Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant.

Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic datasets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.

Adenosine-binding motif mimicry and cellular effects of a thieno[2,3-d]pyrimidine-based chemical inhibitor of atypical protein kinase C isoenzymes.

The aPKC [atypical PKC (protein kinase C)] isoforms ι and ζ play crucial roles in the formation and maintenance of cell polarity and represent attractive anti-oncogenic drug targets in Ras-dependent tumours. To date, few isoform-specific chemical biology tools are available to inhibit aPKC catalytic activity. In the present paper, we describe the identification and functional characterization of potent and selective thieno[2,3-d]pyrimidine-based chemical inhibitors of aPKCs. A crystal structure of human PKCι kinase domain bound to a representative compound, CRT0066854, reveals the basis for potent and selective chemical inhibition. Furthermore, CRT0066854 displaces a crucial Asn-Phe-Asp motif that is part of the adenosine-binding pocket and engages an acidic patch used by arginine-rich PKC substrates. We show that CRT0066854 inhibits the LLGL2 (lethal giant larvae 2) phosphorylation in cell lines and exhibits phenotypic effects in a range of cell-based assays. We conclude that this compound can be used as a chemical tool to modulate aPKC activity in vitro and in vivo and may guide the search for further aPKC-selective inhibitors.

Children's exposure to metals: a community-initiated study.

In 2007, it was shown that the shipping of lead (Pb) through Esperance Port in Western Australia resulted in contamination and increased Pb concentrations in children. A clean-up strategy was implemented; however, little attention was given to other metals. In consultation with the community, a cross-sectional exposure study was designed. Thirty-nine children aged 1 to 12 years provided samples of hair, urine, drinking water, residential soil and dust. Concentrations of nickel (Ni) and Pb were low in biological and environmental samples. Hair aluminium (Al) (lower than the detection limit [DL] to 251 µg/g) and copper (Cu) (7 to 415 µg/g), as well as urinary Al (

Prognostic and diagnostic significance of DNA methylation patterns in high grade serous ovarian cancer.

OBJECTIVE: Altered DNA methylation patterns hold promise as cancer biomarkers. In this study we selected a panel of genes which are commonly methylated in a variety of cancers to evaluate their potential application as biomarkers for prognosis and diagnosis in high grade serous ovarian carcinoma (HGSOC); the most common and lethal subtype of ovarian cancer. METHODS: The methylation patterns of 10 genes (BRCA1, EN1, DLEC1, HOXA9, RASSF1A, GATA4, GATA5, HSULF1, CDH1, SFN) were examined and compared in a cohort of 80 primary HGSOC and 12 benign ovarian surface epithelium (OSE) samples using methylation-specific headloop suppression PCR. RESULTS: The genes were variably methylated in primary HGSOC, with HOXA9 methylation observed in 95% of cases. Most genes were rarely methylated in benign OSE, with the exception of SFN which was methylated in all HGSOC and benign OSE samples examined. Methylation of DLEC1 was associated with disease recurrence, independent of tumor stage and suboptimal surgical debulking (HR 3.5 (95% CI:1.10-11.07), p=0.033). A combination of the methylation status of HOXA9 and EN1 could discriminate HGSOC from benign OSE with a sensitivity of 98.8% and a specificity of 91.7%, which increased to 100% sensitivity with no loss of specificity when pre-operative CA125 levels were also incorporated. CONCLUSIONS: This study provides further evidence to support the feasibility of detecting altered DNA methylation patterns as a potential diagnostic and prognostic approach for HGSOC.

Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers.

To identify epigenetic-based biomarkers for diagnosis of ovarian cancer we performed MeDIP-Chip in A2780 and CaOV3 ovarian cancer cell lines. Validation by Sequenom massARRAY methylation analysis confirmed a panel of six gene promoters (ARMCX1, ICAM4, LOC134466, PEG3, PYCARD & SGNE1) where hypermethylation discriminated 27 serous ovarian cancer clinical samples versus 12 normal ovarian surface epithelial cells (OSE) (ROC of 0.98). Notably, CpG sites across the transcription start site of a potential long-intergenic non-coding RNA (lincRNA) gene (LOC134466), was shown to be hypermethylated in 81% of serous EOC and could differentiate tumours from OSE (p<0.05). We propose that this potential biomarker panel holds great promise as a diagnostic test for high-grade (Type II) serous ovarian cancer.

Assessing urinary levoglucosan and methoxyphenols as biomarkers for use in woodsmoke exposure studies.

A major contributor to particle concentrations in urban airsheds is domestic woodsmoke and smoke arising from wildfires or management burns. Particle concentrations in urban airsheds have been associated with a wide range of health effects. There has been little research into the contribution of biomass burning to studies of human health due to the complexity of attributing effects in the presence of multiple sources of pollutants and the variability in the nature and conditions of biomass burning. A significant advance is the use of biomarkers of exposure; methoxyphenol and levoglucosan; specific compounds produced following the combustion of lignins and detected in urine. Levoglucosan has not previously been assessed for its usefulness as a marker of human exposure. We report for the first time levoglucosan concentrations in urine. Twelve participants were recruited and asked to provide spot urine samples pre- and post-exposure to a fire training exercise. Both levoglucosan and methoxyphenol were detected in the urine of participants. There was no significant increase in these compounds post-exposure to smoke arising from the fire training. Further work is required to assess this biomarker for human exposure studies and in particular the role of diet and previous exposure.

DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment.

OBJECTIVE: To review epigenetic changes identified in ovarian cancer, focusing on their potential as clinical markers for detection, monitoring of disease progression and as markers of therapeutic response. METHODS: A comprehensive review of English language scientific literature on the topics of methylation and ovarian cancer was conducted. RESULTS: Genome-wide demethylation of normally methylated and silenced chromosomal regions, and hypermethylation and silencing of genes including tumor suppressors are common features of cancer cells. Epigenetic alterations, including CpG island DNA methylation, occur in ovarian cancer and the identification of specific genes that are altered by epigenetic events is an area of intense research. Aberrant DNA methylation in ovarian cancer is observed in early cancer development, can be detected in DNA circulating in the blood and hence provides the promise of a non-invasive cancer detection test. In addition, identification of ovarian cancer-specific epigenetic changes has promise in molecular classification and disease stratification. CONCLUSIONS: The detection of cancer-specific DNA methylation changes heralds an exciting new era in cancer diagnosis as well as evaluation of prognosis and therapeutic responsiveness and warrants further investigation.

Acid sulphate soil disturbance and metals in groundwater: implications for human exposure through home grown produce.

A significant emerging environmental problem is the disturbance and oxidation of soils with high levels of iron sulphide minerals resulting in acidification and causing the mobilization of metals into groundwater. This process is occurring in many parts of the world. In Western Australia, impacted groundwater is extracted by residents for domestic use. We sought to establish domestic use patterns of bore water and the concentration of metals. Sixty-seven domestic bore water samples clearly indicated oxidation of sulphidic materials with heavy metal concentrations ranging for aluminium (

Involvement of both intrinsic and extrinsic pathways in IFN-gamma-induced apoptosis that are enhanced with cisplatin.

IFN-gamma has direct anti-proliferative effects on ovarian cancer cell lines and tumour cells isolated from ovarian cancer ascites. The aim of this study was to further elucidate the mechanisms involved. An IFN-gamma-mediated cell cycle blockade was detectable in synchronised cell populations. Apoptosis, which was caspase dependent, was also induced. When caspase activity was blocked, the anti-proliferative effect of IFN-gamma was only partially reduced indicating independent roles for both growth inhibition and apoptosis in its actions. We have demonstrated involvement of the intrinsic apoptotic pathway; IFN-gamma treatment resulted in mitochondrial membrane depolarisation, cytochrome c release into the cytosol and activation of caspase 9. Cytochrome c release was blocked by the presence of a general caspase inhibitor, suggesting a role for caspases upstream of the mitochondria. One candidate is caspase 8, which was also activated in cells treated with IFN-gamma. Levels of Bid, a pro-apoptotic molecule that can mediate mitochondrial membrane permeabilisation when cleaved by caspase 8, were also decreased and indicated a potential link between these two pathways in IFN-gamma-induced apoptosis. Furthermore, together with cisplatin, IFN-gamma exerted a more powerful anti-proliferative effect.

IFN-gamma induces apoptosis in ovarian cancer cells in vivo and in vitro.

PURPOSE: The purpose of this study was to compare in vitro and in vivo responses of primary human tumor cells to IFN-gamma. EXPERIMENTAL DESIGN: IFN-gamma may have therapeutic activity in patients with ovarian cancer. We showed previously that this cytokine had direct antiproliferative activity against human ovarian cancer cell lines and xenografts in nude mice. To further understand the role of IFN-gamma in ovarian cancer, we compared its action on 8 ovarian cancer cell lines with the response of 14 primary cultures of ovarian tumor cells isolated from patients with ascitic disease. A pilot clinical study was then conducted to see whether IFN-gamma would also induce apoptosis in human tumor cells in vivo. Six patients with ascites and advanced disease were given IFN-gamma by i.p. injection, and sequential samples of ascites were analyzed. RESULTS: IFN-gamma had antiproliferative activity in 8 of 8 ovarian cancer cell lines and 11 of 14 primary cultures. This activity was dose related, and cleaved poly(ADP-ribose) polymerase in protein isolates provided evidence of apoptosis. In the clinical study, there was a 3 log(10) pharmacokinetic advantage in peritoneal compared with plasma levels of IFN-gamma. In two of six patients, there was a 90% reduction in tumor cells in ascites after IFN-gamma treatment, and this was related to clinical benefit as assessed by intervals between paracentesis. In all six patients, there were increased amounts of cleaved poly(ADP-ribose) polymerase in protein extracts of ascitic cells sampled during IFN-gamma treatment. CONCLUSIONS: IFN-gamma induces apoptosis in vitro and in vivo in human epithelial ovarian cancer.