scholarly journals Colony size measurement of the yeast gene deletion strains for functional genomics

2021 ◽  
Author(s):  
Negar Memarian ◽  
Matthew Jessulat ◽  
Javad Alirezaie ◽  
Nadereh Mir-Rashed ◽  
Jianhua Xu ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Colony Size ◽  
Large Scale ◽  
Model Organism ◽  
Antifungal Compound ◽  
Image Analysis System ◽  
Yeast Saccharomyces Cerevisiae ◽  
Inspection Method ◽  
Manual Inspection ◽  
Growth Differences

Background Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences. Results Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research. Conclusion GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations.

scholarly journals Colony size measurement of the yeast gene deletion strains for functional genomics

2021 ◽  
Author(s):  
Negar Memarian ◽  
Matthew Jessulat ◽  
Javad Alirezaie ◽  
Nadereh Mir-Rashed ◽  
Jianhua Xu ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Colony Size ◽  
Large Scale ◽  
Model Organism ◽  
Antifungal Compound ◽  
Image Analysis System ◽  
Yeast Saccharomyces Cerevisiae ◽  
Inspection Method ◽  
Manual Inspection ◽  
Growth Differences

Background Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences. Results Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research. Conclusion GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations.

scholarly journals Meeting Highlights: Genome Sequencing and Biology 2001

2001 ◽  
Vol 2 (4) ◽  
pp. 243-251
Author(s):  
Jo Wixon
Keyword(s):  
Comparative Genomics ◽  
Functional Genomics ◽  
Genome Sequencing ◽  
Large Scale ◽  
Model Organism

We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.

scholarly journals In Vivo Production of RNA Aptamers and Nanoparticles: Problems and Prospects

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1422
Author(s):  
Ousama Al Shanaa ◽  
Andrey Rumyantsev ◽  
Elena Sambuk ◽  
Marina Padkina
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Large Scale ◽  
Potential Model ◽  
Model Organism ◽  
Rna Aptamers ◽  
Early Stages ◽  
Near Future

RNA aptamers are becoming increasingly attractive due to their superior properties. This review discusses the early stages of aptamer research, the main developments in this area, and the latest technologies being developed. The review also highlights the advantages of RNA aptamers in comparison to antibodies, considering the great potential of RNA aptamers and their applications in the near future. In addition, it is shown how RNA aptamers can form endless 3-D structures, giving rise to various structural and functional possibilities. Special attention is paid to the Mango, Spinach and Broccoli fluorescent RNA aptamers, and the advantages of split RNA aptamers are discussed. The review focuses on the importance of creating a platform for the synthesis of RNA nanoparticles in vivo and examines yeast, namely Saccharomyces cerevisiae, as a potential model organism for the production of RNA nanoparticles on a large scale.

New Data and New Features of the FunRiceGenes (Functionally Characterized Rice Genes) Database: 2021 Update

2021 ◽  
Author(s):  
Fangfang Huang ◽  
Yingru Jiang ◽  
Tiantian Chen ◽  
Haoran Li ◽  
Mengjia Fu ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Rice Genome ◽  
Model Organism ◽  
Gene Families ◽  
Food Crop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Major Food

Abstract As a major food crop and model organism, rice has been mostly studied with the largest number of functionally characterized genes among all crops. We previously built the funRiceGenes database including ∼2800 functionally characterized rice genes and ∼5000 members of different gene families. Since being published, the funRiceGenes database has been accessed by more than 49,000 users with over 490,000 page views. The funRiceGenes database has been continuously updated with newly cloned rice genes and newly published literature, based on the progress of rice functional genomics studies. Up to Nov 2021, ≥4100 functionally characterized rice genes and ∼6000 members of different gene families were collected in funRiceGenes, accounting for 22.3% of the 39,045 annotated protein-coding genes in the rice genome. Here, we summarized the update of the funRiceGenes database with new data and new features in the last five years.

