A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix

AIM: An outstanding challenge in epigenome studies is the estimation of cell-type proportions in complex epithelial tissues. MATERIALS & METHODS: Here, we construct and validate a DNA methylation reference and algorithm for complex tissues that contain epithelial, immune and nonimmune stromal cells. RESULTS: Using this reference, we show that easily accessible tissues such as saliva, buccal and cervix exhibit substantial variation in immune cell (IC) contamination. We further validate our reference in the context of oral cancer, where it correctly predicts an increased IC infiltration in cancer but suppressed in patients with highest smoking exposure. Finally, our method can improve the specificity of differentially methylated CpG calls in epithelial cancer. CONCLUSION: The degree and variation of IC contamination in complex epithelial tissues is substantial. We provide a valuable resource and tool for assessing the epithelial purity and IC contamination of samples and for identifying differential methylation in such complex tissues

An optimised saliva collection method to produce high-yield, high-quality RNA for translational research

Saliva represents an ideal matrix for diagnostic biomarker development as it is readily available and requires no invasive collection procedures. However, salivary RNA is labile and rapidly degrades. Previous attempts to isolate RNA from saliva have yielded poor quality and low concentrations. Here we compare collection and processing methods and propose an approach for future studies. The effects of RNA stabilisers, storage temperatures, length of storage and fasting windows were investigated on pooled saliva samples from healthy volunteers. Isolated RNA was assessed for concentration and quality. Bacterial growth was investigated through RT-PCR using bacterial and human primers. Optimal conditions were implemented and quality controlled in a clinical setting. The addition of RNAlater increased mean RNA yield from 4912 ng/μl to 15,473 ng and RNA Integrity Number (RIN) from 4.5 to 7.0. No significant changes to RNA yield were observed for storage at room temperature beyond 1 day or at -80 °C. Bacterial growth did not occur in samples stored at ambient temperature for up to a week. There was a trend towards higher RNA concentration when saliva was collected after overnight fasting but no effect on RIN. In the clinic, RNA yields of 6307 ng and RINs of 3.9 were achieved, improving on previous reports. The method we describe here is a robust, clinically feasible saliva collection method using preservative that gives high concentrations and improved RINs compared to saliva collected without preservative

Three-dimensional cephalometric evaluation of maxillary growth following in utero repair of cleft lip and alveolar-like defects in the mid-gestational sheep model

Objective: To evaluate maxillary growth following in utero repair of surgically created cleft lip and alveolar (CLA)-like defects by means of three-dimensional (3D) computer tomographic (CT) cephalometric analysis in the mid-gestational sheep model. Methods: In 12 sheep fetuses a unilateral CLA-like defect was created in utero (untreated control group: 4 fetuses). Four different bone grafts were used for the alveolar defect closure. After euthanasia, CT scans of the skulls of the fetuses, 3D re-constructions, and a 3D-CT cephalometric analysis were performed. Results: The comparisons between the operated and nonoperated skull sides as well as of the maxillary asymmetry among the experimental groups revealed no statistically significant differences of the 12 variables used. Conclusions: None of the surgical approaches used for the in utero correction of CLA-like defects seem to affect significantly postsurgical maxillary growth; however, when bone graft healing takes place, a tendency for almost normal maxillary growth can be observed. Copyright (c) 2006 S. Karger AG, Basel

Measuring health-related quality of life in adolescents and young adults: Swedish normative data for the SF-36 and the HADS, and the influence of age, gender, and method of administration

