Biology subjects

Morales, M.

Publications and source records attributed to Morales, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Select properties of supramammillary input to adult-born dentate gyrus neurons

The hypothalamic supramammillary nucleus (SUM) projects to the hippocampal dentate gyrus (DG), a brain area crucial for learning, memory, and adult neurogenesis. How SUM inputs regulate adult-born DG (abDG) neurons to support memory processing remains unclear. Here, using monosynaptic tracing in adult mice, we identified a distinct subpopulation of abDG-targeting SUM neurons defined by large somata and low firing rate. Electrophysiological recordings revealed that these SUM neurons co-release glutamate and GABA onto abDGs, and that voluntary running selectively enhances GABAergic transmission. Chemogenetic silencing of SUM-DG GABAergic projections impaired pattern separation, the ability to make fine distinctions between similar stimuli, but not fear conditioning and spatial navigation memory. Altogether, our findings reveal that a distinct SUM subpopulation provides inhibitory modulation to abDG neurons, establishing a novel circuit mechanism for sparse encoding during pattern separation.

neuroscience↗

bioRxiv2026

Microglia support regeneration of rod photoreceptors in larval zebrafish retina through Nrf2-independent mechanisms

The molecular and cellular components of successful regeneration of complex tissues in zebrafish are a major area of investigation. Previous work by our lab indicates a redox function for retinal microglia in the first 48 hours following acute injury to rod photoreceptors in the larval zebrafish retina. In addition, recent literature suggests that microglia provide signals that impact the regenerative response in the damaged retina. Here, we investigate the requirement of microglia and the redox-responsive transcription factor Nrf2 in the spontaneous regeneration of rod photoreceptors in the larval zebrafish retina. We used irf8 mutants which are deficient in microglia, and mutant zebrafish lacking a functional copy of the gene nfe2l2a, which encodes a zebrafish ortholog of Nfe2l2/Nrf2. Our results indicate that microglia support the production of regenerated rods following their ablation. However, although detection of reactive oxygen species was increased in nfe2l2a mutant microglia following rod ablation, the regeneration of rods was not impacted in nfe2l2a mutants. Collectively, our results indicate a role for microglia in supporting the production of regenerated retinal neurons while also indicating that Nrf2-independent mechanisms can likely provide redox functions during rod regeneration.

neuroscience↗

bioRxiv2026

Epstein-Barr Virus in HIV-Associated Conjunctival Squamous Cell Carcinoma and Transcriptional Reprogramming of Conjunctival Epithelial Cells

The involvement of Epstein-Barr virus (EBV) in conjunctival squamous cell carcinoma (cSCC) remains incompletely defined. This study integrated analyses of primary tumors with an experimental model of the conjunctival epithelium. Five Nigerian tumors from patients with HIV and three Japanese tumors from patients without HIV were examined by EBV-encoded RNA in situ hybridization (EBER-ISH), EBV DNA PCR, and virome analysis of RNA sequencing data. EBER localized to epithelial tumor cells in four Nigerian specimens and none of the Japanese specimens. EBV DNA and RNA were each detected in three Nigerian tumors, with every EBER-positive tumor supported by at least one additional assay. Human telomerase reverse transcriptase-immortalized conjunctival epithelial cells infected with Akata-GFP-EBV expressed latency-associated and lytic viral genes. Comparison of three infected and three control cultures identified 96 differentially expressed host genes and 23 enriched Hallmark gene sets at a false discovery rate below 0.05. RT-qPCR confirmed increased HES1, CXCL8, CXCL2, and LOX and decreased FGFBP1, CSTA, SAPCD2, and TMEM40 expression. Prominent responses involved inflammatory signaling, epithelial remodeling, metabolism, and cell-cycle regulation. These findings identify tumor-cell-associated EBV in a subset of HIV-associated cSCC and establish an epithelial model for investigating infection-associated host responses.

microbiology↗

bioRxiv2026

A Human Accelerated Region Drives Opposing Heterochronic Changes in Craniofacial and Limb Development

