Biochemical Genetics[JOURNAL]
Sun
200 papers
Microsatellite Markers Display High Diversity in Bean Anthracnose Pathogen Colletotrichum lindemuthianum in Kashmir.
Fayaz T, Nabi A, Nabi N … +13 more , Lateef I, Junaid R, Nisa Q, Khursheed S, Bashir A, Rashid Z, Itoo H, Shah RA, Banday S, Zargar SM, Khan I, Shah MD, Padder BA
Biochem Genet · 2026 Jan · PMID 41579225 · Publisher ↗
Common bean (Phaseolus vulgaris) anthracnose, caused by Colletotrichum lindemuthianum affects and decreases its yield substantially. Fifty Simple Sequence Repeat (SSR) markers were used to analyze the genetic and genotyp...
Common bean (Phaseolus vulgaris) anthracnose, caused by Colletotrichum lindemuthianum affects and decreases its yield substantially. Fifty Simple Sequence Repeat (SSR) markers were used to analyze the genetic and genotypic variation among 36 C. lindemuthianum isolates. Among the 50 SSRs, 24 were polymorphic and amplified 66 alleles. Most of the SSRs had polymorphic information content (PIC) values > 0.30, indicating their strong discriminative competence. Distance based dendrogram analysis and population structure analysis divided 36 C. lindemuthianum isolates into three clusters. Analysis of molecular variance at spatiotemporal levels showed high genetic variation among the populations. The six C. lindemuthianum subpopulations had high Shannon-Wiener indices. The multilocus genotype and genetic diversity indices show that C. lindemuthianum populations in Kashmir are diverse. The three geographic subpopulations of C. lindemuthianum rejected the null hypothesis of linkage equilibrium (p = 0.001). Before this study, all PCR based genetic diversity studies on C. lindemuthianum relied on dominant markers. This study is the first to identify 24 robust SSRs, which can be utilized to elucidate the population structure of the common bean anthracnose pathogen.
Genetic Diversity and Population Structure of Tunisian Festuca Arundinacea Schreb. Revealed by Functional Gene-Based Markers.
Chadded H, Guenni K, Crespan M … +2 more , Sai-Kachout S, Chtourou-Ghorbel N
Biochem Genet · 2026 Jan · PMID 41557072 · Publisher ↗
Tall fescue (Festuca arundinacea Schreb.), taxonomically synonymous with Lolium arundinaceum (Schreb.) Darbysh., is a cool-season perennial grass valued for adaptability, forage quality, and stress tolerance. This study...
Tall fescue (Festuca arundinacea Schreb.), taxonomically synonymous with Lolium arundinaceum (Schreb.) Darbysh., is a cool-season perennial grass valued for adaptability, forage quality, and stress tolerance. This study evaluated the genetic diversity and population structure of 32 Tunisian spontaneous populations and 3 local varieties using CAAT-box Derived Polymorphism (CBDP) and Conserved DNA-Derived Polymorphism (CDDP) markers. Out of 16 tested primers (8 CBDP and 8 CDDP), 12 (7 CBDP and 5 CDDP) generated reproducible and polymorphic banding patterns, producing a total of 124 bands for CBDP and 121 bands for CDDP. High polymorphism was observed (86.29% for CBDP; 74.38% for CDDP), with a mean polymorphism information content (PIC) of 0.378, confirming the informativeness of both marker systems. Clustering analyses based on CBDP, CDDP, and combined data revealed some grouping tendencies among populations, but these groupings were not strictly associated with geographic origin, bioclimatic stage, or whether populations were spontaneous or cultivated. STRUCTURE analysis suggested two clusters for each marker system, but accessions showed overlapping membership, indicating weak population structure. The combined dataset detected four admixed groups, yet all populations displayed high admixture, reflecting high genetic diversity and extensive gene flow in this outcrossing species. Analysis of molecular variance (AMOVA) indicated that over 97% of the total genetic variation occurred within regions, while PhiPT values were low but significant (P = 0.004). No isolation by distance was detected with the Mantel test (CBDP: r = 0.011, p = 0.419; CDDP: r = 0.087, p = 0.078). This study is the first to apply CBDP and CDDP markers in Tunisian tall fescue populations, demonstrating their efficiency in revealing genetic diversity. The findings highlight substantial genetic diversity among populations within regions and underscore the value of this germplasm for breeding and conservation efforts.
Mechanisms of DDR1 in Reinforcing the Resistance to Radiotherapy in Breast Cancer Through the AMPK/SIRT1/PGC-1α Pathway.
Wang S, Chen Y, Wei J … +2 more , Wu H, Li J
Biochem Genet · 2026 Jan · PMID 41557071 · Publisher ↗
Breast cancer (BC) is the leading cause of cancer mortality in women. The emergence of resistance to radiotherapy (RT) is a great challenge for BC treatment. Discoidin domain receptor 1 (DDR1) can modulate the proliferat...
Breast cancer (BC) is the leading cause of cancer mortality in women. The emergence of resistance to radiotherapy (RT) is a great challenge for BC treatment. Discoidin domain receptor 1 (DDR1) can modulate the proliferation, migration, and apoptosis of cancer cells, but its role in RT of BC has not been illuminated. This project evaluated the expression of DDR1 in BC based on single-cell RNA sequencing data. We established RT-resistant strains through radiation and detected the expression of DDR1 using qPCR. The proliferation and apoptosis abilities of BC cells were evaluated using CCK-8, colony formation assay, and flow cytometry. Western blot and IHC were applied to detect the levels of proteins related to the AMPK/SIRT1/PGC-1α pathway. The effect of the DDR1-mediated pathway on resistance to RT in BC was explored in combination with an AMPK inhibitor. DDR1 was highly expressed in BC. In vitro experiments demonstrated that knocking down DDR1 repressed the viability of BC cells during RT, curbed cell proliferation, facilitated apoptosis, and elevated the levels of p-AMPK, SIRT1, and PGC-1α proteins. The addition of an AMPK inhibitor reversed the effects of DDR1 knockdown on cell proliferation and apoptosis. In vivo experiments showed that knocking down DDR1 inhibited tumor growth, and the inhibitory effect was stronger when combined with radiation therapy. This study revealed that the upregulation of DDR1 in BC may reinforce RT resistance by modulating the AMPK/SIRT1/PGC-1α pathway, thus providing a new therapeutic target for improving the sensitivity of BC to RT.
A Boruta-SMOTE Integrated Approach for Rapid Donkey Breed Classification Using SNP Data: Addressing High-Dimensionality and Small Sample Challenges.
Li C, Xu S, Li D … +2 more , Hu X, Jia B
Biochem Genet · 2026 Jan · PMID 41533190 · Publisher ↗
With the increasing complexity of genomic data, traditional classification methods face dual challenges of the "curse of dimensionality" and class imbalance when processing multiple single nucleotide polymorphism (SNP) m...
With the increasing complexity of genomic data, traditional classification methods face dual challenges of the "curse of dimensionality" and class imbalance when processing multiple single nucleotide polymorphism (SNP) markers. To address these challenges, this study proposes an innovative approach integrating the Boruta dimensionality reduction algorithm with the Synthetic Minority Over-sampling Technique (SMOTE). The methodology involves two key steps: Feature optimization using the Boruta algorithm to identify the most representative genetic markers, thereby significantly reducing the complexity of high-dimensional data. Application of SMOTE technology to generate synthetic samples, balancing minority class distributions and alleviating data imbalance issues. Experimental results demonstrate that the proposed method outperforms traditional classifiers (Random Forest [RF], K-Nearest Neighbors [KNN], Extreme Gradient Boosting [XGBoost] and Convolutional Neural Network [CNN]) without Boruta-SMOTE integration across multiple metrics including accuracy, precision, recall, and F1-score. This study provides new insights for the conservation of donkey genetic resources, breed improvement, and commercial applications, while offering an effective solution for genomic data classification challenges.
Spectrum of DNA Variants Underlying Deafness in an Ecuadorian Cohort.
Reinoso-Castillo A, Ramzan M, Carrera-Gonzalez A … +6 more , Rivas-Iglesias C, Montufar S, Vinueza-Gavilanes R, Smith C, Llamos-Paneque A, Tekin M
Biochem Genet · 2026 Jan · PMID 41513900 · Publisher ↗
The genetic etiology of hearing loss (HL) in Ecuador remains largely unexplored. This study investigates the spectrum of genetic variants associated with HL in a cohort of 66 Ecuadorian families using Exome or Genome seq...
The genetic etiology of hearing loss (HL) in Ecuador remains largely unexplored. This study investigates the spectrum of genetic variants associated with HL in a cohort of 66 Ecuadorian families using Exome or Genome sequencing (ES/GS). We identified pathogenic and likely pathogenic variants underlying HL in 27 families (41%). While variants were detected in 15 different genes, only GJB2 (in 12 families) and TMC1 (in 3 families) variants were identified in more than one family. The NM_004004.6 (GJB2):c.19 C > T (p.Gln7*) and NM_004004.6 (GJB2):c.35delG (p.Gly12Valfs*2) variants were more common than other alleles in GJB2. In some families, we detected variants of uncertain significance (VUS) in well-established HL genes and classified them as "possibly solved" due to their rarity and equivocal functional predictions. This study provides valuable insights into the genetic basis of HL in Ecuador and lays the groundwork for improved regional genetic diagnostics and management.
Identification of Susceptibility Genes for Hypertension in the Dong Ethnic Population of Tongdao.
Zhou T, Yang Z, Wang H … +4 more , Song Z, Xiao Y, Hang Y, Yang T
Biochem Genet · 2026 Jan · PMID 41507431 · Publisher ↗
This study aimed to identify susceptibility genes of hypertension in Tongdao Dong ethnic group. 38 hypertension candidate genes with their 42 single nucleotide polymorphisms (SNPs) screened from our previous study were s...
This study aimed to identify susceptibility genes of hypertension in Tongdao Dong ethnic group. 38 hypertension candidate genes with their 42 single nucleotide polymorphisms (SNPs) screened from our previous study were selected for genotyping using MALDI-TOF mass spectrometry in a total of 359 participants, including 242 hypertensive patients and 117 healthy controls. The genotype and allele frequencies of these 42 SNPs were compared between the normotensive and hypertensive groups. 7 SNPs (KLK2 rs198972, MGAT1 rs634501, ABCA1 rs2066714, ADRB1 rs1801253, CLCN2 rs2228291, FOLH1 rs202680, and SCNN1G rs5735) exhibiting significant differences in genotypic and/or allelic frequencies between the two groups were subsequently selected for hypertension risk analysis. Logistic regression analysis with adjustment for the same factors revealed that the homozygous mutant GG genotype of MGAT1 SNP rs634501 enhanced the risk of hypertension, whereas carriers of the T minor allele of KLK2 SNP rs198972 showed a decreased risk of hypertension. Association analysis of SNPs with hypertension-related risk factors showed that MGAT1 rs634501 was significantly associated with SBP and DBP. Thus, our study suggests that MGAT1 may be a susceptibility gene for hypertension in the Dong Ethnic Population of Tongdao.
Complete Genome Sequencing of Streptomyces sp. Qhu-M197 Isolated from Alpine Meadows in the Qinghai-Tibetan Plateau Uncovers Biosynthetic Gene Clusters Encoding Bioactive Natural Products.
Xiang X, Fan J, Liu X … +3 more , Li G, Sun C, Zhang B
Biochem Genet · 2026 Jan · PMID 41504849 · Publisher ↗
Streptomyces spp. is a crucial source for the drug discovery and development, especially those from extreme environments. The complete genome was sequenced to uncover the biosynthetic potential of the strain Qhu-M197 pro...
Streptomyces spp. is a crucial source for the drug discovery and development, especially those from extreme environments. The complete genome was sequenced to uncover the biosynthetic potential of the strain Qhu-M197 producing mithramycin isolated from the alpine meadow of the Qinghai-Tibetan Plateau. The results revealed that the genome consists of one linear chromosome and two plasmids with the size of 9.12 megabases (Mb) and the guanine-cytosine (G + C) content of 71.52%. The phylogenetic analyses of 16S rRNA gene and genome of strain Qhu-M197 suggested the strain belonged to Streptomyces genus, and the closest phylogenetic relationship between the strain Qhu-M197 and S. phaeoluteigriseus DSM 41896. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between Qhu-M197 and S. phaeoluteigriseus DSM 41896 are 97.47% and 84.1%, respectively, indicating that they likely belong to the same species. However, comparative genomic analysis with closely related species reveals that Qhu-M197 may represent a novel strain of S. phaeoluteigriseus, highlighting its potential distinction at the strain level. The biosynthetic gene clusters (BGCs) analyzed by antiSMASH v7.0 revealed that Qhu-M197 had 33 BGCs encoding secondary metabolites. Interestingly, about 64% BGCs show less than 50% similarity to those annotated, which provides new opportunities for the discovery of novel natural products.
FBXW7 Inhibited M2 Macrophage Polarization in Endometrial Cancer by Reducing CCL2 Secretion Through Ubiquitination of MYBL2 Subtitle: The Role of FBXW7 on M2 Macrophage Polarization in EC.
Wu J, Zhang X, Xu W … +1 more , Shen X
Biochem Genet · 2026 Jan · PMID 41484508 · Publisher ↗
Impeding M2 macrophage polarization has been suggested to slow the progression of endometrial cancer (EC). F-box and WD repeat domain containing 7 (FBXW7) reportedly regulates the polarization and migration of macrophage...
Impeding M2 macrophage polarization has been suggested to slow the progression of endometrial cancer (EC). F-box and WD repeat domain containing 7 (FBXW7) reportedly regulates the polarization and migration of macrophages in a multitude of cancers. Our pre-existing bioinformatics predictions showed a negative association between FBXW7 and M2-TAM infiltration in EC. This study aimed to investigate the role of FBXW7 in M2 macrophage polarization in EC by regulating the MYBL2/CCL2 axis. Cancer and adjacent cancerous tissues from patients with EC were collected to detect the differential expression of each factor. CCL2 levels in the cell culture medium were examined using enzyme-linked immunosorbent assay. Immunofluorescence staining was performed to determine the localization of FBXW7 and MYBL2 in EC cells. The number of M2 macrophages marker was determined by flow cytometry. The protein levels of FBXW7, MYBL2, CCL2, CD206, CD163, Arg1, and IL-10 were assessed using western blotting. The ubiquitination level of MYBL2 and the binding relationship between FBXW7 and MYBL2 were verified using co-immunoprecipitation. The effect of FBXW7/MYBL2/CCL2 axis on the malignant progression of EC in vivo was evaluated using tumor xenografts in nude mice. FBXW7 levels were decreased, whereas MYBL2 levels were increased in EC. Overexpression of FBXW7 downregulated CCL2 secretion in EC and inhibited M2 macrophage polarization. FBXW7 promoted the degradation of MYBL2 in a ubiquitination-dependent manner. FBXW7 knockdown inhibited CCL2 secretion by EC cells to restrain M2 macrophage polarization, which was countered by MYBL2 downregulation. In vivo functional assays demonstrated that FBXW7 overexpression significantly suppressed EC xenograft growth and enhanced tumor cell apoptosis. FBXW7 enhanced the ubiquitination and degradation of MYBL2 to reduce CCL2 secretion from EC, which inhibited macrophage polarization to the M2 type.
Translation Initiation Fidelity Defective Mutations in eIF5 and eIF2β Show Distinct Sensitivity to the Sequence Context for Recognition of the UUG Start Codon.
Ram AK, Kole T, Alone PV
Biochem Genet · 2025 Dec · PMID 41460464 · Publisher ↗
In Saccharomyces cerevisiae, the AUG codon typically signals translation initiation to set an open reading frame, with a preference for the AAA/U(AUG)U sequence context. The mutant eIF5 or eIF2β proteins cause translatio...
In Saccharomyces cerevisiae, the AUG codon typically signals translation initiation to set an open reading frame, with a preference for the AAA/U(AUG)U sequence context. The mutant eIF5 or eIF2β proteins cause translation initiation fidelity defect by initiating translation at a near cognate UUG codon, in addition to the AUG start codon (suppressor of initiation codon; Sui¯ phenotype). However, the critical role of the - 3 to - 1 sequences in selecting the UUG start codon by these Sui¯ mutants is not fully explored. Different HIS4-LacZ reporter constructs were made with UUG as the start codon and varied nucleotides at the - 3 and - 2 positions or individually at -1 positions. These constructs were transformed to yeast cells having eIF5 or eIF2β mutation, and the β-galactosidase activity was measured. The HIS4-LacZ transcripts carrying a purine (A/G) at the - 3 position showed higher reporter activity than those with a pyrimidine (U/C). Additionally, purines were favored at the - 1 position within an AA (- 3 and - 2) context for efficient UUG start codon selection. Our findings demonstrate that UUG start codon recognition by Sui¯ mutants eIF5 and eIF2β is greatly influenced by the surrounding nucleotide context, each showing distinct context preferences. This highlights the nuanced role of sequence context in the near-cognate UUG codon initiation by the Sui¯ mutants.
Genetic Variants in EMT-Related lncRNAs Modulate the Risk of Colorectal Cancer in the Chinese Population.
Gu S, Zhang Z, Cheng K … +5 more , Yeerken A, Qian S, Guo F, Jin M, Chen K
Biochem Genet · 2025 Dec · PMID 41405661 · Publisher ↗
Epithelial-mesenchymal transition (EMT) is critical in tumor progression and metastasis, with long non-coding RNAs (lncRNAs) as key regulatory elements. This study explored the association between genetic variants in EMT...
Epithelial-mesenchymal transition (EMT) is critical in tumor progression and metastasis, with long non-coding RNAs (lncRNAs) as key regulatory elements. This study explored the association between genetic variants in EMT-related lncRNAs and colorectal cancer (CRC) risk in a Chinese population. A case-control study was conducted involving 1,888 untreated CRC cases and 1,888 cancer-free controls. Multivariate logistic regression models were used to assess effects of SNPs on CRC risk, while expression quantitative trait loci (eQTL) analysis used data from the Genotype-Tissue Expression (GTEx) project, and gene expression was evaluated using The Cancer Genome Atlas (TCGA) database. Four functionally relevant SNPs (AC106786.1 rs76180806, rs2277930, LINC00578 rs28711160, and RP1-193H18.2 rs17823238) were significantly associated with CRC risk (OR = 1.52, 95% CI = 1.26-1.83, P = 1.57 × 10 ; OR = 1.34, 95% CI = 1.15-1.57, P = 3.30 × 10 ; OR = 1.21, 95% CI = 1.09-1.33, P = 3.30 × 10 ; OR = 0.83, 95% CI = 0.75-0.92, P = 3.30 × 10 ). Notably, rs28711160 exhibited a significant eQTL effect on LINC00578 expression (P = 2.09 × 10), and LINC00578 expression levels correlated strongly with CRC risk. These findings indicate that genetic variants in EMT-related lncRNAs (AC106786.1, LINC00578, RP1-193H18.2) may contribute to CRC susceptibility and could serve as candidate biomarkers, providing new insights into the genetic architecture of CRC.
FABP7 Enhances Endometrial Cancer Cell Migration and Stemness by Activating the Wnt/β-catenin Pathway.
Xu Y, Wang X, Tang L … +2 more , Shi L, Li M
Biochem Genet · 2025 Dec · PMID 41402614 · Publisher ↗
Endometrial cancer is a common malignancy of the female reproductive system and poses a significant threat to women's health. Fatty acid binding protein 7 (FABP7) plays a key role in regulating lipid metabolism, signal t...
Endometrial cancer is a common malignancy of the female reproductive system and poses a significant threat to women's health. Fatty acid binding protein 7 (FABP7) plays a key role in regulating lipid metabolism, signal transduction, and gene expression, and has been implicated in the progression of various cancers. However, its role in endometrial cancer remains unclear. The mRNA and protein expression levels were assessed by RT-qPCR and western blot analysis. Cell proliferation was evaluated using the CCK-8 and colony formation assays. Cell migration and invasion were assessed through wound healing and Transwell assays, while cancer stemness was evaluated using the sphere formation assay. FABP7 was found to be highly expressed in endometrial cancer cells. Knockdown of FABP7 significantly suppressed cell proliferation, migration, and invasion. Furthermore, FABP7 silencing reduced stemness capacity, as evidenced by diminished sphere-forming ability. Mechanistically, downregulation of FABP7 led to inhibition of the Wnt/β-catenin signaling pathway. This study demonstrates that FABP7 can promote cell migration and stemness in endometrial cancer by activating the Wnt/β-catenin pathway, supporting FABP7 as a potential therapeutic target for the clinical management of endometrial cancer.
Transcription Activation of DEPDC1B Upon EBF1 Loss Contributes to Cell Cycle Progression and Epithelial-Mesenchymal Transition in Colon Adenocarcinoma.
Li Y, Shi X, Ling B … +2 more , Su X, Zhang J
Biochem Genet · 2025 Dec · PMID 41402613 · Publisher ↗
Grounded on bioinformatics insights, this study investigates the interaction between DEP domain containing 1B (DEPDC1B) and early B cell factor 1 (EBF1), their expression patterns, and their functions in the progression...
Grounded on bioinformatics insights, this study investigates the interaction between DEP domain containing 1B (DEPDC1B) and early B cell factor 1 (EBF1), their expression patterns, and their functions in the progression of colon adenocarcinoma (COAD). DEPDC1B was identified as a potential oncogene aberrantly expressed in COAD, and its high expression was detected in COAD cell lines. DEPDC1B silencing in COAD cell lines while blocking epithelial-mesenchymal transition (EMT), dissemination, and expansion of COAD cells in vitro. Additionally, DEPDC1B knockdown suppressed tumorigenic activity and metastasis of mouse CT26 cells in isograft tumor models. EBF1, poorly expressed in COAD, was found to repress DEPDC1B transcription. EBF1 overexpression reduced DEPDC1B expression, thus diminishing the malignant properties of cancer cells. Nevertheless, its tumor-suppressive effects were negated by DEPDC1B restoration. EBF1 presented a promoter hypermethylation pattern in COAD cell lines, in which its expression was restored upon treatment of the methylation inhibitor 5-azacytidine. In conclusion, this study highlights that the hypermethylation of EBF1 leads to transcription activation of DEPDC1B, which promotes cell cycle progression, EMT, and malignant progression in COAD. Restoring EBF1 levels or suppressing DEPDC1B expression may be promising strategies for COAD management.
Integrating RNA-seq and Single-Cell RNA-seq to Uncover Transcriptional Signature of Fibroblasts in Oral Squamous Cell Carcinoma.
Wen N, Gai L, Tao Y … +1 more , Shen Z
Biochem Genet · 2025 Dec · PMID 41402612 · Publisher ↗
This study aimed to explore the transcriptional profile of fibroblasts in oral squamous cell carcinoma (OSCC) to identify novel therapeutic targets. We utilized data from two sources: The Cancer Genome Atlas Head and Nec...
This study aimed to explore the transcriptional profile of fibroblasts in oral squamous cell carcinoma (OSCC) to identify novel therapeutic targets. We utilized data from two sources: The Cancer Genome Atlas Head and Neck Squamous Cell Carcinoma (TCGA-HNSC) dataset and single-cell RNA sequencing (scRNA-seq) data. The TCGA-HNSC dataset was used to identify differentially expressed genes (DEGs), while the scRNA-seq data was used to explore fibroblast heterogeneity and their interactions within the tumor microenvironment. Integrated analyses, including CNV analysis, enrichment analysis, transcription factor prediction, and protein–protein interaction network construction, were conducted to explore fibroblast regulation in OSCC. HGF-1 fibroblasts were transfected with siRNAs targeting COL1A1 or ITGA5, and conditioned media (CM) was collected from the silenced cells. CAL-27 oral squamous carcinoma cells were then treated with these CM to evaluate changes in proliferation, migration, invasion, and epithelial mesenchymal transition related signaling. We identified 19 DEGs shared by both datasets and highlighted six genes potentially involved in OSCC progression, which are involved in focal adhesion. Silencing COL1A1 or ITGA5 in fibroblasts reduced CAL-27 cell viability, migration, and invasion. CM from knockdown fibroblasts promoted E-cadherin expression while suppressing vimentin, indicating inhibition of EMT and decreased FAK and AKT phosphorylation, suggesting impaired focal adhesion–mediated signaling. This study reveals fibroblast-specific transcriptional features and identifies potential therapeutic targets for OSCC. Functional validation highlights COL1A1 and ITGA5 as key promoters of OSCC progression. These findings emphasize the critical role of fibroblasts in the OSCC microenvironment and provide promising molecular targets for therapeutic development.
Do Genomic Patterns and Fibonacci-Like Regularity Hold the Key to Reproductive Fitness in Livestock?
Nayak SS, Parida S, Dutt T … +1 more , Panigrahi M
Biochem Genet · 2025 Dec · PMID 41385028 · Publisher ↗
The recurring Fibonacci sequence in various biological systems proves that mathematical ideas are frequently mirrored in natural patterns. This work assumes the compelling theory that cattle genomes may exhibit similar p...
The recurring Fibonacci sequence in various biological systems proves that mathematical ideas are frequently mirrored in natural patterns. This work assumes the compelling theory that cattle genomes may exhibit similar periodic and recursive patterns, particularly in regions associated with reproductive fitness. Unregulated crossbreeding can jeopardize indigenous germplasm and disturb natural genomic configurations, endangering genetic diversity and the structural integrity of the genome. We suggest that animal genomes may follow observable mathematical patterns by looking at haplotype and single-nucleotide polymorphism (SNP) distributions. Finding these hidden patterns through whole genome sequencing (WGS) is crucial for rethinking genetic improvement strategies in livestock breeding programs and providing insights into optimising reproductive traits.
Comparative Analysis of Codon Usage Patterns in Chloroplast Genomes of Maple (Genus Acer).
Zhang Y, Ma Y, Gao J … +2 more , Ma W, Yu T
Biochem Genet · 2025 Dec · PMID 41359224 · Publisher ↗
Maple (Acer genus), deciduous perennial trees belong to the Sapindaceae family, thrive naturally across Asia, Europe and North America. In addition to their wide use in woodwork and pharmaceuticals, Acer species are favo...
Maple (Acer genus), deciduous perennial trees belong to the Sapindaceae family, thrive naturally across Asia, Europe and North America. In addition to their wide use in woodwork and pharmaceuticals, Acer species are favored choices for contemporary landscape design because of their large stature, intricate foliage patterns, vibrant colors, distinctive fruit shapes (paired winged samaras), and extensive genetic diversity. Understandably, they play a pivotal role in enhancing urban ecosystems and contributing to landscape construction. The aim of this study was to investigate the genomic characteristics and extent of codon usage bias (CUB) variation in the chloroplast (cp.) genome of ten sections of the genus Acer. Synonymous codon usage order (SCUO) indicated a weak codon usage bias (CUB) in the cp. genes of various Acer species. Notably, the third position of the codons exhibited a significant correlation with the overall nucleotide composition, suggesting that both natural selection and mutation pressure may have influenced the CUB. The Effective Number of Codon (ENC)-plot, Parity Rule 2 (PR2), and neutrality analyses showed that the codon bias of Acer cp. genetic material was influenced by several factors. While our analyses suggest a significant role for natural selection in shaping codon usage bias, as indicated by the ENC-plot analysis deviating from neutrality expectations, the contribution of mutation pressure and potentially genetic drift cannot be entirely excluded. These findings provide insights into codon usage patterns, which may be useful for future studies aiming to optimize codon usage for exogenous gene expression in the Acer cp. genome.
Annexin-A1 Regulates Apoptosis-Autophagy Switch in a 5-FU-Resistant Colorectal Cancer Stem-Like Model Through the PI3K/AKT/mTOR Axis.
Ganesan T, Ramasamy TS, Alshawsh MA … +1 more , Sinniah A
Biochem Genet · 2025 Dec · PMID 41354954 · Publisher ↗
Colorectal cancer (CRC) remains a leading cause of cancer-related deaths globally, primarily due to treatment failure associated with metastasis and recurrence driven by chemoresistant cancer stem-like cells (CSCs). Anne...
Colorectal cancer (CRC) remains a leading cause of cancer-related deaths globally, primarily due to treatment failure associated with metastasis and recurrence driven by chemoresistant cancer stem-like cells (CSCs). Annexin A1 (Anx-A1) is implicated in regulating apoptosis and autophagy, two crucial mechanisms contributing to chemoresistance. However, the precise role of Anx-A1 in modulating these mechanisms in CRC CSCs, specifically via the PI3K/AKT/mTOR pathway, is not well understood. This study aimed to explore the role of Anx-A1 in modulating apoptosis-autophagy interplay in a 5-FU-resistant colorectal CSC model using HCT 116, particularly through its regulatory effects on the PI3K/AKT/mTOR signaling pathway. A 5-FU-resistant CRC CSC model was developed by sequentially exposing HCT 116 cells to 5-fluorouracil (5-FU). The model was characterized by assessing CSC markers (CD133, ALDH1, ABCG2, Oct-3/4) via flow cytometry and Simple Western analysis. Anx-A1 knockdown and overexpression were performed using siRNA and expression plasmids, respectively. Chemosensitivity was evaluated through cell viability assays, while apoptosis and autophagy markers were assessed by caspase assays, proteome profiler arrays, Western blotting, and autophagy flux analysis. The expression levels of PI3K, p-PI3K, AKT, p-AKT, and mTOR were quantified using Simple Western analysis. The 5-FU-resistant HCT 116 demonstrated significantly elevated IC values, heightened expression of CSC markers, and increased Anx-A1 expression. Knockdown of Anx-A1 markedly enhanced chemosensitivity, significantly reduced cell viability, and modulated CSC marker expression. Anx-A1 knockdown led to mild induction of apoptosis characterized by increased caspase activity, concurrent downregulation of multiple apoptotic proteins, and substantial autophagy induction demonstrated by increased LC3-II and p62 expression, and enhanced autophagosome degradation. Analysis of the PI3K/AKT/mTOR pathway revealed that Anx-A1 knockdown significantly increased phosphorylated PI3K p85α and AKT1/2/3, and substantially downregulated mTOR, illustrating the dynamic regulation of apoptosis-autophagy interplay. Anx-A1 modulates 5-FU induced-chemoresistance in colorectal CSCs by orchestrating the apoptosis-autophagy balance through the PI3K/AKT/mTOR pathway. Targeting Anx-A1 provides a promising therapeutic strategy to enhance chemosensitivity and overcome resistance in CRC treatment.
Tanshinone IIA Inhibits Microglial Activation and Inflammation and Relieves Cerebral Ischemia‒Reperfusion Injury Through TGM2/PANX1.
Yu H, Zhang R, Wang Q … +7 more , Zhang H, Lei Z, Li R, Shen W, Zhang Y, Lv S, Qian Y
Biochem Genet · 2025 Dec · PMID 41351813 · Publisher ↗
Microglial activation and induced inflammation play important roles in cerebral ischemia‒reperfusion injury (CIRI). Tanshinone IIA (Tan IIA) is a natural extract from Chinese herbal medicines that has anti-inflammatory,...
Microglial activation and induced inflammation play important roles in cerebral ischemia‒reperfusion injury (CIRI). Tanshinone IIA (Tan IIA) is a natural extract from Chinese herbal medicines that has anti-inflammatory, antioxidant, antiapoptotic and neuroprotective properties and has a protective effect against CIRI. This study aimed to investigate the effects of Tan IIA on microglial activation and inflammation under CIRI and the underlying molecular mechanism. Experimental investigations were conducted using rat and cellular models of CIRI induced by middle cerebral artery occlusion (MCAO) and oxygen‒glucose deprivation/reperfusion (OGD/R), respectively. The neuroprotective effects of Tan IIA on CIRI rats were evaluated through neurological deficit scores, TTC staining, and H&E staining. Immunofluorescence staining and ELISA were used to detect microglial activation and the expression of inflammatory molecules. In this study, treatment with Tan IIA significantly improved neurological deficits, reduced infarct size, and ameliorated pathological damage to the cerebral cortex in CIRI rats. It also decreased the expression of microglial marker Iba-1 and activation marker TSPO, as well as the expression of pro-inflammatory factors TNF-α, IL-1β and IL-6. In terms of molecular mechanisms, the expression of PANX1 and TGM2 is upregulated in this disease, and TGM2 binds to PANX1. The overexpression of PANX1 or TGM2 attenuated the inhibitory effect of Tan IIA on OGD/R-induced microglial activation and inflammation. Overall, Tan IIA inhibits the expression of PANX1 by downregulating TGM2 expression, thereby suppressing microglial activation and inflammation and alleviating CIRI. These findings provide new insights into the role of Tan IIA in the treatment of CIRI.
Network Pharmacology and Experimental Validation Reveal Wu Miao Pill's Therapeutic Effects on Acute Gouty Arthritis Through P2X7R Regulation.
Gao WQ, Gong XZ, Chang C … +3 more , Li L, Gu YY, He DY
Biochem Genet · 2025 Dec · PMID 41351812 · Publisher ↗
Acute gouty arthritis (AGA) is a common inflammatory joint disease with limited therapeutic options and notable side effects from conventional treatments. This study investigated the anti-inflammatory effects and underly...
Acute gouty arthritis (AGA) is a common inflammatory joint disease with limited therapeutic options and notable side effects from conventional treatments. This study investigated the anti-inflammatory effects and underlying mechanisms of the traditional Chinese herbal formula Wu Miao Pill (WMP) in a rat model of AGA induced by monosodium urate crystals. WMP administration markedly alleviated joint inflammation and swelling, improved synovial histopathology, and reduced the expression of P2X7 receptor (P2X7R) and pro-inflammatory cytokines IL-1β, IL-18, and TNF-α. P2X7R inhibition and knockdown experiments confirmed its central role in the therapeutic effect of WMP. Network pharmacology further revealed multiple active compounds targeting inflammatory pathways, notably IL-17 and NF-κB signaling. Overall, WMP exhibits significant anti-inflammatory efficacy through modulation of P2X7R and related pathways, providing experimental and mechanistic evidence for its potential as a novel therapeutic agent for AGA.
Candidate Prognostic LncRNAs Including C2orf49-DT, CAPN10-DT, LOC105371795 as Potential Biomarkers for Colorectal Cancer.
Karimi A, Ashari Z, Momeni S … +3 more , Kamarei S, Zamani A, Mahdevar M
Biochem Genet · 2025 Dec · PMID 41348314 · Publisher ↗
Long non-coding RNAs (lncRNAs) have regulatory functions and are linked to various disorders, including cancer. In this study, we investigated signature lncRNAs that may be associated with the pathogenesis of colorectal...
Long non-coding RNAs (lncRNAs) have regulatory functions and are linked to various disorders, including cancer. In this study, we investigated signature lncRNAs that may be associated with the pathogenesis of colorectal cancer (CRC) and could serve as diagnostic and prognostic biomarkers. The relationship between lncRNA expression and patient mortality rates was identified using data from The Cancer Genome Atlas. Next, linear models determined the differential expression of lncRNAs in cancer and healthy samples. The association of lncRNA expression with patient prognosis was examined using a Cox regression test, and the risk model was constructed using a subset of lncRNAs. The co-expression network was analyzed to identify the pathways associated with candidate lncRNAs. The expression levels of specific lncRNAs were examined in 35 tumor samples from the Iranian Tumor Bank to validate the in-silico analyses. RNAs were extracted using TRIzol, and their quality was assessed. The qRT-PCR method determined candidate gene expression levels after cDNA synthesis. Our findings showed that C2orf49-DT, CAPN10-DT, and LOC105371795 levels were higher in CRC samples and linked to patients with poor prognoses. The co-expression network data demonstrated that the examined lncRNAs were connected to crucial genes involved in cell proliferation, like E2F3. The RT-qPCR results showed a significant increase in C2orf49-DT, CAPN10-DT, and LOC105371795 compared to healthy tissue samples. We found a significant correlation between the levels of the mentioned lncRNAs and E2F3 expression in the ex vivo data. Our findings suggest that elevated levels of C2orf49-DT, CAPN10-DT, and LOC105371795 may be associated with increased mortality rates in CRC patients. These non-coding RNAs are associated with pathways that promote cell proliferation and are proposed as potential biomarkers for diagnosing and predicting CRC.
Knockdown of MEPE Promotes Cranial Defect Repair and Activates the cAMP/PKA Signaling Pathway.
Hong K, Wu J, Zhi X … +2 more , Shi W, Xu H
Biochem Genet · 2025 Dec · PMID 41348313 · Publisher ↗
Cranial defect repair remains a clinical challenge in current surgical practice. Matrix extracellular phosphoglycoprotein (MEPE) plays a role in mineralization, but its specific mechanism in calvarial bone repair, partic...
Cranial defect repair remains a clinical challenge in current surgical practice. Matrix extracellular phosphoglycoprotein (MEPE) plays a role in mineralization, but its specific mechanism in calvarial bone repair, particularly concerning oxidative stress, remains unclear. Bioinformatics analysis identified hub genes and pathways from the calvarial defect dataset GSE20980 using differentially expressed genes screening (p < 0.05, |log2Foldchange|≥3) and weighted gene co-expression network analysis. In vivo, a rat critical-sized calvarial defect (CSD) model was established. MEPE was knocked down via lentiviral siRNA delivery. Bone repair was assessed 8 weeks post-surgery using micro-computed tomography (bone volume/total volume [BV/TV] and trabecular number [Tb.N]), histology (hematoxylin-eosin staining and tartrate-resistant acid phosphatase staining). Enzyme-linked immunosorbent assay was performed to evaluate levels of inflammatory cytokines and oxidative stress indicators. MEPE-associated pathways were screened, and the protein levels were measured by western blot. Bioinformatics analyses identified MEPE as a key upregulated hub gene in bone defects. In vivo, MEPE expression was significantly elevated in CSD rats. MEPE knockdown enhanced bone repair (increased BV/TV and Tb.N), and promoted bone formation and angiogenesis. Furthermore, knockdown of MEPE reduced inflammation (decreased tumor necrosis factor alpha, interleukin 6, interleukin-1β), reactive oxygen species level, increased antioxidants (elevated catalase, glutathione, superoxide dismutase) and upregulated osteogenic markers (runt-related transcription factor 2, osteocalcin, alkaline phosphatase). Bioinformatics analysis of intersecting genes implicated the cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) pathway as the downstream pathway of MEPE. Mechanistically, MEPE knockdown reversed CSD-induced suppression of cAMP and PKA protein expression. MEPE knockdown promotes calvarial bone repair by mitigating oxidative stress, reducing inflammation, enhancing osteogenesis, and activating the cAMP/PKA signaling pathway, representing a potential therapeutic target for bone regeneration.
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