Advances and applications in single-cell and spatial genomics.

The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics.

snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses.

Differences in prognostic outcomes are prevalent in patients with colorectal cancer liver metastases. Comparative analysis of tissue samples, particularly applying single-cell transcriptome sequencing technology, can provide a deeper understanding of potential impacting factors. However, long-term monitoring for prognosis determination necessitates extended preservation of tissue samples using formalin-fixed and paraffin-embedded (FFPE) treatments, which can cause substantial RNA degradation, presenting challenges to single-cell or single-nucleus sequencing.

High-Throughput Single-Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer.

Puncture biopsy, especially those preserved by formalin fixed paraffin embedding (FFPE) samples, play an important role in various research purposes. Diverse single-nucleus RNA sequencing (snRNA-seq) techniques have been developed for FFPE samples, however, how to perform high-throughput snRNA-seq on small FFPE puncture samples is still a challenge. Here, the previously developed snRNA-seq technique (snRandom-seq) is optimized by implementing a pre-indexing procedure for the minimal puncture FFPE samples.

2-Acetamidophenol (2-AAP) Suppresses the Progression of Atherosclerosis by Alleviating Hyperlipidemia and Attenuating the Ferroptosis Pathway.

Hyperlipidemia and consequent endothelial inflammation, along with foam cell generation, promote the progression of atherosclerosis (AS). Here, we aimed to investigate the effects of 2-acetamidophenol (2-AAP), which was selected by zebrafish phenotypic screening, in alleviating AS by relieving hyperlipidemia and inhibiting foam cell formation, as well as the underlying mechanisms. In a zebrafish hyperlipidemia model, 2-AAP increased lipid-lowering efficacy; alleviated TC, TG, LDL-C, and MDA levels; elevated HDL-C and T-SOD levels; significantly improved intravascular macrophage aggregation; and improved blood flow.

Study on the enhancement of low carbon-to-nitrogen ratio urban wastewater pollutant removal efficiency by adding sulfur electron acceptors.

The effective elimination of nitrogen and phosphorus in urban sewage treatment was always hindered by the deficiency of organic carbon in the low C/N ratio wastewater. To overcome this organic-dependent barrier and investigate community changes after sulfur electron addition. In this study, we conducted a simulated urban wastewater treatment plant (WWTP) bioreactor by using sodium sulfate as an electron acceptor to explore the removal efficiency of characteristic pollutants before and after the addition of sulfur electron acceptor.

Characterization of the flavor profile of four major Chinese carps using HS-SPME-GC-MS combined with ultra-fasted gas chromatography-electronic nose.

The four major Chinese carps are highly popular for their distinctive nutritional benefits. However, the differences in flavor among these carps remain unclear. This study investigated the flavor profiles of these carps using headspace solid-phase micro-extraction gas chromatography-mass spectrometry (HS-SPME-GC/MS) combined with ultra-fasted gas chromatography electronic nose (GC E-nose).

Exposure to per- and polyfluoroalkyl substances is associated with impaired cardiovascular health: a cross-sectional study.

Background: Per- and polyfluoroalkyl substance (PFAS) exposure and cardiovascular disease are controversial. We aimed to assess the association between serum PFAS exposure and cardiovascular health (CVH) in U.S.

Shift Work Increases the Risk of Circadian Syndrome Rather than Metabolic Syndrome: A Cross-Sectional Study of NHANES 2005-2010.

Shift work disrupts sleep-wake cycles and may lead to adverse health outcomes, including cardiovascular disease and metabolic disorders. This study examines the association between shift work and the risks of metabolic syndrome (MetS) and circadian syndrome (CircS) in U.S.

Hosts manipulate lifestyle switch and pathogenicity heterogeneity of opportunistic pathogens in the single-cell resolution.

Host-microbe interactions are virtually bidirectional, but how the host affects their microbiome is poorly understood. Here, we report that the host is a critical modulator to regulate the lifestyle switch and pathogenicity heterogeneity of the opportunistic pathogens utilizing the and bacterium model system. First, we find that larvae efficiently outcompete and typically drive a bacterial switch from pathogenicity to commensalism toward the fly.

