Biology subjects

Mohamed, A.

Publications and source records attributed to Mohamed, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

standR: a Bioconductor package for analysing transcriptomic Nanostring GeoMx DSP data

To gain a better understanding of the complexity of gene expression in normal and diseased tissues it is important to account for the spatial context and identity of cell in situ. State-of-the-art spatial profiling technologies, such as the Nanostring GeoMx Digital Spatial Profiler (DSP), now allow quantitative spatially resolved measurement of the transcriptome in tissues. However, the bioinformatics pipelines currently used to analyse GeoMx data often fail to successfully account for the technical variability within the data and the complexity of experimental designs, thus limiting the accuracy and reliability of subsequent analysis. Carefully designed quality control workflows, that include in-depth experiment-specific investigations into technical variation and appropriate adjustment for such variation can address this issue. Here we present standR, a R/Bioconductor package that enables an end-to-end analysis of GeoMx DSP data. With four case studies from previously published experiments, we demonstrate how the standR workflow can enhance the statistical power of GeoMx DSP data analysis and how application of standR enables scientists to develop in-depth insights into the biology of interest.

bioinformatics↗

bioRxiv2023

Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation

T-cells are critical components of the adaptive immune system. Upon activation, they acquire effector functions through a complex interplay between mRNA transcripts and proteins, the landscape of which remains to be fully elucidated. In this resource article, we present an integrative temporal proteomic and transcriptomic analysis of primary human CD4+ and CD8+ T-cells following ex vivo activation with anti-CD3/CD28 Dynabeads. Our data reveal a time-dependent dissociation between the T-cell transcriptome and proteome during activation. A transient downregulation of GLUT1, the central glucose transporter in T-cells, marked the onset of reprogramming in both CD4+ and CD8+ T-cells. At late activation, CD4+ T-cells upregulated enzymes associated with degradation of fatty acids while CD8+ T-cells preferentially upregulated enzymes in the metabolism of cofactors and vitamins. Surprisingly, we found that activated CD4+ and CD8+ T-cells became transcriptionally more divergent at the same time their proteome became more similar. In addition to the metabolic reprogramming highlighted in our analysis, this dataset provides a public resource for understanding temporal molecular changes governing the acquisition of effector functions by T-cells.

systems biology↗

bioRxiv2022

Cdkn2a regulates beige fat maintenance through BECN1-mediated autophagy

A potential therapeutic target to curb the obesity and diabetes epidemic is thermogenic beige adipocytes. However, beige adipocytes quickly transition into white adipocytes upon removing stimuli. Here, we define the critical role of Cdkn2a as a molecular pedal for the beige-to-white transition. Beige adipocytes lacking Cdkn2a exhibit prolonged lifespan, and mice are more resistant to diet-induced obesity, along with enhanced energy expenditure and improved glucose tolerance. Mechanistic studies demonstrate that Cdkn2a promotes the expression and activity of BECN1 by directly binding to its mRNA and its negative regulator BCL2L1, activating autophagy and accelerating the beige-to-white transition. Notably, reactivating autophagy by pharmacological or genetic methods abolishes beige adipocyte maintenance induced by Cdkn2a-ablation. Furthermore, hyperactive BECN1 alone significantly accelerates the beige-to-white transition. Collectively, these findings show that Cdkn2a-mediated autophagy serves as a brake system for beige adipocyte maintenance and is a highly promising target for anti-obesity and anti-diabetes therapy. HighlightsO_LICdkn2a ablation promotes beige fat maintenance and ameliorates diet-induced obesity C_LIO_LILoss of Cdkn2a retains beige adipocytes by inhibiting BECN1-mediated autophagy C_LIO_LICdkn2a modulates BECN1 by binding to its mRNA and its inhibitor BCL2L1, respectively C_LIO_LIHyperactive BECN1 is sufficient to accelerate the beige-to-white transition C_LI

cell biology↗

bioRxiv2022

Mushroom body output neurons MBONa1/a2 define an odor intensity channel that regulates behavioral odor discrimination learning in larval Drosophila

