Biology subjects

Brown, A.

Publications and source records attributed to Brown, A..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

Context-induced renewal of passive but not active coping behaviours in the shock-probe defensive burying task

Renewal is the return of extinguished responding after removal from the extinction context. Renewal has been extensively studied using classical aversive conditioning procedures that measure a passive freezing response to an aversive conditioned stimulus. However, coping responses to aversive stimuli are complex and can be reflected in passive and active behaviours. Using the shock-probe defensive burying task, we investigated whether different coping responses are susceptible to renewal. During conditioning, male, Long-Evans rats were placed into a specific context (context A) where an electrified shock-probe delivered a 3 mA shock upon contact. During extinction, the shock-probe was unarmed in either the same (context A) or a different context (context B). Renewal of conditioned responses was assessed in the conditioning context (ABA) or in a novel context (ABC or AAB). Renewal of passive coping responses, indicated by an increased latency and a decreased duration of shock-probe contacts, was observed in all groups. However, renewal of passive coping, measured by increased time spent on the side of the chamber opposite the shock-probe, was only found in the ABA group. Renewal of active coping responses linked to defensive burying was not observed in any group. The present findings highlight the presence of multiple psychological processes underlying even basic forms of aversive conditioning and demonstrate the importance of assessing a broader set of behaviours to tease apart these different underlying mechanisms. The current findings suggest that passive coping responses may be more reliable indicators for assessing renewal than active coping behaviours associated with defensive burying.

animal behavior and cognition↗

bioRxiv2022

Molecular Basis for Interferon-mediated Pathogen Restriction in Human Cells

To define novel mechanisms for cellular immunity to the intracellular pathogen Toxoplasma gondii, we performed a genome-wide CRISPR loss-of-function screen to provide an unbiased assessment of genes important for IFN-{gamma}-dependent growth restriction. We revealed a previously unknown role for the tumor suppressor NF2/Merlin for maximum induction of Interferon Stimulated Genes (ISG), which are positively regulated by the transcription factor IRF-1. We then performed an additional focused ISG-targeted CRISPR screen that identified the host E3 ubiquitin ligase RNF213 as essential for IFN-{gamma} mediated control of T. gondii. RNF213 mediated ubiquitination of targets on the parasite-containing vacuole and growth restriction in response to IFN-{gamma} in a variety of cell types, thus identifying a conserved factor that plays a prominent role in human cells. Surprisingly, growth inhibition did not require the autophagy protein ATG5, indicating that RNF213 initiates restriction independent of a non-canonical autophagy pathway that has previously been implicated in control of T. gondii. RNF213 was also important for control of unrelated intracellular pathogens in human cells treated with IFN, as shown here for Mycobacterium tuberculosis and Vesicular Stomatitis Virus. Collectively, our findings establish RNF213 as a critical component of cell-autonomous immunity to a broad spectrum of intracellular pathogens in human cells.

microbiology↗

bioRxiv2022

Neural correlates of extinction in a rat model of appetitive Pavlovian conditioning

Extinction is a fundamental form of inhibitory learning that is important for adapting to changing environmental contingencies. While numerous studies have investigated the neural correlates of extinction using Pavlovian fear conditioning and appetitive operant reward-seeking procedures, less is known about the neural circuitry mediating the extinction of appetitive Pavlovian conditioned responding. Here, we aimed to generate an extensive brain activation map of extinction learning in a rat model of appetitive Pavlovian conditioning. Male Long-Evans rats were trained to associate a conditioned stimulus (CS; 20 s white noise) with the delivery of a 10% sucrose unconditioned stimulus (US; 0.3 ml/CS) to a fluid port. Control groups also received CS presentations, but sucrose was delivered either during the inter-trial interval or in the home-cage. After conditioning, 1 or 6 extinction sessions were conducted in which the CS was presented but sucrose was withheld. We performed Fos immunohistochemistry and network connectivity analyses on a set of cortical, striatal, thalamic, and amygdalar brain regions. Neural activity in the prelimbic cortex, ventral orbitofrontal cortex, nucleus accumbens core, and paraventricular nucleus of the thalamus was greater during recall relative to extinction. Conversely, prolonged extinction following 6 sessions induced increased neural activity in the infralimbic cortex, medial orbitofrontal cortex, and nucleus accumbens shell compared to home-cage controls. All these structures were similarly recruited during recall on the first extinction session. These findings provide novel evidence for the contribution of brain areas and neural networks that are differentially involved in the recall versus extinction of appetitive Pavlovian conditioned responding.

