High-throughput phenotyping of seeds is the assessment of seed morphometry to aid in the prediction of yield, tolerance, resistance, and development of seeds in various environmental conditions. The paper focuses on the application of 3D graphics to image processing as a means to conduct seed phenotyping better. The paper proposes two algorithms - similar in the outcome, but different in implementation. The algorithms perform image processing on a variety of seeds such as wheat, soy, sorghum, rough rice, white rice, and canola to arrive at their morphometric estimations. In the area of static image processing, addressed are at least three common yet significant problems of seed clusters on images, skewed images, and poor image quality. As a means to address the problems, we propose the use of low-cost physical components. The algorithms provide the estimated count, area, perimeter, length, and width of seeds within an image.. Keyphrases: 3D graphics, high-throughput phenotyping, image ...
Introduction: Functional movement disorders (FMD) refer to a group of movement disorders that present with clinical characteristics incongruent to those due to established pathophysiologic processes, as for example in the case of neurodegeneration or lesions. The aim of this study was to assess clinical features that contribute to the specific phenotypic presentations and disease course of FMD.Methods: The study consisted of 100 patients with FMD treated at Clinic for Neurology, Clinical Center of Serbia, who were longitudinally observed. Comprehensive clinical and psychiatric assessment was performed at the baseline, when initial FMD phenotype was defined. Follow-up assessment of phenotypic pattern over the time and clinical course was done after 3.2 ± 2.5 years at average.Results: We showed that 48% of FMD patients were prone to changes of phenotypic pattern during the disease course. Dystonia had tendency to remains as single and unchanged phenotype over the time (68.2%), while patients initially
Genomic selection (GS) and high-throughput phenotyping (HTP) have great potential to increase the efficiency of wheat, Triticum aestivum L., breeding programs. GS is the use of markers covering the whole genome for selection. With GS, reviewed by Lorenz et al. (2011), a training set that has been phenotyped and genotyped is used to calibrate a prediction model, which is then used predict the breeding values of a test set of genotyped selection candidates. This enables indirect selection for quantitative traits prior to phenotyping. Genomic selection has already been implemented in dairy cattle breeding to increase rates of genetic gain (Pryce and Daetwyler 2012), and simulation studies have demonstrated that GS can increase rates of genetic gain in crop plants (Bernardo and Yu 2007; Wong and Bernardo 2008; Heffner et al. 2010). In contrast to GS, HTP is the use of remote and proximal sensing to measure a large number of phenotypes across time and space at low cost and with less labor ...
In this dissertation we expose the results of two research conducted using high-throughput phenotyping techniques with the aim of discovery the genetic bases underling drought adaptive traits in maize and durum wheat. In the first study, we used a maize Introgression Library (IL) derived from the cross between Gaspé Flint (an early flowering Canadian landrace) and B73 (an elite genetics reference line) which was previously shown to segregate for phenology and seminal root architecture (SRA). The IL was phenotypically evaluated in the high-throughput platform PhenoArch (INRA, Montpellier), for large-scale automated imagery and evapotranspiration measurements of potted plants in controlled environment, under well-watered and water-deficit conditions. Biomass accumulation for each plant was estimated by software and model-assisted imaging analysis. Several QTLs were detected (Dunnet test p-value , 0.05) for biomass accumulation and water-use efficiency (WUE) on chr. 1, 2, 3, 4, 7, 8, and 9). In ...
High-throughput phenotyping has opened whole new perspectives for crop improvement and better understanding of quantitative traits in plants. Generation of loss-of-function and gain-of-function plant
Although a phenotype is the ensemble of observable characteristics displayed by an organism, the word phenome is sometimes used to refer to a collection of traits, while the simultaneous study of such a collection is referred to as phenomics.[12][13] Phenomics is an important field of study because it can be used to figure out which genomic variants affect phenotypes which then can be used to explain things like health, disease, and evolutionary fitness.[14] Phenomics forms a large part of the Human Genome Project[15]. Phenomics has widespread applications in the agricultural industry. With an exponentially growing population and inconsistent weather patterns due to global warming, it has become increasingly difficult to cultivate enough crops to support the worlds population. Advantageous genomic variations, like drought and heat resistance, can be identified through the use of phenomics to create more durable GMOs.[16][17]. Phenomics is also a crucial stepping stone towards personalized ...
In field and laboratory studies of birds, positive associations between male phenotype and success at obtaining extra-pair copulations or extra pair fertilizations are often interpreted as providing evidence that females are using extra-pair copulations to obtain indirect benefits for their offspring, either through genes for increased viability, or for a fisherian mating advantage. I describe a simple model, in which functional fertility (the success of ejaculates in fertilizing eggs) covaries with male phenotype, which can explain the observed associations equally well. Under such a model, females pursue extra-pair copulations as insurance against the functional infertility of their mate, and obtain only direct benefits for themselves in their current reproductive event. Several studies of birds suggest that a relation between male phenotype and functional fertility is often likely to exist and that there are many potential causes of functional infertility. Non-manipulative field studies are unlikely
Autor: Müller, Oliver et al.; Genre: Zeitschriftenartikel; Im Druck veröffentlicht: 2004; Keywords: bioorganic chemistry • combinatorial chemistry • library screening • medicinal chemistry • signal transduction; Titel: Identification of potent Ras signaling inhibitors by pathway-selective phenotype-based screening
Abstract Motivation Determining the relative contributions of functional genetic categories is fundamental to understanding the genetic etiology of complex human traits and diseases. Here, we present Annotation Informed-MiXeR, a likelihood-based method for estimating the number of variants influencing a phenotype and their effect sizes across different functional annotation categories of the genome using summary statistics from genome-wide association studies. Results Extensive simulations demonstrate that the model is valid for a broad range of genetic architectures. The model suggests that complex human phenotypes substantially differ in the number of causal variants, their localization in the genome and their effect sizes. Specifically, the exons of protein-coding genes harbor more than 90% of variants influencing type 2 diabetes and inflammatory bowel disease, making them good candidates for whole-exome studies. In contrast, <10% of the causal variants for schizophrenia, bipolar disorder ...
The Mammalian Phenotype (MP) Ontology is a community effort to provide standard terms for annotating phenotypic data. You can use this browser to view terms, definitions, and term relationships in a hierarchical display. Links to summary annotated phenotype data at MGI are provided in Term Detail reports.
The Mammalian Phenotype (MP) Ontology is a community effort to provide standard terms for annotating phenotypic data. You can use this browser to view terms, definitions, and term relationships in a hierarchical display. Links to summary annotated phenotype data at MGI are provided in Term Detail reports.
Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environment-friendly way becomes increasingly important. Therefore, rice research community needs to share resources to better understand functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants.|br| We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93,000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the database at Taiwan Rice Insertional Mutants Database (http://trim.sinica.edu.tw).|br| Detailed analyses of
Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environment-friendly way becomes increasingly important. Therefore, rice research community needs to share resources to better understand functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants.|br| We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93,000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the database at Taiwan Rice Insertional Mutants Database (http://trim.sinica.edu.tw).|br| Detailed analyses of
Purpose : Age-related macular degeneration (AMD) is a multifactorial disease with a highly variable phenotypic presentation. Recently, a Genome-Wide Association Study identified 52 single nucleotide polymorphisms (SNPs) that showed an association with AMD. These genetic variants may represent different pathways involved in AMD pathogenesis and contribute to the variability of the phenotype. We performed a Deep Phenotype Association Study (DeePAS) in Age-Related Eye Disease Study 2 (AREDS2) to identify variants that are related to specific AMD and non-AMD phenotypes. Methods : Genotyping information of the 52 GWAS SNPs was available for 1826 AREDS2 participants. AREDS2 participants have had detailed phenotyping for AMD characteristics and have been assessed for phenotypes related to other retinal disease, cataract, cardiovascular disease, neurological disease, cognitive function, gastro-intestinal and endocrine disease, nutrient serum levels and other. In total, we distinguished 138 phenotypes. ...
TY - JOUR. T1 - Age-related M1/M2 phenotype changes in circulating monocytes from healthy/unhealthy individuals. AU - Costantini, Andrea. AU - Viola, Nadia. AU - Berretta, Antonella. AU - Galeazzi, Roberta. AU - Matacchione, Giulia. AU - Sabbatinelli, Jacopo. AU - Storci, Gianluca. AU - De Matteis, Serena. AU - Butini, Luca. AU - Rippo, Maria Rita. AU - Procopio, Antonio Domenico. AU - Caraceni, Daniele. AU - Antonicelli, Roberto. AU - Olivieri, Fabiola. AU - Bonafè, Massimiliano. PY - 2018/6/1. Y1 - 2018/6/1. N2 - Macrophage polarization is a candidate biomarker of disease-related inflammatory status, but its modulation during aging has not been investigated. To do this, the M1/M2 profile was assessed by CD80/CD163 gating in classical (CD14++CD16-), intermediate (CD14++CD16+), and non-classical (CD14lowCD16+) monocytes from 31 healthy subjects (CTRs) of different ages. Cytofluorimetric analysis showed a significantly different CD80/CD163 distribution in the three subsets, as more than 80% of ...
This study had three objectives: (1) to determine the degree to which within-source genetic variation and genetic correlations differ among elevational sources of Douglas-fir [Pseudotsuga menziesii (Mirb). Franco var. menziesii]; (2) to ascertain the degree to which phenotypic stability differs among and within elevational sources; and (3) to compare the relationships among four measures of stability (variance, regression slope coefficient, deviation from regression and ecovalence). To accomplish the objectives seeds were collected from 10 parent trees in three populations from each of three elevations. Nine traits were measured on two-year-old seedlings grown in four test environments that factorially combined heated and unheated air and soil. Results support the hypothesis that the magnitude of within-source genetic variation is homogeneous among elevations. However1 genetic correlations between growth and phenological traits varied by elevation. For example, increased height was positively ...
Polyphyly of the genus Canoparmelia- uncovering incongruences between phenotype-based classification and molecular phylogeny within lichenized Ascomycota (Parmeliaceae)
The mechanisms by which adaptive phenotypes spread within an evolving population after their emergence are understood fairly well. Much less is known about the factors that influence the evolutionary accessibility of such phenotypes, a pre-requisite for their emergence in a population. Here, we investigate the influence of environmental quality on the accessibility of adaptive phenotypes of Escherichia colis central metabolic network. We used an established flux-balance model of metabolism as the basis for a genotype-phenotype map (GPM). We quantified the effects of seven qualitatively different environments (corresponding to both carbohydrate and gluconeogenic metabolic substrates) on the structure of this GPM. We found that the GPM has a more rugged structure in qualitatively poorer environments, suggesting that adaptive phenotypes could be intrinsically less accessible in such environments. Nevertheless, on average approximately 74% of the genotype can be altered by neutral drift, in the ...
Autor: Dauwe, R. et al.; Genre: Zeitschriftenartikel; Im Druck veröffentlicht: 2007; Keywords: metabolomics|br/|transcriptomics|br/|ccr|br/|cad|br/|oligolignol|br/|cinnamyl-alcohol-dehydrogenase|br/|ammonia-lyase gene|br/|transgenic tobacco|br/|down-regulation|br/|arabidopsis-thaliana|br/|o-methyltransferase|br/|coa reductase|br/|phenylpropanoid metabolism|br/|chlorophyll fluorescence|br/|transcriptome analysis; Titel: Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration
When ordering genetic testing or triaging candidate variants in exome and genome sequencing studies, it is critical to generate and test a comprehensive list of candidate genes that succinctly describe the complete and objective phenotypic features of disease. Significant efforts have been made to curate gene:disease associations both in academic research and commercial genetic testing laboratory settings. However, many of these valuable resources exist as islands and must be used independently, generating static, single-resource gene:disease association lists. Here we describe genepanel.iobio (https://genepanel.iobio.io) an easy to use, free and open-source web tool for generating disease- and phenotype-associated gene lists from multiple gene:disease association resources, including the NCBI Genetic Testing Registry (GTR), Phenolyzer, and the Human Phenotype Ontology (HPO). We demonstrate the utility of genepanel.iobio by applying it to complex, rare and undiagnosed disease cases that had reached a
THAP1 mutations have been shown to be the cause of DYT6. A number of different mutation types and locations in the THAP1 gene have been associated with a range of severity and dystonia phenotypes, but, as yet, it has been difficult to identify clear genotype phenotype patterns. Here, we screened the THAP1 gene in a further series of dystonia cases and evaluated the mutation pathogenicity in this series as well as previously reported mutations to investigate possible phenotype-genotype correlations. THAP1 mutations have been identified throughout the coding region of the gene, with the greatest concentration of variants localized to the THAP1 domain. In the additional cases analyzed here, a further two mutations were found. No obvious, indisputable genotype-phenotype correlation emerged from these data. However, we managed to find a correlation between the pathogenicity of mutations, distribution, and age of onset of dystonia. THAP1 mutations are an important cause of dystonia, but, as yet, no ...