The sensitivity of animals to sensory input must be regulated to ensure that signals are detected and also discriminable. However, how circuits regulate the dynamic range of sensitivity to sensory stimuli is not well understood. A given odor is represented in the insect mushroom bodies (MBs) by sparse combinatorial coding by Kenyon cells (KCs), forming an odor quality representation. To address how intensity of sensory stimuli is processed at the level of the MB input region, the calyx, we characterized a set of novel mushroom body output neurons that respond only to high odor concentrations. We show that a pair of MB calyx output neurons, MBONa1/2, are postsynaptic in the MB calyx, where they receive extensive synaptic inputs from KC dendrites, the inhibitory feedback neuron APL, and octopaminergic sVUM1 neurons, but relatively few inputs from projection neurons. This pattern is broadly consistent in the third instar larva as well as in the first instar connectome. MBONa1/a2 presynaptic terminals innervate a region immediately surrounding the MB medial lobe output region in the ipsilateral and contralateral brain hemispheres. By monitoring calcium activity using jRCamP1b, we find that MBONa1/a2 responses are odor-concentration dependent, responding only to ethyl acetate (EA) concentrations higher than a 200-fold dilution, in contrast to MB neurons which are relatively concentration-invariant and respond to EA dilutions as low as 10-4. Optogenetic activation of the calyx-innervating sVUM1 modulatory neurons originating in the SEZ (Subesophageal zone), did not show a detectable effect on MBONa1/a2 odor responses. Optogenetic activation of MBONa1/a2 using CsChrimson impaired odor discrimination learning compared to controls. We propose that MBONa1/a2 form an output channel of the calyx, summing convergent sensory and modulatory input, firing only to high odor concentration, and might affect the activity of downstream MB targets.

neuroscience↗

bioRxiv2022

Biosphere functional integrity for people and Planet

Defining a safe and just biosphere space requires a synthetic scaleable measure of biosphere functional integrity to secure Natures Contributions to People (NCP). Using a systematic review of 153 peer-reviewed studies we estimated the minimum level of functional integrity needed to secure multiple critical NCP, including pollination, pest and disease control, water quality regulation, soil protection, recreation and natural hazards mitigation in human-modified landscapes. We characterise functional integrity by the quantity, quality and spatial configuration of (semi-)natural habitat within any landscape. We find that at least 20-25% of structurally complex and biologically diverse (semi-)natural habitat in each 1 km2 of land area is needed to maintain the supply of multiple NCP simultaneously. Exact quantity, quality and spatial configuration required is dependent on local context, and may differ for individual NCP. Today, about 50-60% of human-modified lands have less than 10% and 20% (semi-)natural habitat per 1 km2 respectively. These areas require immediate attention to regenerate functional integrity in order to secure ecological functioning in those landscapes.

ecology↗

bioRxiv2022

p38 MAPK Signaling Enhances Reovirus Replication by Facilitating Efficient Virus Entry, Virus Capsid Uncoating and Post-Uncoating Steps.

Mammalian orthoreovirus serotype 3 Dearing an orphan human virus currently being pursued as an oncolytic virus in multiple phase I/II clinical trials. Previous clinical trials have emphasized the importance of patient pre-screening for prognostic markers to improve therapeutic success. However, currently, only generic cancer markers such as EGFR, Hras, Kras, Nras, Braf and/or p53 are utilized and have exhibited limited benefit in predicting therapeutic efficacy. Utilization of more specific markers that influence specific steps during reovirus replication could prove beneficial as prognostic markers. This study delineated the role of p38 MAPK signaling during reovirus infection and illustrated a connection between specific p38 MAPK isoforms and reovirus infection. Using a panel of specific p38 MAPK inhibitors and an inactive inhibitor analogue, we demonstrated that p38 MAPK signaling is essential for establishment of reovirus infection by enhancing reovirus endocytosis, facilitating efficient reovirus uncoating at the endo-lysosomal stage, and augmenting post uncoating replication steps. Using a broad panel of human breast cancer cell lines, we observed susceptibility of reovirus infection corresponded with virus binding and uncoating efficiency, which was strongly correlated with status of the p38{beta} isoform. Together, our study proposes p38{beta} as a potential prognostic marker for early stages of reovirus infection that are crucial to establishment of successful reovirus infection.

cell biology↗

bioRxiv2022

Dissecting neural computations of the human auditory pathway using deep neural networks for speech

