Biology subjects

Murphy, E.

Publications and source records attributed to Murphy, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Passage through submersible and Archimedes pumps results in decreased migration survival in coho salmon yearlings

Flood-control pumpstations compromise connectivity and survival for migratory fish globally, yet field evaluations of modern "fish-friendly" designs remain scarce. We evaluated out-migration survival and behavior of yearling coho salmon (Oncorhynchus kisutch) entrained through an open-Archimedes screw station (Hammersley) and a conventional radial station (Barrowtown) in the lower Fraser River floodplain, British Columbia. Using acoustic telemetry over two migration seasons (2024-2025), we tracked smolts across an 84-km corridor to New Westminster and modeled apparent survival using a Cormack-Jolly-Seber framework. Baseline natural mortality in downstream controls averaged 60% across years (cumulative survival: ~40%). Entrainment through the conventional radial station caused 87.5% mortality. The open-Archimedes station conferred an improvement over the conventional facility but still induced 11.5% mortality. Notably, pump-induced losses at the Archimedes pump were predominantly latent: while acute survival through immediate tailrace receivers was high (95-98%), survival deficits diverged downstream in the mainstem Fraser River. Entrainment also prolonged out-migration, causing up to a 10-day delay in 2024 driven by forebay holding and depressed downstream transit speeds. Our findings demonstrate that while open-Archimedes screws improve survival relative to legacy radial impellers, they still impose substantial latent mortality. In heavily altered basins where baseline smolt mortality is already high, additive losses from drainage infrastructure may exacerbate survival bottlenecks.

ecology↗

bioRxiv2026

Mutation of a single cysteine in CaMKIIδ protects the heart from ischemia-reperfusion Injury

CaMKII{delta} is the dominant isozyme of Ca2+/calmodulin-dependent protein kinase II in the heart. Under certain pathological conditions, it can be oxidized, causing a constitutive activation that can lead to cardiac failure. We recently showed that, in purified CaMKII{delta} exposed to oxidative conditions, a disulfide link formed between Cys273 and Cys290 causes this autonomous activation. Cys273 has a low pKa that facilitates the oxidation of its thiol to a sulfenic acid at physiological pH. Does this matter in vivo? To answer that question, we created a transgenic mouse with Cys273 mutated to serine (CaMKII{delta}C273S) to prevent disulfide formation. We conducted a detailed assessment of cardiac function at rest and in a dobutamine stress test. We found that the CaMKII{delta} Cys273Ser mutation does not have deleterious effects on cardiac physiology. Then, we assessed whether the mutation would protect the heart from ischemia-reperfusion in the Langendorff model. The CaMKII{delta}C273S mouse had improved cardiac function and decreased infarct size compared to the wild-type mouse. We conclude that blocking disulfide formation at Cys273 protects the heart against ischemia-reperfusion injury. Drugs that specifically target Cys 273 may be therapeutic in human cardiac disease.

biochemistry↗

bioRxiv2026

CAR T cell therapy selectively depletes disease-driving mutant calreticulin cells in xenotransplants and human organoid models of myelofibrosis

Targeted immunotherapies have revolutionized outcomes for lymphoid malignancies, but success in myeloid neoplasms is limited by the lack of amenable targets and immunologically hostile tumor microenvironment (TME). Myeloproliferative neoplasms are chronic myeloid blood cancers, a third of which are driven by mutations in calreticulin (mutCALR). This yields a common neoepitope that binds to, and activates, the thrombopoietin receptor and results in display of the oncoprotein on the extracellular membrane of disease-driving cells, exposing a therapeutic vulnerability. Here, we present a first-in-class chimeric antigen receptor (CAR) T-cell therapy that specifically targets mutCALR+ cells, both in vitro and in vivo. The CAR T-cell therapy selectively depleted mutCALR+ stem cells from patients with myelofibrosis while sparing healthy stem cells, and improved survival in mutCALR leukemia xenografts. To mimic myelofibrotic marrow, we developed a bespoke human chimeroid model and showed no decrease in the potency of CAR T cell-mediated target cell killing even in a fibrotic tumor microenvironment. We also devised a method to boost cell surface expression of mutCALR in CD34+ cells isolated from patients with accelerated/blast phase MPN (defined as >10 % blasts in peripheral blood or bone marrow), enhancing CAR T targeting. This study presents a therapeutic with potential to eradicate mutCALR-driven malignancies and highlights an innovative strategy to evaluate blood cancer-targeting immunotherapies in a relevant TME. One Sentence SummaryA first-in-class CAR T-cell therapy targeting mutant calreticulin selectively depletes malignant stem cells in vivo and in fibrotic human organoids.

