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A review of analytical techniques and their application in disease diagnosis in breathomics and salivaomics research

- Beale, David, Jones, Oliver, Karpe, Avinash, Dayalan, Saravanan, Oh, Ding, Kouremenos, Konstantinos, Ahmed, Warish, Palombo, Enzo

  • Authors: Beale, David , Jones, Oliver , Karpe, Avinash , Dayalan, Saravanan , Oh, Ding , Kouremenos, Konstantinos , Ahmed, Warish , Palombo, Enzo
  • Date: 2017
  • Type: Text , Journal article
  • Relation: International Journal of Molecular Sciences Vol. 18, no. 1 (2017), p. 1-26
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  • Description: The application of metabolomics to biological samples has been a key focus in systems biology research, which is aimed at the development of rapid diagnostic methods and the creation of personalized medicine. More recently, there has been a strong focus towards this approach applied to non-invasively acquired samples, such as saliva and exhaled breath. The analysis of these biological samples, in conjunction with other sample types and traditional diagnostic tests, has resulted in faster and more reliable characterization of a range of health disorders and diseases. As the sampling process involved in collecting exhaled breath and saliva is non-intrusive as well as comparatively low-cost and uses a series of widely accepted methods, it provides researchers with easy access to the metabolites secreted by the human body. Owing to its accuracy and rapid nature, metabolomic analysis of saliva and breath (known as salivaomics and breathomics, respectively) is a rapidly growing field and has shown potential to be effective in detecting and diagnosing the early stages of numerous diseases and infections in preclinical studies. This review discusses the various collection and analyses methods currently applied in two of the least used non-invasive sample types in metabolomics, specifically their application in salivaomics and breathomics research. Some of the salient research completed in this field to date is also assessed and discussed in order to provide a basis to advocate their use and possible future scientific directions. © 2016 by the authors; licensee MDPI, Basel, Switzerland.

Bioacoustic and multi-locus DNA data of Ninox owls support high incidence of extinction and recolonisation on small, low-lying islands across Wallacea

- Gwee, Chyi, Christidis, Les, Eaton, James, Norman, Janette, Trainor, Colin, Verbelen, Philippe, Rheindt, Frank

  • Authors: Gwee, Chyi , Christidis, Les , Eaton, James , Norman, Janette , Trainor, Colin , Verbelen, Philippe , Rheindt, Frank
  • Date: 2017
  • Type: Text , Journal article
  • Relation: Molecular Phylogenetics and Evolution Vol. 109, no. (2017), p. 246-258
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  • Description: Known for their rich biodiversity and high level of endemism, the islands of Wallacea serve as natural laboratories for the study of spatio-temporal evolution and patterns of species diversification. Our study focuses on the owl genus Ninox, particularly the Southern Boobook (N. novaeseelandiae) and Moluccan Boobook (N. squamipila) complexes, which are widely distributed across Australasia. We conducted bioacoustic and multi-locus DNA analyses of 24 Ninox owl taxa to evaluate relationships and levels of divergence within the two complexes and ultimately assess the relationship between patterns of taxonomic differentiation and bioclimatic factors. We found that taxa that are vocally and/or genetically distinct from populations on the Australian mainland are found on islands that are significantly larger and higher in altitude than taxa that are vocally and/or genetically indistinct from populations on the Australian mainland. This pattern suggests that taxa occurring on small, low-lying Wallacean islands are likely to be recent colonisers that have dispersed from Australia. Overall, our observations demonstrate that the genus Ninox is likely to have colonised the Wallacean region multiple times as small, low-lying islands undergo frequent extinction, whereas populations on large and high-altitude islands are more resilient. (C) 2017 Elsevier Inc. All rights reserved.

Isolating DNA sourced non-invasively from koala scats: a comparison of four commercial DNA stool kits

