The rockefeller university

Cell types are fundamental functional units that can be traced across the tree of life. Rapid advances in single-cell technologies, coupled with the phylogenetic expansion in genome sequencing, present opportunities for the molecular characterization of cells across a broad range of organisms. Despite these developments, our understanding of eukaryotic cell diversity remains limited and we are far from decoding this diversity from genome sequences. Here we introduce the Biodiversity Cell Atlas initiative, which aims to create comprehensive single-cell molecular atlases across the eukaryotic tree of life. This community effort will be phylogenetically informed, rely on high-quality genomes and use shared standards to facilitate comparisons across species. The Biodiversity Cell Atlas aspires to deepen our understanding of the evolution and diversity of life at the cellular level, encompassing gene regulatory programs, differentiation trajectories, cell-type-specific molecular profiles and inter-organismal interactions.

Caloric restriction (CR) is a well-studied intervention that extends lifespan and slows cognitive decline across species, yet the specific cell populations and molecular pathways involved remain elusive. In this study, we profiled >500,000 cells from 36 control and CR mouse brains across three age groups with EasySci single-nucleus transcriptomics and performed imaging-free IRISeq spatial transcriptomics on twelve brain sections from CR and control aged mice. We thereby explored the impact of CR in >300 cellular states and 11 brain regions. CR delayed expansion of inflammatory cell populations, preserved neural precursor cells, and broadly reduced the expression of aging-associated genes involved in cellular stress, senescence, inflammation, and DNA damage. CR restored the expression of region-specific genes linked to cognitive function, myelin maintenance, and circadian rhythm. In summary, we provide a high-resolution spatiotemporal map of the aging mouse brain's response to CR, detailing precise cellular and molecular mechanisms behind its neuroprotective effects.

Fluorescence imaging enables visualization of the specific molecules of interest with high contrast, and the use of multiple fluorophores in a single tissue sample allows visualization of complex relationships between biological molecules, cell types, and anatomy. The utility of fluorescence imaging in human tissue has been limited by endogenous pigments that can block the light path or emit an autofluorescence, thereby interfering with the specific imaging of target molecules. Although photobleachers have been developed to quench endogenous pigments, the lack of customizability limits their utility for a broad range of applications. Here, we present a high luminous-intensity photobleacher that is based on rigorous simulations of illumination patterns, along with the framework to maximize bleaching efficiency. This open-source project is designed to help scientists customize and scale the device according to their research goals. The photobleacher is applicable to both thin tissue slices and large-volume cleared tissue samples to enable serial three-dimensional imaging of postmortem human brain using multiplexed antibody or oligonucleotide probes.

Measurements of the production yields of charm baryons (Lambda(+)(c)) and charm mesons (D-0) in proton-lead collisions at a nucleon-nucleon center-of-mass energy of 8.16 TeV are presented. The data were collected in 2016 with the CMS experiment and correspond to an integrated luminosity of 186 nb(-1). The Lambda(+)(c) baryon is reconstructed from the decay channel Lambda(+)(c) -> K(S)(0)p, while the D-0 meson is reconstructed via D-0 -> K- pi(+). The Lambda(+)(c) baryon and D-0 meson yields are extracted in several charged-particle multiplicity classes. No strong multiplicity dependence of the Lambda(+)(c) -to-D-0 yield ratio is observed, unlike the observed strange baryon to strange meson yield ratio of Lambda/(Lambda) over bar to K-S(0), which shows a strong multiplicity dependence. This observation indicates different mechanisms for the multiplicity evolution of hadronization processes for charm and strange quarks and provides new constraints to the understanding of heavy flavor production and collectivity in small collision systems.

Human monogenic traits can confer resistance to viral disease in infected individuals. Enhanced susceptibility can be driven directly by mutations in genes essential for control of the virus or indirectly via the production of autoantibodies against components of host defense. While the impact of viruses on individuals carrying these genotypes permitted their identification and has been amply studied, little is known about the impact of these human genotypes on the natural history of viruses, including not only persisting but also emerging viruses. We envisage several scenarios, including the possibility that genetically susceptible individuals serve as patient zeros, superspreaders, or mutation incubators, or that genetically resistant individuals even permit the selection of new viral mutants. Viruses are continually shared between individuals and even host species, where they can benefit from adaption to new environments. Current human viruses, as well as novel viruses from animal reservoirs, will continue to threaten the human population. Improvements in the scale of human genomic sequencing and analysis will permit testing hypotheses about the impact of human genetics on the origin and trajectory of viral infections, including future pandemics, which may ultimately help to prevent or curtail impending outbreaks.

