Biology subjects

Williams, M. A.

Publications and source records attributed to Williams, M. A..

12 recordsLinked to original sources

bioRxiv2024

Investigating the impact of X-rays on decay: X-ray computed tomography as a non-invasive visualisation technique for sediment-based decay experiments

Decay experiments are ever increasing in complexity to better understand taphonomic processes. However, adding new variables, such as sediment, can create methodological biases, such as artificial anatomical character loss during exhumation. Non-invasive in situ imaging techniques such as X-ray computed tomography (XCT scanning) could mitigate this, but the consequences of exposing carcasses to X-rays are not fully understood, and evidence regarding the impact of X-rays on internal microbial faunas that drive decay is conflicting. Here, we test whether XCT scanning impacts the decay of Danio rerio carcasses within a substrate. Our control experiments show that quartz sand sediment physically stabilises the carcass throughout decay and the sequence of anatomical character loss remains constant, however, both the onset and rate of decay of soft tissues are initially accelerated. Our XCT data show that exposure to X-rays does not cause a deviation from the normal sequence of decay, validating XCT as a non-destructive visualisation method for decay experiments. Furthermore, when accompanied with traditional exhumation and dissection, XCT provides decay data with higher accuracy of character analysis than traditional methods, and allows novel quantitative techniques to monitor physical changes in the decaying carcass (e.g., total volume, build-up of gases, collapse of the body cavity etc.). We also underline limitations with the technique, but our experiment acts as an important stepping stone for progression toward non-invasive designs of decay experiments.

paleontology↗

bioRxiv2023

Partial information transfer from peripheral visual streams to foveal visual streams is mediated through local primary visual circuits

A classic view holds that visual object recognition is driven through the what pathway in which perceptual features of increasing abstractness are computed in a sequence of different visual cortical regions. The cortical origin of this pathway, the primary visual cortex (V1), has a retinotopic organization such that neurons have receptive fields tuned to specific regions of the visual field. That is, a neuron that responds to a stimulus in the center of the visual field will not respond to a stimulus in the periphery of the visual field, and vice versa. However, despite this fundamental design feature, the overall processing of stimuli in the periphery - while clearly dependent on processing by neurons in the peripheral regions of V1 - can be clearly altered by the processing of neurons in the fovea region of V1. For instance, it has been shown that task-relevant, non-retinotopic feedback information about peripherally presented stimuli can be decoded in the unstimulated foveal cortex, and that the disruption of this feedback - through Transcranial Magnetic Stimulation or behavioral masking paradigms - has detrimental effects on same/different discrimination behavior. Here, we used fMRI multivariate decoding techniques and functional connectivity analyses to assess the nature of the information that is encoded in the periphery-to-fovea feedback projection and to gain insight into how it may be anatomically implemented. Participants performed a same/different discrimination task on images of real-world stimuli (motorbikes, cars, female and male faces) displayed peripherally. We were able to decode only a subset of these categories from the activity measured in peripheral V1, and a further reduced subset from the activity measured in foveal V1, indicating that the feedback from periphery to fovea may be subject to information loss. Functional connectivity analysis revealed that foveal V1 was functionally connected only to the peripheral V1 and not to later-stage visual areas, indicating that the feedback from peripheral to foveal V1 is likely implemented by neural circuits local to V1.

neuroscience↗

bioRxiv2023

ARF6-dependent endocytic trafficking of the Interferon-γ receptor drives adaptive immune resistance in cancer.

Adaptive immune resistance (AIR) is a protective process used by cancer to escape elimination by CD8+ T cells. Inhibition of immune checkpoints PD-1 and CTLA-4 specifically target Interferon-gamma (IFN{gamma})-driven AIR. AIR begins at the plasma membrane where tumor cell-intrinsic cytokine signaling is initiated. Thus, plasma membrane remodeling by endomembrane trafficking could regulate AIR. Herein we report that the trafficking protein ADP-Ribosylation Factor 6 (ARF6) is critical for IFN{gamma}-driven AIR. ARF6 prevents transport of the receptor to the lysosome, augmenting IFN{gamma}R expression, tumor intrinsic IFN{gamma} signaling and downstream expression of immunosuppressive genes. In murine melanoma, loss of ARF6 causes resistance to immune checkpoint blockade (ICB). Likewise, low expression of ARF6 in patient tumors correlates with inferior outcomes with ICB. Our data provide new mechanistic insights into tumor immune escape, defined by ARF6-dependent AIR, and support that ARF6-dependent endomembrane trafficking of the IFN{gamma} receptor influences outcomes of ICB.

