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Biology subjects

Kennedy, J.

Publications and source records attributed to Kennedy, J..

At least 19 recordsLinked to original sources

Why diabetes matters in dementia studies. Excluding diabetes status masks regional mitochondrial DNA copy number changes in human hippocampus, amygdala, and cerebellum in Alzheimers disease

STRUCTURED ABSTRACTO_ST_ABSINTRODUCTIONC_ST_ABSDiabetes is a major risk factor for Alzheimers disease (AD), and both diseases involve mitochondrial dysfunction. We hypothesised that AD is associated with reduced mitochondrial DNA copy number (mtDNA-CN) in vulnerable brain regions, and that diabetes modifies these changes. METHODSPost-mortem hippocampus, amygdala, and cerebellum samples (N=66-77) from non-cognitively impaired (NCI) and AD donors, with and without diabetes, were analysed. mtDNA-CN was quantified by absolute quantification. RESULTSOverall, mtDNA-CN was lower in AD. However, stratification by diabetes revealed opposite changes: non-diabetic AD cases showed reduced mtDNA-CN, whereas diabetic cases showed higher mtDNA-CN across all regions irrespective of cognitive status. DISCUSSIONThese findings confirm multiregional loss of mtDNA-CN in the AD brain, most evident in the absence of diabetes. The functional significance of higher mtDNA-CN in the diabetic brain remains unclear, but evidence that diabetes can mask effects has important implications for dementia studies.

neuroscience↗

Embryonic origin of cancer in newborn twins

Studying monozygotic twins who present with identical cancers informs on the developmental origins of childhood tumours. Here, we performed whole genome sequencing on multiple tumour, normal, and placental samples to reconstruct the phylogeny of a soft tissue cancer that spread in utero between monozygotic twins. This generalisable and scalable approach allows us to dissect the earliest stages of twinning, revealing unexpected asymmetrical contributions of embryonic lineages to the placenta and each twin.

cancer biology↗

Drought tolerance of Aedes aegypti mosquito eggs is influenced by adaptation to local climate conditions and associations with humans

Urbanization is intensifying human interactions with mosquitoes, exacerbating public health challenges. Densely populated areas provide ideal conditions for container-dwelling mosquitoes, with increased host availability and the presence of artificial breeding sites. These anthropophilic mosquitoes often exhibit distinct ecological adaptations compared to their rural counterparts. Since mosquito eggs are immobile and remain at the site of oviposition, they provide a valuable lens for assessing how urbanization, climate-driven shifts in temperature, and drought affect mosquito reproductive success. This study examined Ae. aegypti egg viability under varying temperature and dry conditions over five months, focusing on lineages with distinct ancestries from West African populations. Mosquitoes collected from urban habitats with a high human preference demonstrated higher egg survival under prolonged arid conditions. Analysis of climatic factors revealed that dry season temperature and precipitation during wet periods are significant predictors of egg drought tolerance. Modeling future climate scenarios based on input from our egg viability results suggests a projected shift and expansion in the seasonal survival window for Ae. aegypti by the end of the century. This study highlights the importance of understanding environmental constraints on the drought tolerance of mosquito eggs to predict and mitigate future mosquito outbreaks.

physiology↗

Extensive and differential platinum chemotherapy mutagenesis in children

Childhood cancer survivors often develop long-term adverse effects, which may be caused by direct mutagenesis of cytotoxic agents. Some of these agents generate distinctive DNA imprints (mutational signatures), as exemplified by platinum chemotherapeutics. Here, we examined chemotherapy mutagenesis in paediatric tissues by deploying a duplex sequencing method (NanoSeq), which enables mutation calling from single DNA molecules. We surveyed whole genomes of paediatric liver, blood and other tissues, obtained from surgical resections and at post-mortem. Platinum signatures pervaded all tissues extensively, elevating mutation burdens of paediatric tissues to levels seen in adults. Remarkably, we found a tissue-specific mutational signature in the liver. We examined the functional potential of mutations by gene focused NanoSeq, which revealed that platinum agents cause a vast repertoire of cancer causing variants across normal tissues, such as leukaemogenic mutations in blood. This finding may conceivably link cancer treatment in childhood to mutation-driven long term sequelae.

