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ABSTRACT Gene family expansion underlies a host of biological innovations across the tree of life. Understanding why specific gene families expand or contract requires comparative genomic investigations clarifying further how species adapt in the wild. This study investigates the gene family change dynamics within several species ofDaphnia, a group of freshwater microcrustaceans that are insightful model systems for evolutionary genetics' research. We employ comparative genomics approaches to understand the forces driving gene evolution and draw upon candidate gene families that change gene numbers acrossDaphnia. Our results suggest that genes related to stress responses and glycoproteins generally expand across taxa, and we investigate evolutionary hypotheses of adaptation that may underpin expansions. Through these analyses, we shed light on the interplay between gene expansions and selection within other ecologically relevant stress response gene families. While we show generalities in gene family turnover in genes related to stress response (i.e., DNA repair mechanisms), most gene family evolution is driven in a species‐specific manner. Additionally, while we show general trends toward positive selection within some expanding gene families, many genes are not under selection, highlighting the complexity of diversification and evolution withinDaphnia. Our research enhances the understanding of individual gene family evolution withinDaphniaand provides a case study of ecologically relevant genes prone to change. 

Abstract Bacterial vaginosis (BV) is the most prevalent vaginal condition among reproductive-age women presenting with vaginal complaints. Despite its significant impact on women’s health, limited knowledge exists regarding the microbial community composition and metabolic interactions associated with BV. In this study, we analyze metagenomic data obtained from human vaginal swabs to generate in silico predictions of BV-associated bacterial metabolic interactions via genome-scale metabolic network reconstructions (GENREs). While most efforts to characterize symptomatic BV (and thus guide therapeutic intervention by identifying responders and non-responders to treatment) are based on genomic profiling, our in silico simulations reveal functional metabolic relatedness between species as quite distinct from genetic relatedness. We grow several of the most common co-occurring bacteria (Prevotella amnii, Prevotella buccalis, Hoylesella timonensis, Lactobacillus iners, Fannyhessea vaginae, andAerrococcus christenssii) on the spent media ofGardnerellaspecies and perform metabolomics to identify potential mechanisms of metabolic interaction. Through these analyses, we identify BV-associated bacteria that produce caffeate, a compound implicated in estrogen receptor binding, when grown in the spent media of other BV-associated bacteria. These findings underscore the complex and diverse nature of BV-associated bacterial community structures and several of these mechanisms are of potential significance in understanding host-microbiome relationships. 

ABSTRACT Shared polymorphisms, loci with identical alleles across species, are of unique interest in evolutionary biology as they may represent cases of selection maintaining ancient genetic variation post‐speciation, or contemporary selection promoting convergent evolution. In this study, we investigate the abundance of shared polymorphism between two members of theDaphnia pulexspecies complex. We test whether the presence of shared mutations is consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting or convergent evolution. We analyzed over 2,000 genomes from six taxa in theD. pulexspecies group and examined the prevalence and distribution of shared alleles between the focal species pair, North American and EuropeanD. pulex. We show that North American and EuropeanD. pulexdiverged over 10 million years ago, yet retained tens of thousands of shared polymorphisms. We suggest that the number of shared polymorphisms between North American and EuropeanD. pulexcannot be fully explained by hybridization or incomplete lineage sorting alone. We show that most shared polymorphisms could be the product of convergent evolution, that a limited number appear to be old trans‐specific polymorphisms, and that balancing selection is affecting convergent and ancient mutations alike. Finally, we provide evidence that a blue wavelength opsin gene with trans‐specific polymorphisms has functional effects on behavior and fitness in the wild. 

