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Search Results: 1 - 10 of 214124 matches for " Kevin L. Childs "
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Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes
Kevin L. Childs,Rebecca M. Davidson,C. Robin Buell
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0022196
Abstract: With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa) gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional annotation of those modules. Additionally, the expression patterns of genes across the treatments/conditions of an expression experiment comprise a second form of useful annotation.
The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
Alicia N. Massa, Kevin L. Childs, Haining Lin, Glenn J. Bryan, Giovanni Giuliano, C. Robin Buell
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026801
Abstract: Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family.
Expression Profiling of Cucumis sativus in Response to Infection by Pseudoperonospora cubensis
Bishwo N. Adhikari, Elizabeth A. Savory, Brieanne Vaillancourt, Kevin L. Childs, John P. Hamilton, Brad Day, C. Robin Buell
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034954
Abstract: The oomycete pathogen, Pseudoperonospora cubensis, is the causal agent of downy mildew on cucurbits, and at present, no effective resistance to this pathogen is available in cultivated cucumber (Cucumis sativus). To better understand the host response to a virulent pathogen, we performed expression profiling throughout a time course of a compatible interaction using whole transcriptome sequencing. As described herein, we were able to detect the expression of 15,286 cucumber genes, of which 14,476 were expressed throughout the infection process from 1 day post-inoculation (dpi) to 8 dpi. A large number of genes, 1,612 to 3,286, were differentially expressed in pair-wise comparisons between time points. We observed the rapid induction of key defense related genes, including catalases, chitinases, lipoxygenases, peroxidases, and protease inhibitors within 1 dpi, suggesting detection of the pathogen by the host. Co-expression network analyses revealed transcriptional networks with distinct patterns of expression including down-regulation at 2 dpi of known defense response genes suggesting coordinated suppression of host responses by the pathogen. Comparative analyses of cucumber gene expression patterns with that of orthologous Arabidopsis thaliana genes following challenge with Hyaloperonospora arabidopsidis revealed correlated expression patterns of single copy orthologs suggesting that these two dicot hosts have similar transcriptional responses to related pathogens. In total, the work described herein presents an in-depth analysis of the interplay between host susceptibility and pathogen virulence in an agriculturally important pathosystem.
Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome
Justin T Reese, Christopher P Childers, Jaideep P Sundaram, C Michael Dickens, Kevin L Childs, Donald C Vile, Christine G Elsik
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-645
Abstract: BGD has provided annotation tools that supported 147 members of the BGSAC in contributing 3,871 gene models over a fifteen-week period, and these annotations have been integrated into the bovine Official Gene Set. Our approach has been to provide an annotation system, which includes a BLAST site, multiple genome browsers, an annotation portal, and the Apollo Annotation Editor configured to connect directly to our Chado database. In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD.We have provided annotation tools that alleviate challenges associated with distributed annotation. Our system provides a consistent set of data to all annotators and eliminates the need for annotators to format data. Involving the bovine research community in genome annotation has allowed us to leverage expertise in various areas of bovine biology to provide biological insight into the genome sequence.The Bovine Genome Sequencing and Analysis Consortium (BGSAC) carried out one of the largest distributed annotation projects for a eukaryotic genome. A goal of the Bovine Genome Database (BGD; http://BovineGenome.org webcite) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in the annotation and analysis of the bovine genome. The central data for BGD are assemblies of the Bos taurus genome, which was sequenced to 7.1 fold coverage [1]. BGD currently provides data for assemblies Btau_3.1 and Btau_4.0 [2], which were generated by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), although alternative assemblies are available elsewhere [3]. Since our initial goal was to support the activities of BGSAC, our effort has been focused on tools and datasets to facilitate annotation and to maintain organization to reduce duplicated efforts.As the project started, we faced a
Computational and transcriptional evidence for microRNAs in the honey bee genome
Daniel B Weaver, Juan M Anzola, Jay D Evans, Jeffrey G Reid, Justin T Reese, Kevin L Childs, Evgeny M Zdobnov, Manoj P Samanta, Jonathan Miller, Christine G Elsik
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-6-r97
