Measuring cell-type specific differential methylation in human brain tissue

The behavior of epigenetic mechanisms in the brain is obscured by tissue heterogeneity and disease-related histological changes. Not accounting for these confounders leads to biased results. We develop a statistical methodology that estimates and adjusts for celltype composition by decomposing neuronal and non-neuronal differential signal. This method provides a conceptual framework for deconvolving heterogeneous epigenetic data from postmortem brain studies. We apply it to find cell-specific differentially methylated regions between prefrontal cortex and hippocampus. We demonstrate the utility of the method on both Infinium 450k and CHARM data.     

Characterization of Botrytis–plant interactions using PathTrack©—an automated system for dynamic analysis of disease development

The measurement of disease development is integral in studies on plant–microbe interactions. To address the need for a dynamic and quantitative disease evaluation, we developed PathTrack^©, and used it to analyse the interaction of plants with Botrytis cinerea. PathTrack^© is composed of an infection chamber, a photography unit and software that produces video files and numerical values of disease progression. We identified a previously unrecognized infection stage and determined numerical parameters of pathogenic development. Using these parameters, we identified differences in disease dynamics between seemingly similar B. cinerea pathogenicity mutants, and revealed new details on plant susceptibility to the fungus. We showed that the difference between the lesion expansion rate on leaves and colony spreading rate on artificial medium reflects the levels of the plant immune system, suggesting that this parameter can be used to quantify plant defence. Our results shed new light and reveal new details of the interaction between the model necrotrophic pathogen B. cinerea and plants. The concept that we present is universal and may be applied to facilitate the study of various types of plant–pathogen association.     

There is more to tomato fruit colour than candidate carotenoid genes

Determining gene sequences responsible for complex phenotypes has remained a major objective in modern biology. The candidate gene approach is attempting to link, through mapping analysis, sequences that have a known functional role in the measured phenotype with quantitative trait loci (QTL) that are responsible for the studied variation. To explore the potential of the candidate approach for complex traits we conducted a mapping analysis of QTL for the intensity of the red colour of the tomato fruit (mainly lycopene) and for probes associated with the well-characterized carotenoid biosynthesis pathway. Seventy-five tomato introgression lines (ILs), each containing a single homozygous RFLP-defined chromosome segment from the green-fruited species Lycopersicon pennellii delimited 107 marker-defined mapping bins. Three of the bins resolved known qualitative colour mutations for yellow (r) and orange (B and Del) fruits resulting from variation in specific carotenoid biosynthesis genes. Based on trials in different environments, 16 QTL that modified the intensity of the red colour of ripe fruit were assigned to bins. Candidate sequences associated with the carotenoid biosynthesis pathway were mapped to 23 loci. Only five of the QTL co-segregated with the same bins that contained candidate genes - a number that is expected by chance alone. Furthermore, similar map location of a QTL and a candidate is far from a direct causative relationship between a gene and a phenotype. This study highlights the wealth and complexity of the variation present in the genus Lycopersicon that could be employed for basic research and genetic improvement of fruit colour in tomato.     

Rutin protects rat liver and kidney from sodium valproate-induce damage by attenuating oxidative stress,ER stress,inflammation, apoptosis and autophagy

Background

The present study investigated the effects of rutin (RUT), which has various biological and pharmacological properties, on liver and kidney damage caused by histone deacetylase inhibitor valproic acid (VPA), which is used in the treatment of many psychiatric disorders.

Methods and results

In the study, 50 or 100 mg/kg RUT treatment was administered 30 min after 500 mg/kg VPA was given to rats for 14 days. Then, some pathways that may be involved in the damage mechanism of VPA in liver and kidney tissues were investigated using biochemical, RT-PCR and Western blotting techniques. The results displayed that the levels of MDA induced by VPA in liver and kidney tissues decreased after RUT treatment, and the levels of SOD, CAT, GPx and GSH suppressed by VPA increased after RUT administration. It was observed that ER stress induced by oxidative stress was alleviated by suppressing the expressions of ATF-6, PERK, IRE1 and GRP78 after RUT treatment. It was observed that the expressions of NF-κB, TNF-α, IL-6, JAK2 and STAT3 in the inflammatory pathway increased after VPA administration, while RUT treatment decreased the levels of these markers. It was also among the data obtained that the levels of markers that played a role in the regulation of apoptosis (Bax, Bcl-2, caspase-3, pERK, pJNK) or autophagy (Beclin-1, LC3A, LC3B) approached the control group after RUT treatment.

