Moreover, dofetilide-sensitive K+ currents with distinctive ‘hooked’ kinetics were considerably smaller in uterine myocytes from late pregnant compared to non-pregnant animals. Expression of mERG1 isoforms did not alter throughout gestation or upon delivery, but the expression of genes encoding auxillary subunits (KCNE) were up-regulated considerably. This study provides the first evidence for a regulation of ERG-encoded K+ channels as a precursor to late pregnancy physiological activity.

Greenwood, I A; Yeung, S Y; Tribe, R M; Ohya, S

2009-01-01

93

The utility of functional gene arrays for assessing community composition, relative abundance, and distribution of ammonia-oxidizing bacteria and archaea.  

PubMed

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) transform ammonium to nitrite, an essential step in the complete mineralization of organic matter, leading to the accumulation of nitrate in oxic environments. The diversity and community composition of both groups have been extensively explored by sequence analysis of both 16S rRNA and amoA (encoding the critical enzyme, ammonia monooxygenase subunit A) genes. In this chapter, the power of the amoA gene as a phylogenetic marker for both AOB and AOA is extended to the development and application of DNA microarrays. Functional gene microarrays provide high throughput, relatively high resolution data on community composition and relative abundance, which is especially useful for comparisons among environments, and between samples in time and space, targeting the microbial group that is responsible for a biogeochemical transformation of interest, such as nitrification. In this chapter, the basic approaches to the design of probes to represent the target groups AOB and AOA are described, and the protocols for preparing hybridization targets from environmental samples are provided. Factors that influence the hybridization results and determine the sensitivity and specificity of the assays are discussed. A few examples of recent applications of amoA microarrays to explore temporal and spatial patterns in AOB and AOA community composition in estuaries and the ocean are presented. Array data are lower resolution than sequencing, but much higher throughput, thus allowing robust statistics and reproducibility that are not possible with large clone libraries. For specific functional groups, arrays provide more direct information in a more economical format than is possible with next generation sequencing. PMID:21514472

Ward, B B; Bouskill, N J

2011-01-01

94

Cost benefit theory and optimal design of gene regulation functions  

Microsoft Academic Search

Cells respond to the environment by regulating the expression of genes according to environmental signals. The relation between the input signal level and the expression of the gene is called the gene regulation function. It is of interest to understand the shape of a gene regulation function in terms of the environment in which it has evolved and the basic

Tomer Kalisky; Erez Dekel; Uri Alon

2007-01-01

95

Increased Attributable Risk Related to a Functional ?-Opioid Receptor Gene Polymorphism in Association with Alcohol Dependence in Central Sweden  

Microsoft Academic Search

The ?-opioid receptor (MOR), through its effects on reward and stress-responsivity, modulates alcohol intake in both animal and human laboratory studies. We have previously demonstrated that the frequently occurring A118G single-nucleotide polymorphism (SNP) in exon 1 of the MORgene (OPRM1), which encodes an amino-acid substitution, is functional and receptors encoded by the variant 118G allele bind the endogenous opioid peptide

Gavin Bart; Mary Jeanne Kreek; Jurg Ott; K Steven LaForge; Dmitri Proudnikov; Lotta Pollak; Markus Heilig

2005-01-01

96

Common Functions or Only Phylogenetically Related? The Large Family of PLAC8 Motif-Containing/PCR Genes  

PubMed Central

PLAC8 motif-containing proteins form a large family and members can be found in fungi, algae, higher plants and animals. They include the PCR proteins of plants. The name giving PLAC8 domain was originally found in a protein residing in the spongiotrophoblast layer of the placenta of mammals. A further motif found in a large number of these proteins including several PCR proteins is the CCXXXXCPC or CLXXXXCPC motif. Despite their wide distribution our knowledge about the function of these proteins is very limited. For most of them two membranespanning ?-helices are predicted, indicating that they are membrane associated or membrane intrinsic proteins. In plants PLAC8 motif-containing proteins have been described to be implicated in two very different functions. On one hand, it has been shown that they are involved in the determination of fruit size and cell number. On the other hand, two members of this family, AtPCR1 and AtPCR2 play an important role in transport of heavy metals such as cadmium or zinc. Transport experiments and approaches to model the 3_D structure of these proteins indicate that they could act as transporters for these divalent cations by forming homomultimers. In this minireview we discuss the present knowledge about this protein family and try to give an outlook on how to integrate the different proposed functions into a common picture about the role of PLAC8 motif-containing proteins.

Song, Won-Yong; Hortensteiner, Stefan; Tomioka, Rie; Lee, Youngsook; Martinoia, Enrico

2011-01-01

97

Molecular Genetic Analysis of the PLP1 Gene in 38 Families with PLP1-related disorders: Identification and Functional Characterization of 11 Novel PLP1 Mutations  

PubMed Central

Background The breadth of the clinical spectrum underlying Pelizaeus-Merzbacher disease and spastic paraplegia type 2 is due to the extensive allelic heterogeneity in the X-linked PLP1 gene encoding myelin proteolipid protein (PLP). PLP1 mutations range from gene duplications of variable size found in 60-70% of patients to intragenic lesions present in 15-20% of patients. Methods Forty-eight male patients from 38 unrelated families with a PLP1-related disorder were studied. All DNA samples were screened for PLP1 gene duplications using real-time PCR. PLP1 gene sequencing analysis was performed on patients negative for the duplication. The mutational status of all 14 potential carrier mothers of the familial PLP1 gene mutation was determined as well as 15/24 potential carrier mothers of the PLP1 duplication. Results and Conclusions PLP1 gene duplications were identified in 24 of the unrelated patients whereas a variety of intragenic PLP1 mutations were found in the remaining 14 patients. Of the 14 different intragenic lesions, 11 were novel; these included one nonsense and 7 missense mutations, a 657-bp deletion, a microdeletion and a microduplication. The functional significance of the novel PLP1 missense mutations, all occurring at evolutionarily conserved residues, was analysed by the MutPred tool whereas their potential effect on splicing was ascertained using the Skippy algorithm and a neural network. Although MutPred predicted that all 7 novel missense mutations would be likely to be deleterious, in silico analysis indicated that four of them (p.Leu146Val, p.Leu159Pro, p.Thr230Ile, p.Ala247Asp) might cause exon skipping by altering exonic splicing elements. These predictions were then investigated in vitro for both p.Leu146Val and p.Thr230Ile by means of RNA or minigene studies and were subsequently confirmed in the case of p.Leu146Val. Peripheral neuropathy was noted in four patients harbouring intragenic mutations that altered RNA processing, but was absent from all PLP1-duplication patients. Unprecedentedly, family studies revealed the de novo occurrence of the PLP1 duplication at a frequency of 20%.

2011-01-01

98

Genomic analysis of cyclic-di-GMP-related genes in rhizobial type strains and functional analysis in Rhizobium etli.  

PubMed

Rhizobia are soil bacteria that can fix nitrogen in symbiosis with leguminous plants or exist free living in the rhizosphere. Crucial to their complex lifestyle is the ability to sense and respond to diverse environmental stimuli, requiring elaborate signaling pathways. In the majority of bacteria, the nucleotide-based second messenger cyclic diguanosine monophosphate (c-di-GMP) is involved in signal transduction. Surprisingly, little is known about the importance of c-di-GMP signaling in rhizobia. We have analyzed the genome sequences of six well-studied type species (Bradyrhizobium japonicum, Mesorhizobium loti, Rhizobium etli, Rhizobium leguminosarum, Sinorhizobium fredii, and Sinorhizobium meliloti) for proteins possibly involved in c-di-GMP signaling based on the presence of four domains: GGDEF (diguanylate cyclase), EAL and HD-GYP (phosphodiesterase), and PilZ (c-di-GMP sensor). We find that rhizobia possess a high number of these proteins. Conservation analysis suggests that c-di-GMP signaling proteins modulate species-specific pathways rather than ancient rhizobia-specific processes. Two hybrid GGDEF-EAL proteins were selected for functional analysis, R. etli RHE_PD00105 (CdgA) and RHE_PD00137 (CdgB). Expression of cdgA and cdgB is repressed by the alarmone (p)ppGpp. cdgB is significantly expressed on plant roots and free living. Mutation of cdgA, cdgB, or both does not affect plant root colonization, nitrogen fixation capacity, biofilm formation, motility, and exopolysaccharide production. However, heterologous expression of the individual GGDEF and EAL domains of each protein in Escherichia coli strongly suggests that CdgA and CdgB are bifunctional proteins, possessing both diguanylate cyclase and phosphodiesterase activities. Taken together, our results provide a platform for future studies of c-di-GMP signaling in rhizobia. PMID:24728599

Gao, Shanjun; Romdhane, Samir Ben; Beullens, Serge; Kaever, Volkhard; Lambrichts, Ivo; Fauvart, Maarten; Michiels, Jan

2014-05-01

99

GOToolBox: functional analysis of gene datasets based on Gene Ontology  

Microsoft Academic Search

We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level

David Martin; Christine Brun; Elisabeth Remy; Pierre Mouren; Denis Thieffry; Bernard Jacq

2004-01-01

100

Genome-wide inventory of metal homeostasis-related gene products including a functional phytochelatin synthase in the hypogeous mycorrhizal fungus Tuber melanosporum  

Microsoft Academic Search

Ectomycorrhizal fungi are thought to enhance mineral nutrition of their host plants and to confer increased tolerance toward toxic metals. However, a global view of metal homeostasis-related genes and pathways in these organisms is still lacking. Building upon the genome sequence of Tuber melanosporum and on transcriptome analyses, we set out to systematically identify metal homeostasis-related genes in this plant-symbiotic

Angelo Bolchi; Roberta Ruotolo; Gessica Marchini; Emanuela Vurro; Luigi Sanità di Toppi; Annegret Kohler; Emilie Tisserant; Francis Martin; Simone Ottonello

2011-01-01

101

A novel functional low-density lipoprotein receptor-related protein 6 gene alternative splice variant is associated with Alzheimer's disease.  

PubMed

We previously found that single nucleotide polymorphisms in the low-density lipoprotein receptor-related protein 6 (LRP6) gene are associated with Alzheimer's disease (AD). Here, we studied the posttranscriptional metabolism of the LRP6 message scanning sequentially the 23 LRP6 exons in human tissues and found a novel LRP6 isoform that completely skips exon 3 (LRP6?3) in all tissues examined and was also conserved in mice. Expression levels of the LRP6 isoforms were determined in 47 cortical brain messenger (m)RNA samples including 22 AD cases, 11 control subjects, and 14 individuals with other neurological disorders. LRP6?3 mRNA levels were significantly augmented in AD brains compared with controls (1.6-fold; p = 0.037) or other pathological samples (2-fold; p = 0.007). Functional analysis in Wnt/?-catenin signaling assays revealed that skipping of exon 3 reduced significantly the signaling activity of the LRP6 coreceptor. We conclude that the LRP6?3 isoform is a novel splice variant, which shows diminished Wnt/?-catenin signaling activity and might have a functional role in individuals with AD. PMID:23218566

Alarcón, Marcelo A; Medina, Matías A; Hu, Qubai; Avila, Miguel E; Bustos, Bernabé I; Pérez-Palma, Eduardo; Peralta, Alexis; Salazar, Paulina; Ugarte, Giorgia D; Reyes, Ariel E; Martin, George M; Opazo, Carlos; Moon, Randall T; De Ferrari, Giancarlo V

2013-06-01

102

Necessity of angiotensin-converting enzyme-related gene for cardiac functions and longevity of Drosophila melanogaster assessed by optical coherence tomography  

NASA Astrophysics Data System (ADS)

Prior studies have established the necessity of an angiotensin-converting enzyme-related (ACER) gene for heart morphogenesis of Drosophila. Nevertheless, the physiology of ACER has yet to be comprehensively understood. Herein, we employed RNA interference to down-regulate the expression of ACER in Drosophila's heart and swept source optical coherence tomography to assess whether ACER is required for cardiac functions in living adult flies. Several contractile parameters of Drosophila heart, including the heart rate (HR), end-diastolic diameter (EDD), end-systolic diameter (ESD), percent fractional shortening (%FS), and stress-induced cardiac performance, are shown, which are age dependent. These age-dependent cardiac functions declined significantly when ACER was down-regulated. Moreover, the lifespans of ACER knock-down flies were significantly shorter than those of wild-type control flies. Thus, we posit that ACER, the Drosophila ortholog of mammalian angiotensin-converting enzyme 2 (ACE2), is essential for both heart physiology and longevity of animals. Since mammalian ACE2 controls many cardiovascular physiological features and is implicated in cardiomyopathies, our findings that ACER plays conserved roles in genetically tractable animals will pave the way for uncovering the genetic pathway that controls the renin-angiotensin system.

Liao, Fang-Tsu; Chang, Cheng-Yi; Su, Ming-Tsan; Kuo, Wen-Chuan

2014-01-01

103

Necessity of angiotensin-converting enzyme-related gene for cardiac functions and longevity of Drosophila melanogaster assessed by optical coherence tomography.  

PubMed

Prior studies have established the necessity of an angiotensin-converting enzyme-related (ACER) gene for heart morphogenesis of Drosophila. Nevertheless, the physiology of ACER has yet to be comprehensively understood. Herein, we employed RNA interference to down-regulate the expression of ACER in Drosophila's heart and swept source optical coherence tomography to assess whether ACER is required for cardiac functions in living adult flies. Several contractile parameters of Drosophila heart, including the heart rate (HR), end-diastolic diameter (EDD), end-systolic diameter (ESD), percent fractional shortening (%FS), and stress-induced cardiac performance, are shown, which are age dependent. These age-dependent cardiac functions declined significantly when ACER was down-regulated. Moreover, the lifespans of ACER knock-down flies were significantly shorter than those of wild-type control flies. Thus, we posit that ACER, the Drosophila ortholog of mammalian angiotensin-converting enzyme 2 (ACE2), is essential for both heart physiology and longevity of animals. Since mammalian ACE2 controls many cardiovascular physiological features and is implicated in cardiomyopathies, our findings that ACER plays conserved roles in genetically tractable animals will pave the way for uncovering the genetic pathway that controls the renin-angiotensin system. PMID:24002232

Liao, Fang-Tsu; Chang, Cheng-Yi; Su, Ming-Tsan; Kuo, Wen-Chuan

2014-01-01

104

Identification of a novel uromodulin-like gene related to predator-induced bulgy morph in anuran tadpoles by functional microarray analysis.  

PubMed

Tadpoles of the anuran species Rana pirica can undergo predator-specific morphological responses. Exposure to a predation threat by larvae of the salamander Hynobius retardatus results in formation of a bulgy body (bulgy morph) with a higher tail. The tadpoles revert to a normal phenotype upon removal of the larval salamander threat. Although predator-induced phenotypic plasticity is of major interest to evolutionary ecologists, the molecular and physiological mechanisms that control this response have yet to be elucidated. In a previous study, we identified various genes that are expressed in the skin of the bulgy morph. However, it proved difficult to determine which of these were key genes in the control of gene expression associated with the bulgy phenotype. Here, we show that a novel gene plays an important role in the phenotypic plasticity producing the bulgy morph. A functional microarray analysis using facial tissue samples of control and bulgy morph tadpoles identified candidate functional genes for predator-specific morphological responses. A larger functional microarray was prepared than in the previous study and used to analyze mRNAs extracted from facial and brain tissues of tadpoles from induction-reversion experiments. We found that a novel uromodulin-like gene, which we name here pirica, was up-regulated and that keratin genes were down-regulated as the period of exposure to larval salamanders increased. Pirica consists of a 1296 bp open reading frame, which is putatively translated into a protein of 432 amino acids. The protein contains a zona pellucida domain similar to that of proteins that function to control water permeability. We found that the gene was expressed in the superficial epidermis of the tadpole skin. PMID:19529781

Mori, Tsukasa; Kawachi, Hiroko; Imai, Chiharu; Sugiyama, Manabu; Kurata, Youichi; Kishida, Osamu; Nishimura, Kinya

2009-01-01

105

Identification of a Novel Uromodulin-Like Gene Related to Predator-Induced Bulgy Morph in Anuran Tadpoles by Functional Microarray Analysis  

PubMed Central

Tadpoles of the anuran species Rana pirica can undergo predator-specific morphological responses. Exposure to a predation threat by larvae of the salamander Hynobius retardatus results in formation of a bulgy body (bulgy morph) with a higher tail. The tadpoles revert to a normal phenotype upon removal of the larval salamander threat. Although predator-induced phenotypic plasticity is of major interest to evolutionary ecologists, the molecular and physiological mechanisms that control this response have yet to be elucidated. In a previous study, we identified various genes that are expressed in the skin of the bulgy morph. However, it proved difficult to determine which of these were key genes in the control of gene expression associated with the bulgy phenotype. Here, we show that a novel gene plays an important role in the phenotypic plasticity producing the bulgy morph. A functional microarray analysis using facial tissue samples of control and bulgy morph tadpoles identified candidate functional genes for predator-specific morphological responses. A larger functional microarray was prepared than in the previous study and used to analyze mRNAs extracted from facial and brain tissues of tadpoles from induction-reversion experiments. We found that a novel uromodulin-like gene, which we name here pirica, was up-regulated and that keratin genes were down-regulated as the period of exposure to larval salamanders increased. Pirica consists of a 1296 bp open reading frame, which is putatively translated into a protein of 432 amino acids. The protein contains a zona pellucida domain similar to that of proteins that function to control water permeability. We found that the gene was expressed in the superficial epidermis of the tadpole skin.

Mori, Tsukasa; Kawachi, Hiroko; Imai, Chiharu; Sugiyama, Manabu; Kurata, Youichi; Kishida, Osamu; Nishimura, Kinya

2009-01-01

106

Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs  

Microsoft Academic Search

Background  Bi-directional gene pairs have received considerable attention for their prevalence in vertebrate genomes. However, their\\u000a biological relevance and exact regulatory mechanism remain less understood. To study the inner properties of this gene organization\\u000a and the difference between bi- and uni-directional genes, we conducted a genome-wide investigation in terms of their sequence\\u000a composition, functional association and regulatory motif discovery.\\u000a \\u000a \\u000a \\u000a \\u000a Results  We identified

Bingchuan Liu; Jiajia Chen; Bairong Shen

2011-01-01

107

Diurnal expression of functional and clock-related genes throughout the rat HPA axis: system-wide shifts in response to a restricted feeding schedule  

PubMed Central

The diurnal rhythm of glucocorticoid secretion depends on the suprachiasmatic (SCN) and dorsomedial (putative food-entrainable oscillator; FEO) nuclei of the hypothalamus, two brain regions critical for coordination of physiological responses to photoperiod and feeding cues, respectively. In both cases, time keeping relies upon diurnal oscillations in clock gene (per1, per2, and bmal) expression. Glucocorticoids may play a key role in synchronization of the rest of the body to photoperiod and food availability. Thus glucocorticoid secretion may be both a target and an important effector of SCN and FEO output. Remarkably little, however, is known about the functional diurnal rhythms of the individual components of the hypothalamic-pituitary-adrenal (HPA) axis. We examined the 24-h pattern of hormonal secretion (ACTH and corticosterone), functional gene expression (c-fos, crh, pomc, star), and clock gene expression (per1, per2 and bmal) in each compartment of the HPA axis under a 12:12-h light-dark cycle and compared with relevant SCN gene expression. We found that each anatomic component of the HPA axis has a unique circadian signature of functional and clock gene expression. We then tested the susceptibility of these measures to nonphotic entrainment cues by restricting food availability to only a portion of the light phase of a 12:12-h light-dark cycle. Restricted feeding is a strong zeitgeber that can dramatically alter functional and clock gene expression at all levels of the HPA axis, despite ongoing photoperiod cues and only minor changes in SCN clock gene expression. Thus the HPA axis may be an important mediator of the body entrainment to the FEO.

Girotti, Milena; Weinberg, Marc S.; Spencer, Robert L.

2009-01-01

108

Glutamine, gene expression, and cell function.  

PubMed

Glutamine is the most abundant free amino acid in the body and is known to play a regulatory role at the gene and protein level in several cell specific processes including metabolism (e.g. oxidative fuel, gluconeogenic precursor and lipogenic precursor), cell integrity (survival, cell proliferation), protein synthesis and degradation, redox potential, respiratory burst, insulin resistance, insulin secretion and extracellular matrix synthesis. Glutamine has been shown to regulate the expression of many genes related to metabolism, signal transduction, cell defense and repair and to activate intracellular signaling pathways. Thus, the function of glutamine goes beyond that of a simple metabolic fuel or protein precursor as previously assumed. In this review, we have attempted to identify some of the common mechanisms underlying glutamine dependent changes in gene and protein expression and cellular function. PMID:17127303

Curi, Rui; Newsholme, Philip; Procopio, Joaquim; Lagranha, Cláudia; Gorjão, Renata; Pithon-Curi, Tânia Cristina

2007-01-01

109

Relation of chromosome structure and gene expression.  

PubMed

We have been able to map specific DNA fragments at the bases of chromatin loops with the help of a novel extraction procedure by using lithium-3',5'-diiodosalicylate. One such scaffold-attached region (SAR) is found in the non-transcribed spacer in each repeat of the histone gene cluster, on a 657 base pair (b.p.) restriction fragment. Exonuclease III digestion has localized two protein-binding domains on the SAR of the histone cluster. Each covers approximately 200 b.p. and they are separated by a nuclease-accessible region of about 100 b.p. These domains are rich in sequences closely related to the topoisomerase II cleavage consensus. We have studied the scaffold association of three developmentally regulated genes of Drosophila melanogaster: alcohol dehydrogenase (Adh), the homoeotic gene fushi tarazu (ftz) and Sgs-4, a gene encoding one of the glue proteins secreted by third-instar larvae. We find regions attached to the nuclear scaffold (SARS) both 5' and 3' of all three genes, defining small domains ranging from 4.5 to 13 kilobases. In the case of Adh, a gene with two promoters, we find two upstream and two downstream SARS. Those 5' of the gene co-map with regulatory regions for the adult and the larval transcripts, respectively. For Sgs-4, the 5' SAR covers 866 b.p. immediately upstream of the transcript, and encompasses the 200 b.p. regulatory region defined by two deletion mutants that produce little or no Sgs-4 protein. In ftz the 5' SAR is found 4.8 kilobases upstream of the start of transcription within a 2.5 kilobase element required for a high level of ftz expression in the early embryo. Sequence analysis of five upstream SARS reveals clusters of sequences closely related to the cleavage consensus of topoisomerase II. In addition, they contain multiple copies of two sequence motifs: a specific 10 b.p. A-rich sequence, and another 10 b.p. T-rich stretch. In conclusion, the intimate association of the SAR with the upstream/enhancer elements, the presence of clustered sequences highly homologous to the topoisomerase II cleavage consensus, and the localization of topoisomerase II in the scaffold, suggest a structure-function relation between chromosome organization and gene expression. PMID:2894689

Mirkovitch, J; Gasser, S M; Laemmli, U K

1987-12-15

110

[Molecular cloning and preliminary function study of a novel human gene AC3-33 related to suppress AP-1 activity].  

PubMed

Activator protein-1(AP-1) is an important transcription factor, and dysregulation of its activity has been associated with many human diseases, including various cancers. A novel human gene AC3-33 (GenBank name: c30rf33, Accession No. FLJ31139), which can suppress PMA and Ionomycin induced activation of AP-1, was identified from 650 human func-tion-known genes by using the high throughput-high content cell-based screening technology. The gene whose full cDNA length is 1391 bp containing 6 exons and 5 introns is located in the human chromosome 3q25.31. The predicted protein encoded by this gene contains 251 amino acids with a theoretical molecular weight of 29 kDa. Expression of the AC3-33 gene is widly found in adrenal glands and cervix. The amino acid sequences of AC3-33 is highly conserved, and has no homology to other known proteins. Subcellular localization studies show that the AC3-33 protein was localized in the cytoplasm. Our preliminary results showed that AC3-33 is an important novel gene related to supress AP-1 activity. PMID:18487146

Liu, Peng; Deng, Wei-Wei; Gao, Peng; Lu, Yang; Sun, Bo; Li, Ming; Zhao, Jie; Shi, Tai-Ping; Zhang, Xiu-Jun

2008-05-01

111

A functional polymorphism in the NAD(P)H oxidase subunit CYBA is related to gene expression, enzyme activity, and outcome in non-Hodgkin lymphoma.  

PubMed

NAD(P)H oxidase is a major endogenous source of reactive oxygen species (ROS). ROS may not only be involved in carcinogenesis but also in efficacy of chemotherapeutic agents like doxorubicin. By a comprehensive genotyping approach covering 48 genetic polymorphisms (single-nucleotide polymorphisms) in five subunits of phagocytic NAD(P)H oxidase, we asked whether they affect gene expression, enzymatic activity, and outcome of CHO(E)P chemotherapy. A highly consistent effect was observed for the CYBA 640A>G variant. In peripheral blood granulocytes of 125 healthy volunteers, the G allele of 640A>G was associated with lower NAD(P)H oxidase activity (P = 0.006). Moreover, the G allele was associated with lower mRNA and protein expression (both P = 0.02). Of clinical importance, the outcome of patients suffering from non-Hodgkin lymphoma and treated with CHO(E)P regimen was dependent on the CYBA 640A>G polymorphism. In an exploratory study (n = 401), carriers of 640GG had an event-free survival (EFS) risk ratio of 1.95 [95% confidence interval (95% CI), 1.31-2.90; P = 0.001] compared with 640AA. In a confirmatory set (n = 477), the risk ratios were 1.53 (1.04-2.25, P = 0.03). The complete set of 878 patients showed a relative risk of 1.72 (1.30-2.26) and 1.59 (1.14-2.21) for EFS and overall survival, respectively. Further molecular-biological experiments showed lower expression and reduced stability of transcripts with the G allele in lymphoblastoid cell lines. Transfection of allele-specific plasmids into HEK293 cells elicited lower activity for the G allele in a luciferase reporter gene construct. Thus, CYBA 640A>G was shown to be a functional polymorphism with possible consequences for patients receiving CHO(E)P chemotherapy and might have further implications for other ROS-mediated modalities. PMID:20215507

Hoffmann, Marion; Schirmer, Markus A; Tzvetkov, Mladen V; Kreuz, Markus; Ziepert, Marita; Wojnowski, Leszek; Kube, Dieter; Pfreundschuh, Michael; Trümper, Lorenz; Loeffler, Markus; Brockmöller, Jürgen

2010-03-15

112

Functional characterization of ether-a-go-go-related gene potassium channels in midbrain dopamine neurons: implications for a role in depolarization block  

PubMed Central

Bursting activity by midbrain dopamine neurons reflects the complex interplay between their intrinsic pacemaker activity and synaptic inputs. Although the precise mechanism responsible for the generation and modulation of bursting in vivo has yet to be established, several ion channels have been implicated in the process. Previous studies with nonselective blockers suggested that ether-a-go-go-related gene (ERG) K+ channels are functionally significant. Here, electrophysiology with selective chemical and peptide ERG channel blockers (E-4031 and rBeKm-1) and computational methods were used to define the contribution made by ERG channels to the firing properties of midbrain dopamine neurons in vivo and in vitro. Selective ERG channel blockade increased the frequency of spontaneous activity as well as the response to depolarizing current pulses without altering spike frequency adaptation. ERG channel block also accelerated entry into depolarization inactivation during bursts elicited by virtual NMDA receptors generated with the dynamic clamp, and significantly prolonged the duration of the sustained depolarization inactivation that followed pharmacologically evoked bursts. In vivo, somatic ERG blockade was associated with an increase in bursting activity attributed to a reduction in doublet firing. Taken together, these results show that dopamine neuron ERG K+ channels play a prominent role in limiting excitability and in minimizing depolarization inactivation. As the therapeutic actions of antipsychotic drugs are associated with depolarization inactivation of dopamine neurons and blockade of cardiac ERG channels is a prominent side effect of these drugs, ERG channels in the central nervous system may represent a novel target for antipsychotic drug development.

Ji, Huifang; Tucker, Kristal R.; Putzier, Ilva; Huertas, Marco A.; Horn, John P.; Canavier, Carmen C.; Levitan, Edwin S.; Shepard, Paul D.

2014-01-01

113

Function of the DISC1 Gene  

NSDL National Science Digital Library

As a result of the human genome project, we now know largely where our genes are, and what structure they have. The search to uncover each gene's function, on the other hand, is only in its infancy. Functional genomics is an area of research dedicated to studying what protein is produced by a gene, and what happens in the body when it is activated. Understanding gene function is the next major hurdle in genomic research, which holds the key to developing revolutionary therapeutics.

2009-04-14

114

Gene disruptions, compositions and methods relating thereto  

US Patent & Trademark Office Database

The present invention relates to transgenic animals, as well as compositions and methods relating to the characterization of gene function. Specifically, the present invention provides transgenic mice comprising disruptions in PRO194, PRO220, PRO241, PRO284, PRO331, PRO354, PRO355, PRO533, PRO541, PRO725, PRO937, PRO1014, PRO1120, PRO1182, PRO1325, PRO1382, PRO1410, PRO1555, PRO1556, PRO1760, PRO1787, PRO1868, PRO4326, PRO4332, PRO4346, PRO4400, PRO6003, PRO6094, PRO6244, PRO9820, PRO9828, PRO10274, PRO16090, PRO19644, PRO21340, PRO92165, PRO85143, PRO1124, PRO1026 or PRO23370 genes. Such in vivo studies and characterizations may provide valuable identification and discovery of therapeutics and/or treatments useful in the prevention, amelioration or correction of diseases or dysfunctions associated with gene disruptions such as neurological disorders; cardiovascular, endothelial or angiogenic disorders; eye abnormalities; immunological disorders; oncological disorders; bone metabolic abnormalities or disorders; lipid metabolic disorders; or developmental abnormalities.

2011-05-24

115

Distribution of typical denitrifying functional genes and diversity of the nirS-encoding bacterial community related to environmental characteristics of river sediments  

NASA Astrophysics Data System (ADS)

Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0-25 cm depth) were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate (narG), nitrite (nirS, nirK and nrfA), and nitrous oxide (nosZ) reductase genes from the sediment samples. Assemblages of nirS, nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5-15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78-94 %) between the nirS sequences recovered from Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic N (DIN: NH4+, NO2genes and the nirS-encoding denitrifier community in the river sediment. Our results also reveal a variety of novel denitrifying bacteria in the river sediment.

Huang, S.; Chen, C.; Wu, Q.; Zhang, R.; Yang, X.

2011-05-01

116

Combining Hierarchical and Associative Gene Ontology Relations with Textual Evidence in Estimating Gene and Gene Product Similarity  

SciTech Connect

Gene and gene product similarity is a fundamental diagnostic measure in analyzing biological data and constructing predictive models for functional genomics. With the rising influence of the Gene Ontology, two complementary approaches have emerged where the similarity between two genes or gene products is obtained by comparing Gene Ontology (GO) annotations associated with the genes or gene products. One approach captures GO-based similarity in terms of hierarchical relations within each gene subontology. The other approach identifies GO-based similarity in terms of associative relations across the three gene subontologies. We propose a novel methodology where the two approaches can be merged with ensuing benefits in coverage and accuracy, and demonstrate that further improvements can be obtained by integrating textual evidence extracted from relevant biomedical literature.

Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Riensche, Roderick M.; Beagley, Nathaniel; Baddeley, Bob L.; Tratz, Stephen C.; Gregory, Michelle L.

2007-03-01

117

Towards integrative gene functional similarity measurement  

PubMed Central

Background In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare gene functional similarities at the molecular level. The existing gene similarity measures, however, solely rely on one or few aspects of MF without utilizing all the rich information available including structure, annotation, common terms, lowest common parents. Results We introduce a rank-based gene semantic similarity measure called InteGO by synergistically integrating the state-of-the-art gene-to-gene similarity measures. By integrating three GO based seed measures, InteGO significantly improves the performance by about two-fold in all the three species studied (yeast, Arabidopsis and human). Conclusions InteGO is a systematic and novel method to study gene functional associations. The software and description are available at http://www.msu.edu/~jinchen/InteGO.

2014-01-01

118

The function of the Aristaless-related homeobox (Arx) gene product as a transcriptional repressor is diminished by mutations associated with X-linked mental retardation (XLMR).  

PubMed

The Aristaless-related homeobox (Arx) is mutated in patients with X-linked mental retardation and a range of other neurological diseases. The molecular consequences of these mutations are unclear. Here, we show that two disease-associated mutations disrupt the function of Arx as a transcriptional repressor. We found that Arx contains two independent repression domains: an N-terminal octapeptide motif/engrailed homology domain and a novel domain located in the C-terminus. The octapeptide motif functions through interaction with members of the Groucho family of co-repressors. The C-terminal domain functions through interaction with C-terminal binding protein (CtBP). PMID:18835247

Fullenkamp, Amy N; El-Hodiri, Heithem M

2008-12-01

119

Cross-Ontological Analytics: Combining Associative and Hierarchical Relations in the Gene Ontologies to Assess Gene Product Similarity  

SciTech Connect

Gene and gene product similarity is a fundamental diagnostic measure in analyzing biological data and constructing predictive models for functional genomics. With the rising influence of the gene ontologies, two complementary approaches have emerged where the similarity between two genes/gene products is obtained by comparing gene ontology (GO) annotations associated with the gene/gene products. One approach captures GO-based similarity in terms of hierarchical relations within each gene ontology. The other approach identifies GO-based similarity in terms of associative relations across the three gene ontologies. We propose a novel methodology where the two approaches can be merged with ensuing benefits in coverage and accuracy.

Posse, Christian; Sanfilippo, Antonio P.; Gopalan, Banu; Riensche, Roderick M.; Beagley, Nathaniel; Baddeley, Bob L.

2006-05-28

120

Overview of available p53 function tests in relation to TP53 and ATM gene alterations and chemoresistance in chronic lymphocytic leukemia.  

PubMed

The ATM-p53 DNA damage response pathway plays a crucial role in chemoresistance in chronic lymphocytic leukemia, as indicated by the adverse prognostic impact of deletions of 17p (locus of TP53) and 11q (locus of ATM) detected by fluorescence in situ hybridization (FISH) analysis. In addition to deletions, mutations in these respective genes are also associated with chemoresistance, and add to the prognostic information provided by FISH. In order to explore the possibility that dysfunction of the ATM-p53 pathway might also result from mechanisms other than ATM/TP53 deletion/mutation, assays have been developed that probe the functional integrity of the ATM-p53 pathway. Currently, four different p53 function assays have been developed that are based on the measurement of p53 and p53-dependent genes at the RNA (real-time polymerase chain reaction [RT-PCR]p21; RT-PCRmiR34a; reverse transcription-multiplex ligation-dependent probe amplification assay [RT-MLPA]p21, bax, puma and CD95) or protein (fluorescence activated cell sorting [FACS]p53-p21) level in untreated cells or following irradiation or drug treatment. Here we provide an overview of these assays based on the available literature. PMID:23614766

te Raa, G Doreen; Malcikova, Jitka; Pospisilova, Sarka; Trbusek, Martin; Mraz, Mark; Garff-Tavernier, Maria Le; Merle-Béral, Hélène; Lin, Ke; Pettitt, Andrew R; Merkel, Olaf; Stankovic, Tatjana; van Oers, Marinus H; Eldering, Eric; Stilgenbauer, Stephan; Zenz, Thorsten; Kater, Arnon P

2013-08-01

121

Distribution of typical denitrifying functional genes and diversity of the nirS-encoding bacterial community related to environmental characteristics of river sediments  

NASA Astrophysics Data System (ADS)

Denitrification in river sediments leads to nitrate removal from the aquatic system; therefore, it is necessary to understand functional diversity of denitrifier communities in the system. Sediment samples (0-25 cm depth) were collected from three typical locations along the Pearl River. The real-time PCR approach was used to measure the abundance of nitrate (narG), nitrite (nirS, nirK and nrfA), and nitrous oxide (nosZ) reductase genes from the sediment samples. Assemblages of nirS, nirK and nosZ indicated that complete denitrification occurred in sediment cores, with the greatest number of gene copies from 5-15 cm depth. Dissimilatory nitrate reduction appeared to be important below 15 cm depth, based on increasing gene copies of narG and nrfA with sediment depth. There was a close match (78-94 %) between the nirS sequences recovered from the Pearl River sediment and those detected in estuarine and marine sediments as well as active sludge, suggesting that the nitrogen source in the Pearl River sediment was affected by domestic sewage inputs and irregular tides. Canonical correspondence analysis indicated that the spatial distribution of denitrifying bacteria was highly correlated with dissolved inorganic nitrogen (including NH4+, NO2- and NO3-) concentrations in sediment. It was concluded that the difference in dissolved inorganic nitrogen concentrations along the sediment profile influenced the distribution of denitrifying genes and the nirS-encoding denitrifier community in the river sediment. In addition, a variety of novel denitrifying bacteria were revealed in the river sediment.

Huang, S.; Chen, C.; Yang, X.; Wu, Q.; Zhang, R.

2011-10-01

122

Analysis of the Interferon Gamma (rs2430561, +874T/A) Functional Gene Variant in Relation to the Presence of Cardiovascular Events in Rheumatoid Arthritis  

PubMed Central

Objective Rheumatoid arthritis (RA) is a chronic inflammatory disease associated with increased cardiovascular (CV) morbidity and mortality. Since interferon-gamma (IFN-?) has a direct effect on inflammation, in this study we assessed the potential association of the IFNG functional gene variant rs2430561 with CV disease in patients with RA. Methods One thousand six hundred and thirty-five patients fulfilling the 1987 American College of Rheumatology classification criteria for RA were genotyped for the IFNG (rs2430561, +874T/A) gene polymorphism using TaqMan genotyping assay. Patients were stratified according to the presence of CV events or not. Logistic regression models to explain the presence of CV disease according to the IFNG rs2430561 allele distribution were performed. The potential influence of this variant in the development of subclinical atherosclerosis was also analyzed in a subgroup of patients with no history of CV events to determine carotid artery intima-media thickness (IMT) (n?=?286) and presence of carotid plaques. Levels of the cytokine were determined in a subgroup of patients by ELISA. Results Adjusted logistic regression model disclosed that presence of the minor allele A was not associated with increased risk of suffering CV events in RA patients. Besides, differences did not achieve statistical significance regarding carotid IMT and presence of carotid plaques in RA patients carrying IFNG rs2430561 variant allele. Levels of IFN-? were higher in patients who had suffered CV events compared to patients who did not. Conclusion Our results do not support a role of IFNG rs2430561 (+874T/A) functional gene variant in the development of CV disease in RA patients.