An ontology of anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. The Xenopus Phenotype Ontology represents and standardizes anatomical, cellular, and gene function phenotypes in Xenopus, the African clawed frogs. The XPO is being designed primarily to support phenotype curation in Xenbase, the model organism database for Xenopus, and to facilitate mappings between frog phenotypes and human disease ...
TY - JOUR. T1 - Lentivirus delivery of IL-10 to promote and sustain macrophage polarization towards an anti-inflammatory phenotype. AU - Boehler, R. M.. AU - Kuo, R.. AU - Shin, S.. AU - Goodman, A. G.. AU - Pilecki, M. A.. AU - Leonard, J. N.. AU - Shea, L. D.. PY - 2014/6. Y1 - 2014/6. N2 - Gene delivery from biomaterials can create an environment that promotes and guides tissue formation. However, the immune response induced upon biomaterial implantation can be detrimental to tissue regeneration. Macrophages play a central role in mediating early phases of this response, and functional polarization of macrophages towards M1 (inflammatory) or M2 (anti-inflammatory) phenotypes may bias the local immune state at the implant site. Since gene delivery from biomaterial scaffolds can confer transgene expression in macrophages in vivo, we investigated whether transduction of macrophages with an IL-10 encoding lentivirus can (1) induce macrophage polarization toward an M2 phenotype even in an ...
Epigenetic phenomena, such as DNA methylation, histone modifications, changes in chromatin structure or effects of non coding RNAs, affect gene expression and thus are expected to have important effects on phenotypes. The phenotypic diversity of a population is the result of both genetic and epigenetic variations, with epigenetics accounting for a portion of the variability of complex traits that is linked to interactions with the environment [1, 2]. The real contribution of epigenetics to phenotypic variation remains to be evaluated, but it is an attractive new path in animal breeding that might help to explain the missing causality of complex traits [3]. In recent years, a growing number of studies have shown that epigenetic information can be transmitted across generations. In particular, the intergenerational transmission of DNA methylation and the influence of epigenetic marks on phenotype variability has been clearly established in plants [4]. These phenomena could also partly explain the ...
The Annual Meeting of the UK Plant Phenomics Network will take place 13:00-16:00 on Friday 8th April, at the Sutton Bonington campus of the University of Nottingham. (This meeting follows directly after the UKPPN root phenotyping workshop).
Phenotype prediction from genome-wide association studies: application to smoking behaviors. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains
Until further notice, in response to COVID-19, I-Share requesting and Statewide Library Delivery are temporarily suspended, and I-Share library materials will not be considered overdue.. As of June 24, 2020, the I-Share catalog and your local library catalog have moved to a new system! This catalog is no longer being updated and you cannot request or renew materials here; it will be retired on Oct. 30, 2020. Please visit https://i-share.carli.illinois.edu to find the new URL to access the new library catalog system. ...
Functional mannose-binding lectin (f-MBL) plays an important role in the innate neonatal immune system. We studied the origin of f-MBL in umbilical cord blood (UCB) by measuring maternal MBL (n=47), collected before elective cesarean section, and neo
Regulation of alveolar epithelial cell phenotypes in fetal sheep: roles of cortisol and lung expansion.: Our aim was to determine whether cortisols effect on a
However, environmental changes during early development may result in the selected trajectory becoming inappropriate, resulting in adverse effects on health. This paradox generates doubts about whether the thrifty phenotype is adaptive for human offspring. Thus, the thrifty phenotype should be considered as the capacity of all offspring to respond to environmental cues during early ontogenetic development. It has been suggested that the thrifty phenotype is the consequence of three unlike adaptive processes: maternal effects, niche construction and developmental plasticity, which all are influenced by the brain. While developmental plasticity demonstrates an adaptation by the offspring, niche construction and parental effects are result of parental selections rather than offspring fitness. Therefore, the thrifty phenotype can be described as a manipulation of offspring phenotype for the benefit of maternal fitness. The information that enters offspring phenotype during early development mirror ...
Enormous progress in mapping complex traits in humans has been made in the last 5 yr. There has been early success for prevalent diseases with complex phenotypes. These studies have demonstrated clearly that, while complex traits differ in their underlying genetic architectures, for many common disorders the predominant pattern is that of many loci, individually with small effects on phenotype. For some traits, loci of large effect have been identified. For almost all complex traits studied in humans, the sum of the identified genetic effects comprises only a portion, generally less than half, of the estimated trait heritability. A variety of hypotheses have been proposed to explain why this might be the case, including untested rare variants, and gene-gene and gene-environment interaction. Effort is currently being directed toward implementation of novel analytic approaches and testing rare variants for association with complex traits using imputed variants from the publicly available 1000 ...
This study focuses on the participants of the Long Life Family Study to elucidate whether biogenetic mechanisms underlying relationships among heritable complex phenotypes in parents function in the same way for the same phenotypes in their children. Our results reveal 3 characteristic groups of relationships among phenotypes in parents and children. One group composed of 3 pairs of phenotypes confirms that associations among some phenotypes can be explained by the same biogenetic mechanisms working in parents and children. Two other groups including 9 phenotype pairs show that this is not a common rule. Our findings suggest that biogenetic mechanisms underlying relationships among different phenotypes, even if they are causally related, can function differently in successive generations or in different age groups of biologically related individuals. The results suggest that the role of aging-related processes in changing environment may be conceptually underestimated in current genetic ...
71.31% of tested genes with null mutations on a B6N genetic background have a phenotype association to embryonic lethality prior to organogenesis (251/352) ...
Human Phenotype Ontology, a standardized vocabulary of phenotypic abnormalities encountered in human disease. With unmatched depth it enables clinicians to record and analyse data with extremely accurate computer interpretable ontology terms. Developed by The Monarch Initiative.
Human Phenotype Ontology, a standardized vocabulary of phenotypic abnormalities encountered in human disease. With unmatched depth it enables clinicians to record and analyse data with extremely accurate computer interpretable ontology terms. Developed by The Monarch Initiative.