Conclusions

Taken together, it was determined that RUT treatment protected against liver and kidney damage by attenuating VPA-induced oxidative stress, ER stress, inflammation, apoptosis and autophagy.

     

Product Quality Research Institute evaluation of cascade impactor profiles of pharmaceutical aerosols, part 1: Background for a statistical method

The purpose of this article is 2-fold: (1) to document in the public domain the considerations that led to the development of a regulatory statistical test for comparison of aerodynamic particle size distribution (APSD) of aerosolized drug formulations, which was proposed in a US Food and Drug Administration (FDA) draft guidance for industry; and (2) to explain the background and process for evaluation of that test through a working group involving scientists from the FDA, industry, academia, and the US Pharmacopeia, under the umbrella of the Product Quality Research Institute (PQRI). The article and the referenced additional statistical information posted on the PQRI Web site explain the reasoning and methods used in the development of the APSD test, which is one of the key tests required for demonstrating in vitro equivalence of orally inhaled and nasal aerosol drug products. The article also describes the process by which stakeholders with different perspectives have worked collaboratively to evaluate properties of the test by drawing on statistical models, historical and practical information, and scientific reasoning. Overall, this article provides background information to accompany the companion article's discussion of the study's methods and results. Published: January 19, 2007 Former address: Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration Rockville, MD     

The Escherichia coli DjlA and CbpA proteins can substitute for DnaJ in DnaK-mediated protein disaggregation

The DnaJ (Hsp40) protein of Escherichia coli serves as a cochaperone of DnaK (Hsp70), whose activity is involved in protein folding, protein targeting for degradation, and rescue of proteins from aggregates. Two other E. coli proteins, CbpA and DjlA, which exhibit homology with DnaJ, are known to interact with DnaK and to stimulate its chaperone activity. Although it has been shown that in dnaJ mutants both CbpA and DjlA are essential for growth at temperatures above 37 degrees C, their in vivo role is poorly understood. Here we show that in a dnaJ mutant both CbpA and DjlA are required for efficient protein dissaggregation at 42 degrees C.     

Microseconds Simulations Reveal a New Sodium-binding Site and the Mechanism of Sodium-coupled Substrate Uptake by LeuT

The bacterial sodium-coupled leucine/alanine transporter LeuT is broadly used as a model system for studying the transport mechanism of neurotransmitters because of its structural and functional homology to mammalian transporters such as serotonin, dopamine, or norepinephrine transporters, and because of the resolution of its structure in different states. Although the binding sites (S1 for substrate, and Na1 and Na2 for two co-transported sodium ions) have been resolved, we still lack a mechanistic understanding of coupled Na⁺- and substrate-binding events. We present here results from extensive (>20 μs) unbiased molecular dynamics simulations generated using the latest computing technology. Simulations show that sodium binds initially the Na1 site, but not Na2, and, consistently, sodium unbinding/escape to the extracellular (EC) region first takes place at Na2, succeeded by Na1. Na2 diffusion back to the EC medium requires prior dissociation of substrate from S1. Significantly, Na⁺ binding (and unbinding) consistently involves a transient binding to a newly discovered site, Na1″, near S1, as an intermediate state. A robust sequence of substrate uptake events coupled to sodium bindings and translocations between those sites assisted by hydration emerges from the simulations: (i) bindings of a first Na⁺ to Na1″, translocation to Na1, a second Na⁺ to vacated Na1″ and then to Na2, and substrate to S1; (ii) rotation of Phe²⁵³ aromatic group to seclude the substrate from the EC region; and (iii) concerted tilting of TM1b and TM6a toward TM3 and TM8 to close the EC vestibule.