Gonzalez-Juanatey, Carlos; Corrales, Alfonso; Robledo, Gema; Castaneda, Santos; Miranda-Filloy, Jose A.; Blanco, Ricardo; Fernandez-Gutierrez, Benjamin; Balsa, Alejandro; Gonzalez-Alvaro, Isidoro; Gomez-Vaquero, Carmen; Llorca, Javier; Gonzalez-Gay, Miguel A.

2012-01-01

123

Amygdalin inhibits genes related to cell cycle in SNU-C4 human colon cancer cells  

Microsoft Academic Search

Abstract Abstract Abstract Abstract Abstract AIM: The,genes,were,divided into seven,categories according to biological function; apoptosis-related, immune response-related, signal transduction-related, cell cycle- related, cell growth-related, stress response-relatedand transcription-related genes. METHODS:We,compared,the gene,expression profiles

Hae-Jeong Park; Seo-Hyun Yoon; Long-Shan Han; Long-Tai Zheng; Kyung-Hee Jung; Yoon-Kyung Uhm; Je-Hyun Lee; Ji-Seon Jeong; Woo-Sang Joo; Sung-Vin Yim; Joo-Ho Chung; Seon-Pyo Hong; Park HJ; Yoon SH; Zheng LT; Jung KH; Uhm YK; Lee JH; Jeong JS; Joo WS; Yim SV; Chung JH

2005-01-01

124

Functional analysis of the Trichoderma harzianum nox1 gene, encoding an NADPH oxidase, relates production of reactive oxygen species to specific biocontrol activity against Pythium ultimum.  

PubMed

The synthesis of reactive oxygen species (ROS) is one of the first events following pathogenic interactions in eukaryotic cells, and NADPH oxidases are involved in the formation of such ROS. The nox1 gene of Trichoderma harzianum was cloned, and its role in antagonism against phytopathogens was analyzed in nox1-overexpressed transformants. The increased levels of nox1 expression in these transformants were accompanied by an increase in ROS production during their direct confrontation with Pythium ultimum. The transformants displayed an increased hydrolytic pattern, as determined by comparing protease, cellulase, and chitinase activities with those for the wild type. In confrontation assays against P. ultimum the nox1-overexpressed transformants were more effective than the wild type, but not in assays against Botrytis cinerea or Rhizoctonia solani. A transcriptomic analysis using a Trichoderma high-density oligonucleotide (HDO) microarray also showed that, compared to gene expression for the interaction of wild-type T. harzianum and P. ultimum, genes related to protease, cellulase, and chitinase activities were differentially upregulated in the interaction of a nox1-overexpressed transformant with this pathogen. Our results show that nox1 is involved in T. harzianum ROS production and antagonism against P. ultimum. PMID:21421791

Montero-Barrientos, M; Hermosa, R; Cardoza, R E; Gutiérrez, S; Monte, E

2011-05-01

125

Cancer module genes ranking using kernelized score functions  

PubMed Central

Background Co-expression based Cancer Modules (CMs) are sets of genes that act in concert to carry out specific functions in different cancer types, and are constructed by exploiting gene expression profiles related to specific clinical conditions or expression signatures associated to specific processes altered in cancer. Unfortunately, genes involved in cancer are not always detectable using only expression signatures or co-expressed sets of genes, and in principle other types of functional interactions should be exploited to obtain a comprehensive picture of the molecular mechanisms underlying the onset and progression of cancer. Results We propose a novel semi-supervised method to rank genes with respect to CMs using networks constructed from different sources of functional information, not limited to gene expression data. It exploits on the one hand local learning strategies through score functions that extend the guilt-by-association approach, and on the other hand global learning strategies through graph kernels embedded in the score functions, able to take into account the overall topology of the network. The proposed kernelized score functions compare favorably with other state-of-the-art semi-supervised machine learning methods for gene ranking in biological networks and scales well with the number of genes, thus allowing fast processing of very large gene networks. Conclusions The modular nature of kernelized score functions provides an algorithmic scheme from which different gene ranking algorithms can be derived, and the results show that using integrated functional networks we can successfully predict CMs defined mainly through expression signatures obtained from gene expression data profiling. A preliminary analysis of top ranked "false positive" genes shows that our approach could be in perspective applied to discover novel genes involved in the onset and progression of tumors related to specific CMs.

2012-01-01

126

Genes2FANs: connecting genes through functional association networks  

PubMed Central

Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Conclusions Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our finding that disease genes in many cancers are mostly connected through PPIs whereas other complex diseases, such as autism and type-2 diabetes, are mostly connected through FANs without PPIs, can guide better strategies for disease gene discovery. Genes2FANs is available at: http://actin.pharm.mssm.edu/genes2FANs.

2012-01-01

127

Discovery of Tumor Suppressor Gene Function.  

ERIC Educational Resources Information Center

This is an update of a 1991 review on tumor suppressor genes written at a time when understanding of how the genes work was limited. A recent major breakthrough in the understanding of the function of tumor suppressor genes is discussed. (LZ)

Oppenheimer, Steven B.

1995-01-01

128

The function of the Aristaless- related homeobox (Arx) gene product as a transcriptional repressor is diminished by mutations associated with X-linked mental retardation (XLMR)  

Microsoft Academic Search

The Aristaless-related homeobox (Arx) is mutated in patients with X-linked mental retardation and a range of other neurological diseases. The molecular consequences of these mutations are unclear. Here, we show that two disease-associated mutations disrupt the function of Arx as a transcriptional repressor. We found that Arx contains two independent repression domains: an N-terminal octapeptide motif\\/engrailed homology domain and a

Amy N. Fullenkamp; Heithem M. El-Hodiri

2008-01-01

129

A method for finding communities of related genes  

PubMed Central

We present a method for creating a network of gene co-occurrences from the literature and partitioning it into communities of related genes. The way in which our method identifies communities makes it likely that the component genes of each community will be related by their function. The method processes a large database of article abstracts, synthesizing information from many sources to shed light on groups of genes that have been shown to interact. It is a tool to be used by researchers in the biomedical sciences to swiftly search for known interactions and to provide insight into unexplored connections. The partitioning procedure is designed to be particularly applicable to large networks in which individual nodes may play a role in more than one community. In this paper, we explain the details of the method, in particular the partitioning process. We also apply the method to produce communities of genes related to colon cancer and show that the results are useful.

Wilkinson, Dennis M.; Huberman, Bernardo A.

2004-01-01

130

Essential Bacterial Functions Encoded by Gene Pairs??  

PubMed Central

To address the need for new antibacterials, a number of bacterial genomes have been systematically disrupted to identify essential genes. Such programs have focused on the disruption of single genes and may have missed functions encoded by gene pairs or multiple genes. In this work, we hypothesized that we could predict the identity of pairs of proteins within one organism that have the same function. We identified 135 putative protein pairs in Bacillus subtilis and attempted to disrupt the genes forming these, singly and then in pairs. The single gene disruptions revealed new genes that could not be disrupted individually and other genes required for growth in minimal medium or for sporulation. The pairwise disruptions revealed seven pairs of proteins that are likely to have the same function, as the presence of one protein can compensate for the absence of the other. Six of these pairs are essential for bacterial viability and in four cases show a pattern of species conservation appropriate for potential antibacterial development. This work highlights the importance of combinatorial studies in understanding gene duplication and identifying functional redundancy.

Thomaides, Helena B.; Davison, Ella J.; Burston, Lisa; Johnson, Hazel; Brown, David R.; Hunt, Alison C.; Errington, Jeffery; Czaplewski, Lloyd

2007-01-01

131

Biological cluster evaluation for gene function prediction.  

PubMed

Abstract Recent advances in high-throughput omics techniques render it possible to decode the function of genes by using the "guilt-by-association" principle on biologically meaningful clusters of gene expression data. However, the existing frameworks for biological evaluation of gene clusters are hindered by two bottleneck issues: (1) the choice for the number of clusters, and (2) the external measures which do not take in consideration the structure of the analyzed data and the ontology of the existing biological knowledge. Here, we address the identified bottlenecks by developing a novel framework that allows not only for biological evaluation of gene expression clusters based on existing structured knowledge, but also for prediction of putative gene functions. The proposed framework facilitates propagation of statistical significance at each of the following steps: (1) estimating the number of clusters, (2) evaluating the clusters in terms of novel external structural measures, (3) selecting an optimal clustering algorithm, and (4) predicting gene functions. The framework also includes a method for evaluation of gene clusters based on the structure of the employed ontology. Moreover, our method for obtaining a probabilistic range for the number of clusters is demonstrated valid on synthetic data and available gene expression profiles from Saccharomyces cerevisiae. Finally, we propose a network-based approach for gene function prediction which relies on the clustering of optimal score and the employed ontology. Our approach effectively predicts gene function on the Saccharomyces cerevisiae data set and is also employed to obtain putative gene functions for an Arabidopsis thaliana data set. PMID:20059365

Klie, Sebastian; Nikoloski, Zoran; Selbig, Joachim

2014-06-01

132

[Research Progress in Cytoplasmic PML Gene Functions].  

PubMed

The promyelocytic leukemia (PML) was originally identified and named as acute promyelocytic leukaemia (APL) . The PML, encoded by PML gene, locates in the nuclear body (NB) and shuttles in the cell nucleus-cytoplasm, so that PML completes many regulation functions. There are many researchs on the function of nuclear PML, but in recent years the foreign datas indicate that cytoplasmic PML gene plays an important role in hematologic malignancies and solid tumors. In this article, the biological functions of PML gene in cytoplasm are reviewed. PMID:24989309

Xu, Xiao-Hong; Sun, Yun-Yan; Zhang, Xue-Mei

2014-05-01

133

DNA Methylation and Gene Function  

Microsoft Academic Search

In most higher organisms, DNA is modified after synthesis by the enzymatic conversion of many cytosine residues to 5-methylcytosine. For several years, control of gene activity by DNA methylation has been recognized as a logically attractive possibility, but experimental support has proved elusive. However, there is now reason to believe, from recent studies, that DNA methylation is a key element

Aharon Razin; Arthur D. Riggs

1980-01-01

134

Evolutionary Approach for Relative Gene Expression Algorithms  

PubMed Central

A Relative Expression Analysis (RXA) uses ordering relationships in a small collection of genes and is successfully applied to classiffication using microarray data. As checking all possible subsets of genes is computationally infeasible, the RXA algorithms require feature selection and multiple restrictive assumptions. Our main contribution is a specialized evolutionary algorithm (EA) for top-scoring pairs called EvoTSP which allows finding more advanced gene relations. We managed to unify the major variants of relative expression algorithms through EA and introduce weights to the top-scoring pairs. Experimental validation of EvoTSP on public available microarray datasets showed that the proposed solution significantly outperforms in terms of accuracy other relative expression algorithms and allows exploring much larger solution space.

Czajkowski, Marcin

2014-01-01

135

Orphan genes: Function, evolution, and composition  

Microsoft Academic Search

The origin and function of orphan genes (OGs) is a mysterious problem in modern molecular biology. The recently developed\\u000a PHOG database helped to shed light on some aspects in the evolution of these genes. Presumably, a rapid evolution is the main\\u000a factor that influences the origin of OGs. The evolutionary rate of particular genes reflects the degree of their conservation,

I. V. Merkeev; A. A. Mironov

2008-01-01

136

Human Intellectual Disability Genes Form Conserved Functional Modules in Drosophila  

PubMed Central

Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules.

Oortveld, Merel A. W.; Keerthikumar, Shivakumar; Oti, Martin; Nijhof, Bonnie; Fernandes, Ana Clara; Kochinke, Korinna; Castells-Nobau, Anna; van Engelen, Eva; Ellenkamp, Thijs; Eshuis, Lilian; Galy, Anne; van Bokhoven, Hans; Habermann, Bianca; Brunner, Han G.; Zweier, Christiane; Verstreken, Patrik; Huynen, Martijn A.; Schenck, Annette

2013-01-01

137

Fungal avirulence genes: structure and possible functions.  

PubMed

Avirulence (Avr) genes exist in many fungi that share a gene-for-gene relationship with their host plant. They represent unique genetic determinants that prevent fungi from causing disease on plants that possess matching resistance (R) genes. Interaction between elicitors (primary or secondary products of Avr genes) and host receptors in resistant plants causes induction of various defense responses often involving a hypersensitive response. Avr genes have been successfully isolated by reverse genetics and positional cloning. Five cultivar-specific Avr genes (Avr4, Avr9, and Ecp2 from Cladosporium fulvum; nip1 from Rhynchosporium secalis; and Avr2-YAMO from Magnaporthe grisea) and three species-specific Avr genes (PWL1 and PWL2 from M. grisea and inf1 from Phytophthora infestans) have been cloned. Isolation of additional Avr genes from these fungi, but also from other fungi such as Uromyces vignae, Melampsora lini, Phytophthora sojae, and Leptosphaeria maculans, is in progress. Molecular analyses of nonfunctional Avr gene alleles show that these originate from deletions or mutations in the open reading frame or the promoter sequence of an Avr gene. Although intrinsic biological functions of most Avr gene products are still unknown, recent studies have shown that two Avr genes, nip1 and Ecp2, encode products that are important pathogenicity factors. All fungal Avr genes cloned so far have been demonstrated or predicted to encode extracellular proteins. Current studies focus on unraveling the mechanisms of perception of avirulence factors by plant receptors. The exploitation of Avr genes and the matching R genes in engineered resistance is also discussed. PMID:9756710

Laugé, R; De Wit, P J

1998-08-01

138

How Often Do Duplicated Genes Evolve New Functions?  

Microsoft Academic Search

A recently duplicated gene can either fix a null allele (becoming a pseudogene) or fix an (advanta- geous) allele giving a slightly different function, starting it on the road to evolving a new function. Here we examine the relative probabilities of these two events under a simple model. Null alleles are assumed to be neutral; linkage effects are ignored, as

J. Bruce Walsh

1995-01-01

139

Drug target-gene signatures that predict teratogenicity are enriched for developmentally related genes  

PubMed Central

Drugs prescribed during pregnancy affect two populations simultaneously: fetuses and their mothers. Drug-induced fetal injury (teratogenicity) has a significant impact on current and future public health. Teratogenic risk designation of many drugs relies on associating rare fetal events with rare environmental exposures. Therefore we aim to develop preclinical predictive models of clinical teratogenicity. We collated public databases for drug-target-gene relationships for 619 drugs spanning the 5 pregnancy risk classes. Genes targeted by high risk but not low risk drugs demonstrated 79% accuracy (p<0.0001 vs. random) for predicting high vs. low fetal risk on cross validation. Functional enrichment analysis revealed that target genes of drugs known to be safe in pregnancy contained no developmentally related terms, while target genes of known teratogens contained 85 developmentally related terms. Drug target gene signatures that are enriched for known developmental genes may provide valuable preclinical predictive information regarding drug pregnancy risk.

Schachter, Asher D.; Kohane, Isaac S.

2010-01-01

140

Functional requirements driving the gene duplication in 12 Drosophila species  

PubMed Central

Background Gene duplication supplies the raw materials for novel gene functions and many gene families arisen from duplication experience adaptive evolution. Most studies of young duplicates have focused on mammals, especially humans, whereas reports describing their genome-wide evolutionary patterns across the closely related Drosophila species are rare. The sequenced 12 Drosophila genomes provide the opportunity to address this issue. Results In our study, 3,647 young duplicate gene families were identified across the 12 Drosophila species and three types of expansions, species-specific, lineage-specific and complex expansions, were detected in these gene families. Our data showed that the species-specific young duplicate genes predominated (86.6%) over the other two types. Interestingly, many independent species-specific expansions in the same gene family have been observed in many species, even including 11 or 12 Drosophila species. Our data also showed that the functional bias observed in these young duplicate genes was mainly related to responses to environmental stimuli and biotic stresses. Conclusions This study reveals the evolutionary patterns of young duplicates across 12 Drosophila species on a genomic scale. Our results suggest that convergent evolution acts on young duplicate genes after the species differentiation and adaptive evolution may play an important role in duplicate genes for adaption to ecological factors and environmental changes in Drosophila.

2013-01-01

141

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle  

PubMed Central

Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the ‘marbling score’ trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

Lim, Dajeong; Lee, Seung-Hwan; Kim, Nam-Kuk; Cho, Yong-Min; Chai, Han-Ha; Seong, Hwan-Hoo; Kim, Heebal

2013-01-01

142

Clock gene evolution and functional divergence.  

PubMed

In considering the impact of the earth's changing geophysical conditions during the history of life, it is surprising to learn that the earth's rotational period may have been as short as 4 h, as recently as 1900 million years ago (or 1.9 billion years ago). The implications of such figures for the origin and evolution of clocks are considerable, and the authors speculate on how this short rotational period might have influenced the development of the "protoclock" in early microorganisms, such as the Cyanobacteria, during the geological periodsin which they arose and flourished. They then discuss the subsequent duplication of clock genes that took place around and after the Cambrian period, 543 million years ago, and its consequences. They compare the relative divergences of the canonical clock genes, which reveal the Per family to be the most rapidly evolving. In addition, the authors use a statistical test to predict which residues within the PER and CRY families may have undergone functional specialization. PMID:15534324

Tauber, Eran; Last, Kim S; Olive, Peter J W; Kyriacou, C P

2004-10-01

143

Gene functional classification from heterogeneous data  

Microsoft Academic Search

In our attempts to understand cellular function at the molecular level, we must be able to synthesize information from disparate types of genomic data. We consider the problem of inferring gene functional classifications from a heterogeneous data set consisting of DNA microarray expression measurements and phylogenetic profiles from whole-genome sequence comparisons. We demonstrate the application of the support vector machine

Paul Pavlidis; Jason Weston; Jinsong Cai; William Noble Grundy

2001-01-01

144

Exploring Patterns, Relations, and Functions.  

ERIC Educational Resources Information Center

Describes three activities using dominoes, playing cards, and the calendar to give students mathematical experiences reinforcing basic skills and problem-solving strategies that involve patterns, relationships, and functions. Students discover mathematical relationships underlying the magic tricks used in the activities. (MDH)

Geer, Charles P.

1992-01-01

145

Morpholinos: Studying gene function in the chick.  

PubMed

The use of morpholinos for perturbing gene function in the chick, Gallus gallus, has led to many important discoveries in developmental biology. This technology makes use of in vivo electroporation, which allows gain and loss of function in a temporally, and spatially controlled manner. Using this method, morpholinos can be transfected into embryonic tissues from early to late developmental stages. In this article, we describe the methods currently used in our laboratory to knock down gene function using morpholinos in vivo. We also detail how morpholinos are used to provide consistency of the results, and describe two protocols to visualise the morpholino after electroporation. In addition, we provide guidance on avoiding potential pitfalls, and suggestions for troubleshooting solutions. These revised techniques provide a practical starting point for investigating gene function in the chick. PMID:24184187

Norris, Anneliese; Streit, Andrea

2014-04-01

146

Molecular Genetic Analysis of the PLP1 Gene in 38 Families with PLP1 -related disorders: Identification and Functional Characterization of 11 Novel PLP1 Mutations  

Microsoft Academic Search

Background  The breadth of the clinical spectrum underlying Pelizaeus-Merzbacher disease and spastic paraplegia type 2 is due to the extensive\\u000a allelic heterogeneity in the X-linked PLP1 gene encoding myelin proteolipid protein (PLP). PLP1 mutations range from gene duplications of variable size found in 60-70% of patients to intragenic lesions present in 15-20%\\u000a of patients.\\u000a \\u000a \\u000a \\u000a \\u000a Methods  Forty-eight male patients from 38 unrelated families

Serena Grossi; Stefano Regis; Roberta Biancheri; Matthew Mort; Susanna Lualdi; Enrico Bertini; Graziella Uziel; Odile Boespflug-Tanguy; Alessandro Simonati; Fabio Corsolini; Ercan Demir; Valentina Marchiani; Antonio Percesepe; Franco Stanzial; Andrea Rossi; Catherine Vaurs-Barrière; David N Cooper; Mirella Filocamo

2011-01-01

147

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function  

PubMed Central

Background Discovering the functions of all genes is a central goal of contemporary biomedical research. Despite considerable effort, we are still far from achieving this goal in any metazoan organism. Collectively, the growing body of high-throughput functional genomics data provides evidence of gene function, but remains difficult to interpret. Results We constructed the first network of functional relationships for Drosophila melanogaster by integrating most of the available, comprehensive sets of genetic interaction, protein-protein interaction, and microarray expression data. The complete integrated network covers 85% of the currently known genes, which we refined to a high confidence network that includes 20,000 functional relationships among 5,021 genes. An analysis of the network revealed a remarkable concordance with prior knowledge. Using the network, we were able to infer a set of high-confidence Gene Ontology biological process annotations on 483 of the roughly 5,000 previously unannotated genes. We also show that this approach is a means of inferring annotations on a class of genes that cannot be annotated based solely on sequence similarity. Lastly, we demonstrate the utility of the network through reanalyzing gene expression data to both discover clusters of coregulated genes and compile a list of candidate genes related to specific biological processes. Conclusions Here we present the the first genome-wide functional gene network in D. melanogaster. The network enables the exploration, mining, and reanalysis of experimental data, as well as the interpretation of new data. The inferred annotations provide testable hypotheses of previously uncharacterized genes.

Costello, James C; Dalkilic, Mehmet M; Beason, Scott M; Gehlhausen, Jeff R; Patwardhan, Rupali; Middha, Sumit; Eads, Brian D; Andrews, Justen R

2009-01-01

148

Predicting gene function using similarity learning  

PubMed Central

Background Computational methods that make use of heterogeneous biological datasets to predict gene function provide a cost-effective and rapid way for annotating genomes. A common framework shared by many such methods is to construct a combined functional association network from multiple networks representing different sources of data, and use this combined network as input to network-based or kernel-based learning algorithms. In these methods, a key factor contributing to the prediction accuracy is the network quality, which is the ability of the network to reflect the functional relatedness of gene pairs. To improve the network quality, a large effort has been spent on developing methods for network integration. These methods, however, produce networks, which then remain unchanged, and nearly no effort has been made to optimize the networks after their construction. Results Here, we propose an alternative method to improve the network quality. The proposed method takes as input a combined network produced by an existing network integration algorithm, and reconstructs this network to better represent the co-functionality relationships between gene pairs. At the core of the method is a learning algorithm that can learn a measure of functional similarity between genes, which we then use to reconstruct the input network. In experiments with yeast and human, the proposed method produced improved networks and achieved more accurate results than two other leading gene function prediction approaches. Conclusions The results show that it is possible to improve the accuracy of network-based gene function prediction methods by optimizing combined networks with appropriate similarity measures learned from data. The proposed learning procedure can handle noisy training data and scales well to large genomes.

2013-01-01

149

Microarray analysis of genes and gene functions in disc degeneration  

PubMed Central

The aim of the present study was to screen differentially expressed genes (DEGs) in human degenerative intervertebral discs (IVDs), and to perform functional analysis on these DEGs. The gene expression profile was downloaded from the Gene Expression Omnibus database (GSE34095)and included six human IVD samples: three degenerative and three non-degenerative. The DEGs between the normal and disease samples were identified using R packages. The online software WebGestalt was used to perform the functional analysis of the DEGs, followed by Osprey software to search for interactions between the DEGs. The Database for Annotation, Visualization and Integrated Discovery was utilized to annotate the DEGs in the interaction network and then the DEGs were uploaded to the Connectivity Map database to search for small molecules. In addition, the active binding sites for the hub genes in the network were obtained, based on the Universal Protein database. By comparing the gene expression profiles of the non-degenerative and degenerative IVDs, the DEGs between the samples were identified. The DEGs were significantly associated with transforming growth factor ? and the extracellular matrix. Matrix metalloproteinase 2 (MMP2) was identified as the hub gene of the interaction network of DEGs. In addition, MMP2 was found to be upregulated in degenerative IVDs. The screened small molecules and the active binding sites of MMP2 may facilitate the development of methods to inhibit overexpression of MMP2.

TANG, YANCHUN; WANG, SHAOKUN; LIU, YING; WANG, XUYUN

2014-01-01

150

Studying Functions of All Yeast Genes Simultaneously  

NASA Technical Reports Server (NTRS)

A method of studying the functions of all the genes of a given species of microorganism simultaneously has been developed in experiments on Saccharomyces cerevisiae (commonly known as baker's or brewer's yeast). It is already known that many yeast genes perform functions similar to those of corresponding human genes; therefore, by facilitating understanding of yeast genes, the method may ultimately also contribute to the knowledge needed to treat some diseases in humans. Because of the complexity of the method and the highly specialized nature of the underlying knowledge, it is possible to give only a brief and sketchy summary here. The method involves the use of unique synthetic deoxyribonucleic acid (DNA) sequences that are denoted as DNA bar codes because of their utility as molecular labels. The method also involves the disruption of gene functions through deletion of genes. Saccharomyces cerevisiae is a particularly powerful experimental system in that multiple deletion strains easily can be pooled for parallel growth assays. Individual deletion strains recently have been created for 5,918 open reading frames, representing nearly all of the estimated 6,000 genetic loci of Saccharomyces cerevisiae. Tagging of each deletion strain with one or two unique 20-nucleotide sequences enables identification of genes affected by specific growth conditions, without prior knowledge of gene functions. Hybridization of bar-code DNA to oligonucleotide arrays can be used to measure the growth rate of each strain over several cell-division generations. The growth rate thus measured serves as an index of the fitness of the strain.

Stolc, Viktor; Eason, Robert G.; Poumand, Nader; Herman, Zelek S.; Davis, Ronald W.; Anthony Kevin; Jejelowo, Olufisayo

2006-01-01

151

Functional characterization of two 13-lipoxygenase genes from olive fruit in relation to the biosynthesis of volatile compounds of virgin olive oil.  

PubMed

Two LOX cDNA clones, Oep1LOX2 and Oep2LOX2, have been isolated from olive ( Olea europaea cv. Picual). Both deduced amino acid sequences showed significant similarity to known plant LOX2, and they contain an N-terminal chloroplastic transit peptide. Genomic Southern blot analyses suggest that at least three copies of Oep1LOX2 and one copy of Oep2LOX2 should be present in the olive genome. Linolenic acid proved to be the preferred substrate for both olive recombinant LOXs, and analyses of reaction products revealed that both enzymes produce primarily 13-hydroperoxides from linoleic and linolenic acids. Expression levels of both genes were measured in the mesocarp and seeds during development and ripening of Picual and Arbequina olive fruit along with the level of volatile compounds in the corresponding virgin olive oils. Biochemical and gene expression data suggest a major involvement of the Oep2LOX2 gene in the biosynthesis of virgin olive oil aroma compounds. PMID:19722522

Padilla, María N; Hernández, M Luisa; Sanz, Carlos; Martínez-Rivas, José M

2009-10-14

152

A search for growth related genes in Kalanchoë blossfeldiana.  

PubMed

Differential display of mRNA from four sets of contrasting phenotypes were carried out in order to identify and isolate genes associated with elongating growth of Kalanchoë blossfeldiana. A total of 17 unique differential expressed cDNA fragments were sequenced and 12 showed homology to genes in other plant species. Three genes were subsequently tested for growth related activity by Virus Induced Gene Silencing (VIGS) in Nicotiana benthamiana. One gene fragment (13C) resulted in plants with significantly reduced growth (N = 20, P = 0.05, one-tailed students t-test) from day 25 after virus infection. Full-length cDNA and genomic DNA sequences were obtained by inverse PCR and thermal asymmetric interlaced (TAIL) PCR and the gene was named KbORF1. The predicted gene is 2244 bp long with three exons of 411 bp in total encoding a protein of 137 amino acid residues with homologs widespread among plants. The protein has no known function, but its expression has been confirmed in a proteomic study of Arabidopsis. Southern blot analysis shows two hybridizing fragments in agreement with the tetraploid nature of K. blossfeldiana. Fragment 13C comprises 446 bp of the gene, and the portion of 13C conferring growth retardation by VIGS is located 10 bp into the second intron indicating a regulatory function of this part of the KbORF1 mRNA. Differential display in combination with VIGS as a screening method proved to be a good functional approach not only to search for genes of interest, but also to isolate expressed genetic regulatory domains. PMID:19819156

Topp, Sine H; Rasmussen, Søren K; Mibus, Heiko; Sander, Lilli

2009-01-01

153

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network  

PubMed Central

AraNet is a functional gene network for the reference plant Arabidopsis and has been constructed in order to identify new genes associated with plant traits. It is highly predictive for diverse biological pathways and can be used to prioritize genes for functional screens. Moreover, AraNet provides a web-based tool with which plant biologists can efficiently discover novel functions of Arabidopsis genes (http://www.functionalnet.org/aranet/). This protocol explains how to conduct network-based prediction of gene functions using AraNet and how to interpret the prediction results. Functional discovery in plant biology is facilitated by combining candidate prioritization by AraNet with focused experimental tests.

Hwang, Sohyun; Rhee, Seung Y; Marcotte, Edward M; Lee, Insuk

2012-01-01

154

Convergence in pigmentation at multiple levels: mutations, genes and function  

PubMed Central

Convergence—the independent evolution of the same trait by two or more taxa—has long been of interest to evolutionary biologists, but only recently has the molecular basis of phenotypic convergence been identified. Here, we highlight studies of rapid evolution of cryptic coloration in vertebrates to demonstrate that phenotypic convergence can occur at multiple levels: mutations, genes and gene function. We first show that different genes can be responsible for convergent phenotypes even among closely related populations, for example, in the pale beach mice inhabiting Florida's Gulf and Atlantic coasts. By contrast, the exact same mutation can create similar phenotypes in distantly related species such as mice and mammoths. Next, we show that different mutations in the same gene need not be functionally equivalent to produce similar phenotypes. For example, separate mutations produce divergent protein function but convergent pale coloration in two lizard species. Similarly, mutations that alter the expression of a gene in different ways can, nevertheless, result in similar phenotypes, as demonstrated by sister species of deer mice. Together these studies underscore the importance of identifying not only the genes, but also the precise mutations and their effects on protein function, that contribute to adaptation and highlight how convergence can occur at different genetic levels.

Manceau, Marie; Domingues, Vera S.; Linnen, Catherine R.; Rosenblum, Erica Bree; Hoekstra, Hopi E.

2010-01-01

155

Gene function prediction with gene interaction networks: a context graph kernel approach  

Microsoft Academic Search

Predicting gene functions is a challenge for biologists in the postgenomic era. Interactions among genes and their products compose networks that can be used to infer gene functions. Most previous studies adopt a linkage assumption, i.e., they assume that gene interactions indicate functional similarities between connected genes. In this study, we propose to use a gene's context graph, i.e., the

Xin Li; Hsinchun Chen; Jiexun Li; Zhu Zhang

2010-01-01

156

Human Cells Display Reduced Apoptotic Function Relative to Chimpanzee Cells  

PubMed Central

Previously published gene expression analyses suggested that apoptotic function may be reduced in humans relative to chimpanzees and led to the hypothesis that this difference may contribute to the relatively larger size of the human brain and the increased propensity of humans to develop cancer. In this study, we sought to further test the hypothesis that humans maintain a reduced apoptotic function relative to chimpanzees by conducting a series of apoptotic function assays on human, chimpanzee and macaque primary fibroblastic cells. Human cells consistently displayed significantly reduced apoptotic function relative to the chimpanzee and macaque cells. These results are consistent with earlier findings indicating that apoptotic function is reduced in humans relative to chimpanzees.

McDonald, John F.

2012-01-01

157

Calcitonin gene-related peptide and menopause  

PubMed Central

The review summarizes recent findings with respect to pathophysiological role of calcitonin gene-related peptide (CGRP), in postmenopausal symptoms and diseases, which has opened horizons in understanding pathophysiology of menopause in a better way. Current evidences strongly propose a need to develop CGRP receptor antagonists, which may prove beneficial in many prevalent menopausal symptom/diseases such as vasomotor symptoms, cardiovascular risk, obesity, and major depressive disorder, in which CGRP levels are elevated.

Sharma, Sudhaa; Mahajan, Annil; Tandon, Vishal R.

2010-01-01

158

Syntenator: Multiple gene order alignments with a gene-specific scoring function  

PubMed Central

Background Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignment softwares like WABA or blastz. In case of conserved syntenies, such regions are defined as conserved gene orders. On the gene order level, homologous regions can even be found between distantly related genomes, which do not align on the nucleotide sequence level. Results We present a novel approach to identify regions of conserved synteny across multiple genomes. Syntenator represents genomes and alignments thereof as partial order graphs (POGs). These POGs are aligned by a dynamic programming approach employing a gene-specific scoring function. The scoring function reflects the level of protein sequence similarity for each possible gene pair. Our method consistently defines larger homologous regions in pairwise gene order alignments than nucleotide-level comparisons. Our method is superior to methods that work on predefined homology gene sets (as implemented in Blockfinder). Syntenator successfully reproduces 80% of the EnsEMBL man-mouse conserved syntenic blocks. The full potential of our method becomes visible by comparing remotely related genomes and multiple genomes. Gene order alignments potentially resolve up to 75% of the EnsEMBL 1:many orthology relations and 27% of the many:many orthology relations. Conclusion We propose Syntenator as a software solution to reliably infer conserved syntenies among distantly related genomes. The software is available from .

Rodelsperger, Christian; Dieterich, Christoph

2008-01-01

159

Functional Genomic and Proteomic Analysis Reveals Disruption of Myelin-Related Genes and Translation in a Mouse Model of Early Life Neglect  

PubMed Central

Early life neglect is an important public health problem which can lead to lasting psychological dysfunction. Good animal models are necessary to understand the mechanisms responsible for the behavioral and anatomical pathology that results. We recently described a novel model of early life neglect, maternal separation with early weaning (MSEW), that produces behavioral changes in the mouse that persist into adulthood. To begin to understand the mechanism by which MSEW leads to these changes we applied cDNA microarray, next-generation RNA-sequencing (RNA-seq), label-free proteomics, multiple reaction monitoring (MRM) proteomics, and methylation analysis to tissue samples obtained from medial prefrontal cortex to determine the molecular changes induced by MSEW that persist into adulthood. The results show that MSEW leads to dysregulation of markers of mature oligodendrocytes and genes involved in protein translation and other categories, an apparent downward biasing of translation, and methylation changes in the promoter regions of selected dysregulated genes. These findings are likely to prove useful in understanding the mechanism by which early life neglect affects brain structure, cognition, and behavior.

Bordner, Kelly A.; George, Elizabeth D.; Carlyle, Becky C.; Duque, Alvaro; Kitchen, Robert R.; Lam, TuKiet T.; Colangelo, Christopher M.; Stone, Kathryn L.; Abbott, Thomas B.; Mane, Shrikant M.; Nairn, Angus C.; Simen, Arthur A.

2011-01-01

160

Cost benefit theory and optimal design of gene regulation functions  

NASA Astrophysics Data System (ADS)

Cells respond to the environment by regulating the expression of genes according to environmental signals. The relation between the input signal level and the expression of the gene is called the gene regulation function. It is of interest to understand the shape of a gene regulation function in terms of the environment in which it has evolved and the basic constraints of biological systems. Here we address this by presenting a cost-benefit theory for gene regulation functions that takes into account temporally varying inputs in the environment and stochastic noise in the biological components. We apply this theory to the well-studied lac operon of E. coli. The present theory explains the shape of this regulation function in terms of temporal variation of the input signals, and of minimizing the deleterious effect of cell-cell variability in regulatory protein levels. We also apply the theory to understand the evolutionary tradeoffs in setting the number of regulatory proteins and for selection of feed-forward loops in genetic circuits. The present cost-benefit theory can be used to understand the shape of other gene regulatory functions in terms of environment and noise constraints.

Kalisky, Tomer; Dekel, Erez; Alon, Uri

2007-12-01

161

Visually Relating Gene Expression and in vivo DNA Binding Data  

SciTech Connect

Gene expression and in vivo DNA binding data provide important information for understanding gene regulatory networks: in vivo DNA binding data indicate genomic regions where transcription factors are bound, and expression data show the output resulting from this binding. Thus, there must be functional relationships between these two types of data. While visualization and data analysis tools exist for each data type alone, there is a lack of tools that can easily explore the relationship between them. We propose an approach that uses the average expression driven by multiple of ciscontrol regions to visually relate gene expression and in vivo DNA binding data. We demonstrate the utility of this tool with examples from the network controlling early Drosophila development. The results obtained support the idea that the level of occupancy of a transcription factor on DNA strongly determines the degree to which the factor regulates a target gene, and in some cases also controls whether the regulation is positive or negative.

