Sorting, typing, classifying

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Privatisierung und Going Public von staatlichen Eisenbahnunternehmen: Versuch eines adaptiven Vergleichs zwischen Japan und Deutschland

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Gene expression studies

Recent technological developments allow genome-wide scans of gene expression levels. The reduction of costs and increasing parallelization of processing enable the quantification of 47,000 transcripts in up to twelve samples on a single microarray. Thereby the data collection of large population-based studies was improved. During my PhD, I first developed a workflow for the statistical analyses of case-control studies of up to 50 samples. With large population-based data sets generated I established a pipeline for quality control, data preprocessing and correction for confounders, which resulted in substantially improved data. In total, I processed more than 3,000 genome-wide expression profiles using the generated pipeline. With 993 whole blood samples from the population-based KORA (Cooperative Health Research in the Region of Augsburg) study we established one of the largest population-based resource. Using this data set we contributed to a number of transcriptome-wide association studies within national (MetaXpress) and international (CHARGE) consortia. Here I will focus on three studies with main contributions: I) Association study of gene expression levels with blood pressure related phenotypes. II) Association study investigating changes of gene expression levels associated with aging. III) Analysis of the impact of genetic variation on the gene expression levels. National and international collaborations substantially increased the power of the studies and ensured independent replication. Within the German consortium we developed protocols for meta-analyses and optimized preprocessing of diverse data sets. Whole blood is particularly useful because of its easy sampling. Especially, we could show that the impact of genetic variation is very robust and replicable within heterogeneous population-based studies.Moderne technologische Entwicklungen erlauben einen genomweiten Einblick in die Expression der Gene. Die Kostenreduzierung und die Möglichkeit der Parallelisierung bei der Probenvorbereitung erlaubt es 47.000 Transkripte in bis zu zwölf Proben mit einem Microarray gleichzeitig zu quantifizieren. Dadurch wird die Datenerhebung von größeren populations-basierten Studien erleichtert. Während meiner PhD Zeit entwickelte ich zunächst einen Arbeitsablauf für die statistische Analyse von Fall-Kontroll-Studien mit weniger als 50 Proben. Mit der Generierung von populations-basierten Datensätzen etablierte ich eine Pipeline für die Qualitätskontrolle, die Vorbereitung der Daten und die Korrektur für Störfaktoren, was zu einem deutlich verbesserten Datensatz führte. Insgesamt habe ich mit dieser Pipeline mehr als 3.000 genomweite Expressionsprofile für die Auswertung vorbereitet. Mit 993 Proben aus Vollblut von Probanden der populations-basierten KORA-Studie (Kooperative Gesundheitsforschung in der Region Augsburg) haben wir dabei eine der größten populations-basierten Ressourcen geschaffen. Mit diesem Datensatz haben wir zu zahlreichen transkriptom-weiten Assoziationsstudien in nationalen (MetaXpress) und internationalen (CHARGE) Konsortien beigetragen. In dieser Arbeit werde ich mich auf drei Studien, an denen wir maßgeblich beteiligt waren, fokussieren: I) Eine Assoziationsstudie der Genexpressionslevel mit Phänotypen, die im Zusammenhang mit Blutdruck stehen. II) Eine Assoziationsstudie, die die Veränderung der Genexpression im Alter untersuchte. III) Eine Studie über den Einfluss der genetischen Variation auf die Genexpressionslevel. Nationale und internationale Kollaborationen haben die Aussagekraft dieser Studien wesentlich erhöht und konnten unabhängige Replikationen sicher stellen. Im Rahmen des deutschen Konsortiums entwickelten wir Protokolle für Meta-Analysen und optimierten die Vorbereitung von verschiedenen Datensätzen. Dabei erwiesen sich Proben aus Vollblut wegen der einfachen Gewinnung als besonders hilfreich. Außerdem konnten wir zeigen, dass vor allem der Einfluss der genetischen Variation sehr robust und replizierbar innerhalb heterogener populations-basierter Studien ist

