Biology subjects

Neely, B. A.

Publications and source records attributed to Neely, B. A..

9 recordsLinked to original sources

bioRxiv2026

Proteomic comparison of Marburg and Kasokero virus infection in natural host Egyptian rousette bat reveals distinct antiviral pathways

Bats are natural reservoir hosts for numerous zoonotic viruses, yet the molecular mechanisms enabling viral persistence without overt disease remain incompletely understood. The Egyptian rousette bat (Rousettus aegyptiacus, ERB) is the sole known natural reservoir of Marburg virus (MARV) and a key host in the enzootic cycle of the tick-borne Kasokero virus (KASV), providing a unique system to compare host responses to different RNA viruses within the same species. Here, we applied serial cross-sectional serum proteomics integrated with tissue-specific viral kinetics to characterize systemic host responses to experimental MARV and KASV infection in captive-reared bats. Nearly 16 % of detected proteins (67/419) were found exclusively in infected animals, yet canonical acute inflammatory signatures driving pathology in other susceptible hosts were absent (e.g., in humans and non-human primates). Differential abundance and detection analyses identified both shared and virus-dependent responses, with MARV infection eliciting limited and transient perturbations, while KASV induced broader and more sustained engagement of complement, lectin pathway, and hepatometabolic proteins. Network-based analysis uncovered coordinated proteasome modules, including circulating immunoproteasome complexes, consistent with enhanced antigen-processing capacity is a feature of these virus-host dynamics. Together, these findings reveal how ERBs mount structured, virus-dependent systemic responses, offering new insight into mechanisms underlying viral infection in natural reservoir hosts.

systems biology↗

bioRxiv2024

Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions

Domoic acid is a neurotoxin secreted by the marine diatom genus, Pseudo-nitzschia, during toxic algal bloom events. California sea lions (Zalophus californianus) are exposed to domoic acid through ingestion of fish that feed on toxic diatoms, resulting in a domoic acid toxicosis (DAT), which can vary from mild to fatal. Sea lions with mild disease can be treated if toxicosis is detected early after exposure, therefore, rapid diagnosis of DAT is essential but also challenging. In this work, we performed multi-omics analyses, specifically proteomic and lipidomic, on blood samples from 31 California sea lions. Fourteen sea lions were diagnosed with DAT based on clinical signs and postmortem histological examination of brain tissue, and 17 had no evidence of DAT. Proteomic analyses revealed three apolipoproteins with statistically significant lower abundance in the DAT individuals compared to the non-DAT individuals. These proteins are known to transport lipids in the blood. Lipidomic analyses highlighted 29 lipid levels that were statistically different in the DAT versus non-DAT comparison, 28 of which were downregulated while only one was upregulated. Furthermore, of the 28 downregulated lipids, 15 were triglycerides, illustrating their connection with the perturbed apolipoproteins and showing their potential for use in rapid DAT diagnoses. SYNOPSISMulti-omics evaluations reveal blood apolipoproteins and triglycerides are altered in domoic acid toxicosis in California sea lions. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/592757v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@b61289org.highwire.dtl.DTLVardef@17ae9f7org.highwire.dtl.DTLVardef@96904eorg.highwire.dtl.DTLVardef@dc299a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions (Zalophus californianus)

Since 1998, California sea lion (Zalophus californianus) stranding events associated with domoic acid toxicosis have consistently increased. Outside of direct measurement of DA in bodily fluids at the time of stranding, currently there are no practical non-lethal clinical tests for the diagnosis of domoic acid toxicosis (DAT) that can be utilized in a large-scale rehabilitation facility. Proteomic analysis was conducted to discover candidate protein markers of DAT using cerebrospinal fluid from stranded California sea lions with acute DAT (n = 8), chronic DAT (n = 19), or without DAT (n = 13). A total of 2005 protein families were identified experiment-wide (FDR < 0.01). Of these proteins, 83 were significantly different in abundance across the three groups (adj. p < 0.05). Cytoplasmic malate dehydrogenase (MDH1), 5-3 exonuclease PLD3, disintegrin and metalloproteinase domain-containing protein 22 (ADAM22), 14-3-3 protein gamma (YWHAG), neurosecretory protein VGF, and calsyntenin-1 (CLSTN1) were able to discriminate California sea lions with or without DAT (ROC > 0.75). Immunoglobulin kappa light chain-like (IGKV2D-28), receptor-type tyrosine-phosphatase F (PTRPF), kininogen-1 (KNG1), prothrombin (F2), and beta-synuclein (SNCB) were able to discriminate acute DAT from chronic DAT (ROC > 0.75). Interestingly, proteins involved in alpha synuclein deposition were over- represented as classifiers of DAT and many of these proteins have been implicated in a variety of neurodegenerative diseases. These proteins should be considered potential markers for DAT in California sea lions, as well as markers to discriminate between acute or chronic DAT, and should be considered priority for future validation studies as biomarkers. All MS data have been deposited in the ProteomeXchange with identifier PXD041356 (http://proteomecentral.proteomexchange.org/dataset/PXD041356).

