scholarly journals Gene Symbol

2020 ◽  
Author(s):  
Keyword(s):  
Gene Symbol

scholarly journals New Alleles, rkcd and rkp, at the Red Kidney Locus for Seedcoat Color in Common Bean

2003 ◽  
Vol 128 (4) ◽  
pp. 552-558 ◽  
Author(s):  
Mark J. Bassett ◽  
Phillip N. Miklas
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Gene Symbol ◽  
Recurrent Parent ◽  
Breeding Line ◽  
Genetic Investigation ◽  
Dry Bean ◽  
Pink Color ◽  
Growing Conditions ◽  
New Alleles

Among light red and dark red kidney common bean (Phaseolus vulgaris L.) varieties, pink seedcoat color (light red kidney) is dominant to dark red, but when Red Mexican varieties (with dark red seedcoats) are crossed with dark red kidney varieties, dark red seedcoat is dominant to the pink segregants observed in an F2 population. A genetic investigation of this reversal of dominance was performed by making crosses in all combinations among standard varieties of the four recessive-red market classes—Light Red Kidney `California Early Light Red Kidney', Pink `Sutter Pink', Red Mexican `NW 63', and Dark Red Kidney `Montcalm'—and observing segregation for seedcoat colors in F2 and F3 progenies. The data were consistent with the hypothesis that `NW 63' carries a new allele at Rk, viz., rkcd, where cd stands for convertible dark red kidney. Thus, C rkcd expresses dark red kidney seedcoats and cu rkcd expresses pink seedcoats. Also, C B rkcd expresses garnet brown seedcoats, whereas C B rkd expresses liver brown seedcoat color. Thus, we propose the gene symbol rkcd for the Rk locus gene in `NW 63'. The rk gene from Light Red Kidney `Redkloud' and `Sutter Pink' was backcrossed (with cu b v) into the recurrent parent 5-593, a Florida dry bean breeding line with seedcoat genotype P [C r] J G B V Rk. In the F2 progenies of BC2 to 5-593, the cu b v rk segregants from `Redkloud' gave true pink seedcoats, whereas those derived from `Sutter Pink' gave consistently very weak pink color under humid Florida growing conditions. We propose the gene symbol rkp, where p stands for pale pink, for the distinctive rk allele in `Sutter Pink'. The more general implications of the above findings were discussed.

scholarly journals Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Ralf C. Mueller ◽  
Nicolai Mallig ◽  
Jacqueline Smith ◽  
Lél Eöery ◽  
Richard I. Kuo ◽  
...  
Keyword(s):  
Bird Species ◽  
Gene Symbol ◽  
Immune Gene ◽  
Command Line ◽  
Biological Processes ◽  
Command Line Interface ◽  
Target List ◽  
Immune Genes ◽  
Front End ◽  
Gene Symbols

Abstract Background Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the “correct” set of genes. In this article, we present and describe the Avian Immunome DB (Avimm) for easy gene property extraction as exemplified by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes. It is a vital trait to study particularly in birds considering that they are a significant driver in spreading zoonotic diseases. With the completion of phase II of the B10K (“Bird 10,000 Genomes”) consortium’s whole-genome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for Avimm. Construction and content A relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up. The foundation stone or the “seed” for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus). Gene annotations, different transcript isoforms, nucleotide sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. Avimm is supplemented by a command-line interface and a web front-end to query the database. Utility and discussion The internal mapping of unique gene symbol identifiers to canonical gene symbols allows for an ambiguous gene property search. The database is organised within core and feature tables, which makes it straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 612 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with download functionality offers sophisticated search functionalities and tracks the origin for each record. Avimm is publicly accessible at https://avimm.ab.mpg.de.

scholarly journals Genetics ofAspergillus flavus: complementation and mapping of aflatoxin mutants

1979 ◽  
Vol 34 (1) ◽  
pp. 1-9 ◽  
Author(s):  
K. E. Papa
Keyword(s):  
Aspergillus Flavus ◽  
Aflatoxin Production ◽  
Gene Symbol ◽  
Linkage Groups ◽  
Parasexual Cycle ◽  
Independent Segregation ◽  
Complementation Groups

