Blood-based profiles of DNA methylation predict the underlying distribution of cell types

The potential influence of underlying differences in relative leukocyte distributions in studies involving blood-based profiling of DNA methylation is well recognized and has prompted development of a set of statistical methods for inferring changes in the distribution of white blood cells using DNA methylation signatures. However, the extent to which this methodology can accurately predict cell-type proportions based on blood-derived DNA methylation data in a large-scale epigenome-wide association study (EWAS) has yet to be examined. We used publicly available data deposited in the Gene Expression Omnibus (GEO) database (accession number GSE37008), which consisted of both blood-derived epigenome-wide DNA methylation data assayed using the Illumina Infinium HumanMethylation27 BeadArray and complete blood cell (CBC) counts among a community cohort of 94 non-diseased individuals. Constrained projection (CP) was used to obtain predictions of the proportions of lymphocytes, monocytes and granulocytes for each of the study samples based on their DNA methylation signatures. Our findings demonstrated high consistency between the average CBC-derived and predicted percentage of monocytes and lymphocytes (17.9% and 17.6% for monocytes and 82.1% and 81.4% for lymphocytes), with root mean squared error (rMSE) of 5% and 6%, for monocytes and lymphocytes, respectively. Similarly, there was moderate-high correlation between the CP-predicted and CBC-derived percentages of monocytes and lymphocytes (0.60 and 0.61, respectively), and these results were robust to the number of leukocyte differentially methylated regions (L-DMRs) used for CP prediction. These results serve as further validation of the CP approach and highlight the promise of this technique for EWAS where DNA methylation is profiled using whole-blood genomic DNA.     

Invasive pulmonary aspergillosis: retrospective case record review

Invasive pulmonary aspergillosis is a severe infection, with a sharp increase during the last decades. Our study aimed at identification of the epidemiological characteristics of invasive pulmonary aspergillosis during a period of four years. All clinical records with pulmonary isolation of Aspergillus species were reviewed, as a part of surveillance program at Reina Sofia University Hospital, from January 1995 to December 1998. Diagnosis of invasive pulmonary aspergillosis was based on criteria of Centers for Disease Control and Prevention. Of the 50 patients identified 78% were males and 44% were current or ex-smokers. Chronic respiratory diseases were identified in 64% of them, and 60% were receiving immunosuppressives. Twenty percent of our patients had been subjected to lung transplantation and 28% to organ transplantation in general. Only 78% had received specific antifungal treatment and 56% had fatal prognosis. Our findings match with previous studies, apart from the high frequency of lung transplantation in our series. We recommend further studies on large prospective cohorts.     

Contrasting Microbial Community Assembly Hypotheses: A Reconciling Tale from the Río Tinto

Background

The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters.

Methodology/Principal Findings

By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns.

Conclusions/Significance

We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.     

Déficit de vitamina D en una cohorte de mayores de 65 años: prevalencia y asociación con factores sociodemográficos y de salud

Introduction

Vitamin D deficiency is common in the elderly, especially among institutionalized and/or hip fracture patients. However, there are few population studies on the prevalence of this deficiency in the general population over 64 years in our environment. The aim of this study was to determine the prevalence of vitamin D deficiency in an urban population cohort of over 64 years, and analyze its relationship with sociodemographic, climatic, and health factors.

Material and methods

Cross-sectional study from «Peñagrande cohort», a population-based cohort consisting of people over 64 years. We determined 25-hydroxyvitamin D levels, and recorded sociodemographic data (age, sex, marital status, education, socioeconomic status), season of measurement and health variables (comorbidity, obesity, malnutrition, renal failure, cognitive impairment, vitamin D supplements, and disability).

Results

A total of 468 individuals with a mean age of 76.0 years (SD: 7.7) were included, of which 53.4% were women. The mean value of vitamin D was 20.3 ± 11.7 ng/mL. The large majority (86.3%, 95% CI: 83.0-89.5) had a vitamin insufficiency (≤ 30 ng/ml), and 35.2% (95% CI: 30.8-39.7) showed severe vitamin deficiency (≤ 15 ng/ml). Vitamin insufficiency increases linearly with age (OR 1.06; 95% CI: 1.01-1.11), and was associated with low socioeconomic status (OR 3.29; 95% CI: 1.55-6.95). Severe vitamin D deficiency increases with age (OR 1.06; 95% CI: 1.02-1.09), female gender (OR 1.80; 95% CI: 1.18-2.75) and with cognitive impairment (OR 1.71; 95% CI: 1.04-2.83).

