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bioRxiv2026

Impact of Water Deficit on Growth, Biochemical, and Physiological Traits in Eggplant MAGIC Lines

Climate change exacerbates agricultural water scarcity, necessitating the development of drought-tolerant crop varieties. This study evaluates 12 eggplant lines from a MAGIC (Multi-parent Advanced Generation Intercross) population, previously selected for contrasting responses to water deficit during the vegetative stage. To validate tolerance under adult production conditions, plants underwent five irrigation-withholding cycles over a 170-day greenhouse growing period. Yield components, the Stress Tolerance Index (STI), and physiological parameters (water status and stomatal conductance) were evaluated. Additionally, photosynthetic pigments, oxidative stress markers, antioxidant compounds, and osmolytes were quantified to characterize the biochemical basis of tolerance alongside final biomass production. The results showed that four of the five lines that were previously classified as tolerant in the vegetative stage remained among the most tolerant at the reproductive stage. Specifically, lines L13, L78 and L179 were the most productive under water-limited conditions. While L13 and L179 exhibited stable tolerance throughout all developmental stages, L78 displayed stage-specific tolerance, manifested only during the reproductive growth phase. These findings emphasise the importance of integrating early-stage screening with adult-stage validation in order to capture the full spectrum of genetic drought tolerance. The most productive lines were characterised by moderate aboveground biomass, high leaf hydration and maintained stomatal conductance. However, the strategies employed differed: while L179 exhibited high photosynthetic pigment content, L13 was characterised by high total sugar accumulation. Overall, these results provide a multi-trait roadmap and identify elite MAGIC parental lines for breeding climate-resilient eggplant cultivars.

plant biology↗

bioRxiv2015

Hyper-variability in Circulating Insulin and Physiological Outcomes in Male High Fat-fed Ins1-/-:Ins2+/- Mice in a Conventional Facility

Insulin is an ancient, multi-functional hormone with essential roles in glucose homeostasis and energy storage. Recently, our group has taken advantage of the ability to limit insulin secretion in vivo by reducing insulin gene dosage to demonstrate that insulin hypersecretion is a requirement for diet-induced obesity. Our previous studies employed male Ins1+/-:Ins2-/- mice that exhibit a complete inhibition of diet-induced hyperinsulinemia relative to Ins1+/+:Ins2-/- littermate controls, as well as female Ins1-/-:Ins2+/- mice with transient, partial reduction in circulating insulin relative to Ins1-/-:Ins2+/+ littermates. In the present study, we sought to extend these studies to male Ins1-/-:Ins2+/- mice on the same chow and high fat diets. Surprisingly, while reduced Ins2 gene dosage appeared capable of reducing Ins2 mRNA, insulin protein levels in these mice were not significantly reduced. Moreover, there was a marked hyper-variability in circulating insulin levels within and between two independent cohorts of mice that persisted over at least the first year of life. In Cohort 1, we observed a paradoxical increase in body weight in some high fat-fed male Ins1-/-:Ins2+/- mice relative to Ins1-/-:Ins2+/+ littermate controls. This phenomenon is consistent with the known satiety effects of insulin and our previous observations with Ins2 can be expressed in the brain. Collectively, our data reveal unexpected complexity associated with the Ins2 gene in male mice, and establish the Ins2 gene as a candidate for studying the effects of modifier genes and/or environmental influences on gene-to-phenotype variability. Further studies are required to define the molecular mechanisms of this phenotypic hyper-variability and to define the role of reduced Ins2 gene dosage in the brain.

