π-HuB: the proteomic navigator of the human body.

The human body contains trillions of cells, classified into specific cell types, with diverse morphologies and functions. In addition, cells of the same type can assume different states within an individual's body during their lifetime. Understanding the complexities of the proteome in the context of a human organism and its many potential states is a necessary requirement to understanding human biology, but these complexities can neither be predicted from the genome, nor have they been systematically measurable with available technologies.

Isolation, characterization, and immobilization of β-galactosidase from Klebsiella michiganensis B5582Y for enhanced transgalactosylation.

β-Galactosidases are highly desirable in various biotechnological applications. However, research on those obtained from Klebsiella strains has been noticeably restricted. The present investigation centers on the isolation, purification, and characterization of a β-galactosidase enzyme derived from Klebsiella michiganensis (GALB5582Y).

The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.

Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.

Effects of microfluidization time on the structural, physiochemical and functional properties of walnut protein.

The effect of microfluidization treatment time under a pressure of 1 MPa on the structural, physiochemical and functional properties of walnut protein (WP) were evaluated. The results showed that the particle size of WP was significantly reduced by 102.10 % and the absolute zeta potential, solubility, water holding capacity, foaming capacity and stability increased by 336.

Dynamic regulation of innate lymphoid cell development during ontogeny.

The helper-like ILC contains various functional subsets, such as ILC1, ILC2, ILC3 and LTi cells, mediating the immune responses against viruses, parasites, and extracellular bacteria, respectively. Among them, LTi cells are also crucial for the formation of peripheral lymphoid tissues, such as lymph nodes. Our research, along with others', indicates a high proportion of LTi cells in the fetal ILC pool, which significantly decreases after birth.

Detecting cell types and densities in the tumor microenvironment improves prognostic risk assessment for breast cancer.

A comprehensive evaluation of the relationship between the densities of various cell types in the breast cancer tumor microenvironment and patient prognosis is currently lacking. Additionally, the absence of a large patch-level whole slide imaging (WSI) dataset of breast cancer with annotated cell types hinders the ability of artificial intelligence to evaluate cell density in breast cancer WSI. We first employed Lasso-Cox regression to build a breast cancer prognosis assessment model based on cell density in a population study.

BioLadder: A bioinformatic platform primarily focused on proteomic data analysis.

BioLadder (https://www.bioladder.cn/) is an online data analysis platform designed for proteomics research, which includes three classes of experimental data analysis modules and four classes of common data analysis modules.

[Patient-derived renal pelvic carcinoma organoids: establishment and sensitivity to chemotherapeutic drugs].

Renal pelvic carcinoma is a common upper urothelial cancer. The lack of an ideal model seriously hinders the research progress in the treatment for this disease. This study established a pipeline for the culture of renal pelvic carcinoma organoids based on the tumor tissue samples derived from the patients and tested the organoids to chemotherapeutic drugs.

Quantitative Proteomics Analysis of Serum and Urine With DIA Mass Spectrometry Reveals Biomarkers for Pediatric Obstructive Sleep Apnea.

Objectives: Identification of suitable biomarkers that facilitate the screening and evaluation of pediatric obstructive sleep apnea (OSA) and its severity was explored.

Methods: Data-independent acquisition quantitative proteomic analysis was employed to identify serum and urine proteins with differential expression patterns between children with OSA and controls. Differentially expressed proteins that gradually increased or decreased with the severity of OSA were retained as potential biomarkers and underwent ELISA validation.

Characterization of a new style tofu coagulated by fermentation of Lactobacillus plantarum SJ-L-1.

A new style of tofu coagulated through the fermentation of Lactobacillus plantarum SJ-L-1 was produced. L. plantarum SJ-L-1 with a high growth rate and excellent acid production ability was isolated and identified from naturally fermented soy yellow whey.

Microencapsulated granaticins from YP1: Optimization, physiochemical characterization and storage stability.