Abstract: Three independent computational surveys of the assembled honey bee genome identified a total of 65 non-redundant candidate miRNAs, several of which appear to have previously unrecognized orthologs in the Drosophila genome. A subset of these candidate miRNAs were screened for expression by quantitative RT-PCR and/or genome tiling arrays and most predicted miRNAs were confirmed as being expressed in at least one honey bee tissue. Interestingly, the transcript abundance for several known and novel miRNAs displayed caste or age-related differences in honey bees. Genes in proximity to miRNAs in the bee genome are disproportionately associated with the Gene Ontology terms 'physiological process', 'nucleus' and 'response to stress'.Computational approaches successfully identified miRNAs in the honey bee and indicated previously unrecognized miRNAs in the well-studied Drosophila melanogaster genome despite the 280 million year distance between these insects. Differentially transcribed miRNAs are likely to be involved in regulating honey bee development, and arguably in the extreme developmental switch between sterile worker bees and highly fertile queens.MicroRNAs (miRNAs) play pivotal roles in diverse biological processes through post-transcriptional regulation of gene expression. These short (approximately 22 nucleotide (nt)) non-coding RNAs repress protein synthesis by binding to partially complementary sites in the 3' untranslated regions (UTRs) of target genes [1-3]. MiRNAs affect biological phenomena such as cell proliferation, embryo and tissue differentiation [4], morphological change [5], and apoptosis, aging and life span [6]. Overall, miRNAs appear to regulate much of the coding transcriptome, influencing the spatial and temporal expression patterns of thousands of genes in plants, nematodes, insects, and vertebrates [7,8]. The pervasive influence of miRNAs exerts strong selective pressures on nucleotide sequences. Either positive selection for, or negative selec
Universal quantum computation with two-level trapped ions
Andrew M. Childs,Isaac L. Chuang
Physics , 2000, DOI: 10.1103/PhysRevA.63.012306
Abstract: Although the initial proposal for ion trap quantum computation made use of an auxiliary internal level to perform logic between ions, this resource is not necessary in principle. Instead, one may perform such operations directly using sideband laser pulses, operating with an arbitrary (sufficiently small) Lamb-Dicke parameter. We explore the potential of this technique, showing how to perform logical operations between the internal state of an ion and the collective motional state and giving explicit constructions for a controlled-not gate between ions.
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
Yoshihiro Kawahara, Melissa de la Bastide, John P Hamilton, Hiroyuki Kanamori, W Richard McCombie, Shu Ouyang, David C Schwartz, Tsuyoshi Tanaka, Jianzhong Wu, Shiguo Zhou, Kevin L Childs, Rebecca M Davidson,, Haining Lin,, Lina Quesada-Ocampo, Brieanne Vaillancourt, Hiroaki Sakai, Sung Shin Lee, Jungsok Kim, Hisataka Numa, Takeshi Itoh, C Robin Buell and Takashi Matsumoto
Rice , 2013, DOI: 10.1186/1939-8433-6-4
Abstract: A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.
Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species
Elsa Góngora-Castillo, Kevin L. Childs, Greg Fedewa, John P. Hamilton, David K. Liscombe, Maria Magallanes-Lundback, Kranthi K. Mandadi, Ezekiel Nims, Weerawat Runguphan, Brieanne Vaillancourt, Marina Varbanova-Herde, Dean DellaPenna, Thomas D. McKnight, Sarah O’Connor, C. Robin Buell
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0052506
Abstract: The natural diversity of plant metabolism has long been a source for human medicines. One group of plant-derived compounds, the monoterpene indole alkaloids (MIAs), includes well-documented therapeutic agents used in the treatment of cancer (vinblastine, vincristine, camptothecin), hypertension (reserpine, ajmalicine), malaria (quinine), and as analgesics (7-hydroxymitragynine). Our understanding of the biochemical pathways that synthesize these commercially relevant compounds is incomplete due in part to a lack of molecular, genetic, and genomic resources for the identification of the genes involved in these specialized metabolic pathways. To address these limitations, we generated large-scale transcriptome sequence and expression profiles for three species of Asterids that produce medicinally important MIAs: Camptotheca acuminata, Catharanthus roseus, and Rauvolfia serpentina. Using next generation sequencing technology, we sampled the transcriptomes of these species across a diverse set of developmental tissues, and in the case of C. roseus, in cultured cells and roots following elicitor treatment. Through an iterative assembly process, we generated robust transcriptome assemblies for all three species with a substantial number of the assembled transcripts being full or near-full length. The majority of transcripts had a related sequence in either UniRef100, the Arabidopsis thaliana predicted proteome, or the Pfam protein domain database; however, we also identified transcripts that lacked similarity with entries in either database and thereby lack a known function. Representation of known genes within the MIA biosynthetic pathway was robust. As a diverse set of tissues and treatments were surveyed, expression abundances of transcripts in the three species could be estimated to reveal transcripts associated with development and response to elicitor treatment. Together, these transcriptomes and expression abundance matrices provide a rich resource for understanding plant specialized metabolism, and promotes realization of innovative production systems for plant-derived pharmaceuticals.