Huang, Min-Yu; Mackey, Lester; Ker?; nen, Soile V. E.; Weber, Gunther H.; Jordan, Michael I.; Knowles, David W.; Biggin, Mark D.; Hamann, Bernd

2011-09-20

162

High presence/absence gene variability in defense-related gene clusters of Cucumis melo  

PubMed Central

Background Changes in the copy number of DNA sequences are one of the main mechanisms generating genome variability in eukaryotes. These changes are often related to phenotypic effects such as genetic disorders or novel pathogen resistance. The increasing availability of genome sequences through the application of next-generation massive sequencing technologies has allowed the study of genomic polymorphisms at both the interspecific and intraspecific levels, thus helping to understand how species adapt to changing environments through genome variability. Results Data on gene presence/absence variation (PAV) in melon was obtained by resequencing a cultivated accession and an old-relative melon variety, and using previously obtained resequencing data from three other melon cultivars, among them DHL92, on which the current draft melon genome sequence is based. A total of 1,697 PAV events were detected, involving 4.4% of the predicted melon gene complement. In all, an average 1.5% of genes were absent from each analyzed cultivar as compared to the DHL92 reference genome. The most populated functional category among the 304 PAV genes of known function was that of stress response proteins (30% of all classified PAVs). Our results suggest that genes from multi-copy families are five times more likely to be affected by PAV than singleton genes. Also, the chance of genes present in the genome in tandem arrays being affected by PAV is double that of isolated genes, with PAV genes tending to be in longer clusters. The highest concentration of PAV events detected in the melon genome was found in a 1.1 Mb region of linkage group V, which also shows the highest density of melon stress-response genes. In particular, this region contains the longest continuous gene-containing PAV sequence so far identified in melon. Conclusions The first genome-wide report of PAV variation among several melon cultivars is presented here. Multi-copy and clustered genes, especially those with putative stress-response functions, were found to be particularly affected by PAV polymorphisms. As cucurbits are known to possess a significantly lower number of defense-related genes compared to other plant species, PAV variation may play an important role in generating new pathogen resistances at the subspecies level. In addition, these results show the limitations of single reference genome sequences as the only basis for characterization and cloning of resistance genes.

2013-01-01

163

Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes  

PubMed Central

The mitochondrial genomes of flowering plants possess a promiscuous proclivity for taking up sequences from the chloroplast genome. All characterized chloroplast integrants exist apart from native mitochondrial genes, and only a few, involving chloroplast tRNA genes that have functionally supplanted their mitochondrial counterparts, appear to be of functional consequence. We developed a novel computational approach to search for homologous recombination (gene conversion) in a large number of sequences and applied it to 22 mitochondrial and chloroplast gene pairs, which last shared common ancestry some 2 billion years ago. We found evidence of recurrent conversion of short patches of mitochondrial genes by chloroplast homologs during angiosperm evolution, but no evidence of gene conversion in the opposite direction. All 9 putative conversion events involve the atp1/atpA gene encoding the alpha subunit of ATP synthase, which is unusually well conserved between the 2 organelles and the only shared gene that is widely sequenced across plant mitochondria. Moreover, all conversions were limited to the 2 regions of greatest nucleotide and amino acid conservation of atp1/atpA. These observations probably reflect constraints operating on both the occurrence and fixation of recombination between ancient homologs. These findings indicate that recombination between anciently related sequences is more frequent than previously appreciated and creates functional mitochondrial genes of chimeric origin. These results also have implications for the widespread use of mitochondrial atp1 in phylogeny reconstruction.

Hao, Weilong; Palmer, Jeffrey D.

2009-01-01

164

Gene-Network Analysis Identifies Susceptibility Genes Related to Glycobiology in Autism  

PubMed Central

The recent identification of copy-number variation in the human genome has opened up new avenues for the discovery of positional candidate genes underlying complex genetic disorders, especially in the field of psychiatric disease. One major challenge that remains is pinpointing the susceptibility genes in the multitude of disease-associated loci. This challenge may be tackled by reconstruction of functional gene-networks from the genes residing in these loci. We applied this approach to autism spectrum disorder (ASD), and identified the copy-number changes in the DNA of 105 ASD patients and 267 healthy individuals with Illumina Humanhap300 Beadchips. Subsequently, we used a human reconstructed gene-network, Prioritizer, to rank candidate genes in the segmental gains and losses in our autism cohort. This analysis highlighted several candidate genes already known to be mutated in cognitive and neuropsychiatric disorders, including RAI1, BRD1, and LARGE. In addition, the LARGE gene was part of a sub-network of seven genes functioning in glycobiology, present in seven copy-number changes specifically identified in autism patients with limited co-morbidity. Three of these seven copy-number changes were de novo in the patients. In autism patients with a complex phenotype and healthy controls no such sub-network was identified. An independent systematic analysis of 13 published autism susceptibility loci supports the involvement of genes related to glycobiology as we also identified the same or similar genes from those loci. Our findings suggest that the occurrence of genomic gains and losses of genes associated with glycobiology are important contributors to the development of ASD.

Poot, Martin; Hochstenbach, Ron; Spierenburg, Henk A.; Vorstman, Jacob A. S.; van Daalen, Emma; de Jonge, Maretha V.; Verbeek, Nienke E.; Brilstra, Eva H.; van 't Slot, Ruben; Ophoff, Roel A.; van Es, Michael A.; Blauw, Hylke M.; Veldink, Jan H.; Buizer-Voskamp, Jacobine E.; Beemer, Frits A.; van den Berg, Leonard H.; Wijmenga, Cisca; van Amstel, Hans Kristian Ploos; van Engeland, Herman; Burbach, J. Peter H.; Staal, Wouter G.

2009-01-01

165

Proteomics – post-genomic cartography to understand gene function  

Microsoft Academic Search

The completion of the genomic sequences of numerous organisms from human and mouse to Caenorhabditis elegans and many microorganisms, and the definition of their genes provides a database to interpret cellular protein-expression patterns and relate them to protein function. Proteomics technologies that are dependent on mass spectrometry and involve two-dimensional gel electrophoresis are providing the main window into the world

Soren Naaby-Hansen; Michael D. Waterfield; Rainer Cramer

2001-01-01

166

Annotation of gene function in citrus using gene expression information and co-expression networks  

PubMed Central

Background The genus Citrus encompasses major cultivated plants such as sweet orange, mandarin, lemon and grapefruit, among the world’s most economically important fruit crops. With increasing volumes of transcriptomics data available for these species, Gene Co-expression Network (GCN) analysis is a viable option for predicting gene function at a genome-wide scale. GCN analysis is based on a “guilt-by-association” principle whereby genes encoding proteins involved in similar and/or related biological processes may exhibit similar expression patterns across diverse sets of experimental conditions. While bioinformatics resources such as GCN analysis are widely available for efficient gene function prediction in model plant species including Arabidopsis, soybean and rice, in citrus these tools are not yet developed. Results We have constructed a comprehensive GCN for citrus inferred from 297 publicly available Affymetrix Genechip Citrus Genome microarray datasets, providing gene co-expression relationships at a genome-wide scale (33,000 transcripts). The comprehensive citrus GCN consists of a global GCN (condition-independent) and four condition-dependent GCNs that survey the sweet orange species only, all citrus fruit tissues, all citrus leaf tissues, or stress-exposed plants. All of these GCNs are clustered using genome-wide, gene-centric (guide) and graph clustering algorithms for flexibility of gene function prediction. For each putative cluster, gene ontology (GO) enrichment and gene expression specificity analyses were performed to enhance gene function, expression and regulation pattern prediction. The guide-gene approach was used to infer novel roles of genes involved in disease susceptibility and vitamin C metabolism, and graph-clustering approaches were used to investigate isoprenoid/phenylpropanoid metabolism in citrus peel, and citric acid catabolism via the GABA shunt in citrus fruit. Conclusions Integration of citrus gene co-expression networks, functional enrichment analysis and gene expression information provide opportunities to infer gene function in citrus. We present a publicly accessible tool, Network Inference for Citrus Co-Expression (NICCE, http://citrus.adelaide.edu.au/nicce/home.aspx), for the gene co-expression analysis in citrus.

2014-01-01

167

Molecular and functional characterization of broccoli EMBRYONIC FLOWER 2 genes.  

PubMed

Polycomb group (PcG) proteins regulate major developmental processes in Arabidopsis. EMBRYONIC FLOWER 2 (EMF2), the VEFS domain-containing PcG gene, regulates diverse genetic pathways and is required for vegetative development and plant survival. Despite widespread EMF2-like sequences in plants, little is known about their function other than in Arabidopsis and rice. To study the role of EMF2 in broccoli (Brassica oleracea var. italica cv. Elegance) development, we identified two broccoli EMF2 (BoEMF2) genes with sequence homology to and a similar gene expression pattern to that in Arabidopsis (AtEMF2). Reducing their expression in broccoli resulted in aberrant phenotypes and gene expression patterns. BoEMF2 regulates genes involved in diverse developmental and stress programs similar to AtEMF2 in Arabidopsis. However, BoEMF2 differs from AtEMF2 in the regulation of flower organ identity, cell proliferation and elongation, and death-related genes, which may explain the distinct phenotypes. The expression of BoEMF2.1 in the Arabidopsis emf2 mutant (Rescued emf2) partially rescued the mutant phenotype and restored the gene expression pattern to that of the wild type. Many EMF2-mediated molecular and developmental functions are conserved in broccoli and Arabidopsis. Furthermore, the restored gene expression pattern in Rescued emf2 provides insights into the molecular basis of PcG-mediated growth and development. PMID:22537758

Liu, Mao-Sen; Chen, Long-Fang O; Lin, Chun-Hung; Lai, Ying-Mi; Huang, Jia-Yuan; Sung, Zinmay Renee

2012-07-01

168

Molecular and Functional Characterization of Broccoli EMBRYONIC FLOWER 2 Genes  

PubMed Central

Polycomb group (PcG) proteins regulate major developmental processes in Arabidopsis. EMBRYONIC FLOWER 2 (EMF2), the VEFS domain-containing PcG gene, regulates diverse genetic pathways and is required for vegetative development and plant survival. Despite widespread EMF2-like sequences in plants, little is known about their function other than in Arabidopsis and rice. To study the role of EMF2 in broccoli (Brassica oleracea var. italica cv. Elegance) development, we identified two broccoli EMF2 (BoEMF2) genes with sequence homology to and a similar gene expression pattern to that in Arabidopsis (AtEMF2). Reducing their expression in broccoli resulted in aberrant phenotypes and gene expression patterns. BoEMF2 regulates genes involved in diverse developmental and stress programs similar to AtEMF2 in Arabidopsis. However, BoEMF2 differs from AtEMF2 in the regulation of flower organ identity, cell proliferation and elongation, and death-related genes, which may explain the distinct phenotypes. The expression of BoEMF2.1 in the Arabidopsis emf2 mutant (Rescued emf2) partially rescued the mutant phenotype and restored the gene expression pattern to that of the wild type. Many EMF2-mediated molecular and developmental functions are conserved in broccoli and Arabidopsis. Furthermore, the restored gene expression pattern in Rescued emf2 provides insights into the molecular basis of PcG-mediated growth and development.

Chen, Long-Fang O.; Lin, Chun-Hung; Lai, Ying-Mi; Huang, Jia-Yuan; Sung, Zinmay Renee

2012-01-01

169

On gene ontology and function annotation.  

PubMed

The effort of function annotation does not merely involve associating a gene with some structured vocabulary that describes action. Rather the details of the actions, the components of the actions, the larger context of the actions are important issues that are of direct relevance, because they help understand the biological system to which the gene/protein belongs. Currently Gene Ontology (GO) Consortium offers the most comprehensive sets of relationships to describe gene/protein activity. However, its choice to segregate gene ontology to subdomains of molecular function, biological process and cellular component is creating significant limitations in terms of future scope of use. If we are to understand biology in its total complexity, comprehensive ontologies in larger biological domains are essential. A vigorous discussion on this topic is necessary for the larger benefit of the biological community. I highlight this point because larger-bio-domain ontologies cannot be simply created by integrating subdomain ontologies. Relationships in larger bio-domain-ontologies are more complex due to larger size of the system and are therefore more labor intensive to create. The current limitations of GO will be a handicap in derivation of more complex relationships from the high throughput biology data. PMID:17597866

Pal, Debnath

2006-01-01

170

A widespread class of reverse transcriptase-related cellular genes.  

PubMed

Reverse transcriptases (RTs) polymerize DNA on RNA templates. They fall into several structurally related but distinct classes and form an assemblage of RT-like enzymes that, in addition to RTs, also includes certain viral RNA-dependent RNA polymerases (RdRP) synthesizing RNA on RNA templates. It is generally believed that most RT-like enzymes originate from retrotransposons or viruses and have no specific function in the host cell, with telomerases being the only notable exception. Here we report on the discovery and properties of a unique class of RT-related cellular genes collectively named rvt. We present evidence that rvts are not components of retrotransposons or viruses, but single-copy genes with a characteristic domain structure that may contain introns in evolutionarily conserved positions, occur in syntenic regions, and evolve under purifying selection. These genes can be found in all major taxonomic groups including protists, fungi, animals, plants, and even bacteria, although they exhibit patchy phylogenetic distribution in each kingdom. We also show that the RVT protein purified from one of its natural hosts, Neurospora crassa, exists in a multimeric form and has the ability to polymerize NTPs as well as dNTPs in vitro, with a strong preference for NTPs, using Mn(2+) as a cofactor. The existence of a previously unknown class of single-copy RT-related genes calls for reevaluation of the current views on evolution and functional roles of RNA-dependent polymerases in living cells. PMID:21876125

Gladyshev, Eugene A; Arkhipova, Irina R

2011-12-20

171

A widespread class of reverse transcriptase-related cellular genes  

PubMed Central

Reverse transcriptases (RTs) polymerize DNA on RNA templates. They fall into several structurally related but distinct classes and form an assemblage of RT-like enzymes that, in addition to RTs, also includes certain viral RNA-dependent RNA polymerases (RdRP) synthesizing RNA on RNA templates. It is generally believed that most RT-like enzymes originate from retrotransposons or viruses and have no specific function in the host cell, with telomerases being the only notable exception. Here we report on the discovery and properties of a unique class of RT-related cellular genes collectively named rvt. We present evidence that rvts are not components of retrotransposons or viruses, but single-copy genes with a characteristic domain structure that may contain introns in evolutionarily conserved positions, occur in syntenic regions, and evolve under purifying selection. These genes can be found in all major taxonomic groups including protists, fungi, animals, plants, and even bacteria, although they exhibit patchy phylogenetic distribution in each kingdom. We also show that the RVT protein purified from one of its natural hosts, Neurospora crassa, exists in a multimeric form and has the ability to polymerize NTPs as well as dNTPs in vitro, with a strong preference for NTPs, using Mn2+ as a cofactor. The existence of a previously unknown class of single-copy RT-related genes calls for reevaluation of the current views on evolution and functional roles of RNA-dependent polymerases in living cells.

Gladyshev, Eugene A.; Arkhipova, Irina R.

2011-01-01

172

Gene functional dynamics: environment as a trigger?  

PubMed

Recent decades have seen the deciphering of the human genome and, also, progress in studies related to the effects of space-weather on humans. The progress in genetics allows us to connect many human pathologies with specific gene abnormalities. Concomitantly it has been shown that many congenital and adherent diseases, and the timing of death are connected with space factors such as solar activity (SA), geomagnetic activity (GMA), cosmic ray activity (CRA), and space neutron and proton flux. Here arises the question to what extent gene expression is affected by the aforementioned space physical activity parameters. This is the motto of this hypothetical paper. In conclusion, the space-weather-related timing of many medical events invites presumption that gene activity is a changing phenomenon and space weather components may be playing a regulatory role in these changes. PMID:24259246

Stoupel, Eliyahu G

2014-05-01

173

Norrie disease gene: Characterization of deletions and possible function  

SciTech Connect

Positional cloning experiments have resulted recently in the isolation of a candidate gene for Norrie disease (pseudoglioma; NDP), a severe X-linked neuro-developmental disorder. Here the authors report the isolation and analysis of human genomic DNA clones encompassing the NDP gene. The gene spans 28 kb and consists of 3 exons, the first of which is entirely contained within the 5{prime} untranslated region. Detailed analysis of genomic deletions in Norrie patients shows that they are heterogeneous, both in size and in position. By PCR analysis, they found that expression of the NDP gene was not confined to the eye or to the brain. An extensive DNA and protein sequence comparison between the human NDP gene and related genes from the database revealed homology with cysteine-rich protein-binding domains of immediate--early genes implicated in the regulation of cell proliferation. They propose that NDP is a molecule related in function to these genes and may be involved in a pathway that regulates neural cell differentiation and proliferation. 19 refs., 2 figs.

Chen, Z.Y.; Battinelli, E.M.; Hendriks, R.W.; Craig, I.W. [Univ. of Oxford (United Kingdom)] [Univ. of Oxford (United Kingdom); Powell, J.F. [Institute of Psychiatry, London (United Kingdom)] [Institute of Psychiatry, London (United Kingdom); Middleton-Price, H. [Univ. of London (United Kingdom)] [Univ. of London (United Kingdom); Sims, K.B.; Breakefield, X.O. [Massachusetts General Hospital, Charlestown, MA (United States)] [Massachusetts General Hospital, Charlestown, MA (United States)

1993-05-01

174

Mutualistic Polydnaviruses Share Essential Replication Gene Functions with Pathogenic Ancestors  

PubMed Central

Viruses are usually thought to form parasitic associations with hosts, but all members of the family Polydnaviridae are obligate mutualists of insects called parasitoid wasps. Phylogenetic data founded on sequence comparisons of viral genes indicate that polydnaviruses in the genus Bracovirus (BV) are closely related to pathogenic nudiviruses and baculoviruses. However, pronounced differences in the biology of BVs and baculoviruses together with high divergence of many shared genes make it unclear whether BV homologs still retain baculovirus-like functions. Here we report that virions from Microplitis demolitor bracovirus (MdBV) contain multiple baculovirus-like and nudivirus-like conserved gene products. We further show that RNA interference effectively and specifically knocks down MdBV gene expression. Coupling RNAi knockdown methods with functional assays, we examined the activity of six genes in the MdBV conserved gene set that are known to have essential roles in transcription (lef-4, lef-9), capsid assembly (vp39, vlf-1), and envelope formation (p74, pif-1) during baculovirus replication. Our results indicated that MdBV produces a baculovirus-like RNA polymerase that transcribes virus structural genes. Our results also supported a conserved role for vp39, vlf-1, p74, and pif-1 as structural components of MdBV virions. Additional experiments suggested that vlf-1 together with the nudivirus-like gene int-1 also have novel functions in regulating excision of MdBV proviral DNAs for packaging into virions. Overall, these data provide the first experimental insights into the function of BV genes in virion formation.

Burke, Gaelen R.; Thomas, Sarah A.; Eum, Jai H.; Strand, Michael R.

2013-01-01

175

Cellular Functions of Genetically Imprinted Genes in Human and Mouse as Annotated in the Gene Ontology  

PubMed Central

By analyzing the cellular functions of genetically imprinted genes as annotated in the Gene Ontology for human and mouse, we found that imprinted genes are often involved in developmental, transport and regulatory processes. In the human, paternally expressed genes are enriched in GO terms related to the development of organs and of anatomical structures. In the mouse, maternally expressed genes regulate cation transport as well as G-protein signaling processes. Furthermore, we investigated if imprinted genes are regulated by common transcription factors. We identified 25 TF families that showed an enrichment of binding sites in the set of imprinted genes in human and 40 TF families in mouse. In general, maternally and paternally expressed genes are not regulated by different transcription factors. The genes Nnat, Klf14, Blcap, Gnas and Ube3a contribute most to the enrichment of TF families. In the mouse, genes that are maternally expressed in placenta are enriched for AP1 binding sites. In the human, we found that these genes possessed binding sites for both, AP1 and SP1.

Hamed, Mohamed; Ismael, Siba; Paulsen, Martina; Helms, Volkhard

2012-01-01

176

Transitive Functional Annotation by Shortest-path Analysis of Gene Expression Data  

Microsoft Academic Search

attribute to link genes of the same biological pathway. Based on large-scale yeast microarray expression data, we use the shortest-path analysis to identify transitive genes between two given genes from the same biological process. We find that not only functionally related genes with correlated expression profiles are identified but also those without. In the latter case, we compare our method

Xianghong Zhou; Ming-Chih J. Kao; Wing Hung Wong

2002-01-01

177

Graph Kernel-Based Learning for Gene Function Prediction from Gene Interaction Network  

Microsoft Academic Search

Prediction of gene functions is a major challenge to biologists in the post-genomic era. Interactions between genes and their products compose networks and can be used to infer gene functions. Most previous studies used heuristic approaches based on either local or global information of gene interaction networks to assign unknown gene functions. In this study, we propose a graph kernel-based

Xin Li; Zhu Zhang; Hsinchun Chen; Jiexun Li

2007-01-01

178

Graph Kernel-Based Learning for Gene Function Prediction from Gene Interaction Network  

Microsoft Academic Search

Prediction of gene functions is a major challenge to biol- ogists in the post-genomic era. Interactions between genes and their products compose networks and can be used to infer gene functions. Most previous studies used heuris- tic approaches based on either local or global informa- tion of gene interaction networks to assign unknown gene functions. In this study, we propose

Xin Li; Zhu Zhang; Hsinchun Chen; Jiexun Li

2007-01-01

179

A global view of pleiotropy and phenotypically derived gene function in yeast  

Microsoft Academic Search

Pleiotropy, the ability of a single mutant gene to cause multiple mutant phenotypes, is a relatively common but poorly understood phenomenon in biology. Perhaps the greatest challenge in the analysis of pleiotropic genes is determining whether phenotypes associated with a mutation result from the loss of a single function or of multiple functions encoded by the same gene. Here we

Aimée Marie Dudley; Daniel Maarten Janse; Amos Tanay; Ron Shamir; George McDonald Church

2005-01-01

180

Age-related changes in task related functional network connectivity.  

PubMed

Aging has a multi-faceted impact on brain structure, brain function and cognitive task performance, but the interaction of these different age-related changes is largely unexplored. We hypothesize that age-related structural changes alter the functional connectivity within the brain, resulting in altered task performance during cognitive challenges. In this neuroimaging study, we used independent components analysis to identify spatial patterns of coordinated functional activity involved in the performance of a verbal delayed item recognition task from 75 healthy young and 37 healthy old adults. Strength of functional connectivity between spatial components was assessed for age group differences and related to speeded task performance. We then assessed whether age-related differences in global brain volume were associated with age-related differences in functional network connectivity. Both age groups used a series of spatial components during the verbal working memory task and the strength and distribution of functional network connectivity between these components differed across the age groups. Poorer task performance, i.e. slower speed with increasing memory load, in the old adults was associated with decreases in functional network connectivity between components comprised of the supplementary motor area and the middle cingulate and between the precuneus and the middle/superior frontal cortex. Advancing age also led to decreased brain volume; however, there was no evidence to support the hypothesis that age-related alterations in functional network connectivity were the result of global brain volume changes. These results suggest that age-related differences in the coordination of neural activity between brain regions partially underlie differences in cognitive performance. PMID:23028536

Steffener, Jason; Habeck, Christian G; Stern, Yaakov

2012-01-01

181

Genotype and Gene Expression Associations with Immune Function in Drosophila  

PubMed Central

It is now well established that natural populations of Drosophila melanogaster harbor substantial genetic variation associated with physiological measures of immune function. In no case, however, have intermediate measures of immune function, such as transcriptional activity of immune-related genes, been tested as mediators of phenotypic variation in immunity. In this study, we measured bacterial load sustained after infection of D. melanogaster with Serratia marcescens, Providencia rettgeri, Enterococcus faecalis, and Lactococcus lactis in a panel of 94 third-chromosome substitution lines. We also measured transcriptional levels of 329 immune-related genes eight hours after infection with E. faecalis and S. marcescens in lines from the phenotypic tails of the test panel. We genotyped the substitution lines at 137 polymorphic markers distributed across 25 genes in order to test for statistical associations among genotype, bacterial load, and transcriptional dynamics. We find that genetic polymorphisms in the pathogen recognition genes (and particularly in PGRP-LC, GNBP1, and GNBP2) are most significantly associated with variation in bacterial load. We also find that overall transcriptional induction of effector proteins is a significant predictor of bacterial load after infection with E. faecalis, and that a marker upstream of the recognition gene PGRP-SD is statistically associated with variation in both bacterial load and transcriptional induction of effector proteins. These results show that polymorphism in genes near the top of the immune system signaling cascade can have a disproportionate effect on organismal phenotype due to the amplification of minor effects through the cascade.

Sackton, Timothy B.; Lazzaro, Brian P.; Clark, Andrew G.

2010-01-01

182

Cancer Proliferation Gene Discovery Through Functional Genomics  

PubMed Central

Retroviral short hairpin RNA (shRNA)–mediated genetic screens in mammalian cells are powerful tools for discovering loss-of-function phenotypes. We describe a highly parallel multiplex methodology for screening large pools of shRNAs using half-hairpin barcodes for microarray deconvolution. We carried out dropout screens for shRNAs that affect cell proliferation and viability in cancer cells and normal cells. We identified many shRNAs to be antiproliferative that target core cellular processes, such as the cell cycle and protein translation, in all cells examined. Moreover, we identified genes that are selectively required for proliferation and survival in different cell lines. Our platform enables rapid and cost-effective genome-wide screens to identify cancer proliferation and survival genes for target discovery. Such efforts are complementary to the Cancer Genome Atlas and provide an alternative functional view of cancer cells.

Schlabach, Michael R.; Luo, Ji; Solimini, Nicole L.; Hu, Guang; Xu, Qikai; Li, Mamie Z.; Zhao, Zhenming; Smogorzewska, Agata; Sowa, Mathew E.; Ang, Xiaolu L.; Westbrook, Thomas F.; Liang, Anthony C.; Chang, Kenneth; Hackett, Jennifer A.; Harper, J. Wade; Hannon, Gregory J.; Elledge, Stephen J.

2010-01-01

183

Microbial functional gene diversity with a shift of subsurface redox conditions during In Situ uranium reduction.  

PubMed

To better understand the microbial functional diversity changes with subsurface redox conditions during in situ uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of dsrAB genes (dissimilatory sulfite reductase genes) and methane generation-related mcr genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from Geobacter sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (E(h)) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the in situ redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation. PMID:22327592

Liang, Yuting; Van Nostrand, Joy D; N'guessan, Lucie A; Peacock, Aaron D; Deng, Ye; Long, Philip E; Resch, C Tom; Wu, Liyou; He, Zhili; Li, Guanghe; Hazen, Terry C; Lovley, Derek R; Zhou, Jizhong

2012-04-01

184

The mouse angiogenin gene family: Structures of an angiogenin-related protein gene and two pseudogenes  

SciTech Connect

Angiogenin, a homologue of pancreatic ribonuclease, is a potent inducer of blood vessel formation. As an initial step toward investigating the in vivo functional role of this protein via gene disruption, we undertook the isolation of the angiogenin gene (Ang) from the 129 strain mouse, which will be used for generating targeting constructs. Unexpectedly, screening of a genomic library with an Ang gene probe obtained previously from the BALB/c strain yielded two new genes closely similar to Ang rather than Ang itself. One of these encodes a protein with 78% sequence identity to angiogenin and is designated {open_quotes}Angrp{close_quotes} for {open_quotes}angiogenin-related protein.{close_quotes} The ribonucleolytic active site of angiogenin, which is critical for angiogenic activity, is completely conserved in Angrp, whereas a second essential site, thought to bind cellular receptors, is considerably different. Thus, the Angrp product may have a function distinct from that of angiogenin. The second gene obtained by library screening is a pseudogene, designated {open_quotes}Ang-ps1,{close_quotes} that contains a frame shift mutation in the early part of the coding region. Although the Ang gene was not isolated from this library, it was possible to amplify this gene from 129 mouse genomic DNA by the polymerase chain reaction (PCR). Sequence analysis showed that the 129 strain Ang gene is identical to the BALB/c gene throughout the coding region. PCR cloning also yielded a second Ang-like pseudogene, designated {open_quotes}Ang-ps2.{close_quotes} Southern blotting of genomic DNA confirmed the presence of Ang, Angrp, and at least one of the pseudogenes in an individual mouse and suggested that the mouse Ang gene family may contain more than the four members identified here. 31 refs., 4 figs., 1 tab.

Brown, W.E.; Nobile, V.; Shapiro, R. [Harvard Medical School, Boston, MA (United States)] [and others] [Harvard Medical School, Boston, MA (United States); and others

1995-09-01

185

Identifying disease feature genes based on cellular localized gene functional modules and regulation networks  

Microsoft Academic Search

Identifying disease-relevant genes and functional modules, based on gene expression profiles and gene functional knowledge,\\u000a is of high importance for studying disease mechanisms and subtyping disease phenotypes. Using gene categories of biological\\u000a process and cellular component in Gene Ontology, we propose an approach to selecting functional modules enriched with differentially\\u000a expressed genes, and identifying the feature functional modules of high

Min Zhang; Jing Zhu; Zheng Guo; Xia Li; Da Yang; Lei Wang; Shaoqi Rao

2006-01-01

186

Mesangial cell-predominant functional gene, megsin.  

PubMed

We obtained the "gene profile" of cultured human mesangial cells, and discovered five unknown genes predominantly expressed in mesangial cells. Megsin is one of these novel genes, and sequencing analysis of megsin showed that megsin belongs to the serpin (serine protease inhibitor) superfamily. The characteristics of megsin as a functional serpin are highly conserved among different species, including mice and rats. Expression of megsin is up-regulated in a variety of diseases with mesangial injury in humans and in animal models. We analyzed the promoter region of megsin and identified one positive regulatory motif, an incomplete activator protein-1 (AP-1) binding site within the region. Transgenic mice overexpressing megsin developed mesangial expansion and hypercellularity, which was associated with glomerular immune complex deposition. Our in vitro assays identified plasmin as a candidate target of megsin, although it is likely that megsin has other biological ligands in vivo. These results suggest that megsin plays an essential role in modulating the biological functions of mesangial cells. Megsin may play a role in the regulation of a wide variety of processes in mesangial cells, such as matrix metabolism, cell proliferation, and apoptosis. Identification of the exact biological functions and target proteases of megsin will lead us to develop novel therapeutic approaches to glomerular diseases. PMID:14586725

Inagi, Reiko; Nangaku, Masaomi; Miyata, Toshio; Kurokawa, Kiyoshi

2003-06-01

187

Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment  

PubMed Central

To determine the potential of DNA array technology for assessing functional gene diversity and distribution, a prototype microarray was constructed with genes involved in nitrogen cycling: nitrite reductase (nirS and nirK) genes, ammonia mono-oxygenase (amoA) genes, and methane mono-oxygenase (pmoA) genes from pure cultures and those cloned from marine sediments. In experiments using glass slide microarrays, genes possessing less than 80 to 85% sequence identity were differentiated under hybridization conditions of high stringency (65°C). The detection limit for nirS genes was approximately 1 ng of pure genomic DNA and 25 ng of soil community DNA using our optimized protocol. A linear quantitative relationship (r2 = 0.89 to 0.94) was observed between signal intensity and target DNA concentration over a range of 1 to 100 ng for genomic DNA (or genomic DNA equivalent) from both pure cultures and mixed communities. However, the quantitative capacity of microarrays for measuring the relative abundance of targeted genes in complex environmental samples is less clear due to divergent target sequences. Sequence divergence and probe length affected hybridization signal intensity within a certain range of sequence identity and size, respectively. This prototype functional gene array did reveal differences in the apparent distribution of nir and amoA and pmoA gene families in sediment and soil samples. Our results indicate that glass-based microarray hybridization has potential as a tool for revealing functional gene composition in natural microbial communities; however, more work is needed to improve sensitivity and quantitation and to understand the associated issue of specificity.

Wu, Liyou; Thompson, Dorothea K.; Li, Guangshan; Hurt, Richard A.; Tiedje, James M.; Zhou, Jizhong

2001-01-01

188

Sex steroid-related candidate genes in psychiatric disorders  

PubMed Central

Sex steroids readily pass the blood-brain barrier, and receptors for them are abundant in brain areas important for the regulation of emotions, cognition and behaviour. Animal experiments have revealed both important early effects of these hormones on brain development and their ongoing influence on brain morphology and neurotransmission in the adult organism. The important effects of sex steroids on human behaviour are illustrated by, for example, the effect of reduced levels of these hormones on sexual drive and conditions such as premenstrual dysphoric disorder, perimenopausal dysphoria, postpartum depression, postpartum psychosis, dysphoria induced by oral contraceptives or hormonal replacement therapy and anabolic steroid–induced aggression. The fact that men and women (as groups) differ with respect to the prevalence of several psychiatric disorders, certain aspects of cognitive function and certain personality traits may possibly also reflect an influence of sex steroids on human behaviour. The heritability of most behavioural traits, including personality, cognitive abilities and susceptibility to psychiatric illness, is considerable, but as yet, only few genes of definite importance in this context have been identified. Given the important role of sex steroids for brain function, it is unfortunate that relatively few studies so far have addressed the possible influence of sex steroid–related genes on interindividual differences with respect to personality, cognition and susceptibility to psychiatric disorders. To facilitate further research in this area, this review provides information on several such genes and summarizes what is currently known with respect to their possible influence on brain function.

Westberg, Lars; Eriksson, Elias

2008-01-01

189

Gene Function Prediction with the Shortest Path in Functional Linkage Graph  

Microsoft Academic Search

This paper presents a new technique for gene function prediction with the shortest path in functional linkage graph. With existing protein-protein interaction data, complex data and gene expression data, a weighted functional linkage graph is inferred. By finding the shortest path in the functional linkage graph, the functions of unknown genes can be predicted with the functions of those that

Xing-Ming Zhao; Luonan Chen; Kazuyuki Aihara

2007-01-01

190

Gene autoregulation via intronic microRNAs and its functions  

PubMed Central

Background MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad range of human diseases. This paper focus on a minimal microRNA-mediated regulatory circuit, in which a protein-coding gene (host gene) is targeted by a microRNA located inside one of its introns. Results Autoregulation via intronic microRNAs is widespread in the human regulatory network, as confirmed by our bioinformatic analysis, and can perform several regulatory tasks despite its simple topology. Our analysis, based on analytical calculations and simulations, indicates that this circuitry alters the dynamics of the host gene expression, can induce complex responses implementing adaptation and Weber’s law, and efficiently filters fluctuations propagating from the upstream network to the host gene. A fine-tuning of the circuit parameters can optimize each of these functions. Interestingly, they are all related to gene expression homeostasis, in agreement with the increasing evidence suggesting a role of microRNA regulation in conferring robustness to biological processes. In addition to model analysis, we present a list of bioinformatically predicted candidate circuits in human for future experimental tests. Conclusions The results presented here suggest a potentially relevant functional role for negative self-regulation via intronic microRNAs, in particular as a homeostatic control mechanism of gene expression. Moreover, the map of circuit functions in terms of experimentally measurable parameters, resulting from our analysis, can be a useful guideline for possible applications in synthetic biology.

2012-01-01

191

Structure-function relationships in telomerase genes.  

PubMed

The TERT (telomerase reverse transcriptase) subunit of telomerase is an intensively studied macromolecule due to its key importance in maintaining genome integrity and role in cellular aging and cancer. In an effort to provide an up-to-date overview of the topic, we discuss the structure of TERT genes, their alternative splicing products and their functions. Nucleotide databases contain more than 90 full-length cDNA sequences of telomerase protein subunits. Numerous in silico, in vitro and in vivo experimental techniques have revealed a great deal of structural and functional data describing particular features of the telomerase subunit in various model organisms. We explore whether particular findings are generally applicable to telomerases or species-specific. We also discuss in an evolutionary context the role of identified functional TERT subdomains. PMID:19419346

Sýkorová, Eva; Fajkus, Jirí

2009-07-01

192

A weighted power framework for integrating multisource information: gene function prediction in yeast.  

PubMed

Predicting the functions of unannotated genes is one of the major challenges of biological investigation. In this study, we propose a weighted power scoring framework, called weighted power biological score (WPBS), for combining different biological data sources and predicting the function of some of the unclassified yeast Saccharomyces cerevisiae genes. The relative power and weight coefficients of different data sources, in the proposed score, are estimated systematically by utilizing functional annotations [yeast Gene Ontology (GO)-Slim: Process] of classified genes, available from Saccharomyces Genome Database. Genes are then clustered by applying k-medoids algorithm on WPBS, and functional categories of 334 unclassified genes are predicted using a P-value cutoff 1 ×10(-5). The WPBS is available online at http://www.isical.ac.in/~ shubhra/WPBS/WPBS.html, where one can download WPBS, related files, and a MATLAB code to predict functions of unclassified genes. PMID:22318478

Ray, Shubhra Sankar; Bandyopadhyay, Sanghamitra; Pal, Sankar K

2012-04-01

193

Gene Profiling of Mta1 Identifies Novel Gene Targets and Functions  

PubMed Central

Background Metastasis-associated protein 1 (MTA1), a master dual co-regulatory protein is found to be an integral part of NuRD (Nucleosome Remodeling and Histone Deacetylation) complex, which has indispensable transcriptional regulatory functions via histone deacetylation and chromatin remodeling. Emerging literature establishes MTA1 to be a valid DNA-damage responsive protein with a significant role in maintaining the optimum DNA-repair activity in mammalian cells exposed to genotoxic stress. This DNA-damage responsive function of MTA1 was reported to be a P53-dependent and independent function. Here, we investigate the influence of P53 on gene regulation function of Mta1 to identify novel gene targets and functions of Mta1. Methods Gene expression analysis was performed on five different mouse embryonic fibroblasts (MEFs) samples (i) the Mta1 wild type, (ii) Mta1 knock out (iii) Mta1 knock out in which Mta1 was reintroduced (iv) P53 knock out (v) P53 knock out in which Mta1 was over expressed using Affymetrix Mouse Exon 1.0 ST arrays. Further Hierarchical Clustering, Gene Ontology analysis with GO terms satisfying corrected p-value<0.1, and the Ingenuity Pathway Analysis were performed. Finally, RT-qPCR was carried out on selective candidate genes. Significance/Conclusion This study represents a complete genome wide screen for possible target genes of a coregulator, Mta1. The comparative gene profiling of Mta1 wild type, Mta1 knockout and Mta1 re-expression in the Mta1 knockout conditions define “bona fide” Mta1 target genes. Further extensive analyses of the data highlights the influence of P53 on Mta1 gene regulation. In the presence of P53 majority of the genes regulated by Mta1 are related to inflammatory and anti-microbial responses whereas in the absence of P53 the predominant target genes are involved in cancer signaling. Thus, the presented data emphasizes the known functions of Mta1 and serves as a rich resource which could help us identify novel Mta1 functions.