Granaticins are natural pigments derived from microorganisms with promising bioactivity. However, their practical applications have been restricted due to inherent instability. To improve the stability of granaticins from the novel strain YP1, microcapsules were prepared using gum Arabic (GA) by a freeze-drying method.

Protocol for identifying and comparing molecular prognosis subtypes of IgAN using R.

By providing a comprehensive view of protein dynamics, quantitative proteomics has emerged as a powerful tool for a better understanding of disease mechanisms. Here, we present a general workflow for identifying and comparing molecular subtypes of disease using proteomics data using R software. We describe steps for data preprocessing, feature selection, determination of subtypes, and functional interpretation of subtypes.

Functionalized electrospun nanofibers to enhance β-Galactosidase immobilization and catalytic activity for efficient galactooligosaccharide synthesis.

This study aimed to immobilize β-galactosidase (β-GAL) into enhanced polystyrene (PS) electrospun nanofiber membranes (ENMs) with functionalized graphene oxide (GO). Initially, GO sheets were functionalized by salinization with 3-aminopropyl triethoxysilane (APTES). Then the ENMs (PS, PS/GO, and PS/GO-APTES) were prepared and characterized.

Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data.

Motivation: Multi-omics data provide a comprehensive view of gene regulation at multiple levels, which is helpful in achieving accurate diagnosis of complex diseases like cancer. However, conventional integration methods rarely utilize prior biological knowledge and lack interpretability.

Results: To integrate various multi-omics data of tissue and liquid biopsies for disease diagnosis and prognosis, we developed a biological pathway informed Transformer, Pathformer.

ACP-DRL: an anticancer peptides recognition method based on deep representation learning.

Cancer, a significant global public health issue, resulted in about 10 million deaths in 2022. Anticancer peptides (ACPs), as a category of bioactive peptides, have emerged as a focal point in clinical cancer research due to their potential to inhibit tumor cell proliferation with minimal side effects. However, the recognition of ACPs through wet-lab experiments still faces challenges of low efficiency and high cost.

Large-Scale Proteome Profiling Identifies Biomarkers Associated with Suspected Neurosyphilis Diagnosis.

Neurosyphilis (NS) is a central nervous system (CNS) infection caused by Treponema pallidum (T. pallidum). NS can occur at any stage of syphilis and manifests as a broad spectrum of clinical symptoms.

SARS-CoV-2-infected hiPSC-derived cardiomyocytes reveal dynamic changes in the COVID-19 hearts.

Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has had an enormous impact on our societies. Moreover, the disease's extensive and sustained symptoms are now becoming a nonnegligible medical challenge. In this respect, data indicate that heart failure is one of the most common readmission diagnoses among COVID-19 patients.

DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis.

Retention time (RT) alignment is a crucial step in liquid chromatography-mass spectrometry (LC-MS)-based proteomic and metabolomic experiments, especially for large cohort studies. The most popular alignment tools are based on warping function method and direct matching method. However, existing tools can hardly handle monotonic and non-monotonic RT shifts simultaneously.

COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods.

Summary: A variety of computational methods have been developed to identify functionally related gene modules from genome-wide gene expression profiles. Integrating the results of these methods to identify consensus modules is a promising approach to produce more accurate and robust results. In this application note, we introduce COMMO, the first web server to identify and analyze consensus gene functionally related gene modules from different module detection methods.

[Deciphering the dynamic characteristics of non-neuronal cells in dorsal root ganglion of rat at different developmental stage based on single cell transcriptome data].

Dorsal root ganglia (DRG) is an essential part of the peripheral nervous system and the hub of the peripheral sensory afferent. The dynamic changes of neuronal cells and their gene expression during the development of dorsal root ganglion have been studied through single-cell RNAseq analysis, while the dynamic changes of non-neuronal cells have not been systematically studied. Using single cell RNA sequencing technology, we conducted a research on the non-neuronal cells in the dorsal root ganglia of rats at different developmental stage.