cancer biology↗

SomaMutDB 2.0: A comprehensive database for exploring somatic mutations and their functional impact in normal human tissues

Recent advances in ultra-accurate sequencing technologies have revealed that somatic mutations accumulate across the human lifespan and may contribute to both normal aging and disease. These mutations are highly diverse, often non-recurrent, and functionally heterogeneous, which makes their biological impact difficult to evaluate systematically. Although many studies have profiled somatic mutations in individual tissues or limited cohorts, a centralized and scalable platform that integrates discoveries and supports functional interpretation has been lacking. To address this gap, we present SomaMutDB 2.0 (https://somamutdb.org/SomaMutDB/), a substantially expanded database that catalogs 8.9 million mutations (8.57 million SNVs and 0.29 million INDELs) from 10,852 samples of 607 human subjects across 47 studies. Beyond expanded data coverage, SomaMutDB 2.0 introduces a comprehensive functional annotation framework that applies 22 predictive models, encompassing coding, regulatory, expression-based, and ensemble predictors, to systematically assess mutational impact. Users can browse pre-annotated variants through an interactive interface or upload their own variants for real-time analysis, with results contextualized against all mutations from normal, non-diseased tissues in the database. Together, these advances establish SomaMutDB 2.0 as the most comprehensive resource currently available for characterizing somatic mosaicism and functional interpretation in human health and aging. Graphical AbstractSomaMutDB 2.0 provides an expanded catalog of 8.9 million somatic mutations across 30 tissues, along with pipelines for mutational signature analysis and 22-tool functional annotation that enable user-submitted variant interpretation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/676124v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1c76484org.highwire.dtl.DTLVardef@1984f71org.highwire.dtl.DTLVardef@8789a9org.highwire.dtl.DTLVardef@5ed54a_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

Comparative Computational Modeling of Approach-Avoidance Biases in Suicidal Populations via Hierarchical Bayesian Inference

Pavlovian "approach or avoid" impulses are critical behavioral biases that, in excess, are linked to multiple psychiatric conditions. To investigate how such biases contribute to suicidal thoughts and behaviors, we analyzed data from two clinical populations completing an aversive Go/NoGo task. This task disentangles motor action (Go or NoGo) from outcome valence (escape from, or avoidance of, an aversive stimulus), enabling the isolation of Pavlovian biases from instrumental learning processes. We compared multiple computational models that had previously been proposed to explain Pavlovian tendencies, including reinforcement learning, active inference, and drift diffusion-based approaches. We employed a hierarchical Bayesian inference procedure that treats model identity as a random factor at the individual level, allowing an unbiased determination of which mechanisms most accurately captured participants behavior. Across both datasets, models featuring Pavlovian context biases plus a value-decay mechanism best accounted for performance. By contrast, policy-based Pavlovian models and more complex approaches, such as those integrating working memory or active inference, were supported by fewer study participants. These findings suggest that reflexive biases exert a persistent influence on decision-making, and that value decay plays a critical role in shaping behavior over time. Our results demonstrate the importance of systematically comparing and accounting for relevant cognitive processes to explain observed task behaviors. Understanding the factors contributing to task performance may help clarify how Pavlovian tendencies relate to psychopathology, including, in our case, elevated suicide risk. Finally, we illustrate how a complete hierarchical model selection framework can be applied to identify the most plausible mechanisms underlying Pavlovian biases, offering a robust approach for advancing our understanding of task behaviors and establishing clinical utility in future studies. Author summaryAutomatic "approach or avoid" reactions shape behavior, particularly in stressful or negative situations. In this study, we explored how these reflex-like tendencies might contribute to suicidal thoughts and behaviors. Two clinical groups completed a computerized task measuring responses to unpleasant sounds. Participants made either active responses (pressing a button to stop a sound) or passive responses (refraining from pressing to avoid starting a sound), allowing us to examine the interplay of automatic impulses and learning from past experiences. Our analysis showed that behavior was best explained by a model combining stable "approach or avoid" impulses with a forgetting process that reduced reliance on past experiences over time. More complex models involving strategies or memory-based control were less effective. These findings suggest that individuals with suicidal tendencies may rely on persistent reflex-like behaviors and over-index recent outcomes, compromising their ability to learn in uncertain environmental conditions. Understanding these cognitive processes provides insights into why some individuals feel trapped in harmful patterns of thought and behavior. Our work highlights how identifying shared traits in clinical populations using model-based methods can inform targeted mental health interventions and improve our understanding of cognitive functioning across disorders.