cancer biology↗

bioRxiv2025

Old Goats: 3,000 years of genetic connectivity of the domestic goat in Ireland

The domestic goat likely first arrived to the island of Ireland as part of the introduction of agriculture approximately 5,900 years ago, and remains a part of the islands biocultural heritage. However, due to the challenges of differentiating goat remains from that of sheep using traditional archaeozoological approaches, there are few specimens specifically identified as goat. To address this we employed genetic, proteomics, and archaeozoological techniques to assess faunal remains from the Late Bronze assemblage of Haugheys Fort (Armagh) and medieval assemblage of Carrickfergus (Antrim). We identify these specimens as goats using proteomics and genetics, and additionally determine their molecular sex. Genomic data recovered from a Haugheys Fort goat reveals a three-millenia genetic connection between herds in the Late Bronze Age, medieval period, and the indigenous Irish breed extant today, the Old Irish Goat. We additionally find varying levels of inbreeding within goats from the settlement of Carrickfergus, suggesting possible mixed use of herds within medieval Irish society. Our results demonstrate the continuing potential of combining archaeological and biomolecular techniques to clarify existing ambiguities and at the same time reveal new facets of the past.

genomics↗

bioRxiv2025

Neural mechanisms of structural inference: an EEG investigation of linguistic phrase structure categorization

Language comprehension is a complex cognitive process of understanding spoken or written language, during which the brain derives meanings and interprets messages by constructing hierarchical structures from word sequences. A key component underlying this process is structural inference. This computation determines the syntactic category ("head") of phrases, such as noun phrases (NP) and verb phrases (VP). Categorization confers distinct semantic and distributional properties. However, isolating neural correlates of structural inference is challenging, as modulations of syntactic category usually alter lexical content. Here, we collected the electroencephalography (EEG) data while participants read Mandarin NPs and VPs, which differ in their syntactic "headedness" but with lexical-semantic, lexical-syntactic categories and word order strictly conserved. We found significant theta power increases at left central-parietal scalp sites in NPs relative to VPs around the presentation (0-210 ms) of the nouns, where only the nouns in NPs project a head. Both NPs and VPs relative to one-word phrases exhibited spatiotemporally consistent low-frequency power increases at the point of linguistic composition, consistent with previous studies. Overall, our findings offer novel constraints on neurocomputational accounts of linguistic structure-building through these previously undocumented signatures of syntactic inference.

neuroscience↗

bioRxiv2025

SHIP1 regulates TREM2 signalling and macrophage functions in a hiPSC-derived model

