Biology subjects

Hill, T.

Publications and source records attributed to Hill, T..

At least 19 recordsLinked to original sources

bioRxiv2026

A Synthetic Consensus Chiroptera IFN-β Induces IFN-I Signaling Across Diverse Bat Taxa

Bat-associated viruses consistently spill over from bats into humans and other animals. Many bat-associated viruses, including Marburg virus and Nipah virus, cause severe disease in humans but their presentation is subclinical in bats. Advancements in tools and resources to study bat innate antiviral immune responses, including the type I IFN (IFN-I) pathway, are needed to evaluate the mechanisms that underlie differential infection outcomes between reservoir bats and spillover hosts. Commercially available IFN-Is are not bat-specific, and conspecific IFN-Is are impractical to produce for the over 1,500 described bat species. Here, we design and validate a bat order-level consensus IFN (Chiroptera IFN-{beta}) that is functional in bat cells from six diverse bat families, including representatives from both suborders. Using Jamaican fruit bat cells, we demonstrate that Chiroptera IFN-{beta} induces an IFN-stimulated gene repertoire comparable to conspecific IFN-{beta}. This valuable resource can accelerate the capacity of the field to study bat innate antiviral responses and illuminate differences between bats and humans.

immunology↗

bioRxiv2026

Chromosome-Level Nuclear Genome of Simulium vittatum Links Black Fly Cytogenetics to Genome Organization and Evolution

Black flies (Diptera: Simuliidae) are important vectors of pathogens affecting human and animal health, yet the absence of a chromosome-level nuclear reference genome has constrained molecular and evolutionary studies of the family. Here, we present the first chromosome-level nuclear genome and a developmental transcriptomic resource for the long-established IS-7 laboratory lineage of Simulium vittatum. Combining Oxford Nanopore long-read sequencing with Hi-C scaffolding, we assembled a 340.4-Mb genome, with 99.1% of the assembly resolved into three chromosome-length scaffolds (N50=104.8 Mb, BUSCO completeness 93.9%), consistent with the known 2n = 6 karyotype. Using the historically mapped molecular landmarks SVAT and SVEP, we assigned the two arms of chromosome III as IIIS and IIIL, respectively, linking sequence coordinates to the classical polytene chromosome map. Repetitive DNA comprises 46.48% of the assembly, including 29.68% unclassified repeats, and annotation identified 14,732 protein-coding genes and 16,417 transcripts. Integration with larval RNA-seq recovered the previously characterized silk gland proteins SGP-1-SGP-3 and resolved the expressed SGP-2 sequence despite a remaining discrepancy with the genomic sequence. This reference genome connects classical black fly cytogenetics with sequence-level analyses of genome organization, structural variation, and gene content, addressing a major genomic gap within Culicomorpha and providing a foundation for comparative studies of chromosome evolution, hematophagy, and vector biology across Simuliidae.

genomics↗

bioRxiv2026

Active Learning Enables Efficient Directed Evolution of a Far-Red Fluorescent Protein with Minimal Experimental Data

Fluorescent proteins are fundamental tools for cellular imaging. Most fluorescent proteins in routine use, including GFP, are derived from the jellyfish Aequorea victoria and emit blue-green light, which is strongly absorbed and scattered by tissue, limiting imaging depth. Far-red and near-infrared fluorescent proteins, engineered from bacteriophytochromes, address this limitation because far-red light penetrates tissue considerably further. However, these proteins are typically much dimmer than their A. victoria -derived counterparts. Improving brightness by conventional directed evolution requires screening large random mutant libraries, a process that is slow, labor-intensive, and often impractical outside specialized laboratories. We utilized an active-learning-guided directed evolution workflow that identified improved variants from substantially less data than conventional screening. Each round coupled automated, miniaturized cell-free protein expression directly from a DNA template without cloning or cell culture, with a machine-learning model retrained on cumulative sequence-function data to nominate the most informative variants for the next round. Applied to miRFP670nano3, this workflow screened 120 variants across successive rounds and identified twelve with improved brightness, the best four-fold brighter in bacterial systems. However, these gains did not translate when the variants were evaluated in mammalian cells, indicating that performance can be strongly dependent on cellular context. Retrospective simulation across benchmark datasets from ProteinGym showed that performing more experimental batches with fewer samples per batch consistently accelerated convergence to high-fitness sequences. Incorporating protein-language-model derived zero-shot fitness priors also accelerated convergence, but only in proportion to how well each prior score correlated with the true fitness landscape. Together, these findings established generalizable design rules, favoring smaller acquisition batches and confidence-weighted priors, for engineering proteins from minimal experimental data. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=55 SRC="FIGDIR/small/744534v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@14cd238org.highwire.dtl.DTLVardef@7d8334org.highwire.dtl.DTLVardef@30e9f2org.highwire.dtl.DTLVardef@14f3a0c_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2026

