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Abstract Wastewater is a geospatially- and temporally-linked microbial fingerprint of a given population, making it a potentially valuable tool for tracking public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (N = 2238 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County, USA, from 2020-2022. We used targeted amplicon sequencing to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with positive PCR tests from University students and Miami-Dade hospital patients. Additionally, in bulk metatranscriptomic data, we demonstrate that the bacterial content of different wastewater sampling locations serving small population sizes can be used to detect putative, host-derived microorganisms that themselves have known associations with human health and diet. We also detect multiple enteric pathogens (e.g., Norovirus) and characterize viral diversity across sites. Moreover, we observed an enrichment of antimicrobial resistance genes (ARGs) in hospital wastewater; antibiotic-specific ARGs correlated to total prescriptions of those same antibiotics (e.g Ampicillin, Gentamicin). Overall, this effort lays the groundwork for systematic characterization of wastewater that can potentially influence public health decision-making.

Abstract Drug-induced gene expression profiles can identify potential mechanisms of toxicity. We focus on obtaining signatures for cardiotoxicity of FDA-approved tyrosine kinase inhibitors (TKIs) in human induced-pluripotent-stem-cell-derived cardiomyocytes, using bulk transcriptomic profiles. We use singular value decomposition to identify drug-selective patterns across cell lines obtained from multiple healthy human subjects. Cellular pathways affected by cardiotoxic TKIs include energy metabolism, contractile, and extracellular matrix dynamics. Projecting these pathways to published single cell expression profiles indicates that TKI responses can be evoked in both cardiomyocytes and fibroblasts. Integration of transcriptomic outlier analysis with whole genomic sequencing of our six cell lines enables us to correctly reidentify a genomic variant causally linked to anthracycline-induced cardiotoxicity and predict genomic variants potentially associated with TKI-induced cardiotoxicity. We conclude that mRNA expression profiles when integrated with publicly available genomic, pathway, and single cell transcriptomic datasets, provide multiscale signatures for cardiotoxicity that could be used for drug development and patient stratification.

Stationary in situ measurements conducted in close proximity to the shoreline present unique challenges. The shallow depth, automated profiling and accessibility for maintenance, particularly in the context of biofouling, are key considerations. The WInch for Long-term MOnitoring (WILMO), a solution designed to meet these requirements, is therefore presented. The fully automated system keeps the sensitive devices outside of the water until a profiling cycle is initiated, reducing the available settling time for species on the surface of the sensors. The design leverages common hardware and is structured in distinct units. This feature facilitates the interchangeability of individual hardware components and the implementation of a unifying software system capable of simultaneously managing all elements of WILMO. Using wireless broadband communications, WILMO can be fully controlled remotely, allowing for adjustments to the setup and monitoring of system functionality through a special web interface. The data are transmitted to a server with adjustable frequency and a post processing tool prepares them for analysis. The system underwent rigorous testing and demonstrated effective performance in northern Bali, Indonesia, between March and December 2022, gathering physical and biogeochemical time series data. The consistency of the data is validated through comparison with other instruments to ensure data quality. The results obtained are employed to ascertain the suitability of the special flow velocity sensor in this context. WILMO is a demonstrably reliable device, easily manageable and perfectly suited for long-term coastal monitoring.

Diet-induced metabolic load is associated with excess body weight and liver steatosis. Here, selected microalgae, known to contain bioactive nutrients, were studied for beneficial metabolic effects in a mouse model of liver steatosis. Adult mice (8 per group) were fed either a Western-style diet (WSD) or a control diet +/− 15 % of the microalgae Chlorella vulgaris (CV), Nannochloropsis oceanica (NO), or Phaeodactylum tricornutum (PT) for 12 weeks. We evaluated liver fat content and liver damage, as well as fecal microbiota and lipopolysaccharide (LPS) translocation. NO supplementation to a WSD reduced the grade of liver steatosis (from 17 % to 4.7 %, p

In the central nervous system of vertebrates, glutamate serves as the primary excitatory neurotransmitter. However, in the retina, glutamate released from photoreceptors causes hyperpolarization in post-synaptic ON-bipolar cells through a glutamate-gated chloride current, which seems paradoxical. Our research reveals that this current is modulated by two excitatory glutamate transporters, EAAT5b and EAAT7. In the zebrafish retina, these transporters are located at the dendritic tips of ON-bipolar cells and interact with all four types of cone photoreceptors. The absence of these transporters leads to a decrease in ON-bipolar cell responses, with eaat5b mutants being less severely affected than eaat5b/eaat7 double mutants, which also exhibit altered response kinetics. Biophysical investigations establish that EAAT7 is an active glutamate transporter with a predominant anion conductance. Our study is the first to demonstrate the direct involvement of post-synaptic glutamate transporters in inhibitory direct synaptic transmission at a central nervous system synapse.

TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X’s predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user’s web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researchers can use to better illuminate understudied proteins.

Abstract Seismic tomography of Earth's mantle images abundant slab remnants, often located in close proximity to active subduction systems. The impact of such remnants on the dynamics of subduction remains underexplored. Here, we use simulations of multi‐material free subduction in a 3‐D spherical shell geometry to examine the interaction between visco‐plastic slabs and remnants that are positioned above, within and below the mantle transition zone. Depending on their size, negatively buoyant remnants can set up mantle flow of similar strength and length scales as that due to active subduction. As such, we find that remnants located within a few hundred km from a slab tip can locally enhance sinking by up to a factor 2. Remnant location influences trench motion: the trench advances toward a remnant positioned in the mantle wedge region, whereas remnants in the sub‐slab region enhance trench retreat. These motions aid in rotating the subducting slab and remnant toward each other, reducing the distance between them, and further enhancing the positive interaction of their mantle flow fields. In this process, the trench develops along‐strike variations in shape that are dependent on the remnant's location. Slab‐remnant interactions may explain the poor correlation between subducting plate velocities and subducting plate age found in recent plate tectonic reconstructions. Our results imply that slab‐remnant interactions affect the evolution of subducting slabs and trench geometry. Remnant‐induced downwelling may also anchor and sustain subduction systems, facilitate subduction initiation, and contribute to plate reorganization events.

Abstract Background Using mouse genetic studies and systematic assessments of brain neuroanatomical phenotypes, we set out to identify which of the 30 genes causes brain defects at the autism-associated 16p11.2 locus. Results We show that multiple genes mapping to this region interact to regulate brain anatomy, with female mice exhibiting far fewer brain neuroanatomical phenotypes. In male mice, among the 13 genes associated with neuroanatomical defects (Mvp, Ppp4c, Zg16, Taok2, Slx1b, Maz, Fam57b, Bola2, Tbx6, Qprt, Spn, Hirip3, and Doc2a), Mvp is the top driver implicated in phenotypes pertaining to brain, cortex, hippocampus, ventricles, and corpus callosum sizes. The major vault protein (MVP), the main component of the vault organelle, is a conserved protein found in eukaryotic cells, yet its function is not understood. Here, we find MVP expression highly specific to the limbic system and show that Mvp regulates neuronal morphology, postnatally and specifically in males. We also recapitulate a previously reported genetic interaction and show that Mvp +/− ;Mapk3 +/− mice exhibit behavioral deficits, notably decreased anxiety-like traits detected in the elevated plus maze and open field paradigms. Conclusions Our study highlights multiple gene drivers in neuroanatomical phenotypes, interacting with each other through complex relationships. It also provides the first evidence for the involvement of the major vault protein in the regulation of brain size and neuroanatomy, specifically in male mice.