biochemistry↗

bioRxiv2022

Serum proteomics identifies immune pathways and candidate biomarkers of coronavirus infection in wild vampire bats

The apparent ability of bats to harbor many virulent viruses without showing disease is likely driven by distinct immune responses that coevolved with mammalian flight and the exceptional longevity of this order. Yet our understanding of the immune mechanisms of viral tolerance is restricted to a small number of bat-virus relationships and remains poor for coronaviruses (CoVs), despite their relevance to human health. Proteomics holds particular promise for illuminating the immune factors involved in bat responses to infection, because it can accommodate especially low sample volumes (e.g., sera) and thus can be applied to both large and small bat species as well as in longitudinal studies where lethal sampling is necessarily limited. Further, as the serum proteome includes proteins secreted from not only blood cells but also proximal organs, it provides a more general characterization of immune proteins. Here, we expand our recent work on the serum proteome of wild vampire bats (Desmodus rotundus) to better understand CoV pathogenesis. Across 19 bats sampled in 2019 in northern Belize with available sera, we detected CoVs in oral or rectal swabs from four individuals (21.1% positivity). Phylogenetic analyses identified all vampire bat sequences as novel -CoVs most closely related to known human CoVs. Across 586 identified serum proteins, we found no strong differences in protein composition nor abundance between uninfected and infected bats. However, receiver operating characteristic curve analyses identified seven to 32 candidate biomarkers of CoV infection, including AHSG, C4A, F12, GPI, DSG2, GSTO1, and RNH1. Enrichment analyses using these protein classifiers identified downregulation of complement, regulation of proteolysis, immune effector processes, and humoral immunity in CoV-infected bats alongside upregulation of neutrophil immunity, overall granulocyte activation, myeloid cell responses, and glutathione processes. Such results denote a mostly cellular immune response of vampire bats to CoV infection and identify putative biomarkers that could provide new insights into CoV pathogenesis in wild and experimental populations. More broadly, applying a similar proteomic approach across diverse bat species and to distinct life history stages in target species could improve our understanding of the immune mechanisms by which wild bats tolerate viruses.

ecology↗

bioRxiv2020

Surveying the vampire bat (Desmodus rotundus) serum proteome: a resource for identifying immunological proteins and detecting pathogens

Bats are increasingly studied as model systems for longevity and as natural hosts for some virulent viruses. Yet our ability to characterize immune mechanisms of viral tolerance and to quantify infection dynamics in wild bats is often limited by small sample volumes and few species-specific reagents. Here, we demonstrate how proteomics can overcome these limitations by using data-independent acquisition-based shotgun proteomics to survey the serum proteome of 17 vampire bats (Desmodus rotundus) from Belize. Using just 2 L of sample and relatively short separations of undepleted serum digests, we identified 361 proteins across five orders of magnitude. Data are available via ProteomeXchange with identifier PXD022885. Levels of immunological proteins in vampire bat serum were then compared to human plasma via published databases. Of particular interest were anti-viral and anti-bacterial components, circulating 20S proteasome complex, and proteins involved in redox activity; whether any results are specific to vampire bats could be assessed by future pan-mammalian analyses. Lastly, we used known virus proteomes to identify Rh186 from Macacine herpesvirus 3 and ORF1a from Middle East respiratory syndrome-related coronavirus, indicating that mass spectrometry-based techniques show promise for pathogen detection. Overall, these results can be used to design targeted mass-spectrometry assays to quantify immunological markers and detect pathogens. More broadly, our findings also highlight the application of proteomics in advancing wildlife immunology and pathogen surveillance.