ELDR-Glo, a biosensor for cell age and quiescence depth

Fluorescent reporters are powerful tools for revealing intercellular heterogeneity among proliferating cells. However, there are few tools to analyze differences among quiescent (G0) cells, though such differences are relevant for development, tissue maintenance, and cancer cell behavior. Quiescence heterogeneity, also known as quiescence depth, typically correlates with time after cell cycle arrest, yet directly measuring cell age is not feasible for all cell types or most tissues. Here, we describe ELDR-Glo, a genetically-encoded fluorescent biosensor that estimates relative cell age, or time since the last cell cycle. The biosensor integrates replication-coupled degradation in S phase with a slow-maturing mCherry and a normalization module. We demonstrate that ELDR-Glo signal correlates with true cell age by both live-cell imaging and in fixed cells. ELDR-Glo distinguishes early and late G0 cells and functions as a relative quiescence depth reporter in situ. The biosensor is compatible with multiplexed immunofluorescence and flow cytometry. ELDR-Glo provides a unique and scalable tool to investigate cell proliferation control. TeaserA fluorescent biosensor to distinguish cells of different ages and thus, likelihood of returning to proliferation from quiescence.

molecular biology↗

bioRxiv2026

The Two Tube Volatile Assay: a non-contact benchtop bioassay for monitoring susceptibility to transfluthrin

IntroductionProgress against malaria has stalled since 2015, with insecticide resistance a key driver. Spatial emanators release volatile insecticides into the air, exposing mosquitoes through a route distinct from the tarsal contact used by treated nets, indoor residual spraying, and standard bioassays. Transfluthrin is currently monitored using the WHO bottle bioassay, which combines contact and vapour exposure and cannot isolate airborne effects. A scalable, vapour-only method is needed to characterise susceptibility to volatile pyrethroids. MethodsWe adapted the WHO tube bioassay to deliver non-contact transfluthrin vapour exposure without contacting treated papers. Non-blood-fed female Anopheles were exposed to acetone control or transfluthrin papers at 0.005, 0.1 and 2 mg/paper. Knockdown was recorded over 60 minutes and mortality at 24 hours. Testing spanned three laboratories (LSTM, AIRID and KEMRI) using susceptible reference and resistant lab colonies. Dose response models estimated EC{square}{square} for knockdown (EC{square}{square}KD) and mortality (EC{square}{square}Mort), with resistance ratios (RR) against the local susceptible reference. ResultsThe assay generated clear concentration- and time-dependent responses. At LSTM, Kisumu gave an EC{square}{square}KD of 0.052 and EC{square}{square}Mort of 0.054 mg/paper; Siaya was comparable (RR{square}{square}KD 1.17, RR{square}{square}Mort 0.89), whereas Tiassale 13 and KDR showed reduced susceptibility (RR{square}{square}KD 2.42 and 2.85; RR{square}{square}Mort 5.56 and 6.65). At AIRID, the resistant Cove strain did not reach 50% knockdown or mortality. At KEMRI, Siaya showed reduced susceptibility (RR{square}{square}KD 3.36/RR{square}{square}Mort 5.65). Kisumu at AIRID and KEMRI was comparable to LSTM (EC{square}{square}KD 0.007/EC{square}{square}Mort 0.030; EC{square}{square}KD 0.044/EC{square}{square}Mort 0.023). Despite inter-laboratory variation, susceptible strains remained distinguishable from resistant ones. Lower RRs than for contact pyrethroids suggest contact-based phenotypes may not predict vapour susceptibility. ConclusionThe assay provides a practical benchtop method using standard WHO hardware, distinguishing susceptible from resistant strains across three laboratories. Twenty-four-hour mortality is the recommended endpoint, 60-minute knockdown secondary. Not yet validated, it provides a foundation for further validation and adaptation to other actives.

