The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome Databases (PGDBs). A microbial community is represented in PTools by generating a PGDB from each metagenome-assembled genome (MAG). PTools computes a metabolic reconstruction for each organism, and predicts its operons. The properties of individual MAGs can be investigated using the many search and visualization operations within PTools. PTools also enables the user to investigate the properties of the microbial community by issuing searches across the full community, and by performing comparative operations across genome and pathway information. The software can generate a metabolic network diagram for the community, and it can overlay community omics datasets on that network diagram. PTools also provides a tool for searching for metabolic transformation routes across an organism community.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580912 | PMC |
| http://dx.doi.org/10.3389/fbinf.2022.869150 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Synthetic biology meets Aspergillus: engineering strategies for next-generation organic acid production.
World J Microbiol Biotechnol
January 2025
School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing, 210023, People's Republic of China.
Organic acids constitute a vital category of chemical raw materials. They have extensive applications in industries such as polymers, food, and pharmaceuticals. Currently, industrial production predominantly relies on microbial fermentation.
View Article and Find Full Text PDFPreparation, mechanism, and biological applications of targeting LDs ratiometric fluorescent probes for HClO detection.
Anal Chim Acta
February 2025
Institute of Environmental Science, Shanxi University, Taiyuan 030006, China.
Hypochlorous acid (HClO) is a well-known inflammatory signaling molecule, while lipid droplets (LDs) are dynamic organelles closely related to inflammation. Using organic small-molecule fluorescence imaging technology to target LDs for precise monitoring of HClO is one of the most effective methods for diagnosing inflammation-related diseases. A thorough investigation of how probes detect biological markers and the influencing factors can aid in the design of probe molecules, the selection of high-performance tools, and the accuracy of disease detection.
View Article and Find Full Text PDFPoint of view: Challenges in implementation of new immunotherapies for Alzheimer's disease.
J Prev Alzheimers Dis
January 2025
Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, BioClinicum, 171 64 Solna, Sweden; Theme Inflammation and Aging, Karolinska University Hospital, 141 86 Stockholm, Sweden.
The advancement of disease-modifying treatments (DMTs) for Alzheimer's disease (AD), along with the approval of three amyloid-targeting therapies in the US and several other countries, represents a significant development in the treatment landscape, offering new hope for addressing this once untreatable chronic progressive disease. However, significant challenges persist that could impede the successful integration of this class of drugs into clinical practice. These challenges include determining patient eligibility, appropriate use of diagnostic tools and genetic testing in patient care pathways, effective detection and monitoring of side effects, and improving the healthcare system's readiness by engaging both primary care and dementia specialists.
View Article and Find Full Text PDFComparative Analysis of Acquired Resistance to Bortezomib in Prostate Cancer Cells Using Proteomic and Bioinformatic Tools.
J Cell Mol Med
January 2025
Department of Medical Biology, Faculty of Medicine, Kutahya Health Sciences University, Kutahya, Turkey.
Chemotherapy is a potent tool against cancer, but drug resistance remains a major obstacle. To combat this, understanding the molecular mechanisms behind resistance in cancer cells and the protein expression changes driving these mechanisms is crucial. Targeting the Ubiquitin-Proteasome System (UPS) has proven effective in treating multiple myeloma and shows promise for solid tumours.
View Article and Find Full Text PDFGrowth Differentiation Factor-15 Is Associated With Congestion-Related Anorexia and Weight Loss in Advanced Heart Failure.
JACC Heart Fail
January 2025
Institute for Clinical and Experimental Medicine (IKEM), Prague, Czech Republic. Electronic address:
Background: Growth differentiation factor (GDF)-15 is a pleiotropic cytokine that is associated with appetite-suppressing effects and weight loss in patients with malignancy.
Objectives: This study aims to investigate the relationships between GDF-15 levels, anorexia, cachexia, and clinical outcomes in patients with advanced heart failure with reduced ejection fraction (HFrEF).
Methods: In this observational, retrospective analysis, a total of 344 patients with advanced HFrEF (age 58 ± 10 years, 85% male, 67% NYHA functional class III), underwent clinical and echocardiographic examination, body composition evaluation by skinfolds and dual-energy x-ray absorptiometry, circulating metabolite assessment, Minnesota Living with Heart Failure Questionnaire, and right heart catheterization.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!