BACKGROUND: There is a paucity of research about health-related quality of life (HRQL) among adolescents, as studies have to a large extent focused on adults. The main aim was to provide information for future studies in this growing field by presenting normative data for the Short Form 36 (SF-36) and the Hospital Anxiety and Depression Scale (HADS) for Swedish adolescents and young adults. Additionally, the influence of age and gender, as well as method of administration, was investigated. METHODS: A sample of 585 persons aged 13–23 was randomly chosen from the general population, and stratified regarding age group (young adolescents: 13–15 years; older adolescents: 16–19 years, and young adults: 20–23 years) and gender (an equal amount of males and females). Within each stratum, the participants were randomized according to two modes of administration, telephone interview and postal questionnaire, and asked to complete the SF-36 and the HADS. Descriptive statistics are presented by survey mode, gender, and age group. A gender comparison was made by independent t-test; and one-way ANOVA was conducted to evaluate age differences. RESULTS: Effects of age and gender were found: males reported better health-related quality of life than females, and the young adolescents (13–15 years old) reported better HRQL than the two older age groups. The older participants (16–23 years old) reported higher scores when interviewed over the telephone than when they answered a postal questionnaire, a difference which was more marked among females. Interestingly, the 13–15-year-olds did not react to the mode of administration to the same extent. CONCLUSION: The importance of taking age, gender, and method of administration into consideration, both when planning studies and when comparing results from different groups, studies, or over time, is stressed

Indigenous Populations of Three Closely Related Lysobacter spp. in Agricultural Soils Using Real-Time PCR

Previous research had shown that three closely related species of Lysobacter, i.e., Lysobacter antibioticus, Lysobacter capsici, and Lysobacter gummosus, were present in different Rhizoctonia-suppressive soils. However, the population dynamics of these three Lysobacter spp. in different habitats remains unknown. Therefore, a specific primer–probe combination was designed for the combined quantification of these three Lysobacter spp. using TaqMan. Strains of the three target species were efficiently detected with TaqMan, whereas related non-target strains of Lysobacter enzymogenes and Xanthomonas campestris were not or only weakly amplified. Indigenous Lysobacter populations were analyzed in soils of 10 organic farms in the Netherlands during three subsequent years with TaqMan. These soils differed in soil characteristics and crop rotation. Additionally, Lysobacter populations in rhizosphere and bulk soil of different crops on one of these farms were studied. In acid sandy soils low Lysobacter populations were present, whereas pH neutral clay soils contained high populations (respectively, <4.0–5.87 and 6.22–6.95 log gene copy numbers g−1 soil). Clay content, pH and C/N ratio, but not organic matter content in soil, correlated with higher Lysobacter populations. Unexpectedly, different crops did not significantly influence population size of the three Lysobacter spp. and their populations were barely higher in rhizosphere than in bulk soil

The assessment of depression in people with multiple sclerosis : a systematic review of psychometric validation studies

Background: The prevalence of depression in people with multiple sclerosis (PwMS) is high; however, symptoms common to both conditions makes measurement difficult. There is no high quality overview of validation studies to guide the choice of depression inventory for this population. Methods: A systematic review of studies validating the use of generic depression inventories in people with MS was conducted using MEDLINE and PsycINFO. Studies validating the use of depression inventories in PwMS and published in English were included; validation studies of tests for cognitive function and general mental health were excluded. Eligible studies were then quality assessed using the COSMIN checklist and findings synthesised narratively by instrument and validity domain. Results: Twenty-one studies (N=5,991 PwMS) evaluating 12 instruments were included in the review. Risk of bias varied greatly between instrument and validity domain. Conclusions: The review of validation studies was constrained by poor quality reporting and outcome reporting bias. Well-conducted evaluations of some instruments are unavailable for some validity domains. This systematic review provides an evidence base for trade-offs in the selection of an instrument for assessing self-reported symptoms of depression in research or clinical practice involving people with MS. We make detailed and specific recommendations for where further research is needed. Registration: PROSPERO CRD42014010597 Keywords Depression; Multiple Sclerosis; Reproducibility of Results; Psychometrics; Chronic Diseas

Sensitivity to heat in MS patients: a factor strongly influencing symptomology - an explorative survey

