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Harris, A.

Publications and source records attributed to Harris, A..

At least 19 recordsLinked to original sources

6-Methylnicotine is a strong agonist at α4β2 and α3β4 nicotinic cholinergic receptors

(-)6-Methylnicotine (6-MN), is a structural analog of (-)nicotine that has been added to some e-cigarette/vape solutions and to nicotine oral pouches. 6-MN binds with high affinity to nicotinic cholinergic receptors (nAChRs) in brain, but its receptor subtype selectivity and its potency to activate and desensitize these receptors is unknown. Also unknown is whether chronic administration of 6-MN increases (upregulates) nAChRs in brain as does nicotine. Currently, 6-MN is unregulated in the U.S. by the FDA. Here we compared 6-MN and nicotine at 4{beta}2 and 3{beta}4 nAChRs, which are two major nAChR subtypes that mediate important functions in the brain and autonomic nervous system. Specifically, we quantitatively compared (-)6-MN and (-)nicotine with respect to receptor binding affinity and functional potency to activate 4{beta}2 and 3{beta}4 nAChRs, as well as its potency to desensitize these receptors, which is one of the key effects of nicotine. In addition, because chronic administration of nicotine upregulates the number of 4{beta}2 nAChRs in rat, mouse and human brain, we measured whether 6-MN also increases these receptors. Our results indicate that 6-MN is a more potent agonist than nicotine at both the 4{beta}2 and 3{beta}4 nAChRs, and it also upregulates nAChRs in brain.

pharmacology and toxicology↗

Source-space EEG functional connectivity and prediction of cognition in Parkinsons disease: No added benefit of individualized head models over standard templates

IntroductionCognitive decline is a major non-motor feature of Parkinsons disease (PD), but reliable and accessible biomarkers remain limited. Resting-state electroencephalography (EEG) is a promising candidate because it is low-cost, portable, and well suited to repeated assessment. Recent work has increasingly focused on source-space functional connectivity (FC) for the prediction of cognition. However, the influence of source modelling based on an individualized MRI-based head model relative to that based on standard template model is unknown. MethodsTo compare these two source-space EEG FC methods, we analysed EEG data from the New Zealand Parkinsons Progression Programme, including 136 people with PD and 51 age-similar controls. Source space resting-state EEG, parcellated with the HCP-MMP1 atlas, was used to derive amplitude envelope correlation (AEC) and debiased weighted phase lag index (dwPLI) across six canonical frequency bands. The resulting twenty-four FC modalities were evaluated using six machine-learning regression algorithms within a nested cross-validation framework. ResultsTheta-, alpha-, and beta-band FC showed the most consistent prediction of global cognition. The strongest performance was observed for theta- and alpha-band AEC and dwPLI features (max R{superscript 2} = 0.170, 95% CI = 0.067-0.262; max r = 0.439, 95% CI = 0.328-0.537). Standard and individualized head models showed comparable predictive performance across nearly all modalities. The feature-importance neuroanatomical patterns for Cole-Anticevic networks were also similar between the two head-model options. ConclusionsWe found that source-space resting-state EEG FC can predict cognitive performance in PD. The comparability of the two head models suggests that the more user-friendly and less resource-intensive standard template head model is sufficient for this purpose. This supports feasible, scalable, and clinically accessible EEG-based FC biomarkers of cognition in PD.

neuroscience↗

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↗

FAST: Filamentous Actin Segmentation Tool for quantifying cytoskeletal organization

Studying how actin filaments are assembled into different subcellular structures can provide insights into both physiological processes and the mechanisms of disease. However, quantifying the size, abundance, and organization of different classes of actin structure from optical microscopy data remains a challenge. To address this, we developed a deep learning based Filamentous Actin Segmentation Tool (FAST) to accurately and efficiently segment and quantify different classes of actin structure from phalloidin stained confocal microscopy images. We evaluated the performance of this tool to segment and quantify the abundance of different classes of actin structure in different cell lines and with dynamic changes in actin organization using lifeact-GFP during drug treatments. FAST enables quantification of different classes of actin structure from actin images alone, without the need for specific antibodies against proteins in different actin structures and hence can be a useful tool for researchers studying for studying actin related pathways involved in cell motility, cancer metastasis, and drug development. Summary StatementWe developed Filamentous Actin Segmentation Tool (FAST), that leverages deep learning and antibody assisted labeling to segment and quantify actin structures from optical microscopy images.