Improving efficiency of disease diagnosis based on phenotype ontology is a critical yet challenging research area. Recently, Human Phenotype Ontology (HPO)-based semantic similarity has been affectively and widely used to identify causative genes and diseases. However, current phenotype similarity measurements just consider the annotations and hierarchy structure of HPO, neglecting the definition description of phenotype terms. In this paper, we propose a novel phenotype similarity measurement, termed as DisPheno, which adequately incorporates the definition of phenotype terms in addition to HPO structure and annotations to measure the similarity between phenotype terms. DisPheno also integrates phenotype term associations into phenotype-set similarity measurement using gene and disease annotations of phenotype terms. Compared with five existing state-of-the-art methods, DisPheno shows great performance in HPO-based phenotype semantic similarity measurement and improves the efficiency of disease
From cell senescence to age-related diseases: differential mechanisms of action of senescence-associated secretory phenotypes - Age-associated diseases;Cell senescence;Differential expression;Senescence-associated secretory phenotypes (SASP);
Human Phenotype Ontology:HP:0000212,MedGen:C0017567,Human Phenotype Ontology:HP:0000316,MedGen:CN000296,Human Phenotype Ontology:HP:0000821,MedGen:C0020676,Human Phenotype Ontology:HP:0001382,MedGen:C1844820,Human Phenotype Ontology:HP:0001636,MedGen:CN001489,Human Phenotype Ontology:HP:0002019,MedGen:C0009806,Human Phenotype Ontology:HP:0004322,MedGen:C0349588,Human Phenotype Ontology:HP:0012471,MedGen:C1836543,MeSH:C536914,MedGen:C0238462,Orphanet:ORPHA1332,SNOMED CT:255032005,MeSH:D013964,MedGen:C0040136,MeSH:D018761,MedGen:C0025267,OMIM:131100,Orphanet:ORPHA652,SNOMED CT:30664006,MeSH:D018813,MedGen:C0025268,OMIM:171400,Orphanet:ORPHA247698,SNOMED CT:61808009,MeSH:D018814,MedGen:C0025269,OMIM:162300,Orphanet:ORPHA247709,SNOMED CT:6153000,SNOMED CT:61530001,MedGen:C0031511,OMIM:171300,MedGen:C1833929,MedGen:C1970712,OMIM:610755,Orphanet:ORPHA276152,MedGen:CN073359,Orphanet:ORPHA653,SNOMED CT:61808009,MedGen:CN169374,MedGen: ...
Candida dubliniensis is closely related to Candida albicans, a major causative agent of candidiasis, and is primarily associated with oral colonization and infection in human immunodeficiency virus (HIV)-positive patients. Despite the high similarity of genomic and phenotypic features between the two species, C. dubliniensis is much less virulent and less prevalent than C. albicans. The ability to change morphological phenotypes is a striking feature of Candida species and is linked to virulence. In this study, we report a novel phenotype, the gray phenotype, in C. dubliniensis. Together with the previously reported white and opaque cell types, the gray phenotype forms a tristable phenotypic switching system in C. dubliniensis that is similar to the white-gray-opaque tristable switching system in C. albicans. Gray cells of C. dubliniensis are similar to their counterparts in C. albicans in terms of several biological aspects including cellular morphology, mating competence, and genetic ...
Typical Rett syndrome (RTT) is a pediatric disorder caused by loss-of-function mutations in the methyl-CpG binding protein 2 (MECP2) gene. The demonstrated reversibility of RTT-like phenotypes in mice suggests that MECP2 gene replacement is a potential therapeutic option in patients. We report improvements in survival and phenotypic severity in Mecp2-null male mice after neonatal intracranial delivery of a single-stranded (ss) AAV9/chicken β-actin (CBA)-MECP2 vector. Median survival was 16.6 weeks for MECP2-treated versus 9.3 weeks for green fluorescent protein (GFP)-treated mice. ssAAV9/CBA-MECP2-treated mice also showed significant improvement in the phenotype severity score, in locomotor function, and in exploratory activity, as well as a normalization of neuronal nuclear volume in transduced cells. Wild-type (WT) mice receiving neonatal injections of the same ssAAV9/CBA-MECP2 vector did not show any significant deficits, suggesting a tolerance for modest MeCP2 overexpression. To test a ...
TY - JOUR. T1 - Molecular phenotyping of HCS-2/8 cells as an in vitro model of human chondrocytes. AU - Saas, J.. AU - Lindauer, K.. AU - Bau, B.. AU - Takigawa, M.. AU - Aigner, Thomas. N1 - Funding Information: Funding sources: This work was supported by the BMBF (grant 01GG9824) and Aventis Pharma Deutschland GmbH. Funding Information: This work was supported by the BMBF (grant 01GG9824) and Aventis Pharma Deutschland GmbH. We are grateful to Drs M.B. Goldring (Boston) and J. Block (Chicago) for the chondrocyte cell lines C28I2 and C28a4 as well as AG and SG. The SW1353 chondrosarcoma cell line was obtained by ATCC (Manassas, Virginia, USA).. PY - 2004/11. Y1 - 2004/11. N2 - Objective: Cultures of primary articular chondrocytes for studying chondrocyte biology are notoriously difficult to handle. One alternative is the use of chondrocytic cell lines. Because the HCS-2/8 cells are the most widely used cell line in cartilage research, we investigated the molecular phenotype of these cells by ...
TY - JOUR. T1 - Phenotype severity in the bladder exstrophy-epispadias complex. T2 - Analysis of genetic and nongenetic contributing factors in 441 families from North America and Europe. AU - Reutter, Heiko. AU - Boyadjiev, Simeon A.. AU - Gambhir, Lisa. AU - Ebert, Anne Karoline. AU - Rösch, Wolfgang H.. AU - Stein, Raimund. AU - Schröder, Annette. AU - Boemers, Thomas M.. AU - Bartels, Enrika. AU - Vogt, Hannes. AU - Utsch, Boris. AU - Müller, Martin. AU - Detlefsen, Birte. AU - Zwink, Nadine. AU - Rogenhofer, Sebastian. AU - Gobet, Rita. AU - Beckers, Goedele M A. AU - Bökenkamp, Arend. AU - Kajbafzadeh, Abdol Mohammad. AU - Jaureguizar, Enrique. AU - Draaken, Markus. AU - Lakshmanan, Yegappan. AU - Gearhart, John Phillip. AU - Ludwig, Michael. AU - Nöthen, Markus M.. AU - Jenetzky, Ekkehart. PY - 2011/11. Y1 - 2011/11. N2 - Objective: To identify genetic and nongenetic risk factors that contribute to the severity of the bladder exstrophy-epispadias complex (BEEC). Study design: ...