Minimally invasive sampling of the skin using tape strips for conducting biomarker research is a growing research area in medical dermatology. The goal of this study was to utilise tape strip sampling to investigate changes in protein skin levels of psoriasis patients after oral treatment with orismilast (a PDE4B/D inhibitor). The proteins were measured in extracts of tape-strip samples taken from the skin of patients with moderate-severe psoriasis participating in a 16-week Ph2b study (IASOS). The proteins were measured using the Olink technology or an ELISA assay. Our results show that protein levels of multiple proteins (32/71) were upregulated at baseline in the lesional skin compared to non-lesional skin, including three key biomarkers of the psoriasis disease pathology (IL-17A, CCL20 and TNF alpha). The protein levels of these three biomarkers were significantly reduced at Week 16, reaching a percent reduction of 52% and 51% for IL-17A, 66% and 60% for TNF alpha, and 41% and 54% for CCL20 for the two doses analysed (20 and 30 mg bid, respectively). In addition, we observed that the clinical response of a 75% reduction in PASI (PASI75) was associated with a 98% reduction in IL-17A protein levels in lesional skin, irrespective of the orismilast dose. In summary, a significant reduction of key proteins related to the TH17 axis and TH1 axis was observed in the skin of psoriasis patients after treatment with oral orismilast, supporting the observed clinical effect. Finally, this constitutes the first report where protein levels from the skin of psoriasis patients are quantified using tape strips as a minimally invasive skin sampling technology in combination with the Olink technology.Trial Registration: ClinicalTrials.gov identifier: NCT05190419

Motivation Large sequencing datasets are being produced and deposited into public archives at unprecedented rates. The availability of tools that can reliably and efficiently generate and store sequencing read summary statistics has become critical.Results As part of the effort by the Vertebrate Genomes Project (VGP) to generate high-quality reference genomes at scale, we sought to address the community's need for efficient sequence data evaluation by developing rdeval, a standalone tool to quickly compute and interactively display sequencing read metrics. Rdeval can either run on the fly or store key sequence data metrics in tiny read 'snapshot' files. Statistics can then be efficiently recalled from snapshots for additional processing. Rdeval can convert fa*[.gz] files to and from other popular formats including BAM and CRAM for better compression. Overall, while CRAM achieves the best compression, the gain compared to BAM is marginal, and BAM achieves the best compromise between data compression and access speed. Rdeval also generates a detailed visual report with multiple data analytics that can be exported in various formats. We showcase rdeval's functionalities using long-read data from different sequencing platforms and species, including human. For PacBio long-read sequencing, our analysis shows dramatic improvements in both read length and quality over time, as well as the benefit of increased coverage for genome assembly, though the magnitude varies by taxa.Availability and implementation Rdeval is implemented in C++ for data processing and in R for data visualization. Precompiled releases (Linux, MacOS, Windows) and commented source code for rdeval are available under MIT license at https://github.com/vgl-hub/rdeval. Documentation is available on ReadTheDocs (https://rdeval-documentation.readthedocs.io). Rdeval is also available in Bioconda and in Galaxy (https://usegalaxy.org). An automated test workflow ensures the consistency of software updates.

The transporter associated with antigen processing (TAP) delivers peptide antigens from the cytoplasm into the endoplasmic reticulum (ER) for loading onto major histocompatibility complex class I (MHC-I) molecules. To examine the mechanisms of peptide transport and release into the ER, we determined cryo-electron microscopy structures of the human TAP heterodimer in multiple functional states along the transport cycle. In the inward-facing conformation, when the peptide translocation cavity within the TAP heterodimer is exposed to the cytosol, ATP binding strengthened intradomain assembly. Transition to the outward-facing conformation, when the transporter opens to the ER lumen, led to a complete reconfiguration of the peptide-binding site, facilitating peptide release. ATP hydrolysis opened the catalytically active nucleotide-binding consensus site, and the subsequent separation of the nucleotide-binding domains reset the transport cycle. These findings establish a comprehensive structural framework for understanding unilateral peptide transport, vanadate trapping, and trans-inhibition-an internal feedback mechanism that prevents excessive peptide accumulation and activation of the ER stress response.

A goal of data visualization is to advance the understanding of multiparameter, large-scale datasets. In astrophysics, scientists map celestial objects to understand the hierarchical structure of the universe. In biology, genetic sequences and biological characteristics uncover evolutionary relationships and patterns (e.g., variation within species and ecological associations). Our highly interdisciplinary project entitled "A Cosmic View of Life on Earth" adapts an immersive astrophysics visualization platform called OpenSpace to contextualize diverse biological data. Dimensionality reduction techniques harmonize biological information to create spatial representations in which data are interactively explored on flat screens and planetarium domes. Visualizations are enriched with geographic metadata, 3-D scans of specimens, and species-specific sonifications (e.g., bird songs). The "Cosmic View" project eases the dissemination of stories related to biological domains (e.g., insects, birds, mammals, and human migrations) and facilitates scientific discovery.

Neurodegenerative diseases present one of the most significant global health challenges. These disorders are defined by the accumulation of abnormal protein aggregates that impair synaptic function and cause progressive neuronal degeneration. Therefore, stimulating protein clearance mechanisms may be neuroprotective. Variants in FBXO7/ PARK15 cause Parkinsonian Pyramidal Syndrome, an early-onset parkinsonian neurodegenerative disorder in humans, and inactivation of this gene in mice recapitulates many phenotypes seen in patients. The proteasome regulator PI31 is a direct binding partner of Fbxo7 and promotes local protein degradation at synapses by mediating fast proteasome transport in neurites. PI31 protein levels are reduced when the function of Fbxo7 is impaired. Here we show that restoring PI31 levels in Fbxo7 mutant fly and mouse strains prevents neuronal degeneration and significantly improves neuronal function, health, and lifespan. Notably, Fbxo7 inactivation in mouse neurons causes hyperphosphorylation of tau, and this was suppressed by transgenic expression of PI31. Our results demonstrate that PI31 is a crucial biological target through which Fbxo7 deficiency drives pathology. Therefore, targeting the PI31-pathway may represent a promising therapeutic approach for treating neurodegenerative disorders.