Rice Functional Genomics by Transposon Mutagenesis

2002 ◽  
Vol 06 (24) ◽  
pp. 930-935 ◽  
Author(s):  
Chang-deok Han
Keyword(s):  
Tissue Culture ◽  
Transposable Elements ◽  
Functional Genomics ◽  
Large Scale ◽  
Expression Patterns ◽  
Transposon Mutagenesis ◽  
Transposon Tagging ◽  
Genomic Sequences ◽  
Knock Out ◽  
Genetic Cross

Transposable elements are powerful mutagens. Along with genomic sequences, knock-out phenotypes and expression patterns are important information to elucidate the function of genes. In this review, I propose a strategy to develop tranposant lines on a large scale by combining genetic cross and tissue culture of Ac and Ds lines. Based on the facts that Ds tends to be inactive in F2 or later generation and Ds becomes reactivated via tissue culture, a large scale of transposants can be produced by tissue culture of seeds carrying Ac and inactive Ds. In this review, I describe limitations and considerations in operating transposon tagging systems in rice. Also, I discuss the efficiency of our gene trap system and technical procedures to clone Ds flanking DNA.

scholarly journals Deletion of two genes improves heterologous secretion of fungal lignin-degrading heme peroxidases in S. cerevisiae

2021 ◽  
Author(s):  
Nikita A. Khlystov
Keyword(s):  
Large Scale ◽  
Screening Method ◽  
Strain Engineering ◽  
Scale Production ◽  
Heterologous Production ◽  
Yeast Saccharomyces Cerevisiae ◽  
Double Deletion ◽  
Large Scale Production ◽  
Crucial Component ◽  
Heme Peroxidases

Efficient, large-scale heterologous production of enzymes is a crucial component of the biomass valorization industry. Whereas cellulose utilization has been successful in applications such as bioethanol, its counterpart lignin remains significantly underutilized despite being an abundant potential source of aromatic commodity chemicals. Fungal lignin-degrading heme peroxidases are thought to be the major agents responsible for lignin depolymerization in nature, but their large-scale production remains inaccessible due to the genetic intractability of basidiomycete fungi and the challenges in the heterologous production of these enzymes. In this study, we employ a strain engineering approach based on functional genomics to identify mutants of the model yeast Saccharomyces cerevisiae with enhanced heterologous production of lignin-degrading heme peroxidases. We show that our screening method coupling an activity-based readout with fluorescence-assisted cell sorting enables identification of two single null mutants of S. cerevisiae, pmt2 and cyt2, with up to 11-fold improved secretion of a versatile peroxidase from the lignin-degrading fungus Pleurotus eryngii. We demonstrate that the double deletion strain pmt2cyt2 displays positive epistasis, improving and even enabling production of members from all three classes of lignin-degrading fungal peroxidases. We anticipate that these mutant strains will be broadly applicable for improved heterologous production of this biotechnologically important class of enzymes.

scholarly journals Functional Genomics of the Chicken—A Model Organism

2007 ◽  
Vol 86 (10) ◽  
pp. 2059-2094 ◽  
Author(s):  
L.A. Cogburn ◽  
T.E. Porter ◽  
M.J. Duclos ◽  
J. Simon ◽  
S.C. Burgess ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Model Organism

Requirements for the nuclear export of the small ribosomal subunit

2002 ◽  
Vol 115 (14) ◽  
pp. 2985-2995 ◽  
Author(s):  
Terence I. Moy ◽  
Pamela A. Silver
Keyword(s):  
Nuclear Export ◽  
Ribosome Biogenesis ◽  
Large Scale ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
Temperature Sensitive ◽  
Yeast Saccharomyces Cerevisiae ◽  
Small Ribosomal Subunit ◽  
Factors Affecting ◽  
The Stability

Eukaryotic ribosome biogenesis requires multiple steps of nuclear transport because ribosomes are assembled in the nucleus while protein synthesis occurs in the cytoplasm. Using an in situ RNA localization assay in the yeast Saccharomyces cerevisiae, we determined that efficient nuclear export of the small ribosomal subunit requires Yrb2, a factor involved in Crm1-mediated export. Furthermore, in cells lacking YRB2, the stability and abundance of the small ribosomal subunit is decreased in comparison with the large ribosomal subunit. To identify additional factors affecting small subunit export, we performed a large-scale screen of temperature-sensitive mutants. We isolated new alleles of several nucleoporins and Ran-GTPase regulators. Together with further analysis of existing mutants,we show that nucleoporins previously shown to be defective in ribosomal assembly are also defective in export of the small ribosomal subunit.

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