Biology subjects

Allen, K.

Publications and source records attributed to Allen, K..

18 recordsLinked to original sources

bioRxiv2026

Understanding Strategic Motor Learning as a Process of Hypothesis Testing

Multiple learning processes contribute to successful goal-directed actions under changing physiological states, biomechanical constraints, and environmental contexts. Among these, explicit strategies enable us to discover new movement patterns when existing ones no longer achieve the desired outcome. Yet, how strategies are discovered during motor learning remains unknown. To address this, we developed a novel behavioral paradigm that isolates strategy discovery in response to a range of visuomotor perturbations. This approach revealed that strategy discovery unfolds through an initial period of systematic exploration across multiple candidate strategies, followed by an 'aha' moment in which behavior converges on a stable solution. To account for these dynamics, we developed a computational model based on hypothesis testing in which learners generate and evaluate visuomotor rules to counteract the perturbation. This hypothesis testing model outperformed a range of alternative accounts, including gradual error reduction, win-stay lose-shift learning, and sudden one-shot insight. Together, these findings identify hypothesis testing as a computational mechanism by which humans discover new strategies during motor learning.

neuroscience↗

bioRxiv2026

Prior experience dynamically determines differential cue weighting in the medial entorhinal cortex

Spatial navigation depends on integrating multiple cue sets whose influence is determined primarily by their inferred reliability. Here we investigated how cue weighting in the medial entorhinal cortex is updated based on previous experience at different time scales (minutes vs. days). In mice recorded in light and darkness while manipulating coherence between distal room cues and local arena cues, grid cells displayed stable firing fields in darkness only when prior light experience maintained coherent cue relationships. Grid activity remained anchored to local cues, and stability continuously increased by repeated exposure. In contrast, mice that experienced cue mismatch in light showed markedly reduced grid stability in darkness. Strikingly, re-establishing cue coherence produced only partial recovery, whereas a single exposure to cue mismatch abolished reliance on local cues. The reference frame shift at different time scales reflects a dynamic balance between flexibility and stability determined by a conservative cue weighting strategy.

neuroscience↗

bioRxiv2026

The Ketogenic Diet Fails to Mitigate Seizures and Neuroinflammatory Responses in a Mouse Model of Virus-Induced Epilepsy

ObjectiveThe ketogenic diet (KD) is a high-fat, low-carbohydrate intervention widely used to treat drug-resistant epilepsy, thought to reduce seizures through a combination of metabolic, neuronal, and microbiota-dependent mechanisms. Additionally, recent studies suggest that the anticonvulsant effects of KD require the gut microbiota, with taxa such as Akkermansia and Parabacteroides contributing to seizure protection by modulating host neurotransmitter balance and neural excitability. While KD has been shown to be effective in reducing seizure burden across different epilepsies, its antiseizure effect on infection-driven seizures, which are often driven by acute neuroinflammation, has not been evaluated. Here, we evaluated the effects of KD on seizure burden, neuroimmune responses, and gut microbiota composition in the Theilers murine encephalomyelitis virus (TMEV) model of virus-induced epilepsy. MethodsMice were maintained on either a KD or a normal diet prior to intracerebral TMEV infection. Seizures were induced by handling and scored twice daily from day 3 to 7 post-infection. Neuroimmune responses were assessed by flow cytometry, and fecal microbial composition was analyzed using 16S rRNA gene sequencing. ResultsDespite achieving ketosis, KD did not reduce seizure incidence, seizure burden, or seizure severity during acute TMEV infection. KD also did not significantly alter overall immune cell infiltration into the central nervous system, indicating limited effects on global neuroinflammation. However, KD significantly reshaped the gut microbiota, reducing alpha diversity (richness, Shannon diversity, and evenness) and strongly altering community structure with clear separation between diet groups, including enrichment of taxa such as Akkermansia, Acetatifactor, Dorea, and Flintibacter, and depletion of fiber-associated taxa including Bifidobacterium and Roseburia. However, these microbial shifts were insufficient to mitigate inflammation-driven seizures. SignificanceThese results demonstrate that KDs anticonvulsant efficacy is highly context-dependent, and that KD-driven changes in microbiota- and metabolite-mediated mechanisms may be ineffective against infection-associated epilepsy, suggesting that inflammation-driven seizures require distinct therapeutic approaches. Key pointsO_LIThe ketogenic diet (KD) does not reduce acute seizure incidence and severity during TMEV infection despite achieving ketosis C_LIO_LIKD does not induce neuroinflammatory changes associated with seizure outcomes C_LIO_LIKD strongly reshapes gut microbiota, reducing diversity and altering community structure. C_LIO_LIMicrobiota changes are insufficient to protect against inflammation-driven seizures C_LIO_LIKD anticonvulsant effects are context-dependent and ineffective in infection-driven epilepsy C_LI