cancer biology↗

bioRxiv2023

Generation of antigen-specific memory CD4 T cells by heterologous immunization enhances the magnitude of the germinal center response upon influenza infection

Current influenza vaccine strategies have yet to overcome significant obstacles, including rapid antigenic drift of seasonal influenza viruses, in generating efficacious long-term humoral immunity. Due to the necessity of germinal center formation in generating long-lived high affinity antibodies, the germinal center has increasingly become a target for the development of novel or improvement of less-efficacious vaccines. However, there remains a major gap in current influenza research to effectively target T follicular helper cells during vaccination to alter the germinal center reaction. In this study, we used a heterologous infection or immunization priming strategy to seed an antigen-specific memory CD4+ T cell pool prior to influenza infection in mice to evaluate the effect of recalled memory T follicular helper cells in increased help to influenza-specific primary B cells and enhanced generation of neutralizing antibodies. We found that heterologous priming with intranasal infection with acute lymphocytic choriomeningitis virus (LCMV) or intramuscular immunization with adjuvanted recombinant LCMV glycoprotein induced increased antigen-specific effector CD4+ T and B cellular responses following infection with a recombinant influenza strain that expresses LCMV glycoprotein. Heterologously primed mice had increased expansion of secondary Th1 and Tfh cell subsets, including increased CD4+ TRM cells in the lung. However, the early enhancement of the germinal center cellular response following influenza infection did not impact influenza-specific antibody generation or B cell repertoires compared to primary influenza infection. Overall, our study suggests that while heterologous infection/immunization priming of CD4+ T cells is able to enhance the early germinal center reaction, further studies to understand how to target the germinal center and CD4+ T cells specifically to increase long-lived antiviral humoral immunity are needed. Author SummaryT follicular helper (Tfh) cells are specialized CD4+ T cells that provide help to B cells and are required to form germinal centers within secondary lymphoid organs during an immune response. Germinal centers are necessary for generating high affinity virus-specific antibodies necessary to clear influenza infections, though current vaccines fail to generate long-lived antibodies that universally recognize different influenza strains. We used a "heterologous priming" strategy in mice using a non-influenza viral infection or viral protein subunit vaccination to form memory CD4+ Tfh cells (in previously naive mice) that can be rapidly recalled into secondary Tfh cells following influenza infection and ideally enhance the germinal center reaction and formation of high affinity antibodies to influenza better than primary Tfh cells. Our study showed that heterologous priming induced an increase in both CD4+ T and B cells early following influenza infection, suggesting we could successfully target enhancement of the germinal center. Despite the enhancement of the early germinal center cellular response, we did not see an increase in influenza-specific antiviral antibodies. Thus, while Tfh cells are critical for the generation of high affinity antibodies, other strategies to target expansion of Tfh cells during influenza vaccination will need to be developed.

immunology↗

bioRxiv2023

Human Rhinoviruses: a novel class of oncolytic virus

While continuing to develop new and improved OVs, researchers have been vigilant in optimizing their ability to safely infect, replicate, and induce an immune response within tumors. There are currently two crucial limitations in OV development, however: modification of viruses often negatively impact their ability to infect, and induction of strong immune responses also promotes rapid viral clearance. In this study, we investigate wild-type HRVs as a novel class of OV. Multiple HRV serotypes were propagated in human melanoma cell lines to produce highly oncolytic populations of virus. A large panel of cancer types were infected, with cytotoxicity evaluated using flow cytometry and real time live imaging. Pro-inflammatory signaling was assessed by cytokine multiplexing. Tumor responses to HRV were assessed in human xenograft and in syngeneic, immune-competent mouse tumor models. We find that HRVs are capable of infecting and killing a wide variety of human cancer cell lines in vitro and in vivo, inducing pro-inflammatory responses and, ultimately, tumor regression. We propose that the natural safety profile of these viruses, coupled with their anti-tumor efficacy and multivalent potential seen in our preclinical model systems, make HRVs ideal candidates for development as oncolytic viruses for clinical testing. Simple SummaryThe idea of utilizing viruses to combat cancer has been around for over a century, yet in practice has seen relatively modest therapeutic success following decades of strategic design to improve safety, efficacy, and tumor selectivity. Engagement of an immune response is critical to have lasting tumor regression upon treatment, but many patients are unable to mount a sufficient response to standard-of-care immunotherapy alone. Oncolytic viruses (OVs) have been shown to synergize with such therapies to accomplish this goal to varying degrees. The purpose of this study is to investigate human rhinoviruses (HRVs) to establish their efficacy as a novel class of anti-cancer agents. We aim to use HRVs to promote longer lasting and more effective immune responses to tumors by fostering viral persistence and immune evasion, in addition to developing multivalent treatment strategies that enhance tumor regression by preventing tumor escape from viral infection.