Many human developmental processes proceed over a prolonged timescale compared to other primates, a phenomenon known as heterochrony. Human accelerated regions (HARs), which encode transcriptional enhancers with human-specific activity, have been implicated in the evolution of novel human traits. However, their contributions to changes in developmental timing remain unknown. Using single-nucleus RNA sequencing and developmental trajectory analyses in a genetically humanized mouse model of the HAR HACNS1, we show that HACNS1 drives heterochronic shifts in opposite directions during craniofacial and limb development. In pharyngeal arches, HACNS1 delays chondrocyte differentiation and the expression of genes involved in cartilage and skeletal maturation. In contrast, in the limb buds, HACNS1 accelerates chondrogenesis and promotes earlier expression of differentiation-associated genes. Consistent with these transcriptomic shifts, SOX9-expressing pre-cartilaginous domains are more diffuse in the pharyngeal arches, but the condensed domains are expanded in the limb buds. Gene regulatory network inference suggests that HACNS1-driven heterochronic shifts are due to changes in the expression of its target gene Gbx2 and resulting downstream effects on the regulatory networks through which Gbx2 functions. Our findings demonstrate that a single human-specific gene regulatory change can alter developmental timing, providing a potential mechanism for how uniquely human genetic changes reshaped conserved developmental programs.

genetics↗

bioRxiv2026

Pooled amplicon sequencing for characterizing mutations in the praziquantel molecular target TRPMPZQ in schistosome populations from Western Kenya

Mass drug administration (MDA) using Praziquantel is central to efforts to eliminate Schistosomiasis. However, regions which respond poorly to MDA ("persistent hotspots") have been reported in many regions of Africa, including in Western Kenya. One possible explanation for persistent hotspots is that these areas contain PZQ resistant schistosome parasites. Recent studies have shown that Sm.TRPMPZQ gene is the molecular target for PZQ in schistosome parasites and that mutations in this gene can result in PZQ resistance. This study characterized mutations within Sm.TRPMPZQ in 23,420 miracidia collected from both hotspot and non-hotspot villages in Siaya County, western Kenya. We collected triplicate pools of 780.67 (SD {+/-} 183.47) miracidia from 135 people in five hotspot villages, where S. mansoni prevalence remains high despite over 5 annual treatments, and from 62 people from 5 non-hotspots villages where annual treatment resulted in reduction in prevalence. We extracted DNA from each miracidia pool, amplified 15 amplicons covering 1,695bp of the Sm.TRPMPZQtransmembrane domain and sequenced these to high read depth (21,110x) using a Miseq at KEMRI-CGHR. We identified five high confidence (frequency [≥] 0.01) Sm.TRPMPZQ variants. These included four synonymous changes and a non-synonymous variant (p.L1476I). p.L1476I is found at similar frequency in non-hotspot (0.040 {+/-} 0.006) and hotspot villages (0.044 {+/-} 0.0050) (Mann Whitney U=18, p= 0.31) and does not impact PZQ-response in Ca2+ reporter assays. Our studies show that resistance variants in Sm.TRPMPZQ are rare or non-existent in the locations studied and do not explain the existence of hotspots in this region.

genomics↗

bioRxiv2026

Direct measurement of in vitro response to Praziquantel in Schistosoma mansoni populations from Western Kenya

Large-scale treatment with praziquantel (PZQ) monotherapy is used to control schistosomiasis, leading to concerns about the emergence of PZQ-resistance. In Western Kenya, schistosome-infected patients frequently remain egg-positive following PZQ treatment, and several "hotspot" villages have been observed where transmission remains high, despite annual mass PZQ treatments. This project asks (i) whether PZQ-resistant parasites are found in Western Kenya and (ii) whether "hotspot" villages can be explained by a higher prevalence of PZQ-resistant parasites. We established a simple platform for directly assaying worm motility following in vitro PZQ-exposure in adult schistosomes isolated from a field setting. To do this, we established snail and hamster breeding colonies, and generated large populations of field-derived adult worms, by (i) harvesting S. mansoni eggs from multiple infected patients; (ii) infecting Biomphalaria spp snails with miracidia; (iii) infecting hamsters with released cercariae; (iv) perfusing adult worms from hamsters, and (iv) examining drug response following exposure to PZQ (1 {micro}g/ml for 1 day) in individual S. mansoni worms using an automated movement assay. We measured PZQ-response in 1,800 adult male parasites, representing an estimated 185 parasite genotypes. We identified a single worm that remained motile after PZQ-exposure among the 185 parasite genotypes surveyed (frequency = 0.54%; 95% CI 0.01 - 2.97%, exact binomial) consistent with PZQ-resistant worms being extremely rare or absent. Our direct phenotypic screening results suggests that (i) PZQ-resistance is not currently an obstacle for S. mansoni control in Western Kenya, and (ii) that other factors explain the existence of persistent hotspots.