neuroscience↗

bioRxiv2026

Shared early impairments of medial entorhinal cortex function across distinct Alzheimer's disease etiologies

The medial entorhinal cortex (MEC) harbors diverse spatially and object-tuned cell types essential for spatial coding and episodic memory, and is among the earliest regions affected in neurodegenerative diseases. Here, we examined how early neurodegeneration alters MEC cellular coding, network dynamics, and behavior in two Alzheimer mouse models of distinct etiology. Specifically, we performed in vivo electrophysiology, immunohistochemistry and behavioral assays in models that reflect the manifestation of a tauopathy and amyloidopathy, respectively, to identify common impairments. In both models, the earliest deficits manifested as instability of spatial context representations at the cellular and behavioral level. These impairments preceded model-specific disruptions in grid cell coding and altered theta oscillations. We further identified reduced parvalbumin-positive (PV+) septal projections as a likely contributor to MEC dysfunction. In contrast, object-vector coding remained intact, highlighting spatial context instability as an early marker of MEC impairment.

neuroscience↗

bioRxiv2026

Autolab HBH: A Rapid Hyperbaric Heating Device for Streamlined, PCR-Ready Sample Preparation Across Diverse Biological Matrices and Organisms

Traditional nucleic acid extraction methods are costly, lengthy, and highly variable depending on the complexity of the sample matrix or the organism of interest. Workflows may exceed twenty steps, require separate kits for RNA and DNA, and demand expensive instrumentation, creating barriers to both speed and scalability. The AutolabTM HBH system addresses these limitations by using hyperbaric heating (HBH) to achieve temperatures above 100 {degrees}C in a sealed, pressurized environment through induction heating, enabling rapid lysis of diverse organisms and neutralization of macromolecular PCR inhibitors within minutes. The combination of extreme heat and HBH-optimized lyophilized reagents rapidly inactivates nucleases while preserving free nucleic acids. The workflow is streamlined to two steps: heating up to 1 mL of sample in the proprietary HBH bullet, followed by a brief centrifugation to pellet additives. The resulting supernatant is immediately compatible with real-time reverse transcription polymerase chain reaction (RT-PCR) and other downstream molecular assays. Here, we evaluate the systems broad compatibility with diverse sample buffers, matrices, and organisms. Comparative testing was conducted alongside Qiagen extraction methods to benchmark performance.