- Wedrowicz, Faye, Mosse, Jennifer, Wright, Wendy, Hogan, Fiona

  • Authors: Wedrowicz, Faye , Mosse, Jennifer , Wright, Wendy , Hogan, Fiona
  • Date: 2018
  • Type: Text , Journal article
  • Relation: Conservation Genetics Resources Vol. , no. (2018), p.
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  • Description: Genetic sampling from faeces is a useful method for obtaining DNA samples non-invasively. The quantity and quality of DNA isolated from faecal samples is, however, an important factor affecting the success of downstream analyses. Commercial DNA isolation kits offer an efficient and convenient means for recovering DNA, but the kit methodology can influence the quantity and quality of DNA obtained. Comparisons of kit performance for the isolation of DNA from non-invasive sources for ecological studies based on genetic analysis are uncommon in the literature. This study compared the quantity and quality of DNA isolated from surface washings of fresh koala (Phascolarctos cinereus) faecal pellets (scats) using four commercial DNA isolation kits: Axygen® AxyPrep™ MAG Soil, Stool, and Water DNA Kit (AX), Bioline ISOLATE Fecal DNA Kit (BL), Qiagen QIAamp® Fast DNA Stool Mini Kit (QFS), and Qiagen QIAamp® DNA Stool Mini Kit (QS). DNA quantitation, standard PCR and electrophoresis, real time PCR and replicate genotyping using capillary electrophoresis were used to compare the performance of resultant DNA isolates. The performance of DNA isolated from koala scats varied substantially with the DNA kit utilised. All kits provided accurate genotypes but with differing amounts of missing data. Overall, kit AX performed best, providing DNA isolates of higher quantity and quality compared to kit QS, which has previously been thoroughly assessed for genotyping reliability using DNA from koala scats. Given the high variability noted, assessing kit performance is an important way to maximise data quality from non-invasively sourced DNA.

The y chromosome : A blueprint for men's health?

- Maan, Akhlaq, Eales, James, Akbarov, Artur, Rowland, Joshua, Xu, Xiaoguang, Jobling, Mark, Charchar, Fadi, Tomaszewski, Maciej

  • Authors: Maan, Akhlaq , Eales, James , Akbarov, Artur , Rowland, Joshua , Xu, Xiaoguang , Jobling, Mark , Charchar, Fadi , Tomaszewski, Maciej
  • Date: 2017
  • Type: Text , Journal article , Review
  • Relation: European Journal of Human Genetics Vol. 25, no. 11 (2017), p. 1181-1188
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  • Description: The Y chromosome has long been considered a genetic wasteland' on a trajectory to completely disappear from the human genome. The perception of its physiological function was restricted to sex determination and spermatogenesis. These views have been challenged in recent times with the identification of multiple ubiquitously expressed Y-chromosome genes and the discovery of several unexpected associations between the Y chromosome, immune system and complex polygenic traits. The collected evidence suggests that the Y chromosome influences immune and inflammatory responses in men, translating into genetically programmed susceptibility to diseases with a strong immune component. Phylogenetic studies reveal that carriers of a common European lineage of the Y chromosome (haplogroup I) possess increased risk of coronary artery disease. This occurs amidst upregulation of inflammation and suppression of adaptive immunity in this Y lineage, as well as inferior outcomes in human immunodeficiency virus infection. From structural analysis and experimental data, the UTY (Ubiquitously Transcribed Tetratricopeptide Repeat Containing, Y-Linked) gene is emerging as a promising candidate underlying the associations between Y-chromosome variants and the immunity-driven susceptibility to complex disease. This review synthesises the recent structural, experimental and clinical insights into the human Y chromosome in the context of men's susceptibility to disease (with a particular emphasis on cardiovascular disease) and provides an overview of the paradigm shift in the perception of the Y chromosome. © 2017 The Author(s).

A meta-analysis of gene expression signatures of blood pressure and hypertension

- Charchar, Fadi

  • Authors: Charchar, Fadi
  • Date: 2015
  • Type: Text , Journal article
  • Relation: PLoS Genetics Vol. 11, no. 3 (2015), p. 1-29
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  • Description: Genome-wide association studies (GWAS) have uncovered numerous genetic variants (SNPs) that are associated with blood pressure (BP). Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression, which in turn affect BP variability. Therefore, characterizing genes whose expression is associated with BP may reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. A meta-analysis of results from six studies of global gene expression profiles of BP and hypertension in whole blood was performed in 7017 individuals who were not receiving antihypertensive drug treatment. We identified 34 genes that were differentially expressed in relation to BP (Bonferroni-corrected p<0.05). Among these genes, FOS and PTGS2 have been previously reported to be involved in BP-related processes; the others are novel. The top BP signature genes in aggregate explain 5%–9% of inter-individual variance in BP. Of note, rs3184504 in SH2B3, which was also reported in GWAS to be associated with BP, was found to be a trans regulator of the expression of 6 of the transcripts we found to be associated with BP (FOS, MYADM, PP1R15A, TAGAP, S100A10, and FGBP2). Gene set enrichment analysis suggested that the BP-related global gene expression changes include genes involved in inflammatory response and apoptosis pathways. Our study provides new insights into molecular mechanisms underlying BP regulation, and suggests novel transcriptomic markers for the treatment and prevention of hypertension. **Please note that there are multiple authors for this article therefore only the name of the Federation University Australia affiliate is provided in this record**

Telomeres, aging and exercise : Guilty by association?

