Biology subjects

Van, D.

Publications and source records attributed to Van, D..

3 recordsLinked to original sources

bioRxiv2025

Discovery and biosynthesis of biffamycin A, a novel glycotetrapeptide antibiotic

The clinical deployment of antibiotics is undermined by antimicrobial resistance. Without new agents to treat antibiotic resistant bacterial infections, mortality rates are predicted to reach 10 million people per year by 2050. Most antibiotics are derived from natural products (NPs) produced by bacteria; however, this resource was abandoned by industry because of high rediscovery rates. We are amid a natural product renaissance fuelled by inexpensive access to genome sequencing and sophisticated bioinformatic tools, which have highlighted that most of the biosynthetic pathways for NPs are not expressed in the laboratory. Here, we engineered the expression of a silent biosynthetic gene cluster harboured by an environmental isolate of Streptomyces albidoflavus. By using a bioinformatics-guided approach, we isolated and structurally characterised a novel glycopeptide antibiotic (GPA) named biffamycin A, which is the smallest GPA known and harbours unprecedented 5-chloro-4-methoxy tryptophan and 3-hydroxy(-O_SCPLOWDC_SCPLOW-mannoysl)-O_SCPLOWDC_SCPLOW-lysine moieties. Biffamycin A possesses antimycobacterial and antistaphylococcal bioactivity, including methicillin-vancomycin-resistant Staphylococcus aureus.

biochemistry↗

bioRxiv2023

DNA barcoding revealed a high percentage of mislabeling in commercial fish products: the first empirical survey in South Texas

Seafood mislabeling is a widespread problem that have produced a growing distrust of seafood industry. In this study, we examined the prevalence of mislabeling in fish samples from regional markets in the greater Houston area and close-by coastal communities. A total of 63 fish fillet samples were purchased, labeled, and stored at -20{degrees}C in individual packages until DNA extraction. DNA fragments of roughly 700 base pairs encoding cytochrome oxidase I (COI) were PCR-amplified from each DNA sample. With 99.6-100% nucleotide identity in the GenBank and BOLD databases, all samples were correctly identified at the species level. The scientific names identified by DNA barcoding were matched with legally acceptable market names using the US Food and Drug Administration (FDA) Seafood List. Out of the 63 samples examined, 13 samples (20.6%) were mislabeled. Moreover, 24 samples (38.1%) did not use the acceptable market names, indicating that the FDA policy is poorly implemented in seafood industry. The first DNA barcoding survey this area warranted the need of continuous monitoring and the dissemination of the regulation combined with taxonomic knowledge.

molecular biology↗

bioRxiv2022

Genomic loss of the HSP70cA gene in the vertebrate lineage

Metazoan 70 kDa heat shock protein (HSP70) genes have been classified into four lineages: cytosolic A (HSP70cA), cytosolic B (HSP70cB), endoplasmic reticulum (HSP70er), and mitochondria (HSP70m). Because previous studies have identified no HSP70cA genes in vertebrates, we hypothesized that this gene has lost on the evolutionary path to vertebrates. To test this hypothesis, the present study conducted a comprehensive database search followed by phylogenetic and synteny analyses. The HSP70cA gene was present in invertebrates and animals that belong to subphyla of Chordata, Cephalochordata (lancelets) and Tunicata (tunicates). However, the genomes of early vertebrates in the subphylum Craniata (lamprey, hagfish, elephant shark, and coelacanth) contained only HSP70cB genes, suggesting the loss of the HSP70cA gene in the early period of vertebrate evolution. Synteny analysis using available genomic resources indicated that the synteny around the HSP70 genes was generally conserved between tunicates, but it was largely different between tunicates and lamprey. These results suggest the presence of dynamic chromosomal rearrangement in early vertebrates, which possibly caused the loss of the HSP70cA gene in the vertebrate lineage.

evolutionary biology↗