molecular biology↗

bioRxiv2024

SEXUAL-DIMORPHISM IN VISUALLY GUIDED APPROACH BEHAVIOR EMERGES UNIQUELY DURING ADOLESCENCE

Studying prey capture behavior in mice offers a fruitful platform for understanding how ecologically relevant visual stimuli are differentially processed by the brain throughout life. For example, specific visual stimuli that indicate prey and that naturally draw appetitive orienting in the adult may be interpreted differently or evoke distinct behaviors during development. What are the neural mechanisms that might allow an animal to flexibly couple the same stimulus information to distinct behavioral outcomes as a function of developmental needs? To begin to address this important question, we quantified visually evoked orienting behaviors between adolescent and adult C57BL6/J mice of both sexes under the natural prey capture context compared to responses in our established virtual motion stimulus paradigm, C-SPOT. Most surprisingly, we discovered that female versus male adolescent mice have opposing innate behavioral biases evoked by the same sweeping motion stimuli which is not present in adulthood. Further, female mice display a robust enhancement of approach towards visual motion over all other groups tested, yet they are the least aggressive in response to live prey. Thus, our work overall revealed that innate approach towards visual motion is robustly dissociated from predatory aggression in female versus male mice specifically during adolescence. This underscores the different natural behavioral goals and physiological states that uniquely apply to female versus male adolescent animals, and reveals that approach towards visual motion is a key sensory-motor process selectively augmented during female adolescence. HighlightsO_LIAdolescent mice of both sexes innately approach insects more than adults C_LIO_LIAdolescent males versus females have distinct response biases to visual motion C_LIO_LIAdolescent males display the strongest hunger-related predatory aggression C_LI

animal behavior and cognition↗

bioRxiv2024

Exogenous ECM in an environmentally-mediated in vitro model for cardiac fibrosis

Few clinical solutions exist for cardiac fibrosis, creating the need for a tunable in vitro model to better understand fibrotic disease mechanisms and screen potential therapeutic compounds. Here, we combined cardiomyocytes, cardiac fibroblasts, and exogenous extracellular matrix (ECM) proteins to create an environmentally-mediated in vitro cardiac fibrosis model. Cells and ECM were combined into 2 types of cardiac tissues-aggregates and tissue rings. The addition of collagen I had a drastic negative impact on aggregate formation, but ring formation was not as drastically affected. In both tissue types, collagen and other ECM did not severely affect contractile function. Histological analysis showed direct incorporation of collagen into tissues, indicating that we can directly modulate the cells ECM environment. This modulation affects tissue formation and distribution of cells, indicating that this model provides a useful platform for understanding how cells respond to changes in their extracellular environment and for potential therapeutic screening.

bioengineering↗

bioRxiv2024

Short-term Electrical Stimulation Impacts Cardiac Cell Structure and Function

Induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) are used to model cardiac development and disease. This requires a robust population of mature CMs and external stimuli to mimic the complex environment of the heart. In effort toward this maturation, previous groups have applied electrical stimulation (ES) to CMs with varying results depending on the stimulation duration, frequency, and pattern. As such, there is uncertainty surrounding the timeline on which stimulated iPSC-CMs begin to show early signs of maturation in comparison to their non-stimulated counterparts, leaving room for additional research into when hallmarks of maturity-such as hypertrophy and changes to sarcomere structure-develop in CMs. Here, we introduce a low-cost custom bioreactor capable of delivering tunable electrical stimulation to standard 2D cell monolayers. We show that, after exposure to short-term ES, stimulated CMs express early signs of maturation compared to the non-stimulated control. The changes to contractility and protein expression indicate that the cells undergo hypertrophy in response to short-term ES, but they do not develop transverse-tubules, which is a key component of a fully mature CM structure. Therefore, while early signs of maturation are present after a short stimulation regimen, additional cellular structures must develop to reach complete maturation. We have shown that our custom electrical stimulator can be easily integrated with standard in vitro cell culture platforms to obtain measurable changes to cells, exhibiting its potential for promoting crucial CM maturation for cardiac tissue engineering applications.

bioengineering↗

bioRxiv2023

Grid cells perform path integration in multiple reference frames during self-motion-based navigation

With their periodic firing pattern, grid cells are considered a fundamental unit of a neural network performing path integration. The periodic firing patterns of grid cells have been observed mainly during behaviors with little navigational demands, and the firing patterns of grid cells in animals navigating 2D environments using path integration are largely unknown. Here, we recorded the activity of grid cells in mice performing the AutoPI task, a task assessing homing based on path integration. Using artificial deep neural networks to decode the animals moment-to-moment movement vectors, we found that grid cells perform path integration over short trajectories and change their reference frames within single trials. More specifically, grid cell modules re-anchor to a task-relevant object via a translation of the grid pattern. The code for movement direction in grid modules drifts as the animal navigates using self-motion cues, and this drift predicts the homing direction of the mouse. These results reveal the computations in grid cell circuits during self-motion-based navigation.

