Biomedical subjects

Zhiyong Liu

Publications and source records attributed to Zhiyong Liu.

5 recordsLinked to original sources

PubMed2026

pSTRminer: integrated bioinformatic software for genome-wide identification and population-scale evaluation of polymorphic short tandem repeats.

Animal forensic genetics plays a critical role in criminal investigations by providing crucial evidence through domestic animal individualization and wildlife species identification. While human forensic genetics benefits from standardized short tandem repeats (STR) genotyping systems, animal forensic applications encounter significant challenges, including the limited availability of validated STR markers, the prevalence of error-prone dinucleotide STRs (di-STRs), and insufficient integration of population data. To address these challenges, we developed pSTRminer, an integrated bioinformatic tool that automates genome-wide STR mining and polymorphism evaluation. By applying pSTRminer to domestic cattle (Bos taurus), we identified 775,444 STRs de novo from the reference genome and genotyped them using whole-genome sequencing data from 60 Chinese and 111 African cattle to evaluate polymorphism across diverse genetic backgrounds. This led to the development of the cattle STR database (CSDB), comprising loci with a genotyping success rate ≥ 40% and polymorphism information content (PIC) ≥ 0.5. Experimental validation of 30 randomly selected tetranucleotide STRs (tetra-STRs) and 33 di-STRs via next-generation sequencing in a local Chinese cattle population (n = 145) confirmed marker reliability. Although tetra-STRs had lower average polymorphism levels, they exhibited significantly lower stutter ratios (p < 0.05), providing a viable path for identifying discriminative markers with fewer artifacts. Systematic screening revealed that certain tetra-STRs could surpass di-STRs in polymorphism. In conclusion, pSTRminer provides a scalable framework for developing standardized STR panels, facilitating the identification of robust and informative markers in forensic applications.

Bioinformatic software↗

PubMed2026

Potential of plasma metagenomic next-generation sequencing to guide antibiotic therapy in acute necrotizing pancreatitis with early fever: a prospective multicenter cohort study.

BACKGROUND: Indiscriminate antibiotic use remains common in febrile patients with acute necrotizing pancreatitis (ANP), particularly during the early phase. Metagenomic next‑generation sequencing (mNGS) has shown diagnostic utility for infected pancreatic necrosis (IPN) and may offer a means to guide antimicrobial therapy. We aimed to explore whether mNGS could potentially improve the appropriateness of antibiotic use in ANP patients presenting with early fever. METHODS: This prospective multicenter cohort study was conducted at five hospitals in China, enrolling ANP patients who developed fever within two weeks of symptom onset. Antibiotic susceptibility was defined per local microbiology laboratory reports. The hypothetical impact of mNGS on reducing inappropriate antibiotic use was evaluated through a retrospective simulation using predefined criteria from the BGI China antimicrobial drug usage card, as mNGS results were not disclosed to the treating teams during the actual clinical course. RESULTS: Between May 2023 and December 2024, 125 ANP patients with early fever were enrolled. Antibiotics were administered to 91.2% (114/125) of patients, whereas only 23.2% (29/125)were eventually confirmed to have IPN, and the rate of appropriate antibiotic use was 14.5% (17/117) based on conventional culture. In our simulated model, if therapy had been guided by plasma mNGS results, the estimated rate of appropriate antibiotic use could have increased to 71.8%. CONCLUSIONS: Plasma mNGS facilitates rapid pathogen identification and shows potential for improving antibiotic appropriateness in ANP patients with early fever.

Adult↗

PubMed2026

Identifying intrinsic piezoelectric contribution in promoting piezocatalytic activity.

Understanding the intrinsic role of piezoelectricity is critical for the rational design of high-efficiency piezocatalytic systems. However, this remains challenging due to the contribution of intrinsic piezoelectricity often being obscured by complex interface effects, specific surface area (size confinement), and other coupled phenomena. In this study, we decouple these factors by employing a model system of piezoceramic thin sheets with a tunable piezoelectric coefficient (d33). We establish a direct and quantitative relationship between d33 and catalytic activity: the sheet with the highest d33 value of 754 pC N-1 exhibited a superior H2O2 production rate of 8.58 μmol h-1 and a Rhodamine B degradation rate constant of 0.073 min-1. Conversely, the sample with the lowest d33 value of 155 pC N-1 showed the minimal activity. Through carrier dynamics analysis and carrier migration simulations, we demonstrate that stronger piezoelectricity enables more efficient polarization rearrangement, greater stress sensitivity, and improved charge separation and transport. These effects lead to a higher transient free carrier concentration and a more robust built-in electric field, which ultimately accelerate the piezocatalytic reaction kinetics. This work establishes a clear and quantitative correlation between intrinsic piezoelectric properties and catalytic activity, while also delivering a high-performance, easily synthesized piezocatalytic platform for sustainable applications.

Piezocatalysts↗

PubMed2026

Full-length single-cell spatial transcriptomics reveals spatial and cell-type-specific transcript isoforms in the primate brain.

The primate brain exhibits complex RNA alternative splicing heterogeneity crucial for functional complexity, yet systematic spatial isoform characterization has been lacking. We developed Fullscope-seq, a full-length single-molecule large field-of-view spatial transcriptomics sequencing method at single-cell resolution, based on programmed concatenation cDNA for multiple long-read sequencing platforms. Applying Fullscope-seq to the macaque brain, we uncovered thousands of genes exhibiting differential transcript usage (DTU) across cortical layers, cell types and brain regions. Fullscope-seq resolved hundreds of major isoform switches across distinct brain regions and identified DTUs between superficial and deep cortical layers. Cortical layer-specific DTUs showed cell-composition dependence, whereas regional DTUs were regulated according to both cellular composition and spatial contexts. These isoform variations showed substantial enrichment for neuropsychiatric disorder-associated genes and were conserved across platforms and species. Our study establishes a scalable framework for spatial isoform analysis and provides a resource for understanding transcriptomic diversity in complex tissues.

Animals↗

PubMed2026

A rare and atypical case of long-distance indirect DNA transfer: Contamination from an investigator never present at the scene.

To maximize the usefulness of DNA obtained from biological samples in forensic genetics, it is crucial to avoid DNA contamination throughout all procedures, from sample collection at crime scenes to STR profile generation in DNA laboratories. This study reports a rare and atypical case of DNA contamination in a forensic setting. During the analysis of biological evidence from a cold case preserved for 18 years, the STR profile obtained from the surface of a plastic bag matched that of an investigator, identified through the DNA elimination database. Case reconstruction confirmed that the investigator-who was located 80 km from the DNA laboratory and had never entered the crime scene or the sample storage room-was not a suspect and that the obtained STR profile originated from contamination. The most plausible explanation for the contamination was indirect transfer: investigator's DNA had adhered to a colleague's clothing and was subsequently dislodged and deposited onto the surface of the plastic bag as the colleague approached the sample pretreatment area. This study integrates trace DNA profiling of challenged samples with rapid contamination investigation and proposes prevention and control measures. This case underscores that, although DNA is widely regarded as the "gold standard" in forensic genetics, its interpretation must be considered within the context of the entire case. Conclusions should not be drawn based solely on a single DNA result.

Humans↗