zoology↗

bioRxiv2026

Widely circulating pyrethroid resistance mechanisms reduce the efficacy of transfluthrin and pose a risk for mosquito-borne disease control with spatial emanators

Spatial emanators (SE) are a promising complement to existing tools for preventing mosquito transmitted diseases. In 2025, the WHO updated the WHO Guidelines for Malaria to include a conditional recommendation for the indoor use of prequalified SE products in malaria control. Both prequalified, and many other SE products contain the volatile pyrethroid transfluthrin, which shares the same target site as other (contact/solid phase) pyrethroids. Therefore, an assessment of cross resistance is critical to predict effectiveness against mosquitoes with existing pyrethroid resistance. Our results show that resistance to solid phase pyrethroids is correlated with resistance to transfluthrin in Anopheles and Aedes species. Moreover, commonly-selected resistance mechanisms including target site mutations and over-expression of P450 detoxification enzymes can confer resistance to transfluthrin. Furthermore, we show that resistant mosquitoes are less impacted by transfluthrin in terms of flight activation (irritancy) and reduced blood feeding inhibition, with the response correlating with resistance strength. Transfluthrin did not elicit an electroantennography response in Anopheles gambiae and surgically ablating mosquitoes antennae did not result in differences in flight activation upon transfluthrin exposure, suggesting the antennae are not required for transfluthrin to elicit behavioral responses. These results provide new insight regarding the mode of action of transfluthrin and the risk of resistance reducing transfluthrins efficacy in vector control interventions.

pharmacology and toxicology↗

bioRxiv2026

D-Methionine Improves Spatial Navigation and Attenuates Oxidative Stress and Amyloid Pathology in a Sex-Specific Manner

BackgroundOxidative stress and maladaptive neuroimmune activation contribute to cognitive decline in Alzheimers disease (AD) and represent therapeutic targets beyond amyloid-centered approaches. ObjectiveTo determine whether oral D-methionine (D-Met), a redox-active amino acid, reduces amyloid pathology and lipid peroxidation and confers disease-modifying benefits in AD mouse models. MethodsMale and female APP/PS1 and APPNL-F mice with advanced AD pathology received oral D-Met or vehicle. Behavioral assessments included locomotor activity and hippocampal-dependent spatial learning and memory. Amyloid burden, lipid peroxidation, peripheral metabolic and inflammatory markers, and hippocampal microglial phenotypes were evaluated using biochemical and histological analyses. ResultsD-Met did not alter locomotor or exploratory behavior but improved spatial memory recall in both sexes of APP/PS1 mice and in female APPNL-F mice. APPNL-F males exhibited improved learning during Morris water maze (MWM) acquisition. Amyloid pathology was modestly and region-specifically reduced, including decreased hippocampal plaque size in male APPNL-F mice, reduced cortical plaque size in female APP/PS1 mice, and lower soluble amyloid-{beta} (A{beta})42 in male APP/PS1 mice. Lipid peroxidation, assessed by malondialdehyde, was reduced only in female APPNL-F mice. D-Met induced pronounced sex-dependent peripheral effects, increasing adiposity and pro-inflammatory adipose signaling in males, while reducing perigonadal white adipose tissue (pgWAT) IL-6 expression in female APPNL-F mice. In the hippocampus, D-Met remodeled microglial signatures, with female APPNL-F mice showing reduced Iba1 and disease-associated microglial (DAM) markers and increased Axl expression. ConclusionShort-term D-Met acts as a metabolic and redox modulator with modest amyloid-lowering effects mediated by improved microglial function. Therapeutic efficacy is strongly sex- and model-dependent, with the greatest benefit observed in female APPNL-F mice.