neuroscience↗

bioRxiv2023

Hypoxia blunts angiogenic signaling and upregulates the antioxidant system in elephant seal endothelial cells

Elephant seals experience extreme hypoxemia during diving bouts. Similar depletions in oxygen availability characterize pathologies including myocardial infarction and ischemic stroke in humans, but seals manage these repeated episodes without injury. However, the real-time assessment of the molecular changes underlying protection against hypoxic injury in seals remains restricted by their at-sea inaccessibility. Hence, we developed a proliferative arterial endothelial cell culture system to assess the molecular response to prolonged hypoxia. Seal and human cells exposed to 1% O2 for up to 6 h demonstrated differential responses to both acute and prolonged hypoxia. Seal cells decouple stabilization of the hypoxia-sensitive transcriptional regulator HIF-1 from angiogenic signaling at both the transcriptional and cellular level. Rapid upregulation of genes involved in the glutathione (GSH) metabolism pathway supported maintenance of GSH pools and increases in intracellular succinate in seal but not human cells during hypoxia exposure. High maximal and spare respiratory capacity in seal cells after hypoxia exposure occurred in concert with increasing mitochondrial branch length and independent from major changes in extracellular acidification rate, suggesting seal cells recover oxidative metabolism without significant glycolytic dependency after hypoxia exposure. In sum, our studies show that in contrast to human cells, seal cells adapt to hypoxia exposure by dampening angiogenic signaling, increasing antioxidant protection, and maintaining mitochondrial morphological integrity and function.

physiology↗

bioRxiv2023

Cryo-EM structures of Kv1.2 potassium channels, conducting and non-conducting

We present near-atomic-resolution cryo-EM structures of the mammalian voltage-gated potassium channel Kv1.2 in open, C-type inactivated, toxin-blocked and sodium-bound states at 3.2 [A], 2.5 [A], 3.2 [A], and 2.9[A]. These structures, all obtained at nominally zero membrane potential in detergent micelles, reveal distinct ion-occupancy patterns in the selectivity filter. The first two structures are very similar to those reported in the related Shaker channel and the much-studied Kv1.2-2.1 chimeric channel. On the other hand, two new structures show unexpected patterns of ion occupancy. First, the toxin -Dendrotoxin, like Charybdotoxin, is seen to attach to the negatively-charged channel outer mouth, and a lysine residue penetrates into the selectivity filter, with the terminal amine coordinated by carbonyls, partially disrupting the outermost ion-binding site. In the remainder of the filter two densities of bound ions are observed, rather than three as observed with other toxin-blocked Kv channels. Second, a structure of Kv1.2 in Na+ solution does not show collapse or destabilization of the selectivity filter, but instead shows an intact selectivity filter with ion density in each binding site. We also attempted to image the C-type inactivated Kv1.2 W366F channel in Na+ solution, but the protein conformation was seen to be highly variable and only a low-resolution structure could be obtained. These findings present new insights into the stability of the selectivity filter and the mechanism of toxin block of this intensively studied, voltage-gated potassium channel.