Perceptions of early adolescent African-American girls concerning virginity and romantic relationships
Childs GD, White R, Hataway C, Moneyham L, Gaioso V
Nursing: Research and Reviews , 2012, DOI: http://dx.doi.org/10.2147/NRR.S37084
Abstract: ceptions of early adolescent African-American girls concerning virginity and romantic relationships Original Research (4884) Total Article Views Authors: Childs GD, White R, Hataway C, Moneyham L, Gaioso V Published Date October 2012 Volume 2012:2 Pages 55 - 65 DOI: http://dx.doi.org/10.2147/NRR.S37084 Received: 16 August 2012 Accepted: 29 September 2012 Published: 25 October 2012 Gwendolyn D Childs, Reashanda White, Connie Hataway, Linda Moneyham, Vanessa Gaioso University of Alabama at Birmingham, School of Nursing, Birmingham, AL, USA Background: Nationally, African-American girls aged 15–19 years have a higher incidence of Chlamydia, gonorrhea, and syphilis compared with White and Hispanic girls in the same age group. To address this epidemic of sexually transmitted infection, it is imperative to target African-American girls during early adolescence and before sexual debut. According to the 2011 National Youth Risk Behavior Survey, approximately 7% of African-American girls initiate sex prior to the age of 13 years. The purpose of this descriptive qualitative study was to explore the perceptions of African-American girls aged 12–14 years about virginity and relationships, and how their perceptions influence their decision to engage in or abstain from sexual activity. Methods: A convenience sample of 64 participants was recruited from community organizations in Alabama. Data were collected using individual interviews and focus groups. Individual interviews focused on values and beliefs about being a virgin, choosing boyfriends, and perceptions about good and bad relationships. Focus groups were held to validate findings from the individual interviews. Verbatim transcripts of audiotapes, observation notes, and demographic data were used as the primary data for analysis. Content analysis was used and interpretation of qualitative data to formulate meaningful categories, themes, and patterns. Qualitative research software (QSR N-Vivo ) was used to code and sort data into categories. Results: The mean age of the study sample was 12.9 years. Of 64 participants, five reported having engaged in sexual activity. The mean age of sexual debut was 13 years. Common themes that emerged included respecting oneself, the ideal boyfriend, and characteristics of a romantic relationship. Conclusion: Findings from this study suggest that the sexually transmitted infection prevention programs should build upon values related to virginity to delay sexual activity. Furthermore, the findings suggest a need for education about healthy relationships.
Perceptions of early adolescent African-American girls concerning virginity and romantic relationships
Childs GD,White R,Hataway C,Moneyham L
Nursing: Research and Reviews , 2012,
Abstract: Gwendolyn D Childs, Reashanda White, Connie Hataway, Linda Moneyham, Vanessa GaiosoUniversity of Alabama at Birmingham, School of Nursing, Birmingham, AL, USABackground: Nationally, African-American girls aged 15–19 years have a higher incidence of Chlamydia, gonorrhea, and syphilis compared with White and Hispanic girls in the same age group. To address this epidemic of sexually transmitted infection, it is imperative to target African-American girls during early adolescence and before sexual debut. According to the 2011 National Youth Risk Behavior Survey, approximately 7% of African-American girls initiate sex prior to the age of 13 years. The purpose of this descriptive qualitative study was to explore the perceptions of African-American girls aged 12–14 years about virginity and relationships, and how their perceptions influence their decision to engage in or abstain from sexual activity.Methods: A convenience sample of 64 participants was recruited from community organizations in Alabama. Data were collected using individual interviews and focus groups. Individual interviews focused on values and beliefs about being a virgin, choosing boyfriends, and perceptions about good and bad relationships. Focus groups were held to validate findings from the individual interviews. Verbatim transcripts of audiotapes, observation notes, and demographic data were used as the primary data for analysis. Content analysis was used and interpretation of qualitative data to formulate meaningful categories, themes, and patterns. Qualitative research software (QSR N-Vivo ) was used to code and sort data into categories.Results: The mean age of the study sample was 12.9 years. Of 64 participants, five reported having engaged in sexual activity. The mean age of sexual debut was 13 years. Common themes that emerged included respecting oneself, the ideal boyfriend, and characteristics of a romantic relationship.Conclusion: Findings from this study suggest that the sexually transmitted infection prevention programs should build upon values related to virginity to delay sexual activity. Furthermore, the findings suggest a need for education about healthy relationships.Keywords: sexual decision-making, sexual risk-taking, sexually transmitted infections, boyfriends
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