Biology subjects

Murphy, M.

Publications and source records attributed to Murphy, M..

68 records · Page 4Linked to original sources

bioRxiv2020

Elicitation of broadly protective immunity to influenza by multivalent hemagglutinin nanoparticle vaccines

Influenza vaccines that confer broad and durable protection against diverse virus strains would have a major impact on global health. However, next-generation vaccine design efforts have been complicated by challenges including the genetic plasticity of the virus and the immunodominance of certain epitopes in its glycoprotein antigens. Here we show that computationally designed, two-component nanoparticle immunogens induce potently neutralizing and broadly protective antibody responses against a wide variety of influenza viruses. The nanoparticle immunogens display 20 hemagglutinin (HA) trimers in a highly immunogenic array, and their assembly in vitro enables precisely controlled co-display of multiple distinct HAs in defined ratios. Nanoparticle immunogens displaying the four HAs of licensed quadrivalent influenza vaccines (QIV) elicited hemagglutination inhibition and neutralizing antibody responses to vaccine-matched strains that were equivalent or superior to commercial QIV in mice, ferrets, and nonhuman primates. The nanoparticle immunogens--but not QIV--simultaneously induced broadly protective antibody responses to heterologous viruses, including H5N1 and H7N9, by targeting the subdominant yet conserved HA stem. Unlike previously reported influenza vaccine candidates, our nanoparticle immunogens can alter the intrinsic immunodominance hierarchy of HA to induce both potent receptor-blocking and broadly cross-reactive stem-directed antibody responses and are attractive candidates for a next-generation influenza vaccine that could replace current seasonal vaccines. One Sentence SummaryNanoparticle immunogens displaying four seasonal influenza hemagglutinins elicit neutralizing antibodies directed at both the immunodominant head and the conserved stem and confer broad protective immunity.

immunology↗

bioRxiv2020

Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays

SARS-CoV-2 enters cells using its Spike protein, which is also the main target of neutralizing antibodies. Therefore, assays to measure how antibodies and sera affect Spike-mediated viral infection are important for studying immunity. Because SARS-CoV-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with Spike. Such pseudotyping has now been described for single-cycle lentiviral, retroviral and VSV particles, but the reagents and protocols are not widely available. Here we detail how to effectively pseudotype lentiviral particles with SARS-CoV-2 Spike and infect 293T cells engineered to express the SARS-CoV-2 receptor, ACE2. We also make all the key experimental reagents available in the BEI Resources repository of ATCC and the NIH. Furthermore, we demonstrate how these pseudotyped lentiviral particles can be used to measure the neutralizing activity of human sera or plasma against SARS-CoV-2 in convenient luciferase-based assays, thereby providing a valuable complement to ELISA-based methods that measure antibody binding rather than neutralization.

microbiology↗

bioRxiv2020

Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome

BackgroundTargeted next generation sequencing offers the potential for consistent, deep coverage of information rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited. MethodsA bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, WGS data were generated for the same controls. ResultsUsing publicly available genomes, 4465 high diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median HE = 0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%) and sensitivity (90% for haplotypes with 5% within sample frequency in DBS with 100 parasites/{micro}L). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic SNP barcodes. DiscussionThe bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.

molecular biology↗

bioRxiv2020

Anopheles stephensi as an emerging malaria vector in the Horn of Africa with high susceptibility to Ethiopian Plasmodium vivax and Plasmodium falciparum isolates

Anopheles stephensi, an efficient Asian malaria vector, recently spread into the Horn of Africa and may increase malaria receptivity in African urban areas. We assessed occurrence, genetic complexity, blood meal source and infection status of An. stephensi in Awash Sebat Kilo town, Ethiopia. We used membrane feeding assays to assess competence of local An. stephensi to P. vivax and P. falciparum isolates from clinical patients. 75.3% of the examined waterbodies were infested with An. stephensi developmental stages that were genetically closely related to isolates from Djibouti and Pakistan. Both P. vivax and P. falciparum were detected in wild-caught adult An. stephensi. Local An. stephensi was more receptive to P. vivax compared to a colony of An. arabiensis. We conclude that An. stephensi is an established vector in this part of Ethiopia, highly permissive for local P. vivax and P. falciparum isolates and presents an important new challenge for malaria control. Summary of the articleAn. stephensi, a metropolitan malaria vector that recently expanded to the Horn of African, was highly susceptible to local P. falciparum and P. vivax isolates from Ethiopia and may increase malariogenic potential of rapidly expanding urban settings in Africa.