microbiology↗

bioRxiv2026

Nucleic acid turnover and lipid remodeling distinguish T cell activation and exhaustion states via label-free Raman spectroscopy

T cell exhaustion impairs immune control of chronic diseases including tuberculosis, HIV, malaria, and cancer. Its clinical implications are vast, predicting HIV-associated malignancy and treatment response and limiting the efficacy of cell therapies. Despite the advantages of monitoring and removing exhausted T cells, current detection methods require expensive antibody labeling, destructive workflows, or days-long functional assays. Here, we introduce Raman spectroscopy as a label-free assay for distinguishing T cell states directly from culture while preserving viability for downstream use. We achieve >97% accuracy in discriminating unstimulated, activated, and exhausted T cells across three donors and multiple hardware setups. We identify vibrational modes associated with nucleic acid turnover and lipid remodeling as key features that distinguish T cell activation and exhaustion. In heterogeneous populations, we quantify exhaustion percentage with R2= 1 and strong correlation to adenine (r= -0.91) and amide II protein (r= 0.94) vibrational modes. This work establishes vibrational fingerprinting as a direct measure of T cell exhaustion beyond surface marker expression towards scalable immune diagnostics, in-line monitoring, and selective immunopheresis.

biophysics↗

bioRxiv2026

Primary productivity declines when species composition and climate are mismatched

Climate change drives shifts in species composition, but turnover in many communities lags behind the current pace of change. Anticipating the impact of the resulting community-climate disequilibria on ecosystem functioning is critical. Present-day communities may already be out of equilibrium with climate, providing an opportunity to estimate the effects of disequilibrium before they become more widespread. We analyzed plant community composition and function data from [~]60,000 rangeland monitoring sites across the western US to measure how community-climate disequilibrium contributes to spatial and temporal variation in net primary productivity (NPP) - a key ecosystem function. We found that communities were already substantially out of equilibrium with climate and accounting for this disequilibrium helped explain patterns of NPP. Communities farthest from equilibrium were less productive than those that were closely matched with climate. Our findings suggest that future increases in community-climate disequilibrium may further impair ecosystem functioning.

ecology↗

bioRxiv2026

Quantification of Mouse Total Body Surface Area: Implications for Preclinical Burn Research

Clinically, burn severity is reported as the size (and depth) of burn wounds relative to total body surface area (TBSA). This nomenclature is also often used in rodent models of burns. Accordingly, accurate determination and reporting of rodent TBSA is required to ensure the rigor and reproducibility of preclinical burn research. Rodent TBSA is typically estimated indirectly as a function of body mass. Further, empirical quantification of rodent TBSA through pelt dissection does not consider differences in rodent and human anatomy, making comparison of relative burn size in rodents and humans a challenge. Here, we compared commonly used approaches to directly determine or indirectly estimate rodent TBSA to demonstrate the impact different approaches can have on the calculation of relative burn size. A total of n=48 C57BL/6J background mice (55% male) ranging from 4 to 45 weeks of age and 17 to 40 grams were used. Mice were weighed prior to euthanasia. After euthanasia, mouse length was measured from the nose to anus. Mice were then placed into clear polypropylene sheet protectors (21.6 x 27.9 cm) to trace the areas of both the dorsal and ventral surfaces as well as all four limbs (dorsal-ventral (DV) tracing). Next, the pelt was carefully excised from the body through cutting a lateral line from the mouth to the genitalia, then again proximally to distally on all four limbs. The pelt was gently placed on a sheet protector and traced when both relaxed and stretched. The ears and tail were removed and traced separately. Photographs were taken of all tracings next to a ruler for scale and analyzed in ImageJ. Stretched pelt measurements of TBSA were 34% (79.4{+/-}7.6 vs. 57.5{+/-}7.5 cm2, P<0.001) and 30% (70.6{+/-}10.9 vs. 52.7{+/-}8.1 cm2, P<0.001) greater than relaxed pelt TBSA measurements in male and female mice respectively. TBSA estimated by DV tracing was 9% greater in males (62.5{+/-}10.9 vs. 57.5{+/-}7.5 cm2) and 15% in females (60.6{+/-}12.3 vs. 52.7{+/-}8.1 cm2) compared to TBSA measurements made on relaxed pelts. Accordingly, empirically derived Meeh constants (k) from DV tracing were greater than those derived from relaxed pelt measurements for both males (7.14{+/-}0.59 vs. 6.58{+/-}0.72) and females (7.72{+/-}0.58 vs. 6.78{+/-}0.80). In contrast k values derived from stretched pelt measures of TBSA were significantly greater than those determined in relaxed pelts for males (8.91{+/-}0.87 vs. 6.58{+/-}0.72, P<0.001) and females (8.85{+/-}1.25 vs. 6.78{+/-}0.80, P>0.001). The combined ears and tail represent approximately 7% and 8% of the TBSA measured by the relaxed pelt approach, respectively. Exclusion of the tail and ears from the calculated TBSA results in derived k values that are [~]16-17% lower. The approach used to determine TBSA in mice significantly influences measured areas and thus derived k values. We suggest that stretching the pelt prior to tracing inflates TBSA values, where measurements made from relaxed pelts or by DV tracing likely provide more accurate estimates of actual TBSA. Further, exclusion of the tail and ears (the latter of which is not typically considered in estimates of TBSA in humans) may be a useful approach relating relative burn sizes of mice to those of humans.

