Biology subjects

Barrett, M.

Publications and source records attributed to Barrett, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Tumbly: An Open-Source Home-Cage Device for Time-Restricted Feeding in Mice

Time-restricted feeding (TRF) is a common tool for studying metabolism, circadian rhythms, aging, and neurodegeneration. Here, we describe a new device called Tumbly, an automated device for performing TRF studies in mouse home-cages. Tumbly controls access to rodent diets at user-set times via a programmable servo-driven food hopper. Tumbly is also battery powered and compatible with multiple types of vivarium home-cages, due to a removable faceplate that can be customized to fit different cage dimensions without modification. Finally, Tumbly is open-source and affordable, with all design files available online, allowing researchers to build and customize it. As a validation test, we deployed Tumbly in two labs at separate institutions, one with singly housed mice (n = 6, within-subject) and one with group-housed mice (n = 22, between-group). We measured daily body weight and food intake. In both labs, mice on an 8-hour TRF schedule maintained their body weight and ate similar amounts of food compared to ad libitum feeding. Our quantified error rates were also low, with no device failures over >1000 hours of operation. We conclude that Tumbly provides a reliable, low-cost option for running TRF studies in mice.

neuroscience↗

bioRxiv2026

Mathematical modelling of thermal death kinetics to describe humane slaughter procedures via hot water immersion in black soldier fly and yellow mealworm larvae

Trillions of black soldier fly (BSFL; Hermetia illucens; Diptera: Stratiomyidae) and yellow mealworm (YML; Tenebrio molitor; Coleoptera: Tenebrionidae) larvae are slaughtered annually for feed. Slaughter standard operating procedures (SOPs) that protect welfare and product quality are essential to ethical and economical industry practice. This study defines humane (less than or equal to 1 second time-to-death) slaughter SOPs for hot water immersion of BSFL and YML. We assessed isothermal critical thermal maxima in water from 32, or 40, to 100 C in YML and BSFL, respectively. We used Weibull probability-based models to characterize survival as a function of processing time at different temperatures, describing the time-temperature conditions required for humane slaughter. We blanched larvae under: 1) a SOP resulting in a ~1 minute time-to-death for 99% of larvae; 2) a SOP resulting in less than or equal to 1 second time-to-death for 99% of larvae; and 3) 99.5-100 C. We compared ash, protein and fat, pH, water activity, lipid oxidation, and color change. Water temperatures kept above 81.3 C (BSFL <0.16 g), and 78.3 C (YML <0.12 g), are predicted to result in humane slaughter for >99% of larvae - though, further research is needed to develop SOPs for larger larvae. The humane SOPs have neutral or beneficial impacts on quality. We recommend producers adopt a 2 C buffer (BSFL: 83.3 C; YML: 80.3 C). Finally, we provide an energy balance model that producers can use to determine the larvae:water ratio and temperature that results in humane slaughter in their facility.

bioengineering↗

bioRxiv2026

Spatial Transcriptomics Reveals Region-Specific Host Responses in Amoebic Gill Disease of Atlantic Salmon

Amoebic gill disease (AGD), caused by the parasite Neoparamoeba perurans, is a major welfare and economic burden for the Atlantic salmon aquaculture industry. However, the spatial organisation of immune functions within the gill, the site of infection, remains poorly resolved. Here, we present the first spatial transcriptomic atlas of the Atlantic salmon gill affected by AGD, generated using 10x Genomics Visium on four AGD-positive fish, confirmed by gill scoring and quantitative PCR for parasite load. As no uninfected gills were included, this study maps the anatomical and immunological organisation of AGD-affected gills rather than defining AGD-specific pathology. Unsupervised clustering of spatial gene expression resolved distinct transcriptional domains that grouped into four principal anatomical compartments of the gill, including (i) epithelial and lamellar regions defined by keratin and osmoregulatory gene expression, (ii) gill arch regions enriched for connective tissue and smooth muscle markers, (iii) an erythroid-associated vascular cluster, and (iv) a skeletal muscle cluster with signatures of glycolysis and oxidative phosphorylation. Across these domains, we identified a spatially organised and diffused immune landscape, with pattern recognition receptors, antimicrobial effectors and chemokines concentrated at the filament surface, and immunoglobulin light chain transcripts consistent with B lymphocyte activity enriched toward the gill arch. Integration of the spatial data with a published single-nucleus reference atlas using reference-based deconvolution resolved the cellular identity underlying these domains and revealed frequent co-localisation of immune and structural cell types, suggesting regulated cell to cell communication within the gill-associated lymphoid tissue. Overall, our results show that the Atlantic salmon gill is not a transcriptionally uniform surface but a regionally specialised organ, with immune functions distributed across, and specialised within, distinct anatomical compartments

immunology↗

bioRxiv2026

Spatial Transcriptomics Reveals Compartment-Specific Immune Activation Signatures in Ileal and Lymph Node Tissue in Treated HIV Infection

People with HIV (PWH) on long-term antiretroviral therapy (ART) continue to experience elevated rates of morbidities and mortality driven by persistent immune activation despite viral suppression. Known contributors include low-level HIV provirus activity, microbial translocation in part from epithelial barrier dysfunction, microbiome dysfunction, and co-infections. However, how these interact and where they predominate across tissue compartments remains incompletely defined. Here, we applied spatial transcriptomics to characterize compartment-specific transcriptional programs in ileum (epithelium, Peyer's patches, lamina propria) and inguinal lymph nodes (B Cell follicles and T cell zone) from ten PWH on long-term ART, stratified by CD4/CD8 ratio into low-ratio and high-ratio groups, with low-ratio as a proxy for immune activation and increased risk for non-AIDS related serious event. Comparison of global expression found significant differences between groups in four of five compartments. Differential expression analysis identified 483 differentially expressed genes across four of five compartments, with the greatest burden in the T-cell zone and none in the lamina propria. Gene set enrichment analysis identified 116 enriched pathways predominantly in the low-ratio group, spanning immune activation, infection-associated, and metabolic programs, with Peyer's patches showing the broadest transcriptional divergence of any compartment. Cross-compartment signals included higher expression of ORMDL3 and ARL17B in the low-ratio group implicating mitochondrial stress and inflammasome activation, lower expression of CCL3L3 and FCMR in the low-ratio group suggesting impaired immune execution, and divergent ribosomal protein programs between B-cell follicles and the T-cell zone. Cell deconvolution identified compartment-specific differences in estimated immune cell proportions, and T-cell zone gene expression showed significant associations with HIV reservoir measures and plasma markers of microbial translocation and immune activation. Together these findings support spatially heterogeneous immune activation as a feature of persistent immune dysregulation in treated HIV infection and provide compartment-resolved, hypothesis-generating evidence for the tissue-specific mechanisms driving inflammation in this population.

bioinformatics↗

bioRxiv2026

Standardized Protocols for Global and Local Thermal Nociception in Black Soldier Fly (Hermetia illucens; Diptera: Stratiomyidae) Larvae

Nociception, the capacity to detect tissue-damaging stimuli such as noxious chemicals or high heat, is increasingly studied across insect orders and life stages, informing our understanding of its adaptive value and molecular mechanisms. The black soldier fly (Hermetia illucens; Diptera: Stratiomyidae) is widely recognized as the star of the growing insects as food and feed industry. Black soldier fly larvae (BSFL) are reared at high densities that, combined with their extraordinary metabolism, can generate lethal overheating on farms. Data on the thermal nocifensive capabilities of BSFL could inform our understanding of larval behaviors during overheating events (and potential welfare impacts of thermal slaughter), and provide a comparative datapoint to the well-studied vinegar fly (Drosophila melanogaster; Diptera: Drosophilidae). Accordingly, we adapted global and local thermal nociception methods from larval vinegar flies for use with BSFL. We find that global assays (akin to boiling) adapt easily to both first and late instar BSFL, that BSFL exhibit slightly different nocifensive behaviors than last instar vinegar fly larvae, and that BSFL have higher thresholds (thrashing begins at 39.70 C in late instar BSFL versus 26.6 C in D. melanogaster). In contrast, the classical local nociception assay did not adapt easily to BSFL, so we modified the assay to test a time-bounded, continuous exposure to the temperature probe instead of response-latency. This assay generated a unique, gradual pattern of increasing responsiveness to the probe in late instar BSFL (>95% responsiveness above 66 C) rather than the sharp cutoff in responsiveness at 52 C demonstrated in D. melanogaster during response-latency assays. Altogether, these protocols open the door for standardized research on BSFL thermal nociception for fundamental and applied purposes.