- Chilton, Warrick, O’Brien, Brendan, Charchar, Fadi

  • Authors: Chilton, Warrick , O’Brien, Brendan , Charchar, Fadi
  • Date: 2017
  • Type: Text , Journal article , Review
  • Relation: International Journal of Molecular Sciences Vol. 18, no. 12 (2017), p. 1-32
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  • Description: Telomeres are repetitive tandem DNA sequences that cap chromosomal ends protecting genomic DNA from enzymatic degradation. Telomeres progressively shorten with cellular replication and are therefore assumed to correlate with biological and chronological age. An expanding body of evidence suggests (i) a predictable inverse association between telomere length, aging and age-related diseases and (ii) a positive association between physical activity and telomere length. Both hypotheses have garnered tremendous research attention and broad consensus; however, the evidence for each proposition is inconsistent and equivocal at best. Telomere length does not meet the basic criteria for an aging biomarker and at least 50% of key studies fail to find associations with physical activity. In this review, we address the evidence in support and refutation of the putative associations between telomere length, aging and physical activity. We finish with a brief review of plausible mechanisms and potential future research directions. © 2017 by the authors. Licensee MDPI, Basel, Switzerland.

The many facets of metzincins and their endogenous inhibitors : Perspectives on ovarian cancer progression

- Escalona, Ruth, Chan, Emily, Kannourakis, George, Findlay, Jock, Ahmed, Nuzhat

  • Authors: Escalona, Ruth , Chan, Emily , Kannourakis, George , Findlay, Jock , Ahmed, Nuzhat
  • Date: 2018
  • Type: Text , Journal article , Review
  • Relation: International Journal of Molecular Sciences Vol. 19, no. 2 (2018), p. 1-33
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  • Description: Approximately sixty per cent of ovarian cancer patients die within the first five years of diagnosis due to recurrence associated with chemoresistance. The metzincin family of metalloproteinases is enzymes involved in matrix remodeling in response to normal physiological changes and diseased states. Recently, there has been a mounting awareness of these proteinases and their endogenous inhibitors, the tissue inhibitors of metalloproteinases (TIMPs), as superb modulators of cellular communication and signaling regulating key biological processes in cancer progression. This review investigates the role of metzincins and their inhibitors in ovarian cancer. We propose that understanding the metzincins and TIMP biology in ovarian cancer may provide valuable insights in combating ovarian cancer progression and chemoresistance-mediated recurrence in patients. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.

Molecular cloning and characterisation of ovine dual oxidase 2

- Lees, Michael, Nagaraj, Shivashankar, Piedrafita, David, Kotze, A., Ingham, Aaron

  • Authors: Lees, Michael , Nagaraj, Shivashankar , Piedrafita, David , Kotze, A. , Ingham, Aaron
  • Date: 2012
  • Type: Text , Journal article
  • Relation: Gene Vol. 500, no. 1 (2012), p. 40-46
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  • Description: The dual oxidases (DUOX1 and DUOX2) are NADPH-dependant hydrogen peroxide-producing enzymes that are reported to function in a physiological capacity and as a component of the mucosal immune response. We have previously reported increased expression of the DUOX2 gene in the gut mucosa of sheep in response to gastrointestinal nematode (GIN) challenge. In this paper, we report the cloning of the full-length ovine DUOX2 transcript, using a PCR based strategy. The ovine DUOX2 transcript includes an ORF of 4644 bases, and encodes a protein with 97% identity to the bovine sequence. We also cloned a fragment of DUOX1 (encompassing nucleotides 2692–2829), and the proximal promoter sequence of DUOX2. Through analysis of sequence data we have confirmed that DUOX1 and DUOX2 are co-located in a head to tail arrangement conserved across many species. Alignment of the sequences to the ovine genome predicts a location of this gene cluster on ovine chromosome 7. We quantified the expression of ovine DUOX1 and DUOX2 transcripts in 24 different sheep tissues, and discovered tissue specific expression signatures. DUOX2 was found to be most highly expressed in tissues of the gastrointestinal tract, while expression of DUOX1 predominated in the bladder. Rapid amplification of cDNA ends (RACE) analysis identified the existence of multiple 5′ UTR variants in DUOX2, ranging in size from 32 to 242 nucleotides, with 3 distinct transcribed regions. Real time PCR quantification of the DUOX2 UTR variants revealed that these were differentially expressed between tissues, and at various stages of the response to GIN parasite infection. The collective evidence suggested a complex regulation of DUOX2, prompting a bioinformatic analysis of the proximal promoter regions of ovine DUOX2 to identify potential transcription factor binding sites (TFBS) that may explain the differences in the observed expression of the transcript variants of DUOX2. Possible transcription factor families that may regulate this process were identified as Kruppel-like factors (KLF), ETS-factors, erythroid growth receptor factors (EGRF) and myogenic differentiation factors (MYOD)