Genetic and functional studies strongly implicate microglia in the pathology of Alzheimers disease (AD). The Triggering Receptor Expressed on Myeloid cells 2 (TREM2) pathway is an important functional regulator of microglia in AD, promoting phagocytosis of apoptotic cells, debris and pathogenic proteins including amyloid beta (A{beta}). Additionally, genome-wide association studies have identified risk bearing polymorphisms in several members of the pathway including INPP5D, encoding the inositol phosphatase SHIP1. Recent studies utilising in vitro macrophage and microglia models and preclinical mouse models have identified a role for SHIP1 in both modulating TREM2 signalling and modulating neurotoxic microglial activation. In this study, we characterised the role of SHIP1 in regulating TREM2 signalling and global microglial functions using human induced pluripotent stem cell (hiPSC)-derived macrophages as a physiologically-relevant in vitro model of microglia. Isogenic parent and SHIP1 knockout (SHIP1 KO) lines were generated and macrophage phenotype and functions investigated. Knocking out SHIP1 was associated with a decreased expression of the lipopolysaccharide (LPS) co-receptor CD14, which translated to lower secretion of pro-inflammatory cytokines on stimulation with LPS. Additionally, SHIP1 KO hiPSC-derived macrophages showed decreased signalling upon TREM2 stimulation, which was further reflected in a reduced level of phagocytosis of apoptotic neurons compared to the parental line. The observed attenuated TREM2 signalling did not correspond to decreased TREM2 protein levels nor increased shedding of the receptor. Examination of macrophage scavenger receptor expression revealed reduced cell surface levels of CD163 and CD206 involved in resolution of inflammation but increased levels of the phagocytic receptor MerTK, while morphological analysis revealed a less amoeboid activated phenotype and increased adhesion. Taken together, our data indicates that SHIP1 plays a key role in regulating global macrophage functions in addition to modulating TREM2 signalling and inflammation.

immunology↗

bioRxiv2025

obABPP-HT*: A Precision-Engineered Activity Proteomics Pipeline for the Streamlined Discovery of Deubiquitinase Inhibitors

Deubiquitinases (DUBs), and the dysregulation thereof, are implicated in human disease. The recent inclusion of selective DUB inhibitors in clinical trials has heightened interest in DUB-focused drug discovery. Current DUB screening methods remain constrained, however, as they often rely on recombinant proteins that are truncated or derived from non-human sources, typically necessitating extensive optimisation of initial hits. We introduce a high-throughput, endogenous human DUB-focused activity proteomics workflow designed for the simultaneous screening and profiling of small, targeted libraries of catalytic group-reactive compounds. In a proof-of-concept screen, this innovative platform expanded the repertoire of electrophilic groups targeting DUBs, leading to the discovery of potent and selective inhibitors for USP47, OTUD7B, and USP5. Remarkably, these inhibitors required minimal or no optimisation to confirm the previously reported biological roles of the three DUBs, underscoring the advantages of this methodology for drug discovery applications.

biochemistry↗

bioRxiv2024

HSV-1 Infection Alters MAPT Splicing and Promotes Tau Pathology in Neural Models of Alzheimer's Disease

INTRODUCTIONHerpes simplex virus 1 (HSV-1) infection alters critical markers of Alzheimers Disease (AD) in neurons. One key marker of AD is the hyperphosphorylation of Tau, accompanied by altered levels of Tau isoforms. However, an imbalance in these Tau splice variants, specifically resulting from altered 3R to 4R MAPT splicing of exon 10, has yet to be directly associated with HSV-1 infection METHODSTo this end, we infected 2D and 3D human neural models with HSV-1 and monitored MAPT splicing and Tau phosphorylation. Further, we transduced SH-SY5Y-neurons with HSV-1 ICP27 which alters RNA splicing to analyze if ICP27 alone is sufficient to induce altered MAPT exon 10 splicing. RESULTSWe show that HSV-1 infection induces altered splicing of MAPT exon 10, increasing 4R-Tau protein levels, Tau hyperphosphorylation, and Tau oligomerization. DISCUSSIONOur experiments reveal a novel link between HSV-1 infection and the development of cytopathic phenotypes linked with AD progression. HIGHLIGHTSO_LIHSV-1 infection in forebrain organoids reduces the neurite length of MAP2-positive neurons. C_LIO_LIHSV-1 infection increases Tau hyperphosphorylation in both two-month-old and four-month-old forebrain organoids. C_LIO_LIHSV-1 infection increases Exon 10 containing (4R) MAPT mRNA and 4R-Tau protein expression in both forebrain organoids and human SH-SY5Y-neurons. C_LIO_LIHSV-1 ICP27 is both necessary and sufficient to induce increased 4R MAPT mRNA and 4R-Tau protein expression in SH-SY5Y-neurons. C_LIO_LIHSV-1 infection increases Tau oligomerization in both forebrain organoids and SH-SY5Y-neurons. C_LI

microbiology↗

bioRxiv2023

The incidence of movement disorders increases with age and contrasts with subtle and limited neuroimaging abnormalities in argininosuccinic aciduria.