neuroscience↗

bioRxiv2025

Five years of national airborne pollen monitoring in South Africa: Biome-specific calendars to inform allergy diagnosis and prevention

Pollen monitoring is crucial for understanding seasonal patterns, supporting allergy diagnosis and informing early-warning tools to mitigate allergic diseases. The Southern Hemisphere lacks long-term data on pollen seasons, with extremely few from Africa. We present pollen calendars based on five-year data from the South African Pollen Monitoring Network (SAPNET). Airborne pollen from 2019 to 2024 in biomes across South Africa was collected using Hirst-type volumetric spore traps and standard protocols. Daily concentrations were analysed by light microscopy. The five-year mean annual pollen integral (APIn, pollen grains/m3 per year) was calculated for each site. The five-year mean APIn was highest in the Grassland Biome (Bloemfontein, 11654 pg/m3; range 8515 to 14454 pg/m3) and lowest in the Albany Thicket Biome (Gqeberha, 1372; range 853 to 2010 pg/m3). The Grassland Biome (Johannesburg) had the highest averaged tree pollen concentration (7558; range 6575 to 8803 pg/m3). The Savanna Biome (Kimberley) had the highest average grass pollen concentration (3150; 1826 to 3785 pg/m3). The grass family (Poaceae) was the most common pollen type across all biomes. Other common contributing taxa were exotic trees Cupressaceae, Platanus, Morus and Betula. Tree seasons were July to September, whilst grass and weed pollen seasons varied across the different biomes. These five-year pollen calendars provide the first biome-specific national reference for airborne pollen exposure in South Africa. The findings provide baseline data for the clinical management of allergic disease.

ecology↗

bioRxiv2025

Surgical Removal of Visceral Adipose Tissue has Therapeutic Benefit in Male APPNL-F Mice

PurposeVisceral white adipose tissue (vWAT) accumulation causes systemic inflammation, insulin resistance, metabolic syndrome, and senescent cell accumulation that are risk factors for Alzheimers disease (AD). Visceral fat removal (VFR) improves metabolism and reduces pro-inflammatory cytokines. We hypothesized that VFR removal in AD mice would improve metabolism and cognition. MethodsMale and female APPNL-F mice underwent sham or vWAT surgical resection (periovarian or epididymal and perirenal) at 4 (pre-symptomatic) and 16 (symptomatic) months of age to understand interventional and therapeutic effects, respectively. At 18 months of age, glucose metabolism and novel object recognition (NOR) memory were assayed followed by assessment of body composition and tissue-specific markers of metabolism, cell senescence, inflammation, or amyloid accumulation. ResultsMale and female APPNL-F mice showed distinct VFR responses. In pre-symptomatic males, increased vWAT lipolysis and hepatic lipogenesis led to ectopic liver lipid accumulation, with reduced adiponectin and leptin, elevated visfatin, and impaired glucose metabolism. Symptomatic males showed reduced vWAT lipogenesis, enhanced hepatic lipolysis, glycolysis, and glycogenesis, lowering liver lipids and improving insulin sensitivity. Only symptomatic males improved NOR, linked to elevated hippocampal learning and memory markers. Female vWAT reaccumulation was due to increased lipogenesis and lower lipolysis. Pre-symptomatic females had lower hepatic lipogenesis, while glycolysis and glycogenesis declined with disease progression. Hippocampal senescence and inflammation were elevated early in the disease that persisted symptomatically. ConclusionsSex-specific differences in glucose and lipid metabolism and lipid accumulation underlie the divergent responses to VFR in APPNL-F mice, with symptomatic males showing the only beneficial outcomes in metabolism and cognition. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/669175v2_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@6ec644org.highwire.dtl.DTLVardef@9ad821org.highwire.dtl.DTLVardef@1e37775org.highwire.dtl.DTLVardef@b7a558_HPS_FORMAT_FIGEXP M_FIG C_FIG Male and female APPNL-F mice exhibited distinct VFR responses to AD progression. In males, early disease stages were marked by vWAT lipolysis and hepatic lipid accumulation with metabolic dysfunction, while symptomatic stages showed a metabolic shift that improved insulin sensitivity and NOR performance. In contrast, females displayed progressive vWAT reaccumulation, reduced hepatic metabolism, and persistent hippocampal senescence and inflammation from early stages onward.

