Strategies for analyzing bisulfite sequencing data

DNA methylation is one of the main epigenetic modifications in the eukaryotic genome and has been shown to play a role in cell-type specific regulation of gene expression, and therefore cell-type identity. Bisulfite sequencing is the gold-standard for measuring methylation over the genomes of interest. Here, we review several techniques used for the analysis of high-throughput bisulfite sequencing. We introduce specialized short-read alignment techniques as well as pre/post-alignment quality check methods to ensure data quality. Furthermore, we discuss subsequent analysis steps after alignment. We introduce various differential methylation methods and compare their performance using simulated and real bisulfite-sequencing datasets. We also discuss the methods used to segment methylomes in order to pinpoint regulatory regions. We introduce annotation methods that can be used further classification of regions returned by segmentation or differential methylation methods. Lastly, we review software packages that implement strategies to efficiently deal with large bisulfite sequencing datasets locally and also discuss online analysis workflows that do not require any prior programming skills. The analysis strategies described in this review will guide researchers at any level to the best practices of bisulfite sequencing analysis

Direct and indirect band gaps in Ge under biaxial tensile strain investigated by photoluminescence and photoreflectance studies

Germanium is an indirect semiconductor which attracts particular interest as an electronics and photonics material due to low indirect-to-direct band separation. In this work we bend the bands of Ge by means of biaxial tensile strain in order to achieve a direct band gap. Strain is applied by growth of Ge on a lattice mismatched InGaAs buffer layer with variable In content. Band structure is studied by photoluminescence and photoreflectance, giving the indirect and direct bands of the material. Obtained experimental energy band values are compared with a k p simulation. Photoreflectance spectra are also simulated and compared with the experiment. The obtained results indicate direct band structure obtained for a Ge sample with 1.94 % strain applied, with preferable Γ valley to heavy hole transition

Voronoia: analyzing packing in protein structures

The packing of protein atoms is an indicator for their stability and functionality, and applied in determining thermostability, in protein design, ligand binding and to identify flexible regions in proteins. Here, we present Voronoia, a database of atomic-scale packing data for protein 3D structures. It is based on an improved Voronoi Cell algorithm using hyperboloid interfaces to construct atomic volumes, and to resolve solvent-accessible and -inaccessible regions of atoms. The database contains atomic volumes, local packing densities and interior cavities calculated for 61 318 biological units from the PDB. A report for each structure summarizes the packing by residue and atom types, and lists the environment of interior cavities. The packing data are compared to a nonredundant set of structures from SCOP superfamilies. Both packing densities and cavities can be visualized in the 3D structures by the Jmol plugin. Additionally, PDB files can be submitted to the Voronoia server for calculation. This service performs calculations for most full-atomic protein structures within a few minutes. For batch jobs, a standalone version of the program with an optional PyMOL plugin is available for download. The database can be freely accessed at: http://bioinformatics.charite.de/voronoia

SuperScent—a database of flavors and scents

Volatiles are efficient mediators of chemical communication acting universally as attractant, repellent or warning signal in all kingdoms of life. Beside this broad impact volatiles have in nature, scents are also widely used in pharmaceutical, food and cosmetic industries, so the identification of new scents is of great industrial interest. Despite this importance as well as the vast number and diversity of volatile compounds, there is currently no comprehensive public database providing information on structure and chemical classification of volatiles. Therefore, the database SuperScent was established to supply users with detailed information on the variety of odor components. The version of the database presented here comprises the 2D/3D structures of approximately 2100 volatiles and around 9200 synonyms as well as physicochemical properties, commercial availability and references. The volatiles are classified according to their origin, functionality and odorant groups. The information was extracted from the literature and web resources. SuperScent offers several search options, e.g. name, Pubchem ID number, species, functional groups, or molecular weight. SuperScent is available online at: http://bioinformatics.charite.de/superscent

Influence of Dynamic Ozone Dry Deposition on Ozone Pollution

Identifying the contributions of chemistry and transport to observed ozone pollution using regional-to-global models relies on accurate representation of ozone dry deposition. We use a recently developed configuration of the NOAA GFDL chemistry-climate model - in which the atmosphere and land are coupled through dry deposition-to investigate the influence of ozone dry deposition on ozone pollution over northern midlatitudes. In our model, deposition pathways are tied to dynamic terrestrial processes, such as photosynthesis and water cycling through the canopy and soil. Small increases in winter deposition due to more process-based representation of snow and deposition to surfaces reduce hemispheric-scale ozone throughout the lower troposphere by 5-12 ppb, improving agreement with observations relative to a simulation with the standard configuration for ozone dry deposition. Declining snow cover by the end of the 21st-century tempers the previously identified influence of rising methane on winter ozone. Dynamic dry deposition changes summer surface ozone by -4 to +7 ppb. While previous studies emphasize the importance of uptake by plant stomata, new diagnostic tracking of depositional pathways reveals a widespread impact of nonstomatal deposition on ozone pollution. Daily variability in both stomatal and nonstomatal deposition contribute to daily variability in ozone pollution. Twenty-first century changes in summer deposition result from a balance among changes in individual pathways, reflecting differing responses to both high carbon dioxide (through plant physiology versus biomass accumulation) and water availability. Our findings highlight a need for constraints on the processes driving ozone dry deposition to test representation in regional-to-global models.Peer reviewe