Argininosuccinate lyase is integral to the urea cycle detoxifying neurotoxic ammonia and the nitric oxide biosynthesis cycle. Inherited argininosuccinate lyase deficiency causes argininosuccinic aciduria (ASA), a rare disease with hyperammonaemia and nitric oxide deficiency. Patients present with developmental delay, epilepsy and movement disorders, associated with nitric oxide-mediated downregulation of central catecholamine biosynthesis. A neurodegenerative phenotype has been proposed in ASA. To better characterise this neurodegenerative phenotype in ASA, we conducted a retrospective study in six paediatric and adult metabolic centres in the UK in 2022. We identified 60 patients and specifically looked for movement disorders-related symptoms: movement disorders such as ataxia, tremor and dystonia, hypotonia and abnormal behaviour. We analysed neuroimaging with diffusion tensor imaging (DTI) magnetic resonance imaging (MRI) in an ASA patient with movement disorders. We assessed conventional and DTI MRI alongside single photon emission computer tomography (SPECT) with dopamine analogue radionuclide 123I-ioflupane, in Asl-deficient mice treated by hASL mRNA with normalised ureagenesis. Movement disorders in ASA appears in the 2nd and 3rd decades of life, becoming more prevalent with ageing and independent from the age of onset of hyperammonaemia. Neuroimaging can show abnormal DTI features affecting both grey and white matter, preferentially basal ganglia. ASA mouse model with normalised ureagenesis did not recapitulate these DTI findings and showed normal 123I-ioflupane SPECT and cerebral dopamine metabolomics. Altogether these findings support the pathophysiology of a late-onset movement disorders with functional central catecholamine dysregulation but without or limited neurodegeneration of dopaminergic neurons, making these symptoms amenable to targeted therapy. SynopsisMovement disorders-related symptoms in ASA appear in the 2nd and 3rd decades of life, becoming more prevalent with age and shows abnormal neuroimaging features of basal ganglia in ASA patients, not recapitulated in ASA mice.

genetics↗

bioRxiv2023

Intercomparison of growth models for Antarctic krill (Euphausia superba): towards a generalised understanding

Antarctic krill is a key species of the Southern Ocean, impacted by climate change and human exploitation. Understanding how these changes affect the distribution and abundance of krill is crucial for generating projections of change for Southern Ocean ecosystems. Krill growth is an important indicator of habitat suitability and a series of models have been developed and used to examine krill growth potential at different spatial and temporal scales. The available models have been developed using a range of empirical and mechanistic approaches, which provide alternative perspectives and cross-validation of analyses of the key processes influencing krill growth. Here we undertake an intercomparison of a suite of the available models to understand their sensitivities to major driving variables. This illustrates that the results are strongly determined by the model structure and technical characteristics, and the data on which they were developed and validated. Our results emphasize the importance of assessing the constraints and requirements of individual krill growth models to ensure their appropriate application. The study also demonstrates the value of the development of alternative modelling approaches to identify key processes affecting the dynamics of krill. Of critical importance for modelling the growth of krill is appropriately assessing and accounting for differences in estimates of food availability resulting from alternative methods of observation. We suggest that an intercomparison approach is particularly valuable in the development and application of models for the assessment of krill growth potential at circumpolar scales and for future projections. As another result of the intercomparison, the implementations of the models used in this study are now publicly available for future use and analyses.

ecology↗

bioRxiv2023

Bulk RNA-Sequencing of small airway cell cultures from IPF and post-COVID lung fibrosis patients illustrates disease signatures and differential responses to TGF-β1 treatment