neuroscience↗

Impaired humidity sensing reduces tick survival by preventing water homeostasis

Off-host periods are critical for ticks, representing a time when environmental stress, particularly dehydration, can impact tick survival. To prevent dehydration, ticks must be able to detect and move into high humidity areas to allow for water vapor uptake. Ionotropic receptor 93a (Ir93a), which is highly expressed in the front forelegs (location of Hallers organ), increases expression following dehydration, suggesting a role for the forelegs in humidity detection. Although the Hallers organ is suggested as the site of humidity detection in ticks, humidity detection has not been extensively examined for ticks. Here, we assessed the ability of ticks to sense humidity and how altered humidity detection impacts tick survival by manipulating the Hallers organ. Permanent (cutting or heat ablation) or temporary blocking (silicone covering) of the Hallers organ impairs the ability of the American dog tick, Dermacentor variabilis, to rest in areas necessary to maintain hydration. Impaired detection of humidity did not impact tick survival when individuals were held under stable optimal conditions. Still, variable conditions (low and high humidity gradient) reduced survival through dehydration stress and decreased energy reserves, as chronic water vapor uptake is energetically expensive. Field validation of these studies in D. variabilis confirmed that humidity detection is critical to tick survival. Lastly, modeling indicates impaired humidity detection will reduce questing tick populations, specifically in the adult stages. These studies confirm that the Hallers organ is critical for humidity sensing in ticks. Without this ability, tick survival will be impaired by potential dehydration or more rapid depletion of energy reserves.

physiology↗

Developmental stage and level of submersion in water impact the viability of lone star and winter tick eggs during flooding

Female ticks deposit large egg clusters that range in size from hundreds to thousands eggs each. These clusters are immobile and restricted to a deposition site, usually under leaf litter and other debris. These sites can be exposed to periodic flooding, where the cluster of tick eggs can float to the surface or remain underneath organic debris entirely submerged underwater. Here, we examined the viability of egg clusters from winter ticks, Dermacentor albipictus, and lone star ticks, Amblyomma americanum, when partially or fully submerged in water and in relation to the developmental stages of the eggs. In general, egg clusters that were older and partially submerged had a higher viability than fully submerged, younger eggs. A. americanum was more resistant to water exposure between the two species. These studies highlight that egg clusters for certain tick species can remain viable when exposed to water for at least two weeks. These studies also suggest that distribution by flooding of egg clusters could occur for some species and flooding will differentially impact tick egg survival based on the specific developmental stage of exposure and species.

ecology↗

Intra-species quantification reveals differences in activity and sleep levels in the yellow fever mosquito, Aedes aegypti

Aedes aegypti is an important mosquito vector of human disease with a wide distribution across the globe. Climatic conditions and ecological pressure drive differences in the biology of several populations of this mosquito, including blood-feeding behavior and vector competence. However, no study has compared activity and/or sleep among different populations/lineages of Ae. aegypti. Having recently established sleep-like states in three mosquito species with observable differences in timing and amount of sleep among species, we investigated differences in activity and sleep levels among 17 Ae. aegypti lines drawn from both its native range in Africa and its invasive range across the global tropics. Activity monitoring indicates that all the lines show consistent diurnal activity, but significant differences in activity level, sleep amount, number of sleep bouts, and bout duration were observed among the lines. Variations in specific activity and sleep parameters were explained by differences in host preference, ancestry, and human population density for the lineages collected in Africa. This study provides evidence that the diurnal sleep and activity profiles for Ae. aegypti are consistent, but there are significant population differences for Ae. aegypti sleep and activity levels and interactions with humans may significantly impact mosquito activity and sleep.

