Biology subjects

Mathis, C.

Publications and source records attributed to Mathis, C..

10 recordsLinked to original sources

bioRxiv2026

Female behavioral cues control male courtship plasticity independent of female pheromones in African Drosophila melanogaster

Sexual interactions involve the exchange of information-including olfactory, auditory, and visual cues-that has been shaped by sexual selection to maximize fitness. While these courtship signals and behaviors are often characterized as stereotypical and species-specific, male courtship is plastic and can depend on the population identity of the courted female. The ability of a male to adjust his courtship behavior based on female identity has significant implications for how selection operates on courtship, potentially driving behavioral divergence between populations and the eventual emergence of new species. A major challenge is identifying the cues that males use to adjust their courtship strategy. We used Drosophila melanogaster to investigate the mechanisms facilitating courtship plasticity, focusing on male song production. Male song is often considered the paramount behavior performed by males and is stimulated by female pheromones. Previous observations have focused on cosmopolitan (non-African) genotypes, whereas the singing rate and singing plasticity is highly variable in African populations. In genotypes from Zimbabwe, females have a different major pheromone compound (5,9-HD) compared to non-African females and show strong behavioral preference for Zimbabwe males. We created a Zimbabwe genotype lacking 5,9-HD by disrupting the gene desat2 in the Zimbabwe Z53 strain. We tested the hypothesis that Zimbabwe male courtship plasticity depends on female pheromones by allowing males to court non-African, wild type Z53, and Z53 desat2 null mutant females. We found that males treated Z53 desat2 null females like wild type Z53 females, not using pheromone cues to determine singing and courtship plasticity. This suggests that other female behavioral feedback influences singing plasticity. This courtship plasticity could contribute to the asymmetrical reproductive isolation between these populations and could provide insight to the broad pattern of asymmetrical reproductive isolation across broad taxonomic groups.

evolutionary biology↗

bioRxiv2025

Convergent Functional Constraints Make Biochemical Reaction Diversity Predictable

The predictability of biochemical evolution remains highly debated, as it is unknown if biological function can be predicted a priori. Here, we explore predictability of function not in individual reactions, but in ensembles. Sampling from 13,777 bacterial, 371 archaeal, and 203 eukaryotic genomes, we use Enzyme Commission (EC) classification to hierarchically group enzyme-catalyzed reactions that perform similar transformations into functional equivalence classes. We show that organisms partition their reaction diversity among these functional equivalence classes in a predictable way, identifying over 120 new, system-size dependent functional scaling relationships. We find distantly related lineages, acting on distinct molecular substrates, can display similar functional scaling, demonstrating that convergence is not driven by phylogeny or common reactions. We demonstrate how transitions in functional scaling can be identified with physiological shifts, using as case studies O2-utilizing oxidoreductases and hexosyltransferases. Taken together, our results open novel avenues for predicting global features of evolving enzyme populations, independent of protein structures. These functional constraints may have broad implications, including for predicting biochemical diversity, designing synthetic organisms, and modeling the evolution of reaction diversity in cases where the exact identity of catalysts is not known, such as during the emergence of life and for potential alternative forms of biochemistry.

biochemistry↗

bioRxiv2025

Exploring sex-specific alterations in early Alzheimer's disease using network MRI analyses

Alzheimers disease (AD) is characterized by the accumulation of amyloid-{beta} plaques and tau neurofibrillary tangles, leading to progressive cognitive decline. Subtle cognitive and neural adaptations mark the preclinical stage of AD, occurring years before mild cognitive impairment and AD diagnosis. Throughout the continuum of AD, women ([~]60% of AD cases) demonstrate faster rates of cognitive decline, greater hippocampal atrophy, and more extensive tau pathology compared to men. This is particularly evident in early AD phases. Therefore, investigating early sex-specific changes is crucial for identifying biomarkers and developing targeted interventions. In the present study, we conducted a longitudinal investigation on the AppNL-F/MAPT double knock-in (dKI) mouse model, to identify sex-specific resting-state functional connectivity (FC) patterns associated with early cognitive deficits. Male and female wild-type and dKI mice were tested for associative and long-term memory deficits, followed by resting-state functional magnetic resonance imaging to examine the default mode network (DMN) connectivity at 2 and 4 months of age. Female dKI mice exhibited earlier and more pronounced memory impairments, with deficits apparent at 2 months, while male deficits emerged at 4 months. FC analyses revealed distinct sex-specific alterations within DMN and between DMN hubs and memory processing nodes. Notably, female dKI mice showed hypersynchrony between the retrosplenial cortex (RSP) and key memory-related regions such as the entorhinal cortex (ENT) and hippocampus (HIP), but also towards subcortical regions overlapping thalamic nuclei, amygdala, and substantia nigra. Meanwhile, male dKI mice exhibited hypoconnectivity along RSP-HIP axis, RSP-reuniens nucleus, and RSP-sensorimotor cortex. Our data particularly highlight sexually dimorphic RSP-ENT and RSP-HIP connectivity. These results underscore the critical role of sex in shaping neural network reorganization and cognitive decline during preclinical AD. These findings position neural network connectivity as a sensitive biomarker of early memory dysfunction and highlight the need for sex-specific investigations and potentially tailored therapeutic strategies in AD.