molecular biology↗

bioRxiv2020

2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study

Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample, as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in core facility settings has been slow. The Association of Biomolecular Resource Facilities conducted a large interlaboratory study to evaluate DIA performance in laboratories with various instrumentation. Participants were supplied with generic methods and a uniform set of test samples. The resulting 49 DIA datasets act as benchmarks and have utility in education and tool development. The sample set consisted of a tryptic HeLa digest spiked with high or low levels of four exogenous proteins. Data are available in MassIVE MSV000086479. Additionally, we demonstrate how the data can be analysed by focusing on two datasets using different library approaches and show the utility of select summary statistics. These data can be used by DIA newcomers, software developers, or DIA experts evaluating performance with different platforms, acquisition settings and skill levels.

bioinformatics↗

bioRxiv2019

Characterization of a Human Liver NIST Reference Material fit for Proteomics Applications

The National Institute of Standards and Technology (NIST) is creating new, economical, qualitative reference materials and data for proteomics comparisons, benchmarking and harmonization. Here we describe a large dataset from shotgun proteomic analysis of RM 8461 Human Liver for Proteomics, a reference material being developed. Consensus identifications using multiple search engines and sample preparations demonstrate a homogeneous and fit-for-purpose material that can be incorporated into automated or manual sample preparation workflows, with the resulting data used to directly assess complete sample-to-data workflows and provide harmonization and benchmarking between laboratories and techniques. Data are available via PRIDE with identifier PXD013608.

biochemistry↗

bioRxiv2018

Proteomic Analysis of Urine from California Sea Lions (Zalophus californianus): a Resource for Urinary Biomarker Discovery

Urinary markers for the assessment of kidney diseases in wild animals are limited, in part, due to the lack of urinary proteome data, especially for marine mammals. One of the most prevalent kidney diseases in marine mammals is caused by Leptospira interrogans, which is the second most common etiology linked to stranding of California sea lions (Zalophus californianus). Urine proteins from eleven sea lions with leptospirosis kidney disease and eight sea lions without leptospirosis or kidney disease were analyzed using shotgun proteomics. In total, 2694 protein groups were identified and 316 were differentially abundant between groups. Major urine proteins in sea lions were similar to major urine proteins in dogs and humans except for the preponderance of resistin, lysozyme C, and PDZ domain containing 1, which appear to be over-represented. Previously reported urine protein markers of kidney injury in humans and animals were also identified. Notably, neutrophil gelatinase-associated lipocalin, osteopontin, and epidermal fatty acid binding protein were elevated over 20-fold in the leptospirosis-infected sea lions. Consistent with leptospirosis infection in rodents, urinary proteins associated with the renin-angiotensin system were depressed, including neprilysin. This study represents a foundation from which to explore the clinical use of urinary protein markers in California sea lions.\n\nAbbreviations

biochemistry↗

bioRxiv2018

Proteomics as a metrological tool to evaluate genome annotation accuracy following de novo genome assembly: a case study using the Atlantic bottlenose dolphin (Tursiops truncatus)

BackgroundThe last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, continued development of genome quality metrics is imperative. The current study utilized the recently updated Atlantic bottlenose dolphin (Tursiops truncatus) genome and annotation to evaluate a proteomics-based metric of genome accuracy.\n\nResultsProteomic analysis of six tissues provided experimental confirmation of 10 402 proteins from 4 711 protein groups, almost 1/3 of the possible predicted proteins in the genome. There was an increased median molecular weight and number of identified peptides per protein using the current T. truncatus annotation versus the previous annotation. Identification of larger proteins with more identified peptides implied reduced database fragmentation and improved gene annotation accuracy. A metric is proposed, NP10, that attempts to capture this quality improvement. When using the new T. truncatus genome there was a 21 % improvement in NP10. This metric was further demonstrated by using a publicly available proteomic data set to compare human genome annotations from 2004, 2013 and 2016, which had a 33 % improvement in NP10.\n\nConclusionsThese results demonstrate that new whole-genome sequencing techniques can rapidly generate high quality de novo genome assemblies and emphasizes the speed of advancing bioanalytical measurements in a non-model organism. Moreover, proteomics may be a useful metrological tool to benchmark genome accuracy, though there is a need for reference proteomic datasets to facilitate this utility in new de novo and existing genomes.

bioinformatics↗