Characterization of the transcriptional response of Candida parapsilosis to the antifungal peptide MAF-1A.

Candida parapsilosis is a major fungal pathogen that leads to sepsis. New and more effective antifungal agents are required due to the emergence of resistant fungal strains. MAF-1A is a cationic antifungal peptide isolated from Musca domestica that is effective against a variety of Candida species.

KIF4A: A potential biomarker for prediction and prognostic of prostate cancer.

Purpose: To investigate the clinical relevance and biological function of the kinesin super-family protein 4A (KIF4A) expression in prostate cancer (PCa).

Methods: We examined 1) the relationship between the expression of KIF4A and clinico-pathological characteristics of PCa patients using a tissue microarray and the Cancer Genome Atlas database, 2) the prognostic value of KIF4A expression in patients using Kaplan-Meier plots and 3) the functions of KIF4A in LNCaP and DU145 cells, such as cell proliferation, cell cycle and cell apoptosis.

Results: Compared with normal prostate, the mRNA and protein expressions of KIF4A were up-regulated in PCa.

Prognostic and predictive value of a DNA methylation-driven transcriptional signature in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. DNA methylation alterations are frequently observed in malignant tumours and play critical roles in the development of cancers, including HCC. To provide novel clinical prognosis biomarkers for HCC patients, we first performed a comprehensive analysis and identified a collection of prognosis-associated genes with DNA methylation-driven expression dysregulation in HCCs.

Autophagy inhibition enhances the inhibitory effects of ursolic acid on lung cancer cells.

The aim of the present study was to identify natural compounds that bear significant anti‑tumor activity. Thus, the effects of 63 small molecules that were isolated from traditional Chinese medicinal herbs on A549 human non‑small cell lung cancer (NSCLC) and MCF‑7 breast cancer cells were examined. It was found that ursolic acid (UA), a natural pentacyclic triterpenoid, exerted significant inhibitory effect on these cells.

Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches.

COVID-19 has recently become the most serious threat to public health, and its prevalence has been increasing at an alarming rate. The incubation period for the virus is ~1-14 days and all age groups may be susceptible to a fatality rate of about 5.9%.

BAP1 regulates AMPK-mTOR signalling pathway through deubiquitinating and stabilizing tumour-suppressor LKB1.

Liver kinase B1 (LKB1), a tumour suppressor, participates in many cellular processes, including cell survival, growth, apoptosis, transformation, and metabolism. Upon performing yeast two-hybrid screening, co-immunoprecipitation, and GST pull-down, we identified that BRCA1-associated protein 1 (BAP1), a deubiquitinase, interacts with LKB1. Immunoblotting was performed to examine the effect of BAP1 on the activation of 5' AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR), downstream of LKB1.

Ubiquitin-specific peptidase 46 promotes tumor metastasis through stabilizing ENO1 in human esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) has high aggressiveness and poor prognosis, and is the major histological subtype of esophageal cancer in East Asia and East Africa. In this study, we found that USP46, a deubiquitinating enzyme, is overexpressed in clinical ESCC samples, especially in patients with positive lymph node metastasis. Moreover, USP46 enhances the migration and invasion of ESCC cells by mediating the EMT process in vitro, and promotes lymph nodes and lung metastasis of ESCC in vivo.

Dietary phosphorus intake and serum prostate-specific antigen in non-prostate cancer American adults: A secondary analysis of the National Health and Nutrition Examination Survey (NHANES), 2003-2010.

Background And Objectives: Previous study has reported phosphorus intake is associated prostate cancer (PCa), but the association between phosphorus intake and serum prostate specific antigen (PSA) levels hasn't been reported in non-history of PCa population. Therefore, we performed a secondary data analysis based on existing data from the public Nutrition Examination Survey (NHANES) (2003-2010) database.

Methods And Study Design: Totally 6403 participants were selected from NHANES (2003-2010) database.

Long Noncoding RNA Regulates the Proliferation, Migration, and Apoptosis of Human Venous Endothelial Cells via SMYD3.

Numerous studies have shown that long noncoding RNAs (lncRNAs) play essential roles in the development and progression of human cardiovascular diseases. However, whether lncRNA ezrin antisense RNA 1 () is associated with the progression of coronary heart disease (CHD) remains unclear. Accordingly, the aim of the present study was to evaluate the role of lncRNA in patients with CHD and in human venous endothelial cells (HUVECs).

Therapeutic effect of 1,25(OH)2-VitaminD3 on fibrosis and angiogenesis of peritoneum induced by chlorhexidine.

The biological activity of vitamin D, which mediated by the vitamin D receptor, is widespread throughout the body. The present study aimed to define whether 1,25-dihydroxy vitamin D3 (1,25-(OH)2D3) can protect against the progression of peritoneum fibrosis (PF) through its impact on the expression of connective tissue growth factor (CTGF) and heat shock protein 47 (HSP47) in vivo and in vitro. The male Sprague-Dawley (SD) rats of PF were induced by daily intraperitoneally injection of chlorhexidine gluconate (CG) for 4 wks.

Ubiquitination of IGF2BP3 by E3 ligase MKRN2 regulates the proliferation and migration of human neuroblastoma SHSY5Y cells.

Neuroblastoma (NB) is a paediatric tumour that shows great biomolecule and clinical heterogeneity, and patients with NB often develop various neurological complications. Currently, the disease is mainly treated by surgery and still lacks specific therapeutic drugs; therefore, targets are urgently needed. Makorin ring finger protein 2 (MKRN2) is an E3 ligase whose effects on neuroblastoma have not been illustrated.

MicroRNA-22-3p alleviates spinal cord ischemia/reperfusion injury by modulating M2 macrophage polarization via IRF5.