Metabolic variations occur during normal pregnancy to provide the growing fetus with a supply of nutrients required for its development and to ensure the health of the woman during gestation. Mass spectrometry-based metabolomics was employed to study the metabolic phenotype variations in the maternal plasma that are induced by pregnancy in each of its three trimesters. Nontargeted metabolomics analysis showed that pregnancy significantly altered the profile of metabolites in maternal plasma. The levels of six metabolites were found to change significantly throughout pregnancy, with related metabolic pathway variations observed in biopterin metabolism, phospholipid metabolism, amino acid derivatives, and fatty acid oxidation. In particular, there was a pronounced elevation of dihydrobiopterin (BH2), a compound produced in the synthesis of dopa, dopamine, norepinephrine, and epinephrine, in the second trimester, whereas it was markedly decreased in the third trimester. The turnover of BH2 and tryptophan
TY - JOUR. T1 - Genotype/Phenotype Correlations in Tuberous Sclerosis Complex. AU - Curatolo, Paolo. AU - Moavero, Romina. AU - Roberto, Denis. AU - Graziola, Federica. PY - 2015/12/1. Y1 - 2015/12/1. N2 - Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by the development of widespread hamartomatous lesions in various organs, including brain, skin, kidneys, heart, and eyes. Central nervous system is almost invariably involved, with up to 85% of patients presenting with epilepsy, and at least half of patients having intellectual disability or other neuropsychiatric disorders including autism spectrum disorder. TSC is caused by the mutation in one of the 2 genes TSC1, at 9q34, and TSC2, at 16p13.3. They respectively encode for hamartin and tuberin, which form an intracellular complex inhibiting the mammalian target of rapamycin. Mammalian target of rapamycin overactivation following the genetic defect determines the cell growth and proliferation responsible for ...
TY - JOUR. T1 - Interferon regulatory factor 3 plays an anti-inflammatory role in microglia by activating the PI3K/Akt pathway. AU - Tarassishin, Leonid. AU - Suh, Hyeon Sook. AU - Lee, Sunhee C.. PY - 2011/12/30. Y1 - 2011/12/30. N2 - Background: Microglia are the principal cells involved in the innate immune response in the CNS. Activated microglia produce a number of proinflammatory cytokines implicated in neurotoxicity but they also are a major source of anti-inflammatory cytokines, antiviral proteins and growth factors. Therefore, an immune therapy aiming at suppressing the proinflammatory phenotype while enhancing the anti-inflammatory, growth promoting phenotype would be of great benefit. In the current study, we tested the hypothesis that interferon regulatory factor 3 (IRF3), a transcription factor required for the induction of IFNβ following TLR3 or TLR4 activation, is critical to the microglial phenotype change from proinflammatory to anti-inflammatory, and that this phenotype change ...
Neurobehavioral phenotype in Prader-Willi syndrome.: The focus of this article is on the lifetime development of people with Prader-Willi syndrome (PWS) and spe
TY - JOUR. T1 - Improving the diagnostic yield of exome-sequencing by predicting gene-phenotype associations using large-scale gene expression analysis. AU - Deelen, Patrick. AU - van Dam, Sipko. AU - Herkert, Johanna C. AU - Karjalainen, Juha M. AU - Brugge, Harm. AU - Abbott, Kristin M. AU - van Diemen, Cleo C. AU - van der Zwaag, Paul A. AU - Gerkes, Erica H. AU - Zonneveld-Huijssoon, Evelien. AU - Boer-Bergsma, Jelkje J. AU - Folkertsma, Pytrik. AU - Gillett, Tessa. AU - van der Velde, K Joeri. AU - Kanninga, Roan. AU - van den Akker, Peter C. AU - Jan, Sabrina Z. AU - Hoorntje, Edgar T. AU - Te Rijdt, Wouter P. AU - Vos, Yvonne J. AU - Jongbloed, Jan D H. AU - van Ravenswaaij-Arts, Conny M A. AU - Sinke, Richard. AU - Sikkema-Raddatz, Birgit. AU - Kerstjens-Frederikse, Wilhelmina S. AU - Swertz, Morris A. AU - Franke, Lude. PY - 2019/6/28. Y1 - 2019/6/28. N2 - The diagnostic yield of exome and genome sequencing remains low (8-70%), due to incomplete knowledge on the genes that cause ...
TY - JOUR. T1 - Genetically predicted body mass index and Alzheimers disease-related phenotypes in three large samples. T2 - Mendelian randomization analyses. AU - Adult Changes in Thought Study Investigators. AU - Religious Orders Study/Memory and Aging Project Investigators. AU - Alzheimers Disease Genetics Consortium. AU - Mukherjee, Shubhabrata. AU - Walter, Stefan. AU - Kauwe, John S K. AU - Saykin, Andrew J.. AU - Bennett, David A.. AU - Larson, Eric B.. AU - Crane, Paul K.. AU - Glymour, M. Maria. AU - Albert, Marilyn S.. AU - Albin, Roger L.. AU - Apostolova, Liana G.. AU - Arnold, Steven E.. AU - Asthana, Sanjay. AU - Atwood, Craig S.. AU - Baldwin, Clinton T.. AU - Barber, Robert C.. AU - Barmada, Michael M.. AU - Barnes, Lisa L.. AU - Beach, Thomas G.. AU - Becker, James T.. AU - Beecham, Gary W.. AU - Beekly, Duane. AU - Bigio, Eileen H.. AU - Bird, Thomas D.. AU - Blacker, Deborah. AU - Boeve, Bradley F.. AU - Bowen, James D.. AU - Boxer, Adam. AU - Burke, James R.. AU - Buxbaum, ...