Abstract BackgroundNeuronal polarity and synaptic connectivity are compromised in Alzheimer’s disease (AD) and other tauopathies. The axon initial segment (AIS) is a key structure for regulating polarity and functions of neurons. It occupies the first 20‐60 µm of the axon, comprises a diffusion barrier that segregates axon‐enriched from somatodendritic‐enriched molecules, and has a high concentration of voltage‐gated ion channels that generate action potentials. Extracellular amyloid‐β oligomers compromise AIS integrity. However, effects on the AIS of toxic tau species, including extracellular oligomers (xcTauOs) that spread tau pathology from neuron to neuron by a prion‐like process, whereas unknown. Therefore, we wanted to test the hypothesis that AIS structure is sensitive to xcTauOs. MethodPrimary cortical neurons derived from either wild type (WT), or tau knockout (KO) mice were exposed to xcTauOs or vehicle. Quantitative western blotting and immunofluorescence microscopy with an antibody against the AIS‐enriched protein TRIM46 was used to monitor effects on the AIS. The same methods were also used to compare TRIM46 and two other AIS proteins, ankyrin‐G and neurofascin‐186 in human hippocampal tissue obtained from AD and age‐matched non‐AD donors. ResultIn cultured WT, but not TKO neurons, xcTauOs cause a trend toward AIS shortening and reduce the concentration of the resident AIS protein, TRIM46, without affecting total TRIM46 levels. Lentiviral‐driven human tau expression in tau KO neurons rescues TRIM46 sensitivity to xcTauOs. In human AD hippocampus, AIS length and TRIM46 concentration within the AIS are reduced in neurons containing neurofibrillary tangles (NFTs), without affecting the overall protein levels of multiple resident AIS proteins. ConclusionThese collective findings demonstrate that in cultured neurons, xcTauOs cause partial AIS damage by a mechanism dependent on intracellular tau, thereby raising the possibility that AIS reduction in AD is caused by xcTauOs working in concert with endogenous neuronal tau. 

Abstract Replicability of divergence after contact is a poorly characterized process, particularly in the contexts of phylogeography and postglacial range dynamics within species. Using contact zones located at the leading‐, mid‐ and rear‐edges of a species' range, we examined variation in outcomes to contact between divergent lineages ofCampanula americana. We investigated whether contact zones vary in quantity and directionality of gene flow, how phylogeographic structure differs between contact zones, and how historic range dynamics may affect outcomes to contact. We found that all contact zones formed at similar times via primary contact yet detected significant admixture in only the rear‐edge (RE) contact zone. In the northern leading‐edge contact zone and the mid‐range Virginia contact zone, gene flow was minimal and asymmetric. In the southern RE contact zone, gene flow was strong and symmetric. Asymmetric admixture in the leading‐edge and Virginia contact zones matches the directionality of a known cosmopolitan cytonuclear incompatibility between lineages ofC. americana. Our results emphasize the dependence of speciation processes on phylogeographic structure, evolutionary history and range dynamics. 

Abstract Parents use joint attention to direct infants to environmental stimuli. We hypothesized that infants whose parents provide more bids for joint attention will display a more complex neural response when viewing social scenes. Sixty‐one 8‐month‐old infants underwent electroencephalography (EEG) while viewing videos of joint‐ and parallel‐play and participated in a free play interaction. EEG data was analyzed using multiscale entropy, which quantifies neural variability. Free play interactions assessed parent alternating gaze, a behavioral mechanism for directing attention to environmental cues. We found a significant positive association between parent alternating gaze and neural entropy in frontal and central regions. These results suggest a relationship between parent behavior and infant neural mechanisms that regulate social attention, underlying the importance of parental cues in forming neural networks. 

