Detection of early prognostic biomarkers for metastasis of Ewing's sarcoma in pediatric patients.

Aims: Ewing's Sarcoma is an extremely aggressive tumor in children. The disease is associated with highly metastatic rate, especially at the time of diagnosis, contributing to a lower survival rate and poor prognosis. The study aimed to identify predictive biomarkers for metastatic Ewing's sarcoma through in-depth analysis of the plasma proteome profile of pediatric Ewing's sarcoma patients.

gtAI: an improved species-specific tRNA adaptation index using the genetic algorithm.

The tRNA adaptation index (tAI) is a translation efficiency metric that considers weighted values ( values) for codon-tRNA wobble interaction efficiencies. The initial implementation of the tAI had significant flaws. For instance, generated weights were optimized based on gene expression in , which is expected to vary among different species.

Integrated multiomics analysis to infer COVID-19 biological insights.

Three years after the pandemic, we still have an imprecise comprehension of the pathogen landscape and we are left with an urgent need for early detection methods and effective therapy for severe COVID-19 patients. The implications of infection go beyond pulmonary damage since the virus hijacks the host's cellular machinery and consumes its resources. Here, we profiled the plasma proteome and metabolome of a cohort of 57 control and severe COVID-19 cases using high-resolution mass spectrometry.

Antitrypanosomal, Antitopoisomerase-I, and Cytotoxic Biological Evaluation of Some African Plants Belonging to Crassulaceae; Chemical Profiling of Extract Using UHPLC/QTOF-MS/MS.

In our continuous study for some African plants as a source for antitrypanosomally and cytotoxic active drugs, nine different plants belonging to the Crassulaceae family have been selected for the present study. leaves extract showed an antitrypanosomal activity against with an IC value of 8.5 µg/mL.

A Novel Approach of SWATH-Based Metabolomics Analysis Using the Human Metabolome Database Spectral Library.

Metabolomics is a potential approach to paving new avenues for clinical diagnosis, molecular medicine, and therapeutic drug monitoring and development. The conventional metabolomics analysis pipeline depends on the data-independent acquisition (DIA) technique. Although powerful, it still suffers from stochastic, non-reproducible ion selection across samples.

Xconnector: Retrieving and visualizing metabolites and pathways information from various database resources.

Metabolomics databases contain crucial information collected from various biological systems and experiments. Developers and scientists performed massive efforts to make the database public and accessible. The diversity of the metabolomics databases arises from the different data types included within the database originating from various sources and experiments can be confusing for biologists and researchers who need further manual investigation for the retrieved data.

UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase).

UniprotR is a software package designed to easily retrieve, cluster and visualize protein data from UniProt knowledgebase (UniProtKB) using R language. The package is implemented mainly to process, parse and illustrate proteomics data in a handy and time-saving approach allowing researchers to summarize all required protein information available at UniProtKB in a readable data frame, Excel CSV file, and/or graphical output. UniprotR generates a set of graphics including gene ontology, chromosomal location, protein scoring and status, protein networking, sequence phylogenetic tree, and physicochemical properties.

Current Understanding of Human Metaproteome Association and Modulation.

During the last decade, metaproteomics has provided a better understanding and functional characterization of the microbiome. A large body of evidence now reveals interspecies, species of bacteria-host interactions, via the secreted modulatory microbial protein "metaproteome". Although high-throughput state-of-art mass spectrometry has recently empowered metaproteomics, its profile remains unclear, and, most importantly, the exact consequences and underlying mechanism of these protein molecules on the host are insufficiently understood.