SUMMARYMutants ofAspergillus flavusimpaired in aflatoxin production were induced withN-methyl-N′-nitrosoguanidine and analysed by means of the parasexual cycle. The gene symbolaflwas assigned to this type of mutation. Diploid complementation tests revealed that most of 14aflmutants belonged to different complementation groups. One mutant (afl-1) failed to complement or only partially complemented all other mutants. Haploidization of one diploid revealed the independent segregation of twoaflmutants. Heterozygous diploids were synthesized between twoaflmutants and tester strains genetically labelled on eight linkage groups. Haploidization of the diploids led to the assignment of two aft mutants to linkage groups. Linkage ofafl-4 tow+andafl-1 toleuon linkage groups II and VII, respectively, was demonstrated.

Terminal ear mutant of maize (Zea mays L.)

1974 ◽  
Vol 82 (3) ◽  
pp. 433-435 ◽  
Author(s):  
D. L. Matthews ◽  
C. O. Grogan ◽  
C. E. Manchester
Keyword(s):  
Zea Mays ◽  
Zea Mays L ◽  
Recessive Gene ◽  
Gene Symbol ◽  
Chromosome 3

SUMMARYA new mutant in maize with an unusual ear location is described. The condition was found to be controlled by a simple recessive gene located near the breakpoint on chromosome 3. The gene symbol, te, is proposed.

Analysis of B-CLL Transcriptomic and Proteomic Profiles: Differences between Molecular Subgroups.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2088-2088
Author(s):  
Eloisa Jantus Lewintre ◽  
Miguel Marin ◽  
Cristina Reinoso ◽  
David Montaner ◽  
Joaquín Dopazo ◽  
...  
Keyword(s):  
Western Blot ◽  
Differentially Expressed Gene ◽  
Progression Free Survival ◽  
Lymphocytic Leukemia ◽  
Gene Symbol ◽  
Differentially Expressed ◽  
2D Electrophoresis ◽  
Molecular Subgroups ◽  
Multiple Test ◽  
Peptide Mass

Abstract INTRODUCTION: B cell chronic lymphocytic leukemia (B-CLL) is a lymphoproliferative disorder with a variable clinical course. Patients (pts) with unmutated (unmut) IgVH gene show a shorter progression free survival and overall survival than the patients with IgVH mutated (mut). To understand the differences between molecular subgroups of B-CLL we have studied transcriptomic and proteomic profiles on samples from 40 B-CLL pts (Binet stage A). MATERIAL AND METHODS: 100 μg of total PBMC proteins were used for IEF followed by 2D electrophoresis. Image analysis of scanned gels was used to identify statistically differentially expressed proteins. Image acquisition and analysis were performed using the Ludesi software (http://www.ludesi.com). Selected spots were subjected to automatic digestion and the proteins were identified by MALDI-TOF (Voyager DE-Pro, Applied Biosystems) peptide mass fingerprint using the Protein Prospector software. To confirm the initial results, sequencing of selected peptide ions was carried out by collision-induced dissociation (CID) with a nESI-QTRAP mass spectrometer from Applied Biosystems. Eight proteins were validated by Western Blot. Total RNA from B cells was used to analyze the expression profile by hybridization with Whole Human Genome U133 Plus 2.0 Array from Affymetrix. Normalization, differential gene expression and functional annotations were analyzed using the GEPAS suite (http://www.gepas.org). qPCR using TaqMan primers/probes was used for validation of the microarray data RESULTS: When we compared IgVH mut vs unmut transcriptomic and proteomic profiles, we found more than 600 differentially expressed genes and 12 proteins ( fdr <0.05 adjusted for multiple test contrast and p<0.05, Mann-Whitney’s test, for gene and proteins, respectively). In tables 1 and 2 we show some of the most differentially expressed gene/proteins in each group of pts. Validation of results from microarrays and proteomic data using qPCR and Western blot are in progress. We obtained positive correlation between transcriptomic and proteomic profiles, (corr=0.21, p=0.04, Pearson’s correation test) suggesting that common features are found using both approximations. CONCLUSION: We found a number of interesting gene/proteins that could be able to differentiate molecular subgroups of B-CLL pts. The study of these proteins and genes may lead to better understand the different clinical behaviour of IgVH mut and unmut B-CLL forms, but validation with a larger group of pts is still necessary. Table 1: Genes differentially expressed IgVH mut IgVH unmut Genes annotated using their gene symbol BCL11A MGC9913 DUSP22 RGS4 PDLIM5 CRY1 RDH13 GGT2 PHF15 DMD SVH TUBB6 ADAM29 LPL ITPKB ITGA9 RBKS BCL7A NFATC1 MYEOV RIN3 PPP1R9A Table 2: Proteins differentially expressed IgVH mut IgVH unmut Proteins were annotated according to their gene symbol VIM ERP29 COTL1 CCT2 S100A9 PSMB10 HSPD1