microbiology↗

bioRxiv2019

Geographical distribution of Anopheles stephensi in eastern Ethiopia

BackgroundThe recent detection of the South Asian malaria vector An. stephensi in Ethiopia and other regions in the Horn of Africa has raised concerns about its potential impact on malaria transmission. We report here findings of survey for this species in eastern Ethiopia using both morphological and molecular methods for species identification.\n\nMethodsAdult and larval/pupal collections were conducted at ten sites in eastern Ethiopia and Anopheles specimens species were determined using standard morphological keys and genetic analysis.\n\nResultsIn total, 2,231 morphologically identified An. stephensi were collected. A molecular approach incorporating both PCR endpoint assay and sequencing of portions of the internal transcribed spacer 2 (ITS2) and cytochrome oxidase I (COI) loci confirmed the identity of the An. stephensi in most cases (119/124 of the morphologically identified An. stephensi confirmed molecularly). Additionally, we observed Aedes aegypti larvae and pupae at many of the An. stephensi larval habitats.\n\nConclusionsOur findings show that An. stephensi is widely distributed in eastern Ethiopia and highlight the need for further surveillance in the southern, western and northern parts of the country and throughout the Horn of Africa.

ecology↗

bioRxiv2019

Novel molecular targets for treating alcohol use disorder and hepatotoxicity

BackgroundNovel treatments for alcohol use disorder (AUD) and alcohol-related liver disease (ALD) are greatly needed. Genetic information can improve drug discovery rates by facilitating the identification of novel biological targets and potential drugs for repurposing. MethodsThe present study utilized a recently developed Bayesian approach, Integrative Risk Gene Selector (iRIGS), to identify additional risk genes for alcohol consumption using SNPs from the largest alcohol consumption GWAS to date (N = 941,280). iRIGS incorporates several genomic features and closeness of these genes in network space to compute a posterior probability for protein coding genes near each SNP. We subsequently used the Target Central Resource Database to search for drug-protein interactions for these newly identified genes and previously identified risk genes for alcohol consumption. ResultsWe identified several genes that are novel contributions to the previously published alcohol consumption GWAS. Namely, ACVR2A, which is critical for liver function and linked to anxiety and cocaine self-administration, and PRKCE, which has been linked to alcohol self-administration. Notably, only a minority of the SNPs (18.4%) were linked to genes with confidence ([≥].75), underscoring the need to apply multiple methods to assign function to loci. Finally, several previously identified risk genes for alcohol consumption code for proteins that are implicated in liver function and are targeted by drugs that are promising candidates for managing hepatotoxicity (e.g., metformin). ConclusionsThis study demonstrates the value of incorporating regulatory information and drug-protein interaction data to highlight additional molecular targets and drug repurposing candidates for treating AUD and ALD.

genetics↗

bioRxiv2019

Differential effects of open- and closed-loop intracortical microstimulation on firing patterns of neurons in distant cortical areas

BackgroundIntracortical microstimulation can be used successfully to modulate neuronal activity. Activity-dependent stimulation (ADS), in which action potentials recorded extracellularly from a single neuron are used to trigger stimulation at another cortical location (closed-loop), is an effective treatment for behavioral recovery after brain lesion in rodents. Neurophysiological changes in cortical communication induced by ADS, and how these changes differ from those induced by open-loop random stimulation (RS) are still not clear. ObjectivesWe investigated the ability of ADS and RS to induce changes in firing patterns in distant populations of neurons in healthy anesthetized rats. MethodsFor this study we used 23 adult Long-Evan rats, recording from a total of 591 neuronal units. Stimulation was delivered to either forelimb or barrel field somatosensory cortex, using either randomly-timed stimulus pulses or ADS triggered from neuronal spikes recorded in the rostral forelimb area (RFA) of the motor cortex. ResultsBoth RS and ADS stimulation protocols rapidly altered spike firing within RFA compared with no stimulation. Changes consisted of increases in mean firing rates and patterns of spike firing as measured by the revised Local Variation metric. ADS was more effective than RS in increasing short-latency evoked spikes during the stimulation periods, by producing a reliable, progressive increase in stimulus-related activity over time. ConclusionsThese results are critical for understanding the efficacy of electrical microstimulation protocols in altering activity patterns in interconnected brain networks. These data further strengthen the idea that activity-dependent microstimulation, can be used to modulate cortical state and functional connectivity.

neuroscience↗

bioRxiv2019

High genetic diversity of Plasmodium falciparum in the low transmission setting of the Kingdom of Eswatini

