ORCID Profile
0000-0003-1221-7023
Current Organisation
University of Sydney
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Publisher: Springer US
Date: 2021
Publisher: Elsevier BV
Date: 10-2018
Publisher: Oxford University Press (OUP)
Date: 03-08-2018
Abstract: Quantification of microbes in water systems is essential to industrial practices ranging from drinking water and wastewater treatment to groundwater remediation. While quantification using DNA-based molecular methods is precise, the accuracy is dependent on DNA extraction efficiencies. We show that the DNA yield is strongly impacted by the cell concentration in groundwater s les (r = -0.92, P < 0.0001). This has major implications for industrial applications using quantitative polymerase chain reaction (qPCR) to determine cell concentrations in water, including bioremediation. We propose a simple normalization method using a DNA recovery ratio, calculated with the total cell count and DNA yield. Application of this method to enumeration of bacteria and archaea in groundwater s les targeting phylogenetic markers (16S rRNA) demonstrated an increased goodness of fit after normalization (7.04 vs 0.94 difference in Akaike's information criteria). Furthermore, normalization was applied to qPCR quantification of functional genes and combined with DNA sequencing of archaeal and bacterial 16S rRNA genes to monitor changes in abundance of methanogenic archaea and sulphate-reducing bacteria in groundwater. The integration of qPCR and DNA sequencing with appropriate normalization enables high-throughput quantification of microbial groups using increasingly affordable and accessible techniques. This research has implications for microbial ecology and engineering research as well as industrial practice.
Publisher: MDPI AG
Date: 04-08-2016
DOI: 10.3390/IJMS17081264
Publisher: Frontiers Media SA
Date: 23-01-2019
Publisher: MDPI AG
Date: 12-05-2017
DOI: 10.3390/IJMS18051047
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.LUNGCAN.2019.06.021
Abstract: To determine the predictive and prognostic roles of three blood-based biomarkers: circulating tumour DNA (ctDNA), circulating tumour cells (CTC) and carcinoembryonic antigen (CEA), in patients with advanced epidermal growth factor receptor-mutated (EGFR+) lung cancer. We recruited 28 patients with 103 serial blood s les. We performed mutational analyses for EGFR mutations using droplet digital PCR (ddPCR) on ctDNA. We evaluated the accuracy of EGFR mutation detection in ctDNA compared with tissue biopsy. We also quantified CTCs, ctDNA and CEA in serially collected blood s les, and evaluated the baseline and changes in these blood-based biomarkers with clinical outcomes. EGFR mutation detection in plasma was highly concordant as compared with tissue biopsy. Detectable baseline ctDNA was associated with higher disease burden (p < 0.01). Early disappearance of ctDNA at 4 weeks was associated with radiological response at 12 weeks of treatment (p = 0.01) and improved progression free survival (PFS) (HR 5.47, 95%CI 1.32-22.72, p = 0.02) and overall survival (OS) (HR 5.46, 95%CI 1.28-23.22, p = 0.02). A decrease in CTC count at 4 weeks was associated with improved PFS (HR 3.81, 95%CI 1.13-12.79, p = 0.03) but not OS. 85% of patients with radiological progression had a ctDNA rise compared with 22% of patients with stable disease (p=0.01). ctDNA rise was seen on average 170 days prior to radiological progression. There is a significant association between the rise of CEA level with radiological progression (p=0.001). Early change in ctDNA, CTC and CEA levels may be long-term predictors of treatment benefit and failure prior to availability of radiological response data.
Publisher: MDPI AG
Date: 27-09-2022
Abstract: Diet, exercise and the gut microbiome are all factors recognised to be significant contributors to cardiometabolic health. However, diet and exercise interventions to modify the gut microbiota to improve health are limited by poor understanding of the interactions between them. In this pilot study, we explored diet–exercise–microbiome dynamics in bodybuilders as they represent a distinctive group that typically employ well-defined dietary strategies and exercise regimes to alter their body composition. We performed longitudinal characterisation of diet, exercise, the faecal microbial community composition and serum metabolites in five bodybuilders during competition preparation and post-competition. All participants reduced fat mass while conserving lean mass during competition preparation, corresponding with dietary energy intake and exercise load, respectively. There was in idual variability in food choices that aligned to in idualised gut microbial community compositions throughout the study. However, there was a common shift from a high protein, low carbohydrate diet during pre-competition to a more macronutrient-balanced diet post-competition, which was associated with similar changes in the gut microbial ersity across participants. The circulating metabolite profiles also reflected in iduality, but a subset of metabolites relating to lipid metabolism distinguished between pre- and post-competition. Changes in the gut microbiome and circulating metabolome were distinct for each in idual, but showed common patterns. We conclude that further longitudinal studies will have greater potential than cross-sectional studies in informing personalisation of diet and exercise regimes to enhance exercise outcomes and improve health.
Publisher: Proceedings of the National Academy of Sciences
Date: 28-03-2014
Abstract: Within-population genetic ersity is an essential evolutionary prerequisite for processes ranging from antibiotic resistance to niche adaptation, but its generation is poorly understood, with most studies focusing on fixed substitutions at the end point of long-term evolution. Using deep sequencing, we analyzed short-term, within-population genetic ersification occurring during biofilm formation of the model bacterium Pseudomonas aeruginosa . We discovered extensive parallel evolution between biological replicates at the level of pathways, genes, and even in idual nucleotides. Short-term ersification featured positive selection of relatively few nonsynonymous mutations, with the majority of the genome being conserved by negative selection. This result is broadly consistent with observations of long-term evolution and suggests ersifying selection may underlie genetic ersification of Pseudomonas aeruginosa biofilms.