neuroscience↗

bioRxiv2024

40 Hz light stimulation restores early brain dynamics alterations and associative memory in Alzheimer's disease model mice

Visual gamma entrainment using sensory stimuli (vGENUS) is a promising non-invasive therapeutic approach for Alzheimers disease (AD), showing efficacy in improving memory function. However, its mechanisms of action remain poorly understood. Using young AppNL-F/MAPT double knock-in (dKI) mice, a model of early AD, we examined brain dynamics alterations before amyloid plaque onset. High-density EEG recordings and novel metrics from fields outside neuroscience were used to assess brain dynamics fluidity--a measure of the brains ability to transition between activity states. We revealed that dKI mice exhibit early, awake state-specific reductions in brain dynamics fluidity associated with cognitive deficits in complex memory tasks. Daily vGENUS sessions over two weeks restored brain dynamics fluidity and rescued memory deficits in dKI mice. Importantly, these effects built up during the stimulation protocol and persisted after stimulation ended, suggesting long-term modulation of brain function. Based on these results, we propose a "brain dynamics repair" mechanism for vGENUS that goes beyond current amyloid-centric hypotheses. This dual insight - that brain dynamics are both a target for repair and a potential diagnostic tool - provides new perspectives on early Alzheimers disease pathophysiology. Significance StatementGamma ENtrainment Using Sensory stimuli (GENUS), involving 40 Hz rhythmic sensory stimulation, shows promise in improving memory function in Alzheimers disease (AD). We hypothesized that brain dynamics changes could be detected before plaque onset and modulated by vGENUS. Applying techniques from climate science to EEG recordings in young AD model mice, we found reduced brain dynamics fluidity associated with early cognitive deficits. Two weeks of vGENUS restored brain dynamics and improved memory, with effects persisting post-treatment. These findings challenge the amyloid-centric view of AD, introduce a potential early biomarker, and suggest vGENUS acts by "repairing" brain dynamics. Our approach offers new perspectives on early diagnosis and non-invasive interventions for AD and other neurological disorders with disrupted brain dynamics.

neuroscience↗

bioRxiv2022

Functional brain-wide network mapping during acute stress exposure in rats: Interaction between the lateral habenula and cortical, amygdalar, hypothalamic and monoaminergic regions.

Upon stress exposure a broad network of structures comes into play in order to provide adequate responses and restore homeostasis. It has been known for decades that the main structures engaged during the stress response are the medial prefrontal cortex, the amygdala, the hippocampus, the hypothalamus, the monoaminergic systems (noradrenaline, dopamine, serotonin), and the periaqueductal gray. The lateral habenula (LHb) is an epithalamic structure directly connected to prefrontal cortical areas and to the amygdala, whereas it functionally interacts with the hippocampus. Also, it is a main modulator of monoaminergic systems. The LHb is activated upon exposure to basically all types of stressors, suggesting it is also involved in the stress response. However, it remains unknown if and how the LHb functionally interacts with the broad stress response network. In the current study we performed in rats a restraint stress procedure followed by immunohistochemical staining of the c-Fos protein throughout the brain. Using Graph Theory-based functional connectivity analyses, we confirm the principal hubs of the stress network (e.g. prefrontal cortex, amygdala, periventricular hypothalamus), and show that the LHb is engaged during stress exposure in close interaction with the medial prefrontal cortex, the lateral septum, and the medial habenula. In addition, we performed DREADD-induced LHb inactivation during the same restraint paradigm in order to explore its consequences on the stress response network. This last experiment gave contrasting results as the DREADD ligand alone, clozapine-N-oxide, was able to modify the network. GRAPHICAL ABSTRACT GRAPHICAL ABSTRACT TEXTIn this study, using immunohistochemical staining of the immediate early gene c-fos and graph theory-based functional correlational analyses, we aimed at unravelling the possible engagement of the lateral habenula (LHb) within the stress response network during acute stress exposure (10-min restraint) in rats. We found that the medial part of the LHb (LHbM) was preferentially engaged, and that this engagement was concomitant to this of structures such as the medial prefrontal cortex (mPFC), the insular cortex (Ins), hypothalamic (PVH) and thalamic (PVT) paraventricular nuclei, the extended amygdala, comprising the Bed nucleus of the stria terminalis (BNST) and the entire amygdala (AMG), as well as the dopaminergic ventral tegmental area (VTA) and the serotonergic dorsal raphe nucleus (RD). This suggests upon stressful situations the LHbM serves as a relay of cortical, thalamic, hypothalamic and temporal information, further transmitted to midbrain monoaminergic systems to probably initiate coping strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/491280v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@a423eeorg.highwire.dtl.DTLVardef@32e1aaorg.highwire.dtl.DTLVardef@7d6106org.highwire.dtl.DTLVardef@16cff53_HPS_FORMAT_FIGEXP M_FIG C_FIG

animal behavior and cognition↗

bioRxiv2022

Virtually the same? Evaluating the effectiveness of remote undergraduate research experiences