Physiology↗

bioRxiv2017

Measuring physiological responses to stressors using a novel Hmox1 reporter mouse

Hmox1 protein holds great promise as a biomarker of organismal health as it is highly expressed in stressed or damaged cells. However, documenting Hmox1 expression patterns has thus far only been feasible in simple model organisms with limited relevance to humans. We now report a new Hmox1 reporter line that makes it possible to access this information in mice, the premiere model system for studying human disease and toxicology. Using a state-of-the-art strategy, we express multiple complementary reporter molecules from the murine Hmox1 locus, including firefly luciferase to allow long-term, non-invasive imaging of Hmox1 expression, and {beta}-galactosidase for high-resolution mapping of expression patterns post-mortem. We validate the model by confirming the absence of haplo-insufficiency effects, the fidelity of reporter expression, and its responsiveness to oxidative and inflammatory stimuli. In addition to providing blueprints for Hmox1 expression in mice that provide novel biological insights for follow-up, this work paves the way for the broad application of this model to regulatory toxicology studies and, also, pre-clinical investigations into human degenerative diseases.

physiology↗

bioRxiv2017

Parametric Imaging Of FDG-PET Data Using Physiology And Iterative Regularization: Application To The Hepatic And Renal Systems

I. AIMS I. AIMS II. METHODS III. RESULTS IV. CONCLUSIONS REFERENCES Positron Emission Tomography (PET) [1] is a nuclear medicine imaging technique capable of detecting the time dependent spatial distribution of pico-molar quantities of a labelled tracer, which is diffused into a living body. FDG-PET is a PET modality in which the radiopharmaceutical [18F]Fluoro-2-deoxy-D-glucose (FDG) is used as a tracer to observe metabolic processes related to glucose consumption. In order to overcome the limits of spatial resolution in PET and to improve the quality of information achievable from PET images, one approach is to develop parametric imaging methods able of showing the tracer metabolism at a local level. Starting from the design of compartmental models appropriate to describe the tracer kinetics in a predefined physiol ...

physiology↗

bioRxiv2017

Physiological factors of importance for load carriage

The energy expenditure during carrying no load, 20, 35 and 50 kg at two walking speeds, 3 and 5 km h-1, was studied in 36 healthy participants, 19 men (30 {+/-} 6 yrs, 82.5 {+/-} 7.0 kg) and 17 women (29 {+/-} 6 yrs, 66.1 {+/-} 8.9 kg). Anthropometric data, leg muscle strength as well as trunk muscle endurance and muscle fibre distribution of the thigh were also obtained. To load the participant a standard backpack filled with extra weight according to the carrying weight tested was used. Extra Load Index (ELI), the oxygen uptake (VO2) during total load over no-load-exercise, was used as a proxy for load carrying ability. In addition to analyzing factors of importance for the ELI values, we also conducted mediator analyzes using sex and long term carrying experience as causal variables for ELI as the outcome value.\n\nFor the lowest load (20 kg), ELI20, was correlated with body mass but no other factors. Walking at 5 km h-1 body mass, body height, leg muscle strength and absolute VO2max were correlated to ELI35 and ELI50, but relative VO2max, trunk muscle endurance and leg muscle fibre distribution were not.\n\nSex as causal factor was evaluated in a mediator analyses with ELI50 as outcome. ELI50 at 5 km h-1 differed between the sexes. The limit for acceptable body load, 40 % of VO2max (according to [A]strand, 1967), was nearly reached for women carrying 35 kg (39%) and surpassed at 50 kg at 3 km h-1, and for men carrying 50 kg at 5 km h-1. This difference was only mediated by difference in body mass. Neither muscle fibre distribution, leg muscle strength, trunk muscle endurance and body height nor did absolute or relative VO2max explain the difference.\n\nParticipants with long term experience of heavy load carrying had significant lower ELI20 and ELI50 values than those with minor or non-experience, but none of the above studied factors could explain this difference.\n\nThe study showed that body mass and experience of carrying heavy loads are important factors for the ability to carry heavy loads.\n\nFundingThis study was founded by the Swedish Military Forces{acute} Research Authority and The Research Funds of The Swedish School of Sport and Health Sciences.\n\nAbbreviations