Eswaran, Jeyanthy; Kumar, Rakesh

2011-01-01

194

Recent Patents Relating to Tumor Suppressor Genes  

Microsoft Academic Search

Researchers in the field of tumor suppressor genes are actively attempting to discover new tumor suppressor genes and\\/or characterize known tumor suppressor genes with the intention of treating and diagnosing cancers. A number of recent patents and patent applications have been published that discuss some of these discoveries. Some of the patents and patent applications discuss newly discovered tumor suppressor

Jason J. Derry; Yijan E. Chang

2007-01-01

195

HDL quality and functionality: what can proteins and genes predict?  

PubMed

Epidemiological and clinical studies have over the years established that dyslipidemia constitutes the main risk factor for atherosclerosis. The inverse correlation between HDL cholesterol (HDL-C) levels and coronary heart disease morbidity and mortality identified HDL-C as an alternative pharmacological target to LDL-C and a potential anti-atherosclerosis marker. However, more recent data reinforced the principle of 'HDL quality' in atherosclerosis that refers to the functionality of HDL particle, as defined by its protein and lipid content, rather than HDL-C levels in plasma. Since HDL functionality depends on the genes and proteins of the HDL metabolic pathway, its apoprotein composition may serve as a surrogate marker of atheroprotection. In this manuscript we review the atheroprotective properties of HDL in relation to the proteins of HDL metabolic pathway and discuss what HDL-associated genes and proteins may reveal about HDL functionality in the assessment of coronary risk. PMID:24650316

Karavia, Eleni A; Zvintzou, Evangelia; Petropoulou, Peristera-Ioanna; Xepapadaki, Eva; Constantinou, Caterina; Kypreos, Kyriakos E

2014-04-01

196

Identification and functional characterization of the novel human ether-a-go-go-related gene (hERG) R744P mutant associated with hereditary long QT syndrome 2.  

PubMed

Mutations of the cyclic nucleotide binding domain (CNBD) may disrupt human ether-a-go-go-related gene (hERG) K(+) channel function and lead to hereditary long QT syndrome (LQTS). We identified a novel missense mutation located in close proximity to the CNBD, hERG R744P, in a patient presenting with recurrent syncope and aborted cardiac death triggered by sudden auditory stimuli. Functional properties of wild type (WT) and mutant hERG R744P subunits were studied in Xenopus laevis oocytes using two-electrode voltage clamp electrophysiology and Western blot analysis. HERG R744P channels exhibited reduced activating currents compared to hERG WT (1.48±0.26 versus 3.40±0.29?A; n=40). These findings were confirmed by tail current analysis (hERG R744P, 0.53±0.07?A; hERG WT, 0.97±0.06?A; n=40). Cell surface trafficking of hERG R744P protein subunits was not impaired. To simulate the autosomal-dominant inheritance associated with LQTS, WT and R744P subunits were co-expressed in equimolar ratio. Mean activating and tail currents were reduced by 32% and 25% compared to hERG WT (n=40), indicating that R744P protein did not exert dominant-negative effects on WT channels. The half-maximal activation voltage was not significantly affected by the R744P mutation. This study highlights the significance of in vitro testing to provide mechanistic evidence for pathogenicity of mutations identified in LQTS. The functional defect associated with hERG R744P serves as molecular basis for LQTS in the index patient. PMID:22314138

Aidery, Parwez; Kisselbach, Jana; Gaspar, Harald; Baldea, Ioana; Schweizer, Patrick A; Becker, Rüdiger; Katus, Hugo A; Thomas, Dierk

2012-02-24

197

Functional imprinting and epigenetic modification of the human SNRPN gene.  

PubMed

The SNRPN gene encodes a small nuclear ribonucleoprotein subunit, SmN, thought to be involved in splicing of pre-mRNA. A closely related protein, SmB/B', is constitutively expressed in all tissues except the brain, where SmN is predominantly expressed. The mouse homolog of the SNRPN gene has been shown to be functionally imprinted in mouse brain, being expressed only from the paternally derived chromosome. SNRPN has been mapped to human chromosome 15q11-q13 within the shortest region of deletion overlap for the Prader-Willi syndrome. We have now demonstrated functional imprinting of the human SNRPN gene using reverse transcription followed by the polymerase chain reaction (RT-PCR). No expression was observed in cultured skin fibroblasts of Prader-Willi patients, but was found in all Angelman patients and normal controls examined. We have also demonstrated a parent-specific DNA methylation imprint within intron 5 of the SNRPN gene, which suggests an epigenetic mechanism by which parent-specific expression of this gene might be inherited. Our findings indicate that SNRPN is expressed only from the paternally derived chromosome 15 in humans and therefore may fulfill one major criterion for being involved in the pathogenesis of the Prader-Willi syndrome. PMID:8111367

Glenn, C C; Porter, K A; Jong, M T; Nicholls, R D; Driscoll, D J

1993-12-01

198

Gene discovery and gene function assignment in filamentous fungi  

Microsoft Academic Search

Filamentous fungi are a large group of diverse and economically important microorganisms. Large-scale gene disruption strategies developed in budding yeast are not applicable to these organisms because of their larger genomes and lower rate of targeted integration (TI) during transformation. We developed transposon-arrayed gene knockouts (TAGKO) to discover genes and simultaneously create gene disruption cassettes for subsequent transformation and mutant

Lisbeth Hamer; Kiichi Adachi; Maria V. Montenegro-Chamorro; Matthew M. Tanzer; Sanjoy K. Mahanty; Clive Lo; Rex W. Tarpey; Amy R. Skalchunes; Ryan W. Heiniger; Sheryl A. Frank; Blaise A. Darveaux; David J. Lampe; Ted M. Slater; Lakshman Ramamurthy; Todd M. Dezwaan; Grant H. Nelson; Jeffrey R. Shuster; Jeffrey Woessner; John E. Hamer

2001-01-01

199

Action Comprehension: Deriving Spatial and Functional Relations  

ERIC Educational Resources Information Center

A perceived action can be understood only when information about the action carried out and the objects used are taken into account. It was investigated how spatial and functional information contributes to establishing these relations. Participants observed static frames showing a hand wielding an instrument and a potential target object of the…

Bach, Patric; Knoblich, Gunther; Gunter, Thomas C.; Friederici, Angela D.; Wolfgang, Prinz

2005-01-01

200

Learning-related effects and functional neuroimaging  

Microsoft Academic Search

A fundamental problem in the study of learning is that learning-related changes may be confounded by nonspecific time effects. There are several strategies for handling this problem. This problem may be of greater significance in functional magnetic resonance imaging (fMRI) compared to positron emission tomography (PET). Using the general linear model, we describe, compare, and discuss two approaches for separating

Karl Magnus Petersson; Christina Elfgren; Martin Ingvar

1999-01-01

201

Poor prognosis in acute lymphoblastic leukemia may relate to promoter hypermethylation of cancer-related genes.  

PubMed

The hallmark of acute lymphoblastic leukemia (ALL) is a progressive appearance of malignant cell behavior that is triggered by the evolution of altered gene function. ALL has traditionally been viewed as a genetic disease; however, epigenetic defects also play an important role. DNA promoter methylation has gained increasing recognition as an important mechanism for transcriptional silencing of tumor-suppressor genes. Hypermethylation may contribute to the pathogenesis of leukemias providing an alternative route to gene mutation. We have reported that gene methylation in ALL cells is the most important way to inactivate cancer-related genes in this disease. In fact, this epigenetic event can help to inactivate tumor-suppressive apoptotic or growth-arresting responses and has prognostic impact in B- and T-ALL. The presence in individual tumors of multiple genes simultaneously methylated is an independent factor of poor prognosis in both childhood and adult ALL in terms of disease-free survival and overall survival. Moreover, methylation status is able to redefine the prognosis of selected ALL groups with well-established prognostic features. PMID:17613754

Roman-Gomez, Jose; Jimenez-Velasco, Antonio; Barrios, Manuel; Prosper, Felipe; Heiniger, Anabel; Torres, Antonio; Agirre, Xabier

2007-07-01

202

Genomic Resources and Tools for Gene Function Analysis in Potato  

PubMed Central

Potato, a highly heterozygous tetraploid, is undergoing an exciting phase of genomics resource development. The potato research community has established extensive genomic resources, such as large expressed sequence tag (EST) data collections, microarrays and other expression profiling platforms, and large-insert genomic libraries. Moreover, potato will now benefit from a global potato physical mapping effort, which is serving as the underlying resource for a full potato genome sequencing project, now well underway. These tools and resources are having a major impact on potato breeding and genetics. The genome sequence will provide an invaluable comparative genomics resource for cross-referencing to the other Solanaceae, notably tomato, whose sequence is also being determined. Most importantly perhaps, a potato genome sequence will pave the way for the functional analysis of the large numbers of potato genes that await discovery. Potato, being easily transformable, is highly amenable to the investigation of gene function by biotechnological approaches. Recent advances in the development of Virus Induced Gene Silencing (VIGS) and related methods will facilitate rapid progress in the analysis of gene function in this important crop.

Bryan, Glenn J.; Hein, Ingo

2008-01-01

203

Implication of synapse-related genes in bipolar disorder by linkage and gene expression analyses  

PubMed Central

Several chromosomal regions have been linked to bipolar disorder (BD). However, the search for specific genes has been hampered by inconsistent findings, partly due to genetic and phenotypic heterogeneity. We focused on lithium-responsive bipolar patients, a subgroup thought to be more homogeneous and conducted a multistage study including an initial linkage study followed up by fine mapping and gene expression. Our sample consisted of 36 families (275 genotyped individuals, 132 affected) recruited through probands who were responders to long-term lithium treatment. We conducted a genome-wide scan with 811 microsatellite markers followed by fine mapping. Gene expression studies of candidate regions were conducted on six post-mortem prefrontal brain regions of 20 individuals (8 BD and 12 controls). We identified regions 3p25, 3p14 and 14q11 as showing the highest genome-wide linkage signal (LOD 2.53, 2.04 and 3.19, respectively). Fine mapping provided further support for 3p25, while only modest support was found in the other two regions. We identified a group of synaptic, mitochondrial and apoptotic genes with altered expression patterns in BD. Analysis of an independent microarray dataset supported the implication of synapse-related and mitochondrial genes in BD. In conclusion, using two complementary strategies, we found evidence of linkage to lithium-responsive BD on 3p25, 3p14 and 14q11 as well as significantly dysregulated genes on these regions suggesting altered synaptic and mitochondrial function in BD. Further studies are warranted to demonstrate the functional role of these genes in BD.

de Lara, Catalina Lopez; Jaitovich-Groisman, Iris; Cruceanu, Cristiana; Mamdani, Firoza; Lebel, Veronique; Yerko, Volodymyr; Beck, Angus; Young, L. Trevor; Rouleau, Guy; Grof, Paul; Alda, Martin; Turecki, Gustavo

2012-01-01

204

Bacterial Genes in the Aphid Genome: Absence of Functional Gene Transfer from Buchnera to Its Host  

PubMed Central

Genome reduction is typical of obligate symbionts. In cellular organelles, this reduction partly reflects transfer of ancestral bacterial genes to the host genome, but little is known about gene transfer in other obligate symbioses. Aphids harbor anciently acquired obligate mutualists, Buchnera aphidicola (Gammaproteobacteria), which have highly reduced genomes (420–650 kb), raising the possibility of gene transfer from ancestral Buchnera to the aphid genome. In addition, aphids often harbor other bacteria that also are potential sources of transferred genes. Previous limited sampling of genes expressed in bacteriocytes, the specialized cells that harbor Buchnera, revealed that aphids acquired at least two genes from bacteria. The newly sequenced genome of the pea aphid, Acyrthosiphon pisum, presents the first opportunity for a complete inventory of genes transferred from bacteria to the host genome in the context of an ancient obligate symbiosis. Computational screening of the entire A. pisum genome, followed by phylogenetic and experimental analyses, provided strong support for the transfer of 12 genes or gene fragments from bacteria to the aphid genome: three LD–carboxypeptidases (LdcA1, LdcA2,?LdcA), five rare lipoprotein As (RlpA1-5), N-acetylmuramoyl-L-alanine amidase (AmiD), 1,4-beta-N-acetylmuramidase (bLys), DNA polymerase III alpha chain (?DnaE), and ATP synthase delta chain (?AtpH). Buchnera was the apparent source of two highly truncated pseudogenes (?DnaE and ?AtpH). Most other transferred genes were closely related to genes from relatives of Wolbachia (Alphaproteobacteria). At least eight of the transferred genes (LdcA1, AmiD, RlpA1-5, bLys) appear to be functional, and expression of seven (LdcA1, AmiD, RlpA1-5) are highly upregulated in bacteriocytes. The LdcAs and RlpAs appear to have been duplicated after transfer. Our results excluded the hypothesis that genome reduction in Buchnera has been accompanied by gene transfer to the host nuclear genome, but suggest that aphids utilize a set of duplicated genes acquired from other bacteria in the context of the Buchnera–aphid mutualism.

Nikoh, Naruo; McCutcheon, John P.; Kudo, Toshiaki; Miyagishima, Shin-ya; Moran, Nancy A.; Nakabachi, Atsushi

2010-01-01

205

Classification using functional data analysis for temporal gene expression data  

Microsoft Academic Search

Motivation: Temporal gene expression profiles provide an important characterization of gene function, as biological systems are pre- dominantly developmental and dynamic. We propose a method of classifying collections of temporal gene expression curves in which individual expression profiles are modeled as independent realizati- ons of a stochastic process. The method uses a recently developed functional logistic regression tool based on

Xiaoyan Leng; Hans-georg Müller

2006-01-01

206

Integrated Analysis of Microarray Data and Gene Function Information  

Microsoft Academic Search

Microarray data should be interpreted in the context of existing biological knowledge. Here we present integrated analysis of microarray data and gene function classification data us- ing homogeneity analysis. Homogeneity analysis is a graphical multivariate statistical method for analyzing categorical data. It converts categorical data into graphical display. By si- multaneously quantifying the microarry-derived gene groups and gene function categories,

Yan Cui; Mi Zhou; Wing Hung Wong

2004-01-01

207

A genome-wide transcriptional activity survey of rice transposable element-related genes  

Microsoft Academic Search

Background  Transposable element (TE)-related genes comprise a significant portion of the gene catalog of grasses, although their functions\\u000a are insufficiently characterized. The recent availability of TE-related gene annotation from the complete genome sequence\\u000a of rice (Oryza sativa) has created an opportunity to conduct a comprehensive evaluation of the transcriptional activities of these potentially\\u000a mobile elements and their related genes.\\u000a \\u000a \\u000a \\u000a \\u000a Results  We conducted

Yuling Jiao; Xing Wang Deng

2007-01-01

208

Structure-function evolution of the Transforming acidic coiled coil genes revealed by analysis of phylogenetically diverse organisms  

Microsoft Academic Search

BACKGROUND: Examination of ancient gene families can provide an insight into how the evolution of gene structure can relate to function. Functional homologs of the evolutionarily conserved transforming acidic coiled coil (TACC) gene family are present in organisms from yeast to man. However, correlations between functional interactions and the evolution of these proteins have yet to be determined. RESULTS: We

Ivan H Still; Ananthalakshmy K Vettaikkorumakankauv; Anthony DiMatteo; Ping Liang

2004-01-01

209

Transport of Magnesium by a Bacterial Nramp-Related Gene  

PubMed Central

Magnesium is an essential divalent metal that serves many cellular functions. While most divalent cations are maintained at relatively low intracellular concentrations, magnesium is maintained at a higher level (?0.5–2.0 mM). Three families of transport proteins were previously identified for magnesium import: CorA, MgtE, and MgtA/MgtB P-type ATPases. In the current study, we find that expression of a bacterial protein unrelated to these transporters can fully restore growth to a bacterial mutant that lacks known magnesium transporters, suggesting it is a new importer for magnesium. We demonstrate that this transport activity is likely to be specific rather than resulting from substrate promiscuity because the proteins are incapable of manganese import. This magnesium transport protein is distantly related to the Nramp family of proteins, which have been shown to transport divalent cations but have never been shown to recognize magnesium. We also find gene expression of the new magnesium transporter to be controlled by a magnesium-sensing riboswitch. Importantly, we find additional examples of riboswitch-regulated homologues, suggesting that they are a frequent occurrence in bacteria. Therefore, our aggregate data discover a new and perhaps broadly important path for magnesium import and highlight how identification of riboswitch RNAs can help shed light on new, and sometimes unexpected, functions of their downstream genes.

Rodionov, Dmitry A.; Freedman, Benjamin G.; Senger, Ryan S.; Winkler, Wade C.

2014-01-01

210

Interpolation of Head-Related Transfer Functions  

Microsoft Academic Search

Using current techniques it is usually impractical to measure head-related transfer functions (HRTFs) at a spatial resolution that does not exceed the minimum audible angle, i.e. 1-2° for a source directly in front, by a considerable amount. As a result, measured HRTFs must be interpolated to generate a display in which auditory space is rendered smoothly. The spatial resolution at

Russell Martin; Ken McAnally

211

Age-Related Changes in Redox Signaling and VSMC Function  

PubMed Central

Abstract Epidemiological studies have shown that advancing age is associated with an increased prevalence of cardiovascular disease (CVD). Vascular smooth muscle cells (VSMC) comprise the major arterial cell population, and changes in VSMC behavior, function, and redox status with age contribute to alterations in vascular remodeling and cell signaling. Over two decades of work on aged animal models provide support for age-related changes in VSMC and/or arterial tissues. Enhanced production of reactive oxygen species (ROS) and insufficient removal by scavenging systems are hallmarks of vascular aging. VSMC proliferation and migration are core processes in vascular remodeling and influenced by growth factors and signaling networks. The intrinsic link between gene regulation and aging often relates directly to transcription factors and their regulatory actions. Modulation of growth factor signaling leads to up- or downregulation of transcription factors that control expression of genes associated with VSMC proliferation, inflammation, and ROS production. Four major signaling pathways related to the transcription factors, AP-1, NF-?B, FoxO, and Nrf2, will be reviewed. Knowledge of age-related changes in signaling pathways in VSMC that lead to alterations in cell behavior and function consistent with disease progression may help in efforts to attenuate age-related CVD, such as atherosclerosis. Antioxid. Redox Signal. 12, 641–655.

Li, Muyao

2010-01-01

212

Concordant gene regulation related to perturbations of three GDP-mannose-related genes.  

PubMed

Glycosylation of proteins is one of the most crucial post-translational modifications. In order to access system-level and state-dependent data related to the regulation of glycosylation events, we cultivated yeast cell strains each harboring a selected conditional knockdown construct for a gene (either SEC53, VRG4 or DPM1) related to GDP-mannose synthesis or its utilization in glycan biosynthesis. In order to carry this out efficiently, we developed automated sampling from bioreactor cultivations, a collection of in silico workflows for data analysis as well as their integration into a large data warehouse. Using the above-mentioned approaches, we could show that conditional knocking down of transcripts related to GDP-mannose synthesis or transportation led to altered levels of over 300 transcripts. These transcripts and their corresponding proteins were characterized by their gene ontology (GO) annotations, and their putative transcriptional regulation was analyzed. Furthermore, novel pathways were generated indicating interactions between GO categories with common proteins, putative transcriptional regulators of such induced GO categories, and the large protein-protein interaction network among the proteins whose transcripts indicated altered expression levels. When these results are always added to an ever-expanding data warehouse as annotations, they will incrementally increase the knowledge of biological systems. PMID:19133071

Törmä, Anssi; Pitkänen, Juha-Pekka; Huopaniemi, Laura; Mattila, Pirkko; Renkonen, Risto

2009-02-01

213

Identification of Colorectal Cancer Related Genes with mRMR and Shortest Path in Protein-Protein Interaction Network  

Microsoft Academic Search

One of the most important and challenging problems in biomedicine and genomics is how to identify the disease genes. In this study, we developed a computational method to identify colorectal cancer-related genes based on (i) the gene expression profiles, and (ii) the shortest path analysis of functional protein association networks. The former has been used to select differentially expressed genes

Bi-Qing Li; Tao Huang; Lei Liu; Yu-Dong Cai; Kuo-Chen Chou

2012-01-01

214

Selective regulation of T-cell development and function by calcitonin gene-related peptide in thymus and spleen. An example of differential regional regulation of immunity by the neuroendocrine system.  

PubMed

In the course of our studies, we have shown the presence of calcitonin gene related peptide (CGRP) by immunocytochemistry in cell bodies and nerve fibers of the murine thymus and in a sparse innervation of the spleen. Receptors for CGRP have been characterized within these glands, and their activation by physiological levels of CGRP was found to suppress Con A-stimulated proliferation of thymocytes and splenic T cells as well as antigen-specific T-cell proliferation. This suppression is blocked by the antagonist for CGRP (CGRP 8-37). Within the thymus cultures, the antagonist CGRP (8-37) alone enhanced proliferation of thymocytes during Con A stimulation, most likely by inhibiting the endogenous release of CGRP into the culture medium by resident thymocytes. Some of the CGRP-induced suppression of mitogenic stimulation of thymocytes, but not of splenocytes, was due to apoptosis. The antagonist, CGRP(8-37), did not block apoptosis caused by Con A or CGRP but rather enhanced it. Flow cytometric analysis of CGRP-treated cultures using antibodies to cluster determinates (CD) showed that the majority of thymocytes undergoing apoptosis induced by CGRP were of the CD4/CD8 double-positive type. These data indicate that apoptosis in the thymocytes is mediated by a CGRP receptor not sensitive to the antagonist CGRP(8-37). Because proliferation of thymocytes and splenocytes induced by Con A is blocked by this antagonist and splenocytes are refractory to CGRP induced apoptosis, CGRP appears to mediate at least two separate functions on subpopulations of thymocytes and T cells via two different CGRP receptors within the gland. These effects of a neuropeptide exemplify the phenomenon of differential regional regulation of immunity by the autonomic and neuroendocrine systems. PMID:9629282

Bulloch, K; McEwen, B S; Nordberg, J; Diwa, A; Baird, S

1998-05-01

215

A Genome-Wide Screen Indicates Correlation between Differentiation and Expression of Metabolism Related Genes  

PubMed Central

Differentiated tissues may be considered as materials with distinct properties. The differentiation program of a given tissue ensures that it acquires material properties commensurate with its function. It may be hypothesized that some of these properties are acquired through production of tissue-specific metabolites synthesized by metabolic enzymes. To establish correlation between metabolism and organogenesis we have carried out a genome-wide expression study of metabolism related genes by RNA in-situ hybridization. 23% of the metabolism related genes studied are expressed in a tissue-restricted but not tissue-exclusive manner. We have conducted the screen on whole mount chicken (Gallus gallus) embryos from four distinct developmental stages to correlate dynamic changes in expression patterns of metabolic enzymes with spatio-temporally unique developmental events. Our data strongly suggests that unique combinations of metabolism related genes, and not specific metabolic pathways, are upregulated during differentiation. Further, expression of metabolism related genes in well established signaling centers that regulate different aspects of morphogenesis indicates developmental roles of some of the metabolism related genes. The database of tissue-restricted expression patterns of metabolism related genes, generated in this study, should serve as a resource for systematic identification of these genes with tissue-specific functions during development. Finally, comprehensive understanding of differentiation is not possible unless the downstream genes of a differentiation cascade are identified. We propose, metabolic enzymes constitute a significant portion of these downstream target genes. Thus our study should help elucidate different aspects of tissue differentiation.

Shende, Akhilesh; Singh, Anupama; Meena, Anil; Ghosal, Ritika; Ranganathan, Madhav; Bandyopadhyay, Amitabha

2013-01-01

216

Isolation of tumor suppressor genes from MEN-1 related neoplasms  

SciTech Connect

Multiple Endocrine Neoplasia type 1 (MEN 1) is a cancer predisposition syndrome marked by the development of tumors in specific endocrine tissues such as the pituitary, parathyroid and pancreatic islets. Genetic linkage studies have mapped the MEN 1 gene to 11q13, and allelic loss in related tumors suggests that the gene is a tumor suppressor. Because inactivation of tumor suppressors may be accompanied by underexpression, subtractive hybridization was used to isolate potential candidate genes underexpressed in MEN 1 tumors. cDNA was synthesized from tumor and normal parathyroid tissue by RT-PCR. Biotinylated tumor cDNA was used as a driver and normal cDNA as a tester in subtractive hybridization. Following annealing of the driver and tester amplicons, the biotinylated strands were removed with streptavidin. The subtracted material was then used as a probe to isolate clones from a normal pancreatic islet library. Screening 2 x 10{sup 5} plaques yielded 14 positive clones. Of 6 clones analyzed, 3 were confirmed to be underexpressed in parathyroid tumors. Sequence analysis identified 2 clones as human ribosomal protein S10 (RPS10, chromosome 6) and 1 as the islet amyloid polypeptide (1AP, chromosome 12). The precise function of human RPS10 is not known but the related RPS6 functions as a tumor suppressor in Drosophila. 1AP has been implicated in modulation of G protein activity. The remaining positive clones will be mapped to determine if any fall on chromosome 11q13, and additional subtractions with parathyroid and pancreatic islet neoplasms are underway.

Yavari, R.; Kinder, B.; Bale, A.E. [Yale Univ. School of Medicine, New Haven, CT (United States)

1994-09-01

217

[Early atrial gene regulation of obesity-related arterial hypertension].  

PubMed

High fat diet (HFD) induces both arterial hypertension and tachycardia in dogs. Changes in heart rate occur early and are in part due to a decrease in the parasympathetic drive to the heart secondary to down-regulation of atrial muscarinic M2 receptors (Pelat et al. Hypertension 1999; 340: 1066-72). These data suggest that HFD is able to modify genic expression at atrial level. Thus, the aim of this work was to perform a systematic study of the genic expression profile in dogs made obese and hypertensive by 9 weeks of HFD. Blood pressure and heart rate were measured by telemetry implanted 15 days before starting regimen in 6 HFD and in 6 control dogs. HFD was the normal canine diet administered to controls but mixed with 300 g of beef fat. At the end of the experience, animals were sacrified and right atria were collected. Gene regulation was assessed in pooled tissue samples from both groups using suppressive substractive hybridization and microarray analysis. Genes with induction or repression rates of at least 20% when compared to controls were sequenced. As previously reported HFD induced a significant increase in body weight, blood pressure and heart rate when compared to controls. The results of SSH experiments led to the identification of 32 genes which are differentially regulated in atria from HFD dogs. Most are genes encoding proteins which have been previously shown to be regulated during various cardiopathies (MMP9, Na/K-ATPase 3...). These changes indicate the existence of early remodeling processes of atrial myocardium secondary to HFD. Other group of genes encodes proteins with no role identified in heart up today (lec-3, ERK-3, TRIP1, nucleophosmin...) or which function remains totally unknown. This work confirms that HFD is associated with early changes in gene expression in atrium. These changes are unlikely to be related to ventricular hypertrophy which is observed only during long-term HFD. Further studies are necessary to demonstrate the role of these modifications in the pathophysiological mechanisms leading to the increase in heart rate in this model of obesity-related arterial hypertension. PMID:12365082

Philip-Couderc, P; Smih, F; Pelat, M; Verwaerde, P; Pathak, A; Buys, S; Montastruc, J L; Senard, J M; Rouet, P

2002-01-01

218

Identification of protein coding genes in genomes with statistical functions based on the circular code.  

PubMed

A new statistical approach using functions based on the circular code classifies correctly more than 93% of bases in protein (coding) genes and non-coding genes of human sequences. Based on this statistical study, a research software called 'Analysis of Coding Genes' (ACG) has been developed for identifying protein genes in the genomes and for determining their frame. Furthermore, the software ACG also allows an evaluation of the length of protein genes, their position in the genome, their relative position between themselves, and the prediction of internal frames in protein genes. PMID:12204444

Arquès, Didier G; Lacan, Jérôme; Michel, Christian J

2002-01-01

219

Tinman Function Is Essential for Vertebrate Heart Development: Elimination of Cardiac Differentiation by Dominant Inhibitory Mutants of the tinman-Related Genes, XNkx2-3and XNkx2-5  

Microsoft Academic Search

InDrosophila,thetinmangene is absolutely required for development of the dorsal vessel, the insect equivalent of the heart. In vertebrates, thetinmangene is represented by a small family oftinman-related sequences, some of which are expressed during embryonic heart development. At present however, the precise importance of this gene family for vertebrate heart development is unclear. Using theXenopusembryo, we have employed a dominant inhibitory

Matthew W Grow; Paul A Krieg

1998-01-01

220

Mining the Gene Wiki for functional genomic knowledge  

PubMed Central

Background Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translating the text of Gene Wiki articles into ontology-based gene annotations. We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology. Results Our system produced 2,983 candidate gene annotations using the Disease Ontology and 11,022 candidate annotations using the Gene Ontology from the text of the Gene Wiki. Based on manual evaluations and comparisons to reference annotation sets, we estimate a precision of 90-93% for the Disease Ontology annotations and 48-64% for the Gene Ontology annotations. We further demonstrate that this data set can systematically improve the results from gene set enrichment analyses. Conclusions The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses.

2011-01-01

221

Function and evolution of the serotonin-synthetic bas-1 gene and other aromatic amino acid decarboxylase genes in Caenorhabditis  

PubMed Central

Background Aromatic L-amino acid decarboxylase (AADC) enzymes catalyze the synthesis of biogenic amines, including the neurotransmitters serotonin and dopamine, throughout the animal kingdom. These neurotransmitters typically perform important functions in both the nervous system and other tissues, as illustrated by the debilitating conditions that arise from their deficiency. Studying the regulation and evolution of AADC genes is therefore desirable to further our understanding of how nervous systems function and evolve. Results In the nematode C. elegans, the bas-1 gene is required for both serotonin and dopamine synthesis, and maps genetically near two AADC-homologous sequences. We show by transformation rescue and sequencing of mutant alleles that bas-1 encodes an AADC enzyme. Expression of a reporter construct in transgenics suggests that the bas-1 gene is expressed, as expected, in identified serotonergic and dopaminergic neurons. The bas-1 gene is one of six AADC-like sequences in the C. elegans genome, including a duplicate that is immediately downstream of the bas-1 gene. Some of the six AADC genes are quite similar to known serotonin- and dopamine-synthetic AADC's from other organisms whereas others are divergent, suggesting previously unidentified functions. In comparing the AADC genes of C. elegans with those of the congeneric C. briggsae, we find only four orthologous AADC genes in C. briggsae. Two C. elegans AADC genes – those most similar to bas-1 – are missing from C. briggsae. Phylogenetic analysis indicates that one or both of these bas-1-like genes were present in the common ancestor of C. elegans and C. briggsae, and were retained in the C. elegans line, but lost in the C. briggsae line. Further analysis of the two bas-1-like genes in C. elegans suggests that they are unlikely to encode functional enzymes, and may be expressed pseudogenes. Conclusions The bas-1 gene of C. elegans encodes a serotonin- and dopamine-synthetic AADC enzyme. Two C. elegans AADC-homologous genes that are closely related to bas-1 are missing from the congeneric C. briggsae; one or more these genes was present in the common ancestor of C. elegans and C. briggsae. Despite their persistence in C. elegans, evidence suggests the bas-1-like genes do not encode functional AADC proteins. The presence of the genes in C. elegans raises questions about how many 'predicted genes' in sequenced genomes are functional, and how duplicate genes are retained or lost during evolution. This is another example of unexpected retention of duplicate genes in eukaryotic genomes.

Hare, Emily E; Loer, Curtis M

2004-01-01

222

Functional Comparison between Genes Dysregulated in Ulcerative Colitis and Colorectal Carcinoma  

PubMed Central

Background Patients with ulcerative colitis (UC) are predisposed to colitis-associated colorectal cancer (CAC). However, the transcriptional mechanism of the transformation from UC to CAC is not fully understood. Methodology Firstly, we showed that CAC and non-UC-associated CRC were very similar in gene expression. Secondly, based on multiple datasets for UC and CRC, we extracted differentially expressed (DE) genes in UC and CRC versus normal controls, respectively. Thirdly, we compared the dysregulation directions (upregulation or downregulation) between DE genes of UC and CRC in CRC-related functions overrepresented with the DE genes of CRC, and proposed a regulatory model to explain the CRC-like dysregulation of genes in UC. A case study for “positive regulation of immune system process” was done to reveal the functional implication of DE genes with reversal dysregulations in these two diseases. Principal Findings In all the 44 detected CRC-related functions except for “viral transcription”, the dysregulation directions of DE genes in UC were significantly similar with their counterparts in CRC, and such CRC-like dysregulation in UC could be regulated by transcription factors affected by pro-inflammatory stimuli for colitis. A small portion of genes in each CRC-related function were dysregulated in opposite directions in the two diseases. The case study showed that genes related to humoral immunity specifically expressed in B cells tended to be upregulated in UC but downregulated in CRC. Conclusions The CRC-like dysregulation of genes in CRC-related functions in UC patients provides hints for understanding the transcriptional basis for UC to CRC transition. A small portion of genes with distinct dysregulation directions in each of the CRC-related functions in the two diseases implicate that their reversal dysregulations might be critical for UC to CRC transition. The cases study indicates that the humoral immune response might be inhibited during the transformation from UC to CRC.

Zhao, Wenyuan; Qi, Lishuang; Qin, Yao; Wang, Hongwei; Chen, Beibei; Wang, Ruiping; Gu, Yunyan; Liu, Chunyang; Wang, Chenguang; Guo, Zheng

2013-01-01

223

FuncBase : a resource for quantitative gene function annotation  

PubMed Central

Summary: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. For example, a custom Cytoscape viewer shows functional linkage graphs relevant to the gene or function of interest. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. Availability: FuncBase as well as all underlying data and annotations are freely available via http://func.med.harvard.edu/ Contact: fritz_roth@hms.harvard.edu

Beaver, John E.; Tasan, Murat; Gibbons, Francis D.; Tian, Weidong; Hughes, Timothy R.; Roth, Frederick P.

2010-01-01

224

Molecular function of tocopherols in age related diseases.  

PubMed

Tocopherols, with a phytyl side chain in its chroman ring, belong to vitamin E family and have several effects on organisms. They are also classified as therapeutics against different types of human diseases. Especially important roles in cell signaling and gene regulatory mechanisms make tocopherols crucial as therapeutic agents. Aging is accompanied with several degenerative disorders including cardiovascular, neuronal and metabolic diseases. The role of free radical damage in aging has been identified and tocopherols were shown to be involved in age related disorders. Recent studies and future directions will be focused in this review regarding the molecular functions of tocopherols. PMID:24079766

Karademir, Betul; Ozer, Nesrin Kartal

2014-01-01

225

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees  

PubMed Central

The data and tools in PANTHER—a comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org—have undergone continual, extensive improvement for over a decade. Here, we describe the current PANTHER process as a whole, as well as the website tools for analysis of user-uploaded data. The main goals of PANTHER remain essentially unchanged: the accurate inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse experimental information from a few model organisms. Yet the focus of PANTHER has continually shifted toward more accurate and detailed representations of evolutionary events in gene family histories. The trees are now designed to represent gene family evolution, including inference of evolutionary events, such as speciation and gene duplication. Subfamilies are still curated and used to define HMMs, but gene ontology functional annotations can now be made at any node in the tree, and are designed to represent gain and loss of function by ancestral genes during evolution. Finally, PANTHER now includes stable database identifiers for inferred ancestral genes, which are used to associate inferred gene attributes with particular genes in the common ancestral genomes of extant species.

Mi, Huaiyu; Muruganujan, Anushya; Thomas, Paul D.

2013-01-01

226

MINING FUNCTIONALLY RELEVANT GENE SETS FOR ANALYZING PHYSIOLOGICALLY NOVEL CLINICAL EXPRESSION DATA  

PubMed Central

Gene set analyses have become a standard approach for increasing the sensitivity of transcriptomic studies. However, analytical methods incorporating gene sets require the availability of pre-defined gene sets relevant to the underlying physiology being studied. For novel physiological problems, relevant gene sets may be unavailable or existing gene set databases may bias the results towards only the best-studied of the relevant biological processes. We describe a successful attempt to mine novel functional gene sets for translational projects where the underlying physiology is not necessarily well characterized in existing annotation databases. We choose targeted training data from public expression data repositories and define new criteria for selecting biclusters to serve as candidate gene sets. Many of the discovered gene sets show little or no enrichment for informative Gene Ontology terms or other functional annotation. However, we observe that such gene sets show coherent differential expression in new clinical test data sets, even if derived from different species, tissues, and disease states. We demonstrate the efficacy of this method on a human metabolic data set, where we discover novel, uncharacterized gene sets that are diagnostic of diabetes, and on additional data sets related to neuronal processes and human development. Our results suggest that our approach may be an efficient way to generate a collection of gene sets relevant to the analysis of data for novel clinical applications where existing functional annotation is relatively incomplete.

Turcan, Sevin; Vetter, Douglas E.; Maron, Jill L.; Wei, Xintao; Slonim, Donna K.

2011-01-01

227

Gene discovery and gene function assignment in filamentous fungi.  

PubMed

Filamentous fungi are a large group of diverse and economically important microorganisms. Large-scale gene disruption strategies developed in budding yeast are not applicable to these organisms because of their larger genomes and lower rate of targeted integration (TI) during transformation. We developed transposon-arrayed gene knockouts (TAGKO) to discover genes and simultaneously create gene disruption cassettes for subsequent transformation and mutant analysis. Transposons carrying a bacterial and fungal drug resistance marker are used to mutagenize individual cosmids or entire libraries in vitro. Cosmids are annotated by DNA sequence analysis at the transposon insertion sites, and cosmid inserts are liberated to direct insertional mutagenesis events in the genome. Based on saturation analysis of a cosmid insert and insertions in a fungal cosmid library, we show that TAGKO can be used to rapidly identify and mutate genes. We further show that insertions can create alterations in gene expression, and we have used this approach to investigate an amino acid oxidation pathway in two important fungal phytopathogens. PMID:11296265

Hamer, L; Adachi, K; Montenegro-Chamorro, M V; Tanzer, M M; Mahanty, S K; Lo, C; Tarpey, R W; Skalchunes, A R; Heiniger, R W; Frank, S A; Darveaux, B A; Lampe, D J; Slater, T M; Ramamurthy, L; DeZwaan, T M; Nelson, G H; Shuster, J R; Woessner, J; Hamer, J E

2001-04-24

228

Gene discovery and gene function assignment in filamentous fungi  

PubMed Central

Filamentous fungi are a large group of diverse and economically important microorganisms. Large-scale gene disruption strategies developed in budding yeast are not applicable to these organisms because of their larger genomes and lower rate of targeted integration (TI) during transformation. We developed transposon-arrayed gene knockouts (TAGKO) to discover genes and simultaneously create gene disruption cassettes for subsequent transformation and mutant analysis. Transposons carrying a bacterial and fungal drug resistance marker are used to mutagenize individual cosmids or entire libraries in vitro. Cosmids are annotated by DNA sequence analysis at the transposon insertion sites, and cosmid inserts are liberated to direct insertional mutagenesis events in the genome. Based on saturation analysis of a cosmid insert and insertions in a fungal cosmid library, we show that TAGKO can be used to rapidly identify and mutate genes. We further show that insertions can create alterations in gene expression, and we have used this approach to investigate an amino acid oxidation pathway in two important fungal phytopathogens.