biophysics↗

bioRxiv2023

Effects of Repeat Test Exposure on Gait Parameters in Naive Lewis Rats

Rodent gait analysis has emerged as a powerful, quantitative behavioral assay to characterize the pain and disability associated with movement-related disorders. In other behavioral assays, the importance of acclimation and the effect of repeated testing have been evaluated. However, for rodent gait analysis, the effects of repeated gait testing and other environmental factors have not been thoroughly characterized. In this study, fifty-two naive male Lewis rats ages 8 to 42 weeks completed gait testing at semi-random intervals for 31 weeks. Gait videos and force plate data were collected and processed using a custom MATLAB suite to calculate velocity, stride length, step width, percentage stance time (duty factor), and peak vertical force data. Exposure was quantified as the number of gait testing sessions. Linear mixed effects models were used to evaluate the effects of velocity, exposure, age, and weight on animal gait patterns. Relative to age and weight, repeated exposure was the dominant parameter affecting gait variables with significant effects on walking velocity, stride length, fore and hind limb step width, fore limb duty factor, and peak vertical force. From exposure 1 to 7, average velocity increased by approximately 15 cm/s. Together, these data indicate arena exposure had large effects on gait parameters and should be considered in acclimation protocols, experimental design, and subsequent data analysis of rodent gait data.

animal behavior and cognition↗

bioRxiv2022

Hippocampal firing fields anchored to a moving object predict homing direction during path-integration-based behavior

Homing based on path integration (H-PI) is a form of navigation in which an animal uses self-motion cues to keep track of its position and return to a starting point. Despite evidence for a role of the hippocampus in H-PI, the firing patterns of hippocampal neurons associated with homing performance are unknown. Here we developed a behavioral task for mice to characterize spatially selective cells during H-PI. The task required a mouse to find a variably placed lever on an arena before returning to its home base. H-PI was assessed in complete darkness. Recordings from CA1 pyramidal neurons in mice showed that several firing fields were anchored to the lever position. The spatial stability of lever-anchored fields was reduced during trials with lower homing accuracy, and the activity of a subset of lever-anchored firing fields predicted homing direction. These results demonstrate how neurons with object-anchored firing fields contribute to navigation.

neuroscience↗

bioRxiv2021

In vivo lentiviral vector gene therapy to cure hereditary tyrosinemia type 1 and prevent development of precancerous and cancerous lesions

Conventional therapy for hereditary tyrosinemia type-1 (HT1) with 2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione (NTBC) delays and in some cases fails to prevent disease progression to liver fibrosis, liver failure, and activation of tumorigenic pathways. Here we demonstrate for the first time a cure of HT1 by direct, in vivo administration of a therapeutic lentiviral vector targeting the expression of a human fumarylacetoacetate hydrolase (FAH) transgene in the porcine model of HT1. This therapy was well tolerated and provided stable long-term expression of FAH in pigs with HT1. Genomic integration displayed a benign profile, with subsequent fibrosis and tumorigenicity gene expression patterns similar to wild-type animals as compared to NTBC-treated or diseased untreated animals. Indeed, the phenotypic and genomic data following in vivo lentiviral vector administration demonstrate comparative superiority over other therapies including ex vivo cell therapy and therefore support clinical application of this approach.

cell biology↗

bioRxiv2020

Learning and motor-impulse control in domestic fowl and crows

Cognitive abilities allow animals to navigate through complex, fluctuating environments. In the present study, we tested the performance of a captive group of eight crows, Corvus corone, and ten domestic chickens, Gallus gallus domesticus, in the cylinder task, as a test of motor inhibitory control, and reversal learning as a measure of learning ability and behavioural flexibility. Four crows and nine chickens completed the cylinder task, eight crows and six chickens completed the reversal learning experiment. Crows performed better in the cylinder task compared to chickens. In the reversal learning experiment, species did not significantly differ in the number of trials until learning criterion was reached. Performance in the reversal learning experiment did not correlate with performance in the cylinder task in chickens. Our results suggest crows to possess better motor inhibitory control compared to chickens. In contrast, learning performance in a reversal learning task did not differ between the species, indicating similar levels of behavioural flexibility. Interestingly, we describe notable individual differences in performance. We stress the importance not only to compare cognitive performance between species but also between individuals of the same species when investigating the evolution of cognitive skills.

animal behavior and cognition↗

bioRxiv2019

In Situ Processing and Efficient Environmental Detection (iSPEED) of pests and pathogens of trees using point-of-use real-time pcr

