A5083199812- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- Fermentation and Sensory Analysis
- Ecology and Vegetation Dynamics Studies
- Forest Insect Ecology and Management
- Crustacean biology and ecology
- Bioinformatics and Genomic Networks
- Viral Infectious Diseases and Gene Expression in Insects
- Advanced Proteomics Techniques and Applications
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Marine Biology and Environmental Chemistry
- Forest Ecology and Biodiversity Studies
- Genomics and Phylogenetic Studies
- Marine and coastal plant biology
- Marine Biology and Ecology Research
- RNA and protein synthesis mechanisms
- thermodynamics and calorimetric analyses
- Enzyme Structure and Function
- Light effects on plants
- Plant and animal studies
- Evolution and Genetic Dynamics
- Metabolomics and Mass Spectrometry Studies
- Plant Gene Expression Analysis
- Biofuel production and bioconversion
University of Gothenburg
2014-2023
University of Sheffield
2018
Australian National University
2018
Université de Montpellier
2018
Centre National de la Recherche Scientifique
2018
University of St Andrews
2018
Utah State University
2018
University College London
2018
University of Oxford
2018
University of Toronto
2018
A fundamental goal in biology is to achieve a mechanistic understanding of how and what extent ecological variation imposes selection for distinct traits favors the fixation specific genetic variants. Key such an detailed mapping natural genomic phenomic space bridging gap that separates these worlds. Here we chart high-resolution map trait one most important model organisms, budding yeast Saccharomyces cerevisiae, its closest wild relatives trace basis timing major phenotype changing events...
In a cell culture of Saccharomyces cerevisiae exponentially growing in basal medium, only 0.02% the cells were osmotolerant, i.e., survived transfer to medium containing 1.4 M NaCl. Short-time conditioning 0.7 NaCl transformed whole population into an osmotolerance phenotype. During this conditioning, rate formation glycerol, main compatible solute S. cerevisiae, increased threefold and specific activity glycerol-3-phosphate dehydrogenase (NAD+) (GPDH) (EC 1.1.1.8) was enhanced sixfold. The...
Abstract A methodology for large‐scale automated phenotypic profiling utilizing quantitative changes in yeast growth has been tested and applied to the analysis of some commonly used laboratory strains. This yeast‐adjusted is based on microcultivation 350 µl liquid medium, where frequently optically recorded, followed by extraction relevant variables from obtained curves. We report that cultivation at this micro‐scale displayed overall features protein expression pattern highly similar well...
We present a methodology for gene functional prediction based on extraction of physiologically relevant growth variables from all viable haploid yeast knockout mutants. This quantitative phenomics approach, here applied to saline cultivation, identified marginal but functionally important phenotypes and allowed the precise determination time adapt an environmental challenge, rate growth, efficiency growth. ≈500 salt-sensitive deletions, majority which were previously uncharacterized...
The existence of specific DL-glycerol-3-phosphatase (EC) activity in extracts Saccharomyces cerevisiae was confirmed by examining strains lacking nonspecific acid and alkaline phosphatase activities. During purification the glycerol-3-phosphatase, two isozymes having very similar molecular weights were isolated gel filtration anion exchange chromatography. By microsequencing trypsin-generated peptides corresponding genes identified as previously sequenced open reading frames unknown...
The salt-instigated protein expression of Saccharomyces cerevisiae during growth in either 0.7 or 1.4 M NaCl was studied by two-dimensional polyacrylamide gel electrophoresis. 73 spots that were identified as more than 3-fold responsive further grouped response class (halometric, low-salt, and high-salt regulation). Roughly 40% these proteins found to decrease expression, while at higher magnitudes change (>8-fold) only induction recorded. Enolase 1 (Eno1p) the most increasing absolute...
Abstract Phenotypic variation arising from populations adapting to different niches has a complex underlying genetic architecture. A major challenge in modern biology is identify the causative variants driving phenotypic variation. Recently, baker’s yeast, Saccharomyces cerevisiae emerged as powerful model for dissecting traits. However, past studies using laboratory strain were unable reveal complete architecture of polygenic Here, we present linkage study 576 recombinant strains obtained...
A glycerol-nonutilizing mutant of the salt-tolerant yeast Debaryomyces hansenii was isolated. When subjected to salt stress produced glycerol, and internal level glycerol increased linearly in proportion increases external salinity as wild-type strain. However, at showed a more pronounced decrease growth rate yield lost surrounding medium than did wild type. Uptake experiments be accumulated against strong concentration gradient, both strains displayed similar kinetic parameters for uptake...
Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying with flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on regions of high differentiation. However, not all architectures potentially are expected to show extreme Here, we develop an approach that combines hybrid zone analysis (i.e., focuses spatial patterns allele frequency change) system-specific simulations identify loci...
We have cloned and characterized a homologue of the previously isolated GPD1 gene, encoding sn ‐glycerol 3‐phosphate dehydrogenase (NAD + ) in Saccharomyces cerevisiae . This second called GPD2 , encodes protein 384 amino acids that shares 69% sequence identity with Like it has an amino‐terminal extension unknown function. is located on chromosome VII cross‐hybridizes at IV as well XV. Disruption gene did not reveal any observable phenotypic effects, whereas overexpression resulted slight,...
Abstract An interlaboratory comparison was conducted on the positional and quantitative reproducibility of yeast proteins resolved by two‐dimensional polyacrylamide gel electrophoresis (2‐D PAGE) using isoelectric focusing with immobilized pH gradient (pH 4–7) in first dimension. The basic experimental set‐up as follows: one laboratory prepared distributed a [ 35 S]methioninelabeled total protein extract (Göteborg, Sweden), another IPG strips to be used all labs this study (Munich, Germany),...
The number of chromosome sets contained within the nucleus eukaryotic organisms is a fundamental yet evolutionarily poorly characterized genetic variable life. Here, we mapped impact ploidy on mitotic fitness baker's yeast and its never domesticated relative Saccharomyces paradoxus across wide swaths their natural genotypic phenotypic space. Surprisingly, environment-specific influences reproduction were found to be rule rather than exception. These ploidy-environment interactions well...
Abstract The fission yeast Schizosaccharomyces pombe has been widely used to study eukaryotic cell biology, but almost all of this work derivatives a single strain. We have studied 81 independent natural isolates and 3 designated laboratory strains pombe. varies significantly in size shows only limited variation proliferation different environments compared with Saccharomyces cerevisiae. Nucleotide diversity, π, at near neutral site, the central core centromere chromosome II is approximately...
A fundamental question in biology is whether variation organisms primarily emerges as a function of adaptation or neutral genetic drift. Trait the model organism baker's yeast follows population bottlenecks rather than environmental boundaries suggesting that it results from Based on life history, we hypothesized population-specific loss-of-function mutations emerging genes recently released selection predominant cause trait within species. As retention one functional copy gene diploid...
The capacity to map traits over large cohorts of individuals-phenomics-lags far behind the explosive development in genomics. For microbes, estimation growth is key phenotype because its link fitness. We introduce an automated microbial phenomics framework that delivers accurate, precise, and highly resolved phenotypes at unprecedented scale. Advancements were achieved through introduction transmissive scanning hardware software technology, frequent acquisition exact colony population size...
Abstract Background Phenomics is a field in functional genomics that records variation organismal phenotypes the genetic, epigenetic or environmental context at massive scale. For microbes, key phenotype growth population size because it contains information directly linked to fitness. Due technical innovations and extensive automation our capacity record complex dynamic microbial data rapidly outpacing dissect visualize this extract fitness components contains, hampering progress all fields...
Anaerobic and aerobic chemostat cultures of Saccharomyces cerevisiae were performed at a constant dilution rate 0.10 h(-1). The glucose concentration was kept constant, whereas the nitrogen gradually decreasing; i.e., conditions changed from energy limitation to excess. This experimental setup enabled glycolytic be separated growth rate. There an extensive uncoupling between anabolic requirements catabolic production when source present in excess both aerobically anaerobically. To increase...
Abstract Background The invasive benthic round goby ( Neogobius melanostomus) is the most successful temperate fish and has spread in aquatic ecosystems on both sides of Atlantic. Invasive species constitute powerful situ experimental systems to study fast adaptation directional selection short ecological timescales present promising case studies understand factors involved impressive ability some colonize novel environments. We seize unique opportunity presented by invasion genomic...
The genes YML070W/DAK1 andYFL053W/DAK2 in the yeast Saccharomyces cerevisiae were characterized by a combined genetic and biochemical approach that firmly functionally classified their encoded proteins as dihydroxyacetone kinases (DAKs), an enzyme present most organisms. kinetic properties of two isoforms similar, exhibiting K m(DHA) 22 5 μm m(ATP) 0.5 0.1 mm for Dak1p Dak2p, respectively. We furthermore show substrate, (DHA), is toxic to cells detoxification dependent on functional DAK....