In-person undergraduate research experiences (UREs) promote students integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration. To address this, we investigated indicators of scientific integration for students who participated in remote life science URE programs in summer 2020. We found that these students experienced gains in their scientific self-efficacy and scientific identity similar to results reported for in-person UREs. We also found that these students perceived high benefits and low costs of doing research at the outset of their programs, and their perceptions did not change despite the remote circumstances. Yet, their perceptions differed by program, indicating that programs differentially affected students perceptions of the costs of doing research. Finally, we observed that students with prior research experience made greater gains in self-efficacy and identity, as well as in their perceptions of the alignment of their values with those of the scientific community, in comparison to students with no prior research experience. This finding suggests that additional programming may be needed for undergraduates with no prior experience to benefit from remote research.

scientific communication and education↗

bioRxiv2021

"How do we do this at a distance?!" A descriptive study of remote undergraduate research programs during COVID-19

The COVID-19 pandemic shut down undergraduate research programs across the U.S. Twenty-three sites offered remote undergraduate research programs in the life sciences during summer 2020. Given the unprecedented offering of remote research experiences, we carried out a study to describe and evaluate these programs. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from the perspectives of participating students. Strengths included the quality of mentorship, opportunities for learning and professional development, and development of a sense of community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote REUs that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.

scientific communication and education↗

bioRxiv2021

Early memory deficits and extensive brain network disorganization in the AppNL-F/MAPT double knock-in mouse model of familial Alzheimer's disease.

A critical challenge in current research on AD is to clarify the relationship between early neuropathology and network dysfunction associated to the emergence of subtle memory alterations which announce disease onset. In the present work, the new generation AppNL-F/MAPT double knock in (dKI) model was used to evaluate early stages of AD. The initial step of tau pathology was restricted to the perirhinal-entorhinal region, sparing the hippocampus. This discrete neuropathological sign was associated with deficits in the object-place associative memory, one of the earliest recognition memories affected in individuals at risk for developing AD. Analyses of task-dependent c-Fos activation was carried out in 22 brain regions across the medial prefrontal cortex, claustrum, retrosplenial cortex, and medial temporal lobe. Initial hyperactivity was detected in the entorhinal cortex and the claustrum of dKI mice. The retention phase was associated to reduced network efficiency especially across cingulate cortical regions, which may be caused by a disruption of information flow through the retrosplenial cortex. Moreover, the relationship between network global efficiency and memory performance in the WT could predict memory loss in the dKI, further linking reduced network efficiency to memory dysfunction. Our results suggest that early perirhinal-entorhinal pathology is associated with local hyperactivity which spreads towards connected regions such as the claustrum, the medial prefrontal cortex and ultimately the key retrosplenial hub which is needed to relay information flow from frontal to temporal lobes. The similarity between our findings and those reported in the earliest stages of AD suggests that the AppNL-F/MAPT dKI model has a high potential for generating key information on the initial stage of the disease.

neuroscience↗

bioRxiv2018

Bioinformatic analysis reveals mechanisms underlying parasitoid venom evolution and function

Introduction Introduction Methods Results and Discussion Conclusions References Parasitoid wasps are a numerous and diverse group of insects that obligately infect other arthropod species. These wasps lay their eggs either on the surface or within the body cavity of their hosts, and the resulting offspring exploit the hosts resources to complete their development [1]. Many parasitoids also introduce venom gland derived proteins or polydnaviruses into the host during infection. These factors act through a variety of mechanisms to manipulate host biology in order to increase the fitness of the developing parasitoid offspring [2-4]. Many hosts mount immune responses to parasitoid infection, and accordingly, parasitoids have evolved multiple venom genes that encode immunom ...

genomics↗

bioRxiv2017

Universal Scaling in Biochemical Networks

The application of network science to biology has advanced our understanding of the metabolism of individual organisms and the organization of ecosystems but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, we constructed biochemical networks using a global database of 28,146 annotated genomes and metagenomes, and 8,658 cataloged biochemical reactions. We uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical networks to random chemical networks reveals the observed biological scaling is not solely a product of the biochemistry shared across life on Earth. Instead, it emerges due to how the global inventory of biochemical reactions is partitioned into individuals. We show the three domains of life are topologically distinguishable, with > 80% accuracy in predicting evolutionary domain based on biochemical network size and average topology. Taken together our results point to a deeper level of organization in biochemical networks than what has been understood so far.

systems biology↗