Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor

The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge due to the vast amounts of data and the large variety of pre-processing and filtering steps employed before the actual analysis is carried out. To guarantee a firm basis for methodological development where results with new methods are compared with previous results it is crucial to ensure that all analyses are completely reproducible for other researchers. We here give a detailed workflow on how to perform reproducible analysis of the GeneChip Human Exon 1.0 ST Array at probe and probeset level solely in R/Bioconductor, choosing packages based on their simplicity of use. To exemplify the use of the proposed workflow we analyse differential splicing and differential gene expression in a publicly available dataset using various statistical methods. We believe this study will provide other researchers with an easy way of accessing gene expression data at different annotation levels and with the sufficient details needed for developing their own tools for reproducible analysis of the GeneChip Human Exon 1.0 ST Array

GMCM: Unsupervised Clustering and Meta-Analysis Using Gaussian Mixture Copula Models

Methods for clustering in unsupervised learning are an important part of the statistical toolbox in numerous scientific disciplines. Tewari, Giering, and Raghunathan (2011) proposed to use so-called Gaussian mixture copula models (GMCM) for general unsupervised learning based on clustering. Li, Brown, Huang, and Bickel (2011) independently discussed a special case of these GMCMs as a novel approach to meta-analysis in highdimensional settings. GMCMs have attractive properties which make them highly flexible and therefore interesting alternatives to other well-established methods. However, parameter estimation is hard because of intrinsic identifiability issues and intractable likelihood functions. Both aforementioned papers discuss similar expectation-maximization-like algorithms as their pseudo maximum likelihood estimation procedure. We present and discuss an improved implementation in R of both classes of GMCMs along with various alternative optimization routines to the EM algorithm. The software is freely available in the R package GMCM. The implementation is fast, general, and optimized for very large numbers of observations. We demonstrate the use of package GMCM through different applications

Cardioprotective effect of succinate dehydrogenase inhibition in rat hearts and human myocardium with and without diabetes mellitus

Abstract Ischemia reperfusion (IR) injury may be attenuated through succinate dehydrogenase (SDH) inhibition by dimethyl malonate (DiMAL). Whether SDH inhibition yields protection in diabetic individuals and translates into human cardiac tissue remain unknown. In isolated perfused hearts from 24 weeks old male Zucker diabetic fatty (ZDF) and age matched non-diabetic control rats and atrial trabeculae from patients with and without diabetes, we compared infarct size, contractile force recovery and mitochondrial function. The cardioprotective effect of a 10 minutes DiMAL administration prior to global ischemia and ischemic preconditioning (IPC) was evaluated. In non-diabetic hearts exposed to IR, DiMAL 0.1 mM reduced infarct size compared to IR (55 ± 7% vs. 69 ± 6%, p < 0.05). Mitochondrial respiration was reduced by DiMAL 0.6 mM compared to sham and DiMAL 0.1 mM (p < 0.05). In diabetic hearts an increased concentration of DiMAL (0.6 mM) was required for protection compared to IR (64 ± 13% vs. 79 ± 8%, p < 0.05). Mitochondrial function remained unchanged. In trabeculae from humans without diabetes, IPC and DiMAL improved contractile force recovery compared to IR (43 ± 12% and 43 ± 13% vs. 23 ± 13%, p < 0.05) but in patients with diabetes only IPC provided protection compared to IR (51 ± 15% vs. 21 ± 8%, p < 0.05). Neither IPC nor DiMAL modulated mitochondrial respiration in patients. Cardioprotection by SDH inhibition is possible in human tissue, but depends on diabetes status. The narrow therapeutic range and discrepancy in respiration between experimental and human studies may limit clinical translation

Oral mucosa tissue gene expression profiling before, during, and after radiation therapy for tonsil squamous cell carcinoma