cell biology↗

A lipoprotein partner for the Escherichia coli outer membrane protein TolC

The outer-membrane protein TolC from Escherichia coli belongs to an extensive superfamily whose members are found throughout the didermal, Gram-negative bacterial lineages. The protein serves as an activated exit duct in multi-drug efflux pumps and protein secretion machinery. Many TolC homologs bear a lipid modification on the N-terminus that embeds into the inner leaflet of the outer membrane and appears to have been a conserved feature; however, the moiety is absent entirely in the E. coli TolC. We have discovered that the E. coli lipoprotein YbjP interacts extensively with the periplasmic surface of TolC and its N-terminal lipid moiety is embedded in the membrane, mimicking the intramolecular and modification-membrane interactions seen in TolC homologs. Here, we present cryo-EM structures of the MacA-MacB-TolC and AcrA-AcrB-TolC tripartite pumps complexed to YbjP. Although the association occurs spontaneously both in vitro and in vivo, the YbjP-TolC interaction is not required for efflux activity under standard laboratory conditions. YbjP may contribute stabilising the orientation and distribution of TolC in the outer membrane as well as the expression of transporters for tryptophan and cyclic peptide toxins.

molecular biology↗

Mapping the canine microbiome: Insights from the Dog Aging Project

Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, the largest population-wide study of the canine gut microbiome to date. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with comprehensive phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as diet, health, and living conditions. Our analyses identify various factors associated with microbiome composition. In addition, we find a gradual shift in microbiome composition with age, which allows us to develop a novel metagenomics-based "clock" to predict biological aging based on microbial signatures. Overall, these findings provide an unprecedented and detailed understanding of the role the gut microbiome plays in our four-legged companions, offering both potential applications in veterinary medicine and an exciting model for aging research.

microbiology↗

DNA methylation of transposons pattern aging differences across a diverse cohort of dogs from the Dog Aging Project

Within a species, larger individuals often have shorter lives and higher rates of age-related disease. Despite this well-known link, we still know little about underlying age-related epigenetic differences, which could help us better understand inter-individual variation in aging and the etiology, onset, and progression of age-associated disease. Dogs exhibit this negative correlation between size, health, and longevity and thus represent an excellent system in which to test the underlying mechanisms. Here, we quantified genome-wide DNA methylation in a cohort of 864 dogs in the Dog Aging Project. Age strongly patterned the dog epigenome, with the majority (66% of age-associated loci) of regions associating age-related loss of methylation. These age effects were non-randomly distributed in the genome and differed depending on genomic context. We found the LINE1 (long interspersed elements) class of TEs (transposable elements) were the most frequently hypomethylated with age (FDR < 0.05, 40% of all LINE1 regions). This LINE1 pattern differed in magnitude across breeds of different sizes- the largest dogs lost 0.26% more LINE1 methylation per year than the smallest dogs. This suggests that epigenetic regulation of TEs, particularly LINE1s, may contribute to accelerated age and disease phenotypes within a species. Since our study focused on the methylome of immune cells, we looked at LINE1 methylation changes in golden retrievers, a breed highly susceptible to hematopoietic cancers, and found they have accelerated age-related LINE1 hypomethylation compared to other breeds. We also found many of the LINE1s hypomethylated with age are located on the X chromosome and are, when considering X chromosome inactivation, counter-intuitively more methylated in males. These results have revealed the demethylation of LINE1 transposons as a potential driver of intra-species, demographic-dependent aging variation.

genomics↗

Aging at scale: Younger dogs and larger breeds from the Dog Aging Project show accelerated epigenetic aging.

Dogs exhibit striking within-species variability in lifespan, with smaller breeds often living more than twice as long as larger breeds. This longevity discrepancy also extends to health and aging-larger dogs show higher rates of age-related diseases. Despite this well-established phenomenon, we still know little about the biomarkers and molecular mechanisms that might underlie breed differences in aging and survival. To address this gap, we generated an epigenetic clock using DNA methylation from over 3 million CpG sites in a deeply phenotyped cohort of 864 companion dogs from the Dog Aging Project, including some dogs sampled annually for 2-3 years. We found that the largest breed size tends to have epigenomes that are, on average, 0.37 years older per chronological year compared to the smallest breed size. We also found that higher residual epigenetic age was significantly associated with increased mortality risk, with dogs experiencing a 34% higher risk of death for each year increase in residual epigenetic age. These findings not only broaden our understanding of how aging manifests within a diverse species but also highlight the significant role that demographic factors play in modulating the biological mechanisms underlying aging. Additionally, they highlight the utility of DNA methylation as both a biomarker for healthspan-extending interventions, a mortality predictor, and a mechanism for understanding inter-individual variation in aging in dogs.