animal behavior and cognition↗

bioRxiv2026

Multi-omics links microbial dysbiosis, systemic inflammation and metabolomic disruptions to SNAE risk in treated HIV

Serious non-AIDS events (SNAEs), including non-AIDS malignancies, cardiovascular disease, and hepatic complications, remain major causes of mortality in treated HIV infection. These outcomes are driven by persistent immune activation, systemic inflammation, and metabolic dysfunction despite effective viral suppression with antiretroviral therapy (ART). To investigate mechanisms underlying SNAE pathogenesis, we performed a cross-site multi-omic analysis integrating plasma proteins, plasma metabolites, and mucosal microbiomes (ileum and rectum) in 82 ART-treated people with HIV (PWH) and 10 people without HIV (PWoH) from the United States and Mexico. Geography was the dominant source of variation, particularly across lipid classes. However, individuals at high risk for SNAEs, defined by low CD4 T cell counts and low CD4/CD8 ratios, shared a consistent signature of systemic inflammation, mitochondrial dysfunction, and microbial dysbiosis including elevated plasma IL-6, {omega}-oxidation products (adipic and suberic acids), and depletion of short-chain fatty acid-producing commensals in the gut mucosa, including Akkermansia muciniphila, Bacteroides uniformis, and Ruminococcus. Notably, A. muciniphila abundance correlated with lower IL-6 levels, fewer HIV RNA-producing cells in lymph nodes, and higher CD4/CD8 ratios. Together, these findings identify a shared inflammatory and metabolic phenotype in PWH and implicate A. muciniphila as a potential microbiome-based target to mitigate immune activation and SNAE risk in treated HIV.

immunology↗

bioRxiv2026

Potential acoustic signatures of stress in black soldier fly (Hermetia illucens; Diptera: Stratiomyidae) larvae

Black soldier fly larvae (BSFL) have quickly become one of the most farmed animals in the world. However, little is known about how to monitor stress and welfare in these animals. The difficulty of welfare assessment is compounded by the fact that BSFL live in their feed and prefer darkness. This behaviour makes it challenging to observe potential welfare indicators without inducing stress via disturbing the larvae or moving them into the light. However, acoustic devices may be able to pick up signatures of stress in the population even while they are out of sight, allowing for remote monitoring of animals in natural conditions (in the feed and/or in the dark). Acoustic monitoring of this type has been deployed for the detection of insects in stored grains, suggesting this method holds some promise for assessing insect behavioural signatures. In this study, we aimed to identify general, acoustic signatures of stress in BSFL by recording them during exposure to two stressors (light or shaking) or in a low-stress control condition. Our data suggest there are consistent differences in the acoustic recordings of the non-stressed and stressed conditions that may indicate the animals behaviours shift consistently in response to stress. Ultimately, the data suggest acoustic monitoring may hold promise for larval behaviour and/or welfare assessment and should be further explored in response to a variety of stressors across the larval life stage.

zoology↗

bioRxiv2026

Sex, head size, and male mate location behavior affect allometric scaling of the eyes in Centris pallida (Hymenoptera: Apidae) bees

Variation in eye structure and function can allow organisms to exploit novel environments or perform unique behaviors. However smaller body sizes may impose morphological constraints on eye investment, limiting adaptive behavioral performance. Males of the solitary desert bee Centris pallida (Hymenoptera: Apidae) are dimorphic in both body size and sensory mate location behaviors: large-morph males are fixed on a scent-based strategy while small-morph males generally use a sight-based strategy. Females are not known to vary categorically in mating behavior but span nearly the full range of male body sizes, allowing for sex comparisons in allometric scaling. We hypothesized that sex, body size, and male mate location behavior would impact eye structure and estimated global and localized visual acuity in C. pallida bees. We predicted that male and female body size would correlate with ommatidia number and size, and visual acuity, due to allometric constraints. We further predicted that small-morph males would have increased relative investment in the eyes and improved visual acuity compared to large-morph males. We found that males had increased ommatidia numbers and larger eyes than similarly-sized females, as well as greater average and maximum ommatidia diameters. Females had improved localized visual acuity in the dorsofrontal hotspot than small-morph males, but similar acuity to large-morph males. Body size thus impacted localized acuity in the dorsofrontal region in males but not in females. Small-morph males had increased relative eye size and ommatidia density but reduced total ommatidia numbers, eye surface areas, and estimated visual acuities compared to large-morph males.