physiology↗

bioRxiv2018

Gradual repression of selenoprotein W ensures physiological bone remodelling

Selenoproteins containing selenium in the form of selenocysteine are critical for bone remodelling. However, their mechanism of action is not well understood. Here, we report the identification of selenoprotein W (SELENOW) through large-scale mRNA profiling of receptor activator of nuclear factor (NF)-{kappa}B ligand (RANKL)-induced osteoclast differentiation, as a protein that is downregulated via RANKL/RANK/tumour necrosis factor receptor-associated factor 6/p38 signalling. RNA sequencing analysis revealed that SELENOW regulates osteoclastogenic genes. SELENOW overexpression enhanced osteoclastogenesis in vitro via nuclear translocation of NF-{kappa}B and nuclear factor of activated T-cells cytoplasmic 1, whereas its loss suppressed osteoclast formation. SELENOW-deficient and SELENOW-overexpressing mice exhibited osteopetrosis and osteoporosis, respectively. Ectopic SELENOW expression stimulated cell-cell fusion critical for osteoclast maturation as well as bone resorption. Thus, RANKL-dependent repression of SELENOW maintains proper osteoclast differentiation and blocks osteoporosis caused by overactive osteoclasts. These findings demonstrate a biological link between selenium and bone metabolism.

physiology↗

bioRxiv2018

Integrative Transcription Start Site Analysis and Physiological Phenotyping Reveal Torpor-Specific Expressions in Mouse Skeletal Muscle

Mice enter an active hypometabolic state, called daily torpor, when they experience a lowered caloric intake under cool ambient temperature (TA). During torpor, the oxygen consumption rate (VO2) drops to less than 30% of the normal rate without harming the body. This safe but severe reduction in metabolism is attractive for various clinical applications; however, the mechanism and molecules involved are unclear. Therefore, here we systematically analyzed the expression landscape of transcription start sites (TSS) in mouse skeletal muscles under various metabolic states to identify torpor-specific transcription patterns. We analyzed the soleus muscles from 38 mice in torpid, non-torpid, and torpor-deprived conditions, and identified 287 torpor-specific promoters. Furthermore, we found that the transcription factor ATF3 was highly expressed during torpor deprivation and that the ATF3-binding motif was enriched in torpor-specific promoters. Our results demonstrate that the mouse torpor has a distinct hereditary genetic background and its peripheral tissues are useful for studying active hypometabolism.

physiology↗

bioRxiv2018

Effects of dietary replacement of broiler litter with Mucuna pruriens utilis forage and seed meal on performance, carcass characteristics, blood biochemical and physiological parameters in indigenous goats

The productivity of indigenous goats in Africa is constrained by shortage of protein-rich feed especially in winter. This study investigated the nutritional value of mucuna forage (MF) and seed meal (MSM) as alternative protein sources for indigenous goats. Mucuna was planted in 3 parallel and adjacent fields and its foliage nutritional composition determined at 4, 8, 12 and 16 weeks after planting (WAP). MF was harvested at 14 WAP whilst mucuna pods were harvested at 28 - 30 WAP, shelled and the MSM chemically analysed. In a completely randomised design (CRD), 20 indigenous goats were randomly offered 5 treatment diets with, respectively, 0%, 25%, 50% and 100% MF and 100% MSM replacing broiler litter (BL), each with 4 replicates, for 82 days. Both mucuna foliage DM and CF contents increased (P < 0.001) whilst foliage CP, EE and ash contents decreased (P<0.001) with maturity. On the other hand, MSM contained high DM (90.7%), EE (3.7% DM) and CP (26.0% DM) but low CF (9.7% DM) and ash (5.5% DM) contents. Both body weight gain (BWG) and feed conversion efficiency (FCE) were not influenced by dietary mucuna incorporation (P > 0.05). However, dietary MF, particularly at the 100% level, decreased goat feed intake (FI) (P < 0.001) whilst 100% MSM increased (P < 0.001) this parameter. Mucuna had no effect on all carcass characteristics (P > 0.05) but increased (P < 0.05), particularly at the 100% MSM level, hot carcass weight and dressing percentage. There were no effects of mucuna on all biochemical and haematological indices (P > 0.05), except for the increase in serum glucose (P < 0.05). In conclusion, the optimal stage for harvesting and utilisation of MF is between 12 and 16 WAP and both MF and MSM, particularly the latter, are rich alternative protein sources for indigenous goats.