neuroscience↗

bioRxiv2025

A secreted fatty acid- and retinol- binding protein from Heligmosomoides polygyrus suppresses host macrophage polarization

Parasitic nematodes are major pathogens of humans, animals, and plants, contributing to global health challenges and substantial agricultural losses. Fatty acid- and retinol-binding proteins (FARs), secreted by parasitic nematodes, are believed to play key roles in host-pathogen interactions, including immune modulation and nutrient acquisition. In this study, we characterize a FAR protein from the gastrointestinal nematode Heligmosomoides polygyrus, Hp-FAR-2. Unlike FARs from Caenorhabditis elegans, Steinernema carpocapsae, and Ancylostoma ceylanicum, Hp-FAR-2 did not influence immunity or survival in a Drosophila melanogaster infection model, suggesting functional divergence within the FAR family. Competitive lipid-binding assays revealed a preference for omega-3 and omega-6 polyunsaturated fatty acids, indicating selective binding to bioactive lipids that may modulate immunity. Using RAW 264.7 macrophages, we found that Hp-FAR-2 suppresses the expression of both M1-associated (TNF-, IL-6) and M2-associated (Chil3) markers during polarization, implicating it as a broad immunomodulator that may inhibit inflammatory responses and tissue repair mechanisms to promote chronic infection. Our findings support a model in which Hp-FAR-2 disrupts host lipid signaling and immune function to favor parasite persistence, suggesting its potential role in the excretory/secretory products of H. polygyrus. Together, these data enhance our understanding of FAR-mediated host manipulation and may inform the development of novel anthelmintic or immunoregulatory therapies.

biochemistry↗

bioRxiv2025

Nutrient requirements for cell differentiation progression in Batrachochytrium dendrobatidis

Batrachochytrium dendrobatidis (Bd) is the causative agent of the deadly amphibian disease chytridiomycosis, which has decimated amphibian populations across the globe. Bd reproduces via a multistage asexual pathway. The Bd life cycle begins with a motile zoospore. Upon contact with a surface, the zoospore anchors itself and forms a cyst. The cyst then develops into a germling that produces rhizoid structures. Finally, the germling matures into a zoosporangium which then releases multiple new zoospores. In this study, we investigated the effects of nutrients on the growth and differentiation of Bd. The presence of carbohydrates, vitamins, and trace minerals had a negligible effect on Bds ability to progress through its life cycle. In contrast, the amino acids L-leucine and L-isoleucine (and to a lesser extent L-arginine) were required for cysts to germinate into germlings. However, none of these amino acids were able to sustain further cellular development. Furthermore, the presence of nitrate or ammonium aided progression from germlings into immature zoosporangia that were not able to produce zoospores. The progression to mature zoosporangia was blocked by nitrite or the combined action of calcium ions and bicarbonate. The addition of soluble and insoluble protein sources alone also allowed Bd to develop into immature zoosporangia and affected the rate of development. Finally, protein sources in combination with L-amino acids allowed the completion of the Bd cycle by allowing development from zoospores to mature zoosporangia that were able to release new zoospores. ImportanceEven though the cell differentiation cycle of Bd has been microscopically described, not much is known about the requirements for Bd to progress throughout its life stages. The identification of the molecular cues that allow Bd cell cycle progression may be crucial to disease mitigation efforts. As a corollary, we have identified conditions that allow for the arrest of Bd at various stages of its life cycle. By changing the metabolite availability, we can efficiently obtain cultures enriched for zoospores, cysts, germlings, immature zoosporangia, or spore-releasing zoosporangia. The ability to temporarily freeze and then restart Bd at different points of its life cycle, can allow for determining the mechanisms behind individual transitions between cell types.

