ORCID Profile
0000-0002-8917-0019
Current Organisations
Meshalkin Research Institute of Circulation Pathology
,
University of Technology Sydney
,
University of Technology Sydney Faculty of Science
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Publisher: CABI
Date: 2017
Publisher: Springer Science and Business Media LLC
Date: 05-05-2018
Publisher: Informa UK Limited
Date: 03-09-2021
Publisher: Cold Spring Harbor Laboratory
Date: 16-05-2017
DOI: 10.1101/138883
Abstract: ‘Who is doing what’ is the ultimate open question in microbiome study. Shotgun metagenomics is often applied to gain knowledge of functional roles for bacteria in microbial communities, where the data can be used to predict protein encoding genes and enzymatic pathways present in the community, sometimes leading to testable hypotheses for microbial function. We describe a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the method to human stool s les and generating sequence data. We evaluate the extent to which ddRADseq data provides an unbiased reduced representation for microbiome profiling. Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.
Publisher: Massachusetts Medical Society
Date: 25-05-2017
Publisher: PeerJ
Date: 20-09-2016
DOI: 10.7717/PEERJ.2492
Abstract: The bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a s le with precision. We describe a method for sequencing near full-length 16S rRNA gene licons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab s les. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. This method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.
Publisher: Oxford University Press (OUP)
Date: 05-2013
Abstract: Seaweeds (macroalgae) form a erse and ubiquitous group of photosynthetic organisms that play an essential role in aquatic ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on rocky shores in temperate waters, providing food and shelter for aquatic life. Like other eukaryotic organisms, macroalgae harbor a rich ersity of associated microorganisms with functions related to host health and defense. In particular, epiphytic bacterial communities have been reported as essential for normal morphological development of the algal host, and bacteria with antifouling properties are thought to protect chemically undefended macroalgae from detrimental, secondary colonization by other microscopic and macroscopic epibiota. This tight relationship suggests that macroalgae and epiphytic bacteria interact as a unified functional entity or holobiont, analogous to the previously suggested relationship in corals. Moreover, given that the impact of diseases in marine ecosystems is apparently increasing, understanding the role of bacteria as saprophytes and pathogens in seaweed communities may have important implications for marine management strategies. This review reports on the recent advances in the understanding of macroalgal-bacterial interactions with reference to the ersity and functional role of epiphytic bacteria in maintaining algal health, highlighting the holobiont concept.
Publisher: Informa UK Limited
Date: 11-06-2020
Publisher: Public Library of Science (PLoS)
Date: 02-04-2013
Publisher: Springer Science and Business Media LLC
Date: 04-11-2010
Publisher: Frontiers Media SA
Date: 22-01-2016
Publisher: Springer Science and Business Media LLC
Date: 21-04-2020
DOI: 10.1038/S41598-020-63729-7
Abstract: Characterisation of protein function based solely on homology searches may overlook functions under specific environmental conditions, or the possibility of a protein having multiple roles. In this study we investigated the role of YtfB, a protein originally identified in a genome-wide screen to cause inhibition of cell ision, and has demonstrated to localise to the Escherichia coli ision site with some degree of glycan specificity. Interestingly, YtfB also shows homology to the virulence factor OapA from Haemophilus influenzae , which is important for adherence to epithelial cells, indicating the potential of additional function(s) for YtfB. Here we show that E. coli YtfB binds to N’acetylglucosamine and mannobiose glycans with high affinity. The loss of ytfB results in a reduction in the ability of the uropathogenic E. coli strain UTI89 to adhere to human kidney cells, but not to bladder cells, suggesting a specific role in the initial adherence stage of ascending urinary tract infections. Taken together, our results suggest a role for YtfB in adhesion to specific eukaryotic cells, which may be additional, or complementary, to its role in cell ision. This study highlights the importance of understanding the possible multiple functions of proteins based on homology, which may be specific to different environmental conditions.