neuroscience↗

bioRxiv2022

Methotrexate inhibition of muropeptide transporter SLC46A2 controls psoriatic skin inflammation

Cytosolic innate immune sensing is critical for protecting barrier tissues. NOD1 and NOD2 are cytosolic sensors of small peptidoglycan fragments (muropeptides) derived from the bacterial cell wall. These muropeptides enter cells, especially epithelial cells, through unclear mechanisms. We previously implicated SLC46 transporters in muropeptide transport in Drosophila immunity. Here we focus on Slc46a2, which is highly expressed in mammalian epidermal keratinocytes, and show that it is critical for delivery of DAP-muropeptides and activation of NOD1 in keratinocytes, while the related transporter Slc46a3 is critical for responding to MDP, the NOD2 ligand. In a mouse model, Slc46a2 and Nod1 deficiency strongly suppressed psoriatic inflammation, while methotrexate, a commonly used psoriasis therapeutic, inhibited Slc46a2-dependent transport of DAP-muropeptides. Collectively these studies define SLC46A2 as a transporter of NOD1 activating muropeptides, with critical roles in the skin barrier, and identify this transporter as an important target for anti-inflammatory intervention.

immunology↗

bioRxiv2022

ESCRT-dependent STING degradation curtails steady-state and cGAMP-induced signaling

STING is an intracellular sensor of cyclic di-nucleotides involved in response to pathogen- or self-derived DNA that induces protective immunity, or if dysregulated, autoimmunity. STING trafficking is tightly linked to its activity. We aimed to systematically characterize genes regulating STING trafficking and to define their impact on STING responses. Based on proximity-ligation proteomics and genetic screens, an ESCRT complex containing HGS, VPS37A and UBAP1 was found to be required for STING degradation and signaling shutdown. Analogous to phosphorylated STING creating a platform for IRF3 recruitment, oligomerization-driven STING ubiquitination by UBE2N formed a platform for ESCRT recruitment at the endosome, responsible for STING signaling shutdown. A UBAP1 mutant that underlies human spastic paraplegia and disrupts ESCRT function led to STING-dependent type I IFN responses at the steady-state, defining ESCRT as a homeostatic regulator of STING signaling.

immunology↗

bioRxiv2022

Cancer-associated SMARCAL1 loss-of-function mutations promote alternative lengthening of telomeres and tumorigenesis in telomerase-negative glioblastoma cells

Telomere maintenance mechanisms are a hallmark of cancer and are required to enable the replicative immortality of malignant cells. While most cancers activate the enzyme telomerase for telomere maintenance, a subset of cancers (~10-15%) use telomerase-independent mechanisms termed alternative lengthening of telomeres (ALT). ALT is characterized by elevated replication stress at telomeres, telomere synthesis via homology directed-repair mechanisms, and is frequently associated with mutations in the ATRX gene. Because ALT is absent in non-malignant proliferating cells, therapeutic strategies targeting ALT-mediated telomere synthesis is an area of significant translational and clinical interest. We previously showed that a subset of adult GBM patients with ATRX-expressing ALT-positive tumors harbored loss-of-function mutations in the SMARCAL1 gene. SMARCAL1 is an annealing helicase involved in replication fork remodeling and the resolution of replication stress. In this study, we used a patient-derived ALT-positive GBM cell line with native SMARCAL1 deficiency to investigate the role of SMARCAL1 in ALT-mediated telomere synthesis and gliomagenesis in vivo. Our results show that inducible rescue of SMARCAL1 expression suppresses ALT indicators and inhibits de novo telomere synthesis in GBM and osteosarcoma cells, suggesting that SMARCAL1 deficiency plays a functional role in ALT induction in cancers that natively lack SMARCAL1 function. Further, SMARCAL1-deficient ALT-positive cells can be serially propagated in vivo in the absence of detectable telomerase activity, suggesting that the SMARCAL1-deficient ALT phenotype maintains telomeres in a manner that promotes tumorigenesis. In summary, we show that SMARCAL1 loss-of-function mutations are permissive to ALT and promote gliomagenesis. We also established isogenic model systems that permit the dynamic modulation of ALT activity, which will be valuable for future studies aimed at understanding the molecular mechanisms of ALT and for identifying novel anti-cancer therapeutics that target the ALT phenotype.

