Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases.

Intestinal lavage fluid (IVF) containing the mucosa-associated microbiota instead of fecal samples was used to study the gut microbiota using different omics approaches. Focusing on the 63 IVF samples collected from healthy and hepatitis B virus-liver disease (HBV-LD), a question is prompted whether omics features could be extracted to distinguish these samples. The IVF-related microbiota derived from the omics data was classified into two enterotype sets, whereas the genomics-based enterotypes were poorly overlapped with the proteomics-based one in either distribution of microbiota or of IVFs.

Strategies to decrease inequalities in cancer therapeutics, care and prevention: Proceedings on a conference organized by the Pontifical Academy of Sciences and the European Academy of Cancer Sciences, Vatican City, February 23-24, 2023.

Analyses of inequalities related to prevention and cancer therapeutics/care show disparities between countries with different economic standing, and within countries with high Gross Domestic Product. The development of basic technological and biological research provides clinical and prevention opportunities that make their implementation into healthcare systems more complex, mainly due to the growth of Personalized/Precision Cancer Medicine (PCM). Initiatives like the USA-Cancer Moonshot and the EU-Mission on Cancer and Europe's Beating Cancer Plan are initiated to boost cancer prevention and therapeutics/care innovation and to mitigate present inequalities.

Tracing the evolving dynamics and research hotspots of microbiota and immune microenvironment from the past to the new era.

Gut microbiota can regulate many physiological processes within gastrointestinal tract and other distal sites. Dysbiosis may not only influence chronic diseases like the inflammatory bowel disease (IBD), metabolic disease, tumor and its therapeutic efficacy, but also deteriorate acute injuries. This article aims to review the documents in this field and summarize the research hotspots as well as developing processes.

The metabolic state of the heart regulates mitochondrial supercomplex abundance in mice.

Mitochondrial supercomplexes are observed in mammalian tissues with high energy demand and may influence metabolism and redox signaling. Nevertheless, the mechanisms that regulate supercomplex abundance remain unclear. In this study, we examined the composition of supercomplexes derived from murine cardiac mitochondria and determined how their abundance changes with substrate provision or by genetically induced changes to the cardiac glucose-fatty acid cycle.

Identification and analysis of lignin biosynthesis genes related to fruit ripening and stress response in banana ( L. AAA group, cv. Cavendish).

Background: Lignin is a key component of the secondary cell wall of plants, providing mechanical support and facilitating water transport as well as having important impact effects in response to a variety of biological and abiotic stresses.

Results: In this study, we identified 104 genes from ten enzyme gene families related to lignin biosynthesis in genome and found the number of gene family was the largest, while s had only two members. s retained the original members, and the number of s in lignin biosynthesis was significantly less than that of flavonoids.

A bibliometric analysis of the role of microbiota in trauma.

Introduction: Over the last several decades, the gut microbiota has been implicated in the formation and stabilization of health, as well as the development of disease. With basic and clinical experiments, scholars are gradually understanding the important role of gut microbiota in trauma, which may offer novel ideas of treatment for trauma patients. In this study, we purposed to summarize the current state and access future trends in gut microbiota and trauma research.

First Evidence Indicates the Physiology- and Axial-Myopia-Dependent Profiles of Steroid Hormones in Aqueous Humor.

The quantitative level of steroid hormones (SHs) in some body fluids have been accepted for clinical diagnosis, whereas their distribution in aqueous humor (AH) is unknown yet. Herein, a profiling study was conducted with a total of 171 AH and 107 plasma samples using liquid chromatography coupled with tandem mass spectrometry (LC MS/MS). For the first time, six kinds of SHs in AH were quantitatively estimated, and their abundances were ranked at cortisol (F), corticosterone (COR), androstenedione (A2), and 11-deoxycortisol (11DOC).

Comparative plastomes of species provide new insights into the plastomes evolution and maternal phylogeny of the genus.

, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of and its two EA and NA major subclades, the maternal phylogeny of still need to be comprehensively evaluated.