Publisher: PeerJ
Date: 19-09-2017
DOI: 10.7717/PEERJ.3837
Abstract: Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool s les and generating sequence data. The ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool s les. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected. Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.
Publisher: Cold Spring Harbor Laboratory
Date: 20-11-2020
DOI: 10.1101/2020.11.19.390815
Abstract: Rod-shaped bacteria such as Escherichia coli can regulate cell ision in response to stress, leading to filamentation, a process where cell growth and DNA replication continues in the absence of ision, resulting in elongated cells. The classic ex le of stress is DNA damage which results in the activation of the SOS response. While the inhibition of cell ision during SOS has traditionally been attributed to SulA in E. coli , a previous report suggests that the e14 prophage may also encode an SOS-inducible cell ision inhibitor, previously named SfiC. However, the exact gene responsible for this ision inhibition has remained unknown for over 35 years. A recent high-throughput over-expression screen in E. coli identified the e14 prophage gene, ymfM , as a potential cell ision inhibitor. In this study, we show that the inducible expression of ymfM from a plasmid causes filamentation. We show that this expression of ymfM results in the inhibition of Z ring formation and is independent of the well characterised inhibitors of FtsZ ring assembly in E. coli , SulA, SlmA and MinC. We confirm that ymfM is the gene responsible for the SfiC + phenotype as it contributes to the filamentation observed during the SOS response. This function is independent of SulA, highlighting that multiple ision inhibition pathways exist during the stress-induced SOS response. Our data also highlight that our current understanding of cell ision regulation during the SOS response is incomplete and raises many questions regarding how many inhibitors there actually are and their purpose for the survival of the organism. Filamentation is an important biological mechanism which aids in the survival, pathogenesis and antibiotic resistance of bacteria within different environments, including pathogenic bacteria such as uropathogenic Escherichia coli . Here we have identified a bacteriophage-encoded cell ision inhibitor which contributes to the filamentation that occurs during the SOS response. Our work highlights that there are multiple pathways that inhibit cell ision during stress. Identifying and characterising these pathways is a critical step in understanding survival tactics of bacteria which become important when combating the development of bacterial resistance to antibiotics and their pathogenicity.
Publisher: Elsevier BV
Date: 04-2018
Publisher: Oxford University Press (OUP)
Date: 18-09-2009
DOI: 10.1093/NAR/GKP746
Publisher: Wiley
Date: 25-03-2022
DOI: 10.1111/JOCN.16233
Abstract: The Early Warning Score (EWS) is a validated tool that has improved patient outcomes internationally. This scoring system is used within the hospital setting to identify potentially deteriorating patients, thus expediting referral to appropriate medical personnel. It is increasingly recognised that there are other influencing factors along with EWS, which impact on nurses’ decisions to escalate care. The aim of this review was to identify and synthesise data from qualitative studies, which examined factors influencing nurses’ escalation of care in response to patients’ EWS. The systematic search strategy and eligibility criteria were guided by the SPIDER (S le Phenomenon of Interest Design Evaluation Type of Research) framework. Eleven databases and five grey literature databases were searched. Titles and abstracts were independently screened in line with pre‐established inclusion and exclusion criteria using the cloud‐based platform, Rayyan. The selected studies underwent quality appraisal using CASP (Critical Appraisal Skills Programme, 2017, www.casp‐asp‐toolschecklists ) and subsequently synthesised using Thomas and Harden's thematic analysis approach. GRADE–CERQual (Grading of Recommendations Assessment Development and Evaluation–Confidence in the Evidence from Reviews of Qualitative research) was used to assess confidence in results. The EQUATOR listed guideline ENTREQ (Tong et al., 2012, BMC Medical Research Methodology, 12) was used to synthesise and report findings. Eighteen studies from seven countries including 235 nurses were identified. Following synthesis, four analytical themes were generated with eighteen derived consequent findings. The four themes identified were as follows: 1) Marrying nurses’ clinical judgement with EWS 2) SMART communication 3) EWS Protocol : Blessing and a Curse 5) Hospital Domain . Nurses strive to find balance by simultaneously navigating within the boundaries of both the EWS protocol and the hospital domain. They view the EWS as a valid essential component in the system but one that does not give a definitive answer and absolute direction. They value the protocols’ ability to identify deteriorating patients and convey the seriousness of a situation to their multidisciplinary colleagues but also find it somewhat restrictive and frustrating and wish to have credence given to their own intuition and clinical judgement.