Abstract Oxytocin (OXT) is a peptide hormone and a neuropeptide that regulates various peripheral physiological processes and modulates behavioral responses in the central nervous system. While the humoral release occurs from the axons arriving at the median eminence, the neuropeptide is also released from oxytocinergic cell axons in various brain structures that contain its receptor, and from their dendrites in hypothalamic nuclei and potentially into the cerebrospinal fluid (CSF). Understanding oxytocin’s complex functions requires the knowledge on patterns of oxytocinergic projections in relationship to its receptor (OXTR). This study provides the first comprehensive examination of the oxytocinergic system in the prairie vole (Microtus ochrogaster), an animal exhibiting social behaviors that mirror human social behaviors linked to oxytocinergic functioning. Using light and electron microscopy, we characterized the neuroanatomy of the oxytocinergic system in this species. OXT+ cell bodies were found primarily in the hypothalamus, and axons were densest in subcortical regions. Examination of the OXT+ fibers and their relationship to oxytocin receptor transcripts (Oxtr) revealed that except for some subcortical structures, the presence of axons was not correlated with the amount ofOxtracross the brain. Of particular interest, the cerebral cortex that had high expression ofOxtrtranscripts contained little to no fibers. Electron microscopy is used to quantify dense cored vesicles (DCV) in OXT+ axons and to identify potential axonal release sites. The ependymal cells that line the ventricles were frequently permissive of DCV-containing OXT+ dendrites reaching the third ventricle. Our results highlight a mechanism in which oxytocin is released directly into the ventricles and circulates throughout the ventricular system, may serve as the primary source for oxytocin that binds to OXTR in the cerebral cortex. 

Bacterial pathogens pose a major risk to human health, leading to tens of millions of deaths annually and significant global economic losses. While bacterial infections are typically treated with antibiotic regimens, there has been a rapid emergence of antimicrobial resistant (AMR) bacterial strains due to antibiotic overuse. Because of this, treatment of infections with traditional antimicrobials has become increasingly difficult, necessitating the development of innovative approaches for deeply understanding pathogen function. To combat issues presented by broad- spectrum antibiotics, the idea of narrow-spectrum antibiotics has been previously proposed and explored. Rather than interrupting universal bacterial cellular processes, narrow-spectrum antibiotics work by targeting specific functions or essential genes in certain species or subgroups of bacteria. Here, we generate a collection of genome-scale metabolic network reconstructions (GENREs) of pathogens through an automated computational pipeline. We used these GENREs to identify subgroups of pathogens that share unique metabolic phenotypes and determined that pathogen physiological niche plays a role in the development of unique metabolic function. For example, we identified several unique metabolic phenotypes specific to stomach pathogens. We identified essential genes unique to stomach pathogens in silico and a corresponding inhibitory compound for a uniquely essential gene. We then validated our in silico predictions with an in vitro microbial growth assay. We demonstrated that the inhibition of a uniquely essential gene,thyX, inhibited growth of stomach-specific pathogens exclusively, indicating possible physiological location-specific targeting. This pioneering computational approach could lead to the identification of unique metabolic signatures to inform future targeted, physiological location-specific, antimicrobial therapies, reducing the need for broad-spectrum antibiotics. 

Background: In Alzheimer’s disease (AD) brain, neuronal polarity and synaptic connectivity are compromised. A key structure for regulating polarity and functions of neurons is the axon initial segment (AIS), which segregates somatodendritic from axonal proteins and initiates action potentials. Toxic tau species, including extracellular oligomers (xcTauOs), spread tau pathology from neuron to neuron by a prion-like process, but few other cell biological effects of xcTauOs have been described. Objective: Test the hypothesis that AIS structure is sensitive to xcTauOs. Methods: Cultured wild type (WT) and tau knockout (KO) mouse cortical neurons were exposed to xcTauOs, and quantitative western blotting and immunofluorescence microscopy with anti-TRIM46 monitored effects on the AIS. The same methods were used to compare TRIM46 and two other resident AIS proteins in human hippocampal tissue obtained from AD and age-matched non-AD donors. Results: Without affecting total TRIM46 levels, xcTauOs reduce the concentration of TRIM46 within the AIS and cause AIS shortening in cultured WT, but not TKO neurons. Lentiviral-driven tau expression in tau KO neurons rescues AIS length sensitivity to xcTauOs. In human AD hippocampus, the overall protein levels of multiple resident AIS proteins are unchanged compared to non-AD brain, but TRIM46 concentration within the AIS and AIS length are reduced in neurons containing neurofibrillary tangles. Conclusion: xcTauOs cause partial AIS damage in cultured neurons by a mechanism dependent on intracellular tau, thereby raising the possibility that the observed AIS reduction in AD neurons in vivo is caused by xcTauOs working in concert with endogenous neuronal tau.