As the human genome project approaches completion, the challenge for mammalian geneticists is to develop approaches for the systematic determination of mammalian gene function. Mouse mutagenesis will be a key element of studies of gene function. Phenotype-driven approaches using the chemical mutagen ethylnitrosourea (ENU) represent a potentially efficient route for the generation of large numbers of mutant mice that can be screened for novel phenotypes. The advantage of this approach is that, in assessing gene function, no a priori assumptions are made about the genes involved in any pathway. Phenotype-driven mutagenesis is thus an effective method for the identification of novel genes and pathways. We have undertaken a genome-wide, phenotype-driven screen for dominant mutations in the mouse. We generated and screened over 26,000 mice, and recovered some 500 new mouse mutants. Our work, along with the programme reported in the accompanying paper, has led to a substantial increase in the mouse mutant
Now that genome-wide association studies (GWAS) are dominating the landscape of genetic research on neuropsychiatric syndromes, investigators are being faced with complexity on an unprecedented scale. It is now clear that phenomics, the systematic study of phenotypes on a genome-wide scale, comprise …
Bergmann glia (Bg) respond to the early postnatal Purkinje cell (Pc) death in Lurcher (Lc) mutant mouse cerebellum by down-regulating expression of the enzyme glycerol-3-phosphate dehydrogenase (GPDH). To determine whether glial GPDH expression requires the continued presence of Pcs in adults, we us …
Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in
Genome-scale metabolic models (GEMs) allow predicting metabolic phenotypes from limited data on uptake and secretion fluxes by defining the space of all the feasible solutions and excluding physio-chemically and biologically unfeasible behaviors. The integration of additional biological information in genome-scale models, e.g., transcriptomic or proteomic profiles, has the potential to improve phenotype prediction accuracy. This is particularly important for metabolic engineering applications where more accurate model predictions can translate to more reliable model-based strain design. Here we present a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO) model of Bacillus subtilis, which uses publicly available proteomic data and enzyme kinetic parameters for central carbon (CC) metabolic reactions to constrain the flux solution space. This model allows more accurate prediction of the flux distribution and growth rate of wild-type and single-gene/operon deletion strains compared to a
Chitosan (C), alginate-crosslinked chitosan (CA), and pectin-crosslinked chitosan (CP) were covalently bonded to Ti-6Al-4V surfaces and tested for their biocompatibility. Compared to the clinically treated Ti-6Al-4V surface (Ti64), C, CA, and CP, had higher contact angles and promoted higher cell proliferation, type I collagen deposition, and mineralization after two weeks (all p|0.05). Cells on C, CA, and CP expressed more alkaline phosphatase (ALP) activity compared to those on Ti64 (p|0.05). The swelling ratios and drug release efficacies of CA and CP were significantly higher and lower, respectively, than those of C (both p|0.05). Only cells on CA expressed ALP activity after three weeks of culture. Generally speaking, crosslinking with alginate and pectin changed surface wettability as well as the swelling and drug release properties of the chitosan coatings. Cells on the coatings had higher proliferation, type I collagen deposition, and degree of mineralization compared to those on Ti64.
TY - JOUR. T1 - The ER-positive / PgR-negative breast cancer phenotype is not associated with mutations within the DNA binding domain. AU - Fuqua, Suzanne A.W.. AU - Allred, D. Craig. AU - Elledge, Richard M.. AU - Krieg, Shelly L.. AU - Benedix, Margaret G.. AU - Nawaz, Zafar. AU - OMalley, Bert W.. AU - Greene, Geoffrey L.. AU - McGuire, William L.. N1 - Copyright: Copyright 2007 Elsevier B.V., All rights reserved.. PY - 1993/1. Y1 - 1993/1. N2 - We have used in vitro DNA binding assays as a measure of estrogen receptor (ER) function in human breast tumors. We found that the majority of ER+ (25 ER+/progesterone receptor [PgR]+, and 25 ER+/PgR-) tumors we examined were capable of binding consensus estrogen response element (ERE) oligonucleotides in this assay system. We found significant proteolytic activity in many of the tumors such that protease inhibitors were found to be essential during the preparation of tumor extracts. We next applied direct sequence analysis of the ER DNA binding ...
Gene expression profiles of multiple breast cancer phenotypes and response to neoadjuvant chemotherapy.s profile, publications, research topics, and co-authors
Multi-Minicore DiseaseSearching for Boundaries: Phenotype Analysis of 38 Cases Ana Ferreiro, MD,* Brigitte Estournet, MD, Danielle Chateau, MSci,* Norma B. Romero,
TY - JOUR. T1 - Berberine inhibits myofibroblast differentiation in nasal polyp-derived fibroblasts via the p38 pathway. AU - Moon, You Mi. AU - Park, Il Ho. AU - Cho, Jung Sun. AU - Um, Ji Young. AU - Kim, Tae-Hoon. AU - Lee, Heung Man. PY - 2013/1/1. Y1 - 2013/1/1. N2 - The purposes of this study were to determine whether berberine has any effect on phenotype changes and extracellular matrix (ECM) production in nasal polyp-derived fibroblasts (NPDFs) and to investigate the underlying molecular mechanism. NPDFs were pre-treated with berberine prior to induction by transforming growth factor (TGF)-β1. The expression of α-smooth muscle actin (SMA) and collagen type I mRNA was determined by a reverse transcription-polymerase chain reaction, and the expression of α-SMA protein and collagen type I was determined by western blotting and/or immunofluorescent staining. The total soluble collagen production was analysed by the SirCol collagen assay. The expression of several signaling molecules of ...
Motor symptoms in Huntingtons Disease (HD) are commonly assessed by the Unified Huntingtons Disease Rating Scale-Total Motor Score (UHDRS-TMS). However, the UHDRS-TMS is limited by interrater variability, its categorical nature, and insensitivity in premanifest subjects. More objective and quantitative measures of motor phenotype may complement the use of the UHDRS-TMS as outcome measure and increase the power and sensitivity of clinical trials. Deficits in tongue protrusion are well acknowledged in HD and constitute a subitem of the UHDRS-TMS. We, therefore, investigated whether objective and quantitative assessment of tongue protrusion forces (TPF) provides measures that (1) correlate to the severity of motor phenotype detected in the UHDRS-TMS in symptomatic HD, (2) detect a motor phenotype in premanifest HD gene-carriers, and (3) exhibit a correlation to the genotype as assessed by a disease burden score (based on CAG-repeat length and age). Using a precalibrated force transducer, the ...
Epigenetic regulation of gene expression is a developing field of study with many potential therapeutic applications. Chromatin remodeling is necessary for proper mammalian development, and misregulation of this process is associated with many human diseases. Three mechanisms by which chromatin structure is modified include methylation of the DNA, covalent modification of histone tails, and repositioning of nucleosomes by ATP dependant chromatin remodeling enzymes. To further increase our knowledge of the mechanisms and proteins involved in the modification of chromatin structure I undertook two projects; the role of DNA methylation in the regulation of human β-globin gene expression, and analysis of the Chd6 ATPase-/- mouse. Methylation status of the human β-globin gene promoters correlates with the expression pattern of the individual genes. However an extensive locus wide analysis of the methylation pattern in primary human tissue has not been performed. We used bisulfite sequencing to ...