cancer biology↗

bioRxiv2022

A living biobank of canine mammary tumor organoids as a comparative model for human breast cancer

Mammary tumors in dogs hold great potential as naturally occurring breast cancer models in translational oncology, as they share the same environmental risk factors, key histological features, hormone receptor expression patterns, prognostic factors, and genetic characteristics as their human counterparts. We aimed to develop in vitro tools that allow functional analysis of canine mammary tumors (CMT), as we have a poor understanding of the underlying biology that drives the growth of these heterogeneous tumors. We established the long-term culture of 24 organoid lines from 16 patients, including organoids derived from normal mammary epithelium or benign lesions. CMT organoids recapitulated key morphological and immunohistological features of the primary tissue from which they were derived, including hormone receptor status. Furthermore, genetic characteristics (driver gene mutations, DNA copy number variations, and single-nucleotide variants) were conserved within tumororganoid pairs. We show how CMT organoids are a suitable model for in vitro drug assays and can be used to investigate whether specific mutations predict therapy outcomes. In addition, we could genetically modify the CMT organoids and use them to perform pooled CRISPR/Cas9 screening, where library representation was accurately maintained. In summary, we present a robust 3D in vitro preclinical model that can be used in translational research, where organoids from normal, benign as well as malignant mammary tissues can be propagated from the same patient to study tumorigenesis.

cancer biology↗

bioRxiv2022

Antibody optimization enabled by artificial intelligence predictions of binding affinity and naturalness

Traditional antibody optimization approaches involve screening a small subset of the available sequence space, often resulting in drug candidates with suboptimal binding affinity, developability or immunogenicity. Based on two distinct antibodies, we demonstrate that deep contextual language models trained on high-throughput affinity data can quantitatively predict binding of unseen antibody sequence variants. These variants span a KD range of three orders of magnitude over a large mutational space. Our models reveal strong epistatic effects, which highlight the need for intelligent screening approaches. In addition, we introduce the modeling of "naturalness", a metric that scores antibody variants for similarity to natural immunoglobulins. We show that naturalness is associated with measures of drug developability and immunogenicity, and that it can be optimized alongside binding affinity using a genetic algorithm. This approach promises to accelerate and improve antibody engineering, and may increase the success rate in developing novel antibody and related drug candidates.