physiology↗

TRPM7-dependent electrical signals drive phagocytic clearance for effective anti-fungal defense

Sentinel phagocytes of the innate immune system have a critical role in detecting and eliminating fungal pathogens. We used patch clamp electrophysiology to explore the electrical signals elicited when macrophages engulf Candida albicans. In the perforated patch configuration, which is least disruptive to intracellular signaling, we detected a composite outwardly rectifying current during the engulfment of C. albicans or zymosan. FTY720, a known inhibitor of ion channel TRPM7, suppressed the current. We then tested the hypothesis that TRPM7 regulates the engulfment and clearance of C. albicans. We found that Trpm7-/- macrophages are highly deficient in the engulfment of C. albicans. Trpm7-/- macrophages initiate phagocytosis of yeast but are defective in sealing the phagocytic cups. While the precise mechanism through which TRPM7 regulates phagosome sealing is not clear, we tested the immunological significance of this discovery using a mouse model of systemic candidiasis. We show that in mice, wherein TRPM7 is deleted selectively in the myeloid cells, infection by C. albicans results in significantly higher lethality, increased colonization of vital organs and increased inflammatory cytokines in the blood. Our study establishes TRPM7 as an ion channel critical for the innate immune responses against fungal pathogens and sets the stage for cell biological studies that define the mechanisms through which TRPM7 regulates phagosome sealing. Significance statementThe worldwide increase in deadly or persistent fungal infections has prompted the research for alternative ways of treatment. We applied the specialized, perforated patch clamp technique to track and identify electrical currents elicited during the detection and engulfment of fungi by macrophages. The ion channel TRPM7 emerged as an important determinant of anti-fungal host defense as its deletion in the murine myeloid cells made the host mice highly susceptible to lethal candidiasis. Ion channels are attractive drug targets whose activation and inhibition can be manipulated with pharmacological therapeutics. This study raises the possibility of enhancing fungal clearance using activators of TRPM7. Such pharmacological strategy may benefit patients of persistent fungal infections that are recalcitrant to anti-fungal drugs.

immunology↗

Partitioning variance in cortical morphometry into genetic, environmental, and subject-specific components using a large adolescent sample

The relative contributions of genetic variation and experience in shaping the morphology of the adolescent brain are not fully understood. Using longitudinal data from 11,665 subjects in the ABCD Study(R), we fit vertex-wise variance components including family effects, genetic effects, and subject-level effects using a computationally efficient framework. Variance in cortical thickness and surface area is largely attributable to genetic influence, whereas sulcal depth is primarily explained by subject-level effects. Our results identify areas with heterogeneous distributions of heritability estimates that have not been seen in previous work using data from cortical regions. We discuss the biological importance of subject-specific variance and its implications for environmental influences on cortical development and maturation.

neuroscience↗

Emergence of High-Order Functional Hubs in the Human Brain

Network theory is often based on pairwise relationships between nodes, which is not necessarily realistic for modeling complex systems. Importantly, it does not accurately capture non-pairwise interactions in the human brain, often considered one of the most complex systems. In this work, we develop a multivariate signal processing pipeline to build high-order networks from time series and apply it to resting-state functional magnetic resonance imaging (fMRI) signals to characterize high-order communication between brain regions. We also propose connectivity and signal processing rules for building uniform hypergraphs and argue that each multivariate interdependence metric could define weights in a hypergraph. As a proof of concept, we investigate the most relevant three-point interactions in the human brain by searching for high-order "hubs" in a cohort of 100 individuals from the Human Connectome Project. We find that, for each choice of multivariate interdependence, the high-order hubs are compatible with distinct systems in the brain. Additionally, the high-order functional brain networks exhibit simultaneous integration and segregation patterns qualitatively observable from their high-order hubs. Our work hereby introduces a promising heuristic route for hypergraph representation of brain activity and opens up exciting avenues for further research in high-order network neuroscience and complex systems.