Epigenetic modifications in essential hypertension

- Wise, Ingrid, Charchar, Fadi

  • Authors: Wise, Ingrid , Charchar, Fadi
  • Date: 2016
  • Type: Text , Journal article , Review
  • Relation: International Journal of Molecular Sciences Vol. 17, no. 4 (2016), p. 1-14
  • Relation: http://purl.org/au-research/grants/nhmrc/1009490
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  • Description: Essential hypertension (EH) is a complex, polygenic condition with no single causative agent. Despite advances in our understanding of the pathophysiology of EH, hypertension remains one of the world’s leading public health problems. Furthermore, there is increasing evidence that epigenetic modifications are as important as genetic predisposition in the development of EH. Indeed, a complex and interactive genetic and environmental system exists to determine an individual’s risk of EH. Epigenetics refers to all heritable changes to the regulation of gene expression as well as chromatin remodelling, without involvement of nucleotide sequence changes. Epigenetic modification is recognized as an essential process in biology, but is now being investigated for its role in the development of specific pathologic conditions, including EH. Epigenetic research will provide insights into the pathogenesis of blood pressure regulation that cannot be explained by classic Mendelian inheritance. This review concentrates on epigenetic modifications to DNA structure, including the influence of non-coding RNAs on hypertension development. © 2016 by the authors; licensee MDPI, Basel, Switzerland.

Measurement of absolute copy number variation reveals association with essential hypertension

- Marques, Francine, Prestes, Priscilla, Pinheiro, Leonardo, Scurrah, Katrina, Emslie, Kerry, Tomaszewski, Maciej, Harrap, Stephen, Charchar, Fadi

  • Authors: Marques, Francine , Prestes, Priscilla , Pinheiro, Leonardo , Scurrah, Katrina , Emslie, Kerry , Tomaszewski, Maciej , Harrap, Stephen , Charchar, Fadi
  • Date: 2014
  • Type: Text , Journal article
  • Relation: BMC Medical Genomics Vol. 7, no. (2014), p. 1-8
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  • Description: Background: The role of copy number variation (CNV) has been poorly explored in essential hypertension in part due to technical difficulties in accurately assessing absolute numbers of DNA copies. Droplet digital PCR (ddPCR) provides a powerful new approach to CNV quantitation. The aim of our study was to investigate whether CNVs located in regions previously associated with blood pressure (BP) variation in genome-wide association studies (GWAS) were associated with essential hypertension by the use of ddPCR. Methods: Using a "power of extreme" approach, we quantified nucleic acids using ddPCR in white subjects from the Victorian Family Heart Study with extremely high (n = 96) and low (n = 92) SBP, providing power equivalent to 1714 subjects selected at random. Results: A deletion of the CNVs esv27061 and esv2757747 on chromosome 1p13.2 was significantly more prevalent in extreme high BP subjects after adjustment for age, body mass index and sex (12.6% vs. 2.2%; P = 0.013). Conclusions: Our data suggests that CNVs within regions identified in previous GWAS may play a role in human essential hypertension.

Antimicrobial sensitivity trends and virulence genes in Shigella spp. from the Oceania region

- Malau, Elisheba, Ford, Rebecca, Valcanis, Mary, Jennison, Amy, Mosse, Jenny, Bean, David, Yoannes, Mition, Pomat, William, Horwood, Paul, Greenhill, Andrew

