Biology subjects

Davis, W. C.

Publications and source records attributed to Davis, W. C..

5 recordsLinked to original sources

bioRxiv2024

Ability of mycobacterial pathogens to establish a persistent infection is lost by deletion of a single gene, rel, regulator of the stringent response

Studies in a mouse model revealed Mycobacterium tuberculosis (Mtb) with a deletion of rel, regulator of the stringent response, could not establish a persistent infection. Studies in cattle with a Mycobacterium. a. paratuberculosis rel deletion mutant revealed inability to establish a persistent infection was associated with development of CD8 cytotoxic T cells (CTL) that kill intracellular bacteria. Further comparative studies ex vivo with Mbv Calmette-Guerin (BCG) and a BCG rel deletion mutant revealed no clear difference in development of CTL in vitro. As reported, a study of the recall response was conducted with cattle vaccinated with either BCG or with BCGrel, to determine if information could be obtained that would show how gene products under control of rel interfere with the CTL response to mycobacterial pathogens in vivo. The study revealed the CTL response elicited by vaccination with BCG was impaired, in comparison with the response elicited by BCGrel. Comparative analysis of the recall response ex vivo revealed the functional impairment was not associated with the timing of appearance of the recall response, expression of IFN-{gamma}, TNF-, IL-17, or IL-22, or molecules that mediate intracellular killing. Further studies are needed to determine how CD8 CTL functional activity is modulated in vivo by gene products regulated by rel.

immunology↗

bioRxiv2023

Vaccination of cattle with a virus-vectored vaccine against a major membrane protein of Mycobacterium a. subsp. paratuberculosis elicits CD8 cytotoxic T cells that kill intracellular bacteria

Infection of cattle with Mycobacterium a. subsp. Paratuberculosis (Map), the causative agent of paratuberculosis, induces an immune response directed toward a 35 kD major membrane protein (MMP) of Map. CD8 cytotoxic T cells (CTL) are elicited when peripheral blood mononuclear cells from healthy cattle are incubated ex vivo with antigen-presenting cells (APC) primed with bacterial recombinant MMP. Ex vivo development of CTL was MHC-restricted and required the presence of both CD4 and CD8 T cells. The gene MAP2121c, encoding MMP, was modified to express a modified form of MMP (p35NN) in a mammalian cell line, also capable of eliciting an ex vivo CTL response. In the present study, the modified gene for p35NN was placed into a BoHV4 vector to determine the potential use of BoHV-4A{Delta}TK-p35NN as a peptide-based vaccine. Subcutaneous vaccination of healthy cattle with BoHV-4A{Delta}TK-p35NN elicited a CTL recall response, as detected ex vivo. Further studies are warranted to conduct a challenge study to determine if CD8 CTL elicited by vaccination with BoHV-4A{Delta}TK-p35NN prevents the establishment of a persistent infection by Map.

immunology↗

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↗

bioRxiv2019

Cognate epitope recognition by bovine CD4 and CD8 T cells is essential for primary expansion of antigen-specific cytotoxic T-cells following ex vivo stimulation with a candidate Mycobacterium avium subsp. paratuberculosis peptide vaccine.

Studies in cattle show CD8 cytotoxic T cells (CTL), with the ability to kill intracellular bacteria, develop following stimulation of monocyte-depleted peripheral blood mononuclear cells (mdPBMC) with conventional dendritic cells (cDC) and monocyte-derived DC (MoDC) pulsed with MMP, a membrane protein from Mycobacterium avium subsp. paratuberculosis (Map) encoded by MAP2121c. CTL activity was diminished if CD4 T cells were depleted from mdPBMC before antigen (Ag) presentation by cDC and MoDC, suggesting simultaneous cognate recognition of MMP epitopes presented by MHC I and MHC II molecules might be essential for development of CTL activity. To clarify whether cognate recognition is essential for CTL development, studies were conducted with mdPBMC cultures in the presence of monoclonal antibodies (mAbs) specific for MHC class I and MHC class II molecules. The CTL response of mdPBMC to MMP-pulsed DC was completely blocked in the presence of mAbs to both MHC I and II molecules and also blocked in the presence of mAbs to either MHC I or MHC II. The results demonstrate CD4 T-cell help is essential for development of a primary CTL response to MMP, and indicate that cognate recognition is required for delivery of CD4 T-cell help during priming. Of importance, the findings provide support for the importance of CD4 and CD8 T-cell cognate antigen recognition in eliciting CTL responses to vaccines against intracellular pathogens. The methods described herein can be used to elucidate the intracellular interactions between lymphocytes and DC in humans and cattle.

immunology↗

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↗