A metagenome-wide association study of the gut microbiota in recurrent aphthous ulcer and regulation by thalidomide.

Recurrent aphthous ulcer (RAU), one of the most common diseases in humans, has an unknown etiology and is difficult to treat. Thalidomide is an important immunomodulatory and antitumor drug and its effects on the gut microbiota still remain unclear. We conducted a metagenomic sequencing study of fecal samples from a cohort of individuals with RAU, performed biochemical assays of cytokines, immunoglobulins and antimicrobial peptides in serum and saliva, and investigated the regulation effects of thalidomide administration and withdrawal.

Spatial transcriptomics technology in cancer research.

In recent years, spatial transcriptomics (ST) technologies have developed rapidly and have been widely used in constructing spatial tissue atlases and characterizing spatiotemporal heterogeneity of cancers. Currently, ST has been used to profile spatial heterogeneity in multiple cancer types. Besides, ST is a benefit for identifying and comprehensively understanding special spatial areas such as tumor interface and tertiary lymphoid structures (TLSs), which exhibit unique tumor microenvironments (TMEs).

Detecting and monitoring bladder cancer with exfoliated cells in urine.

Current methods for the diagnosis and monitoring of bladder cancer are invasive and have suboptimal sensitivity. Liquid biopsy as a non-invasive approach has been capturing attentions recently. To explore the ability of urine-based liquid biopsy in detecting and monitoring genitourinary tumors, we developed a method based on promoter-targeted DNA methylation of urine sediment DNA.

[Corrigendum] TP53 and RET may serve as biomarkers of prognostic evaluation and targeted therapy in hepatocellular carcinoma.

Subsequently to the publication of the above article, the authors have realized that a couple of clerical errors were made when writing the article, and wish to correct these errors in a corrigendum statement. First, in the Materials and methods section on p. 2216, the final sentence of the '' subsection, the authors wish to add a further definition, so that the text reads as follows (changes highlighted in bold): '; high expression was defined as ≥40% staining of a tumor section, and low expression as <40%'.

Single-Cell Transcriptomics Reveals Killing Mechanisms of Antitumor Cytotoxic CD4 TCR-T Cells.

T cell receptor-engineered T cells (TCR-Ts) have emerged as potent cancer immunotherapies. While most research focused on classical cytotoxic CD8 T cells, the application of CD4 T cells in adoptive T cell therapy has gained much interest recently. However, the cytotoxic mechanisms of CD4 TCR-Ts have not been fully revealed.

Identification of a 3-Gene Model as Prognostic Biomarker in Patients With Gastric Cancer.

Objective: Although the incidence of gastric cancer (GC) is decreasing, GC remains one of the leading cancers in the world. Surgical resection, radiotherapy, chemotherapy, and neoadjuvant therapy have advanced, but patients still face the risk of recurrence and poor prognosis. This study provides new insights for assessment of prognosis and postoperative recurrence of GC patients.

Whole-Genome Resequencing Deciphers New Insight Into Genetic Diversity and Signatures of Resistance in Cultivated Cotton Gossypium hirsutum.

Cotton is an important crop that produces fiber and cottonseed oil for the textile and oil industry. However, cotton leaf curl virus disease (CLCuD) stress is limiting its yield in several Asian countries. In this study, we have sequenced Mac7 accession, a Gossypium hirsutum resistance source against several biotic stresses.

Automated Multi-View Multi-Modal Assessment of COVID-19 Patients Using Reciprocal Attention and Biomedical Transform.

Automated severity assessment of coronavirus disease 2019 (COVID-19) patients can help rationally allocate medical resources and improve patients' survival rates. The existing methods conduct severity assessment tasks mainly on a unitary modal and single view, which is appropriate to exclude potential interactive information. To tackle the problem, in this paper, we propose a multi-view multi-modal model to automatically assess the severity of COVID-19 patients based on deep learning.