neuroscience↗

Ocean acidification increases susceptibility to sub-zero air temperatures in ecosystem engineers (Mytilus sp.): a limit to poleward range shifts

Ongoing climate change has caused rapidly increasing temperatures, and an unprecedented decline in seawater pH, known as ocean acidification. Increasing temperatures are redistributing species towards higher and cooler latitudes which are most affected by ocean acidification. Whilst the persistence of intertidal species in cold environments is related to their capacity to resist sub-zero air temperatures, studies have never considered the interacting impacts of ocean acidification and freeze stress on species survival and distribution. A full-factorial experiment was used to study whether ocean acidification increases mortality in Mytilus spp. following sub-zero air temperature exposure. We examined physiological processes behind variation in freeze tolerance using 1H NMR metabolomics, analyses of fatty acids, and amino acid composition. We show that low pH conditions (pH = 7.5) significantly decrease freeze tolerance in both intertidal and subtidal populations of Mytilus spp. Under current day pH conditions (pH = 7.9), intertidal M. trossulus were more freeze tolerant than subtidal M. trossulus and M. galloprovincialis. Opposite, under low pH conditions, subtidal M. trossulus was more freeze tolerant than the other groups. We observed a marked shift from negative to positive metabolite-metabolite correlations across species under low pH conditions, but there was no evidence that the concentration of individual metabolites or amino acids affected freeze tolerance. Finally, pH-induced changes in the composition of cell membrane phospholipid fatty acids had no effect on survival. These results suggest that ocean acidification can offset the poleward expanding facilitated by warming, and that reduced freeze tolerance could result in a niche squeeze if temperatures become lethal at the equatorward edge.

ecology↗

Global, regional, and cryptic population structure in a high gene-flow transatlantic fish

1Lumpfish (Cyclopterus lumpus) is a transatlantic marine fish displaying large population sizes and a high potential for dispersal and gene-flow. These features are expected to result in weak population structure. Here, we investigated population genetic structure of lumpfish throughout its natural distribution in the North Atlantic using two approaches: I) 4393 genome wide SNPs and 95 individuals from 10 locations, and II) 139 discriminatory SNPs and 1,669 individuals from 40 locations. Both approaches identified extensive population genetic structuring with a major split between the East and West Atlantic and a distinct Baltic Sea population, as well as further differentiation of lumpfish from the English Channel, Iceland, and Greenland. The targeted discriminatory loci displayed [~]2-5 times higher divergence than the genome wide approach, revealing further evidence of local population substructures. Lumpfish from Isfjorden in Svalbard were highly distinct but resembled most fish from Greenland. The Kattegat area in the Baltic transition zone, formed a previously undescribed distinct genetic group. Also, further subdivision was detected within North America, Iceland, West Greenland, Barents Sea, and Norway. Although lumpfish have considerable potential for dispersal and gene-flow, the observed high levels of population structuring throughout the Atlantic suggests that this species displays natal homing and potentially local populations with adaptive differences. This fine-scale population structure calls for consideration when defining management units for lumpfish fishing stocks and in decisions related to sourcing and moving lumpfish for farming and cleaner fish use.

evolutionary biology↗

Cooperative escape in ants and robots

The solution of complex problems by the collective action of simple agents in both biologically evolved and synthetically engineered systems involves cooperative action. Understanding the resulting emergent solutions requires integrating across the organismal behaviors of many individuals. Here we investigate an ecologically relevant collective task in black carpenter ants Camponotus pennsylvanicus: escape from a soft, erodible confining corral. Individual ants show a transition from individual exploratory excavation at random locations to spatially localized collective exploitative excavation and escape from the corral. A minimal continuum theory that coarse-grains over individual actions and considers their integrated influence on the environment leads to the emergence of an effective phase space of behaviors in terms of excavation strength and cooperation intensity. To test the theory over the range of predicted behaviors, we used custom-built robots (RAnts) that respond to stimuli and show the emergence (and failure) of cooperative excavation and escape. Overall, our approach shows how the cooperative completion of tasks can arise from relatively simple rules that involve the interaction of simple agents with a dynamically changing environment that serves as an enabler and modulator of behavior.