The human auditory system extracts rich linguistic abstractions from the speech signal. Traditional approaches to understand this complex process have used classical linear feature encoding models, with limited success. Artificial neural networks have recently achieved remarkable speech recognition performance and offer potential alternative computational models of speech processing. We used the speech representations learned by state-of-the-art deep neural network (DNN) models to investigate neural coding across the ascending auditory pathway from the peripheral auditory nerve to auditory speech cortex. We found that representations in hierarchical layers of the DNN correlated well to neural activity throughout the ascending auditory system. Unsupervised speech models achieve the optimal neural correlations among all models evaluated. Deeper DNN layers with context-dependent computations were essential for populations of high order auditory cortex encoding, and the computations were aligned to phonemic and syllabic context structures in speech. Accordingly, DNN models trained on a specific language (English or Mandarin) predicted cortical responses in native speakers of each language. These results reveal convergence between representations learned in DNN models and the biological auditory pathway and provide new approaches to modeling neural coding in the auditory cortex.

neuroscience↗

bioRxiv2022

Molecular profiling of XPO1 inhibitor and gemcitabine-nab-paclitaxel combination in cellular and LSL-Kras G12D/+; Trp53 fl/+; Pdx1-Cre (KPC) pancreatic cancer model

The majority of pancreatic ductal adenocarcinoma (PDAC) patients experience disease progression while on treatment with gemcitabine and nab-Paclitaxel (GemPac) treatment indicating the need for more effective combinations for this recalcitrant disease. Earlier we showed that nuclear exporter protein exportin 1 (XPO1) is a valid therapeutic target in PDAC and the selective inhibitor of nuclear export (SINE) selinexor (Sel), synergistically enhances the efficacy of GemPac in pancreatic cancer cells, spheroids, patient derived tumors and had promising activity in a phase I study in patients with PDAC. Here we investigated the mechanisms of synergy by molecular profiling of Sel or Sel-GemPac treated PDAC cells, in vitro and by utilizing genetically modified LSL-Kras G12D/+; Trp53 fl/+; Pdx1-Cre (KPC) mouse model. In KPC model, Sel given with GemPac at a sub-MTD dose enhanced the survival compared to controls (p < 0.05). Molecular analysis of residual KPC tumors showed re-organization of tumor stromal architecture, suppression of proliferation and nuclear retention of tumor suppressors. Single cell nuclear RNA sequencing (snRNAseq) revealed significant loss of cellular clusters in the Sel-GemPac treated mice including CD44 stem cell population. RNA-seq, Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) analysis showed inhibition of several tumor promoting molecules. Prioritized RNA-seq identified molecules were validated in in vitro or in the PDAC patient samples through siRNA mediated silencing, quantitative gene expression, cytotoxicity assays and confirmed their role in observed synergy. Sel or Sel-GemPac caused broad penetration in PDAC supporting signaling networks.

cancer biology↗

bioRxiv2022

vissE: A versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis

Functional analysis of high throughput experiments using pathway analysis is now ubiquitous. Though powerful, these methods often produce thousands of redundant results owing to knowledgebase redundancies upstream. This scale of results hinders extensive exploration by biologists and often leads to investigator biases due to previous knowledge and expectations. To address this issue, we present vissE, a flexible network-based analysis method that summarises redundancies into biological themes and provides various analytical modules to characterise and visualise them with respect to the underlying data, thus providing a comprehensive view of the biological system. We demonstrate vissEs versatility by applying it to three different technologies: bulk, single-cell and spatial transcriptomics. Applying vissE to a factor analysis of a breast cancer spatial transcriptomic data, we identified stromal phenotypes that support tumour dissemination. Its adaptability allows vissE to enhance all existing gene-set enrichment and pathway analysis workflows, removing investigator bias from molecular discovery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/483195v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1c384b0org.highwire.dtl.DTLVardef@13c6bd3org.highwire.dtl.DTLVardef@1cb1d91org.highwire.dtl.DTLVardef@24cbf_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2021

SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed over 6 million individuals worldwide and continues to spread in countries where vaccines are not yet widely available, or its citizens are hesitant to become vaccinated. Therefore, it is critical to unravel the molecular mechanisms that allow SARS-CoV-2 and other coronaviruses to infect and overtake the host machinery of human cells. Coronavirus replication triggers endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR), a key host cell pathway widely believed essential for viral replication. We examined the master UPR sensor IRE1 kinase/RNase and its downstream transcription factor effector XBP1s, which is processed through an IRE1-mediated mRNA splicing event, in human lung-derived cells infected with betacoronaviruses. We found human respiratory coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome coronavirus (MERS-CoV), and murine coronavirus (MHV) all induce ER stress and strongly trigger the kinase and RNase activities of IRE1 as well as XBP1 splicing. In contrast, SARS-CoV-2 only partially activates IRE1 through autophosphorylation, but its RNase activity fails to splice XBP1. Moreover, while IRE1 was dispensable for replication in human cells for all coronaviruses tested, it was required for maximal expression of genes associated with several key cellular functions, including the interferon signaling pathway, during SARS-CoV-2 infection. Our data suggest that SARS-CoV-2 actively inhibits the RNase of autophosphorylated IRE1, perhaps as a strategy to eliminate detection by the host immune system. IMPORTANCESARS-CoV-2 is the third lethal respiratory coronavirus after MERS-CoV and SARS-CoV to emerge this century, causing millions of deaths world-wide. Other common coronaviruses such as HCoV-OC43 cause less severe respiratory disease. Thus, it is imperative to understand the similarities and differences among these viruses in how each interacts with host cells. We focused here on the inositol-requiring enzyme 1 (IRE1) pathway, part of the host unfolded protein response to virus-induced stress. We found that while MERS-CoV and HCoV-OC43 fully activate the IRE1 kinase and RNase activities, SARS-CoV-2 only partially activates IRE1, promoting its kinase activity but not RNase activity. Based on IRE1-dependent gene expression changes during infection, we propose that SARS-CoV-2 prevents IRE1 RNase activation as a strategy to limit detection by the host immune system.

microbiology↗

bioRxiv2021

Alpha-Gal Syndrome: Involvement of Amblyomma americanum α-D-galactosidase and β-1,4 Galactosyltransferase enzymes in α-gal metabolism

Alpha-Gal Syndrome (AGS) is an IgE-mediated delayed-type hypersensitivity reaction to the oligosaccharide galactose--1,3-galactose (-gal) injected into humans from the lone star tick (Amblyomma americanum) bite. This study aims at the functional characterization of two tick enzymes, -D-galactosidase (ADGal) and -1,4 galactosyltransferase ({beta}-1,4GalT) in -gal metabolism. The ADGal enzyme cleaves terminal -galactose moieties from glycoproteins and glycolipids, whereas {beta}-1,4GalT transfers -galactose to a {beta}1,4 terminal linkage acceptor sugars: GlcNAc, Glc, and Xyl in various processes of glycoconjugate synthesis. An RNA interference approach was utilized to silence ADGal and {beta}-1,4GalT in Am. americanum to examine their functional role in -gal metabolism and AGS onset. Silencing of ADGal led to the significant down regulation of genes involved in galactose metabolism and transport in Am. americanum. Immunoblot and N-glycan analysis of the Am. americanum salivary glands showed a significant reduction in -gal levels in silenced tissues. However, there was no significant difference in the level of -gal in {beta}-1,4GalT silenced tick salivary glands. A basophil-activation test showed a decrease in the frequency of activated basophil by ADGal silenced salivary glands. These results provide an insight into the role of -D galactosidase & {beta}-1,4GalT in tick biology and the probable involvement in the onset of AGS.

molecular biology↗

bioRxiv2021

Cannabidiol Inhibits SARS-CoV-2 Replication and Promotes the Host Innate Immune Response

The rapid spread of COVID-19 underscores the need for new treatments. Here we report that cannabidiol (CBD), a compound produced by the cannabis plant, inhibits SARS-CoV-2 infection. CBD and its metabolite, 7-OH-CBD, but not congeneric cannabinoids, potently block SARS-CoV-2 replication in lung epithelial cells. CBD acts after cellular infection, inhibiting viral gene expression and reversing many effects of SARS-CoV-2 on host gene transcription. CBD induces interferon expression and up-regulates its antiviral signaling pathway. A cohort of human patients previously taking CBD had significantly lower SARS-CoV-2 infection incidence of up to an order of magnitude relative to matched pairs or the general population. This study highlights CBD, and its active metabolite, 7-OH-CBD, as potential preventative agents and therapeutic treatments for SARS-CoV-2 at early stages of infection.