Epigenetic regulation of gene expression is a developing field of study with many potential therapeutic applications. Chromatin remodeling is necessary for proper mammalian development, and misregulation of this process is associated with many human diseases. Three mechanisms by which chromatin structure is modified include methylation of the DNA, covalent modification of histone tails, and repositioning of nucleosomes by ATP dependant chromatin remodeling enzymes. To further increase our knowledge of the mechanisms and proteins involved in the modification of chromatin structure I undertook two projects; the role of DNA methylation in the regulation of human β-globin gene expression, and analysis of the Chd6 ATPase-/- mouse. Methylation status of the human β-globin gene promoters correlates with the expression pattern of the individual genes. However an extensive locus wide analysis of the methylation pattern in primary human tissue has not been performed. We used bisulfite sequencing to ...
For example, there is 70% penetrance if only 700 individuals express red phenotype out of 1,000 HairredHairred individuals. If penetrance of a phenotype is not 100%, then it has reduced penetrance. Mechanisms of reduced penetrance are not always clear. Expressivity is another important concept in describing genotype-phenotype correlation. Expressivity describes the severity of a phenotype among individuals with the same genotype. For example, if a condition has variable expressivity then one individual might have mild symptoms while another might have severe symptoms (although they have the same genotype). If a trait has constant expressivity then individuals with the same genotype will have the same degree of symptoms.. Mechanisms of variable expressivity are not always clear. Although there is typically a clear genotype-phenotype correlation that associates a specific allele with a specific phenotype, this link is frequently muddled. Even individuals with identical genotypes can have different ...
Islet leukocytic infiltration (insulitis) is first obvious at around 4 weeks of age in the NOD mouse - a model for human type 1 diabetes (T1D). The molecular events that lead to insulitis and initiate autoimmune diabetes are poorly understood. Since TID is caused by numerous genes, we hypothesized that multiple molecular pathways are altered and interact to initiate this disease. We evaluated the molecular phenotype (mRNA and protein expression) and molecular networks of ex vivo unfractionated spleen leukocytes from 2 and 4 week-old NOD mice in comparison to two control strains. Analysis of the global gene expression profiles and hierarchical clustering revealed that the majority (∼90%) of the differentially expressed genes in NOD mice were repressed. Furthermore, analysis using a modern suite of multiple bioinformatics approaches identified abnormal molecular pathways that can be divided broadly into 2 categories: metabolic pathways, which were predominant at 2 weeks, and immune response pathways,
We initially established ENU mutagenesis conditions for the rat in setting up gene-driven knockout technology using target-selected mutagenesis (Smits et al. 2004). However, the same F1 animals are also suited for forward genetic, phenotype-driven approaches. Indeed, several phenotypes caused by dominant mutations were readily identified in our experiments (Smits et al. 2004) as well as by others (Zan et al. 2003). Gould and colleagues (Zan et al. 2003) identified 74 visually aberrant mutants in a screen for dominant phenotypes in nearly 5000 F1 progeny from ENU-treated Sprague Dawley rats. About half of them were found to be fertile and to inherit the phenotype. Here, we describe a small-scale study on recessive phenotypes after ENU mutagenesis in the rat and the subsequent cloning of the mutated gene using a novel SNP mapping panel. Although the SNP mapping panel is of relatively low density and specifically designed for mapping crosses between Wistar and Brown Norway, it can easily be adapted ...
Amyotrophic lateral sclerosis (ALS) is a disease of variable severity in terms of speed of progression of the disease course. We found a similar variability in disease onset and progression of 2 familial ALS mouse strains, despite the fact that they carry the same transgene copy number and express the same amount of mutant SOD1G93A messenger RNA and protein in the central nervous system. Comparative analysis of 2 SOD1G93A mouse strains highlights differences associated with the disease severity that are unrelated to the degree of motor neuron loss but that appear to promote early dysfunction of these cells linked to protein aggregation. Features of fast progressing phenotype are (1) abundant protein aggregates containing mutant SOD1 and multiple chaperones; (2) low basal expression of the chaperone alpha-B-crystallin (CRYAB) and β5 subunits of proteasome; and (3) downregulation of proteasome subunit expression at disease onset. In contrast, high levels of functional chaperones such as ...
Since pharmacogenetic clinical recommendations are based on phenotype, the assignment of phenotype based on genotype is an important aspect to clinical implementation and reporting of different inferred phenotypes across laboratories and guidelines has created considerable confusion and inconsistencies in recommendations. To maximize the utility of pharmacogenetic test results, it is desirable to standardize the phenotype prediction from genotype data. The purpose of this project was to determine consensus among CYP2D6 experts as to the definitions used to assign CYP2D6 phenotype based on genotype.. ...
hi ml-stat-talks a reminder that barbara engelhardt is speaking tomorrow. she does top notch research at the intersection of graphical models and computational biology. best dave ---------- Forwarded message ---------- From: David Mimno ,mimno at cs.princeton.edu, Date: Sun, Sep 18, 2011 at 8:55 PM Subject: [Ml-stat-talks] Wed 9/21: Barbara Englehardt on genome-wide associations To: ml-stat-talks at lists.cs.princeton.edu For our first ML talk of the year, we have Barbara Englehardt from Duke. The talk will be this Wednesday (9/21) at 12:30 in CS 402. Title: Genome-wide associations studies with complex phenotypes: How statistics can help Abstract: Genome-wide association studies (GWAS), or studies to identify genetic variants that are associated with a particular phenotype or disease, can be performed trivially using available software given sufficient numbers of individuals and simple quantitative or case-control phenotypes. However, when the phenotype of interest is complex (e.g., ...
PURPOSE: Mutations in murine and human versions of an ancestrally related gene usually result in similar phenotypes. However, interspecies differences exist, and in the case of two forkhead transcription factor genes (FOXC1 and FOXC2), these differences include corneal or anterior segment phenotypes, respectively. This study was undertaken to determine whether such discrepancies provide an opportunity for identifying novel human-murine ocular phenotypes. METHODS: Four pedigrees with early-onset glaucoma phenotypes secondary to segmental chromosomal duplications or deletions encompassing FOXC1 and 18 individuals from 9 FOXC2 mutation pedigrees underwent detailed ocular phenotyping. Subsequently, mice with mutations in Foxc1 or a related forkhead gene, Foxe3, were assessed for features of the human phenotypes. RESULTS: A significant increase in central corneal thickness was present in affected individuals from the segmental duplication pedigrees compared with their unaffected relatives (mean
Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance (r(2) | 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial
In order to identify the function of genes, the consortium uses a series of response (ABR) test conducted at 14 weeks of age. Hearing is assessed at five frequencies - 6kHz, 12kHz, 18kHz, 24kHz and 30kHz - as well as a broadband click stimulus. Increased thresholds are indicative of abnormal hearing. Abnormalities in adult ear morphology are recorded as part of the Combined SHIRPA and Dysmorphology (CSD) protocol, which includes a response to a click box test (absence is indicative of a strong hearing deficit) and visual inspection for behavioural signs that may indicate vestibular dysfunction e.g. head bobbing or circling. ...