immunology↗

bioRxiv2022

Transcription coactivator OCA-B/Pou2af1 is necessary and sufficient to promote T cell-intrinsic CD4 memory

The molecular mechanisms leading to the establishment of immunological memory are inadequately understood, limiting the development of effective vaccines and durable anti-tumor immune therapies. Here we show that ectopic OCA-B expression is sufficient to improve antiviral memory recall responses, while having minimal effects on primary effector responses. At peak viral response short lived effector T cell populations are expanded but show increased Gadd45b and Socs2 expression, while memory precursor effector cells show increased expression of Bcl2, Il7r and Tcf7 on a per-cell basis. Using an OCA-B mCherry reporter mouse line, we observe high OCA-B expression in CD4+ TCM cells. We show that early in viral infection, endogenously elevated OCA-B expression prospectively identifies memory precursor cells with increased survival capability and memory recall potential. Cumulatively, the results demonstrate that OCA-B is both necessary and sufficient to promote CD4 T cell memory in vivo and can be used to prospectively identify memory precursor cells. SignificanceCD4+ T cell memory is incompletely defined and memory progenitors difficult to identify. Here, we show that expression of the OCA-B transcription coactivator in CD4+ T cells is necessary and sufficient to drive productive memory. Using a novel mCherry reporter mouse line, we show that OCA-B expression enriches for responding effector cells with elevated memory potential. The results show that OCA-B expression in T cells is sufficient to promote CD4+ memory formation and marks memory precursor cells.

immunology↗

bioRxiv2021

Unipolar peptidoglycan synthesis in the Rhizobiales requires an essential class A penicillin-binding protein

Members of the Rhizobiales are polarly-growing bacteria that lack homologs of the canonical rod complex. To investigate the mechanisms underlying polar cell wall synthesis, we systematically probed the function of cell wall synthesis enzymes in the plant-pathogen Agrobacterium tumefaciens. The development of fluorescent O_SCPLOWDC_SCPLOW-amino acid dipeptide (FDAAD) probes, which are incorporated into peptidoglycan by penicillin-binding proteins in A. tumefaciens, enabled us to monitor changes in growth patterns in the mutants. Use of these fluorescent cell wall probes and peptidoglycan compositional analysis convincingly demonstrate that a single class A penicillin-binding protein is essential for polar peptidoglycan synthesis. Furthermore, we find evidence of an alternative mode of cell wall synthesis that likely requires O_SCPLOWLDC_SCPLOW-transpeptidase activity. Genetic analysis and cell wall targeting antibiotics reveal that the mechanism of unipolar growth is conserved in Sinorhizobium and Brucella. This work provides insights into unipolar peptidoglycan biosynthesis employed by the Rhizobiales during cell elongation.

microbiology↗

bioRxiv2021

Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2

Terminating the SARS-CoV-2 pandemic relies upon pan-global vaccination. Current vaccines elicit neutralizing antibody responses to the virus spike derived from early isolates. However, new strains have emerged with multiple mutations: P.1 from Brazil, B.1.351 from South Africa and B.1.1.7 from the UK (12, 10 and 9 changes in the spike respectively). All have mutations in the ACE2 binding site with P.1 and B.1.351 having a virtually identical triplet: E484K, K417N/T and N501Y, which we show confer similar increased affinity for ACE2. We show that, surprisingly, P.1 is significantly less resistant to naturally acquired or vaccine induced antibody responses than B.1.351 suggesting that changes outside the RBD impact neutralisation. Monoclonal antibody 222 neutralises all three variants despite interacting with two of the ACE2 binding site mutations, we explain this through structural analysis and use the 222 light chain to largely restore neutralization potency to a major class of public antibodies.

