A5063782623- Genomics and Phylogenetic Studies
- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- Bacterial Genetics and Biotechnology
- Environmental DNA in Biodiversity Studies
- RNA and protein synthesis mechanisms
- Virus-based gene therapy research
- COVID-19 diagnosis using AI
- Microbial Community Ecology and Physiology
- Respiratory viral infections research
- Genetic diversity and population structure
- Bacteriophages and microbial interactions
- Escherichia coli research studies
- Viral Infectious Diseases and Gene Expression in Insects
- Parasite Biology and Host Interactions
- Viral gastroenteritis research and epidemiology
- Influenza Virus Research Studies
- CAR-T cell therapy research
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- Animal Virus Infections Studies
- Evolutionary Game Theory and Cooperation
- Evolution and Genetic Dynamics
- Neutropenia and Cancer Infections
- Gut microbiota and health
University of Auckland
2021-2024
Massey University
2016-2023
Australian National University
2023
Education New Zealand
2023
University of Basel
2016
Board of the Swiss Federal Institutes of Technology
2008
ETH Zurich
2008
Naval Health Research Center
2004-2007
Naval Medical Center San Diego
2006
United States Department of Defense
2004
Abstract Rapid and cost-efficient whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes disease 2019, is critical for understanding viral transmission dynamics. Here we show using a new multiplexed set primers in conjunction with Oxford Nanopore Barcode library kit allows faster, simpler, less expensive SARS-CoV-2 genome sequencing. This primer results amplicons exhibit lower levels variation coverage compared to other commonly used...
<ns3:p>Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations biological concern were reported, one the United Kingdom and South Africa. Using a combination data from routine surveillance, genomic sequencing international travel we track dispersal lineages B.1.1.7 B.1.351 (variant 501Y-V2). We account for potential biases surveillance efforts by including passenger volumes location where lineage was first London Africa...
<ns3:p>Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations biological concern were reported, one the United Kingdom and South Africa. Using a combination data from routine surveillance, genomic sequencing international travel we track dispersal lineages B.1.1.7 B.1.351 (variant 501Y-V2). We account for potential biases surveillance efforts by including passenger volumes location where lineage was first London Africa...
Epidemic respiratory infections are responsible for extensive morbidity and mortality within both military civilian populations. We describe a high-throughput method to simultaneously identify genotype species of bacteria from complex mixtures in samples. The process uses electrospray ionization mass spectrometry base composition analysis PCR amplification products highly conserved genomic regions determine the relative quantity pathogenic present sample. High-resolution genotyping specific...
Abstract Background The first step in understanding ecological community diversity and dynamics is quantifying membership. An increasingly common method for doing so through metagenomics. Because of the rapidly increasing popularity this approach, a large number computational tools pipelines are available analysing metagenomic data. However, majority these have been designed benchmarked using highly accurate short read data (i.e. Illumina), with few studies benchmarking classification...
Background.High levels of morbidity caused by adenovirus among US military recruits have returned since the loss vaccines in 1999.The transmission dynamics never been well understood, which complicates prevention efforts.Methods.Enrollment and end-of-study samples were obtained active surveillance for febrile respiratory illnesses (FRIs) was performed 341 support personnel.Environmental collected simultaneously.Classic advanced diagnostic techniques used.Results.Seventy-nine percent...
Genetically identical populations of unicellular organisms often show marked variation in some phenotypic traits. To investigate the molecular causes and possible biological functions this noise, it would be useful to have a method identify genes whose expression varies stochastically on certain time scale. Here, we developed such used for identifying with high levels noise Salmonella enterica ssp. I serovar Typhimurium (S. Typhimurium). We created genomic plasmid library fused green...
Abstract Real-time genomic sequencing has played a major role in tracking the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contributing greatly to disease mitigation strategies. In August 2020, after having eliminated virus, New Zealand experienced second outbreak. During that outbreak, used primary role, leading elimination virus. We generated genomes from 78% laboratory-confirmed samples SARS-CoV-2 outbreak and compared them with available data. Genomic...
ABSTRACT We have developed a PCR/electrospray ionization mass spectrometry (PCR/ESI-MS) assay for the rapid detection, identification, and serotyping of human adenoviruses. The employs high-performance spectrometer to “weigh” amplicons obtained from PCR using primers designed amplify known Masses are converted base compositions and, by comparison against database genetic sequences, serotype present in sample is determined. performance was demonstrated with quantified viral standards...
ABSTRACT Infections of adenovirus type 4 (Ad4) and Ad7 were discovered among previously vaccinated individuals through febrile respiratory illness surveillance at military recruit camps. Genetic analysis was performed on these isolates a sample from unvaccinated patients. Antigenic regions the hexon gene 21 31 patients sequenced compared to homologous Ad4 vaccine strains other representative sequences archived in GenBank. The phylogenetic distribution closely resembled those individuals....
