Regulation of protein abundance in normal human tissues.

We report a systematic quantification of 10,841 unique proteins from over 700 GTEx samples, representing five human tissues. Sex, age and genetic factors are associated with variation in protein abundance. In total, 1981 cis-protein quantitative trait loci (cis-pQTL) are identified, of which a majority of protein targets have not been assayed in the recent plasma-based proteogenomic studies.

The 40S ribosomal subunit recycling complex modulates mitochondrial dynamics and endoplasmic reticulum - mitochondria tethering at mitochondrial fission/fusion hotspots.

The 40S ribosomal subunit recycling pathway is an integral link in the cellular quality control network, occurring after translational errors have been corrected by the ribosome-associated quality control (RQC) machinery. Despite our understanding of its role, the impact of translation quality control on cellular metabolism remains poorly understood. Here, we reveal a conserved role of the 40S ribosomal subunit recycling (USP10-G3BP1) complex in regulating mitochondrial dynamics and function.

Improving design and normalization of multiplex proteomics study.

Advances in multiplex mass spectrometry-based technologies have enabled high-throughput, quantitative proteome profiling of large cohort. However, certain experimental design configurations can amplify sample variability and introduce systematic biases. To address these challenges, we incorporated two novel features in a recent proteogenomic investigation: (1) the inclusion of two reference samples within each mass spectrometry run to serve as internal standards, and (2) the analysis of each specimen as technical replicates across two distinct mass spectrometry runs.

Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis.

Familial adenomatous polyposis (FAP) is a genetic disease causing hundreds of premalignant polyps in affected persons and is an ideal model to study transitions of early precancer states to colorectal cancer (CRC). We performed deep multiomic profiling of 93 samples, including normal mucosa, benign polyps and dysplastic polyps, from six persons with FAP. Transcriptomic, proteomic, metabolomic and lipidomic analyses revealed a dynamic choreography of thousands of molecular and cellular events that occur during precancerous transitions toward cancer formation.

Structure and topography of the synaptic V-ATPase-synaptophysin complex.

Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a well-defined interface between the synaptic vesicle V-ATPase and synaptophysin by in situ cryo-electron tomography and single-particle cryo-electron microscopy of functional synaptic vesicles isolated from mouse brains. The synaptic vesicle V-ATPase is an ATP-dependent proton pump that establishes the proton gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters.

Integrative multi-omics profiling in human decedents receiving pig heart xenografts.

In a previous study, heart xenografts from 10-gene-edited pigs transplanted into two human decedents did not show evidence of acute-onset cellular- or antibody-mediated rejection. Here, to better understand the detailed molecular landscape following xenotransplantation, we carried out bulk and single-cell transcriptomics, lipidomics, proteomics and metabolomics on blood samples obtained from the transplanted decedents every 6 h, as well as histological and transcriptomic tissue profiling. We observed substantial early immune responses in peripheral blood mononuclear cells and xenograft tissue obtained from decedent 1 (male), associated with downstream T cell and natural killer cell activity.

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease.

Unlabelled: To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment.

Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice.

Genetic variation accounts for much of the risk for developing a substance use disorder, but the underlying genetic factors and their genetic effector mechanisms are mostly unknown. Inbred mouse strains exhibit substantial and heritable differences in the extent of voluntary cocaine self-administration. Computational genetic analysis of cocaine self-administration data obtained from twenty-one inbred strains identified Nav1, a member of the neuron navigator family that regulates dendrite formation and axonal guidance, as a candidate gene.

Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos.

As our closest living relatives, non-human primates uniquely enable explorations of human health, disease, development, and evolution. Considerable effort has thus been devoted to generating induced pluripotent stem cells (iPSCs) from multiple non-human primate species. Here, we establish improved culture methods for chimpanzee (Pan troglodytes) and pig-tailed macaque (Macaca nemestrina) iPSCs.

Transcriptome variation in human tissues revealed by long-read sequencing.

Regulation of transcript structure generates transcript diversity and plays an important role in human disease. The advent of long-read sequencing technologies offers the opportunity to study the role of genetic variation in transcript structure. In this Article, we present a large human long-read RNA-seq dataset using the Oxford Nanopore Technologies platform from 88 samples from Genotype-Tissue Expression (GTEx) tissues and cell lines, complementing the GTEx resource.

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes.

A central question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into 'co-essential' pathways, but this approach has been limited by ubiquitous false positives. In the present study, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules.

Intriguing hierarchical Co@NC microflowers in situ assembled by nanoneedles: Towards enhanced reduction of nitroaromatic compounds via interfacial synergistic catalysis.

Developing highly efficient and cost-effective catalyst with tuned microstructure holds great promise in the reduction of nitroaromatic compounds under mild reaction conditions. Herein, we report a new Co@NC-MF catalyst with a fascinating hierarchical flower-like architecture in situ assembled from uniform Co@NC nanoneedles, which can function as a favorable platform for the efficient reduction of nitroaromatic compounds in the presence of NaBH. In addition with the structural advantage, the characterization and experimental results demonstrate the enormous advantage of interfacial synergistic catalysis in enhancing the catalytic performance.

RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data.

Motivation: Data normalization is an important step in processing proteomics data generated in mass spectrometry experiments, which aims to reduce sample-level variation and facilitate comparisons of samples. Previously published methods for normalization primarily depend on the assumption that the distribution of protein expression is similar across all samples. However, this assumption fails when the protein expression data is generated from heterogenous samples, such as from various tissue types.

A Quantitative Proteome Map of the Human Body.

Determining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from over 12,000 genes across 32 normal human tissues. Tissue-specific or tissue-enriched proteins were identified and compared to transcriptome data.

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding.

Background: Macaque species share >93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g., HIV and neurodegenerative diseases).

Density functional theory study of selective aerobic oxidation of cyclohexane: the roles of acetic acid and cobalt ion.

A computational study of cyclohexane autoxidation and catalytic oxidation to a cyclohexyl hydroperoxide intermediate (CyOOH), cyclohexanol, and cyclohexanone has been conducted using a hybrid density functional theory method. The activation of cyclohexane and O is the rate-determining step in the formation of CyOOH due to its relatively high energy barrier of 41.2 kcal/mol, and the subsequent reaction behavior of CyOOH controls whether the production of cyclohexanol or cyclohexanone is favored.

Highly selective oxidation of styrene to benzaldehyde over a tailor-made cobalt oxide encapsulated zeolite catalyst.

A tailor-made catalyst with cobalt oxide particles encapsulated into ZSM-5 zeolites (CoO@HZSM-5) was prepared via a hydrothermal method with the conventional impregnated CoO/SiO catalyst as the precursor and Si source. Various characterization results show that the CoO@HZSM-5 catalyst has well-organized structure with CoO particles compatibly encapsulated in the zeolite crystals. The CoO@HZSM-5 catalyst was employed as an efficient catalyst for the selective oxidation of styrene to benzaldehyde with hydrogen peroxide as a green and economic oxidant.