A5080767805- Bacterial Genetics and Biotechnology
- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- DNA Repair Mechanisms
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Reproductive Physiology in Livestock
- RNA modifications and cancer
- Peptidase Inhibition and Analysis
- Advanced Proteomics Techniques and Applications
- Quality and Supply Management
- Bacteriophages and microbial interactions
- Amino Acid Enzymes and Metabolism
- Ubiquitin and proteasome pathways
- Bioinformatics and Genomic Networks
- Genetic and phenotypic traits in livestock
- Enzyme Catalysis and Immobilization
- Innovative Microfluidic and Catalytic Techniques Innovation
- Gene Regulatory Network Analysis
- Advanced Fluorescence Microscopy Techniques
- Monoclonal and Polyclonal Antibodies Research
- Resilience and Mental Health
- Biochemical and Structural Characterization
- Transgenic Plants and Applications
- Nuclear Structure and Function
ETH Zurich
2016-2025
University of Waikato
2020
University of Guelph
2002-2012
University of Toronto
2004-2008
QB3
2008
University of California, San Francisco
2008
Montana State University
2005
Memorial Sloan Kettering Cancer Center
2004
McGill University
2004
A genetic interaction network containing approximately 1000 genes and 4000 interactions was mapped by crossing mutations in 132 different query into a set of 4700 viable gene yeast deletion mutants scoring the double mutant progeny for fitness defects. Network connectivity predictive function because often occurred among functionally related genes, similar patterns tended to identify components same pathway. The exhibited dense local neighborhoods; therefore, position on partially is other...
Recent findings suggest important roles for nuclear organization in gene expression. In contrast, little is known about how contributes to genome stability. Epistasis analysis (E-MAP) using DNA repair factors yeast indicated a functional relationship between pore subcomplex and Slx5/Slx8, small ubiquitin-like modifier (SUMO)-dependent ubiquitin ligase, which we show physically interact. Real-time imaging chromatin immunoprecipitation confirmed stable recruitment of damaged pores. Relocation...
Green fluorescent proteins (GFPs) are invaluable tools for modern cell biology. Even though many properties of GFP have been successfully engineered, a retaining brightness at low pH has not emerged. This limits the use in quantitative studies performed fluctuating or acidic conditions. We report engineering and characterisation tandem dimer (pH-tdGFP), bright stable that can be efficiently excited maintains its fluorescence Therefore, pH-tdGFP could act as marker cellular processes occur...
RTT107 (ESC4, YHR154W) encodes a BRCA1 C-terminal-domain protein that is important for recovery from DNA damage during S phase. Rtt107 substrate of the checkpoint kinase Mec1, although mechanism by which targeted Mec1 after activation currently unclear. Slx4, component Slx1-Slx4 structure-specific nuclease, formed complex with Rtt107. Deletion SLX4 conferred many same DNA-repair defects observed in rtt107delta, including sensitivity, prolonged activation, and increased spontaneous damage....
The bacterial envelope plays a critical role in maintaining essential cellular functions by selectively regulating import and export. selectivity of this can restrict the utilisation externally provided compounds, thereby restricting functional space engineering. This study systematically investigates potential large pore outer membrane proteins (OMPs) to enhance permeability for diverse challenging compounds. We focus on general porin OmpF, which facilitates diffusion water small molecules,...
RTT107 (ESC4, YHR154W) encodes a BRCA1 C-terminal domain protein that is important for recovery from DNA damage during S phase. Rtt107 substrate of the checkpoint kinase Mec1, and it forms complexes with repair enzymes, including nuclease subunit Slx4, but role in response remains unclear. We find interacts chromatin when cells are treated compounds cause replication forks to arrest. This damage-dependent binding requires acetyltransferase Rtt109, does not require acetylation known Rtt109...
Abstract Multiplexed gene expression optimization via modulation of translation efficiency through ribosome binding site (RBS) engineering is a valuable approach for optimizing artificial properties in bacteria, ranging from genetic circuits to production pathways. Established algorithms design smart RBS-libraries based on single partially-degenerate sequence that efficiently samples the entire space initiation rates. However, accessible when integrating library by CRISPR/Cas9-based genome...
Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive are typically identified transposon mutagenesis on a case-by-case basis, limiting scalability their exploitation as system-wide protein engineering tool.We developed apporach predicting stretches (PSs) in based the identification length-variable regions (regions containing indels) homologous proteins.We...