zoology↗

bioRxiv2025

Minimizing inferential bias in the theory and design of nutritional experiments through the application of the equilateral mixture triangle

Animal nutritionists seek to understand how animals regulate the intake and balance of multiple nutrients, yet the design and analysis of such experiments are often limited by how nutrient spaces are represented. The geometric framework for nutrition (GFN) provides a powerful means to visualize nutrient interactions, but when more than two nutrients are considered, most empirical studies employ right-angled mixture triangles (RMTs). While convenient, this coordinate system can introduce visual artifacts that can bias inference. Here, we reintroduce the equilateral mixture triangle (EMT) as a complementary and biologically meaningful framework that preserves proportional relationships among nutrients and connects directly with the design principles of mixture experiments in engineering disciplines, where it is more commonly known as a simplex. The simplex provides a consistent bridge between theory and experimentation, allowing the same geometric representation to be used for choice and no-choice assays. For choice experiments, we extend GFN theory to show that animal feeding trajectories are bounded by the convex hull of available foods, show how it can scale to higher-dimensional nutrient systems, and develop statistical tests to distinguish between random choice and the defense of an intake target. For no-choice experiments, we demonstrate how simplex mixture designs can be integrated with response surface methodologies to model multivariate performance landscapes, identify optimal nutrient ratios, and avoid biologically unrealistic regions of nutrient space. For both types of experiments, we provide simulated case studies on how to design studies around the simplex. Together, these developments refine both the theoretical and experimental foundations of nutritional ecology, providing clear guidance for designing, visualizing, and interpreting multidimensional studies of nutrient regulation with diverse applications across ecological and agricultural disciplines.

animal behavior and cognition↗

bioRxiv2025

High protein diets early in life improve survival, reduce cannibalism, and increase growth and yield in farmed yellow mealworms

In the wild, animals may be able to compensate for nutritional inadequacies through foraging for novel resources; however, on farms, animals have more limited nutritional options. Therefore, providing adequate and accessible nutrition is essential to positive farmed animal welfare. Billions of yellow mealworms (Tenebrio molitor; Coleoptera: Tenebrionidae) are farmed as mini-livestock each year for use as food and feed. The major feedstock used, wheat bran, can sustain complete development of the species, but has been shown to have significantly lower protein content than yellow mealworms would typically self-select, particularly at early developmental stages. This can reduce growth, survival, and adult oviposition, and may contribute to high rates of cannibalistic behaviour among larvae (as larvae may have few options but to seek protein from the bodies of conspecifics). In this study, we use 20% nutritional yeast as a dietary protein supplement for larvae in early (0-4 weeks) and later life (4-8 weeks) to assess the effects on survival, growth rate, and rates of cannibalism, as well as any effects on growth, development timing, and adult body size. We also investigated the impact of this higher protein diet, when fed to either larvae or adults, on fecundity. We find that protein supplementation in larval diets increased survival by 23%, growth rate by 200%, and total biomass at eight weeks by up to 272%. Larval cannibalistic behaviour was reduced and development time was shorter. The high protein diet, whether fed to adults or to larvae, increased the number of offspring per female by 34-36%. Survival and growth benefits of protein supplementation were especially pronounced when fed to early juvenile instars, but can benefit mealworms across the entire first eight weeks of development. We highlight the need for further research into dietary protein supplementation for yellow mealworms across development to better align with their dietary choices, thereby improving fitness, yield, and welfare.

zoology↗

bioRxiv2025

Pupation substrate and prepupal handling affect eclosion rate, timing, and adult morphology in black soldier flies (Hermetia illucens; Diptera: Stratiomyidae)

