Biology subjects

McKay, L.

Publications and source records attributed to McKay, L..

6 recordsLinked to original sources

bioRxiv2025

Genetic evidence for a periplasmic protein as a component for a subset of NtrYX two-component systems

PlrSR, a member of the NtrYX family of two-component regulatory systems (TCSs), is required for the classical bordetellae, including the causative agent of whooping cough, Bordetella pertussis, to persist in the lower respiratory tract. The plrSR genes are in the middle of a six-gene cluster whose regulation and roles during infection were unknown. rsmB and plrP are often found 5 to plrSR homologs in {beta}- and {gamma}- proteobacteria, while trkAH are often found 3 to plrSR homologs in -proteobacteria. We investigated these genes to determine if they have a functional link to plrSR. We found that this gene cluster does not function as an operon. Rather, it contains two internal promoters: a weaker promoter in the 3 end of rsmB and a stronger promoter in the 3 end of plrS. Additionally, our results indicate that PlrP functions as a third component of the PlrSR TCS. Genetic manipulations of plrP, plrS, and plrR indicate that PlrP is essential in vitro and inhibits PlrS phosphatase activity, likely through PlrSs PDC domain. Since our results indicate that PlrR can be phosphorylated by another unknown phosphodonor in vitro, limiting PlrS phosphatase activity ensures PlrR[~]P is not dephosphorylated to lethally low levels. Using natural-host models, we determined that high levels of PlrR[~]P are required for in vivo survival, and PlrP affects PlrS activity in vivo. Given that plrP homologs always colocalize with ntrYX homologs, we propose that PlrP may fulfill similar functions in other {beta}- and {gamma}-proteobacteria that encode NtrYX- family TCSs, including nonpathogens. ImportanceBordetella species, including B. pertussis, the causal agent of whooping cough, cause respiratory infections in humans and other animals. Their PlrSR two component regulatory systems, members of the NtrYX family, are required for survival in the lower respiratory tract. We characterized the six-gene cluster that includes plrS and plrR, identifying one promoter within the first gene that drives expression of the second gene, which we named plrP, as well as plrS, and another promoter near the 3 end of plrS that drives expression of plrR and the downstream trkAH genes. Our data indicate that the plrP gene product is an essential third component of the PlrSR TCS, functioning to prevent PlrS from acting as a strong phosphatase in vitro. Comparative analyses suggest that PlrP homologs are present, and may function similarly, in NtrYX-family TCSs in other {beta}- and {gamma}-proteobacteria. Our results are important because they provide insight into how bacteria sense and respond to their environment, including those they experience while causing human infection, and this understanding could inform therapeutic and vaccine development.

microbiology↗

bioRxiv2022

A pan-variant mRNA-LNP T cell vaccine protects HLA transgenic mice from mortality after infection with SARS-CoV-2 Beta

Clinically licensed COVID-19 vaccines ameliorate viral infection by inducing vaccinee production of neutralizing antibodies that bind to the SARS-CoV-2 Spike protein to inhibit viral cellular entry (Walsh et al., 2020; Baden et al., 2021), however the clinical effectiveness of these vaccines is transitory as viral variants arise that escape antibody neutralization (Tregoning et al., 2021; Willett et al., 2022). Vaccines that solely rely upon a T cell response to combat viral infection could be transformational because they can be based on highly conserved short peptide epitopes that hold the potential for pan-variant immunity, but a mRNA-LNP T cell vaccine has not been shown to be sufficient for effective antiviral prophylaxis. Here we show that a mRNA-LNP vaccine based on highly conserved short peptide epitopes activates a CD8+ and CD4+ T cell response that prevents mortality in HLA-A*02:01 transgenic mice infected with the SARS-CoV-2 Beta variant of concern (B.1.351). In mice vaccinated with the T cell vaccine, 24% of the nucleated cells in lung were CD8+ T cells on day 7 post infection. This was 5.5 times more CD8+ T cell infiltration of the lungs in response to infection compared to the Pfizer-BioNTech Comirnaty(R) vaccine. Between days 2 and 7 post infection, the number of CD8+ T cells in the lung increased in mice vaccinated with the T cell vaccine and decreased in mice vaccinated with Comirnaty(R). The T cell vaccine did not produce neutralizing antibodies, and thus our results demonstrate that SARS-CoV-2 viral infection can be controlled by a T cell response alone. Our results suggest that further study is merited for pan-variant T cell vaccines, and that T cell vaccines may be relevant for individuals that cannot produce neutralizing antibodies or to help mitigate Long COVID.

immunology↗

bioRxiv2022

Comparative pathogenicity of SARS-CoV-2 Omicron and Delta variants in Syrian hamsters mirrors the attenuated clinical outlook of Omicron in COVID-19 irrespective of age

