Biology subjects

Nunn, B.

Publications and source records attributed to Nunn, B..

3 recordsLinked to original sources

bioRxiv2020

Survey of metaproteomics software tools for functional microbiome analysis.

To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional role of expressed microbial genes/proteins. This can be accomplished through metaproteomics, which characterizes the protein complement of the microbiome. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, so that researchers can make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental carie plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! Tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN6, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the Universal Protein Knowledgebase revealed that the sensitivity and specificity of functional annotation differed between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated the most precise GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.

bioinformatics↗

bioRxiv2019

Physiological and Molecular Responses Suggest Local Adaptation of the Lobe Coral Porites lobata to the Nearshore Environment

Corals in nearshore marine environments are increasingly exposed to reduced water quality, which is the primary local threat to Hawaiian coral reefs. It is unclear if corals surviving in such conditions have adapted to withstand sedimentation, pollutants, and other environmental stressors. Lobe coral populations from Maunalua Bay, Hawaii showed clear genetic differentiation between the polluted, high-stress nearshore site and the lower-stress offshore site. To understand the driving force of the observed genetic partitioning, reciprocal transplant and common-garden experiments were conducted to assess phenotypic differences between these two populations. Physiological responses were significantly different between the populations, revealing more stress-resilient traits in the nearshore corals. Changes in protein profiles between the two populations highlighted the inherent differences in the cellular metabolic processes and activities; nearshore corals did not significantly alter their proteome between the sites, while offshore corals responded to nearshore transplantation with increased abundances of proteins associated with detoxification, antioxidant defense, and regulation of cellular metabolic processes. The response differences across multiple phenotypes between the populations suggest local adaptation of nearshore corals to reduced water quality. Our results provide insight into corals adaptive potential and its underlying processes, and reveal potential protein biomarkers that could be used to predict resiliency.

ecology↗

bioRxiv2018

Characterization of Pacific oyster (Crassostrea gigas) proteomic response to natural environmental differences

Global climate change is rapidly altering coastal marine ecosystems important for food production. A comprehensive understanding of how organisms will respond to these complex environmental changes can come only from observing and studying species within their natural environment. To this end, the effects of environmental drivers -- pH, dissolved oxygen content, salinity, and temperature -- on Pacific oyster (Crassostrea gigas) physiology were evaluated in an outplant experiment. Sibling juvenile oysters were outplanted to eelgrass and unvegetated habitat at five different estuarine sites within the Acidification Nearshore Monitoring Network in Washington State, USA to evaluate how regional environmental drivers influence molecular physiology. Within each site, we also determined if eelgrass presence that buffered pH conditions changed the oysters expressed proteome. A novel, two-step, gel-free proteomic approach was used to identify differences in protein abundance in C. gigas ctenidia tissue after a 29 day outplant by 1) identifying proteins in a data independent acquisition survey step and 2) comparing relative quantities of targeted environmental response proteins using selected reaction monitoring. While there was no difference in protein abundance detected between habitats or among sites within Puget Sound, C. gigas outplanted at Willapa Bay had significantly higher abundances of antioxidant enzymes and molecular chaperones. Environmental factors at Willapa Bay, such as higher average temperature, may have driven this protein abundance pattern. These findings generate a suite of new hypotheses for lab and field experiments to compare the effects of regional conditions on physiological responses of marine invertebrates.

ecology↗