Cell death after spinal cord ischemia/reperfusion (I/R) can occur through necrosis, apoptosis, and autophagy, resulting in changes to the immune environment. However, the molecular mechanism of this immune regulation is not clear. Accumulating evidence indicates that microRNAs (miRs) play a crucial role in the pathogenesis of spinal cord I/R injury.

Ubiquitin Linkage Specificity of Deubiquitinases Determines Cyclophilin Nuclear Localization and Degradation.

Ubiquitin chain specificity has been described for some deubiquitinases (DUBs) but lacks a comprehensive profiling in vivo. We used quantitative proteomics to compare the seven lysine-linked ubiquitin chains between wild-type yeast and its 20 DUB-deletion strains, which may reflect the linkage specificity of DUBs in vivo. Utilizing the specificity and ubiquitination heterogeneity, we developed a method termed DUB-mediated identification of linkage-specific ubiquitinated substrates (DILUS) to screen the ubiquitinated lysine residues on substrates modified with certain chains and regulated by specific DUB.

High expression of the gene might promote apoptosis through downregulation of the Ras/ERK signalling pathway in the intestinal type of gastric cancer.

Objective: To investigate the effect of the casein kinase 2 interacting protein 1 (CKIP-1) on the apoptosis of the intestinal type of gastric cancer (GC).

Methods: The levels of CKIP-1 protein and the rates of apoptosis were measured in tissue samples of the intestinal type of GC and human GC cell lines. The rate of apoptosis and the protein levels of B cell lymphoma-2 (Bcl-2), Bcl-2 associated X protein (Bax), cleaved cysteinyl aspartate specific protease 3 (cleaved caspase-3), cleaved caspase-9, rat sarcoma (Ras), extracellular signal-regulated kinase 1 and 2 (ERK1/2) and phosphorylated extracellular signal-regulated kinase 1 and 2 (p-ERK1/2) were analysed in SGC7901 cells expressing CKIP-1 short hairpin RNA (shRNA; knockdown) and SGC7901 cells overexpressing CKIP-1.

Metformin Activates the AMPK-mTOR Pathway by Modulating lncRNA to Induce Autophagy and Inhibit Atherosclerosis.

Background: Metformin has been shown to inhibit the proliferation and migration of vascular wall cells. However, the mechanism through which metformin acts on atherosclerosis (AS) via the long non-coding RNA taurine up-regulated gene 1 (lncRNA ) is still unknown. Thus, this research investigated the effect of metformin and lncRNA on AS.

Gclust: A Parallel Clustering Tool for Microbial Genomic Data.

The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources. Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering analysis is essential. However, existing clustering algorithms perform poorly on long genomic sequences.

Casein kinase 2 interacting protein 1 positively regulates caudal-related homeobox 1 in intestinal-type gastric cancer.

Background: Gastric cancer (GC) is one of the most common malignancies, and intestinal-type GC is the main histopathologic type of GC in China. We previously reported that casein kinase 2 interacting protein 1 (CKIP-1) acts as a candidate tumor suppressor in intestinal-type GC. CKIP-1 participates in the regulation of multiple signaling pathways, including the Wnt/β-catenin pathway, of which caudal-related homeobox 1 (CDX1) may be a downstream target gene.

Specific and Unbiased Detection of Polyubiquitination via a Sensitive Non-Antibody Approach.

Polyubiquitination encompasses complex topologies through various linkage types to deliver diverse cellular signals, which has been recognized as a sophisticated ubiquitin code. Accurate comparison of polyubiquitination signals is critical for revealing the dynamic cellular ubiquitination-regulated events. Western blotting (WB) is the most widely used biochemical method to quantify proteins and posttranslational modifications under diverse physiological conditions.

How Big Data and High-performance Computing Drive Brain Science.

Brain science accelerates the study of intelligence and behavior, contributes fundamental insights into human cognition, and offers prospective treatments for brain disease. Faced with the challenges posed by imaging technologies and deep learning computational models, big data and high-performance computing (HPC) play essential roles in studying brain function, brain diseases, and large-scale brain models or connectomes. We review the driving forces behind big data and HPC methods applied to brain science, including deep learning, powerful data analysis capabilities, and computational performance solutions, each of which can be used to improve diagnostic accuracy and research output.

Translational Informatics for Parkinson's Disease: from Big Biomedical Data to Small Actionable Alterations.

Parkinson's disease (PD) is a common neurological disease in elderly people, and its morbidity and mortality are increasing with the advent of global ageing. The traditional paradigm of moving from small data to big data in biomedical research is shifting toward big data-based identification of small actionable alterations. To highlight the use of big data for precision PD medicine, we review PD big data and informatics for the translation of basic PD research to clinical applications.

Ac-LysargiNase Complements Trypsin for the Identification of Ubiquitinated Sites.

Mass spectrometry (MS)-based identification of ubiquitinated sites requires trypsin digestion prior to MS analysis, and a signature peptide was produced with a diglycine residue attached to the ubiquitinated lysine (K-ε-GG peptide). However, the missed cleavage of modified lysines by trypsin results in modified peptides with increased length and charge, whose detection by MS analysis is suppressed by the vast majority of internally unmodified peptides. LysargiNase, the mirrored trypsin, is reported to cleave before lysine and arginine residues and to be favorable for the identification of methylation and phosphorylation, but its digestive characteristics related to ubiquitination are unclear.

Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue.

In recent years, high-throughput technologies have contributed to the development of a more precise picture of the human proteome. However, 2129 proteins remain listed as missing proteins (MPs) in the newest neXtProt release (2019-02). The main reasons for MPs are a low abundance, a low molecular weight, unexpected modifications, membrane characteristics, and so on.