<p>Abstract</p> <p>Background</p> <p>Many individuals diagnosed with Multiple Sclerosis (MS) are sensitive to increased body temperature, which has been recognized as correlating with the symptom of fatigue. The need to explore this association has been highlighted. The aim of this study was to investigate the occurrence of heat sensitivity and its relations to disease course, disability, common MS-related symptoms and ongoing immunosuppressive treatments among individuals 65 years of age or younger diagnosed with MS.</p> <p>Methods</p> <p>A cross-sectional designed survey was undertaken. A questionnaire was sent to MS-patients with an Expanded Disability Status Score (EDSS) in the interval of 0-6.5 and who were between 20 and 65 years of age, living in an eastern region of Sweden (n = 334). Besides occurrence of heat sensitivity (Yes/No) and corresponding questions, the Fatigue Severity Scale (FSS), the MS-related symptom checklist and the Perceived Deficit Questionnaire (PDQ) were included. Data were analysed in relation to data level using Chi-square, Mann Whitney U-test, and Student's t-test. Pearson's and Spearman's correlations were calculated. In the logistic regression analyses (enter) dichotomized MS-symptoms were used as dependent variables, and EDSS, disease-course, time since onset, heat-sensitivity, age and sex (female/male) were independent variables. In the linear regression analyses, enter, mean FSS and summarized PDQ were entered as dependent variables and EDSS, disease-course, time since onset, heat sensitivity, age and sex (female/male) were independent variables.</p> <p>Results</p> <p>Of the responding patients (n = 256), 58% reported heat sensitivity. The regression analyses revealed heat sensitivity as a significant factor relating not only to fatigue (p < 0.001), but also to several other common MS symptoms such as pain (p < 0.001), concentration difficulties (p < 0.001), and urination urgency (p = 0.009).</p> <p>Conclusions</p> <p>Heat sensitivity in MS patients is a key symptom that is highly correlated with disabling symptoms such as fatigue, pain, concentration difficulty and urination urgency.</p

Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism.

Most differentiated cells convert glucose to pyruvate in the cytosol through glycolysis, followed by pyruvate oxidation in the mitochondria. These processes are linked by the mitochondrial pyruvate carrier (MPC), which is required for efficient mitochondrial pyruvate uptake. In contrast, proliferative cells, including many cancer and stem cells, perform glycolysis robustly but limit fractional mitochondrial pyruvate oxidation. We sought to understand the role this transition from glycolysis to pyruvate oxidation plays in stem cell maintenance and differentiation. Loss of the MPC in Lgr5-EGFP-positive stem cells, or treatment of intestinal organoids with an MPC inhibitor, increases proliferation and expands the stem cell compartment. Similarly, genetic deletion of the MPC in Drosophila intestinal stem cells also increases proliferation, whereas MPC overexpression suppresses stem cell proliferation. These data demonstrate that limiting mitochondrial pyruvate metabolism is necessary and sufficient to maintain the proliferation of intestinal stem cells

Algometry to measure pain threshold in the horse's back - An in vivo and in vitro study

Abstract Background The aim of this study was to provide information on algometric transmission of pressure through the dorsal thoracolumbar tissues of the equine back. Using a commercially available algometer, measurements were carried out with six different tips (hemispheric and cylindrical surfaces, contact areas 0.5 cm2, 1 cm2, and 2 cm2). In nine live horses the threshold of pressure that lead to any reaction was documented. In postmortem specimens of five euthanized horses the transmission of algometer pressure onto a pressure sensor placed underneath the dorsal thoracolumbar tissues at the level of the ribs or the transverse lumbar processes respectively was measured. Results Algometer tips with a contact area of 1 cm2 led to widely similar results irrespective of the surface shape; these measurements also had the lowest variance. Contact areas of 0.5 cm2 resulted in a lower pressure threshold, and those of 2 cm2 resulted in a higher pressure threshold. The hemispheric shape of the contact area resulted in a higher pressure threshold, than the cylindrical contact area. Compared to the thoracic region, a significantly higher pressure threshold was found in the lumbar region in the live horses. This result corresponds to the increased tissue thickness in the lumbar region compared to the thoracic region, also documented as less pressure transmission in the lumbar region on the in vitro specimens. Conclusions Algometry is an easily practicable and well tolerated method to quantify pain but it is important to consider the many factors influencing the results obtained