On farms, the conditions experienced by black soldier fly (BSF) prepupae may impact their development and survival, altering production goals by changing the fitness of breeding adults. Few studies have addressed the impact of environmental variables (such as substrate type or moisture content), or stressors like handling, on the development and survival of BSF as they transition from prepupae through adulthood. This study examined the effects of pupation substrate (corn cob grits, potting soil, vermiculite, wood chips, and frass), moisture content (20%, 60%, and 100%), and handling during the prepupal period (daily handling, no handling) on eclosion rate and timing, morphology (mass, head width, thorax length), and abdominal window fullness of adult BSF. Handling delayed adult emergence by over three days, reduced eclosion rates by 30.6%, reduced head width and wet mass in adult males, and reduced window fullness and head width in adult females. Frass resulted in the lowest eclosion rate (72.1 {+/-} 2.4%) while corn cob grits (82.2 {+/-} 2.3%) and wood chips (81.5 {+/-} 2.2%) had the highest. Wood chips also resulted in the highest wet and dry mass, head width, and thorax length for adult males and females. Wood chips may be the best pupation substrate for BSF as it enhances body size and has a good eclosion rate. Significant prepupal handling delays adult emergence, reduces eclosion/survival rates, and reduces adult body size; however, more research is necessary to determine if the less chronic handling regimes that are likely present on farms produce similar effects.

zoology↗

bioRxiv2024

How does Gloger's rule predict near- and mid-infrared radiation in birds?

Animal coloration has diverse functions such as camouflage, communication, thermoregulation, protection from UV damage and more, and can be shaped by environmental selective pressures. Some climactic selective pressures are strong enough to produce consistent patterns in many species across large-scale geographic gradients. One pattern in endothermic animals is Glogers rule, which predicts that populations in hot, humid areas will be darker than those in cool, dry areas. This pattern has been demonstrated in several species across latitudinal gradients and is expected to relate to the selective effects of both local thermoregulatory pressures and humidity. However, shortwave radiation from sunlight extends beyond the visible spectrum [400-700 nm] into the near-infrared; thus, thermal pressures often result in changes in surface reflectance characteristics beyond the visible [e.g., 700-2500 nm]. Further, heat exchange with the environment extends into the mid-infrared, including MIR heat loss through the atmospheric transmission window [7.5 - 14 um]. Here, we examine both UV-NIR absorption and MIR emittance in five species of birds that have been shown to follow, or not follow, Glogers rule. We show that NIR absorption varies by species and population in ways that correspond to their habitat and thermoregulatory strategies. MIR emittance, by contrast, was very stable across both species and populations but differed across populations of Northern Bobwhites. We conclude by highlighting the importance of extending coloration research into the NIR and MIR. Further consideration of infrared radiation is necessary for a complete view of animals phenotypic diversity and possible responses to thermal challenge.

ecology↗

bioRxiv2024

Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses

The grass family (Poaceae, Poales) holds immense economic and ecological significance, exhibiting unique metabolic traits, including dual starch and lignin biosynthetic pathways. To investigate when and how the metabolic innovations known in grasses evolved, we sequenced the genomes of four Poales species, including Joinvillea ascendens and Ecdeiocolea monostachya representing the sister clade to Poaceae. The rho whole genome duplication ({rho}WGD) in the ancestral lineage for all grasses contributed to the gene family expansions underlying cytosolic starch biosynthesis, whereas an earlier tandem duplication of phenylalanine ammonia lyase (PAL) gave rise to phenylalanine/tyrosine ammonia lyase (PTAL) responsible for the dual lignin biosynthesis. Integrated functional genomic and biochemical analyses of grass relatives further revealed the molecular basis of key metabolic innovations predating the evolution of grasses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/622220v2_ufig1.gif" ALT="Figure 1"> View larger version (108K): org.highwire.dtl.DTLVardef@117dd71org.highwire.dtl.DTLVardef@1cb5daborg.highwire.dtl.DTLVardef@72a331org.highwire.dtl.DTLVardef@38124e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Transcutaneous Vagus Nerve Stimulation Reduces Pain and OA Progression in Mouse Models of Post-Traumatic Osteoarthritis