IPF is a condition in which an injury to the lung leads to the accumulation of scar tissue. This fibrotic tissue reduces lung compliance and impairs gas exchange. Studies have shown that infection with COVID-19 significantly worsens the clinical outcomes of IPF patients. The exact etiology of IPF is unknown, but recent evidence suggests that the distal small airways, (those having a diameter less than 2 mm in adults), play a role in the early pathogenesis of IPF. TGF-{beta}1 is a main driver of fibrosis in a variety of tissues; the binding of TGF-{beta}1 to its receptor triggers a signaling cascade that results in inflammatory signaling, accumulation of collagen and other components of the extracellular matrix, and immune system activation. This study aimed to investigate possible mechanisms that contribute to worsening lung fibrosis in IPF patients after being diagnosed with COVID-19, with a particular focus on the role of TGF-{beta}1. Small airway cell cultures derived from IPF and post-COVID-19 IPF patient transplant tissues were submitted for RNA-sequencing and differential gene expression analysis. The genetic signatures for each disease state were determined by comparing the differentially expressed genes present in the cells cultured under control conditions to cells cultured with TGF-{beta}1. The genes shared between the culture conditions laid the framework for determining the genetic signatures of each disease. Our data found that genes associated with pulmonary fibrosis appeared to be more highly expressed in the post-COVID fibrosis samples, under both control and TGF-{beta}1-treated conditions. A similar trend was noted for genes involved in the TGF-{beta}1 signaling pathway; the post-COVID fibrosis cell cultures seemed to be more responsive to treatment with TGF-{beta}1. Gene expression analysis, RT-PCR, and immunohistochemistry confirmed increased levels of BMP signaling in the IPF small airway cell cultures. These findings suggest that TGF-{beta}1 signaling in IPF small airway cells could be inhibited by BMP signaling, leading to the differences in genetic signatures between IPF and post-COVID fibrosis.

cell biology↗

bioRxiv2023

Mono-ADP-ribosyltransferase 1 (Artc1)-deficiency decreases tumorigenesis, increases inflammation, decreases cardiac contractility, and reduces survival

Arginine-specific mono-ADP-ribosylation is a reversible post-translational modification; arginine-specific, cholera toxin-like mono-ADP-ribosyltransferases (ARTCs) transfer ADP-ribose from NAD+ to arginine, followed by cleavage of ADP-ribose-(arginine)protein bond by ADP-ribosylarginine hydrolase 1 (ARH1), generating unmodified (arginine)protein. ARTC1 has been shown to enhance tumorigenicity as does Arh1 deficiency. In this study, Artc1-KO and Artc1/Arh1-double-KO mice showed decreased spontaneous tumorigenesis and increased age-dependent, multi-organ inflammation with upregulation of pro-inflammatory cytokine TNF-. In a xenograft model using tumorigenic Arh1-KO mouse embryonic fibroblasts (MEFs), tumorigenicity was decreased in Artc1-KO and heterozygous recipient mice, with tumor infiltration by CD8+ T cells and macrophages, leading to necroptosis, suggesting that ARTC1 promotes the tumor microenvironment. Furthermore, Artc1/Arh1-double-KO MEFs showed decreased tumorigenesis in nude mice, showing that tumor cells as well as tumor microenvironment require ARTC1. By echocardiography and MRI, Artc1-KO and heterozygous mice showed male-specific, reduced myocardial contractility. Furthermore, Artc1-KO male hearts exhibited enhanced susceptibility to myocardial ischemia-reperfusion-induced injury with increased receptor-interacting protein kinase 3 (RIP3) protein levels compared to WT mice, suggesting that ARTC1 suppresses necroptosis. Overall survival rate of Artc1-KO was less than their Artc1-WT counterparts, primarily due to enhanced immune response and inflammation. Thus, anti-ARTC1 agents may reduce tumorigenesis but may increase multi-organ inflammation and decrease cardiac contractility. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/527366v1_ufig1.gif" ALT="Figure 1"> View larger version (84K): org.highwire.dtl.DTLVardef@1cded54org.highwire.dtl.DTLVardef@9851ceorg.highwire.dtl.DTLVardef@22cd8aorg.highwire.dtl.DTLVardef@e42e7a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Optimization of genomewide CRISPR screens using AsCas12a and multi-guide arrays