Small-molecule conversion of toxic oligomers to nontoxic β-sheet-rich amyloid fibrils

Several lines of evidence indicate that prefibrillar assemblies of amyloid-{beta} (A{beta}) polypeptides, such as soluble oligomers or protofibrils, rather than mature, end-stage amyloid fibrils cause neuronal dysfunction and memory impairment in Alzheimer's disease. These findings suggest that reducing the prevalence of transient intermediates by small molecule-mediated stimulation of amyloid polymerization might decrease toxicity. Here we demonstrate the acceleration of A{beta} fibrillogenesis through the action of the orcein-related small molecule O4, which directly binds to hydrophobic amino acid residues in A{beta} peptides and stabilizes the self-assembly of seeding-competent, {beta}-sheet-rich protofibrils and fibrils. Notably, the O4-mediated acceleration of amyloid fibril formation efficiently decreases the concentration of small, toxic A{beta} oligomers in complex, heterogeneous aggregation reactions. In addition, O4 treatment suppresses inhibition of long-term potentiation by A{beta} oligomers in hippocampal brain slices. These results support the hypothesis that small, diffusible prefibrillar amyloid species rather than mature fibrillar aggregates are toxic for mammalian cells

RHYTHM—a server to predict the orientation of transmembrane helices in channels and membrane-coils

RHYTHM is a web server that predicts buried versus exposed residues of helical membrane proteins. Starting from a given protein sequence, secondary and tertiary structure information is calculated by RHYTHM within only a few seconds. The prediction applies structural information from a growing data base of precalculated packing files and evolutionary information from sequence patterns conserved in a representative dataset of membrane proteins (‘Pfam-domains’). The program uses two types of position specific matrices to account for the different geometries of packing in channels and transporters (‘channels’) or other membrane proteins (‘membrane-coils’). The output provides information on the secondary structure and topology of the protein and specifically on the contact type of each residue and its conservation. This information can be downloaded as a graphical file for illustration, a text file for analysis and statistics and a PyMOL file for modeling purposes. The server can be freely accessed at: URL: http://proteinformatics.de/rhyth

Primary versus secondary contributions to particle number concentrations in the European boundary layer

It is important to understand the relative contribution of primary and secondary particles to regional and global aerosol so that models can attribute aerosol radiative forcing to different sources. In large-scale models, there is considerable uncertainty associated with treatments of particle formation (nucleation) in the boundary layer (BL) and in the size distribution of emitted primary particles, leading to uncertainties in predicted cloud condensation nuclei (CCN) concentrations. Here we quantify how primary particle emissions and secondary particle formation influence size-resolved particle number concentrations in the BL using a global aerosol microphysics model and aircraft and ground site observations made during the May 2008 campaign of the European Integrated Project on Aerosol Cloud Climate Air Quality Interactions (EUCAARI). We tested four different parameterisations for BL nucleation and two assumptions for the emission size distribution of anthropogenic and wildfire carbonaceous particles. When we emit carbonaceous particles at small sizes (as recommended by the Aerosol Intercomparison project, AEROCOM), the spatial distributions of campaign-mean number concentrations of particles with diameter >50 nm (N50) and >100 nm (N100) were well captured by the model (R2≥0.8) and the normalised mean bias (NMB) was also small (−18% for N50 and −1% for N100). Emission of carbonaceous particles at larger sizes, which we consider to be more realistic for low spatial resolution global models, results in equally good correlation but larger bias (R2≥0.8, NMB = −52% and −29%), which could be partly but not entirely compensated by BL nucleation. Within the uncertainty of the observations and accounting for the uncertainty in the size of emitted primary particles, BL nucleation makes a statistically significant contribution to CCN-sized particles at less than a quarter of the ground sites. Our results show that a major source of uncertainty in CCN-sized particles in polluted European air is the emitted size of primary carbonaceous particles. New information is required not just from direct observations, but also to determine the "effective emission size" and composition of primary particles appropriate for different resolution models

Reasons for (Non)Participating in a Telephone-Based Intervention Program for Families with Overweight Children

Willingness to participate in obesity prevention programs is low; underlying reasons are poorly understood. We evaluated reasons for (non)participating in a novel telephone-based obesity prevention program for overweight children and their families. percentile) aged 3.5–17.4 years were screened via the CrescNet database, a representative cohort of German children, and program participation (repetitive computer aided telephone counseling) was offered by their local pediatrician. Identical questionnaires to collect baseline data on anthropometrics, lifestyle, eating habits, sociodemographic and psychosocial parameters were analyzed from 433 families (241 participants, 192 nonparticipants). Univariate analyses and binary logistic regression were used to identify factors associated with nonparticipation. percentile) was higher in participants (58.9% vs.38%,p<0.001). Participating girls were younger than boys (8.8 vs.10.4 years, p<0.001). 87.3% and 40% of participants, but only 72.2% and 24.7% of nonparticipants, respectively, reported to have regular breakfasts (p = 0.008) and 5 regular daily meals (p = 0.003). Nonparticipants had a lower household-net-income (p<0.001), but higher subjective physical wellbeing than participants (p = 0.018) and believed that changes in lifestyle can be made easily (p = 0.05).An important reason for nonparticipation was non-awareness of their child's weight status by parents. Nonparticipants, who were often low-income families, believed that they already perform a healthy lifestyle and had a higher subjective wellbeing. We hypothesize that even a low-threshold intervention program does not reach the families who really need it