Currently, there are no disease-modifying osteoarthritis (OA) drugs (DMOAD) to prevent OA progression and there are limitations on pain relieving therapeutics. Vagus nerve stimulation (VNS) delivered by an implantable device is FDA-approved for refractory epilepsy and severe depression. Here, we investigated the efficacy of transcutaneous VNS (tVNS) for preventing OA progression and providing pain relief in two mouse models of post-traumatic OA (PTOA): the surgical destabilized medial meniscus (DMM) and the non-surgical forced tibial compression anterior cruciate ligament rupture (ACLR). Here, we show that 2 weeks of tVNS significantly reduced histological OA scores in male and female mice after ACLR compared to sham stimulation. In female, but not male, mice, tVNS reduced hyperalgesia and mechanical allodynia. In the slower DMM model, 8 weeks of tVNS improved weight bearing in male and female mice, but only female mice had improved hyperalgesia. Male mice had lower OA histological scores. Serum proinflammatory cytokines were significantly reduced by tVNS in both models but differed by gender and model. Overall, these results provide strong pre-clinical evidence that tVNS reduces OA progression, improves pain, and suppresses pro-inflammatory cytokines, making it a promising DMOAD.

physiology↗

bioRxiv2024

Reconstructing signaling history of single cells with imaging-based molecular recording

The intensity and duration of biological signals encode information that allows a few pathways to regulate a wide array of cellular behaviors. Despite the central importance of signaling in biomedical research, our ability to quantify it in individual cells over time remains limited. Here, we introduce INSCRIBE, an approach for reconstructing signaling history in single cells using endpoint fluorescence images. By regulating a CRISPR base editor, INSCRIBE generates mutations in genomic target sequences, at a rate proportional to signaling activity. The number of edits is then recovered through a novel ratiometric readout strategy, from images of two fluorescence channels. We engineered human cell lines for recording WNT and BMP pathway activity, and demonstrated that INSCRIBE faithfully recovers both the intensity and duration of signaling. Further, we used INSCRIBE to study the variability of cellular response to WNT and BMP stimulation, and test whether the magnitude of response is a stable, heritable trait. We found a persistent memory in the BMP pathway. Progeny of cells with higher BMP response levels are likely to respond more strongly to a second BMP stimulation, up to 3 weeks later. Together, our results establish a scalable platform for genetic recording and in situ readout of signaling history in single cells, advancing quantitative analysis of cell-cell communication during development and disease.

synthetic biology↗

bioRxiv2024

Title Longitudinal Observational (single cohort) Study on the Causes of Trypanocide Failure in cases of African Animal Trypanosomosis in Cattle Near Wildlife Protected Areas of Northern Tanzania

African animal trypanosomosis (AAT) in cattle is primarily managed through trypanocide administration and insecticide application. Trypanocides can be used for both treatment and prophylaxis, but failure is often reported; this may occur due to resistance, substandard drugs, or inappropriate administration. This study in Tanzania aims to quantify reasons for trypanocide failure. An observational year-long longitudinal study was conducted in high-risk AAT areas in Serengeti District from December 2019-October 2022. Purposive sampling targeted herds with high utilization of the prophylactic trypanocide isometamidium chloride (ISM). When a farmer administered a trypanocide (ISM, diminazine aceturate, homidium), the project veterinarian assessed administration and treatment outcomes were determined based on PCR results from blood samples. A multivariable mixed model was utilized to evaluate risk factors for prophylaxis failure. Quality analysis was performed on trypanocide samples using High Performance Liquid Chromatography. A total of 630 cattle from 21 farms were monitored for a year-long period. A total of 295 trypanocide administrations were reported, predominantly being ISM (56%) used for prophylaxis (87%). One-third of trypanocide administrations were not given adequately, and many trypanocides were given to animals that tested negative for trypanosome infections by PCR. Failures occurred in 7% (95% CI 3.0-14%) of curative treatments, and 44% (95% CI 35-42%) of prophylactic administrations. The brand of ISM was significantly associated with odds of prophylaxis failure (p = 0.011). On quality analysis, two ISM samples had no detectable ISM isomers, but the remainder of ISM and DA samples (n=46) fell within the range of acceptable levels. Drug counterfeiting, inadequate use of trypanocides, and resistance are all contributing to trypanocide failure, limiting effective AAT control and with implications for human disease risk. In order to curb trypanocide failure a multi-modal approach to managing the use of trypanocides is required to address all contributing factors. Author SummaryAfrican animal trypanosomosis (AAT) in cattle is commonly controlled through the use of medications called trypanocides. However, these interventions often fail to control AAT due to reasons such as drug resistance, poor-quality medicines, or incorrect administration. This study, conducted in Tanzania between December 2019 and October 2022, aimed to understand why trypanocides fail. Researchers focused particularly on cattle herds that used a preventive drug called isometamidium chloride (ISM). During the study, a veterinarian monitored how farmers administered trypanocides like ISM, diminazine aceturate (DA), or homidium, ensuring proper dosage and storage. Blood samples from cattle were tested to check if treatments were effective. The study found that one-third of trypanocide treatments were not given correctly, and many cattle treated with trypanocides were not actually infected. It was determined that 7% of treatments and 44% of preventive doses failed. The type of ISM brand used played a significant role in failure rates, with some brands performing worse than others. Additionally, tests revealed that some ISM samples lacked the active ingredients necessary for effectiveness. The study highlights that counterfeit drugs, improper use, and drug resistance all contribute to the problem, and a more comprehensive strategy is needed to tackle these issues.