scholarly journals Transport of Drugs and Endogenous Compounds Mediated by Human OCT1: Studies in Single- and Double-Transfected Cell Models

2021 ◽  
Vol 12 ◽  
Author(s):  
Bastian Haberkorn ◽  
Martin F. Fromm ◽  
Jörg König
Keyword(s):  
Drug Interactions ◽  
Molecular Mechanisms ◽  
Transport Processes ◽  
Gene Symbol ◽  
Cell Models ◽  
Cell Systems ◽  
Endogenous Compounds ◽  
Substrate Spectrum ◽  
Hepatobiliary Elimination

Organic Cation Transporter 1 (OCT1, gene symbol: SLC22A1) is predominately expressed in human liver, localized in the basolateral membrane of hepatocytes and facilitates the uptake of endogenous compounds (e.g. serotonin, acetylcholine, thiamine), and widely prescribed drugs (e.g. metformin, fenoterol, morphine). Furthermore, exogenous compounds such as MPP+, ASP+ and Tetraethylammonium can be used as prototypic substrates to study the OCT1-mediated transport in vitro. Single-transfected cell lines recombinantly overexpressing OCT1 (e.g., HEK-OCT1) were established to study OCT1-mediated uptake and to evaluate transporter-mediated drug-drug interactions in vitro. Furthermore, double-transfected cell models simultaneously overexpressing basolaterally localized OCT1 together with an apically localized export protein have been established. Most of these cell models are based on polarized grown MDCK cells and can be used to analyze transcellular transport, mimicking the transport processes e.g. during the hepatobiliary elimination of drugs. Multidrug and toxin extrusion protein 1 (MATE1, gene symbol: SLC47A1) and the ATP-driven efflux pump P-glycoprotein (P-gp, gene symbol: ABCB1) are both expressed in the canalicular membrane of human hepatocytes and are described as transporters of organic cations. OCT1 and MATE1 have an overlapping substrate spectrum, indicating an important interplay of both transport proteins during the hepatobiliary elimination of drugs. Due to the important role of OCT1 for the transport of endogenous compounds and drugs, in vitro cell systems are important for the determination of the substrate spectrum of OCT1, the understanding of the molecular mechanisms of polarized transport, and the investigation of potential drug-drug interactions. Therefore, the aim of this review article is to summarize the current knowledge on cell systems recombinantly overexpressing human OCT1.

scholarly journals Bibliome Variant Database: Automated Identification and Annotation of Genetic Variants in Primary Literature

2020 ◽  
Author(s):  
Samuel W. Baker ◽  
Arupa Ganguly
Keyword(s):  
Human Genome ◽  
Genetic Variants ◽  
Gene Symbol ◽  
Reference Database ◽  
Variant Interpretation ◽  
Automated Identification ◽  
Primary Literature ◽  
Time Required ◽  
Variant Database ◽  
Gene Symbols

ABSTRACTThe Bibliome Variant Database (BVdb) is a freely available reference database containing over 1 million human genetic variants mapped to the human genome that have been mined from primary literature. The BVdb is designed to facilitate variant interpretation in clinical and research contexts by reducing or eliminating the time required to search for literature describing a given variant. Users can search the database using gene symbols, HGVS variant nomenclature, genomic positions, or rsIDs. Each variant page lists references in the database that describe the variant, as well as the exact gene symbol and variant text description identified in each reference.AVAILABILITY AND IMPLEMENTATIONThe BVdb is freely available at http://bibliome.ai

scholarly journals Allelism Found between Two Common Bean Genes, Hilum Ring Color (D) and Partly Colored Seedcoat Pattern (Z), formerly Assumed to Be Independent