microbiology↗

bioRxiv2019

Foveal feedback supports peripheral perception of both object color and form

Evidence from neuroimaging and brain stimulation studies suggest that visual information about objects in the periphery is fed back to foveal retinotopic cortex in a separate representation that is essential for peripheral perception. The characteristics of this phenomenon has important theoretical implications for the role fovea-specific feedback might play in perception. In this work, we employed a recently developed behavioral paradigm to explore whether late disruption to central visual space impaired perception of color. First, participants performed a shape discrimination task on colored novel objects in the periphery while fixating centrally. Consistent with the results from previous work, a visual distractor presented at fixation ~100ms after presentation of the peripheral stimuli impaired sensitivity to differences in peripheral shapes more than a visual distractor presented at other stimulus onset asynchronies. In a second experiment, participants performed a color discrimination task on the same colored objects. In a third experiment, we further tested for the foveal distractor effect with stimuli restricted to a low-level feature by using homogenous color patches. These two latter experiments resulted in a similar pattern of behavior: a central distractor presented at the critical stimulus onset asynchrony impaired sensitivity to peripheral color differences, but, importantly, the magnitude of the effect depended on whether peripheral objects contained complex shape information. These results taken together suggest that feedback to the foveal confluence is a component of visual processing supporting perception of both object form and color.

neuroscience↗

bioRxiv2019

Meaningful patterns of information in the brain revealed through analysis of errors

Great excitement has surrounded our ability to decode task information from human brain activity patterns, reinforcing the dominant view of the brain as an information processor. We tested a fundamental but overlooked assumption: that such decodable information is actually used by the brain to generate cognition and behaviour. Participants performed a challenging stimulus-response task during fMRI. Our novel analyses trained a pattern classifier on data from correct trials, and used it to examine stimulus and rule coding on error trials. There was a striking interaction in which frontoparietal cortex systematically represented incorrect rule but correct stimulus information when participants used the wrong rule, and incorrect stimulus but correct rule information on other types of errors. Visual cortex, by contrast, did not code correct or incorrect information on error. Thus behaviour was tightly linked to coding in frontoparietal cortex and only weakly linked to coding in visual cortex. Human behaviour may indeed result from information-like patterns of activity in the brain, but this relationship is stronger in some brain regions than in others. Testing for information coding on error can help establish which patterns constitute behaviourally-meaningful information.

neuroscience↗

bioRxiv2018

Altered Stool Microbiota of Infants with Cystic Fibrosis Shows Reduction in Genera Associated with Immune Programming

Previous work from our group indicated a connection between the gastrointestinal microbiota of infants and children with cystic fibrosis (CF) and airway disease in this population. Here we examine the stool microbiota of infants with CF and from the general population who did not have CF over the first year of life. CF children had reduced gastrointestinal Bacteroides and Bifidobacterium beginning in infancy, even after adjusting for antibiotic treatment. We also identify several metabolic pathways that are enriched or under represented among the microbial communities in the stool of these young patients with CF as compared to children without CF. In vitro studies demonstrated that exposure of the apical face of a polarized Intestinal cell line to Bacteroides thetaiotaomicron significantly reduced production of IL-8 secreted from both the apical and basolateral face of these cells, suggesting a mechanism whereby changes in the intestinal microflora could impact systemic inflammation. This work further establishes a link between gastrointestinal microbiota, systemic inflammation and airway disease, and presents the opportunity for therapeutic probiotic interventions.\n\nSignificance statementThere is a surprising link between gastrointestinal microbial communities and airway disease progression in CF. Here we show that infants with CF [≤]1 year of age show a distinct stool microbiota compared with children of a comparable age from a general population cohort. We detect associations between stool microbes and airway exacerbation events in the cohort of infants with CF, and in vitro studies provide a possible mechanism for this observation. These data argue that current therapeutics do not establish a healthy-like gastrointestinal microbiota in young patients with CF, and we suggest that interventions that direct the gastrointestinal microbiota closer to a healthy state may provide benefit to these patients.

microbiology↗

bioRxiv2017

COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool \"COREMIC\" meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com), developed using Google App Engine, to help in the process of database mining to identify the \"core microbiome\" associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (5 environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val < 0.05% for Fishers exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.

microbiology↗