Hamer, Lisbeth; Adachi, Kiichi; Montenegro-Chamorro, Maria V.; Tanzer, Matthew M.; Mahanty, Sanjoy K.; Lo, Clive; Tarpey, Rex W.; Skalchunes, Amy R.; Heiniger, Ryan W.; Frank, Sheryl A.; Darveaux, Blaise A.; Lampe, David J.; Slater, Ted M.; Ramamurthy, Lakshman; DeZwaan, Todd M.; Nelson, Grant H.; Shuster, Jeffrey R.; Woessner, Jeffrey; Hamer, John E.

2001-01-01

229

Network Analysis of EtOH-Related Candidate Genes  

PubMed Central

Recently, we collected many large-scale datasets for alcohol dependence and EtOH response in five organisms and deposited them in our EtOH-related gene resource database (ERGR, http://bioinfo.mc.vanderbilt.edu/ERGR/). Based on multidimensional evidence among these datasets, we prioritized 57 EtOH-related candidate genes. To explore their biological roles, and the molecular mechanisms of EtOH response and alcohol dependence, we examined the features of these genes by the Gene Ontology (GO) term-enrichment test and network/pathway analysis. Our analysis revealed that these candidate genes were highly enriched in alcohol dependence/alcoholism and highly expressed in brain or liver tissues. All the significantly enriched GO terms were related to neurotransmitter systems or EtOH metabolic processes. Using the Ingenuity Pathway Analysis system, we found that these genes were involved in networks of neurological disease, cardiovascular disease, inflammatory response, and small molecular metabolism. Many key genes in signaling pathways were in the central position of these networks. Furthermore, our protein–protein interaction (PPI) network analysis suggested some novel candidate genes which also had evidence in the ERGR database. This study demonstrated that our candidate gene selection is effective and our network/pathway analysis is useful for uncovering the molecular mechanisms of EtOH response and alcohol dependence. This approach can be applied to study the features of candidate genes of other complex traits/phenotypes.

Guo, An-Yuan; Sun, Jingchun; Jia, Peilin

2010-01-01

230

A Hidden Markov Model approach to predicting yeast gene function from sequential gene expression data.  

PubMed

Existing data mining tools can only achieve about 40% precision in function prediction of unannotated genes. We developed a gene function prediction tool based on profile Hidden Markov Models (HMMs). Each function class was modelled using a distinct HMM whose parameters were trained using yeast time-series gene expression profiles. Two structural variants of HMMs were designed and tested, each of them on 40 function classes. The highest overall prediction precision achieved was 67% using double-split HMM with leave-one-out cross-validation. We also attempted to generalise HMMs to dynamic Bayesian networks for gene function prediction using heterogeneous data sets. PMID:18640903

Deng, Xutao; Geng, Huimin; Ali, Hesham H

2008-01-01

231

Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities.  

PubMed

Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale. PMID:24806276

Paula, Fabiana S; Rodrigues, Jorge L M; Zhou, Jizhong; Wu, Liyou; Mueller, Rebecca C; Mirza, Babur S; Bohannan, Brendan J M; Nüsslein, Klaus; Deng, Ye; Tiedje, James M; Pellizari, Vivian H

2014-06-01

232

Reconstruction of a Functional Human Gene Network, with an Application for Prioritizing Positional Candidate Genes  

PubMed Central

Most common genetic disorders have a complex inheritance and may result from variants in many genes, each contributing only weak effects to the disease. Pinpointing these disease genes within the myriad of susceptibility loci identified in linkage studies is difficult because these loci may contain hundreds of genes. However, in any disorder, most of the disease genes will be involved in only a few different molecular pathways. If we know something about the relationships between the genes, we can assess whether some genes (which may reside in different loci) functionally interact with each other, indicating a joint basis for the disease etiology. There are various repositories of information on pathway relationships. To consolidate this information, we developed a functional human gene network that integrates information on genes and the functional relationships between genes, based on data from the Kyoto Encyclopedia of Genes and Genomes, the Biomolecular Interaction Network Database, Reactome, the Human Protein Reference Database, the Gene Ontology database, predicted protein-protein interactions, human yeast two-hybrid interactions, and microarray coexpressions. We applied this network to interrelate positional candidate genes from different disease loci and then tested 96 heritable disorders for which the Online Mendelian Inheritance in Man database reported at least three disease genes. Artificial susceptibility loci, each containing 100 genes, were constructed around each disease gene, and we used the network to rank these genes on the basis of their functional interactions. By following up the top five genes per artificial locus, we were able to detect at least one known disease gene in 54% of the loci studied, representing a 2.8-fold increase over random selection. This suggests that our method can significantly reduce the cost and effort of pinpointing true disease genes in analyses of disorders for which numerous loci have been reported but for which most of the genes are unknown.

Franke, Lude; Bakel, Harm van; Fokkens, Like; de Jong, Edwin D.; Egmont-Petersen, Michael; Wijmenga, Cisca

2006-01-01

233

Evaluation of Genetic Variants in MicroRNA-Related Genes and Risk of Bladder Cancer  

Microsoft Academic Search

MicroRNAs (miRNA) are small noncoding RNA molecules involved in a diversity of cellular functions. Although it has been reported that global suppression of the miRNA biogen- esis pathway leads to enhanced tumorigenesis, the effect of common genetic variants of miRNA-related genes on cancer predisposition is unclear. To better understand this effect, we genotyped 41 single-nucleotide polymorphisms (SNP) from 24miRNA-related genes

Hushan Yang; Colin P. Dinney; Yuanqing Ye; H. Barton Grossman; Xifeng Wu

2008-01-01

234

Validation of Reference Genes for the Relative Quantification of Gene Expression in Human Epicardial Adipose Tissue  

Microsoft Academic Search

BackgroundRelative quantification is a commonly used method for assessing gene expression, however its accuracy and reliability is dependent upon the choice of an optimal endogenous control gene, and such choice cannot be made a priori. There is limited information available on suitable reference genes to be used for studies involving human epicardial adipose tissue. The objective of the current study

Kanta Chechi; Yves Gelinas; Patrick Mathieu; Yves Deshaies; Denis Richard

2012-01-01

235

Amplification of a Gene Related to Mammalian mdr Genes in Drug-Resistant Plasmodium falciparum  

NASA Astrophysics Data System (ADS)

The malaria parasite Plasmodium falciparum contains at least two genes related to the mammalian multiple drug resistance genes, and at least one of the P. falciparum genes is expressed at a higher level and is present in higher copy number in a strain that is resistant to multiple drugs than in a strain that is sensitive to the drugs.

Wilson, Craig M.; Serrano, Adelfa E.; Wasley, Annemarie; Bogenschutz, Michael P.; Shankar, Anuraj H.; Wirth, Dyann F.

1989-06-01

236

Microbial functional genes associated with coral health and disease.  

PubMed

Both the incidence and prevalence of coral disease are rapidly increasing, and as a consequence, many studies involving coral microbial associates have been conducted. However, very few of these have considered microbial functional genes. This is an underutilized approach for studying coral disease etiology which is capable of revealing the molecular processes of the coral microbial community. This review presents a summary of the known microbial functional genes that have been linked to coral health and disease. Overall functional gene diversity tended to be lower in healthy corals than diseased or bleached corals, and respiration and photosynthesis functional genes appeared to be crucial to coral health. Genes associated with the nitrogen cycle were the most studied, were highly represented within the coral holobiont, and their expression often shifted in diseased or stressed individuals. Carbon metabolism, such as fatty acid and amino acid catabolism, also tended to shift in unhealthy corals. Genes associated with sulfite respiration as well as dimethylsulfoniopropionate degradation have been detected, although they have yet to be directly associated with coral disease. In addition, genes associated with xenobiotic degradation, antibiotic resistance, virulence, and oxidative stress may all be involved in maintaining coral health. However, the links between these functional genes and their roles in interacting with the coral host are not clear. Continuing identification of coral-associated microbial functional genes within the coral holobiont should facilitate advances in the field of coral health and disease. PMID:24334358

Pratte, Zoe A

2013-12-12

237

Genetic variations in interleukin-12 related genes in immune-mediated diseases.  

PubMed

The interleukin-12 (IL-12) family comprises a group of heterodimeric cytokines and their respective receptors that play key roles in immune responses. A growing number of autoimmune diseases has been found to be associated with genetic variation in these genes. Based on their respective associations with the IL-12 genes, autoimmune diseases appear to cluster in two groups that either show strong associations with the Th1/Th17 pathway (as indicated by genetic association with IL12B and IL23R) or the Th1/IL-35 pathway as the consequence of their association with polymorphisms in the IL12A gene region. The genetic associations are described in relation to what is known of the functionality of these genes in the various diseases. Comparing association data for gene families in different diseases may lead to better insight in the function of the genes in the onset and course of the disease. PMID:22819329

van Wanrooij, R L J; Zwiers, A; Kraal, G; Bouma, G

2012-12-01

238

Predicting function: from genes to genomes and back1  

Microsoft Academic Search

Predicting function from sequence using computational tools is a highly complicated procedure that is generally done for each gene individually. This review focuses on the added value that is provided by completely sequenced genomes in function prediction. Various levels of sequence annotation and function prediction are discussed, ranging from genomic sequence to that of complex cellular processes. Protein function is

Peer Bork; Thomas Dandekar; Yolande Diaz-Lazcoz; Frank Eisenhaber; Martijn Huynen; Yanping Yuan

1998-01-01

239

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

PubMed Central

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?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.

2013-01-01

240

Prediction of Drosophila melanogaster gene function using Support Vector Machines  

PubMed Central

Background While the genomes of hundreds of organisms have been sequenced and good approaches exist for finding protein encoding genes, an important remaining challenge is predicting the functions of the large fraction of genes for which there is no annotation. Large gene expression datasets from microarray experiments already exist and many of these can be used to help assign potential functions to these genes. We have applied Support Vector Machines (SVM), a sigmoid fitting function and a stratified cross?validation approach to analyze a large microarray experiment dataset from Drosophila melanogaster in order to predict possible functions for previously un?annotated genes. A total of approximately 5043 different genes, or about one?third of the predicted genes in the D. melanogaster genome, are represented in the dataset and 1854 (or 37%) of these genes are un?annotated. Results 39 Gene Ontology Biological Process (GO?BP) categories were found with precision value equal or larger than 0.75, when recall was fixed at the 0.4 level. For two of those categories, we have provided additional support for assigning given genes to the category by showing that the majority of transcripts for the genes belonging in a given category have a similar localization pattern during embryogenesis. Additionally, by assessing the predictions using a confidence score, we have been able to provide a putative GO?BP term for 1422 previously un?annotated genes or about 77% of the un?annotated genes represented on the microarray and about 19% of all of the un?annotated genes in the D. melanogaster genome. Conclusions Our study successfully employs a number of SVM classifiers, accompanied by detailed calibration and validation techniques, to generate a number of predictions for new annotations for D. melanogaster genes. The applied probabilistic analysis to SVM output improves the interpretability of the prediction results and the objectivity of the validation procedure.

2013-01-01

241

Relating significance and relations of differentially expressed genes in response to Aspergillus flavus infection in maize  

PubMed Central

Aspergillus flavus is a pathogenic fungus infecting maize and producing aflatoxins that are health hazards to humans and animals. Characterizing host defense mechanism and prioritizing candidate resistance genes are important to the development of resistant maize germplasm. We investigated methods amenable for the analysis of the significance and relations among maize candidate genes based on the empirical gene expression data obtained by RT-qPCR technique from maize inbred lines. We optimized a pipeline of analysis tools chosen from various programs to provide rigorous statistical analysis and state of the art data visualization. A network-based method was also explored to construct the empirical gene expression relational structures. Maize genes at the centers in the network were considered as important candidate genes for maize DNA marker studies. The methods in this research can be used to analyze large RT-qPCR datasets and establish complex empirical gene relational structures across multiple experimental conditions.

Asters, Matthew C.; Williams, W. Paul; Perkins, Andy D.; Mylroie, J. Erik; Windham, Gary L.; Shan, Xueyan

2014-01-01

242

Relating significance and relations of differentially expressed genes in response to Aspergillus flavus infection in maize.  

PubMed

Aspergillus flavus is a pathogenic fungus infecting maize and producing aflatoxins that are health hazards to humans and animals. Characterizing host defense mechanism and prioritizing candidate resistance genes are important to the development of resistant maize germplasm. We investigated methods amenable for the analysis of the significance and relations among maize candidate genes based on the empirical gene expression data obtained by RT-qPCR technique from maize inbred lines. We optimized a pipeline of analysis tools chosen from various programs to provide rigorous statistical analysis and state of the art data visualization. A network-based method was also explored to construct the empirical gene expression relational structures. Maize genes at the centers in the network were considered as important candidate genes for maize DNA marker studies. The methods in this research can be used to analyze large RT-qPCR datasets and establish complex empirical gene relational structures across multiple experimental conditions. PMID:24770700

Asters, Matthew C; Williams, W Paul; Perkins, Andy D; Mylroie, J Erik; Windham, Gary L; Shan, Xueyan

2014-01-01

243

Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma  

PubMed Central

Background This study aimed at the identification of prognostic gene expression markers in early primary colorectal carcinomas without metastasis at the time point of surgery by analyzing genome-wide gene expression profiles using oligonucleotide microarrays. Methods Cryo-conserved tumor specimens from 45 patients with early colorectal cancers were examined, with the majority of them being UICC stage II or earlier and with a follow-up time of 41–115 months. Gene expression profiling was performed using Whole Human Genome 4x44K Oligonucleotide Microarrays. Validation of microarray data was performed on five of the genes in a smaller cohort. Results Using a novel algorithm based on the recursive application of support vector machines (SVMs), we selected a signature of 44 probes that discriminated between patients developing later metastasis and patients with a good prognosis. Interestingly, almost half of the genes was related to the patients’ immune response and showed reduced expression in the metastatic cases. Conclusions Whereas up to now gene signatures containing genes with various biological functions have been described for prediction of metastasis in CRC, in this study metastasis could be well predicted by a set of gene expression markers consisting exclusively of genes related to the MHC class II complex involved in immune response. Thus, our data emphasize that the proper function of a comprehensive network of immune response genes is of vital importance for the survival of colorectal cancer patients.

2014-01-01

244

Predicting gene ontology functions from protein's regional surface structures  

PubMed Central

Background Annotation of protein functions is an important task in the post-genomic era. Most early approaches for this task exploit only the sequence or global structure information. However, protein surfaces are believed to be crucial to protein functions because they are the main interfaces to facilitate biological interactions. Recently, several databases related to structural surfaces, such as pockets and cavities, have been constructed with a comprehensive library of identified surface structures. For example, CASTp provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities. Results A novel method was proposed to predict the Gene Ontology (GO) functions of proteins from the pocket similarity network, which is constructed according to the structure similarities of pockets. The statistics of the networks were presented to explore the relationship between the similar pockets and GO functions of proteins. Cross-validation experiments were conducted to evaluate the performance of the proposed method. Results and codes are available at: . Conclusion The computational results demonstrate that the proposed method based on the pocket similarity network is effective and efficient for predicting GO functions of proteins in terms of both computational complexity and prediction accuracy. The proposed method revealed strong relationship between small surface patterns (or pockets) and GO functions, which can be further used to identify active sites or functional motifs. The high quality performance of the prediction method together with the statistics also indicates that pockets play essential roles in biological interactions or the GO functions. Moreover, in addition to pockets, the proposed network framework can also be used for adopting other protein spatial surface patterns to predict the protein functions.

Liu, Zhi-Ping; Wu, Ling-Yun; Wang, Yong; Chen, Luonan; Zhang, Xiang-Sun

2007-01-01

245

Functional Hypervariability and Gene Diversity of Cardioactive Neuropeptides*  

PubMed Central

Crustacean cardioactive peptide (CCAP) and related peptides are multifunctional regulatory neurohormones found in invertebrates. We isolated a CCAP-related peptide (conoCAP-a, for cone snail CardioActive Peptide) and cloned the cDNA of its precursor from venom of Conus villepinii. The precursor of conoCAP-a encodes for two additional CCAP-like peptides: conoCAP-b and conoCAP-c. This multi-peptide precursor organization is analogous to recently predicted molluscan CCAP-like preprohormones, and suggests a mechanism for the generation of biological diversification without gene amplification. While arthropod CCAP is a cardio-accelerator, we found that conoCAP-a decreases the heart frequency in Drosophila larvae, demonstrating that conoCAP-a and CCAP have opposite effects. Intravenous injection of conoCAP-a in rats caused decreased heart frequency and blood pressure in contrast to the injection of CCAP, which did not elicit any cardiac effect. Perfusion of rat ventricular cardiac myocytes with conoCAP-a decreased systolic calcium, indicating that conoCAP-a cardiac negative inotropic effects might be mediated via impairment of intracellular calcium trafficking. The contrasting cardiac effects of conoCAP-a and CCAP indicate that molluscan CCAP-like peptides have functions that differ from those of their arthropod counterparts. Molluscan CCAP-like peptides sequences, while homologous, differ between taxa and have unique sequences within a species. This relates to the functional hypervariability of these peptides as structure activity relationship studies demonstrate that single amino acids variations strongly affect cardiac activity. The discovery of conoCAPs in cone snail venom emphasizes the significance of their gene plasticity to have mutations as an adaptive evolution in terms of structure, cellular site of expression, and physiological functions.

Moller, Carolina; Melaun, Christian; Castillo, Cecilia; Diaz, Mary E.; Renzelman, Chad M.; Estrada, Omar; Kuch, Ulrich; Lokey, Scott; Mari, Frank

2010-01-01

246

Chemical genomics for studying parasite gene function and interaction.  

PubMed

With the development of new technologies in genome sequencing, gene expression profiling, genotyping, and high-throughput screening of chemical compound libraries, small molecules are playing increasingly important roles in studying gene expression regulation, gene-gene interaction, and gene function. Here we briefly review and discuss some recent advancements in drug target identification and phenotype characterization using combinations of high-throughput screening of small-molecule libraries and various genome-wide methods such as whole-genome sequencing, genome-wide association studies (GWAS), and genome-wide expression analysis. These approaches can be used to search for new drugs against parasite infections, to identify drug targets or drug resistance genes, and to infer gene function. PMID:24215777

Li, Jian; Yuan, Jing; Cheng, Ken Chih-Chien; Inglese, James; Su, Xin-zhuan

2013-12-01

247

[Identification of gastric cancer-related differentially expressed genes by combining PCA and ICA].  

PubMed

Screening potential differentially expressed genes can help us to understand the functions of the genes and their roles in disease development. Due to the different emphases of the principal component analysis and independent component analysis, a novel method that combines principal component analysis and independent component analysis is proposed to identify differentially expressed genes associated with gastric cancer for the improvement of accuracy and credibility of results. This method screens out 16 differentially expressed genes which is significantly related to the occurrence and development of gastric cancer from gastric cancer gene expression data with 7129 genes and 29 samples. These genes are worthy to be studied experimentally. The results of this paper are helpful for revealing the occurrence and development mechanism of gastric cancer. PMID:24459943

Chen, Zhanlei; Li, Boyu; Li, Yi; Rao, Nini

2013-10-01

248

Prediction and Analysis of Retinoblastoma Related Genes through Gene Ontology and KEGG  

PubMed Central

One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB) is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). 119 RB genes were compiled from two previous RB related studies, while 5,500 non-RB genes were randomly selected from Ensemble genes. Ten datasets were constructed based on all these RB and non-RB genes. Each gene was encoded with a 13,126-dimensional vector including 12,887 Gene Ontology enrichment scores and 239 KEGG enrichment scores. Finally, an optimal feature set including 1061 GO terms and 8 KEGG pathways was obtained. Analysis showed that these features were closely related to RB. It is anticipated that the method can be applied to predict the other cancer related genes as well.

Li, Zhen; Chen, Lei; Zhang, Jian; Liu, Lin; Huang, Tao

2013-01-01

249

Prediction and analysis of retinoblastoma related genes through gene ontology and KEGG.  

PubMed

One of the most important and challenging problems in biomedicine is how to predict the cancer related genes. Retinoblastoma (RB) is the most common primary intraocular malignancy usually occurring in childhood. Early detection of RB could reduce the morbidity and promote the probability of disease-free survival. Therefore, it is of great importance to identify RB genes. In this study, we developed a computational method to predict RB related genes based on Dagging, with the maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). 119 RB genes were compiled from two previous RB related studies, while 5,500 non-RB genes were randomly selected from Ensemble genes. Ten datasets were constructed based on all these RB and non-RB genes. Each gene was encoded with a 13,126-dimensional vector including 12,887 Gene Ontology enrichment scores and 239 KEGG enrichment scores. Finally, an optimal feature set including 1061 GO terms and 8 KEGG pathways was obtained. Analysis showed that these features were closely related to RB. It is anticipated that the method can be applied to predict the other cancer related genes as well. PMID:23998122

Li, Zhen; Li, Bi-Qing; Jiang, Min; Chen, Lei; Zhang, Jian; Liu, Lin; Huang, Tao

2013-01-01

250

Neuroimaging, nutrition, and iron-related genes.  

PubMed

Several dietary factors and their genetic modifiers play a role in neurological disease and affect the human brain. The structural and functional integrity of the living brain can be assessed using neuroimaging, enabling large-scale epidemiological studies to identify factors that help or harm the brain. Iron is one nutritional factor that comes entirely from our diet, and its storage and transport in the body are under strong genetic control. In this review, we discuss how neuroimaging can help to identify associations between brain integrity, genetic variations, and dietary factors such as iron. We also review iron's essential role in cognition, and we note some challenges and confounds involved in interpreting links between diet and brain health. Finally, we outline some recent discoveries regarding the genetics of iron and its effects on the brain, suggesting the promise of neuroimaging in revealing how dietary factors affect the brain. PMID:23817740

Jahanshad, Neda; Rajagopalan, Priya; Thompson, Paul M

2013-12-01

251

FUNCTIONAL NANOPARTICLES FOR MOLECULAR IMAGING GUIDED GENE DELIVERY  

PubMed Central

Gene therapy has great potential to bring tremendous changes in treatment of various diseases and disorders. However, one of the impediments to successful gene therapy is the inefficient delivery of genes to target tissues and the inability to monitor delivery of genes and therapeutic responses at the targeted site. The emergence of molecular imaging strategies has been pivotal in optimizing gene therapy; since it can allow us to evaluate the effectiveness of gene delivery noninvasively and spatiotemporally. Due to the unique physiochemical properties of nanomaterials, numerous functional nanoparticles show promise in accomplishing gene delivery with the necessary feature of visualizing the delivery. In this review, recent developments of nanoparticles for molecular imaging guided gene delivery are summarized.

Liu, Gang; Swierczewska, Magdalena; Lee, Seulki; Chen, Xiaoyuan

2010-01-01

252

Computational analysis of tissue-specific gene networks: application to murine retinal functional studies  

PubMed Central

Motivation: The vertebrate retina is a complex neuronal tissue, and its development, normal functioning and response to injury and disease is subject to a variety of genetic factors. To understand better the regulatory and functional relationships between the genes expressed within the retina, we constructed an interactive gene network of the mouse retina by applying a Bayesian statistics approach to information derived from a variety of gene expression, protein–protein interaction and gene ontology annotation databases. Results: The network contains 673 retina-related genes. Most of them are obtained through manual literature-based curation, while the others are the genes preferentially expressed in the retina. These retina-related genes are linked by 3403 potential functional associations in the network. The prediction on the gene functional association using the Bayesian approach outperforms predictions using only one source of information. The network includes five major gene clusters, each enriched in different biological activities. There are several applications to this network. First, we identified ?50 hub genes that are predicted to play particularly important roles in the function of the retina. Some of them are not yet well studied. Second, we can predict novel gene functions using ‘guilt by association’ method. Third, we also predicted novel retinal disease-associated genes based on the network analysis. Availability: To provide easy access to the retinal network, we constructed an interactive web tool, named MoReNet, which is available at http://bioinfo.wilmer.jhu.edu/morenet/ Contact: jiang.qian@jhmi.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Hu, Jianfei; Wan, Jun; Hackler, Laszlo; Zack, Donald J.; Qian, Jiang

2010-01-01

253

Studies of the regulation and function of the Gs? gene Gnas using gene targeting technology  

PubMed Central

The heterotrimeric G protein ?-subunit Gs? is ubiquitously expressed and mediates receptor-stimulated intracellular cAMP generation. Its gene Gnas is a complex imprinted gene which uses alternative promoters and first exons to generate other gene products, including the Gs? isoform XL?s and the chromogranin-like protein NESP55, which are specifically expressed from the paternal and maternal alleles, respectively. Gs? itself is imprinted in a tissue-specific manner, being biallelically expressed in most tissues but paternally silenced in a few tissues. Gene targeting of specific Gnas transcripts demonstrates that heterozygous mutation of Gs? on the maternal (but not the paternal) allele leads to early lethality, perinatal subcutaneous edema, severe obesity, and multihormone resistance, while the paternal mutation leads to only mild obesity and insulin resistance. These parent-of-origin differences are the consequence of tissue-specific Gs? imprinting. XL?s deficiency leads to a perinatal suckling defect and a lean phenotype with increased insulin sensitivity. The opposite metabolic effects of Gs? and XL?s deficiency are associated with decreased and increased sympathetic nervous system activity, respectively. NESP55 deficiency has no metabolic consequences. Other gene targeting experiments have shown Gnas to have two independent imprinting domains controlled by two different imprinting control regions. Tissue-specific Gs? knockout models have identified important roles for Gs? signaling pathways in skeletal development, renal function, and glucose and lipid metabolism. Our present knowledge gleaned from various Gnas gene targeting models are discussed in relation to the pathogenesis of human disorders with mutation or abnormal imprinting of the human ortholog GNAS.

Weinstein, Lee S.; Xie, Tao; Zhang, Qing-Hong; Chen, Min

2007-01-01

254

Family business: the multidrug-resistance related protein (MRP) ABC transporter genes in Arabidopsis thaliana.  

PubMed

Despite the completion of the sequencing of the entire genome of Arabidopsis thaliana (L.) Heynh., the exact determination of each single gene and its function remains an open question. This is especially true for multigene families. An approach that combines analysis of genomic structure, expression data and functional genomics to ascertain the role of the members of the multidrug-resistance-related protein ( MRP) gene family, a subfamily of the ATP-binding cassette (ABC) transporters from Arabidopsis is presented. We used cDNA sequencing and alignment-based re-annotation of genomic sequences to define the exact genic structure of all known AtMRP genes. Analysis of promoter regions suggested different induction conditions even for closely related genes. Expression analysis for the entire gene family confirmed these assumptions. Phylogenetic analysis and determination of segmental duplication in the regions of AtMRP genes revealed that the evolution of the extraordinarily high number of ABC transporter genes in plants cannot solely be explained by polyploidisation during the evolution of the Arabidopsis genome. Interestingly MRP genes from Oryza sativa L. (rice; OsMRP) show very similar genomic structures to those from Arabidopsis. Screening of large populations of T-DNA-mutagenised lines of A. thaliana resulted in the isolation of AtMRP insertion mutants. This work opens the way for the defined analysis of a multigene family of important membrane transporters whose broad variety of functions expands their traditional role as cellular detoxifiers. PMID:12430019

Kolukisaoglu, H Uner; Bovet, Lucien; Klein, Markus; Eggmann, Thomas; Geisler, Markus; Wanke, Dierk; Martinoia, Enrico; Schulz, Burkhard

2002-11-01

255

Quantitative analysis of gene function in the Drosophila embryo.  

PubMed Central

The specific functions of gene products frequently depend on the developmental context in which they are expressed. Thus, studies on gene function will benefit from systems that allow for manipulation of gene expression within model systems where the developmental context is well defined. Here we describe a system that allows for genetically controlled overexpression of any gene of interest under normal physiological conditions in the early Drosophila embryo. This regulated expression is achieved through the use of Drosophila lines that express a maternal mRNA for the yeast transcription factor GAL4. Embryos derived from females that express GAL4 maternally activate GAL4-dependent UAS transgenes at uniform levels throughout the embryo during the blastoderm stage of embryogenesis. The expression levels can be quantitatively manipulated through the use of lines that have different levels of maternal GAL4 activity. Specific phenotypes are produced by expression of a number of different developmental regulators with this system, including genes that normally do not function during Drosophila embryogenesis. Analysis of the response to overexpression of runt provides evidence that this pair-rule segmentation gene has a direct role in repressing transcription of the segment-polarity gene engrailed. The maternal GAL4 system will have applications both for the measurement of gene activity in reverse genetic experiments as well as for the identification of genetic factors that have quantitative effects on gene function in vivo.

Tracey, W D; Ning, X; Klingler, M; Kramer, S G; Gergen, J P

2000-01-01

256

RNA interference can be used to disrupt gene function in tardigrades  

PubMed Central

How morphological diversity arises is a key question in evolutionary developmental biology. As a long-term approach to address this question, we are developing the water bear Hypsibius dujardini (Phylum Tardigrada) as a model system. We expect that using a close relative of two well-studied models, Drosophila (Phylum Arthropoda) and Caenorhabditis elegans (Phylum Nematoda), will facilitate identifying genetic pathways relevant to understanding the evolution of development. Tardigrades are also valuable research subjects for investigating how organisms and biological materials can survive extreme conditions. Methods to disrupt gene activity are essential to each of these efforts, but no such method yet exists for the Phylum Tardigrada. We developed a protocol to disrupt tardigrade gene functions by double-stranded RNA-mediated RNA interference (RNAi). We show that targeting tardigrade homologs of essential developmental genes by RNAi produced embryonic lethality, whereas targeting green fluorescent protein did not. Disruption of gene functions appears to be relatively specific by two criteria: targeting distinct genes resulted in distinct phenotypes that were consistent with predicted gene functions, and by RT-PCR, RNAi reduced the level of a target mRNA and not a control mRNA. These studies represent the first evidence that gene functions can be disrupted by RNAi in the phylum Tardigrada. Our results form a platform for dissecting tardigrade gene functions for understanding the evolution of developmental mechanisms and survival in extreme environments.

Tenlen, Jennifer R.; McCaskill, Shaina; Goldstein, Bob

2012-01-01

257

Systems-wide Chicken DNA Microarrays, Gene Expression Profiling, and Discovery of Functional Genes  

Microsoft Academic Search

The goal of our current consortium project is to launch a new era—functional genomics of poultry— by providing genomic resources (expressed sequence tags (EST) and DNA microarrays) and by examining global gene expression in target tissues of chickens. DNA mi- croarray analysis has been a fruitful strategy for the iden- tification of functional genes in several model organisms (i.e., human,

L. A. Cogburn; X. Wang; W. Carre; L. Rejto; T. E. Porter; S. E. Aggrey; J. Simon

2003-01-01

258

DING proteins: numerous functions, elusive genes, a potential for health.  

PubMed

DING proteins, named after their conserved N-terminus, form an overlooked protein family whose members were generally discovered through serendipity. It is characterized by an unusually high sequence conservation, even between distantly related species, and by an outstanding diversity of activities and ligands. They all share a demonstrated capacity to bind phosphate with high affinity or at least a predicted phosphate-binding site. However, DING protein genes are conspicuously absent from databases. The many novel family members identified in recent years have confirmed that DING proteins are ubiquitous not only in animals and plants but probably also in prokaryotes. At the functional level, there is increasing evidence that they participate in many health-related processes such as cancers as well as bacterial (Pseudomonas) and viral (HIV) infections, by mechanisms that are now beginning to be understood. They thus represent potent targets for the development of novel therapeutic approaches, especially against HIV. The few genomic sequences that are now available are starting to give some clues on why DING protein genes and mRNAs are well conserved and difficult to clone. This could open a new era of research, of both fundamental and applied importance. PMID:23743708

Bernier, François

2013-09-01

259

Screening miRNA and their target genes related to tetralogy of Fallot with microarray.  

PubMed

Our aim is to screen miRNAs and genes related to tetralogy of Fallot and construct a co-expression network based on integrating miRNA and gene microarrays. We downloaded the gene expression profile GSE35490 (miRNA) and GSE35776 (mRNA) of tetralogy of Fallot from the Gene Expression Omnibus database, which includes eight normal and 15 disease samples from infants, and screened differentially expressed miRNAs and genes between normal and disease samples (cut-off: p < 0.05; FDR < 0.05; and log FC > 2 or log FC < -2); in addition, we downloaded human miRNA and their targets, which were collected in the miRNA targets prediction database TargetScan, and selected ones that also appeared in our differentially expressed miRNAs and their predicted targets (score >0.9) and then made a relationship of diff_miRNAs and diff_genes of our results. Finally, we uploaded all the diff_target genes into String, constructed a co-expression network regulated by diff_miRNAs, and performed functional analysis with the software DAVID. Comparing normal and disease lesion tissue, we got 32 and 875 differentially expressed miRNAs and genes, respectively, and found hsa-miR-124 with 34 diff_target genes and hsa-miR-138 with two diff_target genes. Then we constructed a co-expression network that contains 231 pairs of genes. Genes in the network were enriched into 14 function clusters, and the most significant one is protein localisation. We screened the tetralogy of Fallot-related hsa-miR-124 and hsa-miR-138 with their direct and indirect differentially expressed target genes, and found that protein localisation is the significant cause affecting tetralogy of Fallot. Our approach may provide the groundwork for a new therapy approach to treating tetralogy of Fallot. PMID:23680813

Wang, Xian-Min; Zhang, Kui; Li, Yan; Shi, Kun; Liu, Yi-Ling; Yang, Yan-Feng; Fang, Yu; Mao, Meng

2014-06-01

260

Spaceflight effects on T lymphocyte distribution, function and gene expression  

PubMed Central

The immune system is highly sensitive to stressors present during spaceflight. The major emphasis of this study was on the T lymphocytes in C57BL/6NTac mice after return from a 13-day space shuttle mission (STS-118). Spleens and thymuses from flight animals (FLT) and ground controls similarly housed in animal enclosure modules (AEM) were evaluated within 3–6 h after landing. Phytohemagglutinin-induced splenocyte DNA synthesis was significantly reduced in FLT mice when based on both counts per minute and stimulation indexes (P < 0.05). Flow cytometry showed that CD3+ T and CD19+ B cell counts were low in spleens from the FLT group, whereas the number of NK1.1+ natural killer (NK) cells was increased (P < 0.01 for all three populations vs. AEM). The numerical changes resulted in a low percentage of T cells and high percentage of NK cells in FLT animals (P < 0.05). After activation of spleen cells with anti-CD3 monoclonal antibody, interleukin-2 (IL-2) was decreased, but IL-10, interferon-?, and macrophage inflammatory protein-1? were increased in FLT mice (P < 0.05). Analysis of cancer-related genes in the thymus showed that the expression of 30 of 84 genes was significantly affected by flight (P < 0.05). Genes that differed from AEM controls by at least 1.5-fold were Birc5, Figf, Grb2, and Tert (upregulated) and Fos, Ifnb1, Itgb3, Mmp9, Myc, Pdgfb, S100a4, Thbs, and Tnf (downregulated). Collectively, the data show that T cell distribution, function, and gene expression are significantly modified shortly after return from the spaceflight environment.

Gridley, Daila S.; Slater, James M.; Luo-Owen, Xian; Rizvi, Asma; Chapes, Stephen K.; Stodieck, Louis S.; Ferguson, Virginia L.; Pecaut, Michael J.

2009-01-01

261

Manipulation of gene function in Xenopus laevis  

PubMed Central

Xenopus laevis embryos are particularly well suited to address questions requiring either knockdown or overexpression of genes in a tissue-specific fashion during vertebrate embryonic development. These manipulations are achieved by targeted injection of either antisense morpholino oligonucleotides, or synthetic mRNAs, respectively, into the early embryo. Herein we offer detailed protocols describing how to design and perform these experiments successfully, as well as a brief discussion of considerations for performing a microarray analysis in this organism.

Mimoto, Mizuho S.; Christian, Jan L.

2012-01-01

262

Insights into SAGA function during gene expression  

Microsoft Academic Search

Histone modifications are a crucial source of epigenetic control. SAGA (Spt–Ada–Gcn5 acetyltransferase) is a chromatin-modifying complex that contains two distinct enzymatic activities, Gcn5 and Ubp8, through which it acetylates and deubiquitinates histone residues, respectively, thereby enforcing a pattern of modifications that is decisive in regulating gene expression. Here, I discuss the latest contributions to understanding the roles of the SAGA

Susana Rodríguez-Navarro

2009-01-01

263

Identification of brassinosteroid-related genes by means of transcript co-response analyses  

PubMed Central

The comprehensive systems-biology database (CSB.DB) was used to reveal brassinosteroid (BR)-related genes from expression profiles based on co-response analyses. Genes exhibiting simultaneous changes in transcript levels are candidates of common transcriptional regulation. Combining numerous different experiments in data matrices allows ruling out outliers and conditional changes of transcript levels. CSB.DB was queried for transcriptional co-responses with the BR-signalling components BRI1 and BAK1: 301 out of 9694 genes represented in the nasc0271 database showed co-responses with both genes. As expected, these genes comprised pathway-involved genes (e.g. 72 BR-induced genes), because the BRI1 and BAK1 proteins are required for BR-responses. But transcript co-response takes the analysis a step further compared with direct approaches because BR-related non BR-responsive genes were identified. Insights into networks and the functional context of genes are provided, because factors determining expression patterns are reflected in correlations. Our findings demonstrate that transcript co-response analysis presents a valuable resource to uncover common regulatory patterns of genes. Different data matrices in CSB.DB allow examination of specific biological questions. All matrices are publicly available through CSB.DB. This work presents one possible roadmap to use the CSB.DB resources.

