Biology subjects

McDonough, K.

Publications and source records attributed to McDonough, K..

5 recordsLinked to original sources

bioRxiv2025

Differential expression of a disease-associated MRE11 variant reveals distinct phenotypic outcomes

The MRE11 DNA nuclease plays central roles in the repair of DNA double-strand breaks (DSBs) as a core component of the heterotrimeric MRE11/RAD50/NBS1 (MRN) complex. MRN localizes to chromosomal DSBs and recruits and activates the apical DSB repair protein kinase, ATM, which phosphorylates downstream substrates to elicit cellular DNA damage responses. Pathogenic variants in MRE11 cause the genome instability disorder ataxia-telangiectasia-like disorder (ATLD). The first ATLD patient allele identified, ATLD1, is a nonsense mutation that deletes 76 amino acids from the MRE11 C-terminus and results in markedly reduced levels of MRE11-ATLD1 and the entire MRN complex. This region of the C-terminus has been demonstrated to function in DNA binding, mediate functional protein interactions, and undergo post-translational modifications that regulate MRE11 nucleolytic activities. We previously demonstrated that transgenic mice expressing low wildtype MRN exhibit severe phenotypes, including small body size, anemia, and cellular DNA DSB repair defects. Thus, it is currently unknown whether reduced MRE11-ATLD1 and MRN levels, loss of the C-terminus, or both cause disease-associated phenotypes. In this study, we generated transgenic mouse models that express near endogenous or significantly reduced levels of MRE11-ATLD1 to determine the in vivo importance of the MRE11 C-terminus. We observe that reduced MRE11-ATLD1 expression leads to anemia, bone marrow failure, extramedullary hematopoiesis, and impaired lymphocyte development, similar to mice expressing low wildtype MRE11. In contrast, higher expression of MRE11-ATLD1 results in a subset of moderate phenotypes, indicating that loss of C-terminus has limited impact on MRN functions in vivo. These findings have implications for clinical predictions of ATLD patients harboring pathogenic MRE11 variants that impair MRE11 function and/or impact MRN protein levels.

genetics↗

bioRxiv2024

Quantitating SARS-CoV-2 Neutralizing Antibodies from Human Dried Blood Spots

BackgroundIn the earliest days of COVID-19 pandemic, the collection of dried blood spots (DBS) enabled public health laboratories to undertake population-scale seroprevalence studies to estimate rates of SARS-CoV-2 exposure. With SARS-CoV-2 seropositivity levels now estimated to exceed 94% in the United States, attention has turned to using DBS to assess functional (neutralizing) antibodies within cohorts of interest. MethodsContrived DBS eluates from convalescent, fully vaccinated and pre-COVID-19 serum samples were evaluated in SARS-CoV-2 plaque reduction neutralization titer (PRNT) assays, a SARS-CoV-2 specific 8-plex microsphere immunoassay, a cell-based pseudovirus assay, and two different spike-ACE2 inhibition assays, an in-house Luminex-based RBD-ACE2 inhibition assay and a commercial real-time PCR-based inhibition assay (NAB-Sure). ResultsDBS eluates from convalescent individuals were compatible with the spike-ACE2 inhibition assays, but not cell-based pseudovirus assays or PRNT. However, the insensitivity of cell-based pseudovirus assays was overcome with DBS eluates from vaccinated individuals with high SARS-CoV-2 antibody titers. ConclusionSARS-CoV-2 neutralizing titers can be derived with confidence from DBS eluates, thereby opening the door to the use of these biospecimens for the analysis of vulnerable populations and normally hard to reach communities.

immunology↗

bioRxiv2023

Imagination as predictive perception: mental imagery predictively biases perceptual judgments of observed action kinematics.

Recent approaches conceptualize mental imagery as a simulatory mode of perceptual experience, which relies on the voluntary engagement of the same top-down prediction processes that shape our perception of the external world. If so, then imagery should induce similar predictive biases as those that are known to govern the perceptual representation of others behaviour. In four experiments, participants saw object-directed approach and avoidance actions and reported the hands last seen location after their sudden disappearance. All revealed robust predictive biases, showing that perceptual judgments are illusorily distorted towards the implied goals of the actions and away from obstacles. Importantly, the experiments also showed that prior action imagery suffices to induce similar biases, so that perceptual judgments become distorted not only towards the actions expected next steps but also the imagined ones. These imagery-induced biases were robust across stimulus sets and measurement methods. They reflect prior knowledge of how people move and can be induced not only through imagery of the actions itself, but also through imagery of situations in which the actions are merely expected. These data show that imagery induces similar perceptual expectations as other prediction processes, in line with the proposal that imagery reflects the voluntary control of predictive pathways that govern an events perceptual representation. Moreover, imagery can drive prediction processes, inducing expectations about events likely to occur in the imagined (not observed) realities, suggesting shared pathways through which imagery and prediction may support mental simulation and counterfactual reasoning. Public Significance StatementThis study uses the perception of other peoples behaviour as a testing bed to advance the hypothesis that imagery can be understood as predicted perception: that, when people imagine, they make voluntary use of the same prediction mechanisms that otherwise allow them to anticipate - and visualise - how a situation will develop further. In four experiments, the study shows (1) that imagining anothers behaviour induces the expectation that their actions will develop in the imagined manner, (2) that imagining situations elicits expectations about how people will behave within them, (3) that these imagery-induced expectations are integrated with other expectations people have about others behaviour and (4) subtly distort how these behaviours are visuospatially represented. The findings demonstrate a link between imagery and predictive perceptual abilities and reveal how imagery can act as a key tool in peoples ability to anticipate relevant futures and explore counterfactual realities.