physiology↗

bioRxiv2026

Rapid residual bead quantification for cell therapy manufacturing using Raman spectroscopy

Adoptive cell therapies are transforming the treatment of cancer and autoimmunity by enhancing patients own immune cells to fight disease. In cell therapy manufacturing, immunomagnetic beads are used to isolate and activate target cells for gene transfer but must be removed downstream to [≤]10 beads per 300,000 cells. Current quantification requires time-intensive and error-prone manual counting using brightfield microscopy, while existing automated approaches struggle with variable bead-cell morphology and tedious sample preparation steps. Raman spectroscopy offers rapid, morphology-independent detection using molecular signatures generated by inelastic light scattering. Here, we leverage immunomagnetic beads strong Raman signatures to quantify them in area scans from dried samples, achieving single bead resolution and accurate counting of bead clusters with and without cells. Using low power ([≤]7 mW) and exposure times ([≥]0.5 s), the average area under 3 signature Raman peaks (1110 cm-1, 1346 cm-1, and 1595 cm-1) are measured and input to a linear regression model, achieving a mean squared error (MSE) of <0.2 beads. Our results show Raman spectroscopy as a robust, automated approach for bead counting in existing pipelines with potential to improve the safety and throughput of cell therapies.

bioengineering↗

bioRxiv2026

Cone photoreceptor ablation in microglia-deficient larval zebrafish retina elicits a regenerative response alongside a compensatory immune cell response

Emerging evidence implicates retinal microglia and inflammation as important components impacting the outcome of retinal regeneration, which is spontaneously achieved in zebrafish retina following acute damage but is limited or blocked in mammals. In this paper, we describe the regenerative response in the larval zebrafish retina following ablation of cone photoreceptors. To investigate the role of microglia in the regenerative response, we used both irf8st95 heterozygote (microglia-sufficient) and irf8st95 homozygous mutant (microglia-deficient) zebrafish. We compared multiple aspects of the regenerative response in irf8+/- and irf8-/- larval retinas, including entry of the Muller glia (MG) into the cell cycle, the amplification of MG-derived progenitor cell (MGPC) proliferation, inflammatory and glial reactivity-associated gene expression, and the regeneration of cones. We found only modest impacts to early and late stages of MGPC proliferation and to inflammatory gene expression in irf8 mutants, with no obvious impacts to the regeneration of cones. Notably, we detected a population of immune cells in irf8 mutants that emerged following cone ablation, which expanded in number then were reduced over time, following a trajectory similar to microglia-sufficient siblings but at markedly reduced abundance. The immune cells detected in irf8 mutants included a subset with L-plastin/4C4 antibody staining patterns different than those in microglia-sufficient siblings, suggesting distinct origins and/or phenotype compared to resident microglia in controls. Though strong conclusions about the role of microglia were limited due to the presence of such immune cell populations in irf8 mutants, our results are consistent with several reports that indicate a role for microglia and inflammation in regulating MGPC proliferation in the regenerating retina. Collectively considered with other reports, our results further indicate that compensatory responses, which may include different immune cells and/or signaling from other retinal cell types such as the Muller glia, are elicited in microglia-deficient retinas upon neuronal damage.