physiology↗

bioRxiv2014

The HVCN1 channel conducts protons into the phagocytic vacuole of neutrophils to produce a physiologically alkaline pH

Activation of the NADPH oxidase (NOX2) of the phagocytic vacuole of neutrophils is essential for innate immunity. Sustained activity of the oxidase requires that charge movements across the membrane are balanced. A role for the proton channel, HVCN1, has been proposed but not proven. Using the ratiometric pH indicator SNARF, introduced into the cytosol and separately into the vacuole coupled to Candida, we used confocal microscopy to measure changes in pH in these two compartments in human and mouse neutrophils. Shortly after phagocytosis by human cells, the vacuolar pH rose to ~9, at which it was maintained for ~20 minutes, while the cytosol showed a small acidification of ~0.25 pH unit. Alkalinisation has important consequences for the microbicidal and digestive functions of vacuolar enzymes. In HVCN1 knock out mouse neutrophils, the phagocytosis induced respiratory burst was halved to ~3 fmols per Candida, the vacuolar pH rose to >11 and the cytosol acidified excessively to pH ~6.75. These changes were prevented by the protonophore CCCP. The rate of extrusion of protons into the extracellular medium following phagocytosis was not significantly different from wild type neutrophils suggesting that cytoplasmic acidification resulted from the loss of the proton sink into the vacuole. HVCN1 phagocytic vacuoles showed considerable swelling, and this was blocked by CCCP and decreased by valinomycin. Stoichiometric considerations indicated that the HVCN1 channel compensates 90-95% of the oxidase-induced charge in normal cells, and in its absence, charge is carried by ions other than protons, including K+.

Cell Biology↗

bioRxiv2016

Dendritic trafficking faces physiologically critical speed-precision tradeoffs

Nervous system function requires intracellular transport of channels, receptors, mRNAs, and other cargo throughout complex neuronal morphologies. Local signals such as synaptic input can regulate cargo trafficking, motivating the leading conceptual model of neuron-wide transport, sometimes called the \"sushi-belt model\" (Doyle and Kiebler, 2011). Current theories and experiments are based on this model, yet its predictions are not rigorously understood. We formalized the sushi belt model mathematically, showing how it can achieve arbitrarily complex spatial distributions of cargo in reconstructed morphologies. However, the model also predicts an unavoidable, morphology dependent tradeoff between speed, precision and metabolic efficiency of cargo transport. With experimental estimates of trafficking kinetics, the model predicts delays of many hours or days for modestly accurate and efficient cargo delivery throughout a dendritic tree. These findings challenge current understanding of the efficacy of nucleus-to-synapse trafficking and may explain the prevalence of local biosynthesis in neurons.

Neuroscience↗

bioRxiv2016

Goggatomy: a Method for Opening Small Cuticular Compartments in Arthropods for Physiological Experiments

Most sense organs of arthropods are ensconced in small exoskeletal compartments that hinder direct access to plasma membranes. We have developed a method for exposing live sensory and supporting cells in such structures. The technique uses a viscous light cured resin to embed and support the structure, which is then sliced with a sharp blade. We term the procedure a goggatomy, from the Khoisan word for a bug, gogga. To demonstrate the utility of the method we show that it can be used to expose the auditory chordotonal organs in the second antennal segment and the olfactory receptor neurons in the third antennal segment of Drosophila melanogaster, preserving the transduction machinery. The procedure can also be used on other small arthropods, like mites, Daphnia, mosquitoes, wasps and ants to expose a variety of cells.