bioinformatics↗

bioRxiv2022

Reshuffling of the coral microbiome during dormancy

Quiescence, or dormancy, is a response to stressful conditions in which an organism slows or halts physiological functioning. Although most species that undergo dormancy maintain complex microbiomes, there is little known about how dormancy influences and is influenced by the hosts microbiome, including in the temperate coral, Astrangia poculata. Northern populations of A. poculata undergo winter quiescence. Here, we characterized wild A. poculata microbiomes in a high-resolution sampling time series before, during, and after quiescence using 16S ribosomal RNA gene sequencing on active (RNA) and present (DNA) microbiomes. We observed a restructuring of the coral microbiome during quiescence that persisted after re-emergence. Upon entering quiescence, corals shed copiotrophic microbes, including putative pathogens, suggesting removal of these taxa as corals cease normal functioning. During and after quiescence, bacteria and archaea associated with nitrification were enriched, suggesting the quiescent microbiome may replace essential functions through supplying nitrate to corals and/or microbes. Overall, this study demonstrates that key microbial groups related to quiescence in A. poculata may play a role in the onset or emergence from dormancy, and long-term regulation of the microbiome composition. The predictability of dormancy in A. poculata provides an ideal natural manipulation system to further identify factors that regulate host-microbial associations. ImportanceUsing a high-resolution sampling time series, we are the first to demonstrate a persistent microbial community shift with quiescence (dormancy) in a marine organism, the temperate coral, Astrangia poculata. Furthermore, during this period of community turnover, there is a shedding of putative pathogens and copiotrophs and an enhancement of the ammonia-oxidizing bacteria (Nitrosococcales) and archaea (Ca. Nitrosopumilus). Our results suggest that quiescence represents an important period during which the coral microbiome can "reset," shedding opportunistic microbes and enriching for the re-establishment of beneficial associates, including those that may contribute nitrate while the coral animal is not actively feeding. We suggest this work provides foundational understanding of the interplay of microbes and the hosts dormancy response in marine organisms.

microbiology↗

bioRxiv2022

Didemnin B and ternatin-4 inhibit conformational changes in eEF1A required for aminoacyl-tRNA accommodation into mammalian ribosomes

Rapid and accurate mRNA translation requires efficient codon-dependent delivery of the correct aminoacyl-tRNA (aa-tRNA) to the ribosomal A site. In mammals, this fidelity-determining reaction is facilitated by the GTPase elongation factor-1 alpha (eEF1A), which escorts aa-tRNA as an eEF1A(GTP)-aa-tRNA ternary complex into the ribosome. Two structurally unrelated cyclic peptides didemnin B and ternatin-4 bind to the eEF1A(GTP)-aa-tRNA ternary complex and inhibit translation. Here, we employ single-molecule fluorescence imaging and cryogenic electron microscopy to determine how these natural products inhibit translational elongation on mammalian ribosomes. By binding to a common allosteric site on eEF1A, didemnin B and ternatin-4 trap eEF1A in its GTPase-activated conformation, preventing aa-tRNA accommodation on the ribosome. We also show that didemnin B and ternatin-4 exhibit distinct effects on aa-tRNA selection that inform on observed disparities in their inhibition efficacies and physiological impacts. These integrated findings highlight the potential of single-molecule methods to reveal how distinct natural products differentially impact the human translation mechanism.

biochemistry↗

bioRxiv2022

Covert detection of own-name and semantic violations in task-irrelevant speech, in a realistic Virtual Cafe

Detecting that someone has said your name is one of the most famous examples for incidental processing of supposedly-unattended speech. However, empirical investigation of this so-called "cocktail party effect" has yielded conflicting results. We present a novel empirical approach for revisiting this effect under highly ecological conditions, by immersing participants in a multisensory virtual cafe environment and using realistic stimuli and tasks. Participants listened to conversational speech from a character sitting across from them, while a barista in the back of the cafe called out food orders. Unbeknownst to them, the barista sometimes called orders containing their own name or semantic violations. We used combined measurements of brain activity (EEG), eye-gaze and galvanic skin response to assess the response-profile to these two probes in the task-irrelevant barista-stream. Both probes elicited unique neural and physiological responses relative to control stimuli, indicating that the system indeed processed these words and detected their unique status, despite being task-irrelevant. Interestingly, these responses were covert in nature and were not accompanied by gaze-shifts towards the barista character. This pattern demonstrates that under these highly ecological conditions, listeners incidentally pick up information from task-irrelevant speech, emphasizing the dynamic and non-binary nature of attention in real-life environments.

neuroscience↗

bioRxiv2022

Inhibitors of ROCK kinases induce multiple mitotic defects and synthetic lethality in BRCA2-deficient cells