microbiology↗

bioRxiv2023

A long-read draft assembly of the Chinese mantis (Mantodea: Mantidae: Tenodera sinensis) genome reveals patterns of ion channel gain and loss across Arthropoda

Praying mantids (Mantodea: Mantidae) are iconic insects that have captivated biologists for decades, especially the species with cannibalistic copulatory behavior. This behavior has been cited as evidence that insects lack nociceptive capacities and cannot feel pain; however, this behaviorally-driven hypothesis has never been rigorously tested at the genetic or functional level. To enable future studies of nociceptive capabilities in mantids, we sequenced and assembled a draft genome of the Chinese praying mantis (Tenodera sinensis) and identified multiple classes of nociceptive ion channels by comparison to orthologous gene families in Arthropoda. Our assembly - produced using PacBio HiFi reads - is not chromosome-scale (Total size = 3.03Gb; N50 = 1.8Mb; 4966 contigs), but is highly complete with respect to gene content (BUSCO complete = 98.7% [odb10_insecta]). The size of our assembly is substantially larger than that of most other insects, but is consistent with the size of other mantid genomes. We found that most families of nociceptive ion channels are present in the T. sinensis genome; that they are most closely related to those found in the damp-wood termite (Zootermopsis nevadensis); and that some families have expanded in T. sinensis while others have contracted relative to nearby lineages. Our findings suggest that mantids are likely to possess nociceptive capabilities and provide a foundation for future experimentation regarding ion channel functions and their consequences for insect behavior.

genomics↗

bioRxiv2023

Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early pre-neoplastic pancreatic lesions

The adult healthy human pancreas has been poorly studied given lack of indication to obtain tissue from the pancreas in the absence of disease and rapid postmortem degradation. We obtained pancreata from brain dead donors thus avoiding any warm ischemia time. The 30 donors were diverse in age and race and had no known pancreas disease. Histopathological analysis of the samples revealed PanIN lesions in most individuals irrespective of age. Using a combination of multiplex immunohistochemistry, single cell RNA sequencing, and spatial transcriptomics, we provide the first ever characterization of the unique microenvironment of the adult human pancreas and of sporadic PanIN lesions. We compared healthy pancreata to pancreatic cancer and peritumoral tissue and observed distinct transcriptomic signatures in fibroblasts, and, to a lesser extent, macrophages. PanIN epithelial cells from healthy pancreata were remarkably transcriptionally similar to cancer cells, suggesting that neoplastic pathways are initiated early in tumorigenesis. Statement of significanceThe causes underlying the onset of pancreatic cancer remain largely unknown, hampering early detection and prevention strategies. Here, we show that PanIN are abundant in healthy individuals and present at a much higher rate than the incidence of pancreatic cancer, setting the stage for efforts to elucidate the microenvironmental and cell intrinsic factors that restrain, or, conversely, promote, malignant progression.

cancer biology↗