microbiology↗

bioRxiv2024

A PI3Kδ-Foxo1-FasL signaling amplification loop rewires CD4+ T helper cell signaling, differentiation and epigenetic remodeling

While inputs regulating CD4+ T helper cell (Th) differentiation are well-defined, the integration of downstream signaling with transcriptional and epigenetic programs that define Th-lineage identity remain unresolved. PI3K signaling is a critical regulator of T cell function; activating mutations affecting PI3K{delta} result in an immunodeficiency with multiple T cell defects. Using mice expressing activated-PI3K{delta}, we found aberrant expression of proinflammatory Th1-signature genes under Th2-inducing conditions, both in vivo and in vitro. This dysregulation was driven by a robust PI3K{delta}-IL-2-Foxo1 signaling loop, fueling Foxo1-inactivation, loss of Th2-lineage restriction, altered chromatin accessibility and global impairment of CTCF-DNA interactions. Surprisingly, ablation of Fasl, a Foxo1-repressed gene, restored normal Th2 differentiation, TCR signaling and CTCF expression. BioID revealed Fas interactions with TCR- signaling components, which were supported by Fas-mediated potentiation of TCR signaling. Our results highlight Fas-FasL signaling as a critical intermediate in phenotypes driven by activated-PI3K{delta}, thereby linking two key pathways of immune dysregulation.

immunology↗

bioRxiv2024

Lifespan of male and female APP/PS1 and APPNL-F/NL-F mouse models of Alzheimer's disease

Alzheimers disease (AD) disproportionately affects women, yet most preclinical research studies are male-centric. We performed lifespan analyses of male and female AD mouse models (APP/PS1 and APPNL-F/NL-F) and their shared genetic background control (C57BL/6). Survival curves support significant sex differences between within genotypes. Minimal longevity revealed increased age in male APP/PS1, and decreased age in APPNL-F/NL-F mice. Maximal longevity revealed an increased average age in males. Furthermore, median lifespan differed between sex and genotype. This study supports sexual dimorphic survival in two mouse models of AD, emphasizing the need to examine mechanisms and treatments in both sexes.

physiology↗

bioRxiv2024

Infrared thermography for plant stress detection in vertical farms: Investigating spatiotemporal variations and exploring solutions via machine learning

Application of infrared thermography (IRT) for real-time plant stress detection has grown rapidly in recent years. Although the technology has been well established for crops grown in fields and glasshouses, its feasibility for vertical farms has not been tested extensively. In this study, temporal monitoring of stress induced by root dehydration in purple basil plantlets inside a vertical farm was performed to identify bottlenecks in real-time stress detection via IRT. Subsequently, potential solutions were investigated via machine learning by implementing support vector machines for supervised classification. Edge effects as well as proximity to air vents were identified as the major causes of positional variation in plant temperature that could lead to misprediction of stress. Binary, ternary, and quaternary classification models were trained using thermal images from two, three, and four levels of stress, respectively, to assess model performance. Binary classification models trained with plants experiencing medial and high levels of stress were able to identify stressed plants with high accuracy (81-94%). Further, binary models trained using plants under medial levels of stress generated a continuous probability distribution for stress prediction when plotted against plant temperature. In contrast, models trained using samples experiencing high stress generated distinct probabilistic clusters for the unstressed and highly stressed plants, but were unable to classify medial stress samples reliably. Similarly, ternary and quaternary models were able to better predict very high and very low levels of stress than intermediate stress levels. Hence, our findings suggest that binary classification models trained using samples under medial levels of stress would be helpful in overcoming spatiotemporal variations in canopy thermal profile by providing reliable probabilistic estimates of plant stress within a vertical farming system. Key pointsO_LIPlant stress detection in vertical farms via thermal imaging may be challenging because perceptible plant temperature can be strongly influenced by its microenvironment. C_LIO_LIThermal image analysis via supervised machine learning allows the development of robust prediction models that can overcome such factors to identify stressed plants. C_LIO_LIBinary classification machine learning models can reliably identify stressed plants as well as provide probabilistic estimates for the degree of stress. C_LI

plant biology↗

bioRxiv2024

Assessing nutritional pigment content and plant health status of green and red leafy vegetables by image analysis: Catching the 'red herring' of plant digital color processing