genomics↗

The role of β-Nicotyrine in E-Cigarette abuse liability I: Drug Discrimination

Background{beta}-Nicotyrine ({beta}-Nic) is a unique minor alkaloid constituent in electronic nicotine delivery systems (ENDS) that is derived from nicotine (Nic) degradation and can reach 25% of Nic concentrations in ENDS aerosol. {beta}-Nic slows Nic metabolism and prolongs systemic Nic exposure, which may alter the discriminability of Nic. The present study sought to examine {beta}-Nic has interoceptive effects itself, and if it alters the subjective effects ENDS products within a drug-discrimination paradigm. MethodsThe pharmacodynamics of {beta}-Nic were examined in vitro, and a nicotine discrimination paradigm was used to determine if {beta}-Nic (0 - 5.0 mg/kg) shares discriminative stimulus properties with Nic (0.2 mg/kg) in male (n = 13) and female (n = 14) rats after 10- & 60-min {beta}-Nic pretreatment delays. A second group of rats was trained to discriminate {beta}-Nic and Nornicotine (Nornic) from saline to determine if {beta}-Nic alone has interoceptive properties and whether they are similar to Nornic. Results{beta}-Nic had similar binding affinity and efficacy at the 4{beta}2 nicotinic receptor subtype as Nornic, [~]50% of Nic efficacy. However, {beta}-Nic only weakly substituted for Nic during substitution testing in female rats, but not males, whereas Nornic fully substituted for Nic. Combination testing at the 10 and 60-min pretreatment intervals showed that {beta}-Nic dose-dependently increased the duration of nicotines discriminative stimulus effects, especially at the 60-min delay. Drug naive rats could reliably discriminate Nornic, but not {beta}-Nic, from Sal. Conclusion{beta}-Nic increased and prolonged the interoceptive stimulus properties of Nic, suggesting it may alter to the abuse liability of ENDS through its ability to slow Nic metabolism.

pharmacology and toxicology↗

IgM plays a prominent role in naturally acquired immunity against Plasmodium falciparum gametocytes

The development of transmission-blocking vaccines against Plasmodium falciparum malaria could facilitate malaria elimination. However, limitations in the knowledge of the human immune responses against P. falciparum transmission stages, known as gametocytes, represent a critical roadblock to vaccine development. We evaluated human antibodies acquired through natural malaria exposure to whole gametocytes and recombinant antigens expressed by transmission stages, including the major transmission-blocking vaccine candidates Pfs230 and Pfs48/45 and other transmission stages, Pf38, Pf12 and Pf41. Among individuals residing in Kenya and Papua New Guinea, we found substantial antibody responses to whole gametocytes and to all recombinant transmission stage antigens with high levels of IgG, IgG subclasses and IgM. Complement fixation by antibodies to gametocytes is key for effective transmission-blocking activity. We found that purified IgM was substantially more potent than IgG at mediating complement fixation and activation. Higher antibody levels were generally observed in individuals positive for P. falciparum infection, including gametocyte positive individuals, and these antibodies generally increased with age. Our findings reveal that IgM is a prominent feature of antibody responses to gametocytes and that antibodies target multiple antigens. The further demonstration that IgM has high functional activity against gametocytes suggests IgM plays an important role in immunity to transmission stages. Our data provide new insights to inform the development of potent transmission-blocking vaccines.

immunology↗

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↗

Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years

The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R2>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.

evolutionary biology↗

Multi-signal regulation of the GSK-3β homolog Rim11 governs meiosis entry in yeast

Starvation of budding yeast diploid cells induces the cell-fate program that drives meiosis and spore formation. Transcription activation of early meiotic genes (EMGs) requires the transcription activator Ime1, its DNA-binding partner Ume6, and GSK-3{beta} kinase Rim11. Phosphorylation of Ume6 by Rim11 is key for EMG activation. We report that Rim11 integrates multiple input signals to control Ume6 phosphorylation and EMG transcription. Under nutrient-rich conditions PKA represses Rim11 to low levels while TORC1 keeps Rim11 localized to the cytoplasm. Inhibiting PKA and TORC1 induces Rim11 expression and nuclear localization. Remarkably, nuclear Rim11 is required, but not sufficient, for Rim11-dependent Ume6 phosphorylation. Additionally, Ime1 is an essential anchor protein for phosphorylating Ume6. Subsequently, Ume6-Ime1 coactivator complexes form that drive EMG transcription. Our results demonstrate how varied signalling inputs (PKA/TORC1/Ime1) integrated by Rim11 determine EMG expression and entry into meiosis. We propose that the signalling-regulatory network described here generates robustness in cell-fate control.