Publisher: American Society for Microbiology
Date: 2009
DOI: 10.1128/AEM.01630-08
Abstract: A novel method has been developed for the selective extraction of DNA from surface-associated bacterial communities from the two model marine benthic algae Ulva australis and Delisea pulchra . The extracted DNA had no detectable contamination with host DNA, was recovered in high yield and quality, and was representative of the bacterial community on the algal surfaces. The DNA is suitable for a variety of subsequent applications, including the construction of large-insert clone libraries and metagenomic sequencing.
Publisher: Springer Science and Business Media LLC
Date: 03-12-2019
DOI: 10.1038/S41598-019-54576-2
Abstract: Chronic wound treatment is becoming increasingly difficult and costly, further exacerbated when wounds become infected. Bacterial biofilms cause most chronic wound infections and are notoriously resistant to antibiotic treatments. The need for new approaches to combat polymicrobial biofilms in chronic wounds combined with the growing antimicrobial resistance crisis means that honey is being revisited as a treatment option due to its broad-spectrum antimicrobial activity and low propensity for bacterial resistance. We assessed four well-characterised New Zealand honeys, quantified for their key antibacterial components, methylglyoxal, hydrogen peroxide and sugar, for their capacity to prevent and eradicate biofilms produced by the common wound pathogen Pseudomonas aeruginosa . We demonstrate that: (1) honey used at substantially lower concentrations compared to those found in honey-based wound dressings inhibited P. aeruginosa biofilm formation and significantly reduced established biofilms (2) the anti-biofilm effect of honey was largely driven by its sugar component (3) cells recovered from biofilms treated with sub-inhibitory honey concentrations had slightly increased tolerance to honey and (4) honey used at clinically obtainable concentrations completely eradicated established P. aeruginosa biofilms. These results, together with their broad antimicrobial spectrum, demonstrate that manuka honey-based wound dressings are a promising treatment for infected chronic wounds, including those with P. aeruginosa biofilms.
Publisher: MDPI AG
Date: 27-02-2023
DOI: 10.3390/LIFE13030656
Abstract: With the advancement in reusable rocket propulsion technology, space tourist trips into outer space are now becoming a possibility at a cost-effective rate. As such, astronauts will face a host of health-related challenges, particularly on long-duration space missions where maintaining a balanced healthy microbiome is going to be vital for human survival in space exploration as well as mission success. The human microbiome involves a whole list of micro-organisms that reside in and on the human host, and plays an integral role in keeping the human host healthy. However, imbalances in the microbiome have been directly linked to many human diseases. Research findings have clearly shown that the outer space environment can directly affect the normal microbiome of astronauts when the astronaut is exposed to the microgravity environment. In this study, we show that the simulation of microgravity on earth can mimic the outer space microgravity environment. Staphylococus aureus (S. aureus) was chosen for this study as it is an opportunistic pathogen, which is part of the normal human skin microflora and the nasal passages. This study’s results show that S. aureus proliferation was significantly increased under a microgravity environment compared to Earth’s gravity conditions, which complements previous work performed on bacteria in the outer space environment in the International Space Station (ISS). This demonstrates that this technology can be utilised here on Earth to mimic the outer space environment and to study challenging health-related questions. This in return saves us the cost on conducting experiments in the ISS and can help advance knowledge at a faster rate and produce countermeasures to mitigate the negative side effects of the hostile outer space environment on humans.