Lisso, Janina; Steinhauser, Dirk; Altmann, Thomas; Kopka, Joachim; Mussig, Carsten

2005-01-01

264

Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome[W  

PubMed Central

In each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. In the rice (Oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the Michigan State University rice genome annotation. We have implemented an integrative approach to analyze their duplication/expansion and function. The analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the expansion of hypothetical genes despite their different contribution rates. A total of 3,769 hypothetical genes have been detected from retrogene, tandem, segmental, Pack-MULE, or long terminated direct repeat-related duplication/expansion. The nonsynonymous substitutions per site and synonymous substitutions per site analyses showed that 21.65% of them were still functional, accounting for 7.47% of total hypothetical genes. Global expression analyses have identified 1,672 expressed hypothetical genes. Among them, 415 genes might function in a developmental stage-specific manner. Antisense strand expression and small RNA analyses have demonstrated that a high percentage of these hypothetical genes might play important roles in negatively regulating gene expression. Homologous searches against Arabidopsis (Arabidopsis thaliana), maize (Zea mays), sorghum (Sorghum bicolor), and indica rice genomes suggest that most of the hypothetical genes could be annotated from recently evolved genomic sequences. These data advance the understanding of rice hypothetical genes as being involved in lineage-specific expansion and that they function in a specific developmental stage. Our analyses also provide a valuable means to facilitate the characterization and functional annotation of hypothetical genes in other organisms.

Jiang, Shu-Ye; Christoffels, Alan; Ramamoorthy, Rengasamy; Ramachandran, Srinivasan

2009-01-01

265

Relating Functional Groups to the Periodic Table  

ERIC Educational Resources Information Center

An introduction to organic chemistry functional groups and their ionic variants is presented. Functional groups are ordered by the position of their specific (hetero) atom in the periodic table. Lewis structures are compared with their corresponding condensed formulas. (Contains 5 tables.)

Struyf, Jef

2009-01-01

266

NOISE ROBUST RELATIVE TRANSFER FUNCTION ESTIMATION  

Microsoft Academic Search

Microphone arrays are suitable for a large range of ap- plications. Two important applications are speaker locali - zation and speech enhancement. For both of these the trans- fer functions from one microphone to the other microphones are needed to form potential algorithms for these applica- tions. In this paper we present a new transfer function esti- mator optimized for

M. Schwab; P. Noll; T. Sikora

2006-01-01

267

On the level: IRGM gene function is all about expression.  

PubMed

Crohn disease is a complex, multigenic, chronic inflammatory bowel disease of uncertain etiology. Recent advances in genetics, including high-throughput single-nucleotide polymorphism typing platforms and deep sequencing technologies have begun to shed light upon disease predisposition and pathogenesis. Autophagy is emerging as a key player in both innate and adaptive immunity, as well as tissue homeostasis and development in the gut. Here we describe our recent studies into the Crohn disease-associated Immunity-Related GTPase family, M (IRGM) gene and our discovery of a large risk-conferring upstream deletion. We discuss the effects of this deletion upon expression levels of IRGM alleles and how tissue-specific expression might be affected by the promoter polymorphism. In addition, we comment upon the potential roles of IRGM in autophagy of intracellular pathogens, and the challenges ahead for further elucidating IRGM function. PMID:19029815

Huett, Alan; McCarroll, Steven A; Daly, Mark J; Xavier, Ramnik J

2009-01-01

268

A Graphic Method for Identification of Novel Glioma Related Genes  

PubMed Central

Glioma, as the most common and lethal intracranial tumor, is a serious disease that causes many deaths every year. Good comprehension of the mechanism underlying this disease is very helpful to design effective treatments. However, up to now, the knowledge of this disease is still limited. It is an important step to understand the mechanism underlying this disease by uncovering its related genes. In this study, a graphic method was proposed to identify novel glioma related genes based on known glioma related genes. A weighted graph was constructed according to the protein-protein interaction information retrieved from STRING and the well-known shortest path algorithm was employed to discover novel genes. The following analysis suggests that some of them are related to the biological process of glioma, proving that our method was effective in identifying novel glioma related genes. We hope that the proposed method would be applied to study other diseases and provide useful information to medical workers, thereby designing effective treatments of different diseases.

Gao, Yu-Fei; Yang, Lei; He, Yi-Chun; Li, Li-Peng; Huang, GuaHua; Li, Hai-Peng

2014-01-01

269

Alpha 1 -antitrypsin gene polymorphism related to respiratory system disease  

Microsoft Academic Search

Summary Restriction fragment length polymorphism (RFLP) in the alpha1-antitrypsin gene region was studied in relation to chronic obstructive airway disease (COAD) and pneumoconiosis. Genomic DNA of 122 studied subjects was digested with Hind III restriction endonuclease and hybridized with the alpha1-antitrypsin gene probe. In eight patients with COAD an unusual 10-kb restriction fragment was found hybridizing with the probe. Three

M. Buraczynska; D. Schött; A. J. Hanzlik; B. Höltmann; W. T. Ulmer

1987-01-01

270

Targeting Fungal Genes by Diced siRNAs: A Rapid Tool to Decipher Gene Function in Aspergillus nidulans  

PubMed Central

Background Gene silencing triggered by chemically synthesized small interfering RNAs (siRNAs) has become a powerful tool for deciphering gene function in many eukaryotes. However, prediction and validation of a single siRNA duplex specific to a target gene is often ineffective. RNA interference (RNAi) with synthetic siRNA suffers from lower silencing efficacy, off-target effects and is cost-intensive, especially for functional genomic studies. With the explosion of fungal genomic information, there is an increasing need to analyze gene function in a rapid manner. Therefore, studies were performed in order to investigate the efficacy of gene silencing induced by RNase III-diced-siRNAs (d-siRNA) in model filamentous fungus, Aspergillus nidulans. Methodology/Principal Findings Stable expression of heterologous reporter gene in A. nidulans eases the examination of a new RNAi-induction route. Hence, we have optimized Agrobacterium tumefaciens-mediated transformation (AMT) of A. nidulans for stable expression of sGFP gene. This study demonstrates that the reporter GFP gene stably introduced into A. nidulans can be effectively silenced by treatment of GFP-d-siRNAs. We have shown the down-regulation of two endogenous genes, AnrasA and AnrasB of A. nidulans by d-siRNAs. We have also elucidated the function of an uncharacterized Ras homolog, rasB gene, which was found to be involved in hyphal growth and development. Further, silencing potency of d-siRNA was higher as compared to synthetic siRNA duplex, targeting AnrasA. Silencing was shown to be sequence-specific, since expression profiles of other closely related Ras family genes in d-siRNA treated AnrasA and AnrasB silenced lines exhibited no change in gene expression. Conclusions/Significance We have developed and applied a fast, specific and efficient gene silencing approach for elucidating gene function in A. nidulans using d-siRNAs. We have also optimized an efficient AMT in A. nidulans, which is useful for stable integration of transgenes.

Kalleda, Natarajaswamy; Naorem, Aruna; Manchikatla, Rajam V.

2013-01-01

271

Consequences of recurrent gene flow from crops to wild relatives.  

PubMed Central

Concern about gene flow from crops to wild relatives has become widespread with the increasing cultivation of transgenic crops. Possible consequences of such gene flow include genetic assimilation, wherein crop genes replace wild ones, and demographic swamping, wherein hybrids are less fertile than their wild parents, and wild populations shrink. Using mathematical models of a wild population recurrently receiving pollen from a genetically fixed crop, we find that the conditions for genetic assimilation are not stringent, and progress towards replacement can be fast, even for disfavoured crop genes. Demographic swamping and genetic drift relax the conditions for genetic assimilation and speed progress towards replacement. Genetic assimilation can involve thresholds and hysteresis, such that a small increase in immigration can lead to fixation of a disfavoured crop gene that had been maintained at a moderate frequency, even if the increase in immigration is cancelled before the gene fixes. Demographic swamping can give rise to 'migrational meltdown', such that a small increase in immigration can lead to not only fixation of a disfavoured crop gene but also drastic shrinkage of the wild population. These findings suggest that the spread of crop genes in wild populations should be monitored more closely.

Haygood, Ralph; Ives, Anthony R; Andow, David A

2003-01-01

272

NHR-23 dependent collagen and hedgehog-related genes required for molting  

SciTech Connect

Highlights: {yields} NHR-23 is a critical regulator of nematode development and molting. {yields} The manuscript characterizes the loss-of-function phenotype of an nhr-23 mutant. {yields} Whole genome expression analysis identifies new potential targets of NHR-23. {yields} Hedgehog-related genes are identified as NHR-23 dependent genes. {yields} New link between sterol mediated signaling and regulation by NHR-23 is found. -- Abstract: NHR-23, a conserved member of the nuclear receptor family of transcription factors, is required for normal development in Caenorhabditis elegans where it plays a critical role in growth and molting. In a search for NHR-23 dependent genes, we performed whole genome comparative expression microarrays on both control and nhr-23 inhibited synchronized larvae. Genes that decreased in response to nhr-23 RNAi included several collagen genes. Unexpectedly, several hedgehog-related genes were also down-regulated after nhr-23 RNAi. A homozygous nhr-23 deletion allele was used to confirm the RNAi knockdown phenotypes and the changes in gene expression. Our results indicate that NHR-23 is a critical co-regulator of functionally linked genes involved in growth and molting and reveal evolutionary parallels among the ecdysozoa.

Kouns, Nathaniel A.; Nakielna, Johana; Behensky, Frantisek [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic)] [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic); Krause, Michael W. [Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (United States)] [Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (United States); Kostrouch, Zdenek [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic)] [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic); Kostrouchova, Marta, E-mail: marta.kostrouchova@lf1.cuni.cz [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic)] [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic)

2011-10-07

273

[The analysis of rbcS gene function by post-transcription gene silencing in Nicotiana benthamiana].  

PubMed

A system of virus-induced post-transcriptional gene silencing for studying rbcS gene function was established and optimized using tobacco rattle virus vector and Nicotiana benthamiana as experimental materiaes. The following analyses were conducted: phenotypic characterization of rbcS gene silenced plants, transcription levels of rbcS gene by RT-PCR; protein levels of rbcS by the antibodies of rbcS and rbcL and photosynthetic pigments wntents in rbcS silenced plants by HPLC method. The results showed that the seedlings at 21-24-day-old and Agrobacterium concentration at OD600 = 1-1.5 gave the best results for gene silencing. The expression level of rbcL was very likely regulated by rbcS, and rbcS gene did not relate to the collection of photosynthetic energy. Probability analysis showed that the tobacco rattle virus vector system is a useful and effective technique to study rbcS gene function via post-transcriptional gene silencing. PMID:16018185

Zhou, Xiao-Fu; Ma, Peng-Da; Wang, Ren-Hou; Zhu, Xiao-Juan; Liu, Bao; Wang, Xing-Zhi

2005-06-01

274

An improved chemically inducible gene switch that functions in the monocotyledonous plant sugar cane.  

PubMed

Chemically inducible gene switches can provide precise control over gene expression, enabling more specific analyses of gene function and expanding the plant biotechnology toolkit beyond traditional constitutive expression systems. The alc gene expression system is one of the most promising chemically inducible gene switches in plants because of its potential in both fundamental research and commercial biotechnology applications. However, there are no published reports demonstrating that this versatile gene switch is functional in transgenic monocotyledonous plants, which include some of the most important agricultural crops. We found that the original alc gene switch was ineffective in the monocotyledonous plant sugar cane, and describe a modified alc system that is functional in this globally significant crop. A promoter consisting of tandem copies of the ethanol receptor inverted repeat binding site, in combination with a minimal promoter sequence, was sufficient to give enhanced sensitivity and significantly higher levels of ethanol inducible gene expression. A longer CaMV 35S minimal promoter than was used in the original alc gene switch also substantially improved ethanol inducibility. Treating the roots with ethanol effectively induced the modified alc system in sugar cane leaves and stem, while an aerial spray was relatively ineffective. The extension of this chemically inducible gene expression system to sugar cane opens the door to new opportunities for basic research and crop biotechnology. PMID:24142380

Kinkema, Mark; Geijskes, R Jason; Shand, Kylie; Coleman, Heather D; De Lucca, Paulo C; Palupe, Anthony; Harrison, Mark D; Jepson, Ian; Dale, James L; Sainz, Manuel B

2014-03-01

275

Independent origin of functional MHC class II genes in humans and New World monkeys.  

PubMed

In previous studies, major histocompatibility complex (MHC) class II DP, DQ, and DR families of genes were characterized in different primate species mostly on the basis of their second exon sequences. Resemblances were found between Old World monkey (OWM) and New World monkey (NWM) genes and were interpreted as being the result of transspecies evolution. Subsequent analysis of intron sequences of catarrhine and platyrrhine DRB genes, however, revealed that the amplifiable genes were not, in fact, orthologous. To test other DRB genes and other families of the class II region Southern blot hybridizations were carried out with tamarin genomic DNA using probes specific for the third exons of the tamarin DQA, DQB, DPB, and DRB genes. The hybridizing bands were extracted from the gel and the third exons of the genes were amplified by PCR, cloned, and sequenced. With two exceptions, all NWM class II genes were found to group separately from the human sequences. Only the sequences of one nonfunctional DQB locus appeared to be more closely related to human genes than to other platyrrhine DQB genes. In the DRB family one gene was found that grouped with sheep and strepsirhine DRB sequences and might represent an old gene lineage. To extend the sequences to the second exon, long PCRs were performed on tamarin genomic DNA. This approach was successful for five of the ten third exon sequences. From these data, we conclude that at least the functional MHC class II genes have expanded independently in catarrhines and platyrrhines. PMID:11165710

Kriener, K; O'hUigin, C; Klein, J

2001-01-01

276

Isolation of p53-target genes and their functional analysis.  

PubMed

Mutations of the p53 gene are the most common genetic alterations found in human cancers, and are known to play crucial roles in tumor development and progression. The p53 gene encodes a protein functioning as a transcription factor, and the biological functions of p53 are manifested through the activities of its downstream genes. Identification of these downstream genes involved in the p53-signaling pathway should provide more detailed insight into the molecular mechanisms that mediate tumor-suppressor activities, as well as various responses to cellular stress. We have been attempting to isolate p53-target genes by means of various approaches, including differential display, cDNA microarray analysis, and direct cloning of the p53-binding sequences from human genomic DNA. Here I review our recent work on isolation of p53-target genes and their functional analysis. The physiological functions of p53-target genes include apoptosis (GML, p53AIP1, and STAG1), DNA repair (p53R2), inhibition of angiogenesis (BAI1), re-entry into the cell cycle (p53RFP), oxidative stress (CSR), and determination of cell fate (p53RDL1). PMID:14720320

Nakamura, Yusuke

2004-01-01

277

Pan-metazoan phylogeny of the DMRT gene family: a framework for functional studies.  

PubMed

The family of Doublesex-Mab-3 Related Transcription factors (DMRTs) includes key regulators of sexual differentiation and neurogenesis. To help understand the functional diversification of this gene family, we examined DMRT gene complements from the whole genome sequences and predicted gene models of 32 animal species representing 12 different phyla and from several non-metazoan outgroups. DMRTs are present in all animals except the sponge Amphimedon queenslandica, but are not found in any of the outgroups, indicating that this gene family is specific to animals and has an ancient pre-eumetazoan origin. Our analyses suggest that DMRT genes diversified independently in bilaterian and non-bilaterian animals. Most clades in the DMRT gene tree, including those containing the well-characterized DMRT1 and doublesex genes, have phylogenetically limited distributions. PMID:24903586

Wexler, Judith R; Plachetzki, David C; Kopp, Artyom

2014-06-01

278

Functional gene-set analysis does not support a major role for synaptic function in attention deficit/hyperactivity disorder (ADHD).  

PubMed

Attention Deficit/Hyperactivity Disorder (ADHD) is one of the most common childhood-onset neuropsychiatric disorders. Despite high heritability estimates, genome-wide association studies (GWAS) have failed to find significant genetic associations, likely due to the polygenic character of ADHD. Nevertheless, genetic studies suggested the involvement of several processes important for synaptic function. Therefore, we applied a functional gene-set analysis to formally test whether synaptic functions are associated with ADHD. Gene-set analysis tests the joint effect of multiple genetic variants in groups of functionally related genes. This method provides increased statistical power compared to conventional GWAS. We used data from the Psychiatric Genomics Consortium including 896 ADHD cases and 2455 controls, and 2064 parent-affected offspring trios, providing sufficient statistical power to detect gene sets representing a genotype relative risk of at least 1.17. Although all synaptic genes together showed a significant association with ADHD, this association was not stronger than that of randomly generated gene sets matched for same number of genes. Further analyses showed no association of specific synaptic function categories with ADHD after correction for multiple testing. Given current sample size and gene sets based on current knowledge of genes related to synaptic function, our results do not support a major role for common genetic variants in synaptic genes in the etiology of ADHD. PMID:25055203

Hammerschlag, Anke R; Polderman, Tinca J C; de Leeuw, Christiaan; Tiemeier, Henning; White, Tonya; Smit, August B; Verhage, Matthijs; Posthuma, Danielle

2014-01-01

279

Rapid evolution of sex-related genes in Chlamydomonas.  

PubMed

Biological speciation ultimately results in prezygotic isolation-the inability of incipient species to mate with one another-but little is understood about the selection pressures and genetic changes that generate this outcome. The genus Chlamydomonas comprises numerous species of unicellular green algae, including numerous geographic isolates of the species C. reinhardtii. This diverse collection has allowed us to analyze the evolution of two sex-related genes: the mid gene of C. reinhardtii, which determines whether a gamete is mating-type plus or minus, and the fus1 gene, which dictates a cell surface glycoprotein utilized by C. reinhardtii plus gametes to recognize minus gametes. Low stringency Southern analyses failed to detect any fus1 homologs in other Chlamydomonas species and detected only one mid homolog, documenting that both genes have diverged extensively during the evolution of the lineage. The one mid homolog was found in C. incerta, the species in culture that is most closely related to C. reinhardtii. Its mid gene carries numerous nonsynonymous and synonymous codon changes compared with the C. reinhardtii mid gene. In contrast, very high sequence conservation of both the mid and fus1 sequences is found in natural isolates of C. reinhardtii, indicating that the genes are not free to drift within a species but do diverge dramatically between species. Striking divergence of sex determination and mate recognition genes also has been encountered in a number of other eukaryotic phyla, suggesting that unique, and as yet unidentified, selection pressures act on these classes of genes during the speciation process. PMID:9238029

Ferris, P J; Pavlovic, C; Fabry, S; Goodenough, U W

1997-08-01

280

Expression of the retinoblastoma-related gene Rb2\\/ p130 is downregulated in atypical endometrial hyperplasia and adenocarcinoma  

Microsoft Academic Search

The retinoblastoma-related gene Rb2\\/p130 encodes a protein that is a negative cell-cycle regulator normally expressed in a number of adult tissues. This protein shares many structural and functional features with the product of the retinoblastoma gene, one of the best-studied tumor-suppressor genes, and plays a fundamental role in growth control. The Rb2\\/p130 gene product associates with specific members of the

Tommaso Susini; Daniela Massi; Milena Paglierani; Valeria Masciullo; Giovanni Scambia; Antonio Giordano; Gianni Amunni; Giambattista Massi; Gian Luigi Taddei

2001-01-01

281

Age-related macular degeneration: Evidence of a major gene  

SciTech Connect

Age-related macular degeneration is a major cause of blindness in developing countries. It remains a very poorly understood disorder. Although environmental and genetic factors have been implicated in its pathogenesis, none have been firmly implicated. The purpose of this study was to use pedigree analysis to evaluate the possible role of a major gene as a determinant of familial aggregation. Information was collected regarding occupation, smoking, sun exposure, associated medical problems and family history. 50 probands with age-related macular degeneration (ARMD) and 39 age, race and sex-matched controls were included in the study. In the ARMD group 15/50 (30%) of probands reported a positive family history; 22 out of 222 first degree relatives over age 60 were reported to be affected. In the control groups, none of the 138 first degree relatives over age 50 had a history of ARMD. This difference is statistically significant (p = 0.0003), indicating that genetic factors may play an important role in the pathogenesis of ARMD. In the ARMD group more siblings as compared to parents (16/127 vs. 5/82) were affected. 5/50 (10%) of the ARMD probands also gave a history of a second degree relative affected with ARMD, compared to none known among the relatives of controls. Data from 50 pedigrees were analyzed by complex segregation analysis under a class A regressive logistic model using the REGD program implemented in the SAGE package. Preliminary results allow rejection of a polygenic model and suggest there is a major gene for ARMD in these families. The inheritance model most compatible with the observed familial aggregation is autosomal recessive. In conclusion, these results are suggestive of a major gene effect in the etiology of ARMD. Identification of a major gene effect is a first step to further pursue linkage analysis and to search for the gene(s) involved in the causation of ARMD.

Bhatt, S.; Warren, C.; Yang, H. [UCLA School of Medicine, Los Angeles, CA (United States)] [and others

1994-09-01

282

The use of gene clusters to infer functional coupling  

PubMed Central

Previously, we presented evidence that it is possible to predict functional coupling between genes based on conservation of gene clusters between genomes. With the rapid increase in the availability of prokaryotic sequence data, it has become possible to verify and apply the technique. In this paper, we extend our characterization of the parameters that determine the utility of the approach, and we generalize the approach in a way that supports detection of common classes of functionally coupled genes (e.g., transport and signal transduction clusters). Now that the analysis includes over 30 complete or nearly complete genomes, it has become clear that this approach will play a significant role in supporting efforts to assign functionality to the remaining uncharacterized genes in sequenced genomes.

Overbeek, Ross; Fonstein, Michael; D'Souza, Mark; Pusch, Gordon D.; Maltsev, Natalia

1999-01-01

283

Evolution, functional divergence and conserved exon-intron structure of bHLH/PAS gene family.  

PubMed

bHLH/PAS genes encode a family of basic helix-loop-helix (bHLH) transcription factors with bHLH, PAS and PAS_3 domain. bHLH/PAS genes are involved in many essential physiological and developmental processes, such as hypoxic response neural development, the circadian clock, and learning ability. Despite their important functions, the origin and evolution of this bHLH/PAS gene family has yet to be elucidated. In this study, we aim to explore the origin, evolution, gene structure conservation of this gene family and provide a model to analyze the evolution of other gene families. Our results show that genes of the bHLH/PAS family only exist in metazoans. They may have originated from the common ancestor of metazoans and expanded into vertebrates. We identified bHLH/PAS genes in more than ten species representing the main lineages and constructed the phylogenetic trees (Beyasian, ML and NJ) to classify them into three groups. The exon-intron structure analysis revealed that a relatively conserved "1001-0210" eight-exon structure exists in most groups and lineages. In addition, we found the exon fusion pattern in several groups in this conserved eight-exon structure. Further analysis indicated that bHLH/PAS protein paralogs evolved from several gene duplication events followed by functional divergence and purifying selection. We presented a phylogenetic model to describe the evolutionary history of the exon structures of bHLH/PAS genes. Taken together, our study revealed the evolutionary model, functional divergence and gene structure conservation of bHLH/PAS genes. These findings provide clues for the functional and evolutionary mechanism of bHLH/PAS genes. PMID:24202550

Yan, Jun; Ma, Zhaowu; Xu, Xiaopeng; Guo, An-Yuan

2014-02-01

284

Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network.  

PubMed

One of the most important and challenging problems in biomedicine and genomics is how to identify the disease genes. In this study, we developed a computational method to identify colorectal cancer-related genes based on (i) the gene expression profiles, and (ii) the shortest path analysis of functional protein association networks. The former has been used to select differentially expressed genes as disease genes for quite a long time, while the latter has been widely used to study the mechanism of diseases. With the existing protein-protein interaction data from STRING (Search Tool for the Retrieval of Interacting Genes), a weighted functional protein association network was constructed. By means of the mRMR (Maximum Relevance Minimum Redundancy) approach, six genes were identified that can distinguish the colorectal tumors and normal adjacent colonic tissues from their gene expression profiles. Meanwhile, according to the shortest path approach, we further found an additional 35 genes, of which some have been reported to be relevant to colorectal cancer and some are very likely to be relevant to it. Interestingly, the genes we identified from both the gene expression profiles and the functional protein association network have more cancer genes than the genes identified from the gene expression profiles alone. Besides, these genes also had greater functional similarity with the reported colorectal cancer genes than the genes identified from the gene expression profiles alone. All these indicate that our method as presented in this paper is quite promising. The method may become a useful tool, or at least plays a complementary role to the existing method, for identifying colorectal cancer genes. It has not escaped our notice that the method can be applied to identify the genes of other diseases as well. PMID:22496748

Li, Bi-Qing; Huang, Tao; Liu, Lei; Cai, Yu-Dong; Chou, Kuo-Chen

2012-01-01

285

Identification of an Orphan Receptor Gene as a Type 1 Calcitonin Gene-Related Peptide Receptor  

Microsoft Academic Search

Calcitonin gene-related peptide (CGRP) is a 37 residue neuropeptide that is distantly related to adrenomedullin, We have recently reported the cloning and expression of an adrenomedullin receptor which is ? 30% homologous to the canine orphan receptor RDC-1. Therefore we tested the hypothesis that RDC-1 was a CGRP receptor. The RDC-1 gene was expressed in COS-7 cells and showed a

S. Kapas; A. J. L. Clark

1995-01-01

286

Functional Conservation of Gsdma Cluster Genes Specifically Duplicated in the Mouse Genome  

PubMed Central

Mouse Gasdermin A3 (Gsdma3) is the causative gene for dominant skin mutations exhibiting alopecia. Mouse has two other Gsdma3-related genes, Gsdma and Gsdma2, whereas human and rat have only one related gene. To date, no skin mutation has been reported for human GSDMA and rat Gsdma as well as mouse Gsdma and Gsdma2. Therefore, it is possible that only Gsdma3 has gain-of-function type mutations to cause dominant skin phenotype. To elucidate functional divergence among the Gsdma-related genes in mice, and to infer the function of the human and rat orthologs, we examined in vivo function of mouse Gsdma by generating Gsdma knockout mice and transgenic mice that overexpress wild-type Gsdma or Gsdma harboring a point mutation (Alanine339Threonine). The Gsdma knockout mice shows no visible phenotype, indicating that Gsdma is not essential for differentiation of epidermal cells and maintenance of the hair cycle, and that Gsdma is expressed specifically both in the inner root sheath of hair follicles and in suprabasal cell layers, whereas Gsdma3 is expressed only in suprabasal layers. By contrast, both types of the transgenic mice exhibited epidermal hyperplasia resembling the Gsdma3 mutations, although the phenotype depended on the genetic background. These results indicate that the mouse Gsdma and Gsdma3 genes share common function to regulate epithelial maintenance and/or homeostasis, and suggest that the function of human GSDMA and rat Gsdma, which are orthologs of mouse Gsdma, is conserved as well.

Tanaka, Shigekazu; Mizushina, Youichi; Kato, Yoriko; Tamura, Masaru; Shiroishi, Toshihiko

2013-01-01

287

Learning Gene Functional Classifications from Multiple Data Types  

Microsoft Academic Search

In our attempts to understand cellular function at the molecular level, we must be able to synthesize information from disparate types of genomic data. We consider the problem of inferring gene functional classi é cations from a heterogeneous data set consisting of DNA microarray expression measurements and phylogenetic pro é les from whole-genome sequence comparisons. We demonstrate the application of

Paul Pavlidis; Jason Weston; Jinsong Cai; William Stafford Noble

2002-01-01

288

Genome-wide identification and functional analyses of calmodulin genes in Solanaceous species  

PubMed Central

Background Calmodulin (CaM) is a major calcium sensor in all eukaryotes. It binds calcium and modulates the activity of a wide range of downstream proteins in response to calcium signals. However, little is known about the CaM gene family in Solanaceous species, including the economically important species, tomato (Solanum lycopersicum), and the gene silencing model plant, Nicotiana benthamiana. Moreover, the potential function of CaM in plant disease resistance remains largely unclear. Results We performed genome-wide identification of CaM gene families in Solanaceous species. Employing bioinformatics approaches, multiple full-length CaM genes were identified from tomato, N. benthamiana and potato (S. tuberosum) genomes, with tomato having 6 CaM genes, N. benthamiana having 7 CaM genes, and potato having 4 CaM genes. Sequence comparison analyses showed that three tomato genes, SlCaM3/4/5, two potato genes StCaM2/3, and two sets of N. benthamiana genes, NbCaM1/2/3/4 and NbCaM5/6, encode identical CaM proteins, yet the genes contain different intron/exon organization and are located on different chromosomes. Further sequence comparisons and gene structural and phylogenetic analyses reveal that Solanaceous species gained a new group of CaM genes during evolution. These new CaM genes are unusual in that they contain three introns in contrast to only a single intron typical of known CaM genes in plants. The tomato CaM (SlCaM) genes were found to be expressed in all organs. Prediction of cis-acting elements in 5' upstream sequences and expression analyses demonstrated that SlCaM genes have potential to be highly responsive to a variety of biotic and abiotic stimuli. Additionally, silencing of SlCaM2 and SlCaM6 altered expression of a set of signaling and defense-related genes and resulted in significantly lower resistance to Tobacco rattle virus and the oomycete pathogen, Pythium aphanidermatum. Conclusions The CaM gene families in the Solanaceous species tomato, N. benthamiana and potato were identified through a genome-wide analysis. All three plant species harbor a small set of genes that encode identical CaM proteins, which may manifest a strategy of plants to retain redundancy or enhanced quantitative gene function. In addition, Solanaceous species have evolved one new group of CaM genes during evolution. CaM genes play important roles in plant disease resistance to a variety of pathogens.

2013-01-01

289

Molecular approaches towards the isolation of sleep-related genes.  

PubMed

Behavioural genetics is one of the most enticing fields in modern biology. Owing to straightforward and semiautomated techniques that can be used to measure locomotor activity, circadian rhythmicity is perhaps the best studied behaviour in animals. Thus, during the past decade, five essential circadian clock genes have been isolated in Drosophila, and homologous counterparts for all of these genes have also been found in mammals. As the sleep-wake cycle is under the control of the circadian clock, these circadian master genes are expected to influence sleeping behaviour. However, different vigilance states are regulated by additional mechanisms that also have a genetic basis. In this article we discuss molecular approaches that may prove useful in the search for sleep-related genes. PMID:10389100

Schibler, U; Tafti, M

1999-06-01

290

Calreticulin: one protein, one gene, many functions.  

PubMed Central

The endoplasmic reticulum (ER) plays a critical role in the synthesis and chaperoning of membrane-associated and secreted proteins. The membrane is also an important site of Ca(2+) storage and release. Calreticulin is a unique ER luminal resident protein. The protein affects many cellular functions, both in the ER lumen and outside of the ER environment. In the ER lumen, calreticulin performs two major functions: chaperoning and regulation of Ca(2+) homoeostasis. Calreticulin is a highly versatile lectin-like chaperone, and it participates during the synthesis of a variety of molecules, including ion channels, surface receptors, integrins and transporters. The protein also affects intracellular Ca(2+) homoeostasis by modulation of ER Ca(2+) storage and transport. Studies on the cell biology of calreticulin revealed that the ER membrane is a very dynamic intracellular compartment affecting many aspects of cell physiology.

Michalak, M; Corbett, E F; Mesaeli, N; Nakamura, K; Opas, M

1999-01-01

291

Functional analysis of fungal polyketide biosynthesis genes  

Microsoft Academic Search

Fungal polyketides have huge structural diversity from simple aromatics to highly modified complex reduced-type compounds. Despite such diversty, single modular iterative type I polyketide synthases (iPKSs) are responsible for their carbon skeleton construction. Using heterologous expression systems, we have studied on ATX, a 6-methylsalicylic acid synthase from Aspergillus terreus as a model iPKS. In addition, iPKS functions involved in fungal

Isao Fujii

2010-01-01

292

Identification of programmed cell death related genes in bamboo.  

PubMed

The event of bamboo flowering and subsequent death of bamboo cells, a rare phenomenon is an interesting model to study gene expression/function in the context of the programmed cell death (PCD) in plant. To identify genes involved in autolytic cell death in bamboo (Bambusa arundinacea/Bambusa bambos Voss), a suppressive subtractive cDNA hybridization (SSH) was performed between cDNA isolated from control (healthy), as driver and test internodal tissue (45days after setting of seeds), as tester. In-silico data revealed that 82% of total ESTs (231) were non-significant (unidentified proteins) while remaining ESTs were classified as protein with known/predicted function/s. Among these, net distribution and differential expression patterns of 11 important B. arundinacea PCD specific ESTs were studied using RNA slot-blot, qRT-PCR and semi-quantitative RT. In-situ localization of mRNA-transcripts for selected bamboo PCD-specific ESTs namely V2Ba48 (Aldehyde dehydrogenase 2) and V2Ba19 (Glycogen phosphorylase) were detected using digoxigenin-labeled corresponding anti-sense RNA probes employing Confocal Laser Scanning Microscope (CLSM). Differential expression-kinetics of the aforementioned genes were confirmed during the progress of PCD after setting of seeds. Global appearance of V2Ba48, V2Ba19, V2Ba95 (Ubiquitin thioesterase) and V2Ba89 (Nebulin isoform 2) genes were identified in monocot (Oryza sativa) and dicots (Arabidopsis thaliana and Nicotiana tabacum). This is the first report on systematic analysis of genes involved in death of bamboo cells that may provide critical information regarding key metabolic/regulatory genes involved in plant PCD. PMID:22326529

Rai, Vineeta; Dey, Nrisingha

2012-04-15

293

Functional Characterization of the dRYBP Gene in Drosophila  

PubMed Central

The Drosophila dRYBP gene has been described to function as a Polycomb-dependent transcriptional repressor. To determine the in vivo function of the dRYBP gene, we have generated mutations and analyzed the associated phenotypes. Homozygous null mutants die progressively throughout development and present phenotypes variable both in their penetrance and in their expressivity, including disrupted oogenesis, a disorganized pattern of the syncytial nuclear divisions, defects in pattern formation, and decreased wing size. Although dRYBP mutations do not show the homeotic-like phenotypes typical of mutations in the PcG and trxG genes, they enhance the phenotypes of mutations of either the Sex comb extra gene (PcG) or the trithorax gene (trxG). Finally, the dRYBP protein interacts physically with the Sex comb extra and the Pleiohomeotic proteins, and the homeotic-like phenotypes produced by the high levels of the dRYBP protein are mediated through its C-terminal domain. Our results indicate that the dRYBP gene functions in the control of cell identity together with the PcG/trxG proteins. Furthermore, they also indicate that dRYBP participates in the control of cell proliferation and cell differentiation and we propose that its functional requirement may well depend on the robustness of the animal.

Gonzalez, Inma; Aparicio, Ricardo; Busturia, Ana

2008-01-01

294

Generation of a preliminary bovine gene atlas, using expression clustering to annotate gene function  

Microsoft Academic Search

Genes whose products function in a common biologi- cal process are often co-regulated. When regulation occurs at the transcriptional level, co-expressed genes can be detected globally by expression arrays or by sequencing non-normalized cDNA li- braries. We examined bovine gene expression in 27 tissues using non-normalized cDNA library sequencing. Contigs were generated from expressed sequence tags whose sequences overlapped. Contigs

O. M. Keane; N. Maqbool; A. F. McCulloch; J. C. McEwan; K. G. Dodds

2009-01-01

295

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

PubMed Central

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.

2011-01-01

296

Mapping of a family of heterogeneous nuclear ribonucleoprotein [hnRNP] genes related to the fragile X gene - fmr1  

SciTech Connect

RNA binding proteins are involved in a wide range of cellular processes in the nucleus and cytoplasm including regulation of pre-mRNA splicing, mRNA stability, translation efficiency and the transport of RNAs between the nucleus and the cytoplasm. The gene involved in the Fragile X syndrome encodes a protein that contains two types of sequence motifs found in RNA binding proteins: an RGG box as seen in hnRNP U and two KH (hnRNP K homology) domains. The FMR1 gene product binds RNA in vitro and a missense mutation in a highly conserved isoleucine residue in the KH domain of fmr1 impairs RNA binding, demonstrating the importance of the KH domain in the RNA binding ability of FMR1. We have identified a new gene, fxr1 (fmr1 cross-hybridizing related), that bears striking homology to the fmr1 gene. The two genes are highly homologous at the amino acid level. Fxr1 has two KH domains, as does fmr1. This suggests that fmr1 may be only one of a family of RNA binding proteins that have yet to be characterized, but are potentially important for normal cellular function. We are systematically mapping hnRNP genes related to fmrl as a first step towards investigating the role of these proteins in human disease states. We have mapped fxr1 to chromosome 12 using a somatic cell hybrid panel and are currently using YACs containing fxr1 to perform FISH to further pinpoint the exact location of fxr1. HnRNP K and U share common sequence motifs with fmr1 and fxr1 that seem to be important for RNA binding function. We are also mapping these genes by both somatic cell hybrid panels and by FISH with the corresponding YACs.

Srinivasan, S.; Siomi, M.; Siomi, H. [Univ. of Pennsylvania, Philadelphia, PA (United States)] [and others

1994-09-01

297

Involvement of Trichoderma trichothecenes in the biocontrol activity and induction of plant defense-related genes.  