ABSTRACTO_ST_ABSBackgroundC_ST_ABSTo better understand transmission dynamics, we characterized Plasmodium falciparum (Pf) genetic diversity in Eswatini, where transmission is low and sustained by importation.\n\nMethods26 Pf microsatellites were genotyped in 66% of all confirmed cases from 2014-2016 (n=582). Population and within-host diversity were used to characterize differences between imported and locally-acquired infections, as determined by travel history. Logistic regression was used to assess the added value of diversity metrics to classify imported and local infections beyond epidemiology data alone.\n\nResultsThe parasite population in Eswatini was highly diverse (HE=0.75) and complex, with 67% polyclonal infections, a mean MOI of 2.2, and mean FWS of 0.84. Imported cases had comparable diversity to local cases, but exhibited higher MOI (2.4 versus 2.0; p=0.004) and lower mean FWS (0.82 vs. 0.85; p=0.03). Addition of MOI and FWS to multivariate analyses did not increase discrimination between imported and local infections.\n\nDiscussionIn contrast to the commonly held perception that Pf diversity declines with decreasing transmission intensity, isolates from Eswatini exhibited high parasite diversity consistent with high rates of malaria importation and limited local transmission. Estimates of malaria transmission intensity from genetic data need to consider the effect of importation, especially as countries near elimination.

genetics↗

bioRxiv2018

FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences

The growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), a next-generation CRISPR/Cas9 diagnostic method that takes advantage of the efficiency, specificity and flexibility of Cas9 to enrich for a programmed set of sequences. FLASH-NGS achieves up to 5 orders of magnitude of enrichment and sub-attomolar gene detection with minimal background. We provide an open-source software tool (FLASHit) for guide RNA design. Here we applied it to detection of antimicrobial resistance genes in respiratory fluid and dried blood spots, but FLASH-NGS is applicable to all areas that rely on multiplex PCR.

microbiology↗

bioRxiv2018

Sulforaphane Alters the Acidification of the Vacuole to Trigger Cell Death

Sulforaphane (SFN) is a compound [1-isothiocyanato-4-(methylsulfinyl)- butane] found in broccoli and other cruciferous vegetables that is currently of interest because of its potential as a chemopreventive and a chemotherapeutic drug. Recent studies in a diverse range of cellular and animal models have shown that SFN is involved in multiple intracellular signaling pathways that regulate cell death, cell cycle progression, and cell invasion. In order to better understand the mechanisms of action behind SFN-induced cell death, we undertook an unbiased genome wide screen with the yeast knockout (YKO) library to identify SFN sensitive (SFNS) mutants. Our mutants were enriched with knockouts in genes linked to vacuolar function suggesting a link between this organelle and SFNs mechanism of action in yeast. Our subsequent work revealed that SFN increases the vacuolar pH of yeast cells and that varying the vacuolar pH can alter the sensitivity of yeast cells to the drug. In fact, several mutations that lower the vacuolar pH in yeast actually made the cells resistant to SFN (SFNR). Finally, we show that human lung cancer cells with more acidic compartments are also SFNR suggesting that SFNs mechanism of action identified in yeast may carry over to higher eukaryotic cells.

cell biology↗

bioRxiv2018

A Framework for Predicting Design Failures in Engineered Genetic Codes

Extreme engineering of an organisms genetic code could impart true genetic incompatibility, even blocking effects of horizontal gene transfer and viral infection. Recent experiments exploring this possibility demonstrate that such radical genome engineering achievements are plausible. However, it is unclear when the modifications will compromise the fitness of an organism. Efforts to reformat an entire genome are difficult and expensive; computational methods predicting fruitful experimental trajectories could play a pivotal role in advancing such efforts. We present a framework for building in silico models to assist genome-scale engineering. Genetic code engineering requires choosing from many possible codon-usage schemes, to find a design that is viable and effective. We use machine learning to identify which alternative codon-usage schemes are likely to result in no observed viable cells. Our data-driven approach employs observations of how modifying codon usage in individual genes impacted observed viability in E. coli, revealing salient features for early identification of problematic genetic code designs. We achieved an average area under the receiver operating characteristic of 0.72 on out-ofsample data.\n\nAuthor SummaryAs machine learning and artificial intelligence play an increasingly central role in science and engineering, it will be important to establish standardized techniques that facilitate the dialogue between experimentation and modeling. Biological experimental techniques are concurrently evolving at a rapid pace, providing unique opportunities to collect high-quality, novel information that was previously unobtainable. This work navigates the landscape of this vast, new territory, identifies interesting landmarks for exploration and posits new approaches towards advancing our research efforts in these areas. In this work, we show that, using a small dataset of 47 observations and rigorous nested cross validation techniques, we can build a model that makes better-than-random predictions of how codon usage changes in essential genes influence viability in E. coli. These predictions can be used to inform experimental trajectories in both genetic code and codon optimization experiments. We discuss ways to improve this model, iteratively, by performing high value experiments that decrease uncertainty in predictions and extrapolation error. Finally, we present novel visualization methods to aid in developing intuitions for how re-coding impacts groups of genes. These methods are also useful tools in building important insights into how well machine learning algorithms can generalize to new data.

