Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 30, P. 1 - 11
Published: Dec. 25, 2024
Language: Английский
Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 2289 - 2303
Published: May 21, 2024
The rapid progression of genomics and proteomics has been driven by the advent advanced sequencing technologies, large, diverse, readily available omics datasets, evolution computational data processing capabilities. vast amount generated these advancements necessitates efficient algorithms to extract meaningful information. K-mers serve as a valuable tool when working with large offering several advantages in speed memory efficiency carrying potential for intrinsic biological functionality. This review provides an overview methods, applications, significance k-mers genomic proteomic analyses, well utility absent sequences, including nullomers nullpeptides, disease detection, vaccine development, therapeutics, forensic science. Therefore, highlights pivotal role addressing current problems underscores their future breakthroughs research.
Language: Английский
Citations
24
Cancer Gene Therapy, Journal Year: 2024, Volume and Issue: 31(6), P. 861 - 870
Published: Feb. 14, 2024
Abstract Early detection of cancer can significantly improve patient outcomes; however, sensitive and highly specific biomarkers for are currently missing. Nullomers the shortest sequences that absent from human genome but emerge due to somatic mutations in cancer. We examine over 10,000 whole exome sequencing matched tumor-normal samples characterize nullomer emergence across exonic regions genome. also identify emerging mutational hotspots within tumor genes. Finally, we provide evidence identification nullomers cell-free RNA peripheral blood samples, enabling multiple types. show classification models with an AUC greater than 0.9, including a hepatocellular carcinoma classifier 0.99.
Language: Английский
Citations
5
npj Microgravity, Journal Year: 2025, Volume and Issue: 11(1)
Published: Jan. 3, 2025
Systemic mitochondrial dysfunction, dopamine loss, sustained structural changes in the basal ganglia including reduced tyrosine hydroxylase, and altered gait- these effects observed space-flown animals astronauts mirrors Parkinson's disease (PD). Evidence of human cells, examined through lens PD, suggests that spaceflight-induced PD-like molecular are important to monitor during deep space exploration. These changes, may potentially elevate risk PD astronauts.
Language: Английский
Citations
0
Journal of Translational Medicine, Journal Year: 2025, Volume and Issue: 23(1)
Published: Jan. 15, 2025
With breast cancer being the most common tumor among women in world today, it is also leading cause of cancer-related deaths. Standard treatments include chemotherapy, surgery, endocrine therapy, and targeted therapy. However, heterogeneity, drug resistance, poor prognosis highlight an urgent need for further exploration its underlying mechanisms. Mitochondria, highly dynamic intracellular organelles, play a pivotal role maintaining cellular energy metabolism. Altered mitochondrial function plays critical various diseases, recent studies have elucidated pathophysiological mechanisms carcinogenesis. This review explores dysfunction pathogenesis assesses potential mitochondria-targeted therapies.
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 8, 2025
Abstract The identification of succinct, universal fingerprints that enable the characterization individual taxonomies can reveal insights into trait development and have widespread applications in pathogen diagnostics, human healthcare, ecology biomes. Here, we investigated existence peptide k-mer sequences are exclusively present a specific taxonomy absent every other taxonomic level, termed quasi-primes. By analyzing proteomes across 24,073 species, identified quasi-prime peptides to superkingdoms, kingdoms, phyla, uncovering their distributions functional relevance. These exhibit remarkable sequence uniqueness at six- seven-amino- acid lengths, offering evolutionary divergence lineage-specific adaptations. Moreover, show loci more prone harboring pathogenic variants, underscoring significance. This study introduces quasi-primes offers contributions proteomic diversity, pathways, adaptations tree life, while emphasizing potential impact on health disease.
Language: Английский
Citations
0
ACS Omega, Journal Year: 2025, Volume and Issue: 10(7), P. 6794 - 6800
Published: Feb. 11, 2025
Analysis of observed protein sequences across all species within the UniProtKB/Swiss-Prot data set reveals CQWW as shortest absent stretch amino acids. While DNA can be found encoding sequence, it has never been to translated or included in manually curated sets proteins, existing only predicted, tentative and a single mature antibody sequence. We have synthesized this "nullomer" peptide, along with 13 derivatives, reversed, truncated, stereoisomers, alanine-scanning peptides, conjugated polyarginine stretches increase cellular uptake. their impact against healthy neuronal line six patient-derived glioblastoma cell lines spanning three clinical subtypes. Results reveal IC50 values averaging 4.9 μM for inhibition survival tested oncogenic lines. High-content phenotypic analysis features reverse-phase arrays failed discern clear mode action nullomer peptide but suggests mitochondrial impairment through GSK3 isoforms, supported by observations reduced stain intensities. With recent interest we see results study starting point further investigation into potentially therapeutic class.
Language: Английский
Citations
0
Jundishapur Journal of Natural Pharmaceutical Products, Journal Year: 2025, Volume and Issue: 20(2)
Published: March 18, 2025
Context: Breast cancer is a major cause of mortality worldwide. It involves the proliferation cells within breast tissues and metastasis to other organs. Currently, several strategies exist address this challenging disease, but none are both promising safe, often exposing patients complications. Consequently, alternative therapeutic agents urgently needed. Anticancer peptides (ACPs), due their considerable efficacy low toxicity, hold high value in combating cancer. Reviewing activity, mechanisms ACPs, as reported original articles from era, can lead better judgment regarding implementation clinical trials. Evidence Acquisition: We conducted search PubMed database for published English 1963 2025. The strategy outlined Appendix 1 Supplementary File. This study included that investigated anticancer effects vivo. Excluded analysis were studies only vitro or those properties peptide, such delivery, imaging, vaccination, without examining peptide on tumors. Additionally, written languages than English, well reviews duplicates, excluded. Results: A yielded 3,552 articles. After removing duplicates review papers, 3,147 deemed suitable qualified analysis. Following screening process based titles abstracts, 3,080 publications excluded lack relevance, leaving 67 met our inclusion criteria full-text (Appendix 2 File). reviewed summarized 3 Conclusions: development ACPs represents hopeful innovative frontier fight against Through ongoing research, could emerge vital component treatment options, providing new hope
Language: Английский
Citations
0
Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 1919 - 1928
Published: April 21, 2024
The decrease in sequencing expenses has facilitated the creation of reference genomes and proteomes for an expanding array organisms. Nevertheless, no established repository that details organism-specific genomic proteomic sequences specific lengths, referred to as kmers, exists our knowledge. In this article, we present kmerDB, a database accessible through interactive web interface provides kmer-based information from systematic way. kmerDB currently contains 202,340,859,107 base pairs 19,304,903,356 amino acids, spanning 54,039 21,865 proteomes, respectively, well 14,658,776 149,264,442 species-specific sequences, termed quasi-primes. Additionally, provide access 5,186,757 nucleic 214,904,089 peptide absent every genome proteome, primes. features user-friendly offering various search options filters easy parsing searching. service is available at: www.kmerdb.com.
Language: Английский
Citations
2
Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 315 - 331
Published: Jan. 1, 2024
Language: Английский
Citations
2
Journal of Computational Biology, Journal Year: 2024, Volume and Issue: unknown
Published: Dec. 23, 2024
An
Language: Английский
Citations
1