Publisher: Public Library of Science (PLoS)
Date: 24-09-2008
Publisher: American Society for Microbiology
Date: 15-02-2011
DOI: 10.1128/AEM.02038-10
Abstract: The functional metagenomic screening of the microbial communities associated with a temperate marine sponge and a green alga identified three novel hydrolytic enzymes with antibacterial activities. The results suggest that uncultured alpha- and gammaproteobacteria contain new classes of proteins that may be a source of antibacterial agents.
Publisher: Frontiers Media SA
Date: 27-08-2021
DOI: 10.3389/FMICB.2021.713703
Abstract: There is a high incidence of upper respiratory viral infections in the human population, with infection severity being unique to each in idual. Upper respiratory viruses have been associated previously with secondary bacterial infection, however, several cross-sectional studies analyzed in the literature indicate that an inverse relationship can also occur. Pathobiont abundance and/or bacterial dysbiosis can impair epithelial integrity and predispose an in idual to viral infection. In this review we describe common commensal microorganisms that have the capacity to reduce the abundance of pathobionts and maintain bacterial symbiosis in the upper respiratory tract and discuss the potential and limitations of localized probiotic formulations of commensal bacteria to reduce the incidence and severity of viral infections.
Publisher: Springer Science and Business Media LLC
Date: 16-06-2015
Publisher: Proceedings of the National Academy of Sciences
Date: 08-08-2011
Abstract: The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis , and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal s les. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between s les), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be “species” (by means of rRNA taxonomy), but rather the more functional level of genes.
Publisher: MDPI AG
Date: 06-04-2023
DOI: 10.3390/NU15071783
Abstract: Background: The gut microbiome, which can be altered by different diets or smoking, has been implicated in the pathogenesis of lung conditions. E-cigarette vaping is now recognised to have detrimental health effects, with several of these being similar to cigarette smoking. However, whether e-cigarettes can alter high-fat diet (HFD)-induced systemic effects and gut microbiota is unknown. In this study, we investigated the effects of HFD in the absence resence of e-cigarette exposure on systemic inflammation, lipid metabolic markers, and the gut microbiome. Methods: Mice were fed a HFD (or chow) in the absence resence of e-vapour exposure (±nicotine) and serum inflammation, lipid levels, and microbial ersity were assessed. Results: HFD increased the circulating levels of both triglycerides and non-esterified fatty acids, which were significantly reduced by e-vapour exposure in HFD-fed mice. Serum TNF-α was increased by HFD consumption or e-vapour. HFD had a significant effect on microbial ersity, but there were no additional effects of e-vapour exposure. Conclusions: This study highlights both similarities and differences in how the body responds to e-cigarette vapours, and it is therefore likely that the long-term sequelae of e-cigarette vapour exposure/vaping might not involve the significant alteration of the gut microbiome.
Publisher: Frontiers Media SA
Date: 27-01-2015
Publisher: Springer Science and Business Media LLC
Date: 15-10-2009
Abstract: Marine Ulvacean algae are colonized by dense microbial communities predicted to have an important role in the development, defense and metabolic activities of the plant. Here we assess the ersity and seasonal dynamics of the bacterial community of the model alga Ulva australis to identify key groups within this epiphytic community. A total of 48 algal s les of U. australis that were collected as 12 in iduals at 3 monthly intervals, were processed by applying denaturing gradient gel electrophoresis (DGGE), and three s les from each season were subjected to catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). CARD-FISH revealed that the epiphytic microbial community was comprised mainly of bacterial cells (90%) and was dominated by the groups Alphaproteobacteria (70%) and Bacteroidetes (13%). A large portion (47%) of sequences from the Alphaproteobacteria fall within the Roseobacter clade throughout the different seasons, and an average relative proportion of 19% was observed using CARD-FISH. DGGE based spatial (between tidal pools) and temporal (between season) comparisons of bacterial community composition demonstrated that variation occurs. Between in iduals from both the same and different tidal pools, the variation was highest during winter (30%) and between seasons a 40% variation was observed. The community also includes a sub-population of bacteria that is consistently present. Sequences from excised DGGE bands indicate that members of the Alphaproteobacteria and the Bacteroidetes are part of this stable sub-population, and are likely to have an important role in the function of this marine epiphytic microbial community.