Unique metabolic biomarkers specific to lung cancer were found through metabolic phenotyping of blood plasma by proton nuclear magnetic resonance (H-NMR), enabling diagnosis of both early-stage and late-stage disease.
Background: The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text.Results: We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits
article{7193339, abstract = {We analyzed 3,872 common genetic variants across the ESR1 locus (encoding estrogen receptor a) in 118,816 subjects from three international consortia. We found evidence for at least five independent causal variants, each associated with different phenotype sets, including estrogen receptor (ER+ or ER-) and human ERBB2 (HER2(+) or HER2(-)) tumor subtypes, mammographic density and tumor grade. The best candidate causal variants for ER-tumors lie in four separate enhancer elements, and their risk alleles reduce expression of ESR1, RMND1 and CCDC170, whereas the risk alleles of the strongest candidates for the remaining independent causal variant disrupt a silencer element and putatively increase ESR1 and RMND1 expression.}, author = {Dunning, Alison M and Michailidou, Kyriaki and Kuchenbaecker, Karoline B and Thompson, Deborah and French, Juliet D and Beesley, Jonathan and Healey, Catherine S and Kar, Siddhartha and Pooley, Karen A and Lopez-Knowles, Elena and Dicks, Ed ...
We have identified DIAPH1 as a novel candidate gene for dominant MTP and sensorineural hearing loss by analysis of the largest ever assembled collection of cases with previously uncharacterized BPD. Essential to this discovery was the annotation of the characteristics of the cases with HPO terms for hematologic features and phenotypes in other organ systems, and then statistical analysis to identify similarities in HPO terms between cases. We have previously shown that cluster analysis of HPO terms within a large BPD case collection enabled identification of causal variants in ACTN1 and MYH9 that have been associated with MTP.7,9 However, the statistical evidence supporting DIAPH1 as a candidate gene could only be obtained by applying a novel similarity regression method to the phenotype and genotype data.19 Specifically, similarity regression revealed a hitherto unidentified association between a characteristic phenotype that was ontologically similar for 2 unrelated index cases and the shared ...
TY - JOUR. T1 - Phenotype harmonization and cross-study collaboration in GWAS consortia. T2 - The GENEVA experience. AU - Bennett, Siiri N.. AU - Caporaso, Neil. AU - Fitzpatrick, Annette L.. AU - Agrawal, Arpana. AU - Barnes, Kathleen. AU - Boyd, Heather A.. AU - Cornelis, Marilyn C.. AU - Hansel, Nadia N.. AU - Heiss, Gerardo. AU - Heit, John A.. AU - Kang, Jae Hee. AU - Kittner, Steven J.. AU - Kraft, Peter. AU - Lowe, William. AU - Marazita, Mary L.. AU - Monroe, Kristine R.. AU - Pasquale, Louis R.. AU - Ramos, Erin M.. AU - van Dam, Rob M.. AU - Udren, Jenna. AU - Williams, Kayleen. PY - 2011/4. Y1 - 2011/4. N2 - Genome-wide association study (GWAS) consortia and collaborations formed to detect genetic loci for common phenotypes or investigate gene-environment (GE) interactions are increasingly common. While these consortia effectively increase sample size, phenotype heterogeneity across studies represents a major obstacle that limits successful identification of these associations. ...
Fingerprint Dive into the research topics of Mac-1-negative B-1b phenotype of natural antibody-producing cells, including those responding to Galα1,3Gal epitopes α1,3-galactosyltransferase-deficient mice. Together they form a unique fingerprint. ...
TY - JOUR. T1 - Dark brown is the more virulent of the switch phenotypes of Candida glabrata. AU - Srikantha, Thyagaraja. AU - Daniels, Karla J.. AU - Wu, Wei. AU - Lockhart, Shawn R.. AU - Yi, Song. AU - Sahni, Nidhi. AU - Ma, Ning. AU - Soll, David R.. PY - 2008. Y1 - 2008. N2 - Candida glabrata undergoes reversible, high-frequency core switching between phenotypes that include dark brown (DB), light brown (LB) and white (Wh). These phenotypes in turn can switch to the irregular wrinkle (IWr) phenotype. Natural isolates, however, express predominantly the DB phenotype, leading to the hypothesis that it has a colonization advantage over the other switch phenotypes. Using the mouse model of systemic infection, results are presented which support this hypothesis. DB has an advantage over other switch phenotypes in colonizing the two major target organs in the mouse model, the spleen and liver. A time-course study reveals that colonization of the major target organs occurs very rapidly (within 2 ...
Cancer clinical outcome prediction using gene expression profiles has been proposed by the field of translational bioinformatics for better diagnostics, prognostics, and further therapeutics [1]. Somatic mutations and regulation abnormalities in a tumor cell cause substantial gene expression changes [2]. Expression of oncogenes or tumor suppressor genes promotes the malignant phenotype of cancer cells or inhibits cell division, development, or survival of cancer cell [2]. Thus, DNA microarray technologies have been widely used to predict clinical phenotypes such as stage, grade, metastatic status, recurrence, and patient survival in several cancers [3-5]. In terms of translational bioinformatics, accurate phenotype prediction based on the molecular signature can be used clinically to choose the best of several available therapies for a cancer patient.. However, clinical phenotype prediction based on gene expression profiles can vary between independent data sets [6, 7]. One possible explanation ...
This was the front page of this project wiki from June 1, 2007 to July 31, 2011, while it was funded (under the title of this page) by NSF grant BDI,nowiki>-,/nowiki>0641025. ==Linking Evolution to Genomics Using Phenotype Ontologies== [[Image:NESCent Logo.png,right]] ===About this project=== What are the developmental and genetic bases of evolutionary differences in morphology across species? Currently it is difficult to approach this question due to a lack of computational tools that allow researchers to integrate developmental genetic and comparative morphological/anatomical data. [[Image:Ctol Logo.jpg,right]] [[Image:Zfinlogo.png,left]] We are addressing this by developing a database of evolutionarily variable morphological characters for a large clade of fishes (the Ostariophysi) and connecting this database to the large collection of mutant phenotypes in the [http://zfin.org ZFIN database], the central database of the zebrafish model organism community. The evolutionary and mutant ...
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