Comprehensive phenotypic analysis of single-gene deletion and overexpression strains of Saccharomyces cerevisiae

Yeast ◽  
2011 ◽  
Vol 28 (5) ◽  
pp. 349-361 ◽  
Author(s):  
Katsunori Yoshikawa ◽  
Tadamasa Tanaka ◽  
Yoshihiro Ida ◽  
Chikara Furusawa ◽  
Takashi Hirasawa ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Deletion ◽  
Single Gene ◽  
Phenotypic Analysis ◽  
Single Gene Deletion

scholarly journals Mutability of demographic noise in microbial range expansions

2021 ◽  
Author(s):  
QinQin Yu ◽  
Matti Gralka ◽  
Marie-Cécilia Duvernoy ◽  
Megan Sousa ◽  
Arbel Harpak ◽  
...  
Keyword(s):  
Gene Deletion ◽  
Genetic Manipulation ◽  
Single Gene ◽  
Population Level ◽  
Growth Conditions ◽  
Establishment Probability ◽  
In The Wild ◽  
Order Of Magnitude ◽  
Demographic Noise ◽  
Single Gene Deletion

AbstractDemographic noise, the change in the composition of a population due to random birth and death events, is an important driving force in evolution because it reduces the efficacy of natural selection. Demographic noise is typically thought to be set by the population size and the environment, but recent experiments with microbial range expansions have revealed substantial strain-level differences in demographic noise under the same growth conditions. Many genetic and phenotypic differences exist between strains; to what extent do single mutations change the strength of demographic noise? To investigate this question, we developed a high-throughput method for measuring demographic noise in colonies without the need for genetic manipulation. By applying this method to 191 randomly-selected single gene deletion strains from the E. coli Keio collection, we find that a typical single gene deletion mutation decreases demographic noise by 8% (maximal decrease: 81%). We find that the strength of demographic noise is an emergent trait at the population level that can be predicted by colony-level traits but not cell-level traits. The observed differences in demographic noise from single gene deletions can increase the establishment probability of beneficial mutations by almost an order of magnitude (compared to in the wild type). Our results show that single mutations can substantially alter adaptation through their effects on demographic noise and suggest that demographic noise can be an evolvable trait of a population.

scholarly journals A Comprehensive Analysis of Replicative Lifespan in 4,698 Single-Gene Deletion Strains Uncovers Conserved Mechanisms of Aging

2015 ◽  
Vol 22 (5) ◽  
pp. 895-906 ◽  
Author(s):  
Mark A. McCormick ◽  
Joe R. Delaney ◽  
Mitsuhiro Tsuchiya ◽  
Scott Tsuchiyama ◽  
Anna Shemorry ◽  
...  
Keyword(s):  
Gene Deletion ◽  
Single Gene ◽  
Comprehensive Analysis ◽  
Replicative Lifespan ◽  
Single Gene Deletion

Evaluation of Low Mean Corpuscular Volume in an Apheresis Donor Population.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4136-4136
Author(s):  
Barbara J. Bryant ◽  
Julie A. Hopkins ◽  
Susan F. Leitman
Keyword(s):  
Iron Deficiency ◽  
Mean Corpuscular Volume ◽  
Gene Deletion ◽  
Single Gene ◽  
Transferrin Saturation ◽  
Hemoglobin S ◽  
Alpha Thalassemia ◽  
Donor Population ◽  
Thalassemia Trait ◽  
Single Gene Deletion