Isothiocyanate metabolism in generalist lepidopteran herbivores

Lepidopterans specialised on brassicaceous plants have been shown to possess biochemical adaptations preventing the formation of isothiocyanates. In faeces of generalist lepidopteran larvae glutathione (GSH) and cysteineglycine conjugates of plant-derived isothiocyanates were detected. The presence of GSH conjugates in larval faeces after consumption of crucifers suggests isothiocyanate-detoxification via GST (glutathione-S-transferase) activity in caterpillars. Active native GSTs were purified from midguts of Spodoptera littoralis larvae.It was shown that under conditions widely used for GST characterisation, S. littoralis-GSTs are capable of catalysing the conjugation reaction of GSH with isothiocyanates of different structures

Sensitivity to cdk1-inhibition is modulated by p53 status in preclinical models of embryonal tumors

Dysregulation of the cell cycle and cyclin-dependent kinases (cdks) is a hallmark of cancer cells. Intervention with cdk function is currently evaluated as a therapeutic option in many cancer types including neuroblastoma (NB), a common solid tumor of childhood. Re-analyses of mRNA profiling data from primary NB revealed that high level mRNA expression of both cdk1 and its corresponding cyclin, CCNB1, were significantly associated with worse patient outcome independent of MYCN amplification, a strong indicator of adverse NB prognosis. Cdk1 as well as CCNB1 expression were readily detectable in all embryonal tumor cell lines investigated. Pharmacological inhibition or siRNA-mediated knockdown of cdk1/CCNB1 induced proliferation arrest independent of MYCN status in NB cells. Sensitivity to cdk1 inhibition was modulated by TP53, which was demonstrated using isogenic cells with wild-type TP53 expressing either dominant-negative p53 or a short hairpin RNA directed against TP53. Apoptosis induced by cdk1 inhibition was dependent on caspase activation and was concomitant with upregulation of transcriptional targets of TP53. Our results confirm an essential role for the cdk1/CCNB1 complex in tumor cell survival. As relapsing embryonal tumors often present with p53 pathway alterations, these findings have potential implications for therapy approaches targeting cdks

Cognitive behavioural therapy for insomnia does not appear to have a substantial impact on early markers of cardiovascular disease: A preliminary randomized controlled trial

According to the World Health Organization, cardiovascular diseases are the leading cause of death in the world. Therefore, early prevention of these diseases is a public health priority. Epidemiological data suggest that insomnia may be a modifiable risk factor for cardiovascular diseases. A randomized controlled trial in a sample of insomnia patients without cardiovascular disease was conducted to investigate the effects of insomnia treatment on early markers of cardiovascular diseases assessed by 24‐hr ambulatory blood pressure, heart rate and heart rate variability monitoring, and morning fasting blood samples. Forty‐six patients with insomnia disorder were randomized to cognitive behavioural therapy for insomnia (CBT‐I; n = 23) or a waitlist control condition (n = 23). Contrary to the hypothesis, intention‐to‐treat analyses did not show any significant treatment effects on early markers of cardiovascular disease (d = 0.0–0.6) despite successful insomnia treatment (d = 1.3). Potential methodological and conceptual reasons for these negative findings are discussed. Future studies might include larger sample sizes that are at risk of cardiovascular diseases and focus on other cardiovascular markers

Robust selection of cancer survival signatures from high-throughput genomic data using two-fold subsampling

Identifying relevant signatures for clinical patient outcome is a fundamental task in high-throughput studies. Signatures, composed of features such as mRNAs, miRNAs, SNPs or other molecular variables, are often non-overlapping, even though they have been identified from similar experiments considering samples with the same type of disease. The lack of a consensus is mostly due to the fact that sample sizes are far smaller than the numbers of candidate features to be considered, and therefore signature selection suffers from large variation. We propose a robust signature selection method that enhances the selection stability of penalized regression algorithms for predicting survival risk. Our method is based on an aggregation of multiple, possibly unstable, signatures obtained with the preconditioned lasso algorithm applied to random (internal) subsamples of a given cohort data, where the aggregated signature is shrunken by a simple thresholding strategy. The resulting method, RS-PL, is conceptually simple and easy to apply, relying on parameters automatically tuned by cross validation. Robust signature selection using RS-PL operates within an (external) subsampling framework to estimate the selection probabilities of features in multiple trials of RS-PL. These probabilities are used for identifying reliable features to be included in a signature. Our method was evaluated on microarray data sets from neuroblastoma, lung adenocarcinoma, and breast cancer patients, extracting robust and relevant signatures for predicting survival risk. Signatures obtained by our method achieved high prediction performance and robustness, consistently over the three data sets. Genes with high selection probability in our robust signatures have been reported as cancer-relevant. The ordering of predictor coefficients associated with signatures was well-preserved across multiple trials of RS-PL, demonstrating the capability of our method for identifying a transferable consensus signature. The software is available as an R package rsig at CRAN (http://cran.r-project.org)