1999 ◽  
Vol 124 (6) ◽  
pp. 649-653 ◽  
Author(s):  
Mark J. Bassett ◽  
Colleen Shearon ◽  
Phil McClean
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Rapd Marker ◽  
Gene Symbol ◽  
Supporting Evidence ◽  
Randomly Amplified Polymorphic Dna ◽  
New Genotype ◽  
The Cross ◽  
Genetic Hypothesis

Inheritance of two phenotypes, the virgarcus pattern of partly colored seedcoats and the margo d seedcoat pattern, were studied in common bean (Phaseolus vulgaris L.) materials that segregated jointly for genes controlling the two phenotypes to test the hypothesis of allelism of two genes, D and Z. The F2 progeny from the cross j margo BC3 5-593 × t z virgarcus BC3 5-593 produced an unexpected phenotypic class, margo d, suggesting possible allelism of D and Z. The F2 also produced another unexpected phenotypic class, white seedcoat, for which the genetic hypothesis t j z was made. The F2 from the cross t j marginata BC3 5-593 × t z virgarcus BC3 5-593 provided supporting evidence for the new genotype, t j z, for a white seedcoat. Analysis of the F2 and F3 progenies of 80 random F2 plants from the cross t z virgarcus BC3 5-593 × d j (margo d) BC3 5-593 provided support for the hypothesis that the D and Z loci are allelic. Production of two different phenotypes (white vs. white with two tiny pale gray dots, one each at the raphe and micropyle) for t J/j z in two different genetic and cytoplasmic backgrounds is discussed. The F2 from the crosses d j (margo d) BC2 5-593 × j v margo BC2 5-593 and d j (margo d) BC3 5-593 × j margo BC3 5-593 segregated for d (vs. D) phenotypes, which were found not to be independent of a randomly amplified polymorphic DNA (RAPD) marker (AM10560) associated (1.4 cM) with the Z locus. Because the Z gene symbol has priority, we propose to retain Z for the locus.

scholarly journals The Hippo signal transduction network for exercise physiologists

2016 ◽  
Vol 120 (10) ◽  
pp. 1105-1117 ◽  
Author(s):  
Brendan M. Gabriel ◽  
D. Lee Hamilton ◽  
Annie M. Tremblay ◽  
Henning Wackerhage
Keyword(s):  
Transcription Factors ◽  
Fiber Type ◽  
Association Studies ◽  
Hippo Pathway ◽  
Muscle Fibers ◽  
Body Height ◽  
Gene Symbol ◽  
Genome Wide Association Studies ◽  
Hippo Signaling ◽  
Key Factor

The ubiquitous transcriptional coactivators Yap (gene symbol Yap1) and Taz (gene symbol Wwtr1) regulate gene expression mainly by coactivating the Tead transcription factors. Being at the center of the Hippo signaling network, Yap and Taz are regulated by the Hippo kinase cassette and additionally by a plethora of exercise-associated signals and signaling modules. These include mechanotransduction, the AKT-mTORC1 network, the SMAD transcription factors, hypoxia, glucose homeostasis, AMPK, adrenaline/epinephrine and angiotensin II through G protein-coupled receptors, and IL-6. Consequently, exercise should alter Hippo signaling in several organs to mediate at least some aspects of the organ-specific adaptations to exercise. Indeed, Tead1 overexpression in muscle fibers has been shown to promote a fast-to-slow fiber type switch, whereas Yap in muscle fibers and cardiomyocytes promotes skeletal muscle hypertrophy and cardiomyocyte adaptations, respectively. Finally, genome-wide association studies in humans have linked the Hippo pathway members LATS2, TEAD1, YAP1, VGLL2, VGLL3, and VGLL4 to body height, which is a key factor in sports.

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