Neuroscience↗

bioRxiv2016

Using MinION nanopore sequencing to generate a de novo eukaryotic draft genome: preliminary physiological and genomic description of the extremophilic red alga Galdieria sulphuraria strain SAG 107.79

We report here the de novo assembly of a eukaryotic genome using only MinION nanopore DNA sequence data by examining a novel Galdieria sulphuraria genome: strain SAG 107.79. This extremophilic red alga was targeted for full genome sequencing as we found that it could grow on a wide variety of carbon sources and could uptake several precious and rare-earth metals, which places it as an interesting biological target for disparate industrial biotechnological uses. Phylogenetic analysis clearly places this as a species of G. sulphuraria. Here we additionally show that the genome assembly generated via nanopore long read data was of a high quality with regards to low total number of contiguous DNA sequences and long length of assemblies. Collectively, the MinION platform looks to rival other competing approaches for de novo genome acquisition with available informatics tools for assembly. The genome assembly is publically released as NCBI BioProject PRJNA330791. Further work is needed to reduce small insertion-deletion errors, relative to short-read assemblies.

Genomics↗

bioRxiv2016

Grow with the flow: a latitudinal cline in physiology is associated with more variable precipitation in Mimulus cardinalis

Local adaptation is commonly observed in nature: organisms perform well in their natal environment, but poorly outside it. Correlations between traits and latitude, or latitudinal clines, are among the most common pieces of evidence for local adaptation, but identifying the traits under selection and the selective agents is challenging. Here, we investigated a latitudinal cline in growth and photosynthesis across 16 populations of the perennial herb Erythranthe cardinalis (Phrymaceae). Using machine learning methods, we identify interannual variation in precipitation as a likely selective agent: Southern populations from more variable environments had higher photosynthetic rates and grew faster. We hypothesize that selection may favor a more annualized life history - grow now rather than save for next year - in environments where severe droughts occur more often. Thus our study provides insight into how species may adapt if Mediterranean climates become more variable due to climate change.

evolutionary biology↗

bioRxiv2017

Single-cell histories in growing populations: relating physiological variability to population growth

Cell size and individual growth rates vary substantially across genetically identical cell populations. This variation cannot entirely be explained by asynchronous cell division cycles, but also needs to take into account the differences in the histories that cells experience during their lifespan. We describe a stochastic framework to characterise cell size histories in an exponentially growing population. We show that these histories differ from cells observed in isolation, such as observed in mother machines. Quantifying these historical fluctuations allows us to predict the population growth rate. We highlight that the maximum attainable population growth cannot exceed the rate at which an average cell grows, but the population doubles faster than an average cell doubles its size. We validate this prediction using recent single-cell data. The theory thus provides fundamental limits on population fitness in terms of individual cell properties.

systems biology↗

bioRxiv2017

Efficacy of the β-lactam\β-lactamase inhibitor combination is linked to WhiB4 mediated changes in redox physiology of Mycobacterium tuberculosis

AimsInhibition of {beta}-lactamase by clavulanate (Clav) sensitizes multi-and extensively drug-resistant Mycobacterium tuberculosis (Mtb) strains towards {beta}-lactams such as amoxicillin (Amox). However, the underlying mechanism of how Mtb responds to Amox-Clav combination (Augmentin; AG) is not characterized.\n\nResultsWe integrated global expression profiling with the protein-protein interaction landscape and generated a genome-scale network of Mtb in response to AG. In addition to specific targets (e.g., peptidoglycan biosynthesis and {beta}-lactamase), the response to AG was also centered on redox-balance, central carbon metabolism (CCM), and respiration in Mtb. We discovered that AG modulates superoxide levels, NADH/NAD+ balance and mycothiol redox potential (EMSH) of Mtb. Higher intra-mycobacterial EMSH potentiates mycobactericidal efficacy of AG, whereas lower EMSH induces tolerance. Further, Mtb responds to AG via a redox-sensitive transcription factor, WhiB4. Mtb{Delta}whiB4 displayed higher expression of genes involved in {beta}-lactam resistance along with those mediating respiration, CCM and redox balance. Moreimportantly, WhiB4 binds to the promoter regions and represses transcription of genes involved in {beta}-lactamase expression in a redox-dependent manner. Lastly, while Mtb{Delta}whiB4 maintained internal EMSH, exhibited greater {beta}-lactamase activity and displayed AG-tolerance, overexpression of WhiB4 induced oxidative shift in EMSH and repressed {beta}-lactamase activity to aggravate AG-mediated killing of drug-sensitive and -resistant strains of Mtb.\n\nInnovation and ConclusionsThis work demonstrate that efficacy of {beta}-lactam\\{beta}-lactamase inhibitor combination can be attenuated by elevating mycobacterial antioxidant capabilities and potentiated by impairing redox buffering capacity of Mtb. The functional linkage between {beta}-lactams, redox balance, and WhiB4 can be exploited to potentiate AG action against drug-resistant Mtb.

