Biology subjects

Tran, H. D.

Publications and source records attributed to Tran, H. D..

4 recordsLinked to original sources

bioRxiv2024

Investigating demic versus cultural diffusion and sex bias in the spread of Austronesian languages in Vietnam

Austronesian (AN) is the second-largest language family in the world, particularly widespread in Island Southeast Asia (ISEA) and Oceania. In Mainland Southeast Asia (MSEA), groups speaking these languages are concentrated in the highlands of Vietnam. However, our knowledge of the spread of AN-speaking populations in MSEA remains limited; in particular, it is not clear if AN languages were spread by demic or cultural diffusion. In this study, we present and analyze new data consisting of complete mitogenomes from 369 individuals and 847 Y-chromosomal single nucleotide polymorphisms (SNPs) from 170 individuals from all five Vietnamese Austronesian groups (VN-AN) and five neighboring Vietnamese Austroasiatic groups (VN-AA). We found genetic signals consistent with matrilocality in some, but not all, of the VN-AN groups. Population affinity analyses indicated connections between the AN-speaking Giarai and certain Taiwanese AN groups (Rukai, Paiwan, and Bunun). However, overall, there were closer genetic affinities between VN-AN groups and neighboring VN-AA groups, suggesting language shifts. Our study provides insights into the genetic structure of AN-speaking communities in MSEA, characterized by some contact with Taiwan and language shift in neighboring groups, indicating that the expansion of AN speakers in MSEA was a combination of cultural and demic diffusion.

genomics↗

bioRxiv2024

Mitochondrial DNA analysis in ayu (Plecoglossus altivelis) raises an urgent conservation need for its southernmost population

The central-marginal hypothesis predicts that genetic diversity decreases and genetic differentiation increases toward the species distribution margin. We analyzed the mitochondrial DNA control region of ayu (Plecoglossus altivelis) collected from different localities, including central and marginal populations, to test the hypothesis. The results show that the ayu populations at southern marginal habitats (Tien Yen River in Vietnam and Yakugachi River in Amami-oshima Island) displayed low genetic diversity (Haplotype diversity, H = 0.52 and 0.67; Nucleotide diversity, Pi = 0.01 and 0.006, respectively) and significantly differed from the central populations (p < 0.001), consistent with the central-marginal hypothesis. However, ayu populations at the center of their distribution range (Shinano River in Honsyu and Hamoji River in Sado Island) and the northern marginal habitats (Yoichi River in Hokkaido and Aonae River in Okushiri Island) exhibited high genetic diversity (H = 1 for all rivers; Pi = 0.024-0.029). The genetic differences between the populations at the center and the northern marginal habitats were insignificant (p > 0.05). This study showed that in ayu, the central-marginal hypothesis is valid in the southern direction but not in the northern direction. Urgent conservation is needed for the genetically distinct population in the degraded southern habitat with severely low genetic diversity.

ecology↗

bioRxiv2021

Direct multiplex recombinase polymerase amplification for rapid detection of Staphylococcus aureus and Pseudomonas aeruginosa in food

Foodborne illness undermines human health by causing fever, stomachache and even lethality. Among foodborne bacterial pathogens, Staphylococcus aureus and Pseudomonas aeruginosa are of extraordinary significance which drive reasons of food and beverage poisoning in numerous cases. Today, PCR has been widely used to examine the presence of different foodborne pathogens. However, PCR requires specialized equipment and skillful personnel which limit its application in the field. Recently, there is an emerging of isothermal PCR methods in which the reactions occur at low and constant temperature, allowing their application in restricted-resource settings. In this work, multiplex Recombinase Polymerase Amplification (RPA) was used to simultaneously detect S. aureus and P. aeruginosa with high sensitivity and specificity. The limit detection of multiplex RPA was 10 and 30 fg/reaction of genomic DNAs of S. aureus and P. aeruginosa, respectively. Besides, the reaction time was reduced to only 25 minutes with a low incubation temperature of 39 {degrees}C. Markedly, multiplex RPA reactions succeeded to directly detect as low as 1 and 5 CFU/reaction of S. aureus and P. aeruginosa cells, respectively without the requirement of extracting DNA genome. Moreover, the multiplex RPA reliably detected the two foodborne bacteria in milk, fruit juice and bottled water samples. In general, the direct multiplex RPA described in this study is a rapid, simple, sensitive and efficient alternative tool that could be used to detect the presence of S. aureus and P. aeruginosa without the necessity of costly devices and high-trained staff.

molecular biology↗

bioRxiv2016

A SUMO-Ubiquitin Relay Recruits Proteasomes to Chromosome Axes to Regulate Meiotic Recombination

Meiosis produces haploid gametes through a succession of chromosomal events including pairing, synapsis and recombination. Mechanisms that orchestrate these events remain poorly understood. We found that the SUMO-modification and ubiquitin-proteasomes systems regulate the major events of meiotic prophase in mouse. Interdependent localization of SUMO, ubiquitin and proteasomes along chromosome axes was mediated largely by RNF212 and HEI10, two E3 ligases that are also essential for crossover recombination. RNF212-dependent SUMO conjugation effected a checkpoint-like process that stalls recombination by rendering the turnover of a subset of recombination factors dependent on HEI10-mediated ubiquitylation. We propose that SUMO conjugation establishes a precondition for designating crossover sites via selective protein stabilization. Thus, meiotic chromosome axes are hubs for regulated proteolysis via SUMO-dependent control of the ubiquitin-proteasome system.\n\nOne Sentence SummaryChromosomal events of meiotic prophase in mouse are regulated by proteasome-dependent protein degradation.

genetics↗