Estimating pigment content in leafy vegetables via digital image analysis is a reliable method for real-time assessment of plant health status and nutritive value. However, the present leaf color analysis models developed using green-leafed plants do not perform reliably while analyzing images of anthocyanin-rich leaves, often giving misleading or "red herring" trends. Hence, the present study investigates variations in different digital color features for six types of leafy vegetables with varying levels of laminar anthocyanin to identify holistic digital color analysis models that could be implemented for real-time assessment of health status as well as nutritional pigment contents of leafy vegetables irrespective of laminar anthocyanin status. For this, datasets from three digital color spaces, viz., RGB (red, green, blue), HSI (hue, saturation, intensity), and L*a*b* (lightness, redness-greenness, yellowness-blueness), were compared with pigment contents of n = 320 leaf samples, and were analyzed via linear and non-linear regression using single variables, multiple linear regression, Support Vector regression, and Random Forest regression to predict chlorophyll and anthocyanin contents. While most digital color features presented abrupt shifts between anthocyanin-rich and low-anthocyanin samples, the R digital color feature did not show any deviation due to leaf anthocyanin content and was found to have the best correlation with SPAD chlorophyll meter readings (R2 = 0.83). Concomitantly, H (R2 = 0.82) and a* (R2 = 0.79) features correlated most strongly with leaf anthocyanin content. In general, prediction of pigment contents was more accurate when data from all channels within a color space was analyzed simultaneously. Further, most reliable estimates of pigment content were provided by Support Vector and Random Forest regression models (0.7 < R2 < 0.85). Thus, the present findings demonstrate how digital color analysis of green as well as anthocyanin-rich leafy vegetables could be implemented for assessing plant health status and nutritional pigment content non-invasively.

plant biology↗

bioRxiv2024

One year of gluten free diet impacts gut function and microbiome in celiac disease

BACKGROUND & AIMSCurrently, the main treatment option for coeliac disease (CD) is a gluten free diet (GFD). This observational cohort study investigated the impact of CD and 1 year of GFD on gut function and microbiome. METHODS36 newly diagnosed patients and 36 healthy volunteers (HV) were studied at baseline and at 12 months follow up. Small bowel water content (SBWC), whole gut transit time (WGTT) and colon volumes were measured by MRI. Stool samples DNA was subjected to shotgun metagenomic sequencing. Species level abundances and gene functions, including carbohydrate active enzymes (CAZymes) were determined. RESULTSSBWC was significantly higher in people with CD 157{+/-}15 mL versus HVs 100{+/-}12 mL (p=0.003). WGTT was delayed in people with CD 68{+/-}8 hours versus HVs 41{+/-}5 hours (p=0.002). The differences reduced after 12 months of GFD but not significantly. Wellbeing in the CD group significantly improved after GFD but did not recover to control values. CD faecal microbiota showed high abundance of proteolytic gene functions, associated with Escherichia coli, Enterobacter and Peptostreptococcus. GFD significantly reduced Bifidobacteria and increased Blautia wexerelae. Microbiome composition correlated positively with WGTT, colonic volume and Akkermansia municphilia but negatively with B.wexerelae. Following GFD the reduction in WGTT and colonic volume significantly associated with increased abundance of B.wexerelae. There were also significant alterations in CAZyme profiles, specifically starch and arabinoxylan degrading families. CONCLUSIONSCD impacted gut function and microbiota. GFD ameliorated but did not reverse these effects, significantly reducing Bifidobacteria associated with reduced intake of resistant starch and arabinoxylan from wheat.

physiology↗

bioRxiv2024

Discordant changes in foliar and reproductive phenology of tropical dry-forest trees under increasing temperature and decreasing wet-season rainfall