microbiology↗

bioRxiv2017

Laboratory cultivation of acidophilic nanoorganisms. Physiological and bioinformatic dissection of a stable laboratory co-culture.

This study describes the laboratory cultivation of ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganisms). After 2.5 years of successive transfers in an anoxic medium containing ferric sulfate as an electron acceptor, a consortium was attained that is comprised of two members of the order Thermoplasmatales, a member of a proposed ARMAN group, as well as a fungus. The 16S rRNA of one archaeon is only 91.6% identical to Thermogymnomonas acidicola as most closely related isolate. Hence, this organism is the first member of a new genus. The enrichment culture is dominated by this microorganism and the ARMAN. The third archaeon in the community seems to be present in minor quantities and has a 100% 16S rRNA identity to the recently isolated Cuniculiplasma divulgatum. The enriched ARMAN species is most probably incapable of sugar metabolism because the key genes for sugar catabolism and anabolism could not be identified in the metagenome. Metatranscriptomic analysis suggests that the TCA cycle funneled with amino acids is the main metabolic pathway used by the archaea of the community. Microscopic analysis revealed that growth of the ARMAN is supported by the formation of cell aggregates. These might enable cross feeding by other community members to the ARMAN.

microbiology↗

bioRxiv2017

Sex chromosome evolution, heterochiasmy and physiological QTL in the salmonid Brook Charr Salvelinus fontinalis

Whole genome duplication can have large impacts on genome evolution. However, much remains unknown about these impacts, such as the mechanisms of coping with a duplicated sex determination system, which may result in increased sex determination mechanism diversity. Sexual conflict (i.e. alleles having different optimums in each sex) can result in sequestration of genes into non-recombining sex chromosomes. Development of sex chromosomes may involve heterochiasmy (i.e. sex-specific recombination rate), which is also poorly understood. Family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have non-homologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species, four genera). Although non-homology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify QTL for 21 unique growth, reproductive and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution.

genomics↗

bioRxiv2017

Basal Ganglia Control Of Reflexive Saccades: A Computational Model Integrating Physiology Anatomy And Behaviour

It is hypothesised that the basal ganglia play a key role in solving the problem of action selection. Here we investigate this hypothesis through computational modelling of the primate saccadic oculomotor system. This system is an excellent target for computational modelling because it is supported by a reasonably well understood functional anatomy, has limited degrees of freedom, and there is a wealth of behavioural and electrophysiological data for model comparison. Here, we describe a computational model of the reflexive saccadic oculomotor system incorporating the basal ganglia, key structures in motor control and competition between possible actions. To restrict the likelihood of overfitting the model it is structured and parameterised by the known anatomy and neurophysiology along with data from a single experimental behavioural paradigm, then validated by testing against several additional behavioural experimental data without modification of the parameters. With this model we reproduce a range of fundamental reflexive saccadic results both qualitatively and quantitatively, comprising: the distribution of saccadic latencies; the effect of eccentricity, luminance and fixation-target interactions on saccadic latencies; and the effect of competing targets on saccadic endpoint. By investigating the model dynamics we are able to provide mechanistic explanations for the sources of these behaviours. Further, because of its accesibility, the oculomotor system has also been used to study general principle of sensorimotor control. We interpret the ability of the basal ganglia to successfully control saccade selection in our model as further evidence for the action selection hypothesis.

neuroscience↗