The increase in global trade is responsible for a surge in foreign invasive species introductions across the world. Early detection and surveillance activities are essential to prevent future invasions. Molecular diagnostics by DNA testing has become an integral part of this process. However, for environmental applications, there is a need for cost-effective and efficient point-of-use DNA testing that would allow for the collection of results in real-time away from laboratory facilities. To achieve this requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We conducted a series of tests using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions to address the first two requirements. We chose to demonstrate the use of this approach with organisms that cover a broad spectrum of known undesirable insects and pathogens: the ascomycete Sphaerulina musiva, the oomycete Phytophthora ramorum, the basidiomycetes Cronartium ribicola and Cronartium comandrae and the insect Lymantria dispar. Tests performed from either infected leaf material or spores (pathogens), or legs and antenna (insects). We were able to obtain positive amplification for the targeted species in all the samples tested. The shelf-life of the lyophilized reactions was assessed, confirming the stability of over a year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable plastics, demonstrating the suitability of the method, named in Situ Processing and Efficient Environment Detection (iSPEED), for field testing. This kit is ideally adapted to field testing as it fits in a backpack and can be carried to remote locations.

plant biology↗

bioRxiv2019

Inspiratory muscle training in young, race-fit Thoroughbred racehorses during a period of detraining

Although inspiratory muscle training (IMT) is reported to improve inspiratory muscle strength in humans little has been reported for horses. We tested the hypothesis that IMT would maintain and/or improve inspiratory muscle strength variables measured in Thoroughbreds during detraining. Thoroughbreds from one training yard were placed into a control (Con, n=3 males n=7 females; median age 2.2{+/-}0.4 years) or treatment group (Tr, n=5 males, n=5 females; median age 2.1{+/-}0.3 years) as they entered a detraining period at the end of the racing/training season. The Tr group underwent eight weeks of IMT twice a day, five days per week using custom-made training masks with resistance valves and an incremental threshold of breath-loading protocol. An inspiratory muscle strength test to fatigue using an incremental threshold of breath-loading was performed in duplicate before (T0) and after four (T1) and eight weeks (T2) of IMT/no IMT using a custom-made testing mask and a commercial testing device. Inspiratory measurements included the total number of breaths achieved during the test, average load, peak power, peak volume, peak flow, energy and the mean peak inspiratory muscle strength index (IMSi). Data was analysed using a linear mixed effects model, P[≤]0.05 significant. There were no differences for inspiratory measurements between groups at T0. Compared to T0, the total number of breaths achieved (P=0.02), load (P=0.003) and IMSi (P=0.01) at T2 had decreased for the Con group while the total number of breaths achieved (P<0.001), load (P=0.03), volume (P=0.004), flow (P=0.006), energy (P=0.01) and IMSi (P=0.002) had increased for the Tr group. At T2 the total number of breaths achieved (P<0.0001), load (P<0.0001), volume (P=0.02), energy (P=0.03) and IMSi (P<0.0001) were greater for the Tr than Con group. In conclusion, our results support that IMT can maintain and/or increase aspects of inspiratory muscle strength for horses in a detraining programme.

physiology↗

bioRxiv2018

Head-direction cells escaping attractor dynamics in the parahippocampal region

Navigation depends on the activity of head-direction (HD) cells. Computational models postulate that HD cells form a uniform population that reacts coherently to changes in landmarks. We tested whether this applied to HD cells of the medial entorhinal cortex and parasubiculum, areas where the HD signal contributes to the periodic firing of grid cells. Manipulations of the visual landmarks surrounding freely-moving mice altered the tuning of HD cells. Importantly, these tuning modifications were often non-coherent across cells, refuting the notion that HD cells form a uniform population constrained by attractor-like dynamics. Instead, examination of theta rhythmicity 1revealed two types of HD cells, theta rhythmic and non-rhythmic cells. Larger tuning alterations were observed predominantly in non-rhythmic HD cells. Moreover, only non-rhythmic HD cells reorganized their firing associations in response to visual land-mark changes. These findings reveal a theta non-rhythmic HD signal whose malleable organization is controlled by visual landmarks.

neuroscience↗