Biomedical subjects

Jilin Zhang

Publications and source records attributed to Jilin Zhang.

6 recordsLinked to original sources

PubMed2026

Modtector: ultra-fast modification signal mining on mapped sequencing reads.

SUMMARY: Existing tools for RNA epitranscriptomic modification and structural signal analysis are often fragmented, inefficiency, and limited to single signal types. We developed Modtector, an unified tool for extracting mutation and reverse-transcription stop signals from aligned sequencing reads. By using a "count-then-correct" strategy, Modtector reduces computational complexity and enables efficient dual-signal analysis. It achieves multi-fold speedups on large-genome and high-coverage datasets, including completing HEK293 22G data analysis in 5 minutes, and show strong scalability on single-cell datasets with speedups exceeding 50-fold. AVAILABILITY: The source code is available at GitHub (https://github.com/TongZhou2017/modtector) and Crates.io (https://crates.io/crates/modtector). The archived source-code snapshot used in this study is available at Zenodo (DOI: 10.5281/zenodo.20967747), corresponding to GitHub commit 7c60e9d. Workflow examples, datasets, and analysis scripts are available at Zenodo (DOI: 10.5281/zenodo.17316476 and 10.5281/zenodo.18523297).

Humans↗

PubMed2026

Transcriptomics reveals species-specific adaptive strategies to calorie restriction in two Argopecten scallops with distinct lifespans.

Calorie restriction (CR) is a well-established non-genetic intervention for lifespan extension in multiple model organisms. Seasonal food shortage in cold and temperate seas may mimic CR, inducing in bivalves a response similar to that in vertebrates and thereby prolonging life expectancy. However, the relationship and the mechanism underlying the food availability and lifespan in bivalves remain largely unexplored. Two closely related scallop species the short-lived warm-water Argopecten irradians (lifespan <2 years) and the longer-lived cold-water Argopecten purpuratus (7-10 years) provide an ideal comparative system to investigate species-specific adaptive strategies. In this study, we subjected both species to CR for 30 and 56 days and performed comparative transcriptomic profiling, weighted gene co-expression network analysis (WGCNA), and physiological assays to elucidate their distinct molecular responses. Transcriptomic analysis revealed that A. purpuratus exhibited substantially more DEGs than A. irradians at both time points under CR, with both species showing downregulation of metabolic pathways but to different extents. A. irradians mounted an early nutrient-sensing response at 30 days (IGF1R, PIK3R3, INSR suppression), indicating acute sensitivity to limitation; by contrast, A. purpuratus displayed delayed FoxO activation at 56 days, along with its downstream effectors NFKBIA, CREB3L4, and SMAD4, suggesting a gradual adaptive program may link to its extended lifespan. WGCNA identified three negatively correlated modules in each species, with coral2 being the most prominent in A. irradians and darkolivegreen in A. purpuratus. The former was dominated by ciliary motility genes, whereas the latter featured coordinated repression of oxidative phosphorylation. Additionally, both species exhibited conserved suppression of mTOR/S6K growth signaling and activation of cellular maintenance programs. Collectively, these findings expand the understanding of CR-mediated longevity regulation in bivalves and provide candidate gene resources for future functional studies and breeding programs.

Pectinidae↗

PubMed2006

Wettability of zinc oxide surfaces with controllable structures.

Zinc oxide (ZnO) surfaces with controllable structures (i.e, microstructure, nanostructure, and micronanobinary structure) have been created by controlling pH at < 4 or > 10.5 in the Zn(gray) + H2O2 reaction. The resulting surface shows superhydrophobicity. It is found that the water contact angle (CA) of the surface with micronanobinary structure is greater than that of nanostructure and that of nanostructure is greater than that of the microstructure. Theoretical analysis is completely in agreement with the experimental results.

Journal Article↗

PubMed2005

Fabrication of gradient colloidal topography.

A rather simple but yet effective way to self-assemble polystyrene (PS) beads in gradient colloidal crystal topography is proposed. The PS bead concentration, solvent, and substrate have a big effect on the colloidal crystal topography. Whether the gradient-shaped crystals can form or not depends on the Bond number [Bo; the ratio of gravitational potential energy (G) to adhesive energy (E(a)), or gravitational to capillary forces]. When Bo < 1, that is, the capillary force dominates over the gravitational force, the liquid meniscus is stable. The gradient-shaped crystals can form. Otherwise, PS beads form a uniform multilayer structure.

Journal Article↗

PubMed2005

Fabrication gradient surfaces by changing polystyrene microsphere topography.

A rather simple yet effective way to fabricate gradient surfaces by changing polystyrene (PS) microsphere topography in a temperature gradient field is proposed. The wettability of the film has an obvious gradient change from 88.7 to 148.1 degrees . The changes of the PS microsphere topography are believed to be responsible for the changing of the wettability.

Journal Article↗

PubMed2003

[Impact of salt stress on peroxidase activity in Populus deltoides cambium and its consequence].

Studies on the impact of salt stress on the peroxidase (POD) activity in Populus deltoides cambium and on the anatomic characteristics of its secondary xylem indicated that the changes of POD activity caused by soil salinity stress behaved differently in dormant and growing period. In low salinity soil, the POD activity of dormant Populus deltoides showed the trend of increasing first, and then, decreasing as the soil salinity was rising gradually. Namely, with the rising of soil salinity in the range of 0.024-->0.094-->0.145%, the POD activity varied in the range of 83.7-->132.1-->63.2 units.min-1.g-1FW accordingly. However, in growing season, with the gradual increase of soil salinity from 0.036 to 0.289%, the POD activity decreased gradually from 405.2 to 107.2 units.min-1.g-1FW. There were regular changes in wood anatomic characteristics of Populus deltoides. Namely, with the increase of soil salinity 0.036-->0.125-->0.289%, the vessel diameters (VD) of both early wood and late wood varied accordingly in the range of 41.8-->56.6-->43.4 microns, and 29.1-->33.1-->33.1 microns, respectively. The vessel frequencies (VF) were 141.8-->113.8-->144.2 and 160.0-->134.8-->206.7 entries mm-2, respectively. Along with the gradual increase of soil salinity from 0.036 to 0.289%, the fiber length gradually decreased from 693.8 to 570.4 microns, and the fiber width decreased from 14.9 to 13.5 microns.

Ecology↗