developmental biology↗

bioRxiv2026

Structural Mechanisms of SAMD9 Autoinhibition and Pathogenic Dysregulation

SAMD9 and SAMD9L (SAMD9/9L) are large cytosolic proteins essential for hematopoietic homeostasis and antiviral defense1-3. Germline gain-of-function (GoF) mutations in SAMD9/9L cause severe multisystem disorders and predisposition to leukemia, yet the mechanisms that regulate SAMD9/9L activity and how pathogenic mutations disrupt these processes, remain poorly understood. Here, we determine cryo-electron microscopy structures of human SAMD9 in multiple conformational and oligomeric states. We show that SAMD9 predominantly adopts a closed, autoinhibited conformation stabilized by a central ATP-bound nucleotide-binding oligomerization domain (NOD) and an extensive network of intramolecular interactions. Recurrent patient-derived GoF mutations localize to and destabilize these intramolecular interfaces, and restoring the disrupted interactions through compensatory mutations reinstates autoinhibition. We further identify low-abundance asymmetric SAMD9 dimers in which one protomer undergoes large conformational changes and establishes intermolecular interactions that are essential for SAMD9 activation. Together, these findings define the structural basis of SAMD9 autoinhibition and explain how human GoF mutations subvert this regulatory mechanism to drive disease.

biophysics↗

bioRxiv2026

Induction of ferroptotic and amyloidogenic signatures linked to Alzheimers disease by chemically distinct air pollutants

Air pollution (AirP) exposure is associated with increased Alzheimers disease (AD) risk, yet AirP is chemically heterogeneous, complicating identification of shared pathogenic drivers. We examined acute cortical responses to two metal-rich AirP sources, diesel exhaust particles (DEP) and World Trade Center (WTC) dust, and compared them to woodsmoke (WS), a particulate exposure with low metal content. DEP and WTC elicited highly convergent transcriptional responses, sharing over 1200 differentially expressed genes linked to inflammation, ferroptosis, neuronal remodeling, and amyloid processing. These changes were accompanied by impaired antioxidant activity and increased lipid peroxidation within lipid rafts, a membrane microdomain critical for amyloid processing, resulting in increased A{beta} generation. In contrast, WS produced a distinct transcriptional signature and failed to induce ferroptotic priming or lipid peroxidation, consistent with its low metal composition. Together, these findings implicate metals as a shared driver linking diverse AirP exposures to amyloidogenic vulnerability and elevated AD risk. Graphical AbstractAcute AirP exposure converges on ferroptotic priming, amyloidogenic processing, and white-matter vulnerability. Acute exposure to metal-rich AirP, such as DEP or WTC introduces redox-active metals and particulate matter that promote lipid peroxidation, amyloidogenesis, and altered transcriptional regulation in the brain. AirP exposure engages xenobiotic metabolism pathways (AhR/ARNT), activates iron and heme handling through ferritinophagy (NCOA4) and heme oxygenase activity (HMOX1), and blunts lipid peroxide detoxification systems, including glutathione peroxidase 4 (GPx4), ferroptosis suppressor protein 1 (FSP1), and glutathione (GSH) synthesis. These changes promote ferroptotic priming and lipid raft oxidation, facilitating amyloid precursor protein (APP) processing by secretases (ADAM10, BACE1, {gamma}-secretase) and increasing amyloid-{beta} (A{beta}) generation. In parallel, transcriptional and cell-state remodeling involving neuronal and oligodendrocyte responses contribute to selective white-matter vulnerability, particularly within the corpus callosum. Together, these pathways provide a mechanistic framework linking acute AirP exposure to convergent oxidative, amyloidogenic, and microstructural changes relevant to Alzheimers disease pathology. O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/696601v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@3a22dcorg.highwire.dtl.DTLVardef@c6ae26org.highwire.dtl.DTLVardef@1d3412forg.highwire.dtl.DTLVardef@5cb011_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Microglia maintain retinal redox homeostasis following ablation of rod photoreceptors in zebrafish

