Leveraging a KRAS-based signature to predict the prognosis and drug sensitivity of colon cancer and identifying SPINK4 as a new biomarker.

KRAS is one of the leading mutations reported in colon cancer. However, there are few studies on the application of KRAS related signature in predicting prognosis and drug sensitivity of colon cancer patient. We identified KRAS related differentially expressed genes (DEGs) using The Cancer Genome Atlas (TCGA) database.

IL-17A-mediated mitochondrial dysfunction induces pyroptosis in colorectal cancer cells and promotes CD8 + T-cell tumour infiltration.

Background: Interleukin-17A (IL-17A), a proinflammatory cytokine primarily secreted by Th17 cells, γδT cells and natural killer T (NKT) cells, performs essential roles in the microenvironment of certain inflammation-related tumours by regulating cancer growth and tumour elimination proved in previous literature. In this study, the mechanism of IL-17A that induces mitochondrial dysfunction promoted pyroptosis has been explored in colorectal cancer cells.

Method: The records of 78 patients diagnosed with CRC were reviewed via the public database to evaluate clinicopathological parameters and prognosis associations of IL-17A expression.

FOXD1 promotes chemotherapy resistance by enhancing cell stemness in colorectal cancer through β‑catenin nuclear localization.

Forkhead box D1 (FOXD1) serves a critical role in colorectal cancer (CRC). FOXD1 expression is an independent prognostic factor in patients with CRC; however, the molecular mechanism and signaling pathway of FOXD1 that regulates cell stemness and chemoresistance has not been fully characterized. The aim of the present study was to further validate the effect of FOXD1 on the proliferation and migration of CRC cells, and to delve into the possible potential of FOXD1 in the clinical treatment of CRC.

Discovery of Drug Candidates for Specific Human Disease Based on Natural Products of Gut Microbes.

The beneficial metabolites of the microbiome could be used as a tool for screening drugs that have the potential for the therapy of various human diseases. Narrowing down the range of beneficial metabolite candidates in specific diseases was primarily a key step for further validation in model organisms. Herein, we proposed a reasonable hypothesis that the metabolites existing commonly in multiple beneficial (or negatively associated) bacteria might have a high probability of being effective drug candidates for specific diseases.

Geptop 2.0: Accurately Select Essential Genes from the List of Protein-Coding Genes in Prokaryotic Genomes.

Computational tool composites alternative way to identify essential genes and it is low-cost and time-efficient. Based on experimental essentiality sets deposited in the databases DEG and OGEE as reference, we developed an automatically computational tool named Geptop to select essential genes from the set of protein-coding genes in a prokaryotic genome, which utilizes the strategy of reciprocally best hit for homology search and evolutionary distance for weight assigning. The latest version of Geptop is 2.

Retrospective research of neoadjuvant therapy on tumor-downstaging, post-operative complications, and prognosis in locally advanced rectal cancer.

Background: Neoadjuvant therapy (NAT) is becoming increasingly important in locally advanced rectal cancer. Hence, such research has become a problem.

Aim: To evaluate the downstaging effect of NAT, its impact on postoperative complications and its prognosis with different medical regimens.

CasLocusAnno: a web-based server for annotating cas loci and their corresponding (sub)types.

In prokaryotes, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) systems constitute adaptive immune systems against mobile genetic elements (MGEs). Here, we introduce the Markov cluster algorithm (MCL) to Makarova et al.'s method in order to select a more reasonable profile.

Geptop 2.0: An Updated, More Precise, and Faster Geptop Server for Identification of Prokaryotic Essential Genes.

Geptop has performed effectively in the identification of prokaryotic essential genes since its first release in 2013. It estimates gene essentiality for prokaryotes based on orthology and phylogeny. Genome-scale essentiality data of more prokaryotic species are available, and the information has been collected into public essential gene repositories such as DEG and OGEE.

Comprehensive review of the identification of essential genes using computational methods: focusing on feature implementation and assessment.

Essential genes have attracted increasing attention in recent years due to the important functions of these genes in organisms. Among the methods used to identify the essential genes, accurate and efficient computational methods can make up for the deficiencies of expensive and time-consuming experimental technologies. In this review, we have collected researches on essential gene predictions in prokaryotes and eukaryotes and summarized the five predominant types of features used in these studies.

Comprehensive exploration of the enzymes catalysing oxygen-involved reactions and COGs relevant to bacterial oxygen utilization.

To better understand the mechanisms of bacterial adaptation in oxygen environments, we explored the aerobic living-associated genes in bacteria by comparing Clusters of Orthologous Groups of proteins' (COGs) frequencies and gene expression analyses and 38 COGs were detected at significantly higher frequencies (p-value less than 1e-6) in aerobes than in anaerobes. Differential expression analyses between two conditions further narrowed the prediction to 27 aerobe-specific COGs. Then, we annotated the enzymes associated with these COGs.

Designing principles of an ecological water storage basin on coastal saline: a case study.

The degradation of water source environment becomes serious problems accompanying with rapid urbanization in China. Ecological engineering provides ecologically sound and cost-effective solution to solving this problem. As a case study, a 15 hm2 ecological water storage basin for a water plant was designed and constructed on the TEDA area in Tianjin City.