Genomewide loss-of-function (LOF) screening using CRISPR (clustered regularly interspaced short palindromic repeats) has facilitated the discovery of novel gene functions across diverse physiological and pathophysiological systems. A challenge with conventional genomewide CRISPR/Cas9 libraries is the unwieldy size (60,000 to 120,000 constructs), which is resource intensive and prohibitive in some experimental contexts. One solution to streamlining CRISPR screening is by multiplexing two or more guides per gene on a single construct, which enables functional redundancy to compensate for suboptimal gene knockout by individual guides. In this regard, AsCas12a (Cpf1) and its derivatives, e.g., enhanced AsCas12a (enAsCas12a), have enabled multiplexed guide arrays to be specifically and efficiently processed for genome editing. Prior studies have established that multiplexed CRISPR/Cas12a libraries perform comparably to the larger equivalent CRISPR/Cas9 libraries, yet the most efficient CRISPR/Cas12a library design remains unresolved. Here, we demonstrate that CRISPR/Cas12a genomewide LOF screening performed optimally with three guides arrayed per gene construct and could be adapted to robotic cell culture without noticeable differences in screen performance. Thus, the conclusions from this study provide novel insight to streamlining genomewide LOF screening using CRISPR/Cas12a and robotic cell culture.

genetics↗

bioRxiv2022

Small molecule inhibition of multiple RNA binding proteins underlies Musashi-2 independent phenotypes

RNA binding proteins (RBPs) are key regulators of gene expression. Small molecules targeting these RBP-RNA interactions are a rapidly emerging class of therapeutics for treating a variety of diseases. Ro-08-2750 (Ro) is a small molecule inhibitor identified as a competitive inhibitor of Musashi(MSI)-RNA interactions. Here we show Ro potently inhibits adrenocortical steroidogenesis and viability independent of MSI2 in multiple cell lines. We identified Ro-interacting proteins using an unbiased proteome-wide approach and discovered it is broadly targeting RBPs. To confirm this finding, we leveraged the large-scale ENCODE data and found a subset of RBPs whose depletion phenocopies Ro inhibition. We conclude that Ro is a promiscuous inhibitor of multiple RBPs, many containing RRM1 domains. Moreover, we provide a general framework for validating the specificity and identifying targets of RBP inhibitors in a cellular context.

molecular biology↗

bioRxiv2022

The spatiotemporal dynamics of semantic integration in the human brain

Language depends critically on the integration of lexical information to derive semantic concepts. The neurobiology of this fundamental aspect of human cognition remains mostly unknown. Limitations of spatiotemporal resolution have previously rendered it difficult to disentangle processes involved in semantic integration from independent computations such as tracking word meaning and establishing referents. We utilized intracranial recordings (n = 58) during the presentation of orthographic descriptions that were either referential or non-referential to a common object. Referential contexts enabled high frequency broadband gamma activation (70-150 Hz) of a distributed network including the inferior frontal sulcus (IFS), medial parietal cortex (MPC) and medial temporal lobe (MTL) in the left, language-dominant hemisphere. Components of this network (IFS, MPC), alongside posterior superior temporal sulcus, showed greater engagement for trials that did not progressively isolate a limited set of referents, relative to trials that did. IFS and posterior middle temporal gyrus activity was modulated by semantic coherence, regardless of whether the sentence picked out a common object. Centered around IFS and spreading out dorsally towards middle frontal gyrus and ventrally towards anterior/posterior inferior frontal gyrus, we uncovered a cortical mosaic of functional specialization for reference, coherence and semantic narrowing. Early processing windows implicated IFS in all aspects of semantics, and in later windows sub-portions of IFS exposed a clearer functional tessellation with some remaining overlap. This work unveils how lateral fronto-temporal regions make distinctly rich semantic contributions and are involved jointly in semantic integration and conflict resolution, depending on the sub-region and processing stage.