PubMed

Trichoderma species produce trichothecenes, most notably trichodermin and harzianum A (HA), by a biosynthetic pathway in which several of the involved proteins have significant differences in functionality compared to their Fusarium orthologues. In addition, the genes encoding these proteins show a genomic organization differing from that of the Fusarium tri clusters. Here we describe the isolation of Trichoderma arundinaceum IBT 40837 transformants which have a disrupted or silenced tri4 gene, a gene encoding a cytochrome P450 monooxygenase that oxygenates trichodiene to give rise to isotrichodiol, and the effect of tri4 gene disruption and silencing on the expression of other tri genes. Our results indicate that the tri4 gene disruption resulted in a reduced antifungal activity against Botrytis cinerea and Rhizoctonia solani and also in a reduced ability to induce the expression of tomato plant defense-related genes belonging to the salicylic acid (SA) and jasmonate (JA) pathways against B. cinerea, in comparison to the wild-type strain, indicating that HA plays an important function in the sensitization of Trichoderma-pretreated plants against this fungal pathogen. Additionally, the effect of the interaction of T. arundinaceum with B. cinerea or R. solani and with tomato seedlings on the expressions of the tri genes was studied. PMID:22562989

Malmierca, M G; Cardoza, R E; Alexander, N J; McCormick, S P; Hermosa, R; Monte, E; Gutiérrez, S

2012-07-01

298

COMT but not serotonin-related genes modulates the influence of childhood abuse on anger traits  

PubMed Central

Anger-related traits are regulated by genes as well as early environmental factors. Both childhood maltreatment and genes underlie vulnerability to suicidal behaviors, possibly by affecting the constitution of intermediate phenotypes such as anger traits. The aim of this study was to test the interaction between nine candidate genes and childhood maltreatment in modulating anger-related traits in 875 adult suicide attempters. The State-Trait Anger Expression Inventory and the Childhood Trauma Questionnaire were used to examine anger traits and traumatic childhood experiences respectively. The functional polymorphism of the catecholamine-O-methyl-transferase (COMT) gene Val158Met significantly modulated the association between sexual abuse and anger-trait level (p=0.001). In the presence of sexual abuse, individuals carrying the Val high-activity allele displayed greater disposition towards anger than individuals homozygous for the Met allele (p=0.0003). Notably, none of the serotonin-related genes influenced the effect of childhood abuse on anger traits. The results of the present study suggest that anger-trait level is influenced by the interaction between childhood abuse and functional polymorphism in the COMT gene. This study was carried out in a population with a high frequency of childhood abuse and a high disposition towards anger, and replication in healthy subjects is needed.

Perroud, Nader; Jaussent, Isabelle; Guillaume, Sebastien; Bellivier, Frank; Baud, Patrick; Jollant, Fabrice; Leboyer, Marion; Lewis, Cathryn; Malafosse, Alain; Courtet, Philippe

2010-01-01

299

GLUTAMATE-RELATED GENE EXPRESSION CHANGES WITH AGE IN THE MOUSE AUDITORY MIDBRAIN  

PubMed Central

Glutamate is the main excitatory neurotransmitter in both the peripheral and central auditory systems. Changes of glutamate and glutamate-related genes with age may be an important factor in the pathogenesis of age-related hearing loss - presbycusis. In this study, changes in glutamate-related mRNA gene expression in the CBA mouse inferior colliculus with age and hearing loss were examined and correlations were sought between these changes and functional hearing measures, such as the auditory brainstem response (ABR) and distortion product otoacoustic emissions (DPOAEs). Gene expression of 68 glutamate-related genes was investigated using both genechip microarray and real-time PCR (qPCR) molecular techniques for four different age/hearing loss CBA mouse subject groups. Two genes showed consistent differences between groups for both the genechip and qPCR. Pyrroline-5-carboxylate synthetase enzyme (Pycs) showed down-regulation with age and a high-affinity glutamate transporter (Slc1a3) showed up-regulation with age and hearing loss. Since Pycs plays a role in converting glutamate to proline, its deficiency in old age may lead to both glutamate increases and proline deficiencies in the auditory midbrain, playing a role in the subsequent inducement of glutamate toxicity and loss of proline neuroprotective effects. The up-regulation of Slc1a3 gene expression may reflect a cellular compensatory mechanism to protect against age-related glutamate or calcium excitoxicity.

Tadros, Sherif F.; D'Souza, Mary; Zettel, Martha L.; Zhu, XiaoXia; Frisina, Robert D.

2007-01-01

300

Functional epigenetic approach identifies frequently methylated genes in Ewing sarcoma.  

PubMed

Using a candidate gene approach we recently identified frequent methylation of the RASSF2 gene associated with poor overall survival in Ewing sarcoma (ES). To identify effective biomarkers in ES on a genome-wide scale, we used a functionally proven epigenetic approach, in which gene expression was induced in ES cell lines by treatment with a demethylating agent followed by hybridization onto high density gene expression microarrays. After following a strict selection criterion, 34 genes were selected for expression and methylation analysis in ES cell lines and primary ES. Eight genes (CTHRC1, DNAJA4, ECHDC2, NEFH, NPTX2, PHF11, RARRES2, TSGA14) showed methylation frequencies of>20% in ES tumors (range 24-71%), these genes were expressed in human bone marrow derived mesenchymal stem cells (hBMSC) and hypermethylation was associated with transcriptional silencing. Methylation of NPTX2 or PHF11 was associated with poorer prognosis in ES. In addition, six of the above genes also showed methylation frequency of>20% (range 36-50%) in osteosarcomas. Identification of these genes may provide insights into bone cancer tumorigenesis and development of epigenetic biomarkers for prognosis and detection of these rare tumor types. PMID:24005033

Alholle, Abdullah; Brini, Anna T; Gharanei, Seley; Vaiyapuri, Sumathi; Arrigoni, Elena; Dallol, Ashraf; Gentle, Dean; Kishida, Takeshi; Hiruma, Toru; Avigad, Smadar; Grimer, Robert; Maher, Eamonn R; Latif, Farida

2013-11-01

301

A completely monotone function related to the Gamma function  

NASA Astrophysics Data System (ADS)

We show that the reciprocal of the functionis a Stieltjes transform. As a corollary we obtain that the derivative of f is completely monotone, in the sense that (-1)n-1f(n)(x)[greater-or-equal, slanted]0 for all n[greater-or-equal, slanted]1 and all x>0. This answers a question raised by Dimitar Dimitrov at the Fifth International Symposium on Orthogonal Polynomials, Special Functions and Applications held in Patras in September 1999. To prove the result we examine the imaginary part of 1/f in the upper half-plane, in particular close to the negative real axis, where Stirling's formula is not valid.

Berg, Christian; Pedersen, Henrik L.

2001-08-01

302

Intra-relation reconstruction from inter-relation: miRNA to gene expression  

PubMed Central

Background In computational biology, a novel knowledge has been obtained mostly by identifying 'intra-relation,' the relation between entities on a specific biological level such as from gene expression or from microRNA (miRNA) and many such researches have been successful. However, intra-relations are not fully explaining complex cancer mechanisms because the inter-relation information between different levels of genomic data is missing, e.g. miRNA and its target genes. The 'inter-relation' between different levels of genomic data can be constructed from biological experimental data as well as genomic knowledge. Methods Previously, we have proposed a graph-based framework that integrates with multi-layers of genomic data, copy number alteration, DNA methylation, gene expression, and miRNA expression, for the cancer clinical outcome prediction. However, the limitation of previous work was that we integrated with multi-layers of genomic data without considering of inter-relationship information between genomic features. In this paper, we propose a new integrative framework that combines genomic dataset from gene expression and genomic knowledge from inter-relation between miRNA and gene expression for the clinical outcome prediction as a pilot study. Results In order to demonstrate the validity of the proposed method, the prediction of short-term/long-term survival for 82 patients in glioblastoma multiforme (GBM) was adopted as a base task. Based on our results, the accuracy of our predictive model increases because of incorporation of information fused over genomic dataset from gene expression and genomic knowledge from inter-relation between miRNA and gene expression. Conclusions In the present study, the intra-relation of gene expression was reconstructed from inter-relation between miRNA and gene expression for prediction of short-term/long-term survival of GBM patients. Our finding suggests that the utilization of external knowledge representing miRNA-mediated regulation of gene expression is substantially useful for elucidating the cancer phenotype.

2013-01-01

303

Functional Interactions between Unlinked Muscle Genes within Haploinsufficient Regions of the Drosophila Genome  

PubMed Central

Mutations in 13 genes affecting muscle development in Drosophila have been examined in pairwise combinations for evidence of genetic interactions. Heterozygous combinations of mutations in five genes, including the gene coding for myosin heavy chain, result in more severe phenotypes than respective single heterozygous mutant controls. The various mutant interactions include examples showing allele-specific intergenic interactions, gene specific interactions, and allele-specific intragenic complementations, suggesting that some interactions result from the manner in which mutant gene products associate. Interactions that result from alterations in ``+'' gene copy number were also uncovered, suggesting that normal myofibril development requires that the relative amounts of respective gene products produced be tightly regulated. The importance of the latter parameter is substantiated by the finding that all five interacting loci map to disperse haploinsufficient or haplolethal regions of the genome. The implications of the present findings are discussed in relation to pursuing the phenomena involving genetic interactions to identify new genes encoding interacting myofibrillar proteins, to examine the nature of intermolecular interactions in mutant and normal development and to decipher the quantitative and temporal regulation of a large family of functionally related gene products.

Homyk-Jr., T.; Emerson-Jr., C. P.

1988-01-01

304

The prediction of candidate genes for cervix related cancer through gene ontology and graph theoretical approach.  

PubMed

With rapidly changing technology, prediction of candidate genes has become an indispensable task in recent years mainly in the field of biological research. The empirical methods for candidate gene prioritization that succors to explore the potential pathway between genetic determinants and complex diseases are highly cumbersome and labor intensive. In such a scenario predicting potential targets for a disease state through in silico approaches are of researcher's interest. The prodigious availability of protein interaction data coupled with gene annotation renders an ease in the accurate determination of disease specific candidate genes. In our work we have prioritized the cervix related cancer candidate genes by employing Csaba Ortutay and his co-workers approach of identifying the candidate genes through graph theoretical centrality measures and gene ontology. With the advantage of the human protein interaction data, cervical cancer gene sets and the ontological terms, we were able to predict 15 novel candidates for cervical carcinogenesis. The disease relevance of the anticipated candidate genes was corroborated through a literature survey. Also the presence of the drugs for these candidates was detected through Therapeutic Target Database (TTD) and DrugMap Central (DMC) which affirms that they may be endowed as potential drug targets for cervical cancer. PMID:24647578

Hindumathi, V; Kranthi, T; Rao, S B; Manimaran, P

2014-06-01

305

Main Functions and Taxonomic Distribution of Virulence Genes in Brucella melitensis 16 M  

PubMed Central

Many virulence genes have been detected in attenuated mutants of Brucella melitensis 16 M; nevertheless, a complete report of these genes, including the main Cluster of Orthologous Groups (COG) represented as well as the taxonomical distribution among all complete bacterial and archaeal genomes, has not been analyzed. In this work a total of 160 virulence genes that have been reported in attenuated mutants in B. melitensis were included and analyzed. Additionally, we obtained 250 B. melitensis randomly selected genes as a reference group for the taxonomical comparisons. The COGs and the taxonomical distribution profile for 789 nonredundant bacterial and archaeal genomes were obtained and compared with the whole-genome COG distribution and with the 250 randomly selected genes, respectively. The main COGs associated with virulence genes corresponded to the following: intracellular trafficking, secretion and vesicular transport (U); cell motility (N); nucleotide transport and metabolism (F); transcription (K); and cell wall/membrane/envelope biogenesis (M). In addition, we found that virulence genes presented a higher proportion of orthologs in the Euryarchaeota and Proteobacteria phyla, with a significant decrease in Chlamydiae, Bacteroidetes, Tenericutes, Firmicutes and Thermotogae. In conclusion, we found that genes related to specific functions are more relevant to B. melitensis virulence, with the COG U the most significant. Additionally, the taxonomical distribution of virulence genes highlights the importance of these genes in the related Proteobacteria, being less relevant in distant groups of organisms with the exception of Euryarchaeota.

Brambila-Tapia, Aniel Jessica Leticia; Armenta-Medina, Dagoberto; Rivera-Gomez, Nancy; Perez-Rueda, Ernesto

2014-01-01

306

Differential expression of apoptosis-related genes in the cochlea of noise-exposed rats  

PubMed Central

Exposure to intense noise induces apoptosis in hair cells in the cochlea. To identify the molecular changes associated with noise-induced apoptosis, we used quantitative real-time PCR to evaluate the changes in 84 apoptosis related genes in cochlear samples from the sensory epithelium and lateral wall. Sprague Dawley rats exposed to a continuous noise at 115 dB SPL for 2 h. The exposure caused a 40–60 dB threshold shift 4 h post-exposure that decreased to 20–30 dB 7 days post-exposure. These functional changes were associated with apoptotic markers including nuclear condensation and fragmentation and TUNEL staining. Immediately after the noise exposure, 12 genes were downregulated, whereas only one gene (Traf4) was upregulated. At 4 h post-exposure, 8 genes were upregulated; 3 (Tnrsf1a, Tnfrsf1b, Tnfrst5) belonged to the Tnfrsf family, 3 (Bir3, Mcl1 and Prok2) have anti-apoptotic properties and 1 (Gadd45a) is a target of p53. At 7 d post-exposure, all the upregulated genes returned to pre-noise levels. Interestingly, the normal control cochlea had high constitutive levels of several apoptosis-related genes. These constitutively expressed genes, together with the inducible genes, may participate in the induction of cochlear apoptotic activity.

Hu, Bo Hua; Cai, Qunfeng; Manohar, Senthilvelan; Jiang, Haiyan; Ding, Dalian; Coling, Donald E.; Zheng, Guiliang; Salvi, Richard

2009-01-01

307

Global Properties and Functional Complexity of Human Gene Regulatory Variation  

PubMed Central

Identification and functional interpretation of gene regulatory variants is a major focus of modern genomics. The application of genetic mapping to molecular and cellular traits has enabled the detection of regulatory variation on genome-wide scales and revealed an enormous diversity of regulatory architecture in humans and other species. In this review I summarise the insights gained and questions raised by a decade of genetic mapping of gene expression variation. I discuss recent extensions of this approach using alternative molecular phenotypes that have revealed some of the biological mechanisms that drive gene expression variation between individuals. Finally, I highlight outstanding problems and future directions for development.

Gaffney, Daniel J.

2013-01-01

308

Breaking restricted taxonomic functionality by dual resistance genes  

PubMed Central

NB-LRR-type disease resistance (R) genes have been used in traditional breeding programs for crop protection. However, functional transfer of NB-LRR-type R genes to plants in taxonomically distinct families to establish pathogen resistance has not been successful. Here we demonstrate that a pair of Arabidopsis (Brassicaceae) NB-LRR-type R genes, RPS4 and RRS1, properly function in two other Brassicaceae, Brassica rapa and B. napus, but also in two Solanaceae, Nicotiana benthamiana and tomato (Solanum lycopersicum). The solanaceous plants transformed with RPS4/RRS1 confer bacterial effector-specific immunity responses. Furthermore, RPS4 and RRS1, which confer resistance to a fungal pathogen Colletotrichum higginsianum in Brassicaceae, also protect against Colletotrichum orbiculare in cucumber (Cucurbitaceae). Thus the successful transfer of two R genes at the family level overcomes restricted taxonomic functionality. This implies that the downstream components of R genes must be highly conserved and interfamily utilization of R genes can be a powerful strategy to combat pathogens.

Narusaka, Mari; Kubo, Yasuyuki; Hatakeyama, Katsunori; Imamura, Jun; Ezura, Hiroshi; Nanasato, Yoshihiko; Tabei, Yutaka; Takano, Yoshitaka; Shirasu, Ken; Narusaka, Yoshihiro

2013-01-01

309

Functional analysis of oocyte-expressed genes using transgenic models.  

PubMed

An oocyte's journey is highly distinct from the vast majority of cells in the body. As one of the largest and rarest cells, oocytes express unique genes required for the genesis of healthy and competent eggs. The function of only a handful of oocyte-specific genes is beginning to be unraveled. Transgenic mouse models have proven to be extremely valuable in studying the effects of gene deletions on oocytes and surrounding somatic cells. Growth differentiation factor 9 (Gdf9), bone morphogenetic protein 15 (Bmp15), zona pellucida genes (Zp1, Zp2 and Zp3), factor in the germline alpha (Figla), and the c-mos protooncogene (c-mos) are some of the genes preferentially expressed in oocytes which play important roles during folliculogenesis. In order to identify other novel genes preferentially expressed in oocytes, we have utilized subtractive hybridization and in silico subtraction. The combination of these identification approaches, coupled with the use of knockout mice, will lead to many future functional studies of genes uniquely devoted to oogenesis and folliculogenesis. PMID:11988305

Rajkovic, Aleksandar; Matzuk, Martin M

2002-02-22

310

Functional specificity among ribosomal proteins regulates gene expression  

PubMed Central

Duplicated genes escape gene loss by conferring a dosage benefit or evolving diverged functions. The yeast Saccharomyces cerevisiae contains many duplicated genes encoding ribosomal proteins. Prior studies have suggested that these duplicated proteins are functionally redundant and affect cellular processes in proportion to their expression. In contrast, through studies of ASH1 mRNA in yeast, we demonstrate paralog-specific requirements for the translation of localized mRNAs. Intriguingly, these paralog-specific effects are limited to a distinct subset of duplicated ribosomal proteins. Moreover, transcriptional and phenotypic profiling of cells lacking specific ribosomal proteins reveals differences between the functional roles of ribosomal protein paralogs that extend beyond effects on mRNA localization. Finally, we show that ribosomal protein paralogs exhibit differential requirements for assembly and localization. Together, our data indicate complex specialization of ribosomal proteins for specific cellular processes, and support the existence of a ribosomal code.

Komili, Suzanne; Farny, Natalie G.; Roth, Frederick P.; Silver, Pamela A.

2008-01-01

311

The relationship between protein sequences and their gene ontology functions  

PubMed Central

Background One main research challenge in the post-genomic era is to understand the relationship between protein sequences and their biological functions. In recent years, several automated annotation systems have been developed for the functional assignment of uncharacterized proteins. The underlying assumption of these systems is that similar sequences imply similar biological functions. However, it has been noted that matching sequences do not always infer similar functions. Results In this paper, we present the correlation between protein sequences and protein functions for the yeast proteome in the context of gene ontology. A novel measure is introduced to define the overall similarity between two protein sequences. The effects of the level as well as the size of a gene ontology group on the degree of similarity were studied. The similarity distributions at different levels of gene ontology trees are presented. To evaluate the theoretical prediction power of similar sequences, we computed the posterior probability of correct predictions. Conclusion The results indicate that protein pairs of similar biological functions tend to have higher sequence similarity, although the similarity distribution in each functional group is heterogeneous and varies from group to group. We conclude that sequence similarity can serve as a key measure in protein function prediction. However, the resulting annotations must be verified through other means. A method that combines a broader range of measures is more likely to provide more accurate prediction. Our study indicates that the posterior probability of a correct prediction could serve as one of the key measures.

Duan, Zhong-Hui; Hughes, Brent; Reichel, Lothar; Perez, Dianne M; Shi, Ting

2006-01-01

312

Searching for functional gene modules with interaction component models  

PubMed Central

Background Functional gene modules and protein complexes are being sought from combinations of gene expression and protein-protein interaction data with various clustering-type methods. Central features missing from most of these methods are handling of uncertainty in both protein interaction and gene expression measurements, and in particular capability of modeling overlapping clusters. It would make sense to assume that proteins may play different roles in different functional modules, and the roles are evidenced in their interactions. Results We formulate a generative probabilistic model for protein-protein interaction links and introduce two ways for including gene expression data into the model. The model finds interaction components, which can be interpreted as overlapping clusters or functional modules. We demonstrate the performance on two data sets of yeast Saccharomyces cerevisiae. Our methods outperform a representative set of earlier models in the task of finding biologically relevant modules having enriched functional classes. Conclusions Combining protein interaction and gene expression data with a probabilistic generative model improves discovery of modules compared to approaches based on either data source alone. With a fairly simple model we can find biologically relevant modules better than with alternative methods, and in addition the modules may be inherently overlapping in the sense that different interactions may belong to different modules.

2010-01-01

313

Deriving transcriptional programs and functional processes from gene expression databases  

PubMed Central

Motivation: A system-wide approach to revealing the underlying molecular state of a cell is a long-standing biological challenge. Developed over the last decade, gene expression profiles possess the characteristics of such an assay. They have the capacity to reveal both underlying molecular events as well as broader phenotypes such as clinical outcomes. To interpret these profiles, many gene sets have been developed that characterize biological processes. However, the full potential of these gene sets has not yet been achieved. Since the advent of gene expression databases, many have posited that they can reveal properties of activities that are not evident from individual datasets, analogous to how the expression of a single gene generally cannot reveal the activation of a biological process. Results: To address this issue, we have developed a high-throughput method to mine gene expression databases for the regulation of gene sets. Given a set of genes, we scored it against each gene expression dataset by looking for enrichment of co-regulated genes relative to an empirical null distribution. After validating the method, we applied it to address two biological problems. First, we deciphered the E2F transcriptional network. We confirmed that true transcriptional targets exhibit a distinct regulatory profile across a database. Second, we leveraged the patterns of regulation across a database of gene sets to produce an automatically generated catalog of biological processes. These demonstrations revealed the power of a global analysis of the data contained within gene expression databases, and the potential for using them to address biological questions. Contact: jeffrey.t.chang@uth.tmc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Chang, Jeffrey T.

2012-01-01

314

Knots in the family tree: evolutionary relationships and functions of knox homeobox genes  

Microsoft Academic Search

Knotted-like homeobox (knox) genes constitute a gene family in plants. Class I knox genes are expressed in shoot apical meristems, and (with notable exceptions) not in lateral organ primordia. Class II genes have more diverse expression patterns. Loss and gain of function mutations indicate that knox genes are important regulators of meristem function. Gene duplication has contributed to the evolution

Leonore Reiser; Patricia Sánchez-Baracaldo; Sarah Hake

2000-01-01

315

A conserved family of cellular genes related to the baculovirus iap gene and encoding apoptosis inhibitors.  

PubMed

The baculovirus inhibitor of apoptosis gene, iap, can impede cell death in insect cells. Here we show that iap can also prevent cell death in mammalian cells. The ability of iap to regulate programmed cell death in widely divergent species raised the possibility that cellular homologs of iap might exist. Consistent with this hypothesis, we have isolated Drosophila and human genes which encode IAP-like proteins (dILP and hILP). Like IAP, both dILP and hILP contain amino-terminal baculovirus IAP repeats (BIRs) and carboxy-terminal RING finger domains. Human ilp encodes a widely expressed cytoplasmic protein that can suppress apoptosis in transfected cells. An analysis of the expressed sequence tag database suggests that hilp is one of several human genes related to iap. Together these data suggest that iap and related cellular genes play an evolutionarily conserved role in the regulation of apoptosis. PMID:8654366

Duckett, C S; Nava, V E; Gedrich, R W; Clem, R J; Van Dongen, J L; Gilfillan, M C; Shiels, H; Hardwick, J M; Thompson, C B

1996-06-01

316

Temporal expression analysis of angiogenesis-related genes in brain development  

PubMed Central

Background The current knowledge on molecular pathogenesis of cerebral vascular malformations (CVM), which are believed to arise during development, is very limited. To unravel the molecular mechanisms involved in CVMs, a detailed understanding of the brain vascular development at molecular level is crucial. In this study, we aimed to explore the temporal and comparative expression profile of angiogenesis-related genes in the establishment of brain vasculature. Methods Expression of a total of 113 angiogenesis-related genes during murine brain development has been analyzed using low-density array systems designed for angiogenesis-related genes. Bai1 (brain specific angiogenesis inhibitor-1), a recently identified novel anti-angiogenic gene, has been selected for further characterization. Results We found that 62 out of 113 analyzed genes have expression in brain development at varying levels. Nineteen of these were differentially expressed between embryonic and postnatal stages (>1.5 fold). Bai1 is strongly expressed on growing blood vessels of cerebral cortex and hippocampus, partially expressed in the lateral regions of striatum, but mostly absent on the thalamus. Conclusion By showing the comparative expression analysis of angiogenesis-related genes throughout brain development, the data presented here will be a crucial addition to further functional studies on cerebrovascular research.

2012-01-01

317

Advances in Pig Genomics and Functional Gene Discovery  

PubMed Central

Advances in pig gene identification, mapping and functional analysis have continued to make rapid progress. The porcine genetic linkage map now has nearly 3000 loci, including several hundred genes, and is likely to expand considerably in the next few years, with many more genes and amplified fragment length polymorphism (AFLP) markers being added to the map. The physical genetic map is also growing rapidly and has over 3000 genes and markers. Several recent quantitative trait loci (QTL) scans and candidate gene analyses have identified important chromosomal regions and individual genes associated with traits of economic interest. The commercial pig industry is actively using this information and traditional performance information to improve pig production by marker-assisted selection (MAS). Research to study the co-expression of thousands of genes is now advancing and methods to combine these approaches to aid in gene discovery are under way. The pig's role in xenotransplantation and biomedical research makes the study of its genome important for the study of human disease. This review will briefly describe advances made, directions for future research and the implications for both the pig industry and human health.

2003-01-01

318

Extending relational algebra and relational calculus with set-valued attributes and aggregate functions  

Microsoft Academic Search

In commercial network database management systems, set-valued fields and aggregate functions are commonly supported. However, the relational database model, as defined by Codd, does not include set-valued attributes or aggregate functions. Recently, Klug extended the relational model by incorporating aggregate functions and by defining relational algebra and calculus languages.In this paper, relational algebra and relational calculus database query languages (as

G. Özsoyo?lu; Z. Meral Özsoyoglu; Victor Matos

1987-01-01

319

Syntenator: Multiple gene order alignments with a gene-specific scoring function  

Microsoft Academic Search

BACKGROUND: Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignment softwares like WABA or blastz. In case of conserved syntenies, such regions are defined as conserved gene orders. On the gene order level, homologous regions can even be found between distantly related genomes, which do

Christian Rödelsperger; Christoph Dieterich

2008-01-01

320

Promoter methylation of tumor-related genes in gastric carcinogenesis.  

PubMed

Aberrant promoter methylation and subsequent silencing of cancer-related genes has been recognized as an important pathway involved in gastric carcinogenesis. In fact, several factors are believed to contribute to its induction in gastric epithelia, including aging, diet, chronic inflammation and infection of Helicobacter pylori (H. pylori) and Epstein-Barr virus (EBV). However, the underling mechanisms are not completely identified, despite the belief that increased expression or activity of DNA methyltransferases (DNMTs), or decreased demethylation activity may contribute to the excessive methylation. A great number of genes with promoter methylation have been observed in gastric cancer (GC), among which p16INK4A (p16), Mut L homologue 1 (MLH1), Epithelial-cadherin (E-cadherin), Runt-related transcription factor 3 (RUNX3), adenomatous polyposis coli (APC), O(6)-methylguanine-DNA methyltransferase (MGMT), Ras association domain family 1A (RASSF1A) and Death-associated protein kinase (DAPK) have been extensively studied. Unlike the distinct methylation characterization in single genes, methylation analysis of multiple genes may provide more information in risk prediction, early detection, prognosis assessment and chemotherapy choice for GC. Specifically, particular monitoring and screening should be performed on those over 45 years old, with precancerous gastric disease or infection of H. pylori or EBV. As an alternative to tumor tissues, methylation detection in patient sera or gastric washes may also be used in risk prediction and early detection. However, what still poses a great challenge as well as a puzzle is the determination of the very genes that should be used in methylation analysis. Because epigenetic alterations are normally reversible, drugs or chemical compounds with demethylating activity, such as 5-aza-2'-deoxycytidine (5-aza-dC) could be used in the treatment of patients with multiple gene methylation. In view of the adverse effects of 5-aza-dC, DNMT-targeted strategy has been proposed and may prove to be more effective than demethylating agents. PMID:22936446

Zhao, Chenghai; Bu, Xianmin

2012-10-01

321

'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration  

PubMed Central

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, ‘RetinoGenetics’, which contains informative knowledge about all known IRD-related genes and mutations for IRD. ‘RetinoGenetics’ currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein–protein interaction, mutational annotations and gene–disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, ‘RetinoGenetics’ could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, ‘RetinoGenetics’ is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/.

Ran, Xia; Cai, Wei-Jun; Huang, Xiu-Feng; Liu, Qi; Lu, Fan; Qu, Jia; Wu, Jinyu; Jin, Zi-Bing

2014-01-01

322

'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration.  

PubMed

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, 'RetinoGenetics', which contains informative knowledge about all known IRD-related genes and mutations for IRD. 'RetinoGenetics' currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein-protein interaction, mutational annotations and gene-disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, 'RetinoGenetics' could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, 'RetinoGenetics' is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/. PMID:24939193

Ran, Xia; Cai, Wei-Jun; Huang, Xiu-Feng; Liu, Qi; Lu, Fan; Qu, Jia; Wu, Jinyu; Jin, Zi-Bing

2014-01-01

323

Functional validation of GWAS gene candidates for abnormal liver function during zebrafish liver development.  

PubMed

Genome-wide association studies (GWAS) have revealed numerous associations between many phenotypes and gene candidates. Frequently, however, further elucidation of gene function has not been achieved. A recent GWAS identified 69 candidate genes associated with elevated liver enzyme concentrations, which are clinical markers of liver disease. To investigate the role of these genes in liver homeostasis, we narrowed down this list to 12 genes based on zebrafish orthology, zebrafish liver expression and disease correlation. To assess the function of gene candidates during liver development, we assayed hepatic progenitors at 48 hours post fertilization (hpf) and hepatocytes at 72 hpf using in situ hybridization following morpholino knockdown in zebrafish embryos. Knockdown of three genes (pnpla3, pklr and mapk10) decreased expression of hepatic progenitor cells, whereas knockdown of eight genes (pnpla3, cpn1, trib1, fads2, slc2a2, pklr, mapk10 and samm50) decreased cell-specific hepatocyte expression. We then induced liver injury in zebrafish embryos using acetaminophen exposure and observed changes in liver toxicity incidence in morphants. Prioritization of GWAS candidates and morpholino knockdown expedites the study of newly identified genes impacting liver development and represents a feasible method for initial assessment of candidate genes to instruct further mechanistic analyses. Our analysis can be extended to GWAS for additional disease-associated phenotypes. PMID:23813869

Liu, Leah Y; Fox, Caroline S; North, Trista E; Goessling, Wolfram

2013-09-01

324

Functional validation of GWAS gene candidates for abnormal liver function during zebrafish liver development  

PubMed Central

SUMMARY Genome-wide association studies (GWAS) have revealed numerous associations between many phenotypes and gene candidates. Frequently, however, further elucidation of gene function has not been achieved. A recent GWAS identified 69 candidate genes associated with elevated liver enzyme concentrations, which are clinical markers of liver disease. To investigate the role of these genes in liver homeostasis, we narrowed down this list to 12 genes based on zebrafish orthology, zebrafish liver expression and disease correlation. To assess the function of gene candidates during liver development, we assayed hepatic progenitors at 48 hours post fertilization (hpf) and hepatocytes at 72 hpf using in situ hybridization following morpholino knockdown in zebrafish embryos. Knockdown of three genes (pnpla3, pklr and mapk10) decreased expression of hepatic progenitor cells, whereas knockdown of eight genes (pnpla3, cpn1, trib1, fads2, slc2a2, pklr, mapk10 and samm50) decreased cell-specific hepatocyte expression. We then induced liver injury in zebrafish embryos using acetaminophen exposure and observed changes in liver toxicity incidence in morphants. Prioritization of GWAS candidates and morpholino knockdown expedites the study of newly identified genes impacting liver development and represents a feasible method for initial assessment of candidate genes to instruct further mechanistic analyses. Our analysis can be extended to GWAS for additional disease-associated phenotypes.

Liu, Leah Y.; Fox, Caroline S.; North, Trista E.; Goessling, Wolfram

2013-01-01

325

Bach2 maintains T cells in a naive state by suppressing effector memory-related genes  

PubMed Central

The transcriptional repressor BTB and CNC homology 2 (Bach2) is thought to be mainly expressed in B cells with specific functions such as class switch recombination and somatic hypermutation, but its function in T cells is not known. We found equal Bach2 expression in T cells and analyzed its function using Bach2-deficient (?/?) mice. Although T-cell development was normal, numbers of peripheral naive T cells were decreased, which rapidly produced Th2 cytokines after TCR stimulation. Bach2?/? naive T cells highly expressed genes related to effector-memory T cells such as CCR4, ST-2 and Blimp-1. Enhanced expression of these genes induced Bach2?/? naive T cells to migrate toward CCR4-ligand and respond to IL33. Forced expression of Bach2 restored the expression of these genes. Using Chromatin Immunoprecipitation (ChIP)-seq analysis, we identified S100 calcium binding protein a, Heme oxigenase 1, and prolyl hydroxylase 3 as Bach2 direct target genes, which are highly expressed in effector-memory T cells. These findings indicate that Bach2 suppresses effector memory-related genes to maintain the naive T-cell state and regulates generation of effector-memory T cells.

Tsukumo, Shin-ichi; Unno, Midori; Muto, Akihiko; Takeuchi, Arata; Kometani, Kohei; Kurosaki, Tomohiro; Igarashi, Kazuhiko; Saito, Takashi

2013-01-01

326

Bach2 maintains T cells in a naive state by suppressing effector memory-related genes.  

PubMed

The transcriptional repressor BTB and CNC homology 2 (Bach2) is thought to be mainly expressed in B cells with specific functions such as class switch recombination and somatic hypermutation, but its function in T cells is not known. We found equal Bach2 expression in T cells and analyzed its function using Bach2-deficient (-/-) mice. Although T-cell development was normal, numbers of peripheral naive T cells were decreased, which rapidly produced Th2 cytokines after TCR stimulation. Bach2(-/-) naive T cells highly expressed genes related to effector-memory T cells such as CCR4, ST-2 and Blimp-1. Enhanced expression of these genes induced Bach2(-/-) naive T cells to migrate toward CCR4-ligand and respond to IL33. Forced expression of Bach2 restored the expression of these genes. Using Chromatin Immunoprecipitation (ChIP)-seq analysis, we identified S100 calcium binding protein a, Heme oxigenase 1, and prolyl hydroxylase 3 as Bach2 direct target genes, which are highly expressed in effector-memory T cells. These findings indicate that Bach2 suppresses effector memory-related genes to maintain the naive T-cell state and regulates generation of effector-memory T cells. PMID:23754397

Tsukumo, Shin-ichi; Unno, Midori; Muto, Akihiko; Takeuchi, Arata; Kometani, Kohei; Kurosaki, Tomohiro; Igarashi, Kazuhiko; Saito, Takashi

2013-06-25

327

Differential expression of inflammation-related genes after intense exercise.  

PubMed

The present study focused on the identification of the difference in expression of inflammation-related genes after intense exercise by oligonucleotide microarray methods. This may finally lead to an improved understanding of underlying cellular and molecular mechanism of the immunological alterations in response to exercises. The study group consisted of three healthy road cyclists. Peripheral blood mononuclear cells (PBMCs) were collected preexercise, immediately post-exercise and after 15 min of recovery. The analysis of the expression profile of genes related to the inflammation was performed in PBMCs using HG-U133A oligonucleotide microarrays. 4 genes were found to be regulated by more than 2.0-fold (IL1R2, IL2RB, IL8, IL8RB). Venn diagram indicated that only one of differentially expressed genes (TXLNA) remains the same in each comparison. The balance of both pro- and anti-inflammatory cytokines after exercise seems to be important for athletes. Optimal inflammatory and immune response may help optimize exercise regimes, link physical activity with health and diagnose or prevent athletes from overtraining. PMID:24874932

Kimsa, Magdalena C; Strzalka-Mrozik, Barbara; Kimsa, Malgorzata W; Gola, Joanna; Kochanska-Dziurowicz, Aleksandra; Zebrowska, Aleksandra; Mazurek, Urszula

2014-01-01

328

Gene Network Analysis in a Pediatric Cohort Identifies Novel Lung Function Genes  

PubMed Central

Lung function is a heritable trait and serves as an important clinical predictor of morbidity and mortality for pulmonary conditions in adults, however, despite its importance, no studies have focused on uncovering pediatric-specific loci influencing lung function. To identify novel genetic determinants of pediatric lung function, we conducted a genome-wide association study (GWAS) of four pulmonary function traits, including FVC, FEV1, FEV1/FVC and FEF25–75% in 1556 children. Further, we carried out gene network analyses for each trait including all SNPs with a P-value of <1.0×10?3 from the individual GWAS. The GWAS identified SNPs with notable trends towards association with the pulmonary function measures, including the previously described INTS12 locus association with FEV1 (pmeta?=?1.41×10?7). The gene network analyses identified 34 networks of genes associated with pulmonary function variables in Caucasians. Of those, the glycoprotein gene network reached genome-wide significance for all four variables. P-value range pmeta?=?6.29×10?4 - 2.80×10?8 on meta-analysis. In this study, we report on specific pathways that are significantly associated with pediatric lung function at genome-wide significance. In addition, we report the first loci associated with lung function in both pediatric Caucasian and African American populations.

McDonough, Joseph M.; Wei, Zhi; Kim, Cecilia; Chiavacci, Rosetta; Mentch, Frank; Caboot, Jason B.; Spergel, Jonathan; Allen, Julian L.; Sleiman, Patrick M. A.; Hakonarson, Hakon

2013-01-01

329

Positive selection and functional divergence after melanopsin gene duplication.  

