A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks

De-novo reverse-engineering of genome-scale regulatory networks is an increasingly important objective for biological and translational research. While many methods have been recently developed for this task, their absolute and relative performance remains poorly understood. The present study conducts a rigorous performance assessment of 32 computational methods/variants for de-novo reverse-engineering of genome-scale regulatory networks by benchmarking these methods in 15 high-quality datasets and gold-standards of experimentally verified mechanistic knowledge. The results of this study show that some methods need to be substantially improved upon, while others should be used routinely. Our results also demonstrate that several univariate methods provide a "gatekeeper" performance threshold that should be applied when method developers assess the performance of their novel multivariate algorithms. Finally, the results of this study can be used to show practical utility and to establish guidelines for everyday use of reverse-engineering algorithms, aiming towards creation of automated data-analysis protocols and software systems.     

Quantitative role of p42/44 and p38 in the production and regulation of cytokines TNF-alpha, IL-1beta and IL-12 by murine peritoneal macrophages in vitro by concanavalin A

In the present study the quantitative role of p42/44 and p38 in the production of TNF-alpha, IL-1beta and IL-12 by murine peritoneal macrophages, in vitro, on treatment with Concanavalin A (ConA) has been investigated. Maximum expression/production of cytokines TNF-alpha, IL-1beta and IL-12 was observed after 16 h by RT-PCR and 24 h by ELISA, on in vitro treatment with ConA. To investigate the role of MAP kinases in the production of cytokines, pharmacological inhibitors of MAP kinases--PD98059, SB202190 and SP600125, were used. The expression of TNF-alpha, IL-1beta and IL-12 was down regulated in the presence of PD98059 and SB202190 in a dose dependent manner, suggesting the involvement of p42/44 and p38 in ConA induced production of TNF-alpha, IL-1beta and IL-12 by macrophages. It was observed that SP600125 did not have any effect on the expression of TNF-alpha, IL-1beta and IL-12. Using different combinations of MAPK inhibitors, it was found that 45% signal is conveyed via p42/44 and 25% via p38 in the production of these cytokines, by ConA treated macrophages while 30% signal passes through unidentified pathways.     

DNA methylation in neonates born to women receiving psychiatric care

Prenatal exposure both to maternal psychiatric illness and psychiatric medication has been linked with adverse child outcomes that affect physiological, emotional and psychiatric development. Studies suggest that epigenetic mechanisms, such as DNA methylation, may facilitate these effects. In this report, we explore the association between maternal psychiatric illness and treatment during pregnancy and neonatal DNA methylation patterns in a prospectively-characterized clinical cohort of 201 dyads. Associations between the percent of umbilical cord blood DNA methylated at 27,578 CpG sites and maternal psychiatric diagnosis, symptoms and antidepressant use were evaluated by fitting a separate linear mixed effects model for each CpG site. There were no significant changes in neonatal DNA methylation attributable to maternal psychiatric diagnosis or depressive symptoms during pregnancy. Exposure to an antidepressant medication was associated with differential methylation of CpG sites in TNFRSF21 and CHRNA2 (false discovery rate < 0.05), but the average difference in methylation for both CpG sites was less than 3% between each group. The results were not specific to type of antidepressant or duration of the exposure. This study suggests that there are no large effects of maternal psychiatric illness, depressive symptoms or prenatal exposure to antidepressants on neonatal DNA methylation. Delineation of the influence of maternal psychiatric illness and pharmacological exposures on the developing fetuses has critical implications for clinical care during pregnancy.     

Structure of the integrin alphaIIb transmembrane segment

Integrin cell-adhesion receptors transduce signals bidirectionally across the plasma membrane via the single-pass transmembrane segments of each alpha and beta subunit. While the beta3 transmembrane segment consists of a linear 29-residue alpha-helix, the structure of the alphaIIb transmembrane segment reveals a linear 24-residue alpha-helix (Ile-966 -Lys-989) followed by a backbone reversal that packs Phe-992-Phe-993 against the transmembrane helix. The length of the alphaIIb transmembrane helix implies the absence of a significant transmembrane helix tilt in contrast to its partnering beta3 subunit. Sequence alignment shows Gly-991-Phe-993 to be fully conserved among all 18 human integrin alpha subunits, suggesting that their unusual structural motif is prototypical for integrin alpha subunits. The alphaIIb transmembrane structure demonstrates a level of complexity within the membrane that is beyond simple transmembrane helices and forms the structural basis for assessing the extent of structural and topological rearrangements upon alphaIIb-beta3 association, i.e. integrin transmembrane signaling.     