O_LIPlant phenology drives population dynamics and forest productivity; it is also impacted by shifting environmental cues under climate change such as more prevalent drought. It is imperative to better understand how species and community phenology respond to climate change in leaf turnover and reproduction, both of which are required to integrate phenology into full life-cycle assessments. C_LIO_LIHowever, relatively few studies to-date examined the quantity and timing of phenology simultaneously. We demonstrate that the simultaneous assessment of phenological quantity and timing across multiple organs reveals more nuanced and holistic insights into the consequences of climate change. C_LIO_LIExtending a regression approach based on Fourier series, we decomposed the long-term (2004-2020) monthly leaf shedding, leaf flush, flowering and fruiting of 617 trees across 94 taxa at a Nigerian seasonally dry tropical forest into three periodic components--mean intensity, amplitude and phase--which respectively represents the total quantity, pulse concentration and peak timing of phenology. We then related each periodic component to warming minimum temperature and drying wet-season rainfall. C_LIO_LIWe found that climate explained more variation in phenological amplitudes (14-66%) compared to mean intensity and timing (6-49%). In drier years, more species (18%) shed leaves earlier (changing timing) or in more concentrated pulses (changing amplitude), while only a few (2%) shed leaves in greater total amounts (changing mean intensity). This combined with the decreased mean intensity of leaf flush imply a lower primary productivity as trees deployed fewer leaves for a shorter period. Some species (30%) produced fewer fruits despite no change or even increase in flowering; in a few species this could be explained by a shortened flowering period that limited pollination. At the community level, reproduction became more synchronous, potentially creating periods of scarcity for consumers. C_LIO_LISynthesis: Our findings highlight several contrasting yet complementary phenology- climate insights, indicating that assessments of forests climate resilience necessitate multiple aspects of phenology rather than a single performance indicator. The decline of leaf and fruit productions, as well as the temporal mismatches in leaf turnover and reproduction, will have cascading impacts on trophic interactions and nutrient cycling. C_LI

ecology↗

bioRxiv2023

Altered Hippocampal Glutamatergic Neurotransmission and Cognitive Impairment in APP Knock-In Mice

BackgroundIt is well established that glutamatergic neurotransmission plays an essential role in learning and memory. Previous studies indicate that glutamate dynamics shift with Alzheimers disease (AD) progression, contributing to negative cognitive outcomes. ObjectiveIn this study, we characterized hippocampal glutamatergic signaling with age and disease progression in a knock-in mouse model of AD (APPNL-F/NL-F). MethodsAt 2-4 and 18+ months old, male and female APPNL/NL, APPNL-F/NL-F, and C57BL/6 mice underwent cognitive assessment using Morris water maze (MWM) and Novel Object Recognition (NOR). Then, basal and 70 mM KCl stimulus-evoked glutamate release was measured in the dentate gyrus (DG), CA3, and CA1 regions of the hippocampus using a glutamate-selective microelectrode in anesthetized mice. ResultsGlutamate recordings support elevated stimulus-evoked glutamate release in the DG and CA3 of young APPNL-F/NL-F male mice that declined with age compared to age-matched control mice. Young female APPNL-F/NL-F mice exhibited increased glutamate clearance in the CA1 that slowed with age compared to age-matched control mice. Male and female APPNL-F/NL-F mice exhibited decreased CA1 basal glutamate levels, while males also showed depletion in the CA3. Cognitive assessment demonstrated impaired spatial cognition in aged male and female APPNL-F/NL-F mice, but only aged females displayed recognition memory deficits compared to age-matched control mice. ConclusionsThese findings confirm a sex-dependent hyper-to-hypoactivation glutamatergic paradigm in APPNL-F/NL-F mice. Further, data illustrate a sexually dimorphic biological aging process resulting in a more severe cognitive phenotype for female APPNL-F/NL-F mice than their male counterparts. Research outcomes mirror that of human AD pathology and provide further evidence of divergent AD pathogenesis between sexes.

neuroscience↗