BRCA2-deficient cells are highly sensitive to poly-ADP-ribose polymerase inhibitors (PARPi) due to their impaired homologous recombination repair. This increased cytotoxicity is triggered by DNA replication stress induced by PARP trapping on DNA. Thus, it is broadly assumed that DNA damage is a prerequisite for BRCA2 synthetic lethality (SL). Here we show that inhibiting ROCK kinases in BRCA2 deficient cells, triggers SL independently from acute replication stress. In contrast, such SL is preceded by enhanced M-phase defects such as anaphase bridges, and abnormal mitotic figures, which were associated with multipolar spindles, supernumerary centrosomes and multinucleation. SL was also triggered by inhibiting Citron Rho-interacting kinase, another enzyme which, similarly to ROCK kinases, regulates cytokinesis. Together, these observations suggest cytokinesis failure as trigger of mitotic abnormalities and SL in BRCA2 cells. Furthermore, preventing mitotic entry by Early mitotic inhibitor 1 (EMI1) depletion promoted survival of BRCA2 deficient cells treated with inhibitors of ROCK kinases, thus reinforcing the association between M-phase and the cell death in BRCA2 deficient cells. This novel mechanism of SL induction is in contrast to the one triggered by PARPi and uncovers mitosis as an Achilles heel of BRCA2 deficient cells.

cancer biology↗

bioRxiv2022

Nutrient limitation mimics artemisinin tolerance in malaria

Mounting evidence demonstrates that nutritional environment can alter pathogen drug sensitivity. While the nutrient-rich media used for standard in vitro culture contains supra-physiological nutrient concentrations, pathogens encounter a relatively restrictive environment in vivo. We assessed the effect of nutrient limitation on the protozoan parasite that causes malaria and demonstrated that short-term growth under physiologically-relevant mild nutrient stress (or "metabolic priming") triggers increased tolerance of the potent antimalarial drug dihydroartemisinin (DHA). We observed beneficial effects using both short-term survival assays and longer-term proliferation studies, where metabolic priming increases parasite survival to a level previously defined as DHA resistant (>1% survival). We performed these assessments by either decreasing single nutrients that have distinct roles in parasite metabolism or using a media formulation with reductions in many nutrients that simulates the human plasma environment. We determined that priming-induced DHA tolerance was restricted to parasites that had newly invaded the host red blood cell but the effect was not dependent on genetic background. The molecular mechanisms of this intrinsic effect mimic aspects of genetic artemisinin tolerance, including translational repression, autophagy, and protein export. This finding suggests regardless of the impact on survival rates, environmental stress could stimulate changes that ultimately directly contribute to drug tolerance. Because metabolic stress is likely to occur more frequently in vivo compared to the stable in vitro environment, priming-induced drug tolerance has ramifications for how in vitro results translate to in vivo studies. Improving our understanding of how pathogens adjust their metabolism to impact survival of current and future drugs is an important avenue of research to prevent and slow the spread of resistance.

microbiology↗

bioRxiv2022

An ecological investigation of the capacity to follow simultaneous speech and preferential detection of ones' own name

Many situations require focusing attention on one speaker, while monitoring the environment for potentially important information. Some have proposed that dividing attention among two speakers involves behavioral tradeoffs, due to limited cognitive resources. However the severity of these tradeoffs, particularly under ecologically-valid circumstances, is not well understood. We investigated the capacity to process simultaneous speech using a dual-task paradigm simulating task demands and stimuli encountered in real-life. Participants listened to conversational narratives (Narrative Stream) and monitored a stream of announcements (Barista Stream), to detect when their order was called. We measured participants performance, neural activity and skin conductance as they engaged in this dual-task. Participants achieved extremely high dual-task accuracy, with no apparent behavioral tradeoffs. Moreover, robust neural and physiological responses were observed for target-stimuli in the Barista Stream, alongside significant neural speech-tracking of the Narrative Stream. These results suggest that humans have substantial capacity to process simultaneous speech and do not suffer from insufficient processing resources, at least for this highly ecological task-combination and level of perceptual load. Results also confirmed the ecological validity of the advantage for detecting ones own name at the behavioral, neural and physiological level, highlighting the contribution of personal relevance when processing simultaneous speech.

