Gene Function Inference From Gene Expression of Deletion Mutants

2007 ◽  
pp. 1-18 ◽  
Author(s):  
Ghislain Bidaut
Keyword(s):  
Gene Expression ◽  
Gene Function ◽  
Deletion Mutants

scholarly journals Transcriptional, Posttranscriptional, and Posttranslational Regulation of SHOOT MERISTEMLESS Gene Expression in Arabidopsis Determines Gene Function in the Shoot Apex

2014 ◽  
Vol 167 (2) ◽  
pp. 424-442 ◽  
Author(s):  
José Antonio Aguilar-Martínez ◽  
Naoyuki Uchida ◽  
Brad Townsley ◽  
Donnelly Ann West ◽  
Andrea Yanez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Shoot Apex ◽  
Gene Function ◽  
Posttranslational Regulation ◽  
Shoot Meristemless

Gene silencing or gene editing: the pros and cons.

2021 ◽  
pp. 47-53
Author(s):  
Huw D. Jones
Keyword(s):  
Gene Expression ◽  
Gene Silencing ◽  
Gene Function ◽  
Gene Editing ◽  
Mutation Breeding ◽  
Gene Transcript ◽  
Commercial Activities ◽  
Targeted Mutation ◽  
Pros And Cons ◽  
Or Gene

Abstract Research into plant genetics often requires the suppression or complete knockout of gene expression to scientifically validate gene function. In addition, the phenotypes obtained from gene suppression can occasionally have commercial value for plant breeders. Until recently, the methodological choices to achieve these goals fell into two broad types: either some form of RNA-based gene silencing; or the screening of large numbers of natural or induced random genomic mutations. The more recent invention of gene editing as a tool for targeted mutation potentially gives researchers and plant breeders another route to block gene function. RNAi is widely used in animal and plant research and functions to silence gene expression by degrading the target gene transcript. Although RNAi offers unique advantages over genomic mutations, it often leads to the formation of a genetically modified organism (GMO), which for commercial activities has major regulatory and acceptance issues in some regions of the world. Traditional methods of generating genomic mutations are more laborious and uncertain to achieve the desired goals but possess a distinct advantage of not being governed by GMO regulations. Gene editing (GE) technologies have some of the advantages of both RNAi and classical mutation breeding in that they can be designed to give simple knockouts or to modulate gene expression more subtly. GE also has a more complex regulatory position, with some countries treating it as another conventional breeding method whilst the EU defines GE as a technique of genetic modification and applies the normal GMO authorization procedures. This chapter explores the pros and cons of RNAi alongside other methods of modulating gene function.

scholarly journals Visual Comparison of Multiple Gene Expression Datasets in a Genomic Context

2008 ◽  
Vol 5 (2) ◽  
Author(s):  
Krzysztof Borowski ◽  
Jung Soh ◽  
Christoph W. Sensen
Keyword(s):  
Gene Expression ◽  
Microarray Data ◽  
Gene Function ◽  
Graphical Representation ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Expression Data ◽  
Genomic Context ◽  
Multiple Gene ◽  
Microarray Datasets

SummaryThe need for novel methods of visualizing microarray data is growing. New perspectives are beneficial to finding patterns in expression data. The Bluejay genome browser provides an integrative way of visualizing gene expression datasets in a genomic context. We have now developed the functionality to display multiple microarray datasets simultaneously in Bluejay, in order to provide researchers with a comprehensive view of their datasets linked to a graphical representation of gene function. This will enable biologists to obtain valuable insights on expression patterns, by allowing them to analyze the expression values in relation to the gene locations as well as to compare expression profiles of related genomes or of di erent experiments for the same genome.

scholarly journals Stable RK2-Derived Cloning Vectors for the Analysis of Gene Expression and Gene Function in Gram-Negative Bacteria

2001 ◽  
Vol 14 (3) ◽  
pp. 426-430 ◽  
Author(s):  
Bruno Dombrecht ◽  
Jos Vanderleyden ◽  
Jan Michiels
Keyword(s):  
Gene Expression ◽  
Gene Function ◽  
Plasmid Stability ◽  
Gram Negative Bacteria ◽  
Cloning Vectors ◽  
Gram Negative ◽  
Gusa Gene ◽  
Vector Sequences ◽  
And Function ◽  
Multiple Cloning Sites

The construction of several stable RK2-derived cloning vectors for the analysis of gene expression and function in gram-negative bacteria is reported. Plasmid stability is conferred by the RK2 par locus or by insertion of the spsAB or spsCD symbiotic plasmid stability loci from pNGR234a of Rhizobium sp. NGR234. The vectors carry multiple cloning sites with protection against read-through transcriptional activity of vector sequences. Vector derivatives with the constitutive nptII promoter or a promoter-less gusA gene are suitable for the study of gene function or regulation in bacteria.

scholarly journals Transcription of the Subtilase Cytotoxin Gene subAB1 in Shiga Toxin-Producing Escherichia coli Is Dependent on hfq and hns

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Laura Heinisch ◽  
Katharina Zoric ◽  
Maike Krause ◽  
Herbert Schmidt
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Shiga Toxin ◽  
Promoter Activity ◽  
Deletion Mutants ◽  
Content Type ◽  
E Coli ◽  
Intensive Investigation ◽  
Subtilase Cytotoxin