Abstract Donors of apheresis blood components are routinely evaluated with a complete blood count (CBC) at the time of each donation. In otherwise healthy donors, recurrent low mean corpuscular volume (MCV) values (< 80 fL) in the presence of an acceptable hemoglobin (≥ 12.5 gm/dL) could be due to iron deficiency or to an hemoglobinopathy, such as alpha thalassemia trait or a beta chain variant trait. Iron deficiency in repeat blood donors may warrant treatment with oral iron supplementation, whereas donors with hemoglobinopathies in the absence of iron deficiency do not need treatment. Pre-donation samples for CBC (Cell-Dyn 4000, Abbott) were obtained from all apheresis donors donating platelets, plasma, granulocytes, lymphocytes, and monocytes. MCV values <80 fL were electronically flagged via a donor database module for review by medical staff. Donors with MCV ≤ 80 fL on two or more occasions were evaluated for iron deficiency and the presence of hemoglobinopathies. CBC, ferritin, serum iron, transferrin, percent transferrin saturation, and hemoglobin electrophoresis were performed at the time of a subsequent donation. Iron deficiency was defined as values below the reference range for ferritin or transferrin saturation. Alpha thalassemia trait was presumed if the red blood cell count was elevated, no variant hemoglobins were detected by electrophoresis, and the ferritin, percent transferrin saturation, serum iron, and transferrin levels were all within normal ranges. In a one-year period, 25 of 1333 healthy apheresis donors had a low MCV on more than one occasion. Donors with low MCV were more likely to be African American (AA) (12 of 25, 48%) or Asian (2 of 25, 8%) compared with donors without a low MCV (AA 193 of 1308, 15%; Asian 37 of 1308, 3%). Iron deficiency was present in 60% (15 of 25) of the low-MCV donors: 36% (9) had isolated iron deficiency, 20% (5) had iron deficiency with probable alpha thalassemia trait, and 4% (1) had hemoglobin C trait with coexistent iron deficiency. Hemoglobinopathy without concomitant iron deficiency was found in 40% (10 of 25) of the low-MCV donors and included 24% (6) with presumed alpha thalassemia trait, 4% (1) with hemoglobin S trait and single gene deletion alpha thalassemia trait (hemoglobin S concentration 34%), 4% (1) with hemoglobin S trait and double gene deletion alpha thalassemia trait (hemoglobin S concentration 28%), 4% (1) with hemoglobin Lepore trait, and 4% (1) with hemoglobin G-Philadelphia trait with at least a single gene deletion alpha thalassemia trait (hemoglobin G-Philadelphia concentration 36%). Although the combination of MCV, hemoglobin, and red cell count available from the routine CBC were often helpful in discriminating iron deficiency from hemoglobinopathy, the frequent coexistence of both processes resulted in a need for further laboratory evaluation, both before and after iron repletion, to confirm the diagnosis. In a sample of American repeat apheresis donors, iron deficiency is present in the majority with recurrent low MCV values and hemoglobin levels ≥ 12.5 gm/dL. Concurrent hemoglobinopathy is also commonly present but may not be easily recognized in the setting of iron deficiency. The MCV is a useful screening tool to detect iron deficiency in a repeat blood donor population, however low MCV values should be further investigated in the blood donor setting to determine if iron replacement therapy is indicated.

scholarly journals Update on the Keio collection of Escherichia coli single‐gene deletion mutants

2009 ◽  
Vol 5 (1) ◽  
pp. 335 ◽  
Author(s):  
Natsuko Yamamoto ◽  
Kenji Nakahigashi ◽  
Tomoko Nakamichi ◽  
Mihoko Yoshino ◽  
Yuki Takai ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gene Deletion ◽  
Single Gene ◽  
Deletion Mutants ◽  
Keio Collection ◽  
Single Gene Deletion

scholarly journals Pcr-Based Construction and Transformation of Cody Gene Deletion Construct in Streptococcus Pneumoniae

2017 ◽  
Vol 16 (1) ◽  
Author(s):  
Aisyah Mohamed Rehan ◽  
Mohammad Izwan Enche Othman ◽  
Nor Munirah Mohd Amin ◽  
Intan Azura Shahdan ◽  
Hanani Ahmad Yusof@Hanafi
Keyword(s):  
Streptococcus Pneumoniae ◽  
Gene Deletion ◽  
Single Gene ◽  
Crystallographic Structure ◽  
Mortality And Morbidity ◽  
Fusion Pcr ◽  
Deletion Construct ◽  
Hyaluronate Lyase ◽  
Pcr Method ◽  
Single Gene Deletion

Introduction: Streptococcus pneumoniae (S. pneumoniae) is a gram-positive diplococci belonging to the genus Streptococcus and it is a well-studied pathogenic bacterium. Pneumococcal diseases such as otitis media, pneumonia, sepsis and meningitis caused by pathogenic strains of S. pneumoniae still brought significant mortality and morbidity worldwide. The pathogenicity of S. pneumoniae is exerted by various virulence factors and one of it is the enzyme hyaluronate lyase. Hyaluronate lyase plays a major role in the invasive capability of S. pneumoniae. Its mechanism of action and crystallographic structure have been determinedbut its regulatory mechanism is still poorly understood. Drawing connections between the nutritional behaviour and invasive property of S. pneumoniae, CodY regulator is hypothesized as a potential hyaluronate lyase regulator. This work was aimed to construct CodY deficient mutant of S. pneumoniae to form foundational work for the study of CodY regulatory effect on hyaluronate lyase. Materials and method: A single gene-deletion method was chosen to create CodY mutant construct containing aphA-3 gene (encoding kanamycin resistance protein) replacement cassette by employing recombinant fusion PCR method. A single band DNA product at the expected size of 2,563 bp after recombinant fusion PCR was visualized on agarose gel electrophoresis. This indicated that the linear recombinant amplicon has been successfully constructed. The recombinant amplicon was transformed into S. pneumoniae cells of Malaysian local clinical isolate by employing the competence stimulating peptide (CSP-1) to enhance and induce natural competence. Results: No viable CodY mutant was evident post-transformation. The negative transformation result was postulated to be due to the essential nature of CodY regulator. Conclusion: This work can provide basis for recombinant fusion PCR method in designing and constructing single gene deletion construct. However, further work is needed to identify the regulatory agent of hyaluronate lyase.

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