neuroscience↗

bioRxiv2022

Arf GTPase activates the WAVE Regulatory Complex through a novel binding site

Crosstalk between Rho- and Arf-family GTPases plays an important role in linking actin cytoskeletal remodeling to membrane protrusion, organelle structure, and vesicle trafficking. The central actin regulator, WAVE Regulatory Complex (WRC), is a converging point of Rac1 (a Rho-family GTPase) and Arf signaling in many processes, but how Arf promotes WRC activation is unknown. Here we reconstituted a direct interaction between Arf and WRC. This interaction can be greatly enhanced by Rac1 binding to the D site of the WRC. Arf1 binds to a newly identified conserved surface on Sra1 located between the D site and the WH2 helix of WAVE1, which can drive WRC activation using a mechanism distinct from that of Rac1. Mutating Arf binding site abolishes Arf1-WRC interaction, disrupts Arf1-mediated WRC activation, and impairs lamellipodia morphology. This work uncovers a new mechanism underlying WRC activation and provides a mechanistic foundation for studying how WRC-mediated actin polymerization links Arf and Rac signaling in the cell.

biochemistry↗

bioRxiv2022

Mapping odorant sensitivities reveals a sparse but structured representation of olfactory chemical space by sensory input to the mouse olfactory bulb.

In olfactory systems, convergence of sensory neurons onto glomeruli generates a map of odorant receptor identity. How glomerular maps relate to sensory space remains unclear. We sought to better characterize this relationship in the mouse olfactory system by defining glomeruli in terms of the odorants to which they are most sensitive. Using high-throughput odorant delivery and ultrasensitive imaging of sensory inputs, we imaged responses to 185 odorants presented at concentrations determined to activate only one or a few glomeruli across the dorsal olfactory bulb. The resulting datasets defined the tuning properties of glomeruli - and, by inference, their cognate odorant receptors - in a low-concentration regime, and yielded consensus maps of glomerular sensitivity across a wide range of chemical space. Glomeruli were extremely narrowly tuned, with ~25% responding to only one odorant, and extremely sensitive, responding to their effective odorants at sub-picomolar to nanomolar concentrations. Such narrow tuning in this concentration regime allowed for reliable functional identification of many glomeruli based on a single diagnostic odorant. At the same time, the response spectra of glomeruli responding to multiple odorants was best predicted by straightforward odorant structural features, and glomeruli sensitive to distinct odorants with common structural features were spatially clustered. These results define an underlying structure to the primary representation of sensory space by the mouse olfactory system.

neuroscience↗

bioRxiv2022

Structures reveal a key mechanism of WAVE Regulatory Complex activation by Rac1 GTPase

Rho-family GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3-mediated actin polymerization in many essential processes. Rac1 binds to WRC at two distinct sites--the A and D sites. Precisely how Rac1 binds and how the binding triggers WRC activation remain unknown. Here we report WRC structures by itself, and when bound to single or double Rac1 molecules, at [~]3 [A] resolutions by cryogenic-electron microscopy. The structures reveal that Rac1 binds to the two sites by distinct mechanisms, and binding to the A site, but not the D site, drives WRC activation. Activation involves a series of unique conformational changes leading to the release of sequestered WCA (WH2- central-acidic) polypeptide, which stimulates the Arp2/3 complex to polymerize actin. Together with biochemical and cellular analyses, the structures provide a novel mechanistic understanding of how the Rac1-WRC-Arp2/3-actin signaling axis is regulated in diverse biological processes and diseases.

biochemistry↗

bioRxiv2022

Phylogeny and Metadata Network Database for Epidemiologic Surveillance

AO_SCPLOWBSTRACTC_SCPLOWThe ongoing SARS-CoV-2 pandemic has highlighted the difficulty in integrating disparate data sources for epidemiologic surveillance. To address this challenge, we have created a graph database to integrate phylogenetic trees, associated metadata, and community surveillance data for phylodynamic inference. As an example use case, we divided 22,713 SARS-CoV-2 samples into 5 groups, generated maximum likelihood trees, and inferred a potential transmission network from a forest of minimum spanning trees built on patristic distances between samples. We then used Cytoscape to visualize the resultant graphs.

evolutionary biology↗