COPid: composition based protein identification

In the past, a large number of methods have been developed for predicting various characteristics of a protein from its composition. In order to exploit the full potential of protein composition, we developed the web-server COPid to assist the researchers in annotating the function of a protein from its composition using whole or part of the protein. COPid has three modules called search, composition and analysis. The search module allows searching of protein sequences in six different databases. Search results list database proteins in ascending order of Euclidian distance or descending order of compositional similarity with the query sequence. The composition module allows calculation of the composition of a sequence and average composition of a group of sequences. The composition module also allows computing composition of various types of amino acids (e.g. charge, polar, hydrophobic residues). The analysis module provides the following options; i) comparing composition of two classes of proteins, ii) creating a phylogenetic tree based on the composition and iii) generating input patterns for machine learning techniques. We have evaluated the performance of composition-based (or alignment-free) similarity search in the subcellular localization of proteins. It was found that the alignment free method performs reasonably well in predicting certain classes of proteins. The COPid web-server is available at http://www.imtech.res.in/raghava/copid/.     

Behavioural and Electrophysiological Responses of Mosquito Vectors <Emphasis Type="Italic">Aedes aegypti,Anopheles stephensi</Emphasis> and <Emphasis Type="Italic">Culex quinquefasciatus</Emphasis> to an Ethyl Ester: Ethyl 2-aminobenzoate

Mosquito control using different methods remains an integral component of intervention programmes which aim to protect humans from various mosquito-borne diseases. The host seeking behaviour of mosquitoes is essentially guided by odorant receptor neurons housed in the antenna, maxillary palps and proboscis. The odorant receptor neurons are responsible for detecting chemical cues from hosts and also useful for developing sustainable mosquito-control strategies that exploit host-seeking behaviours. The present investigation evaluates host seeking behavioural responses of a novel, non-toxic and environment friendly repellent, ethyl 2-aminobenzoate against three known vector species of mosquitoes viz. Aedes aegypti, Anopheles stephensi and Culex quinquefasciatus maintained in laboratory. The flight orientation of the test mosquitoes was studied using Y-tube olfactometer, whereas the antennae of adult female mosquitoes were used to investigate the effect of ethyl 2-aminobenzoate on the peripheral olfactory system using electroantennogram (EAG). The findings demonstrate that ethyl 2-aminobenzoate exhibited significant response in Y-tube olfactometer against all the three known vector species of mosquitoes. However, only Anopheles stephensi significantly elicited responses in EAG experiments, while the responses obtained for Aedes aegypti and Culex quinquefasciatus were not statistically significant. The results conclude that currently evaluated chemical ethyl 2-aminobenzoate has potential against some well established mosquito vector species and could be exploited to develop new and comparatively more effective anti-mosquito formulations.     

Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial

Advancements in mass spectrometry‐based proteomics have enabled experiments encompassing hundreds of samples. While these large sample sets deliver much‐needed statistical power, handling them introduces technical variability known as batch effects. Here, we present a step‐by‐step protocol for the assessment, normalization, and batch correction of proteomic data. We review established methodologies from related fields and describe solutions specific to proteomic challenges, such as ion intensity drift and missing values in quantitative feature matrices. Finally, we compile a set of techniques that enable control of batch effect adjustment quality. We provide an R package, "proBatch", containing functions required for each step of the protocol. We demonstrate the utility of this methodology on five proteomic datasets each encompassing hundreds of samples and consisting of multiple experimental designs. In conclusion, we provide guidelines and tools to make the extraction of true biological signal from large proteomic studies more robust and transparent, ultimately facilitating reliable and reproducible research in clinical proteomics and systems biology.