Conclusion

The prevalence of vitamin D deficiency in people over 65 years of age in our community is high. It would be advisable to determine the vitamin D values in the high risk elderly in order to introduce measures of pharmacological supplementation in those with inadequate levels.     

Biochemical characteristics of the outer membranes of plant mitochondria

Like the outer membranes of liver mitochondria, those of plant mitochondria are impermeable to cytochrome c when intact and can be ruptured by osmotic shock. Isolated plant outer mitochondrial membranes are also similar to the corresponding liver membranes in terms of phospholipid and sterol content. Sodium dodecyl sulfate-polyacrylamide gradient gel electrophoresis experiments indicate that a single class of proteins (apparent molecular weight 30 000) comprises the bulk of the plant outer membrane protein. There are also considerable amounts of polysaccharide associated with these membranes, which may contribute to their osmotic stability.     

Modulation of histamine-induced Ca2+ release by protein kinase C. Effects on cytosolic and mitochondrial [Ca2+] peaks

In HeLa cells, histamine induces production of inositol 1,4,5-trisphosphate (InsP3) and release of Ca2+ from the endoplasmic reticulum (ER). Ca2+ release is typically biphasic, with a fast and brief initial phase, followed by a much slower and prolonged one. In the presence of inhibitors of protein kinase C (PKC), including staurosporine and the specific inhibitors GF109203X and Ro-31-8220, the fast phase continued until the ER became fully empty. On the contrary, treatment with phorbol 12,13-dibutyrate inhibited Ca2+ release. Staurosporine had no effect on InsP3-induced Ca2+ release in permeabilized cells and did not modify either histamine-induced InsP3 production. These data suggest that histamine induces Ca2+ release and with a short lag activates PKC to down-regulate it. Consistently, Ca2+ oscillations induced by histamine were increased in amplitude and decreased in frequency in the presence of PKC inhibitors. We show also that mitochondrial [Ca2+] was much more sensitive to changes in ER-Ca2+ release induced by PKC modulation than cytosolic [Ca2+]. PKC inhibitors increased the histamine-induced mitochondrial [Ca2+] peak by 4-fold but increased the cytosolic [Ca2+] peak only by 20%. On the contrary, PKC activation inhibited the mitochondrial [Ca2+] peak by 90% and the cytosolic one by only 50%. Similarly, the combination of PKC inhibitors with the mitochondrial Ca2+ uniporter activator SB202190 led to dramatic increases in mitochondrial [Ca2+] peaks, with little effect on cytosolic ones. This suggests that activation of ER-Ca2+ release by PKC inhibitors could be involved in apoptosis induced by staurosporine. In addition, these mechanisms allow flexible and independent regulation of cytosolic and mitochondrial [Ca2+] during cell stimulation.     

Stability of Benzocaine Formulated in Commercial Oral Disintegrating Tablet Platforms

Pharmaceutical excipients contain reactive groups and impurities due to manufacturing processes that can cause decomposition of active drug compounds. The aim of this investigation was to determine if commercially available oral disintegrating tablet (ODT) platforms induce active pharmaceutical ingredient (API) degradation. Benzocaine was selected as the model API due to known degradation through ester and primary amino groups. Benzocaine was either compressed at a constant pressure, 20 kN, or at pressure necessary to produce a set hardness, i.e., where a series of tablets were produced at different compression forces until an average hardness of approximately 100 N was achieved. Tablets were then stored for 6 months under International Conference on Harmonization recommended conditions, 25°C and 60% relative humidity (RH), or under accelerated conditions, 40°C and 75% RH. Benzocaine degradation was monitored by liquid chromatography–mass spectrometry. Regardless of the ODT platform, no degradation of benzocaine was observed in tablets that were kept for 6 months at 25°C and 60% RH. After storage for 30 days under accelerated conditions, benzocaine degradation was observed in a single platform. Qualitative differences in ODT platform behavior were observed in physical appearance of the tablets after storage under different temperature and humidity conditions.