  • Authors: Malau, Elisheba , Ford, Rebecca , Valcanis, Mary , Jennison, Amy , Mosse, Jenny , Bean, David , Yoannes, Mition , Pomat, William , Horwood, Paul , Greenhill, Andrew
  • Date: 2018
  • Type: Text , Journal article
  • Relation: Infection, Genetics and Evolution Vol. 64, no. (2018), p. 52-56
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  • Description: Shigella is a common cause of diarrhoea in Papua New Guinea (PNG) and other Oceania countries. However, little is known about the strains causing infection. Archived Shigella isolates (n = 72) were obtained from research laboratories in PNG and reference laboratories in Australia. Shigella virulence genes were detected by PCR, and antimicrobial susceptibility was determined by disk diffusion. The ipaH virulence gene was present in all 72 isolates. The prevalence of other virulence genes was variable, with ial, invE, ipaBCD, sen/ospD3 and virF present in 60% of isolates and set1A and set1B genes present in 42% of isolates. Most S. flexneri isolates contained genes encoding enterotoxin 1 and/or enterotoxin 2. Resistance to antibiotics was common, with 51/72 isolates resistant to 2–4 antimicrobials. A greater proportion of bacteria isolated since 2010 (relative to pre-2010 isolates) were resistant to commonly used antibiotics such as ampicillin, chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole; suggesting that antimicrobial resistance (AMR) in Shigella is increasing over time in the Oceania region. There is a need for improved knowledge regarding Shigella circulation in the Oceania region and further monitoring of AMR patterns. © 2018 Elsevier B.V.

Wave 2 strains of atypical Vibrio cholerae El Tor caused the 2009-2011 cholera outbreak in Papua New Guinea

- Greenhill, Andrew, Mutreja, Ankur, Bulach, Dieter, Belousoff, Matthew, Jonduo, Marinjho, Collins, Deirdre, Kas, Monalisa, Wapling, Johanna, Seemann, Torsten, Lafana, Alice, Dougan, Gordon, Brown, Mark, Horwood, Paul

  • Authors: Greenhill, Andrew , Mutreja, Ankur , Bulach, Dieter , Belousoff, Matthew , Jonduo, Marinjho , Collins, Deirdre , Kas, Monalisa , Wapling, Johanna , Seemann, Torsten , Lafana, Alice , Dougan, Gordon , Brown, Mark , Horwood, Paul
  • Date: 2019
  • Type: Text , Journal article
  • Relation: Microbial genomics Vol. 5, no. 3 (2019), p. 1-5
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  • Description: Vibrio cholerae is the causative agent of cholera, a globally important human disease for at least 200 years. In 2009-2011, the first recorded cholera outbreak in Papua New Guinea (PNG) occurred. We conducted genetic and phenotypic characterization of 21 isolates of V. cholerae, with whole-genome sequencing conducted on 2 representative isolates. The PNG outbreak was caused by an atypical El Tor strain harbouring a tandem repeat of the CTX prophage on chromosome II. Whole-genome sequence data, prophage structural analysis and the absence of the SXT integrative conjugative element was indicative that the PNG isolates were most closely related to strains previously isolated in South-East and East Asia with affiliations to global wave 2 strains. This finding suggests that the cholera outbreak in PNG was caused by an exotic (non-endemic) strain of V. cholerae that originated in South-East Asia.

A non-invasive tool for assessing pathogen prevalence in koala (Phascolarctos cinereus) populations: detection of Chlamydia pecorum and koala retrovirus (KoRV) DNA in genetic material sourced from scats

- Wedrowicz, Faye, Saxton, Tom, Mosse, Jennifer, Wright, Wendy, Hogan, Fiona

  • Authors: Wedrowicz, Faye , Saxton, Tom , Mosse, Jennifer , Wright, Wendy , Hogan, Fiona
  • Date: 2016
  • Type: Text , Journal article
  • Relation: Conservation Genetics Resources Vol. 8, no. 4 (2016), p. 511-521
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  • Description: Pathogenic diseases may threaten the viability of wild animal populations, especially when already vulnerable. The mitigation of risks associated with pathogenic infections in populations is an important factor in conservation strategies. Koalas are of conservation concern across the north of their range and are affected by two main pathogens; Chlamydia pecorum and the koala retrovirus (KoRV). This study tested whether DNA from C. pecorum and KoRV could be detected in genetic material isolated from koala scats. Detection of C. pecorum in scat isolated DNA samples was compared with results obtained from urogenital swabs collected from the same individuals as part of an independent study. The ability to detect KoRV in scats from both northern and southern regions of the koala’s range was also assessed. There was a high level of concordance (5/6) between the detection of C. pecorum in DNA isolated from scats and urogenital swabs from the same individual. In positive samples, C. pecorumompA genotypes were identical between DNA from scats and urogenital swabs in two out of three cases. In samples from the south of the koala’s range, KoRV copy number was higher in DNA isolated from scats compared to DNA isolated from ear tissue, potentially indicating the detection of horizontally acquired infections. Our results demonstrate the ability to detect C. pecorum and KoRV in DNA isolated from koala scats. This method will be useful for studying the prevalence, transmission and impact of these pathogens in wild populations which may subsequently inform conservation management strategies. © 2016, Springer Science+Business Media Dordrecht.
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