Publisher: MDPI AG
Date: 12-07-2018
DOI: 10.3390/MICROORGANISMS6030068
Abstract: The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a role in their health. This study provides an initial characterization of the cloacal microbiota of the northern quoll, as well as other marsupials including possums and kangaroos which were opportunistically s led. The northern quoll cloaca microbiota was dominated by Enterococcus and Lactobacillus and had a relatively high proportion of members of the Proteobacteria phylum, which has been observed in other carnivorous marsupials. The ersity and structure of the microbiota was not influenced by presence of Chlamydiales which are intracellular bacteria and potential pathogens. The microbiota of the other marsupials was quite varied, which may be related to their health status. Characterization of the northern quoll microbiota will help to better understand the biology of this endangered animal.
Publisher: CSIRO Publishing
Date: 19-05-2021
DOI: 10.1071/MA21022
Abstract: The human cervicovaginal microbiome has an important role in the health and homoeostasis of the female reproductive tract. A eubiotic microbiome is typically dominated with lactic acid producing bacteria and is categorised into five community state types. Issues arise when the microbiome becomes dysbiotic, with the microbial composition shifting to contain a greater relative abundance of strict and facultative anaerobes. This shift will lead to several adverse changes in the vaginal environment including compromised epithelial cells, cell death, inflammation, and greater susceptibility to infection. These changes are associated with various adverse outcomes including infections, preterm birth, and infertility. In this review, we discuss how the cervicovaginal microbiome influences these outcomes and possible future directions of treatment and research.
Publisher: Informa UK Limited
Date: 06-03-2018
Publisher: Informa UK Limited
Date: 04-05-2019
Publisher: BMJ
Date: 02-2021
DOI: 10.1136/BMJOPEN-2020-042493
Abstract: Crohn’s disease and ulcerative colitis are common chronic idiopathic inflammatory bowel diseases (IBD), which cause considerable morbidity. Although the precise mechanisms of disease remain unclear, evidence implicates a strong multidirectional interplay between diet, environmental factors, genetic determinants/immune perturbations and the gut microbiota. IBD can be brought into remission using a number of medications, which act by suppressing the immune response. However, none of the available medications address any of the underlying potential mechanisms. As we understand more about how the microbiota drives inflammation, much interest has focused on identifying microbial signals/triggers in the search for effective therapeutic targets. We describe the establishment of the Australian IBD Microbiota (AIM) Study, Australia’s first longitudinal IBD bioresource, which will identify and correlate longitudinal microbial and metagenomics signals to disease activity as evaluated by validated clinical instruments, patient-reported surveys, as well as biomarkers. The AIM Study will also gather extensive demographic, clinical, lifestyle and dietary data known to influence microbial composition in order to generate a more complete understanding of the interplay between patients with IBD and their microbiota. The AIM Study is an Australian multicentre longitudinal prospective cohort study, which will enrol 1000 participants 500 patients with IBD and 500 healthy controls over a 5-year period. Assessment occurs at 3 monthly intervals over a 24-month period. At each assessment oral and faecal s les are self-collected along with patient-reported outcome measures, with clinical data also collected at baseline, 12 and 24 months. Intestinal tissue will be s led whenever a colonoscopy is performed. Dietary intake, general health and psychological state will be assessed using validated self-report questionnaires. S les will undergo metagenomic, transcriptomic, proteomic, metabolomic and culturomic analyses. Omics data will be integrated with clinical data to identify predictive biomarkers of response to therapy, disease behaviour and environmental factors in patients with IBD. Ethical approval for this study has been obtained from the South Eastern Sydney Local Health District Research Ethics Committee (HREC 2019/ETH11443). Findings will be reported at national and international gastroenterology meetings and published in peer-reviewed journals. ACTRN12619000911190.