Abstract Despite the success of adenovirus vaccine administered to US military trainees, acute respiratory disease (ARD) surveillance still detected breakthrough infections (respiratory illnesses associated with serotypes specifically targeted by vaccine). To explore role adenoviral co-infection (simultaneous infection multiple pathogenic species) in disease, we examined specimens from patients ARD using 3 methods detect species: a DNA microarray, polymerase chain reaction...
Gene essentiality - whether or not a gene is necessary for cell growth fundamental component of function. It well established how quickly can change, as few studies have compared empirical measures between closely related organisms.Here we present the results Tn-seq experiment designed to detect essential protein coding genes in bacterial pathogen Shigella flexneri 2a 2457T on genome-wide scale. Superficial analysis this data suggested that 481 protein-coding strain are critical robust...
Evolutionary biology was previously considered a historical science with predictions about evolutionary trajectories believed to be near impossible. The development of high throughput sequencing and data analysis technologies has challenged this belief, provided an abundance that yields novel insights into processes. are now increasingly being used develop fundamental knowledge evolving systems and/or demonstrate control. Here we investigate the factors make repeatability more or less likely...
To enable faster, easier sequencing of SARS-COV2 genomes with fewer steps than current methods, we use multiplexed 1200 base pair PCR amplicons the Oxford Nanopore RAPID barcoding kit. UPDATE: The Rapid protocol is now (March 2021) available on website for 1-96 samples "PCR tiling SARS-CoV-2 virus rapid (SQK-RBK110.96)" https://community.nanoporetech.com/protocols/pcr-tiling-of-sars-cov-2-virus-with-rapid-barcoding-sqk-rbk110/v/PCTR_9125_v110_revA_24Mar2021 This a modification ARTIC amplicon...
Abstract Rapid and cost-efficient whole-genome sequencing of SARS-CoV-2, the virus that causes COVID-19, is critical for understanding viral transmission dynamics. Here we show using a new multiplexed set primers in conjunction with Oxford Nanopore Barcode library kit allows faster, simpler, less expensive SARS-CoV-2 genome sequencing. This primer results amplicons exhibit lower levels variation coverage compared to other commonly used sets. Using five patient samples C q values between 20...
To enable faster, easier sequencing of SARS-COV2 genomes with fewer steps than current methods, we use multiplexed 1200 base pair PCR amplicons the Oxford Nanopore RAPID barcoding kit. UPDATE: The Rapid protocol is now (March 2021) available on website for 1-96 samples "PCR tiling SARS-CoV-2 virus rapid (SQK-RBK110.96)" https://community.nanoporetech.com/protocols/pcr-tiling-of-sars-cov-2-virus-with-rapid-barcoding-sqk-rbk110/v/PCTR_9125_v110_revA_24Mar2021 This a modification ARTIC amplicon...
This protocols is part of the ANU Biosecurity mini-research project #2 "An SARS-COV2 incursion scenario: Genomics, phylogenetics, and incursions." modeled on yearly Quality Assurance Program The Royal College Pathologists Australia (RCPAQAP), we take in together with ACT Pathology. research split into two major parts, identical to how official RCPAQAP run every year. Part #1 focusing 'wet- lab' by sequencing from real world RNA samples provided Pathology especially for our biosecurity course...
Abstract Background The first step in understanding ecological community diversity and dynamics is quantifying membership. An increasingly common method for doing so through metagenomics. Because of the rapidly increasing popularity this approach, a large number computational tools pipelines are available analysing metagenomic data. However, majority these have been designed benchmarked using highly accurate short read data (i.e. illumina), with few studies benchmarking classification...
Abstract Population genetic structure in the marine environment can be influenced by life‐history traits such as developmental mode (biphasic, with distinct adult and larval morphology, direct development, which larvae resemble adults) or habitat specificity, well geography selection. Developmental is thought to significantly influence dispersal, developers expected have much lower dispersal potential. However, this prediction complicated presence of geophysical barriers dispersal. In study,...
Transposon mutagenesis is a method that allows gene disruption via the random genomic insertion of piece DNA called transposon. The protocol below outlines for high efficiency transfer between bacterial strains plasmid harboring transposon containing kanamycin resistance marker. plasmid-borne transposase encoded by variant tnp inserts into genome recipient strain with very low insertional bias. This thus creation large mutant libraries in which transposons have been inserted unique positions...
Most animal mitochondrial genomes are small, circular and structurally conserved. However, recent work indicates that diverse taxa possess unusual genomes. In Isopoda, species in multiple lineages have atypical rearranged more of this speciose taxon need to be evaluated understand the evolutionary origins group. study, we report presence an structure New Zealand endemic marine isopod, Isocladus armatus. Data from long- short-read DNA sequencing suggest I. armatus has two chromosomes. The...