ABSTRACT Certain foodborne Shiga toxin-producing Escherichia coli (STEC) strains carry genes encoding the subtilase cytotoxin (SubAB). Although the mode of action of SubAB is under intensive investigation, information about the regulation of subAB gene expression is currently not available. In this study, we investigated the regulation of the chromosomal subAB1 gene in laboratory E. coli strain DH5α and STEC O113:H21 strain TS18/08 using a luciferase reporter gene assay. Special emphasis was given to the role of the global regulatory protein genes hfq and hns in subAB1 promoter activity. Subsequently, quantitative real-time PCR was performed to analyze the expression of Shiga toxin 2a (Stx2a), SubAB1, and cytolethal distending toxin V (Cdt-V) genes in STEC strain TS18/08 and its isogenic hfq and hns deletion mutants. The deletion of hfq led to a significant increase of up to 2-fold in subAB1 expression, especially in the late growth phase, in both strains. However, deletion of hns showed different effects on the promoter activity during the early and late exponential growth phases in both strains. Furthermore, upregulation of stx2a and cdt-V was demonstrated in hfq and hns deletion mutants in TS18/08. These data showed that the expression of subAB1, stx2a, and cdt-V is integrated in the regulatory network of global regulators Hfq and H-NS in Escherichia coli. IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) strains are responsible for outbreaks of foodborne diseases, such as hemorrhagic colitis and the hemolytic uremic syndrome. The pathogenicity of those strains can be attributed to, among other factors, the production of toxins. Recently, the subtilase cytotoxin was detected in locus of enterocyte effacement (LEE)-negative STEC, and it was confirmed that it contributes to the cytotoxicity of those STEC strains. Although the mode of action of SubAB1 is under intensive investigation, the regulation of gene expression is currently not known. The global regulatory proteins H-NS and Hfq have impact on many cellular processes and have been described to regulate virulence factors as well. Here, we investigate the role of hns and hfq in expression of subAB1 as well as stx2a and cdt-V in an E. coli laboratory strain as well as in wild-type STEC strain TS18/08.

scholarly journals Systems Metabolic Alteration in a Semi-Dwarf Rice Mutant Induced by OsCYP96B4 Gene Mutation

2020 ◽  
Vol 21 (6) ◽  
pp. 1924 ◽  
Author(s):  
Limiao Jiang ◽  
Rengasamy Ramamoorthy ◽  
Srinivasan Ramachandran ◽  
Prakash P. Kumar
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Secondary Metabolism ◽  
Gene Mutation ◽  
Gene Function ◽  
Nucleotide Metabolism ◽  
Expression Levels ◽  
Rice Mutant ◽  
Choline Metabolism ◽  
Gene Expression Levels

Dwarfism and semi-dwarfism are among the most valuable agronomic traits in crop breeding, which were adopted by the “Green Revolution”. Previously, we reported a novel semi-dwarf rice mutant (oscyp96b4) derived from the insertion of a single copy of Dissociator (Ds) transposon into the gene OsCYP96B4. However, the systems metabolic effect of the mutation is not well understood, which is important for understanding the gene function and developing new semi-dwarf mutants. Here, the metabolic phenotypes in the semi-dwarf mutant (M) and ectopic expression (ECE) rice line were compared to the wild-type (WT) rice, by using nuclear magnetic resonance (NMR) metabolomics and quantitative real-time polymerase chain reaction (qRT-PCR). Compared with WT, ECE of the OsCYP96B4 gene resulted in significant increase of γ-aminobutyrate (GABA), glutamine, and alanine, but significant decrease of glutamate, aromatic and branched-chain amino acids, and some other amino acids. The ECE caused significant increase of monosaccharides (glucose, fructose), but significant decrease of disaccharide (sucrose); induced significant changes of metabolites involved in choline metabolism (phosphocholine, ethanolamine) and nucleotide metabolism (adenosine, adenosine monophosphate, uridine). These metabolic profile alterations were accompanied with changes in the gene expression levels of some related enzymes, involved in GABA shunt, glutamate and glutamine metabolism, choline metabolism, sucrose metabolism, glycolysis/gluconeogenesis pathway, tricarboxylic acid (TCA) cycle, nucleotide metabolism, and shikimate-mediated secondary metabolism. The semi-dwarf mutant showed corresponding but less pronounced changes, especially in the gene expression levels. It indicates that OsCYP96B4 gene mutation in rice causes significant alteration in amino acid metabolism, carbohydrate metabolism, nucleotide metabolism, and shikimate-mediated secondary metabolism. The present study will provide essential information for the OsCYP96B4 gene function analysis and may serve as valuable reference data for the development of new semi-dwarf mutants.

scholarly journals Gene expression in placentation of farm animals: An overview of gene function during development

2011 ◽  
Vol 76 (4) ◽  
pp. 589-597 ◽  
Author(s):  
R.S.N. Barreto ◽  
F.F. Bressan ◽  
L.J. Oliveira ◽  
F.T.V. Pereira ◽  
F. Perecin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Function ◽  
Farm Animals

Biochemical genetics of the mouse IgM system

1984 ◽  
Vol 62 (4) ◽  
pp. 217-224 ◽  
Author(s):  
Marc J. Shulman ◽  
Robert G. Hawley ◽  
Atsuo Ochi ◽  
W. O. T. Baczynsky ◽  
Catherine Collins ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Heavy Chain ◽  
Mutant Cell ◽  
Immunoglobulin M ◽  
Structural Basis ◽  
Deletion Mutants ◽  
Transfer System ◽  
Biochemical Genetics ◽  
Chain Synthesis

Using a mouse hybridoma system, we have developed methods of isolating a variety of mutant cell lines in which immunoglobulin function or synthesis is defective. The analysis of mutants defective in κ chain synthesis has defined a class of murine transposons. The deletion mutants produce immunoglobulin M (IgM) bearing μ heavy chain fragments and provide information on the requirements of IgM assembly and μ gene expression. We also describe a transfer system for the μ and κ genes which will be useful in analyzing the structural basis of IgM function.

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