microbiology↗

bioRxiv2020

Sclerostin depletion induces inflammation in the bone marrow of mice

Romosozumab, a humanized monoclonal antibody specific for sclerostin, has been approved for treatment of post-menopausal women with osteoporosis at high risk for fracture. In several Phase III clinical trials, romosozumab decreased the risk of vertebral fractures up to 73% and increased total hip area bone mineral density by 3.2%. Previous work in 12 to 15-week-old sclerostin-knockout (Sost-/-) mice indicated that changes in immune cell development occur in the bone marrow (BM), which could be a possible side effect to follow in human patients. Our overall goal was to define the mechanisms that guide behavior of long-term hematopoietic stem cells (LT-HSCs) after exposure to an irregular BM microenvironment. SOST plays an important role in maintaining bone homeostasis, as demonstrated by the increased ratio of bone volume to total volume observed in Sost-/- mice. Here, we examined the effects of short-term sclerostin depletion in the BM on hematopoiesis in young (8 week-old) mice receiving sclerostin-antibody (Scl-Ab) treatment for 6 weeks, and the effects of long-term Sost-deficiency on wild-type (WT) LT-HSCs transplanted into older (16-22 week-old) cohorts of Sost-/- mice. Our analyses revealed an increased frequency of granulocytes and decreased frequency of lymphocytes in the BM of Scl-Ab treated mice and WT[->]Sost-/- hematopoietic chimeras, indicating myeloid-biased differentiation in Sost-deficient BM microenvironments. This myeloid bias extended to extramedullary hematopoiesis in the spleen and was correlated with an increase in inflammatory cytokines TNF, IL-1 and MCP-1 in the serum of the Sost-/- BM. Additionally, we observed alterations in erythrocyte differentiation in the BM and spleen of Sost-/- mice. Taken together, our current study indicates novel roles for Sost in the regulation of myelopoiesis and control of inflammation in the BM. Our animal studies strongly recommend tracking of hematopoietic function in patients treated with romosozumab.

immunology↗

bioRxiv2020

Integrated transcriptome, DNA methylome and chromatin state accessibility landscapes reveal regulators of Atlantic salmon maturation

Despite sexual development being ubiquitous to vertebrates, the epigenetic mechanisms controlling this fundamental transition remain largely undocumented in many organisms. Through whole-methylome, whole-transcriptome and chromatin landscape sequencing, we discovered global control mechanisms as well as specific regulators of sexual maturation in Atlantic salmon. This large integrated study was based on an experimental time course that successfully sampled the period when Atlantic salmon commence their trajectory towards sexual maturation. Co-analysis of DNA methylome and gene expression changes revealed chromatin remodelling genes arid1b and smarca2 were both significantly hypermethylated and upregulated in the ovary during the onset of maturation. We also observed changes in chromatin state landscape occurred early in the transition and were strongly correlated with fundamental remodelling of gene expression. Finally, we integrated our multiomics datasets to identify trim25 and znf423 as key regulators in the pituitary that underwent 60 fold change in connectivity during the transition to sexual maturation. The study provides a comprehensive view of the spatiotemporal changes involved in a complex trait and opens the door to future efforts aiming to manipulate puberty in an economically important aquaculture species.

genomics↗

bioRxiv2020

Comparative study of a 3CLpro inhibitor and remdesivir against both major SARS-CoV-2 clades in human airway models

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of Coronavirus Disease 2019 (COVID-19). There is a dire need for novel effective antivirals to treat COVID-19, as the only approved direct-acting antiviral to date is remdesivir, targeting the viral polymerase complex. A potential alternate target in the viral life cycle is the main SARS-CoV-2 protease 3CLpro (Mpro). The drug candidate PF-00835231 is the active compound of the first anti-3CLpro regimen in clinical trials. Here, we perform a comparative analysis of PF-00835231, the pre-clinical 3CLpro inhibitor GC-376, and the polymerase inhibitor remdesivir, in alveolar basal epithelial cells modified to express ACE2 (A549+ACE2 cells). We find PF-00835231 with at least similar or higher potency than remdesivir or GC-376. A time-of-drug-addition approach delineates the timing of early SARS-CoV-2 life cycle steps in A549+ACE2 cells and validates PF-00835231s early time of action. In a model of the human polarized airway epithelium, both PF-00835231 and remdesivir potently inhibit SARS-CoV-2 at low micromolar concentrations. Finally, we show that the efflux transporter P-glycoprotein, which was previously suggested to diminish PF-00835231s efficacy based on experiments in monkey kidney Vero E6 cells, does not negatively impact PF-00835231 efficacy in either A549+ACE2 cells or human polarized airway epithelial cultures. Thus, our study provides in vitro evidence for the potential of PF-00835231 as an effective SARS-CoV-2 antiviral and addresses concerns that emerged based on prior studies in non-human in vitro models. ImportanceThe arsenal of SARS-CoV-2 specific antiviral drugs is extremely limited. Only one direct-acting antiviral drug is currently approved, the viral polymerase inhibitor remdesivir, and it has limited efficacy. Thus, there is a substantial need to develop additional antiviral compounds with minimal side effects and alternate viral targets. One such alternate target is its main protease, 3CLpro (Mpro), an essential component of the SARS-CoV-2 life cycle processing the viral polyprotein into the components of the viral polymerase complex. In this study, we characterize a novel antiviral drug, PF-00835231, which is the active component of the first-in-class 3CLpro-targeting regimen in clinical trials. Using 3D in vitro models of the human airway epithelium, we demonstrate the antiviral potential of PF-00835231 for inhibition of SARS-CoV-2.