neuroscience↗

bioRxiv2022

Biomechanical Investigation of Ancient Maya Warfare at Mayapan, Yucatan, Mexico

Despite significant advancements in the reconstruction of activity patterns from skeletal remains and growing scholarly interest in ancient warfare, few biomechanical studies have investigated weaponry use. We adopt a biomechanical approach to investigate who participated in ancient Maya warfare and the types of weaponry used at the Late Postclassic (ca. 1200-1450 A.D.) regional political capital of Mayapan located in northwestern Yucatan, Mexico. This has implications for the nature and scale of Maya warfare and the size of territories that could be controlled by Maya polities. Comparative Finite Element Analysis is a powerful, non-destructive method that can be applied to skeletal remains to model strain, stress and deformation of structures in response to a defined loading regime. Here, biomechanical data extracted using cross-sectional geometry were combined with Finite Element Analysis models of three ancient Maya humeri from Mayapan: one elite male, one elite female, and one commoner female. Models were created with loading conditions of archery and spear use to assess evidence for skeletal adaptation to habitual weapon use. Following suggestions by some Mayanists that elite status males were the principal participants in warfare, we hypothesized that the elite male humerus would exhibit lower strains than the two female humeri in all the loading conditions. This was supported by the Finite Element model results, with the exception of spear throwing. The elite female humerus showed similar trends to the elite male humerus, suggesting the possibility of elite female participation in warfare.

paleontology↗

bioRxiv2022

Performance of novel antibodies for lipoarabinomannan to develop diagnostic tests for Mycobacterium tuberculosis

Lipoarabinomannan (LAM), a component of the Mycobacterium tuberculosis (MTB) cell wall, is detectable in the urine of MTB infected patients with active tuberculosis (TB). LAM-specific antibodies (Igs) have been developed by a variety of traditional and recombinant methods for potential use in a rapid diagnostic test (RDT). We evaluated the analytical performance of the TB LAM Igs to identify pairs that offer superior performance over existing urine LAM tests. We assessed 25 new and 4 existing Igs in a matrixed format using a multiplex electrochemiluminescence-based liquid immunoassay. A total of 841 paired Ig combinations were challenged with in vitro cultured LAM (cLAM) derived from MTB strains representing diverse phylogenetic lineages, alongside urinary LAM (uLAM) from the urine of adults with active pulmonary TB. Analytical sensitivity of down-selected Ig pairs was determined using MTB Aoyama-B cLAM, while diagnostic accuracy was determined using clinical samples. When testing cLAM, the reactivity of Ig pairs was similar across MTB lineages 1-4 but lineage 5:6 had significantly more reactivity among Ig pairs. Overall, 41 Ig pairs had a strong binding affinity to cLAM, as compared to the reference pair of S4-20/A194-01, and 28 Ig pairs therein exhibited a strong affinity for both cLAM and uLAM. Retrospective testing on clinical urine specimens demonstrated varying sensitivities (12-80%) and specificities (14-100%). The five top pairs had a similar analytical limit of detection to the reference pair but in four instances, the sensitivity and specificity with clinical uLAM samples was poor. Overall, epitopes presented by uLAM are different from cLAM, which may affect antibody performance when testing uLAM in patient samples. Several new Ig pairs had similar ranges of high sensitivity to cLAM but overall, there were no new candidate Ig pairs identified in this round of screening with increased performance with uLAM as compared to an existing optimal pair.

microbiology↗

bioRxiv2022

Millennium-Old Pathogenic Mendelian Mutation Discovery for MultipleOsteochondromas from a Gaelic Medieval Graveyard.

Only a limited number of genetic diseases are diagnosable in archaeological individuals and none have had causal mutations identified in genome-wide screens. Two individuals from the Gaelic Irish Medieval burial ground of Ballyhanna, Co. Donegal, showed evidence of bone tumors consistent with the autosomal dominant condition multiple osteochondromas. Genome sequencing of the earlier individual uncovered a missense mutation in the second exon of EXT1, a specific lesion that has been identified in several modern patients. The later individual lacked this but displayed a novel frameshift mutation leading to a premature stop codon and loss of function in the same gene. These molecular confirmations of a paleopathological diagnosis within a single rural ancient context are surprisingly disjunct, given the observation of clusters of this disease in modern isolated populations and a de novo mutation rate of only 10%.

genomics↗