Biology subjects

LIN, X.

Publications and source records attributed to LIN, X..

4 recordsLinked to original sources

bioRxiv2025

Detecting the Indo-Pacific finless porpoises (Neophocaena phocaenoides) in Hong Kong waters using environmental DNA

The Indo-Pacific finless porpoise (Neophocaena phocaenoides), a coastal cetacean species widely distributed from the Taiwan Strait to the Persian Gulf, is an iconic species that may represent an overall status indicator of marine ecosystems. However, growing anthropogenic pressures have led to declines in the population of this species in many regions such as Hong Kong waters, highlighting the need for more efficient and reliable monitoring methods. In this study, we applied two environmental DNA (eDNA) analysis methods, species-specific quantitative PCR (qPCR) and cetacean-targeting metabarcoding using {micro}Ceta primers, to detect Indo-Pacific finless porpoises eDNA in Hong Kong waters. First, we empirically validated the performance of the qPCR primers previously designed in another study. Then, in March 2025, water samples were collected from surface and bottom water layers in 20 locations in the Soko Islands area, a major habitat of the Indo-Pacific finless porpoises. The qPCR analysis detected the finless porpoise eDNA in eight out of 40 samples, but all of the eDNA concentrations were below the limit of quantification. {micro}Ceta metabarcoding detected the finless porpoise eDNA from seven out of 40 samples. The qPCR and {micro}Ceta metabarcoding approaches showed comparable detection rates for Indo-Pacific finless porpoise. Interestingly, the {micro}Ceta metabarcoding method detected a transient cetacean species, the false killer whale (Pseudorca crassidens), from a single location. Both methods showed consistent detection rates between surface and bottom water layers, with no statistically significant difference. Overall, the two eDNA analysis methods successfully detected the finless porpoise eDNA in Hong Kong waters, demonstrating the potential of these approaches for monitoring the Indo-Pacific finless porpoises and other cetaceans in this region. Taken together, our findings provide a basis for an eDNA-based cetacean monitoring framework in Hong Kong waters.

ecology↗

bioRxiv2023

Reversibly-bonded Microfluidic Devices for Stable Cell Culture and Rapid, Gentle Cell Extraction

Microfluidics chips have emerged as significant tools in cell culture due to their capacity for supporting cells to adopt more physiologically relevant morphology in 3D compared with traditional cell culture in 2D. Currently, irreversible bonding methods commonly used in chip fabrication mean that chips cannot be detached from their substrate without destroying the chip structure, which makes it challenging to do further analysis on cells that have been cultured on-chip. Some reversible bonding techniques exist but are restricted to certain materials, or require complex processing procedures. Here, we demonstrate a simple and reversible polydimethylsiloxane (PDMS)-polystyrene (PS) bonding technique that allows devices to withstand extended operation while pressurized, and supports long-term stable cell cultures. Importantly, it allows rapid and gentle live cell extraction for further downstream manipulation and characterization after long-term on-chip culturing, or even further subculturing. Our new approach could greatly facilitate microfluidic chip-based tissue and cell cultures, overcoming current analytical limitations and opening up new avenues for downstream uses of on-chip cultures, including 3D-engineered tissue structures for biomedical applications.

bioengineering↗

bioRxiv2021

Isolation, screening, degradation characteristics of a quinclorac-degrading bacteria D and its potential of bioremediation for rice field environment polluted by quinclorac

Quinclorac (QNC) is a highly selective, hormonal, and low-toxic herbicide with a long duration. And the growth and development of subsequent crops are easily affected by QNC accumulated in the soil. In this paper, a QNC-degrading strain D was isolated and screened from the rice paddy soil. Through morphology, physiological and biochemical tests and 16Sr DNA gene analysis, strain D was identified as Cellulosimicrobium cellulans sp. And the QNC degradation characteristics of strain D were studied. Under the optimal culture conditions, the QNC-degrading rate was 45.9% after culturing for 21 days. The QNC-degrading efficiency of strain D in the field was evaluated by a simulated pot experiment. The results show that strain D can promote the growth of rice and QNC-degrading effectively. This research could provide a new bacterial species for microbial degradation of QNC and lay a theoretical foundation for further research on QNC remediation. ImportanceAt present, some QNC-degrading bacteria have been isolated from different environments, but there are no reports of Cellulosimicrobium cellulans sp. bacterial that could degrade QNC. In this study, a new QNC-degradation strain was selected from the paddy soil. The degradation characteristics of strain D were studied in detail. The results shown that strain D had a satisfactory quinclorac-degrading efficiency. Two degradation products of QNC by strain D were identified by HPLC-Q-TOF/MS: 3-pyridylacetic acid (138.0548 m/z) and 3-ethylpyridine (108.0805 m/z), which have not been reported before. The strain D had a potential ability of quinclorac-degrading effectively in the quinclorac-polluted paddy field environment.

microbiology↗

bioRxiv2020

Butyribacter intestini gen. nov., sp. nov., a butyric acid-producing bacterium of the family Lachnospiraceae isolated from the human faeces, and reclassification of Acetivibrio ethanolgignens as Acetanaerobacter ethanolgignens gen. nov., comb. nov.

A novel, non-motile, Gram-stain-positive, non-spore-forming, obligate anaerobic bacterium, designated strain TF01-11T, was isolated from human faeces. The isolate was characterized by phylogenetic and phenotypic properties, as well as by determination of its whole genome sequence. The growth temperature and pH ranges were 30-42 {degrees}C and 6.0-8.5, respectively. The end products of glucose fermentation were butyric acid and a small amount of acetic acid. The genome was estimated to be 3.61Mbp with G+C content of 36.79 mol%. Genes related to biosynthesis of diaminopimelic acid, polar lipids, polyamines, teichoic and lipoteichoic acids were present. The predominant fatty acids were C16:0 (37.9 %), C14:0 (16.4 %), C13:0 OH/iso-C15:1 H (11.1 %) and C18:1{omega} 9c (10.6 %). Phylogenetic analyses based on 16S rRNA gene sequences, the isolate was a member of family Lachnospiraceae, with the highest sequence similarity to the type strain of Roseburia intestinalis DSM 14610T at 92.18 % followed by Acetivibrio ethanolgignens ATCC 33324T at 91.99 %. The average nucleotide identity (ANI) calculated for the genomes between strain TF01-11T and these closest relatives were 70.5 % and 68.1 %. Based on results of phenotypic characteristics and genotypic properties presented in this study, strain TF01-11T represent a novel species in a new genus, for which the name Butyribacter intestini gen. nov., sp. nov. is proposed. The type strain of the type species is TF01-11T (CGMCC 1.5203T = CGMCC 10984T = DSM 105140T). In addition, Acetivibrio ethanolgignens is proposed to be reclassified as Acetanaerobacter ethanolgignens gen. nov., comb. nov.

microbiology↗