microbiology↗

bioRxiv2020

Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes

High-throughput Plasmodium genomic data is increasingly useful in assessing prevalence of clinically important mutations and malaria transmission patterns. Understanding parasite diversity is important for identification of specific human or parasite populations that can be targeted by control programs, and to monitor the spread of mutations associated with drug resistance. An up-to-date understanding of regional parasite population dynamics is also critical to monitor the impact of control efforts. However, this data is largely absent from high-burden nations in Africa, and to date, no such analysis has been conducted for malaria parasites in Tanzania country-wide. To this end, over 1,000 P. falciparum clinical isolates were collected in 2017 from 13 sites in seven administrative regions across Tanzania, and parasites were genotyped at 1,800 variable positions genome-wide using molecular inversion probes. Population structure was detectable among Tanzanian P. falciparum parasites, roughly separating parasites from the northern and southern districts and identifying genetically admixed populations in the north. Isolates from geographically close districts were more likely to be genetically related compared to parasites sampled from more distant districts. Known drug resistance mutations were seen at increased frequency in northern districts, and additional variants with undetermined significance for antimalarial resistance also varied by geography. Malaria Indicator Survey (2017) data corresponded with genetic findings, including average region-level complexity-of-infection and malaria prevalence estimates. The parasite populations identified here provide important information on extant spatial patterns of genetic diversity of Tanzanian parasites, to which future surveys of genetic relatedness can be compared. SIGNIFICANCEDocumenting dynamics of malaria parasite genomics in high-transmission settings at scale in sub-Saharan Africa is critical for policy and decision making to support ongoing malaria elimination initiatives. Using molecular inversion probes, we genotyped over 1,000 Tanzanian Plasmodium falciparum samples collected country-wide in 2017 at hundreds of variable polymorphic positions across the genome. Frequencies of known drug resistance mutations were higher in northern districts of the country compared to the south. Results also showed a distinct isolation-by-distance pattern (whereby increasing geographic distance was correlated with decreasing genetic relatedness), as well as signals of higher genetic sharing between several southern districts. These results provide, for the first time, a picture of current within-country diversity of Tanzanian P. falciparum populations.

genomics↗

bioRxiv2020

Non-invasive surveys of mammalian viruses using environmental DNA

O_LIEnvironmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively to mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA have been applied to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent. C_LIO_LITo detect and identify known and novel mammalian viruses from eDNA/iDNA sources, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing. C_LIO_LIWe detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes. C_LIO_LIOur results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence. C_LI

molecular biology↗

bioRxiv2019

Hif-1alpha stabilisation is protective against infection in a zebrafish model of co-morbidity

Multi-drug resistant tuberculosis is a worldwide problem and there is an urgent need for host-derived therapeutic targets, circumventing emerging drug resistance. We have previously shown that hypoxia inducible-1 (Hif-1) stabilisation helps the host to clear mycobacterial infection via neutrophil activation. However, Hif-1 stabilisation has also been implicated in chronic inflammatory diseases caused by prolonged neutrophilic inflammation. Comorbid infection and inflammation can be found together in disease settings, so it is unclear as to whether Hif-1 stabilisation would be beneficial in a holistic disease setting. Here, we set out to understand the effects of Hif-1 on neutrophil behaviour in disease-relevant settings by combining two well-characterised in vivo zebrafish models: TB infection (Mycobacterium marinum infection) and wounding (tailfin transection). We demonstrate during systemic infection, that wounding leads to increased infection burden, but the protective effect of Hif-1 stabilisation remains. A local Mm infection near to the tailfin wound site caused neutrophil migration between sites that was reduced by Hif-1 stabilisation. Our data indicate that the protective effect of Hif-1 against Mm is maintained in the presence of inflammation, highlighting its potential as a host-derived target against TB infection in a disease relevant setting.

immunology↗