Publisher: Wiley
Date: 02-11-2007
DOI: 10.1111/J.1462-2920.2006.01177.X
Abstract: A large insert library was created in Escherichia coli from the DNA of the surface-associated marine bacterium Pseudoalteromonas tunicata. Screening of the library for antifungal activity resulted in the detection and identification of a large gene cluster encoding for the biosynthesis of an antifungal tambjamine. A biosynthetic pathway has been proposed based on analysis and annotation of the gene cluster.
Publisher: Elsevier BV
Date: 09-2021
Publisher: Elsevier BV
Date: 06-2019
DOI: 10.1016/J.JAD.2019.04.097
Abstract: Depression is the leading cause of disability worldwide with evidence suggesting that decreased gut barrier function and inflammation are correlated with depressive symptoms. We conducted a clinical trial to determine the effect of consumption of probiotic supplements (Winclove's Ecologic® Barrier) on depressive symptoms in a s le of participants with mild to severe depression. 71 participants were randomly allocated to either probiotic or placebo, which was, consumed daily over eight weeks. Pre- and post-intervention measures of symptoms and vulnerability markers of depression as well as gut microbiota composition were compared. Clinical trial participants were also compared on psychological variables and gut microbiota composition to a non-depressed group (n = 20). All clinical trial participants demonstrated improvement in symptoms, suggesting non-specific therapeutic effects associated with weekly monitoring visits. Participants in the probiotic group demonstrated a significantly greater reduction in cognitive reactivity compared with the placebo group, particularly in the mild/moderate subgroup. Probiotics did not significantly alter the microbiota of depressed in iduals, however, a significant correlation was found between Ruminococcus gnavus and one depression metric. There was a high attrition rate, which may be attributed to weekly monitoring visits. Additionally, modulation of the gut microbiota may need more specific testing to distinguish subtle changes. While microbiota composition was similar between all groups, probiotics did affect a psychological variable associated with susceptibility to depression. Further research is needed to investigate how probiotics can be utilised to modify mental wellbeing, and whether they can act as an adjunct to existing treatments.
Publisher: American Association for Cancer Research (AACR)
Date: 2010
DOI: 10.1158/1078-0432.CCR-09-0948
Abstract: Purpose: The three main treatment options for primary prostate cancer are surgery, radiation, and active surveillance. Surgical and radiation intervention for prostate cancer can be associated with significant morbidity. Therefore, accurate stratification predictive of outcome for prostate cancer patients is essential for appropriate treatment decisions. Nomograms that use clinical and pathologic variables are often used for risk prediction. Favorable outcomes exist even among men classified by nomograms as being at high risk of recurrence. Experimental Design: Previously, we identified a set of DNA-based biomarkers termed Genomic Evaluators of Metastatic Prostate Cancer (GEMCaP) and have shown that they can predict risk of recurrence with 80% accuracy. Here, we examined the risk prediction ability of GEMCaP in a high-risk cohort and compared it to a Kattan nomogram. Results: We determined that the GEMCaP genotype alone is comparable with the nomogram, and that for a subset of cases with negative lymph nodes improves upon it. Conclusion: Thus, GEMCaP shows promise for predicting unfavorable outcomes for negative lymph node high-risk cases, where the nomogram falls short, and suggests that addition of GEMCaP to nomograms may be warranted. Clin Cancer Res 16(1) 195–202
Publisher: Frontiers Media SA
Date: 28-02-2018
Publisher: Springer Science and Business Media LLC
Date: 29-10-2018
Publisher: Cambridge University Press (CUP)
Date: 10-2020
DOI: 10.1017/JBR.2020.93
Publisher: PeerJ
Date: 25-03-2014
DOI: 10.7717/PEERJ.326
Publisher: American Society for Microbiology
Date: 07-05-2021
DOI: 10.1128/JB.00646-20
Abstract: Filamentation is an important biological mechanism that aids in the survival, pathogenesis, and antibiotic resistance of bacteria within different environments, including pathogenic bacteria such as uropathogenic Escherichia coli . Here, we have identified a bacteriophage-encoded cell ision inhibitor which contributes to the filamentation that occurs during the SOS response.