neuroscience↗

bioRxiv2021

AbmR is a mycobacterial dual-function transcription factor and ribonucleoprotein with distinct DNA and RNA-binding determinants

The bacterium Mycobacterium tuberculosis (Mtb) must adapt to myriad host-associated stressors. A recently identified transcription factor, AbmR (ATP-binding mcr11-regulator), regulates expression of an essential stress-responsive small RNA (Mcr11) and inhibits the growth of Mtb. Previously, AbmR was found to make 39S complexes of unknown function. Here we report that AbmR 39S complexes are comprised of AbmR and co-purifying RNAs and that RNA-binding inhibits AbmRs DNA-binding function. While AbmR binds DNA and regulates gene expression in a sequence specific manner, RNA-binding is not sequence specific. Amino acid R146 is important for DNA-binding but completely dispensable for RNA-binding and 39S complex formation, establishing that the RNA- and DNA-binding functions of AbmR are distinct. RNA bound by AbmR was protected from RNase digestion, supporting an RNA modulatory function for the 39S complex. We also found that abmR is required for optimal survival during treatment with the ATP-depleting antibiotic bedaquiline, which is associated with extended RNA stability. These data establish a paradigm wherein a transcription factor assembles into large complexes to transition between mutually exclusive DNA-binding gene regulatory and RNA-binding RNA modulatory functions. Our findings indicate that AbmR is a dual-function protein that may have novel RNA regulatory roles in stress adapted Mtb.

molecular biology↗

bioRxiv2019

Small RNA Mcr11 regulates genes involved in the central metabolism of Mycobacterium tuberculosis and requires 3 sequence along with the transcription factor AbmR for stable expression

Mycobacterium tuberculosis (Mtb), the etiologic agent of tuberculosis, must adapt to host-associated environments during infection by modulating gene expression. Small regulatory RNAs (sRNAs) are key regulators of bacterial gene expression, but their roles in Mtb are not well understood. Here, we address the expression and function of the Mtb sRNA Mcr11, which is associated with slow bacterial growth and latent infections in mice. We found, by using biochemical and genetic approaches, that the AbmR transcription factor and an extended region of native sequence 3 to the mcr11 gene enhance production of mature Mcr11. Additionally, we found that expression of Mcr11 was unstable in the saprophyte Mycobacterium smegmatis, which lacks an mcr11 orthologue. Bioinformatic analyses used to predict regulatory targets of Mcr11 identified 9-11 nucleotide regions immediately upstream of Rv3282 and lipB with potential for direct base-pairing with Mcr11. mcr11-dependent regulation of Rv3282, lipB, Rv2216 and pknA was demonstrated using qRT-PCR in wild type versus mcr11-deleted Mtb and found to be responsive to the presence of fatty acids. These studies establish that Mcr11 has roles in regulating growth and central metabolism in Mtb that warrant further investigation. In addition, our finding that multiple factors are required for production of stable, mature Mcr11 emphasizes the need to study mechanisms of sRNA expression and stability in TB complex mycobacteria to understand their roles in TB pathogenesis.\n\nAuthor SummaryBacterial pathogens must continuously modulate their gene expression in response to changing conditions to successfully infect and survive within their hosts. Transcription factors are well known regulators of gene expression, but there is growing recognition that small RNAs (sRNAs) also have critically important roles in bacterial gene regulation. Many sRNAs have been identified in M. tuberculosis (Mtb), but little is known about their expression, regulatory targets or roles in Mtb biology. In this study, we found that the Mtb sRNA Mcr11, which is expressed at high levels in slowly replicating Mtb and during mouse infection, regulates expression of several target genes involved in central metabolism. Importantly, we also discovered that mcr11 has unexpected requirements for stable expression in mycobacteria. In particular, we identified RNA sequence elements immediately downstream of mcr11 that enhance transcription termination and production of mature Mcr11 RNA in TB-complex mycobacteria. Meanwhile, ectopic expression of Mcr11 was unstable in a non-pathogenic strain of mycobacteria, suggesting that factors specific to pathogenic mycobacteria are required for the stable production of Mcr11. These studies identify sRNA stability as a new frontier for understanding gene expression in Mtb.

microbiology↗