Radiation-therapy (RT) induces mucositis, a clinically challenging condition with limited prophylactic interventions and no predictive tests. In this pilot study, we applied global gene-expression analysis on serial human oral mucosa tissue and blood cells from patients with tonsil squamous cell cancer (TSCC) to identify genes involved in mucositis pathogenesis.Eight patients with TSCC each provided consecutive buccal biopsies and blood cells before, after 7 days of RT treatment, and 20 days following RT. We monitored clinical mucositis and performed gene-expression analysis on tissue samples. We obtained control tissue from nine healthy individuals. After RT, expression was upregulated in apoptosis inducer and inhibitor genes, EDA2R and MDM2, and in POLH, a DNA-repair polymerase. Expression was downregulated in six members of the histone cluster family, e.g., HIST1H3B. Gene expression related to proliferation and differentiation was altered, including MKI67 (downregulated), which encodes the Ki-67-proliferation marker, and KRT16 (upregulated), which encodes keratin16. These alterations were not associated with the clinical mucositis grade. However, the expression of LY6G6C, which encodes a surface immunoregulatory protein, was upregulated before treatment in three cases of clinical none/mild mucositis, but not in four cases of ulcerative mucositis.RT caused molecular changes related to apoptosis, DNA-damage, DNA-repair, and proliferation without a correlation to the severity of clinical mucositis. LY6G6C may be a potential protective biomarker for ulcerative mucositis. Based on these results, our study model of consecutive human biopsies will be useful in designing a prospective clinical validation trial to characterize molecular mucositis and identify predictive biomarkers

Effekter av redusert jordarbeiding og forbedrede jordarbeidingsteknikker på klimagassutslipp i planteproduksjon – et forprosjekt.

Norsk: Denne rapporten er resultatet av et forprosjekt gjennomført som et samarbeid mellom Ruralis – Institutt for rural- og regionalforskning og Høgskolen i Innlandet. Tilnærmingen er todelt; der del 1 er en innledende litteraturstudie som gir oversikt over relevant norsk og internasjonal forskning omkring redusert jordarbeiding og forbedrede jordarbeidingsteknikker, med hensyn på reduserte klimagassutslipp og miljøbelastninger. Del 2 er hoveddelen av rapporten, og er en pilotstudie som omhandler bønders interesse for og erfaring med redusert jordarbeiding i sin daglige drift, og er basert på intervjuer med i alt 12 gårdbrukere på Østlandet og i Trøndelag. Med redusert jordarbeiding menes endringer i antall operasjoner og tilpasning til nye redskapstyper, slik at det benyttes færre operasjoner enn tidligere for å bearbeide og bruke jorda. I mange tilfeller betyr redusert jordarbeiding bortfall av veltefjølsplog, men ikke alltid. Vi belyser bøndenes teknikker for jordarbeiding, som harving og andre arbeidsoperasjoner på jordbruksarealene. Valgene av teknikker og operasjoner tas for eksempel hos enkelte bønder som følge av tilpasninger til værforhold, økonomisering av drift, eller forsøk på å redusere klimagassutslipp, i noen tilfeller alt sammen. Andre bønder kjenner til mulighetene for, eller har forsøkt å endre teknikker og operasjoner, men har likevel valgt å fortsette som tidligere. Alle bøndenes valg bunner ifølge dem selv i deres ideer om best mulig bruk av jorda. Rapporten inneholder funn som det vil bygges videre på i utformingen av hovedprosjekt innen fremtidige valg av jordarbeidingsstrategier i Norge, tilpasset et endret klima, krav til lavere energibruk ved jordarbeiding og bedret virkningsgrad i arbeidsoperasjonene tilknyttet jordarbeiding og planteetablering.English: This report is the result of a preliminary project conducted in a collaboration between Ruralis – Institute for Rural and Regional Research and HINN – Inland Norway University of Applied Sciences. Our approach consists of two parts; Part 1 is a literature review of relevant Norwegian and international research on reduced soil tilling and improved techniques of soil cultivation, including effects on climate gas emissions and environmental hazards. Part 2 is the main part of the report and, is a pilot study about farmers’ interest in and experiences with reduced soil tillage in their daily farming operations. This qualitative study is based on interviews with 12 farmers in two areas, the Østlandet area in the eastern part of Norway and Trøndelag county in the middle part of Norway. What is meant by reduced soil tillage is changes in number of operations and adjustments to new equipment, resulting in reduction in number of operations compared to former practices to cultivate the soil. In many instances reduced soil tillage is involves exclusion of the tillage plough, but this is not always so. We investigate the farmers’ techniques for soil tillage, such as harrowing and other operations in the fields. Their choice of techniques and operations are based on, amongst other things, the weather conditions, economization of the farming, or attempts in reducing climate gas emissions, in some instances all of them at once. Other farmers know about the opportunities for, or have tried to change, techniques and operations, but have chosen to continue previous procedures. All the farmers’ choices are, according to themselves, based on their own ideas regarding how to best cultivate the soil. The report contains results which we will build on in our preparations for a main project researching future choices of soil tillage strategies in Norway, that is, strategies adapted to a changing climate, resulting in reduced energy consumption and improved efficiency in the operations on soil and plant cultivation