bioengineering↗

bioRxiv2018

Endogenous protection from ischemic brain injury by preconditioned monocytes

Exposure to low dose lipopolysaccharide prior to cerebral ischemia is neuroprotective in stroke models, a phenomenon termed preconditioning. While it is well established that lipopolysaccharide-preconditioning induces central and peripheral immune responses, the cellular mechanisms modulating ischemic injury remain unclear. Here, we investigated the role of immune cells in the brain protection afforded by preconditioning and we tested whether monocytes may be reprogrammed by ex vivo lipopolysaccharide exposure thus modulating the inflammatory injury after cerebral ischemia in male mice. We found that systemic injection of low-dose lipopolysaccharide induces a distinct subclass of CD115+Ly6Chi monocytes that protect the brain after transient middle cerebral artery occlusion in mice. Remarkably, adoptive transfer of monocytes isolated from preconditioned mice into naive mice 7 hours after transient middle cerebral artery occlusion reduced brain injury. Gene expression and functional studies showed that IL-10, iNOS and CCR2 in monocytes are essential for the neuroprotection. This protective activity was elicited even if mouse or human monocytes were exposed ex vivo to lipopolysaccharide and then injected into male mice after stroke. Cell tracking studies showed that protective monocytes are mobilized from the spleen and reach brain and meninges, wherein they suppressed post-ischemic inflammation and neutrophils influx into the brain parenchyma. Our findings unveil a previously unrecognized subpopulation of splenic monocytes capable to protect the brain with an extended therapeutic window, and provide the rationale for cell therapies based on the delivery of autologous or allogeneic protective monocytes into patients with ischemic stroke.\n\nSignificance StatementInflammation is a key component of the pathophysiology of the brain in stroke, a leading cause of death and disability with limited therapeutic options. Here, we investigate endogenous mechanisms of protection against cerebral ischemia. Using LPS preconditioning as an approach to induce ischemic tolerance in mice, we found the generation of neuroprotective monocytes within the spleen from where they traffic to the brain and meninges suppressing post-ischemic inflammation. Importantly, systemic LPS preconditioning can be mimicked by adoptive transfer of in vitro-preconditioned mouse or human monocytes at translational relevant time points after stroke. This model of neuroprotection may facilitate clinical efforts to increase the efficacy of bone marrow mononuclear cell treatments in acute neurological diseases such as cerebral ischemia.

neuroscience↗

bioRxiv2017

Restriction of dietary protein leads to conditioned protein preference and elevated palatability of protein-containing food in rats.

The mechanisms by which intake of dietary protein is regulated are poorly understood despite their potential involvement in determining food choice and appetite. In particular, it is unclear whether protein deficiency results in a specific appetite for protein and whether influences on diet are immediate or develop over time. To determine the effects of protein restriction on consumption, preference, and palatability for protein we assessed patterns of intake for casein (protein) and maltodextrin (carbohydrate) solutions in adult rats. To induce a state of protein restriction, rats were maintained on a low protein diet (5% casein) and compared to control rats on non-restricted diet (20% casein). Under these dietary conditions, relative to control rats, protein-restricted rats exhibited hyperphagia without weight gain. After two weeks, on alternate conditioning days, rats were given access to either isocaloric casein or maltodextrin solutions that were saccharin-sweetened and distinctly flavoured whilst consumption and licking patterns were recorded. This allowed rats to learn about the post-ingestive nutritional consequences of the two different solutions. Subsequently, during a preference test when rats had access to both solutions, we found that protein-restricted rats exhibited a preference for casein over carbohydrate whereas non-restricted rats did not. Analysis of lick microstructure revealed that this preference was associated with an increase in cluster size and number, reflective of an increase in palatability. In conclusion, protein-restriction induced a conditioned preference for protein, relative to carbohydrate, and this was associated with increased palatability.

neuroscience↗

bioRxiv2017

p53 suppresses mutagenic RAD52 and POLθ pathways by orchestrating DNA replication restart homeostasis

Classically, p53 tumor-suppressor acts in transcription, apoptosis, and cell-cycle arrest. Yet, replication-mediated genomic instability is integral to oncogenesis, and p53 mutations promote tumor progression and drug-resistance. By delineating human and murine separation-of-function p53 alleles, we find that p53 null and gain-of-function (GOF) mutations exhibit defects in restart of stalled or damaged DNA replication forks driving genomic instability independent of transcription activation. By assaying protein-DNA fork interactions in single cells, we unveil a p53-MLL3-enabled recruitment of MRE11 DNA replication restart nuclease. Importantly, p53 defects or depletion unexpectedly allow mutagenic RAD52 and POL{theta} pathways to hijack stalled forks, which we find reflected in p53 defective breast-cancer patient COSMIC mutational signatures. These data uncover p53 as a keystone regulator of replication homeostasis within a DNA restart network. Mechanistically, this has important implications for development of resistance in cancer therapy. Combined, these results define an unexpected role for p53 suppression of replication genome instability.

genetics↗