Integration of novel compounds into biological processes holds significant potential for modifying or expanding existing cellular functions. However, the uptake these is often hindered by selectively permeable membranes. We present a bacterial transport system that has been rationally designed to address this challenge. Our approach utilizes highly promiscuous sulfonate membrane transporter, which allows passage cargo molecules attached as amides sulfobutanoate vector molecule cytoplasm...
Abstract Saccharomyces cerevisiae cells grown in a small volume of chemically defined media neither reach the desired cell density nor grow at fast enough rate to scale down and increase sample number classical biochemical assays, as detection limit readout often requires high an input. To ameliorate this problem, we developed optimised new (HCD) medium for S. . Starting from widely used synthetic composition, systematically varied concentrations all components without addition other...
The susceptibility of Pseudomonas aeruginosa (PA01) bacteria to ultraviolet-A (UV-A) light in photocatalytic and non-photocatalytic systems was investigated. Thin films TiO 2 were deposited on glass slides using a dip-coating method. Disinfection both planktonic biofilm bacterial cells studied over coated uncoated exposed low intensity (1.0 mW/cm ) UV-A irradiation. Photocatalytic treatment PA01 cultures pro-vided 4-log reduction the number viable 3 h whereas UV alone produced 1-log...
T7 RNA polymerase (RNAP) is a valuable tool in biotechnology, basic research and synthetic biology due to its robust, efficient selective transcription of genes. Here, we expand the scope RNAP include plasmid replication. We present novel type plasmid, termed ori plasmids that replicate, an engineered Escherichia coli, with phage origin as sole find while replication proteins; DNA polymerase, single-stranded binding proteins helicase-primase are dispensable for replication, required,...
CRM66 (cross-reactive 66 kDa protein) is an inactive mutant form of Pseudomonas aeruginosa exotoxin A that has been isolated from a strain P. derived nitrosoguanidine-based mutagenesis. The mutation within this enzyme toxin was previously identified as H426Y and it shown to possess significantly reduced enzymic activity. Furthermore, suggested His-426 may directly participate in the catalytic mechanism also play important role binding protein substrate A, critical factor eukaryotic...
Xenobiology is an emerging field that focuses on the extension and redesign of biological systems through use laboratory-derived xenomolecules, which are molecules new to metabolism cell. Despite enormous potential using xenomolecules in living organisms, most noncanonical building blocks still need be supplied externally, often poor uptake into cells limits wider applicability. To improve cytosolic availability molecules, a synthetic transport system based portage was developed, interest...
All known bacterial tRNAs adopt the canonical cloverleaf 2D and L-shaped 3D structures. We aimed to explore whether alternative tRNA structures could be introduced in translation. To this end, we crafted a vitamin-based genetic system evolve Escherichia coli toward activity of structurally non-canonical tRNAs. The reliably couples (escape frequency <10-12) growth with activities novel orthogonal histidine suppressor (HisTUAC) cognate ARS (HisS) via suppression GTA valine codon mRNA an enzyme...
Transfer ribonucleic acids (tRNAs) are essential for protein synthesis, decoding mRNA sequences into amino acids. In E. coli K-12 MG1655, 86 tRNA genes organized in 43 transcription units (TUs) and the essentiality of individual TUs bacterial physiology remains unclear. To address this, we systematically generated deletion strains which each TU was replaced by a kanamycin resistance gene. We found that 33 not survival, while 10 require corresponding to be provided on plasmid. The analysis...
Teaching social work students in Aotearoa New Zealand during the Covid-19 crisis produced an acute awareness of impact lockdown levels 3 and 4 on student wellbeing. Students were required to rapidly adapt study a fully online environment without face-to-face support university campus life. Normal academic pressures immediately intensified, with no immediate relief sight. Student resilience was tested further due multiple factors such as: suddenly reduced incomes, parenting lockdown, caring...
Saccharomyces cerevisiae cells grown in a small volume of defined media neither reach the desired cell density nor grow at fast enough rate to scale down and increase sample number classical biochemical assays, as detection limit readout often requires high an input. To ameliorate this problem, we developed optimised new (HCD) medium for S. . Starting from widely-used synthetic composition, systematically varied concentrations all components without addition other compounds. We used response...