Dataset Information

Analysis of 58 Families of Holins Using a Novel Program, PhyST.

ABSTRACT: We have designed a freely accessible program, PhyST, which allows the automated characterization of any family of homologous proteins within the Transporter Classification Database. The program performs an NCBI-PSI-BLAST search and reports (1) the average protein sequence length with standard deviations, (2) the average predicted number of transmembrane segments, (3) the total number of homologues retrieved, (4) a quantitative list of all source phyla, and (5) potential fusion proteins of sizes considerably exceeding the average size of the proteins retrieved. We have applied this program to 58 families of holins, and the results are presented. The results show that holins are very rarely fused to other protein domains, suggesting that holins form transmembrane pores as homooligomers without the participation of other proteins or protein domains.

SUBMITTER: Kuppusamykrishnan H

PROVIDER: S-EPMC5591648 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Analysis of 58 Families of Holins Using a Novel Program, PhyST.

Kuppusamykrishnan Harikrishnan H Chau Larry M LM Moreno-Hagelsieb Gabriel G Saier Milton H MH

Journal of molecular microbiology and biotechnology 20160824 6

We have designed a freely accessible program, PhyST, which allows the automated characterization of any family of homologous proteins within the Transporter Classification Database. The program performs an NCBI-PSI-BLAST search and reports (1) the average protein sequence length with standard deviations, (2) the average predicted number of transmembrane segments, (3) the total number of homologues retrieved, (4) a quantitative list of all source phyla, and (5) potential fusion proteins of sizes ...[more]

PMID: 27553295

Similar Datasets

Project description:BackgroundThe Strengthening Families Program (SFP) is an evidence-based parent training and youth life skills and drug prevention program traditionally delivered in group settings. Families attend parent and youth classes conducted by trained facilitators. Recently, a 2-disk home-use DVD series was created with the same SFP skills as the group classes for parents and the youth to watch together at home. Additional lesson material was added that included healthy brain development, school success, anger management, dangers of alcohol and drugs, and mindfulness. The SFP DVD reduces SFP delivery costs for agencies and logistic burdens to families. Creative applications of the DVD include holding SFP DVD family discussion groups of multiple families and using SFP DVD video clips as part of a shorter 10-week group class version for parents and the youth.ObjectiveThis study aimed to examine three different DVD implementation scenarios using a noninferiority trial, contrasting target outcomes with an age-matched sample culled from a national norm database of families who completed a standard SFP 14-week class.MethodsThe partial eta-square was used to compare effect sizes between the different delivery modalities for relevant programmatic outcomes. We adjusted the effect sizes by demographic measures to determine whether there were site-specific features influencing program outcomes.ResultsFor the unadjusted effect size comparisons, 13 of the 15 indicated that the home-use DVD outperformed group norms with an average 0.13 effect size estimate difference across the comparisons (28% improvement in the effect size for DVD condition). Comparisons of the home-use DVD condition with the mixed DVD use conditions showed no discernable pattern where one condition consistently outperformed another. Adjusted effect sizes still reinforced the superiority of the DVD conditions; however, there was some shrinkage in the effect sizes as expected with the inclusion of relevant covariates.ConclusionsThe home-use DVD shows that it is possible to effectively deliver an affordable family-based intervention using alternative technology outside of the traditional group-based class format. In almost all of the comparisons, the DVD conditions outperformed the group norms, underscoring that low-cost DVDs or viewing the videos on the Web may provide a useful surrogate for costly group-based formats. Future studies may want to improve on the quasi-experimental design by examining programmatic differences based on delivery format using a randomized controlled trial, thus strengthening the causal framework regarding program effects. In addition, the assessment protocol relied on retrospective reporting, which, although this can limit response shift bias, does not separate data collection in time as with a true pre- and posttest design.

Project description:Coevolutionary networks can encapsulate information about the dynamics of presence and absence of gene families in organisms. Analysis of such networks should reveal fundamental principles underlying the evolution of cellular systems and the functionality of sets of genes. In this study, we describe a new approach for analyzing coevolutionary networks. Our method detects Mutually Exclusive Orthologous Modules (MEOMs). A MEOM is composed of two sets of gene families, each including gene families that tend to appear in the same organisms, such that the two sets tend to mutually exclude each other (if one set appears in a certain organism the second set does not). Thus, a MEOM reflects the evolutionary replacement of one set of genes by another due to reasons such as lineage/environmental specificity, incompatibility, or functional redundancy. We use our method to analyze a coevolutionary network that is based on 383 microorganisms from the three domains of life. As we demonstrate, our method is useful for detecting meaningful evolutionary clades of organisms as well as sets of proteins that interact with each other. Among our results, we report that: 1) MEOMs tend to include gene families whose cellular functions involve transport, energy production, metabolism, and translation, suggesting that changes in the metabolic environments that require adaptation to new sources of energy are central triggers of complex/pathway replacement in evolution. 2) Many MEOMs are related to outer membrane proteins, such proteins are involved in interaction with the environment and could thus be replaced as a result of adaptation. 3) MEOMs tend to separate organisms with large phylogenetic distance but they also separate organisms that live in different ecological niches. 4) Strikingly, although many MEOMs can be identified, there are much fewer cases where the two cliques in the MEOM completely mutually exclude each other, demonstrating the flexibility of protein evolution. 5) CO dehydrogenase and thymidylate synthase and the glycine cleavage genes mutually exclude each other in archaea; this may represent an alternative route for generation of methyl donors for thymidine synthesis.

Dataset Information

Analysis of 58 Families of Holins Using a Novel Program, PhyST.

Publications

Analysis of 58 Families of Holins Using a Novel Program, PhyST.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets