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Yifei Wang

Publications and source records attributed to Yifei Wang.

At least 19 recordsLinked to original sources
PubMed2026

A horizontally transferred bacterial gene for pantothenic acid biosynthesis regulates diapause and reproduction in the spider mite Amphitetranychus viennensis.

Horizontal gene transfer (HGT) has contributed substantially to the evolution of arthropod genomes, yet the functional significance of many horizontally acquired genes remains poorly understood. The hawthorn spider mite, Amphitetranychus viennensis, is a devastating agricultural pest whose high fecundity and overwintering diapause afford its exceptional ecological resilience. Through a genome-wide screen, we identified 37 high-confidence horizontally transferred genes (HTGs) in A. viennensis. Among these candidates, we prioritized AvPBL, a gene encoding pantothenate-β-alanine ligase, for functional characterization because it controls the rate-limiting step of a distinctly non-metazoan pantothenic acid (vitamin B5) biosynthesis pathway. RNAi-mediated suppression of AvPBL significantly reduced transcript abundance and endogenous pantothenic acid levels, triggering a 23.7% reduction in cumulative fecundity and severely compromising the mites' ability to enter winter diapause. Importantly, exogenous pantothenic acid supplementation rescued these reproductive and diapause defects, directly linking the observed phenotypes to the disruption of pantothenic acid biosynthesis. Our results demonstrate that the horizontally transferred bacterial gene AvPBL has been functionally integrated into the endogenous metabolic network of A. viennensis, playing a critical role in vitamin B5 biosynthesis, reproduction, and diapause regulation. These findings provide direct evidence that horizontally acquired metabolic genes can shape key life-history traits and drive adaptive evolution in arthropods.

Amphitetranychus viennensis↗
PubMed2026

Development and evaluation of a multiplex PCR-based dual-platform targeted sequencing framework for precise differentiation of lumpy skin disease virus.

BACKGROUND: Lumpy skin disease virus (LSDV) shares over 96% genomic identity with goatpox and sheeppox viruses, presenting severe diagnostic challenges due to cross-reactivity. METHODS: To address this bottleneck, we established a targeted sequencing framework integrating multiplex PCR with short-read and long-read platforms. By sequentially screening target pathogens, identifying low-homology genes, and designing short and gradient long-fragment primer pools, we evaluated these dual-platform panels using highly homologous poxvirus samples. RESULTS: The short-read panel stably detected target viruses at inputs as low as 5.26 ×101 copies/μL. Under strict alignment criteria, LSDV mapping rates reached 42.91%, suppressing non-target signals to 3.05%. The Nanopore-Targeted Sequencing (NTS) long-amplicon strategy successfully eliminated homologous interference. By applying length-dependent diagnostic thresholds (≥ 100 reads for short amplicons; ≥ 50 reads for long amplicons), precise species-level identification was achieved, maintaining near-zero cross-reads (0-5) in ultra-long regions. Crucially, the field-deployable NTS workflow enabled complete detection in approximately 4 h. CONCLUSION: This complementary strategy seamlessly meets both laboratory demands for high-sensitivity enrichment and frontline requirements for rapid typing, providing a reliable tool for LSDV surveillance, mutation tracking, and outbreak control.

Capripoxvirus differentiation↗
PubMed2026

MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis.

Emerging evidence suggests that MYC binds RNAs, but its functional consequences remain unclear. Here, we integrate multiomics data and reveal that MYC broadly binds enhancer RNAs (eRNAs), which exhibit high cancer- and tissue-specific expression in cancer cell lines and patient tumors. Moreover, we developed a computational pipeline to identify potential cis-regulatory MYC-eRNA target genes, with most predicted eRNA-target pairs supported by RNA polymerase II-mediated chromatin interaction data. Among these, we functionally characterized MERG1 as an oncogenic eRNA that promotes breast cancer tumorigenesis. Mechanistically, MERG1 interacts with MYC to enhance its occupancy at the GREB1 promoter, driving chromatin remodeling and epigenetic activation. This process specifically amplifies GREB1 expression and promotes tumor progression. Last, nanoparticle-mediated delivery of antisense oligonucleotides targeting MERG1 suppresses MYC-mediated breast cancer growth. These results advance our understanding of the enhancer-driven regulation of gene expression and tumorigenesis and provide insights into the regulatory landscape of MYC in cancer.

Humans↗
PubMed2025

Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae).

The hawthorn spider mite, Amphitetranychus viennensis, is a major pest of orchards and ornamentals in the Palaearctic region, with adaptability and acaricide resistance. The lack of high-quality genomic resources limits understanding of its detoxification mechanisms and the development of RNAi-based pest control strategies. In this study, we utilized Illumina, Pacific Biosciences (PacBio), and Hi-C sequencing technologies to assemble a chromosome-level reference genome of A. viennensis. The assembled genome spans 141.96 Mb, with a contig N50 of 1.35 Mb. BUSCO analysis confirmed a high level of completeness, covering 91.6% of annotated genes. The assembly includes 50.97 Mb of repetitive sequences, representing 35.93% of the genome, and annotates 13,968 protein-coding genes. Using Hi-C sequencing, we anchored 47 contigs to three chromosomes, accounting for 97.27% of the estimated nuclear genome and achieving a contig N50 of 45.83 Mb. This high-quality genome assembly provides a valuable foundation for evolutionary and genomic research on spider mites, while also serving as a genetic resource to inform molecular control strategies and support sustainable pest management.

Animals↗
PubMed2024

Reducing competition between msd and genomic DNA improves retron editing efficiency.

Retrons, found in bacteria and used for defense against phages, generate a unique molecule known as multicopy single-stranded DNA (msDNA). This msDNA mimics Okazaki fragments during DNA replication, making it a promising tool for targeted gene editing in prokaryotes. However, existing retron systems often exhibit suboptimal editing efficiency. Here, we identify the msd gene in Escherichia coli, which encodes the noncoding RNA template for msDNA synthesis and carries the homologous sequence of the target gene to be edited, as a critical bottleneck. Sequence homology causes the msDNA to bind to the msd gene, thereby reducing its efficiency in editing the target gene. To address this issue, we engineer a retron system that tailors msDNA to the leading strand of the plasmid containing the msd gene. This strategy minimizes msd gene editing and reduces competition with target genes, significantly increasing msDNA availability. Our optimized system achieves very high retron editing efficiency, enhancing performance and expanding the potential for in vivo techniques that rely on homologous DNA synthesis.

Gene Editing↗
PubMed2006

Overexpression of the gene for transmembrane 4 superfamily member 4 accelerates liver damage in rats treated with CCl4.

BACKGROUND/AIMS: Transmembrane 4 superfamily member 4 (TM4SF4) is up-regulated in regenerating liver after partial hepatectomy in rats, but the in vivo functions of this protein are still largely unknown. Therefore, we investigated the role of TM4SF4 during liver injury. METHODS: Expression of TM4SF4 was analyzed by RT-PCR and Western blotting in normal and CCl4-injured rats. Overexpression or reduced expression of TM4SF4 in the liver was achieved by injection of sense or antisense TM4SF4 expression plasmids. Assessment of liver injury (histology, serum ALT and AST levels), apoptosis by TUNEL assay were performed. Expression of injury-related genes was analyzed by quantitative real-time PCR. RESULTS: Overexpression of TM4SF4 in rats after CCl4 treatment showed extensive liver damage and increased levels of serum ALT and AST. Decreased TM4SF4 gene expression showed minimal liver necrosis and depressed ALT and AST levels. Increased expression of TM4SF4 affected the expression levels of growth factors and receptors, such as TNF-alpha, TNFR1 and c-met. Furthermore, pro-apoptotic and anti-apoptotic gene expression was altered after TM4SF4 administration. CONCLUSIONS: Rat TM4SF4 is overexpressed in acutely injured liver induced by CCl4 and plays a crucial role in accelerating liver injury, which may be mediated by the TNF-alpha and HGF/c-met signaling pathways.

Alanine Transaminase↗
PubMed2006

Characterization and quantification of mRNA transcripts in ejaculated spermatozoa of fertile men by serial analysis of gene expression.

BACKGROUND: Accumulated evidence proves that mature spermatozoa contain a complex yet specific array of mRNA, which could provide information on the past events of spermatogenesis. OBJECTIVE: To quantitatively microdissect these mRNA transcripts by a digital approach. METHODS: Serial analysis of gene expression (SAGE) was used to study the mRNA transcripts from ejaculate of a fertile individual and of a pool of 10 fertile men. Online DAVID software suite was also utilized to cluster the UniGene data. RESULTS: A SAGE library from the individual produced 20,237 raw tags representing 2459 unique tags and that from pooled 10 men generated 21,052 raw tags representing 2712 unique tags. When the unique tags occurring > or = 4 times were analysed, 564 overlapping tags were produced by 638 unique tags from the individual and 682 from the pooled library. Fifty-four of these overlapped tags were considered to be novel genes. Online analysis of the overlapping tags revealed 25 functional gene groups, with the dominant one comprising 96 nuclear protein genes involving transcription and transcription regulation and also a group with 84 ribosomal subunit genes involving protein synthesis. CONCLUSION: A SAGE analysis of ejaculate from fertile men has revealed a large number of transcripts, which occur in steady frequencies and probably have important roles in spermatogenesis and fertilization.

Adult↗
PubMed2006

An RNA folding algorithm including pseudoknots based on dynamic weighted matching.

On the basis of maximum weighted matching (MWM) algorithm, we introduced a dynamic weight related with stem length and used a recursive algorithm to predict RNA secondary structures by searching the stem structure with maximum weight summation step-by-step. This algorithm not only avoids the complicated free energy calculation, but also it could attain higher prediction accuracy. Moreover, our algorithm can predict most types of potential pseudoknots in the RNA structure.

Algorithms↗
PubMed2006

[Egg cluster pattern of two coexisting melitaeine butterfly species and oviposition site selection of their adult females].

In this study, the oviposition sites of Euphydryas aurinia and Meiltaea phoebe adult females in the same habitat network were investigated, aimed to identify the factors affecting the patch quality. The results showed that the egg-laying females of both melitaeine butterfly species preferred to oviposit in the open areas with large-sized host plants and surrounded by short vegetations, especially on warm and sunny slopes. For E. aurinia, most of its egg clusters were concentrated within the area less than 3 m to the edge of cropland, and the average distance from each egg cluster to the edge of nearest cropland was 3.55 +/- 0.33 m (n = 246); but for M. phoebe, a few of its egg clusters distributed in the area less than 3 m to the edge, and the average distance was 7.43 +/- 1.53 m (n = 25). It was suggested that the criteria to evaluate the patch quality and the conservation strategies for the two butterfly species should be different, due to their special habitat requirements of ovipositing females.

Animals↗
PubMed2005

Construction of a eukaryotic expression plasmid encoding partial S gene fragments of the SARS-CoV and its potential utility as a DNA vaccine.

The spike (S) protein, a main surface antigen of the SARS coronavirus (SARS-CoV), is considered to be one of the most important protective antigen candidates for targets for vaccine design against the virus. In this study, a secreted recombinant expression plasmid, pVAX-S1, encoding the partial S protein with a signal peptide, was constructed and used to immunize BALB/c mice through electroporation. It was demonstrated that the eukaryotic expression vector pVAX-S1 was successfully constructed by restriction enzyme and sequence analysis. The expressed protein could be detected specifically by Western blot analysis. The serum IgG level of the vaccine group mice was significantly higher than that of the corresponding control group at day 14 after vaccination (P < 0.05). The vaccine group demonstrated significantly higher S1 protein lymphocyte proliferation index (LPI) than the control groups (P < 0.05). Furthermore, in the experimental group, a decrease in the ratio of CD4(+) to CD8(+) T-lymphocytes and an increase level of IFN-gamma in serum were observed. However, interleukin-4 (IL-4) was not detectable in two groups. These results strongly demonstrated that the pVAX-S1 plasmid could induce humoral and cellular immune responses in mice, and may be a potential candidate for a DNA vaccine against the SARS coronavirus.

Animals↗
PubMed2005

[Purification and analysis of polysaccharides from the caudex of Undaria pinnatifida].

To isolate polysaccharides with hot water from the caudex of Undaria pinnatifida, and precipitate with ethanol. The protein in polysaccharides was removed by sevage way. DEAE-52 and Sephadex G-200 column chromatography were used to isolate and purification polysaccharides, three purified polysaccharides F2, F3 and F4 were obtained. It was identified that they were homogeneity. The ultraviolet spectrum showed there was no proteins and nucleic acids in F2, F3 and F4. Through thin-layer chromatography analysis, F2, F3 and F4 were mainly composed of Gal, Fuc, Man and Glu acid. F2 also contained Glu and Rha.

Chromatography, Gel↗
PubMed2004

Methylation profiles of thirty four promoter-CpG islands and concordant methylation behaviours of sixteen genes that may contribute to carcinogenesis of astrocytoma.

BACKGROUND: Astrocytoma is a common aggressive intracranial tumor and presents a formidable challenge in the clinic. Association of altered DNA methylation patterns of the promoter CpG islands with the expression profile of cancer-related genes, has been found in many human tumors. Therefore, DNA methylation status as such may serve as an epigenetic biomarker for both diagnosis and prognosis of human tumors, including astrocytoma. METHODS: We used the methylation specific PCR in conjunction with sequencing verification to establish the methylation profile of the promoter CpG island of thirty four genes in astrocytoma tissues from fifty three patients (The WHO grading: I: 14, II: 15, III: 12 and IV: 12 cases, respectively). In addition, compatible tissues (normal tissues distant from lesion) from three non-astrocytoma patients were included as the control. RESULTS: Seventeen genes (ABL, APC, APAF1, BRCA1, CSPG2, DAPK1, hMLH1, LKB1, PTEN, p14ARF, p15INK4b, p27KIP1, p57KIP2, RASSF1C, RB1, SURVIVIN, and VHL) displayed a uniformly unmethylated pattern in all the astrocytoma and non-astrocytoma tissues examined. However, the MAGEA1 gene that was inactivated and hypermethylated in non-astrocytoma tissues, was partially demethylated in 24.5% of the astrocytoma tissues (co-existence of the hypermethylated and demethylated alleles). Of the astrocytoma associated hypermethylated genes, the methylation pattern of the CDH13, cyclin a1, DBCCR1, EPO, MYOD1, and p16INK4a genes changed in no more than 5.66% (3/53) of astrocytoma tissues compared to non-astrocytoma controls, while the RASSF1A, p73, AR, MGMT, CDH1, OCT6, MT1A, WT1, and IRF7 genes were more frequently hypermethylated in 69.8%, 47.2%, 41.5%, 35.8%, 32%, 30.2%, 30.2%, 30.2% and 26.4% of astrocytoma tissues, respectively. Demethylation mediated inducible expression of the CDH13, MAGEA1, MGMT, p73 and RASSF1A genes was established in an astrocytoma cell line (U251), demonstrating that expression of these genes is likely regulated by DNA methylation. AR gene hypermethylation was found exclusively in female patients (22/27, 81%, 0/26, 0%, P < 0.001), while the IRF7 gene hypermethylation preferentially occurred in the male counterparts (11/26, 42.3% to 3/27, 11%, P < 0.05). Applying the mathematic method "the Discovery of Association Rules", we have identified groups consisting of up to three genes that more likely display the altered methylation patterns in concert in astrocytoma. CONCLUSIONS: Of the thirty four genes examined, sixteen genes exhibited astrocytoma associated changes in the methylation profile. In addition to the possible pathological significance, the established concordant methylation profiles of the subsets consisting of two to three target genes may provide useful clues to the development of the useful prognostic as well as diagnostic assays for astrocytoma.

Adolescent↗
PubMed2004

[Expression of the cystatin-related epididymal spermatogenic gene in mouse testes and epididymis at different postnatal stages].

OBJECTIVE: To investigate the expression pattern of the cystatin-related epididymal spermatogenic (Cres) gene in mouse testes and epididymis during postnatal development. METHODS: Semi-quantitative RT-PCR was used to detect the Cres mRNA level in postnatal mouse testes and epididymis on day 14, 20, 22, 28, 35, 49, 70 and 400. RESULTS: Low-level Cres mRNA was detected on day 14 in both the testes and the epididymis. The expression of the Cres gene increased gradually with the development of the mouse, and it reached the peak on day 70 in the testes and on day 400 in the epididymis. CONCLUSION: The time-dependent expression pattern of the Cres gene in postnatal mouse testes and epididymis suggested that the Cres gene might be involved in the regulation of spermatogenesis and sperm maturation.

Age Factors↗
PubMed2004

[Study on extraction process of the volatile oil for biyuan dropping pills].

OBJECTIVE: To determine the optimal extracting process of the volatile oil for Biyuan Dropping Pills. METHODS: Conditions for the extraction were studied by orthogonal design guided by the increasement of the volatile oil. RESULTS: The distilling time is the main factor,and the fineness of the herbal material is the second. The optimal process is as follows: crush the herbal material into coarse powder, macerate 1 hour with 9 times water and distill 4 hours. CONCLUSION: The optimized process is feasible and stable.

Analysis of Variance↗
PubMed2003

Anatomy of specific interactions between lambda repressor and operator DNA.

Recognition of specific DNA sequences by proteins is essential for regulation of gene expression. To fully understand the recognition mechanism, it is necessary to understand not only the structure of the specific protein-DNA interactions but also the energetics. We therefore performed a computer analysis in which a phage DNA-binding protein, lambda repressor, was used to examine the changes in binding free energy (DeltaDeltaG) and its energy components caused by single base mutations. We then determined which of the calculated energy components best correlated with the experimental data. The experimental DeltaDeltaG values were well reproduced by the calculations. Component analysis revealed that the electrostatic and hydrogen bond energies were most strongly correlated with the experimental data. Among the 51 single base-substitution mutants examined, positive DeltaDeltaG values, corresponding to weakened binding, were caused by the loss of favorable electrostatic interactions and hydrogen bonds, the introduction of steric collisions and electrostatic repulsion, the loss of favorable interactions with a thymine methyl group, and the increase of unfavorable hydration energy from isolated DNA. This analysis also showed distinct patterns of recognition at A-T and G-C positions, as different combinations of energy components were involved in DeltaDeltaG caused by the two substitution types. We have thus been able to identify the energy components that most strongly correlate with sequence-dependent DeltaDeltaG and determine their contribution to the specificity of DNA sequence recognition by the lambda repressor. Application of this method to other systems should provide additional insight into the molecular mechanism of protein-DNA recognition.

Amino Acids↗
PubMed2003

Genetic differentiation within metapopulations of Euphydryas aurinia and Melitaea phoebe in China.

We analyzed genetic differentiation within metapopulations of two species of checkerspot butterfly, Euphydryas aurinia and Melitaea phoebe, in China. To generate genetic information, we used a new molecular technique, DALP - direct amplified length polymorphism. AMOVA results showed that most of the variation occurred among individuals within local populations of both E. aurinia and M. phoebe. However, while there was differentiation among local population in E. aurinia (P < 0.001), there was no subdivision in metapopulation of M. phoebe (P = 0.210). This is consistent with the behavior of M. phoebe adults being more dispersive than E. aurinia. Within the M. phoebe metapopulation, three neighboring patches were always occupied during the observation period (1998-2000). In addition, the number of individuals in these three populations accounted for the majority of M. phoebe larvae, and hence we conclude that the M. phoebe metapopulation might exist as a source-sink metapopulation. On the other hand, the E. aurinia metapopulation is an example of a classical metapopulation. Therefore, the conservation management of these two species should reflect these differences.

Analysis of Variance↗
PubMed2003

Inhibiting severe acute respiratory syndrome-associated coronavirus by small interfering RNA.

OBJECTIVE: To evaluate the effectiveness of small interfering RNA (siRNA) on inhibiting severe acute respiratory syndrome (SARS)-associated coronavirus replication, and to lay bases for the future clinical application of siRNA for the treatment of viral infectious diseases. METHODS: Vero-E6 cells was transfected with siRNA before SARS virus infection, and the effectiveness of siRNA interference was evaluated by observing the cytopathic effect (CPE) on Vero-E6 cells. RESULTS: Five pairs of siRNA showed ability to reduce CPE dose dependently, and two of them had the best effect. CONCLUSION: siRNA may be effective in inhibiting SARS-associated coronavirus replication.

Animals↗