Coronavirus disease 2019 continues to batter the world with the unceasing introduction of new variants of the causative virus, SARS-CoV-2. In order to understand differences in disease caused by variants of concern and to develop variant-specific vaccines, suitable small animal models are required that mimic disease progression in humans at various stages of life. In this study, we compared the dynamics of infection with two SARS-CoV-2 variants of concern (Delta and Omicron) in aged (>1 year 3 months old) and young (<5 weeks old) Syrian hamsters (Mesocricetus auratus). We show that no weight loss occurred in Omicron infected groups regardless of age, while infection with the Delta variant caused weight loss of up to 10% by day 7 post-infection with slower and incomplete recovery in the aged group. Omicron replicated to similar levels as Delta in the lungs, trachea and nasal turbinates, with no significant differences in the tissue viral loads of aged versus young animals for either variant. In contrast to rare necrosis observed in Omicron-infected animals regardless of age, severe necrosis was observed in the olfactory epithelium in Delta-infected animals. Omicron infection also resulted in mild pulmonary disease in both young and aged animals compared to the moderate acute necrotizing bronchointerstitial pneumonia seen in Delta-infected animals. These results suggest that Omicron infection results in an attenuated clinical disease outlook in Syrian hamsters compared to infection with the Delta variant irrespective of age.

microbiology↗

bioRxiv2021

Memory B cell repertoire for recognition of evolving SARS-CoV-2 spike

Memory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted memory B cell receptor-encoded monoclonal antibodies (mAbs) from 19 COVID-19 convalescent subjects against SARS-CoV-2 spike (S) and found 7 major mAb competition groups against epitopes recurrently targeted across individuals. Inclusion of published and newly determined structures of mAb-S complexes identified corresponding epitopic regions. Group assignment correlated with cross-CoV-reactivity breadth, neutralization potency, and convergent antibody signatures. mAbs that competed for binding the original S isolate bound differentially to S variants, suggesting the protective importance of otherwise-redundant recognition. The results furnish a global atlas of the S-specific memory B cell repertoire and illustrate properties conferring robustness against emerging SARS-CoV-2 variants.

immunology↗

bioRxiv2020

The Guaymas Basin Subseafloor Sedimentary Archaeome Reflects Complex Environmental Histories

We explore archaeal distribution and environmental niche differentiation in sedimentary subseafloor habitats of Guaymas Basin and the adjacent Sonora Margin, located in the Gulf of California, Mexico. Specifically, we survey diverse subseafloor habitats on the Guaymas Basin flanking regions that are extending from the spreading center, termed here "off-axis" sites. Sampling locations include (i) control sediments without hydrothermal or seep influence, (ii) Sonora Margin sediments underlying oxygen minimum zone water, (iii) compacted, highly reduced sediments from a pressure ridge with numerous seeps at the base of the Sonora Margin, and (iv) sediments impacted by hydrothermal circulation at the off-axis Ringvent site. Generally, archaeal 16S rRNA gene datasets are largely comprised of Bathyarchaeal lineages, members of the Hadesarchaea, MBG-D, TMEG, and ANME-1 groups. The most frequently observed 25 OTUs belong to members of these lineages, and correspond to approx. 40 to 80% of the sequence dataset in each sediment sample. Differential distribution patterns of these archaeal groups in downcore sediments uniquely characterize each major sedimentary environment. Variations in archaeal community composition reflect locally specific environmental challenges throughout the greater Guaymas Basin area. Background sediments are divided into surface and subsurface niches, reflecting increased selection of the archaeal community downcore. In sum, the environmental setting and history of a particular site, not isolated biogeochemical properties out of context, control the subseafloor archaeal communities in Guaymas Basin and Sonora Margin sediments.

ecology↗

bioRxiv2019

Framework for determining accuracy of RNA sequencing data for gene expression profiling of single samples

BackgroundThe accuracy of gene expression as measured by RNA sequencing (RNA-Seq) is dependent on the amount of sequencing performed. However, some types of reads are not informative for determining this accuracy. Unmapped and non-exonic reads do not contribute to gene expression quantification. Duplicate reads can be the product of high gene expression or technical errors. FindingsWe surveyed bulk RNA-Seq datasets from 2179 tumors in 48 cohorts to determine the fractions of uninformative reads. Total sequence depth was 0.2-668 million reads (median (med.) 61 million; interquartile range (IQR) 53 million). Unmapped reads constitute 1-77% of all reads (med. 3%; IQR 3%); duplicate reads constitute 3-100% of mapped reads (med. 27%; IQR 30%); and non-exonic reads constitute 4-97% of mapped, non-duplicate reads (med. 25%; IQR 21%). Informative reads--Mapped, Exonic, Non-duplicate (MEND) reads--constitute 0-79% of total reads (med. 50%; IQR 31%). Further, we find that MEND read counts have a 0.22 Pearson correlation to the number of genes expressed above 1 Transcript Per Million, while total reads have a correlation of -0.05. ConclusionsSince the fraction of uninformative reads vary, we propose using only definitively informative reads, MEND reads, for the purposes of asserting the accuracy of gene expression measured in a bulk RNA-Seq experiment. We provide a Docker image containing 1) the existing required tools (RSeQC, sambamba and samblaster) and 2) a custom script. We recommend that all results, sensitivity studies and depth recommendations use MEND units.

genomics↗