PubMed

A newly discovered melanopsin gene (Opn4) encodes a member of the opsins, melanopsin. Two melanopsin genes, mammalian-like Opn4m and Xenopus-like Opn4x, have been described in nonmammalian vertebrates, but the underlying evolutionary mechanisms behind the duplication of melanopsin genes remain unclear. We conducted a comprehensive evolutionary analysis within a phylogenetic framework. In our phylogenetic tree, the duplication of Opn4m and Opn4x probably occurred prior to the emergence of vertebrates, and subsequently Opn4x disappeared in the lineages leading to mammalian species. Evolutionary analyses show strong purifying selection during melanopsin evolution. We also provide evidence that Opn4x underwent positive selection after the early gene duplication events. It has been indicated that functional divergence and altered functional constraints occurred between Opn4m and Opn4x duplicates with the identification of positively selected amino acids. Our findings highlight the evolutionary malleability in vertebrate melanopsin genes and provide a genetic basis for comparative studies of functional properties of these two melanopsins. PMID:21952875

Dong, Changgui; Zhang, Junpeng; Qiao, Jian; He, Guimei

2012-04-01

330

New gene functions in megakaryopoiesis and platelet formation  

PubMed Central

Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes controlling both traits. Here we carried out a high-powered meta-analysis of genome-wide association studies (GWAS) in up to 66,867 individuals of European ancestry, followed by extensive biological and functional assessment. We identified 68 genomic loci reliably associated with platelet count and volume mapping to established and putative novel regulators of megakaryopoiesis and platelet formation. These genes show megakaryocyte-specific gene expression patterns and extensive network connectivity. Using gene silencing in Danio rerio and Drosophila melanogaster, we identified 11 of the genes as novel regulators of blood cell formation. Taken together, our findings advance understanding of novel gene functions controlling fate-determining events during megakaryopoiesis and platelet formation, providing a new example of successful translation of GWAS to function.

Gieger, Christian; Radhakrishnan, Aparna; Cvejic, Ana; Tang, Weihong; Porcu, Eleonora; Pistis, Giorgio; Serbanovic-Canic, Jovana; Elling, Ulrich; Goodall, Alison H.; Labrune, Yann; Lopez, Lorna M.; Magi, Reedik; Meacham, Stuart; Okada, Yukinori; Pirastu, Nicola; Sorice, Rossella; Teumer, Alexander; Voss, Katrin; Zhang, Weihua; Ramirez-Solis, Ramiro; Bis, Joshua C.; Ellinghaus, David; Gogele, Martin; Hottenga, Jouke-Jan; Langenberg, Claudia; Kovacs, Peter; O'Reilly, Paul F.; Shin, So-Youn; Esko, Tonu; Hartiala, Jaana; Kanoni, Stavroula; Murgia, Federico; Parsa, Afshin; Stephens, Jonathan; van der Harst, Pim; van der Schoot, C. Ellen; Allayee, Hooman; Attwood, Antony; Balkau, Beverley; Bastardot, Francois; Basu, Saonli; Baumeister, Sebastian E.; Biino, Ginevra; Bomba, Lorenzo; Bonnefond, Amelie; Cambien, Francois; Chambers, John C.; Cucca, Francesco; D'Adamo, Pio; Davies, Gail; de Boer, Rudolf A.; de Geus, Eco J. C.; Doring, Angela; Elliott, Paul; Erdmann, Jeanette; Evans, David M.; Falchi, Mario; Feng, Wei; Folsom, Aaron R.; Frazer, Ian H.; Gibson, Quince D.; Glazer, Nicole L.; Hammond, Chris; Hartikainen, Anna-Liisa; Heckbert, Susan R.; Hengstenberg, Christian; Hersch, Micha; Illig, Thomas; Loos, Ruth J. F.; Jolley, Jennifer; Khaw, Kay Tee; Kuhnel, Brigitte; Kyrtsonis, Marie-Christine; Lagou, Vasiliki; Lloyd-Jones, Heather; Lumley, Thomas; Mangino, Massimo; Maschio, Andrea; Leach, Irene Mateo; McKnight, Barbara; Memari, Yasin; Mitchell, Braxton D.; Montgomery, Grant W.; Nakamura, Yusuke; Nauck, Matthias; Navis, Gerjan; Nothlings, Ute; Nolte, Ilja M.; Porteous, David J.; Pouta, Anneli; Pramstaller, Peter P.; Pullat, Janne; Ring, Susan M.; Rotter, Jerome I.; Ruggiero, Daniela; Ruokonen, Aimo; Sala, Cinzia; Samani, Nilesh J.; Sambrook, Jennifer; Schlessinger, David; Schreiber, Stefan; Schunkert, Heribert; Scott, James; Smith, Nicholas L.; Snieder, Harold; Starr, John M.; Stumvoll, Michael; Takahashi, Atsushi; Tang, W. H. Wilson; Taylor, Kent; Tenesa, Albert; Thein, Swee Lay; Tonjes, Anke; Uda, Manuela; Ulivi, Sheila; van Veldhuisen, Dirk J.; Visscher, Peter M.; Volker, Uwe; Wichmann, H.-Erich; Wiggins, Kerri L.; Willemsen, Gonneke; Yang, Tsun-Po; Zhao, Jing Hua; Zitting, Paavo; Bradley, John R.; Dedoussis, George V.; Gasparini, Paolo; Hazen, Stanley L.; Metspalu, Andres; Pirastu, Mario; Shuldiner, Alan R.; van Pelt, L. Joost; Zwaginga, Jaap-Jan; Boomsma, Dorret I.; Deary, Ian J.; Franke, Andre; Froguel, Philippe; Ganesh, Santhi K.; Jarvelin, Marjo-Riitta; Martin, Nicholas G.; Meisinger, Christa; Psaty, Bruce M.; Spector, Timothy D.; Wareham, Nicholas J.; Akkerman, Jan-Willem N.; Ciullo, Marina; Deloukas, Panos; Greinacher, Andreas; Jupe, Steve; Kamatani, Naoyuki; Khadake, Jyoti; Kooner, Jaspal S.; Penninger, Josef; Prokopenko, Inga; Stemple, Derek; Toniolo, Daniela; Wernisch, Lorenz; Sanna, Serena; Hicks, Andrew A.; Rendon, Augusto; Ferreira, Manuel A.; Ouwehand, Willem H.; Soranzo, Nicole

2012-01-01

331

Identification of Lung-Cancer-Related Genes with the Shortest Path Approach in a Protein-Protein Interaction Network  

PubMed Central

Lung cancer is one of the leading causes of cancer mortality worldwide. The main types of lung cancer are small cell lung cancer (SCLC) and nonsmall cell lung cancer (NSCLC). In this work, a computational method was proposed for identifying lung-cancer-related genes with a shortest path approach in a protein-protein interaction (PPI) network. Based on the PPI data from STRING, a weighted PPI network was constructed. 54 NSCLC- and 84 SCLC-related genes were retrieved from associated KEGG pathways. Then the shortest paths between each pair of these 54 NSCLC genes and 84 SCLC genes were obtained with Dijkstra's algorithm. Finally, all the genes on the shortest paths were extracted, and 25 and 38 shortest genes with a permutation P value less than 0.05 for NSCLC and SCLC were selected for further analysis. Some of the shortest path genes have been reported to be related to lung cancer. Intriguingly, the candidate genes we identified from the PPI network contained more cancer genes than those identified from the gene expression profiles. Furthermore, these genes possessed more functional similarity with the known cancer genes than those identified from the gene expression profiles. This study proved the efficiency of the proposed method and showed promising results.

Li, Bi-Qing; You, Jin; Chen, Lei; Zhang, Jian; Zhang, Ning; Li, Hai-Peng; Huang, Tao; Kong, Xiang-Yin; Cai, Yu-Dong

2013-01-01

332

Expression profiling of immune-related genes from Japanese flounder Paralichthys olivaceus kidney cells using cDNA microarrays.  

PubMed

A Japanese flounder Paralichthys olivaceus cDNA microarray containing 871 unique cDNAs including 91 putative immune-related genes from our EST studies was constructed and used to characterize of gene expression of in vitro grown kidney cells stimulated with mitogens such as ConA, PMA, LPS or infected with hirame rhabdovirus (HRV). The numbers of genes whose expressions were increased or decreased by these factors were: 17 by Con A, 139 by PMA, 76 by LPS and 182 by HRV infection. The treatment of Con A for 1 and 6h affected the expression of only a few of the immune-related genes. PMA down-regulated far more genes than it up-regulated. Apoptosis-related factors, such as c-fos, NGF induced protein IB and NR13 genes, were among the genes whose expressions were induced by PMA. LPS induced the expression of inflammation-related genes, such as IL-1beta, monocyte chemotactic protein 1 and collagenase. The expressions of many genes were induced after 3h HRV infection but some of them were decreased to the basal level after 6h HRV infection. The expression of some genes of unknown function were induced or reduced by Con A, PMA or LPS or by HRV infection in different time periods. From all of the gene expression profiling in this study, we could get lots of information about the dynamic changes in the gene expression of the kidney cells under different stress or stimulations. PMID:15752548

Kurobe, Tomofumi; Yasuike, Motoshige; Kimura, Takuto; Hirono, Ikuo; Aoki, Takashi

2005-01-01

333

Inflammatory genes and neural activity: involvement of immune genes in synaptic function and behavior.  

PubMed

The function of pro-inflammatory cytokines and chemokines in brain injury and autoimmune diseases has been long recognized. There is however, a significant lack of information regarding the role of constitutively expressed immune genes in the normal brain. The current evidence points to the involvement of certain cytokines and major histocompatibility complex (MHC) molecules in synaptic function and plasticity. Furthermore, constitutively expressed chemokines in neurons provide an additional indication of a role for these molecules in neural function. In addition, clinical data suggests a dysregulation of immune genes in the cerebrospinal fluid of psychiatric patients who have neither brain injury nor autoimmune diseases. This review will discuss recent data indicating a role for immune genes in synaptic stability and will also discuss the implications for specific brain functions involving mood and cognition. PMID:15569608

Tonelli, Leonardo H; Postolache, Teodor T; Sternberg, Esther M

2005-01-01

334

Retinal Gene Expression Changes Related to IOP Exposure and Axonal Loss in DBA/2J Mice  

PubMed Central

Purpose. To determine the effects of cumulative IOP exposure and axonal damage on retinal gene expression in DBA/2 mice. Methods. DBA/2J, DBA/2Jpe (pearl), and C57BL/6 mice from 3 to 12 months of age were used. IOP was measured with a rebound tonometer, and optic nerve (ON) damage was determined by grading of ON sections. Retinal RNA was subjected to microarray analysis. Comparisons explored the effects of cumulative IOP exposure (cIOPx) as well as ON damage (ONd) in the DBA/2J animals compared with that in the C57BL/6 and pearl mice. RT-PCR was performed to confirm some of the genes and bioinformatic analysis to identify affected gene networks. Results. Microarrays revealed that an increasing number of genes were up- or downregulated in 9- and 12-month DBA/2J mice with various degrees of ONd. A smaller number of genes were expressed differentially between eyes with different cIOPx at the same age, from 6 months on. Expression of 1385 and 1133 genes differed between DBA/2J animals and C57BL/6 or pearl mice, respectively, and some them were confirmed by RT-PCR. Bioinformatics analysis identified functional gene networks, including members of the complement system, that appeared to be related to cIOPx, ONd, or both. Conclusions. Gene expression changes occur in retinas of DBA/2 mice with various amounts of cIOPx as well as ONd. Genes involved, code for proteins with diverse cellular functions and include among others the complement system. cIOPx and ONd affect common as well as unique gene sets.

Panagis, Lambros; Zhao, Xiujun; Ge, Yongchao; Ren, Lizhen; Mittag, Thomas W.

2011-01-01

335

The mammalian gene function resource: the International Knockout Mouse Consortium.  

PubMed

In 2007, the International Knockout Mouse Consortium (IKMC) made the ambitious promise to generate mutations in virtually every protein-coding gene of the mouse genome in a concerted worldwide action. Now, 5 years later, the IKMC members have developed high-throughput gene trapping and, in particular, gene-targeting pipelines and generated more than 17,400 mutant murine embryonic stem (ES) cell clones and more than 1,700 mutant mouse strains, most of them conditional. A common IKMC web portal (www.knockoutmouse.org) has been established, allowing easy access to this unparalleled biological resource. The IKMC materials considerably enhance functional gene annotation of the mammalian genome and will have a major impact on future biomedical research. PMID:22968824

Bradley, Allan; Anastassiadis, Konstantinos; Ayadi, Abdelkader; Battey, James F; Bell, Cindy; Birling, Marie-Christine; Bottomley, Joanna; Brown, Steve D; Bürger, Antje; Bult, Carol J; Bushell, Wendy; Collins, Francis S; Desaintes, Christian; Doe, Brendan; Economides, Aris; Eppig, Janan T; Finnell, Richard H; Fletcher, Colin; Fray, Martin; Frendewey, David; Friedel, Roland H; Grosveld, Frank G; Hansen, Jens; Hérault, Yann; Hicks, Geoffrey; Hörlein, Andreas; Houghton, Richard; Hrabé de Angelis, Martin; Huylebroeck, Danny; Iyer, Vivek; de Jong, Pieter J; Kadin, James A; Kaloff, Cornelia; Kennedy, Karen; Koutsourakis, Manousos; Lloyd, K C Kent; Marschall, Susan; Mason, Jeremy; McKerlie, Colin; McLeod, Michael P; von Melchner, Harald; Moore, Mark; Mujica, Alejandro O; Nagy, Andras; Nefedov, Mikhail; Nutter, Lauryl M; Pavlovic, Guillaume; Peterson, Jane L; Pollock, Jonathan; Ramirez-Solis, Ramiro; Rancourt, Derrick E; Raspa, Marcello; Remacle, Jacques E; Ringwald, Martin; Rosen, Barry; Rosenthal, Nadia; Rossant, Janet; Ruiz Noppinger, Patricia; Ryder, Ed; Schick, Joel Zupicich; Schnütgen, Frank; Schofield, Paul; Seisenberger, Claudia; Selloum, Mohammed; Simpson, Elizabeth M; Skarnes, William C; Smedley, Damian; Stanford, William L; Stewart, A Francis; Stone, Kevin; Swan, Kate; Tadepally, Hamsa; Teboul, Lydia; Tocchini-Valentini, Glauco P; Valenzuela, David; West, Anthony P; Yamamura, Ken-ichi; Yoshinaga, Yuko; Wurst, Wolfgang

2012-10-01

336

A geminivirus-induced gene silencing system for gene function validation in cassava.  

PubMed

We have constructed an African cassava mosaic virus (ACMV) based gene-silencing vector as a reverse genetics tool for gene function analysis in cassava. The vector carrying a fragment from the Nicotiana tabacum sulfur gene (su), encoding one unit of the chloroplast enzyme magnesium chelatase, was used to induce the silencing of the cassava orthologous gene resulting in yellow-white spots characteristic of the inhibition of su expression. This result suggests that well developed sequence databases from model plants like Arabidopsis thaliana, Nicotiana benthamiana, N. tabacum, Lycopersicon esculentum and others could be used as a major source of information and sequences for functional genomics in cassava. Furthermore, a fragment of the cassava CYP79D2 endogenous gene, sharing 89% homology with CYP79D1 endogenous gene was inserted into the ACMV vector. The resultant vector was inducing the down regulation of the expression of these two genes which catalyze the first-dedicated step in the synthesis of linamarin, the major cyanogenic glycoside in cassava. At 21 days post-inoculation (dpi), a 76% reduction of linamarin content was observed in silenced leaves. Using transgenic plants expressing antisense RNA of CYP79D1 and CYP79D2, Siritunga and Sayre (2003) obtained several lines with a reduction level varying from 60% to 94%. This result provides the first example of direct comparison of the efficiency of a virus-induced gene silencing (VIGS) system and the transgenic approach for suppression of a biosynthetic pathway. The ACMV VIGS system will certainly be a complement and in some cases an alternative to the transgenic approach, for gene discovery and gene function analysis in cassava. PMID:15630624

Fofana, Ismael B F; Sangaré, Abdourahamane; Collier, Ray; Taylor, Christopher; Fauquet, Claude M

2004-11-01

337

Genome Holography: Deciphering Function-Form Motifs from Gene Expression Data  

PubMed Central

Background DNA chips allow simultaneous measurements of genome-wide response of thousands of genes, i.e. system level monitoring of the gene-network activity. Advanced analysis methods have been developed to extract meaningful information from the vast amount of raw gene-expression data obtained from the microarray measurements. These methods usually aimed to distinguish between groups of subjects (e.g., cancer patients vs. healthy subjects) or identifying marker genes that help to distinguish between those groups. We assumed that motifs related to the internal structure of operons and gene-networks regulation are also embedded in microarray and can be deciphered by using proper analysis. Methodology/Principal Findings The analysis presented here is based on investigating the gene-gene correlations. We analyze a database of gene expression of Bacillus subtilis exposed to sub-lethal levels of 37 different antibiotics. Using unsupervised analysis (dendrogram) of the matrix of normalized gene-gene correlations, we identified the operons as they form distinct clusters of genes in the sorted correlation matrix. Applying dimension-reduction algorithm (Principal Component Analysis, PCA) to the matrices of normalized correlations reveals functional motifs. The genes are placed in a reduced 3-dimensional space of the three leading PCA eigen-vectors according to their corresponding eigen-values. We found that the organization of the genes in the reduced PCA space recovers motifs of the operon internal structure, such as the order of the genes along the genome, gene separation by non-coding segments, and translational start and end regions. In addition to the intra-operon structure, it is also possible to predict inter-operon relationships, operons sharing functional regulation factors, and more. In particular, we demonstrate the above in the context of the competence and sporulation pathways. Conclusions/Significance We demonstrated that by analyzing gene-gene correlation from gene-expression data it is possible to identify operons and to predict unknown internal structure of operons and gene-networks regulation.

Roth, Dalit; Regev, Tamar; Bransburg-Zabary, Sharron; Jacob, Eshel Ben

2008-01-01

338

Functional association networks as priors for gene regulatory network inference  

PubMed Central

Motivation: Gene regulatory network (GRN) inference reveals the influences genes have on one another in cellular regulatory systems. If the experimental data are inadequate for reliable inference of the network, informative priors have been shown to improve the accuracy of inferences. Results: This study explores the potential of undirected, confidence-weighted networks, such as those in functional association databases, as a prior source for GRN inference. Such networks often erroneously indicate symmetric interaction between genes and may contain mostly correlation-based interaction information. Despite these drawbacks, our testing on synthetic datasets indicates that even noisy priors reflect some causal information that can improve GRN inference accuracy. Our analysis on yeast data indicates that using the functional association databases FunCoup and STRING as priors can give a small improvement in GRN inference accuracy with biological data. Contact: matthew.studham@scilifelab.se Supplementary information: Supplementary data are available at Bioinformatics online.

Studham, Matthew E.; Nordling, Torbjorn E.M.; Nelander, Sven; Sonnhammer, Erik L. L.

2014-01-01

339

Characterization of a novel prospero -related homeobox gene, Prox2  

Microsoft Academic Search

prospero-related homeobox genes have been identified from various multi-cellular organisms and play important roles in development\\u000a as a cell fate determinant. Mouse Prox1 is essential for embryogenesis and is required to differentiate horizontal cells in the retina. Here we describe a novel\\u000a prospero family member, Prox2. Transcriptional reporter assays demonstrated that mouse Prox2 is a transcriptional activator and the N-terminal

Ichiko Nishijima; Akihira Ohtoshi

2006-01-01

340

Functions of rol genes in plant secondary metabolism.  

PubMed

For a long time, the Agrobacterium rhizogenes rolA, rolB and rolC oncogenes have been considered to be modulators of plant growth and cell differentiation. A new function of the rol genes in plant-Agrobacterium interaction became apparent with the discovery that these genes are potential activators of secondary metabolism in transformed cells from the Solanaceae, Araliaceae, Rubiaceae, Vitaceae and Rosaceae families. In some cases, the activator effect of individual rol genes is sufficient to overcome the inability of cultured plant cells to produce large amounts of secondary metabolites. Here, I summarize the available evidence that shows that genetic transformation by single Agrobacterium rol genes may be used as a powerful tool to manipulate secondary metabolites in cultured plant cells. Although it is known that the rol genes act via transcriptional activation of defense genes, the mechanism of activation is unclear. In this review, evidence is presented to support the hypothesis that the rol genes mediate uncommon signal transduction pathways in plants. PMID:18434069

Bulgakov, Victor P

2008-01-01

341

Cancer Genes: Discovery and Function - Michael Dean, Ph.D.  

Cancer.gov

April 29, 2014 1:00 PM - 2:00 PM Shady Grove, Room TE408/410 + Add to Outlook Calendar Speaker: Michael Dean, Ph.D. Chief, Human Genetics Section Laboratory of Experimental Immunology, CCR, NCI Print This Page Cancer Genes: Discovery and Function

342

Presence and functionality of mating type genes in the supposedly asexual filamentous fungus Aspergillus oryzae.  

PubMed

The potential for sexual reproduction in Aspergillus oryzae was assessed by investigating the presence and functionality of MAT genes. Previous genome studies had identified a MAT1-1 gene in the reference strain RIB40. We now report the existence of a complementary MAT1-2 gene and the sequencing of an idiomorphic region from A. oryzae strain AO6. This allowed the development of a PCR diagnostic assay, which detected isolates of the MAT1-1 and MAT1-2 genotypes among 180 strains assayed, including industrial tane-koji isolates. Strains used for sake and miso production showed a near-1:1 ratio of the MAT1-1 and MAT1-2 mating types, whereas strains used for soy sauce production showed a significant bias toward the MAT1-2 mating type. MAT1-1 and MAT1-2 isogenic strains were then created by genetic manipulation of the resident idiomorph, and gene expression was compared by DNA microarray and quantitative real-time PCR (qRT-PCR) methodologies under conditions in which MAT genes were expressed. Thirty-three genes were found to be upregulated more than 10-fold in either the MAT1-1 host strain or the MAT1-2 gene replacement strain relative to each other, showing that both the MAT1-1 and MAT1-2 genes functionally regulate gene expression in A. oryzae in a mating type-dependent manner, the first such report for a supposedly asexual fungus. MAT1-1 expression specifically upregulated an ?-pheromone precursor gene, but the functions of most of the genes affected were unknown. The results are consistent with a heterothallic breeding system in A. oryzae, and prospects for the discovery of a sexual cycle are discussed. PMID:22327593

Wada, Ryuta; Maruyama, Jun-Ichi; Yamaguchi, Haruka; Yamamoto, Nanase; Wagu, Yutaka; Paoletti, Mathieu; Archer, David B; Dyer, Paul S; Kitamoto, Katsuhiko

2012-04-01

343

Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting  

PubMed Central

Sequences involved in the regulation of genetic and genomic processes are primarily located in noncoding regions. Identifying such cis-acting sequences from sequence data is difficult because their patterns are not readily apparent, and, to date, identification has concentrated on regions associated with gene-coding functions. Here, we used phylogenetic footprinting to look for gene-independent noncoding elements in the ribosomal RNA gene repeats from several Saccharomyces species. Similarity plots of ribosomal intergenic spacer alignments from six closely related Saccharomyces species allowed the identification of previously characterized functional elements, such as the origin-of-replication and replication-fork barrier sites, demonstrating that this method is a powerful predictor of noncoding functional elements. Seventeen previously uncharacterized elements, showing high levels of conservation, were also discovered. The conservation of these elements suggests that they are functional, and we demonstrate the functionality of two classes of these elements, a putative bidirectional noncoding promoter and a series of conserved peaks with matches to the origin-of-replication core consensus. Our results paint a comprehensive picture of the functionality of the Saccharomyces ribosomal intergenic region and demonstrate that functional elements not involved in gene-coding function can be identified by using comparative genomics based on sequence conservation.

Ganley, Austen R. D.; Hayashi, Kouji; Horiuchi, Takashi; Kobayashi, Takehiko

2005-01-01

344

Fast integration of heterogeneous data sources for predicting gene function with limited annotation  

PubMed Central

Motivation: Many algorithms that integrate multiple functional association networks for predicting gene function construct a composite network as a weighted sum of the individual networks and then use the composite network to predict gene function. The weight assigned to an individual network represents the usefulness of that network in predicting a given gene function. However, because many categories of gene function have a small number of annotations, the process of assigning these network weights is prone to overfitting. Results: Here, we address this problem by proposing a novel approach to combining multiple functional association networks. In particular, we present a method where network weights are simultaneously optimized on sets of related function categories. The method is simpler and faster than existing approaches. Further, we show that it produces composite networks with improved function prediction accuracy using five example species (yeast, mouse, fly, Esherichia coli and human). Availability: Networks and code are available from: http://morrislab.med.utoronto.ca/˜sara/SW Contact: smostafavi@cs.toronto.edu; quaid.morris@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Mostafavi, Sara; Morris, Quaid

2010-01-01

345

A candidate gene approach for virally induced cancer with application to HIV-related Kaposi's sarcoma.  

PubMed

Like other members of the ?-herpesvirus family, human herpes virus 8, the etiologic agent of classic and HIV-related Kaposi's sarcoma (HIV-KS) acquired and evolved several human genes with key immune modulatory and cellular growth control functions. The encoded viral homologs substitute for their human counterparts but escape cellular regulation, leading to uncontrolled cell proliferation. We postulated that DNA variants in the human homologs of viral genes that potentially alter the expression or the binding of the encoded factors controlling the antiviral response may facilitate viral interference. To test whether cellular homologs are candidate susceptibility genes, we evaluated the association of DNA variants in 92 immune-related genes including seven cellular homologs with the risk for HIV-KS in a matched case and control study nested in the Multicenter AIDS Cohort Study. Low- and high-risk gene-by-gene interactions were estimated by multifactor dimensionality reduction and used as predictors in conditional logistic models. Among the most significant gene interactions at risk (OR=2.84-3.92; Bonferroni- adjusted p=9.9 × 10(-3) - 2.6 × 10(-4) ), three comprised human homologs of two latently expressed viral genes, cyclin D1 (CCND1) and interleukin-6 (IL-6), in conjunction with angiogenic genes (VEGF, EDN-1 and EDNRB). At lower significance thresholds (adjusted p < 0.05), human homologs related to apoptosis (CFLAR) and chemotaxis (CCL2) emerged as candidates. This "proof of concept" study identified human homologs involved in the regulation of type I interferon-induced signaling, cell cycle and apoptosis potentially as important determinants of HIV-KS. PMID:23818101

Aissani, Brahim; Wiener, Howard W; Zhang, Kui; Kaslow, Richard A; Ogwaro, Kisani M; Shrestha, Sadeep; Jacobson, Lisa P

2014-01-15

346

Molecular cloning of allelopathy related genes and their relation to HHO in Eupatorium adenophorum.  

PubMed

In this study, conserved sequence regions of HMGR, DXR, and CHS (encoding 3-hydroxy-3-methylglutaryl-CoA reductase, 1-deoxyxylulose-5-phosphate reductoisomerase and chalcone synthase, respectively) were amplified by reverse transcriptase (RT)-PCR from Eupatorium adenophorum. Quantitative real-time PCR showed that the expression of CHS was related to the level of HHO, an allelochemical isolated from E. adenophorum. Semi-quantitative RT-PCR showed that there was no significant difference in expression of genes among three different tissues, except for CHS. Southern blotting indicated that at least three CHS genes are present in the E. adenophorum genome. A full-length cDNA from CHS genes (named EaCHS1, GenBank ID: FJ913888) was cloned. The 1,455 bp cDNA contained an open reading frame (1,206 bp) encoding a protein of 401 amino acids. Preliminary bioinformatics analysis of EaCHS1 revealed that EaCHS1 was a member of CHS family, the subcellular localization predicted that EaCHS1 was a cytoplasmic protein. To the best of our knowledge, this is the first report of conserved sequences of these genes and of a full-length EaCHS1 gene in E. adenophorum. The results indicated that CHS gene is related to allelopathy of E. adenophorum. PMID:21127986

Guo, Huiming; Pei, Xixiang; Wan, Fanghao; Cheng, Hongmei

2011-10-01

347

Gene-Gene Interaction and Functional Impact of Polymorphisms on Innate Immune Genes in Controlling Plasmodium falciparum Blood Infection Level  

PubMed Central

Genetic variations in toll-like receptors and cytokine genes of the innate immune pathways have been implicated in controlling parasite growth and the pathogenesis of Plasmodium falciparum mediated malaria. We previously published genetic association of TLR4 non-synonymous and TNF-? promoter polymorphisms with P.falciparum blood infection level and here we extend the study considerably by (i) investigating genetic dependence of parasite-load on interleukin-12B polymorphisms, (ii) reconstructing gene-gene interactions among candidate TLRs and cytokine loci, (iii) exploring genetic and functional impact of epistatic models and (iv) providing mechanistic insights into functionality of disease-associated regulatory polymorphisms. Our data revealed that carriage of AA (P?=?0.0001) and AC (P?=?0.01) genotypes of IL12B 3?UTR polymorphism was associated with a significant increase of mean log-parasitemia relative to rare homozygous genotype CC. Presence of IL12B+1188 polymorphism in five of six multifactor models reinforced its strong genetic impact on malaria phenotype. Elevation of genetic risk in two-component models compared to the corresponding single locus and reduction of IL12B (2.2 fold) and lymphotoxin-? (1.7 fold) expressions in patients'peripheral-blood-mononuclear-cells under TLR4Thr399Ile risk genotype background substantiated the role of Multifactor Dimensionality Reduction derived models. Marked reduction of promoter activity of TNF-? risk haplotype (C-C-G-G) compared to wild-type haplotype (T-C-G-G) with (84%) and without (78%) LPS stimulation and the loss of binding of transcription factors detected in-silico supported a causal role of TNF-1031. Significantly lower expression of IL12B+1188 AA (5 fold) and AC (9 fold) genotypes compared to CC and under-representation (P?=?0.0048) of allele A in transcripts of patients' PBMCs suggested an Allele-Expression-Imbalance. Allele (A+1188C) dependent differential stability (2 fold) of IL12B-transcripts upon actinomycin-D treatment and observed structural modulation (P?=?0.013) of RNA-ensemble were the plausible explanations for AEI. In conclusion, our data provides functional support to the hypothesis that de-regulated receptor-cytokine axis of innate immune pathway influences blood infection level in P. falciparum malaria.

Basu, Madhumita; Das, Tania; Ghosh, Alip; Majumder, Subhadipa; Maji, Ardhendu Kumar; Kanjilal, Sumana Datta; Mukhopadhyay, Indranil; Roychowdhury, Susanta; Banerjee, Soma; Sengupta, Sanghamitra

2012-01-01

348

The haplolethal region at the 16F gene cluster of Drosophila melanogaster: structure and function.  

PubMed Central

Extensive aneuploid analyses had shown the existence of a few haplolethal (HL) regions and one triplolethal region in the genome of Drosophila melanogaster. Since then, only two haplolethals, 22F1-2 and 16F, have been directly linked to identified genes, dpp and wupA, respectively. However, with the possible exception of dpp, the actual bases for this dosage sensitivity remain unknown. We have generated and characterized dominant-lethal mutations and chromosomal rearrangements in 16F and studied them in relation to the genes in the region. This region extends along 100 kb and includes at least 14 genes. The normal HL function depends on the integrity of a critical 4-kb window of mostly noncoding sequences within the wupA transcription unit that encodes the muscle protein troponin I (TNI). All dominant lethals are breakpoints within that window, which prevent the functional expression of TNI and other adjacent genes in the proximal direction. However, independent mutations in these genes result in recessive lethal phenotypes only. We propose that the HL at 16F represents a long-range cis regulatory region that acts upon a number of functionally related genes whose combined haploidy would yield the dominant-lethal effect.

Prado, A; Canal, I; Ferrus, A

1999-01-01

349

Functional Communication Patterns and Relational Concern in Interpersonal Conflict.  

ERIC Educational Resources Information Center

A study explored the relationship between the functional communication patterns occurring in conflict and post conflict impressions of relational concern. The first part of the study involved the development and testing of an instrument to measure perceived relational concern, while the second part investigated whether varying styles of functional

Spear, Stephen J.; Miller, Larry D.

350

Analyzing protein structure and function using ancestral gene reconstruction  

PubMed Central

Summary Protein families with functionally diverse members can illuminate the structural determinants of protein function and the process by which protein structure and function evolve. To identify the key amino acid changes that differentiate one family member from another, most studies have taken a “horizontal” approach, swapping candidate residues between present-day family members. This approach has often been stymied, however, by the fact that shifts in function often require multiple interacting mutations; chimeric proteins are often non-functional, either because one lineage has amassed mutations that are incompatible with key residues that conferred a new function on other lineages, or because it lacks mutations required to support those key residues. These difficulties can be overcome by using a vertical strategy, which reconstructs ancestral genes and uses them as the appropriate background in which to study the effects of historical mutations on functional diversification. In this review, we discuss the advantages of the vertical strategy and highlight several exemplary studies that have used ancestral gene reconstruction to reveal the molecular underpinnings of protein structure, function, and evolution.

Harms, Michael J.

2010-01-01

351

Ascorbate peroxidase-related (APx-R) is not a duplicable gene  

PubMed Central

Phylogenetic, genomic and functional analyses have allowed the identification of a new class of putative heme peroxidases, so called APx-R (APx-Related). These new class, mainly present in the green lineage (including green algae and land plants), can also be detected in other unicellular chloroplastic organisms. Except for recent polyploid organisms, only single-copy of APx-R gene was detected in each genome, suggesting that the majority of the APx-R extra-copies were lost after chromosomal or segmental duplications. In a similar way, most APx-R co-expressed genes in Arabidopsis genome do not have conserved extra-copies after chromosomal duplications and are predicted to be localized in organelles, as are the APx-R. The member of this gene network can be considered as unique gene, well conserved through the evolution due to a strong negative selection pressure and a low evolution rate.

Dunand, Christophe; Mathe, Catherine; Lazzarotto, Fernanda; Margis, Rogerio; Margis-Pinheiro, Marcia

2011-01-01

352

Differential expression of cell wall related genes in the elongation zone of rice roots under water deficit  

Microsoft Academic Search

Growth in the apical elongation zone of plant roots is central to the development of functional root systems. It has been\\u000a known that rice seminal root elongation could be enhanced by water stress. In the present study, 17 cell-wall related genes\\u000a were identified by cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique. Five genes encoded cell-wall loosening\\u000a enzymes and six genes were

L. Yang; C. C. Wang; W. D. Guo; X. B. Li; M. Lu; C. L. Yu

2006-01-01

353

Functional requirements for bacteriophage growth: Gene essentiality and expression in Mycobacteriophage Giles  

PubMed Central

Summary Bacteriophages represent a majority of all life forms, and the vast, dynamic population with early origins is reflected in their enormous genetic diversity. A large number of bacteriophage genomes have been sequenced. They are replete with novel genes without known relatives. We know little about their functions, which genes are required for lytic growth, and how they are expressed. Furthermore, the diversity is such that even genes with required functions – such as virion proteins and repressors – cannot always be recognized. Here we describe a functional genomic dissection of mycobacteriophage Giles, in which the virion proteins are identified, genes required for lytic growth are determined, the repressor is identified, and the transcription patterns determined. We find that although all of the predicted phage genes are expressed either in lysogeny or in lytic growth, 45% of the predicted genes are non-essential for lytic growth. We also describe genes required for DNA replication, show that recombination is required for lytic growth, and that Giles encodes a novel repressor. RNAseq analysis reveals abundant expression of a small non-coding RNA in a lysogen and in late lytic growth, although it is non-essential for lytic growth and does not alter lysogeny.

Dedrick, Rebekah M.; Marinelli, Laura J.; Newton, Gerald L.; Pogliano, Kit; Pogliano, Joseph; Hatfull, Graham F.

2013-01-01

354

ETS-related Gene (ERG) Controls Endothelial Cell Permeability via Transcriptional Regulation of the Claudin 5 (CLDN5) Gene*  

PubMed Central

ETS-related gene (ERG) is a member of the ETS transcription factor family. Our previous studies have shown that ERG expression is highly enriched in endothelial cells (EC) both in vitro and in vivo. ERG expression is markedly repressed in response to inflammatory stimuli. It has been shown that ERG is a positive regulator of several EC-restricted genes including VE-cadherin, endoglin, and von Willebrand factor, and a negative regulator of other genes such as interleukin (IL)-8 and intercellular adhesion molecule (ICAM)-1. In this study we have identified a novel role for ERG in the regulation of EC barrier function. ERG knockdown results in marked increases in EC permeability. This is associated with a significant increase of stress fiber and gap formation in EC. Furthermore, we identify CLDN5 as a downstream target of ERG in EC. Thus, our results suggest that ERG plays a pivotal role in regulating EC barrier function and that this effect is mediated in part through its regulation of CLDN5 gene expression.

Yuan, Lei; Le Bras, Alexandra; Sacharidou, Anastasia; Itagaki, Kiyoshi; Zhan, Yumei; Kondo, Maiko; Carman, Christopher V.; Davis, George E.; Aird, William C.; Oettgen, Peter

2012-01-01

355

Noncommutative Symmetric Functions Vi: Free Quasi-Symmetric Functions and Related Algebras  

Microsoft Academic Search

This article is devoted to the study of several algebras which are related to symmetric functions, and which admit linear bases labelled by various combinatorial objects: per- mutations (free quasi-symmetric functions), standard Young tableaux (free symmetric functions) and packed integer matrices (matrix quasi-symmetric functions). Free quasi- symmetric functions provide a kind of noncommutative Frobenius characteristic for a certain category of

Gérard Duchamp; Florent Hivert; Jean-yves Thibon

2002-01-01

356

Genetic variation in cytokine-related genes and migraine susceptibility.  

PubMed

Migraine is classified by the World Health Organization (WHO) as being one of the top 20 most debilitating diseases. According to the neurovascular hypothesis, neuroinflammation may promote the activation and sensitisation of meningeal nociceptors, inducing the persistent throbbing headache characterized in migraine. The tumor necrosis factor (TNF) gene cluster, made up of TNF?, lymphotoxin ? (LTA), and lymphotoxin ? (LTB), has been implicated to influence the intensity and duration of local inflammation. It is thought that sterile inflammation