molecular biology↗

The Transcriptional Regulator Ume6 is a Major Driver of Early Gene Expression during Gametogenesis

The process of gametogenesis is orchestrated by a dynamic program of gene expression, where a vital subset constitutes the early meiotic genes (EMGs). In budding yeast, the transcription factor Ume6 represses EMG expression during mitosis. However, during mitosis to meiosis transition, EMGs are activated in response to the meiotic regulator Ime1 through its interaction with Ume6. While it is known that binding of Ime1 to Ume6 promotes EMG expression, the mechanism of EMG activation remains elusive. Two competing models have been proposed whereby Ime1 either forms a coactivator complex with Ume6 or promotes Ume6 degradation. Here, we resolve this controversy. First, we identify the set of genes that are directly regulated by Ume6, including UME6 itself. While Ume6 levels increase in response to Ime1, Ume6 degradation occurs much later in meiosis. Importantly, we found that depletion of Ume6 shortly before meiotic entry is detrimental to EMG activation and gamete formation, whereas tethering of Ume6 to a heterologous activation domain is sufficient to trigger EMG expression and produce viable gametes in the absence of Ime1. We conclude that Ime1 and Ume6 function as a coactivator complex. While Ume6 is indispensable for EMG expression, Ime1 primarily serves as a transactivator for Ume6.

genetics↗

The classic psychedelic DOI induces a persistent desynchronized state in medial prefrontal cortex

Administration or consumption of classic psychedelics (CPs) leads to profound changes in experience which are often described as highly novel and meaningful. They have shown substantial promise in treating depressive symptoms and may be therapeutic in other situations. Although research suggests that the therapeutic response is correlated with the intensity of the experience, the neural circuit basis for the alterations in experience caused by CPs requires further study. The medial prefrontal cortex (mPFC), where CPs have been shown to induce rapid, 5-HT2A receptor-dependent structural and neurophysiological changes, is believed to be a key site of action. To investigate the acute neural circuit changes induced by CPs, we recorded single neurons and local field potentials in the mPFC of freely behaving mice after administration of the 5-HT2A/2C receptor-selective CP, 2,5-Dimethoxy-4-iodoamphetamine (DOI). We segregated recordings into active and rest periods in order to examine cortical activity during desynchronized (active) and synchronized (rest) states. We found that DOI induced a robust decrease in low frequency power and decoupled rhythmic activity from neural population dynamics when animals were at rest, attenuating the usual synchronization that occurs during less active behavioral states. DOI also increased broadband gamma power and suppressed activity in fast-spiking neurons in both active and rest periods. Together, these results show that the CP DOI induces persistent desynchronization in mPFC, including during rest when mPFC typically exhibits more synchronized activity. This shift in cortical dynamics may in part underlie the longer-lasting effects of CPs on plasticity, and may be critical to their therapeutic properties.

neuroscience↗

Conditioning electrical stimulation fails to enhance sympathetic axon regeneration

Peripheral nerve injuries are common, and there is a critical need for the development of novel treatments to complement surgical repair. Conditioning electrical stimulation (CES) is a novel variation of the well-studied perioperative electrical stimulation treatment paradigm. CES is a clinically attractive alternative because of its ability to be performed at the bedside prior to a scheduled nerve repair surgery. Although 60 minutes of CES has been shown to enhance motor and sensory axon regeneration, the effects of CES on sympathetic regeneration are unknown. We investigated how two clinically relevant CES paradigms (10 minutes and 60 minutes) impact sympathetic axon regeneration and distal target reinnervation. Our results indicate that the growth of sympathetic axons is inhibited by CES at acute time points, and at a longer survival time point post-injury, there is no difference between sham CES and the CES groups. We conclude sympathetic axons may retain some regenerative ability, but no enhancement is exhibited after CES, which may be accounted for by the inability of the electrical stimulation paradigm to recruit the small-caliber sympathetic axons into activity. Furthermore, 10-minute CES did not enhance motor and sensory regeneration with a direct repair, and neither 60-minute nor 10-minute CES enhanced motor and sensory regeneration through a graft. Further studies will be needed to optimize electrical stimulation parameters to enhance the regeneration of all neuron types.

neuroscience↗

Deletion of genes linked to the C1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum

Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C1) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO2) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C1-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions - hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950) - directly adjacent and expressed at similar levels to the C1-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both {Delta}hp and {Delta}nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO2 and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C1-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.

synthetic biology↗

Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness

Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has already been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for routine bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on a minimal medium with one strain, named "LAbrini" (LT1), exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of sporulation-related mutations in genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism, which we named "LAbrini".

bioengineering↗