Microglia rapidly respond to injury, stress, and perturbations to neurons in the brain and retina and perform phagocytosis to clear dying cells and debris. Oxidative stress is a frequent feature of neurodegeneration, and while glia are crucial for managing such stress, microglia may also be dysfunctional in diseased tissue. Here we examine the role of microglia in management of oxidative stress upon death of rod photoreceptors in the larval zebrafish retina. Using rho:nfsb-eGFP transgenic zebrafish and treatment with the pro-drug metronidazole (MTZ), we coupled the generation of reactive oxygen species (ROS) in dying rods to their ablation. Microglia efficiently engulfed and cleared the ROS-laden rods, effectively undertaking the oxidative load. Despite abundant ROS upon MTZ-mediated cell death, oxidative stress overall was minimal in retinal tissue when microglia were present, indicating that they rapidly and efficiently performed redox functions. In irf8-/- mutants, which are deficient in microglia, retinas with MTZ-induced rod ablation showed widespread ROS that localized, at least in part, to Muller glia. Further, there was evidence of increased oxidative stress, and increased numbers of "off-target" inner retinal neurons that stained positive for the cell death marker TUNEL. Supplementation with the antioxidant Glutathione (GSH) reduced the number of off-target TUNEL+ cells detected in microglia-deficient retinas following rod ablation. Our results indicate that microglial redox functions are important in restoring homeostasis following acute retinal damage.

neuroscience↗

bioRxiv2025

Hippocampal input-driven plasticity of prefrontal interneurons reveals a circuit basis for impaired spatial working memory.

Long-range projections from ventral hippocampus (vHPC) to medial prefrontal cortex (mPFC) support cognitive functions including spatial working memory (SWM). vHPC input targets multiple prefrontal interneuron classes, yet how hippocampal input recruits these populations in vivo, whether this recruitment is plastic, and how such plasticity influences cognition remain unknown. Here, we combined optical stimulation of mouse vHPC inputs with calcium recordings from discrete mPFC interneuron populations, revealing persistent activity-induced reweighting of hippocampal recruitment across prefrontal inhibitory microcircuits. Ex vivo electrophysiology and computational modeling implicated weakened monosynaptic hippocampal drive onto vasoactive intestinal polypeptide (VIP)-expressing interneurons in this circuit reconfiguration. Prior vHPC input stimulation and the schizophrenia-associated Df(16)A+/- mutation, which also yielded reduced hippocampal input onto VIP interneurons, produced convergent alterations in task-related VIP interneuron activity associated with poorer SWM task learning. These findings implicate hippocampal input to VIP interneurons as a key locus of plasticity capable of reconfiguring inhibitory microcircuit activity linked to impaired working memory task learning. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/665987v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@e26cb0org.highwire.dtl.DTLVardef@14d9d6borg.highwire.dtl.DTLVardef@9a0fc2org.highwire.dtl.DTLVardef@80afd1_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

neuroscience↗

bioRxiv2024

Abundant genetic variation is retained in many laboratory schistosome populations

Schistosomes are obligately sexual blood flukes that can be maintained in the laboratory using freshwater snails as intermediate and rodents as definitive hosts. The genetic composition of laboratory schistosome populations is poorly understood: whether genetic variation has been purged due to serial inbreeding or retained is unclear. We sequenced 19 - 24 parasites from each of five laboratory Schistosoma mansoni populations and compared their genomes with published exome data from four S. mansoni field populations. We found abundant genomic variation (0.897 - 1.22 million variants) within laboratory populations: these retained on average 49% ({pi} = 3.27e-04 - 8.94e-04) of the nucleotide diversity observed in the four field parasite populations ({pi} = 1.08e-03 - 2.2e-03). However, the pattern of variation was very different in laboratory and field populations. Tajimas D was positive in all laboratory populations except SmBRE, indicative of recent population bottlenecks, but negative in all field populations. Current effective population size estimates of laboratory populations were lower (2 - 258) compared to field populations (3,174 - infinity). The distance between markers at which linkage disequilibrium (LD) decayed to 0.5 was longer in laboratory populations (59 bp - 180 kb) compared to field populations (9 bp - 9.5 kb). SmBRE was the least variable; this parasite also shows low fitness across the lifecycle, consistent with inbreeding depression. The abundant genetic variation present in most laboratory schistosome populations has several important implications: (i) measurement of parasite phenotypes, such as drug resistance, using laboratory parasite populations will determine average values and underestimate trait variation; (ii) genome-wide association studies (GWAS) can be conducted in laboratory schistosome populations by measuring phenotypes and genotypes of individual worms; (iii) genetic drift may lead to divergence in schistosome populations maintained in different laboratories. We conclude that the abundant genetic variation retained within many laboratory schistosome populations can provide valuable, untapped opportunities for schistosome research.