Publisher: PeerJ
Date: 20-07-2017
DOI: 10.7717/PEERJ.3543
Abstract: Type II diabetes is a chronic health condition which is associated with skin conditions including chronic foot ulcers and an increased incidence of skin infections. The skin microbiome is thought to play important roles in skin defence and immune functioning. Diabetes affects the skin environment, and this may perturb skin microbiome with possible implications for skin infections and wound healing. This study examines the skin and wound microbiome in type II diabetes. Eight type II diabetic subjects with chronic foot ulcers were followed over a time course of 10 weeks, s ling from both foot skin (swabs) and wounds (swabs and debrided tissue) every two weeks. A control group of eight control subjects was also followed over 10 weeks, and skin swabs collected from the foot skin every two weeks. S les were processed for DNA and subject to 16S rRNA gene PCR and sequencing of the V4 region. The diabetic skin microbiome was significantly less erse than control skin. Community composition was also significantly different between diabetic and control skin, however the most abundant taxa were similar between groups, with differences driven by very low abundant members of the skin communities. Chronic wounds tended to be dominated by the most abundant skin Staphylococcus , while other abundant wound taxa differed by patient. No significant correlations were found between wound duration or healing status and the abundance of any particular taxa. The major difference observed in this study of the skin microbiome associated with diabetes was a significant reduction in ersity. The long-term effects of reduced ersity are not yet well understood, but are often associated with disease conditions.
Publisher: Informa UK Limited
Date: 03-06-2020
Publisher: Springer Science and Business Media LLC
Date: 21-11-2017
Publisher: American Society for Microbiology
Date: 09-2010
DOI: 10.1128/AEM.00695-10
Abstract: Marine bacteria are a rich, yet underexplored, resource of compounds with inhibitory bioactivity against a range of eukaryotic target organisms. Identification of those inhibitors, however, requires a culturable or genetically tractable producer strain, a prerequisite that is not often fulfilled. This study describes a novel functional genomic screen that is based on expression of inhibitors in a heterogeneous recombinant host (i.e., Escherichia coli ). Functional libraries were screened by selective grazing by the nematode Caenorhabditis elegans , in a simple, rapid, high-throughput manner. We applied our approach to discover inhibitors of C. elegans produced by the marine bacterium Pseudoalteromonas tunicata D2, a model organism for exploring a range of antagonistic activities between bacteria and eukaryotes and a known producer of several toxic compounds. Expression of P. tunicata DNA in E. coli and grazing selection by the nematode Caenorhabditis elegans identified two clones, with slow- and fast-killing modes of action. Genomic analysis of the slow-killing clone revealed that the activity was due to a small molecule, tambjamine, while the fast-killing activity involved a gene encoding for a novel protein. Microscopic analysis showed substantial colonization of the intestinal lumen, or rapid death of the nematode without colonization, for the two activities, respectively. The novel functional genomic screen presented here therefore detects new eukaryotic inhibitors with different chemical structures, kinetics, and predicted modes of actions.
Publisher: American Society for Microbiology
Date: 06-02-2020
DOI: 10.1128/MRA.01523-19
Abstract: We report the availability of a high-quality metagenomic Hi-C data set generated from a fecal s le taken from a healthy fecal microbiome transplant donor subject. We report on basic features of the data to evaluate their quality.
Location: Russian Federation
Location: Australia
No related grants have been discovered for Catherine Burke.