Developments of electrospinning technology in membrane bioreactor: A review.

The necessity for effective wastewater treatment and purification has grown as a result of the increasing pollution issues brought on by industrial and municipal wastewater. Membrane bioreactor (MBR) technology stands out when compared to other treatment methods because of its high efficiency, environmental friendliness, small footprint, and ease of maintenance. However, the development and application of membrane bioreactors has been severely constrained by the higher cost and shorter service life of these devices brought on by membrane biofouling issues resulting from contaminants and bacteria in the water.

Association between frailty index based on laboratory tests and all-cause mortality in critically ill patients with heart failure.

Background: The frailty index based on laboratory tests (FI-lab) can identify individuals at increased risk for adverse health outcomes. The association between the FI-lab and all-cause mortality in patients with heart failure (HF) in the intensive care unit (ICU) remains unknown. This study aimed to determine the correlation between FI-lab and all-cause mortality to evaluate the impact of FI-lab on the prognosis of critically ill patients with HF.

Single Nucleus Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Gliomas.

Gliomas, the predominant form of brain cancer, comprise diverse malignant subtypes with limited curative therapies available. The insufficient understanding of their molecular diversity and evolutionary processes hinders the advancement of new treatments. Technical complexities associated with formalin-fixed paraffin-embedded (FFPE) clinical samples hinder molecular-level analyses of gliomas.

Efficacy and safety of the Chinese herbal medicine Bu-Shen-Huo-Xue granule for the treatment of coronary heart disease: study protocol for a multicenter, randomized, double-blinded, placebo-controlled clinical trial.

Background: Coronary heart disease (CHD) is representative of cardiovascular disease and the leading cause of death in humans. Previous studies have shown that kidney disease is associated with CHD, and current treatment options that can improve both cardiac and renal functions still have some limitations. The traditional Chinese medicine Bu-Shen-Huo-Xue granule (BSHXG) can promote blood rheology, inhibit platelet agglutination, and improve heart and kidney functions.

Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome.

Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome.

High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome.

Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications in health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve comprehensive understanding of complex microbial communities together with their hosts is therefore utterly needed.

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nuclei using Microwell-seq3.

Single cell chromatin accessibility profiling and transcriptome sequencing are the most widely used technologies for single-cell genomics. Here, we present Microwell-seq3, a high-throughput and facile platform for high-sensitivity single-nucleus chromatin accessibility or full-length transcriptome profiling. The method combines a preindexing strategy and a penetrable chip-in-a-tube for single nucleus loading and DNA amplification and therefore does not require specialized equipment.

Association between dietary live microbe intake and Life's Essential 8 in US adults: a cross-sectional study of NHANES 2005-2018.

Background: Assessing the impact of dietary live microbe intake on health outcomes has gained increasing interest. This study aimed to elucidate the relationship between dietary live microbe intake and Life's Essential 8 (LE8) scores, a metric for cardiovascular health (CVH), in the U.S.

Bibliometric analysis of residual cardiovascular risk: trends and frontiers.

Background: The presence of residual cardiovascular risk is an important cause of cardiovascular events. Despite the significant advances in our understanding of residual cardiovascular risk, a comprehensive analysis through bibliometrics has not been performed to date. Our objective is to conduct bibliometric studies to analyze and visualize the current research hotspots and trends related to residual cardiovascular risk.

Pan-Cancer Single-Nucleus Total RNA Sequencing Using snHH-Seq.

Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single-cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA-seq amplify the termini of polyadenylated transcripts, making it challenging to perform total RNA analysis and somatic mutation analysis.

OpenNAU: An open-source platform for normalizing, analyzing, and visualizing cancer untargeted metabolomics data.

Objective: As an important part of metabolomics analysis, untargeted metabolomics has become a powerful tool in the study of tumor mechanisms and the discovery of metabolic markers with high-throughput spectrometric data which also poses great challenges to data analysis, from the extraction of raw data to the identification of differential metabolites. To date, a large number of analytical tools and processes have been developed and constructed to serve untargeted metabolomics research. The different selection of analytical tools and parameter settings lead to varied results of untargeted metabolomics data.