genomics↗

bioRxiv2024

Rapid phenotypic and genotypic change in a laboratory schistosome population

BackgroundGenomic analysis has revealed extensive contamination among laboratory-maintained microbes including malaria parasites, Mycobacterium tuberculosis and Salmonella spp. Here, we provide direct evidence for recent contamination of a laboratory schistosome parasite population, and we investigate its genomic consequences. The Brazilian Schistosoma mansoni population SmBRE has several distinctive phenotypes, showing poor infectivity, reduced sporocysts number, low levels of cercarial shedding and low virulence in the intermediate snail host, and low worm burden and low fecundity in the vertebrate rodent host. In 2021 we observed a rapid change in SmBRE parasite phenotypes, with a [~]10x increase in cercarial production and [~]4x increase in worm burden. MethodsTo determine the underlying genomic cause of these changes, we sequenced pools of SmBRE adults collected during parasite maintenance between 2015 and 2023. We also sequenced another parasite population (SmLE) maintained alongside SmBRE without phenotypic changes. ResultsWhile SmLE allele frequencies remained stable over the eight-year period, we observed sudden changes in allele frequency across the genome in SmBRE between July 2021 and February 2023, consistent with expectations of laboratory contamination. (i) SmLE-specific alleles rose in the SmBRE population from 0 to 41-46% across the genome between September and October 2021, documenting the timing and magnitude of the contamination event. (ii) After contamination, strong selection (s = [~]0.23) drove replacement of low fitness SmBRE with high fitness SmLE alleles. (iii) Allele frequency changed rapidly across the whole genome, except for a region on chromosome 4 where SmBRE alleles remained at high frequency. ConclusionsWe were able to detect contamination in this case because SmBRE shows distinctive phenotypes. However, this would likely have been missed with phenotypically similar parasites. These results provide a cautionary tale about the importance of tracking the identity of parasite populations, but also showcase a simple approach to monitor changes within populations using molecular profiling of pooled population samples to characterize fixed single nucleotide polymorphisms. We also show that genetic drift results in continuous change even in the absence of contamination, causing parasites maintained in different labs (or sampled from the same lab at different times) to diverge.

genomics↗

bioRxiv2024

Wireless, Multimodal Monitoring of Organ Health Using 3D-Printed, Barbed, Bioresorbable Stretchable Microneedle Sensor Arrays

Comprehensive and continuous assessment of organ physiology and biochemistry, beyond the capabilities of conventional monitoring tools, can enable timely interventions for intraoperative complications like organ ischemia and nerve injuries and postoperative conditions such as organ dysfunction and transplant rejection. Here, we report a wireless implant with a 3D-printed, barbed, bioresorbable stretchable microneedle sensor array that offers multimodal monitoring of organ metabolism, oxygenation, and electrophysiology as well as spatiotemporal mapping of biomarkers across different organ regions. The development of a deformation-coupled 3D-printing technique enables 3D-programmable manufacturing of microneedles with monolithic backward-facing barbs, offering conformal yet robust 3D probing of organs with dynamic mechanics. Electrochemical functionalization of microneedle tips serves as a universal approach for localized sensing of physiological and biochemical parameters, enabling concurrent monitoring of up to 36 parameters (glucose, uric acid, oxygen, etc.) and spatiotemporal mapping of up to 32 sites. An electrically programmable self-destruction mechanism based on crevice corrosion and bioresorption eliminates the need for traumatic retrieval of microneedles. Demonstrations in clinically relevant complications like kidney ischemia and gut disorders in animal models highlight the broad applications of this device in intra- and postoperative monitoring.

bioengineering↗