Publisher: Springer Science and Business Media LLC
Date: 15-10-2018
DOI: 10.1038/S41396-018-0296-5
Abstract: Despite the significance of biogenic methane generation in coal beds, there has never been a systematic long-term evaluation of the ecological response to biostimulation for enhanced methanogenesis in situ . Biostimulation tests in a gas-free coal seam were analysed over 1.5 years encompassing methane production, cell abundance, planktonic and surface associated community composition and chemical parameters of the coal formation water. Evidence is presented that sulfate reducing bacteria are energy limited whilst methanogenic archaea are nutrient limited. Methane production was highest in a nutrient amended well after an oxic preincubation phase to enhance coal biofragmentation (calcium peroxide amendment). Compound-specific isotope analyses indicated the predominance of acetoclastic methanogenesis. Acetoclastic methanogenic archaea of the Methanosaeta and Methanosarcina genera increased with methane concentration. Acetate was the main precursor for methanogenesis, however more acetate was consumed than methane produced in an acetate amended well. DNA stable isotope probing showed incorporation of 13 C-labelled acetate into methanogenic archaea, Geobacter species and sulfate reducing bacteria. Community characterisation of coal surfaces confirmed that methanogenic archaea make up a substantial proportion of coal associated biofilm communities. Ultimately, methane production from a gas-free subbituminous coal seam was stimulated despite high concentrations of sulfate and sulfate-reducing bacteria in the coal formation water. These findings provide a new conceptual framework for understanding the coal reservoir biosphere.
Publisher: Baishideng Publishing Group Inc.
Date: 21-02-2018
Publisher: Cold Spring Harbor Laboratory
Date: 06-06-2018
DOI: 10.1101/340679
Abstract: The hypervirulent Group B Streptococcus ( Streptococcus agalactiae , GBS) serogroup III clonal cluster 17 has been associated with neonatal GBS invasive disease and meningits. Serogroup III, ST283 has recently been implicated in invasive disease among non-pregnant adults in Asia. These strains cluster with strains from freshwater fishes from aquaculture and a foodborne outbreak of sepsis, especially with septic arthritis, had been linked to such consumption in Singapore in 2015. Through comparative genome analyses of invasive and non-invasive strains of ST283, we identified a truncated response regulator gene in the non-invasive strain. This two component response gene, previously named a DNA binding regulator, is conserved among GBS strains and is a homologue of Bacillus subtilis BceR , the response regulator of the BceRSAB system. Loss of function of the BceR response gene in the invasive GBS strain demonstrated bacitracin susceptibility in ΔBceR mutant with MICs of 256-fold and four-fold reduction in bacitracin and human cathelicin LL-37 compared to wild type and complementation strains. Upregulation of dltA of wild type strain vs ΔBceR mutant was demonstrated ( p .0001), and was previously shown in Staphylococcus aureus to resist and repel cationic peptides through excess positive charges with D-alanylation of teichoic acids on the cell wall. In addition, ΔBceR mutant was less susceptible under oxidative stress under H 2 O 2 stress when compared to wild type strain ( p .001) and inhibited biofilm formation ( p .05 and p 0.0001 for crystal violet staining and cfu counts). The ΔBceR mutant also showed reduced mortality as compared to wild type strain ( p .01) in a murine infection model. Taken together, BceRS is involved in bacitracin and antimicrobial peptide resistance, survival under oxidative stress, biofilm formation and play an important role in the virulence of GBS. Two-component systems (TCSs) play an important role in virulence in bacteria, and are involved in detecting environmental changes. Although S. agalactiae was reported to contain more predicted TCSs than Streptococcus pneumoniae, few have been studied in detail. In this work, comparative genomic analysis of GBS invasive (hyper-virulent) and non-invasive serotype III-4 strains were performed to determine any gene differences that may account for severity of disease in humans. BceR-like TCS was selected and suspected to be involved in virulence, and thus BceR was deleted in a hyper-virulent GBS serotype III-4 strain. We demonstrated that this BceR-like TCS is involved in GBS virulence and induced proinflammatory host immune responses. Our study of TCS BceR may guide further research into the role of other TCSs in GBS pathogenicity, and further explore therapeutic targets for GBS disease.
Publisher: Springer Science and Business Media LLC
Date: 08-06-2021
DOI: 10.1038/S42255-021-00393-9
Abstract: Reduced protein intake, through dilution with carbohydrate, extends lifespan and improves mid-life metabolic health in animal models. However, with transition to industrialised food systems, reduced dietary protein is associated with poor health outcomes in humans. Here we systematically interrogate the impact of carbohydrate quality in diets with varying carbohydrate and protein content. Studying 700 male mice on 33 isocaloric diets, we find that the type of carbohydrate and its digestibility profoundly shape the behavioural and physiological responses to protein dilution, modulate nutrient processing in the liver and alter the gut microbiota. Low (10%)-protein, high (70%)-carbohydrate diets promote the healthiest metabolic outcomes when carbohydrate comprises resistant starch (RS), yet the worst outcomes were with a 50:50 mixture of monosaccharides fructose and glucose. Our findings could explain the disparity between healthy, high-carbohydrate diets and the obesogenic impact of protein dilution by glucose-fructose mixtures associated with highly processed diets.
Publisher: Wiley
Date: 29-03-2019
Location: No location found
No related grants have been discovered for Alison Luk.