animal behavior and cognition↗

TGFβ drives mitochondrial dysfunction in peripheral blood NK cells during metastatic breast cancer

Natural Killer (NK) cells provide important protection from cancer and are a key requirement for particular immunotherapies. In activated NK cells, a metabolic response towards increased glycolysis and oxidative phosphorylation is crucial for NK cell effector functions. However, there is accumulating evidence that NK cells become dysfunctional during chronic inflammatory diseases, such as human breast cancer. This dysfunction is apparent in peripheral blood NK cells and can impact on normal NK cell immune responses and their effective targeting during immunotherapy. Herein, we demonstrate that prolonged cytokine stimulation combined with metabolic restriction, through inhibition of mTORC1, is sufficient to induce persistent dysfunction in human NK cells. TGF{beta}, also restricted NK cell metabolism and promoted persistent NK cell dysfunction. NK cells from patients with metastatic breast cancer had profound metabolic defects in glycolysis and mitochondrial function, and clear structural differences in NK cell mitochondrial morphology. Importantly, blocking elevated TGF{beta} improved readouts of metabolism and restored IFN{gamma} production in patient NK cells.

immunology↗

Theta-Gamma Cascades and Running Speed

The local field potentials (LFPs) of the hippocampus are primarily generated by the spatiotemporal accretion of electrical currents via activated synapses. Oscillations in the hippocampal LFP at theta and gamma frequencies are prominent during awake-behavior and have demonstrated several behavioral correlates. In particular, both oscillations have been observed to increase in amplitude and frequency as a function of running velocity. Previous investigations, however, have examined the relationship between velocity and each of these oscillation bands separately. Based on energy cascade models where \"...perturbations of slow frequencies cause a cascade of energy dissipation at all frequency scales\" (Buzsaki 2006), we hypothesized that the cross-frequency interactions between theta and gamma should increase as a function of velocity. We examined these relationships across multiple layers of the CA1 subregion and found a reliable correlation between the power of theta and the power of gamma, indicative of an amplitude-amplitude relationship. Moreover, there was an increase in the coherence between the power of gamma and the phase of theta, demonstrating increased phase-amplitude coupling with velocity. Finally, at higher velocities, phase entrainment between theta and gamma becomes stronger. These results have important implications and provide new insights regarding how theta and gamma are integrated for neuronal circuit dynamics, with coupling strength determined by the excitatory drive within the hippocampus.

neuroscience↗

Serial quantification of brain oxygenation in acute stroke using streamlined-qBOLD

It has been proposed that metabolic markers of baseline brain oxygenation have a role to play in the early identification of the ischemic penumbra. Streamlined-qBOLD is a magnetic resonance imaging technique that does not require exogenous contrast. It is a refinement of the quantitative BOLD methodology that provides a simplified approach to mapping and quantifying baseline brain oxygenation related parameters (reversible transverse relaxation rate (R2'), deoxygenated blood volume (DBV) and deoxyhaemoglobin concentration ([dHb])) in a clinically relevant manner. Streamlined-qBOLD was applied to an exploratory cohort of acute stroke patients in a serial imaging study. Detailed voxel-level analysis was used to quantify the metabolic profile of ischaemic tissue on presentation and investigate these metrics in relation to tissue outcome. Individual patient examples illustrate the appropriate interpretation of R2', DBV and [dHb] in acute stroke and demonstrate the ability of this method to deliver regional information related to oxygen metabolism in the ischaemic tissue. Regional analysis confirms that R2', DBV and [dHb] vary between regions of ischaemia with different tissue outcomes.

neuroscience↗