Urine-Derived Stem Cells Express 571 Neuromuscular Disorders Causing Genes, Making Them a Potential Model for Rare Genetic Diseases.

Neuromuscular disorders (NMDs) are a heterogeneous group of genetic diseases, caused by mutations in genes involved in spinal cord, peripheral nerve, neuromuscular junction, and muscle functions. To advance the knowledge of the pathological mechanisms underlying NMDs and to eventually identify new potential drugs paving the way for personalized medicine, limitations regarding the availability of neuromuscular disease-related biological samples, rarely accessible from patients, are a major challenge. We characterized urinary stem cells (USCs) by in-depth transcriptome and protein profiling to evaluate whether this easily accessible source of patient-derived cells is suitable to study neuromuscular genetic diseases, focusing especially on those currently involved in clinical trials.

Network of Interactions Between Gut Microbiome, Host Biomarkers, and Urine Metabolome in Carotid Atherosclerosis.

Comprehensive analyses of multi-omics data may provide insights into interactions between different biological layers concerning distinct clinical features. We integrated data on the gut microbiota, blood parameters and urine metabolites of treatment-naive individuals presenting a wide range of metabolic disease phenotypes to delineate clinically meaningful associations. Trans-omics correlation networks revealed that candidate gut microbial biomarkers and urine metabolite feature were covaried with distinct clinical phenotypes.

Chromosome-scale assembly and high-density genetic map of the yellow drum, Nibea albiflora.

The yellow drum (Nibea albiflora) is an economically important sciaenid fish in East Asian countries. In this study, we sequenced and assembled a near-complete gynogenetic yellow drum genome. We generated 45.

"Integrating China in the International Consortium for Personalized Medicine": The Coordination and Support Action to Foster Collaboration in Personalized Medicine Development between Europe and China.

"Integrating China in the International Consortium for Personalized Medicine" (IC2PerMed) is a coordination and support action funded within the Horizon 2020 work program. Following the guidance of the International Consortium for Personalized Medicine (ICPerMed), the project's overarching aim is to align the European Union and China's research agendas in the field of personalized medicine (PM) to enable a swift development of PM approaches in the EU with strong leverage upon EU-Chinese collaboration. Living in the CO-VID-19 era, we are witnessing how the challenges imposed by the pandemic all around the globe have been acting as a catalyst for collaborations and knowledge sharing among national health systems worldwide.

Colonic Dopaminergic Neurons Changed Reversely With Those in the Midbrain via Gut Microbiota-Mediated Autophagy in a Chronic Parkinson's Disease Mice Model.

The role of gut-brain axis in the pathogenesis of Parkinson's disease (PD) have become a research hotspot, appropriate animal model to study gut-brain axis in PD is yet to be confirmed. Our study employed a classical PD mice model achieved by chronic MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) injection to study concurrent changes of dopaminergic neurons in the midbrain and the colon of mice. Our results showed such a PD model exhibited apparent locomotor deficits but not gastrointestinal dysfunction.

Application of Copy Number Variation Detection to Fetal Diagnosis of Echogenic Intracardiac Focus During Pregnancy.

Echogenic intracardiac focus (EIF) is one of the most common ultrasound soft markers (USMs) in prenatal screening. However, the association of EIF with chromosomal abnormalities is still controversial. From January 2018 to April 2020, a total of 571 fetuses with USMs in our center were enrolled, among which 150 (26.

PacBio Long Reads Improve Metagenomic Assemblies, Gene Catalogs, and Genome Binning.

PacBio long reads sequencing presents several potential advantages for DNA assembly, including being able to provide more complete gene profiling of metagenomic samples. However, lower single-pass accuracy can make gene discovery and assembly for low-abundance organisms difficult. To evaluate the application and performance of PacBio long reads and Illumina HiSeq short reads in metagenomic analyses, we directly compared various assemblies involving PacBio and Illumina sequencing reads based on two anaerobic digestion microbiome samples from a biogas fermenter.