Becoming a Viking: DNA testing, genetic ancestry and placeholder identity

A consensus has developed among social and biological scientists around the problematic nature of genetic ancestry testing, specifically that its popularity will lead to greater genetic essentialism in social identities. Many of these arguments assume a relatively uncritical engagement with DNA, under ‘highstakes’ conditions. We suggest that in a biosocial society, more pervasive ‘lowstakes’ engagement is more likely. Through qualitative interviews with participants in a study of the genetic legacy of the Vikings in Northern England, we investigate how genetic ancestry results are discursively worked through. The identities formed in ‘becoming a Viking’ through DNA are characterized by fluidity and reflexivity, rather than essentialism. DNA results are woven into a wider narrative of selfhood relating to the past, the value of which lies in its potential to be passed on within families. While not unproblematic, the relatively banal nature of such narratives within contemporary society is characteristic of the ‘biosociable’

Persistent Pesticides in Human Breast Milk and Cryptorchidism

INTRODUCTION: Prenatal exposure to some pesticides can adversely affect male reproductive health in animals. We investigated a possible human association between maternal exposure to 27 organochlorine compounds used as pesticides and cryptorchidism among male children. DESIGN: Within a prospective birth cohort, we performed a case–control study; 62 milk samples from mothers of cryptorchid boys and 68 from mothers of healthy boys were selected. Milk was collected as individual pools between 1 and 3 months postpartum and analyzed for 27 organochlorine pesticides. RESULTS: Eight organochlorine pesticides were measurable in all samples (medians; nanograms per gram lipid) for cases/controls: 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (p,p′-DDE): 97.3/83.8; β-hexachlorocyclohexane (β-HCH): 13.6/12.3; hexachlorobenzene (HCB): 10.6/8.8; α -endosulfan: 7.0/6.7; oxychlordane: 4.5/4.1; 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (p,p′-DDT): 4.6/4.0; dieldrin: 4.1/3.1; cis-heptachloroepoxide (cis-HE): 2.5/2.2. Five compounds [octachlorostyrene (OCS); pentachlorobenzene, 1,1-dichloro-2,2-bis(4-chlorophenyl)ethane (p,p′-DDD); o,p′-DDT; mirex] were measurable in most samples (detection rates 90.8–99.2%) but in lower concentrations. For methoxychlor, cis-chlordane, pentachloroanisole (PCA), γ -HCH, 1,1-dichloro-2-(2-chlorophenyl)-2,2(4-chlorophenyl)ethane, trans-chlordane, α -HCH, and o,p′-DDE, both concentrations and detection rates were low (26.5–71.5%). Heptachlor, HCH (δ, ɛ ), aldrin, β-endosulfan and trans-heptachloroepoxide were detected at negligible concentrations and low detection rates and were not analyzed further. Seventeen of 21 organochlorine pesticides [p,p′-DDT, p,p′-DDE, p,p′-DDD, o,p′-DDT, HCH (α , β, γ ), HCB, PCA, α -endosulfan, cis-HE, chlordane (cis-, trans-) oxychlordane, methoxychlor, OCS, and dieldrin] were measured in higher median concentrations in case milk than in control milk. Apart from trans-chlordane (p = 0.012), there were no significant differences between cryptorchid and healthy boys for individual chemicals. However, combined statistical analysis of the eight most abundant persistent pesticides showed that pesticide levels in breast milk were significantly higher in boys with cryptorchidism (p = 0.032). CONCLUSION: The association between congenital cryptorchidism and some persistent pesticides in breast milk as a proxy for maternal exposure suggests that testicular descent in the fetus may be adversely affected