Search Results (110)

Expression quantitative trait locus (eQTL) mapping is an effective tool for identifying genetic variations that regulate gene expression. An increasing number of studies suggested that SNPs associated with complex traits in farm animals are considered as expression quantitative trait loci. Identifying eQTLs associated with gene expression levels in the endometrium helps to unravel the regulatory mechanisms of genes related to reproductive functions in this tissue and provides molecular markers for the genetic improvement of high-fertility sow breeding. In this study, 218 RNA-seq data from pig endometrial tissue were used for eQTL analysis to identify genetic variants regulating gene expression. Additionally, weighted gene co-expression network analysis (WGCNA) was performed to identify hub genes involved in reproductive functions. The eQTL analysis identified 34,876 significant cis-eQTLs regulating the expression of 5632 genes (FDR ≤ 0.05), and 90 hub genes were identified by WGCNA analysis. By integrating eQTL and WGCNA results, 14 candidate genes and 16 fine-mapped cis-eQTLs were identified, including FRK, ARMC3, SLC35F3, TMEM72, FFAR4, SOWAHA, PSPH, FMO5, HPN, FUT2, RAP1GAP, C6orf52, SEL1L3, and CLGN, which were involved in the physiological processes of reproduction in sows through hormone regulation, cell adhesion, and amino acid and lipid metabolism. These eQTLs regulate the high expression of candidate genes in the endometrium, thereby affecting reproductive-related physiological functions. These findings enhance our understanding of the genetic basis of reproductive traits and provide valuable genetic markers for marker-assisted selection (MAS), which can be applied to improve sow fecundity and optimize breeding strategies for high reproductive performance. Full article

Background: Acute myeloid leukemia (AML), a malignant blood disease, is caused by the excessive growth of undifferentiated myeloid cells, which disrupt normal hematopoiesis and may invade several organs. Given the high heterogeneity in prognosis, identifying stable prognostic biomarkers is crucial for improved risk stratification and personalized treatment strategies. Although glycolysis has been extensively studied in cancer, its prognostic significance in AML remains unclear. Methods: Glycolysis-related prognostic genes were identified by differential expression profiles. We modeled prognostic risk by least absolute shrinkage and selection operator (LASSO) regression and validated it by Kaplan–Meier (KM) survival analysis, receiver operating characteristic (ROC) curves, and independent datasets (BeatAML2.0, GSE37642, GSE71014). Mechanisms were further explored through immune microenvironment analysis and drug sensitivity scores. Results: Differential expression and survival correlation analysis across the genes associated with glycolysis revealed multiple glycolytic genes associated with the outcomes of AML. We constructed a seven-gene prognostic model (G6PD, TFF3, GALM, SOD1, NT5E, CTH, FUT8). Kaplan–Meier analysis demonstrated significantly reduced survival in high-risk patients (hazard ratio (HR) = 3.4, p < 0.01). The model predicted the 1-, 3-, and 5-year survival outcomes, achieving area under the curve (AUC) values greater than 0.8. Immune profiling indicated distinct cellular compositions between risk groups: high-risk patients exhibited elevated monocytes and neutrophils but reduced Th1 cell infiltration. Drug sensitivity analysis showed that high-risk patients exhibited resistance to crizotinib and lapatinib but were more sensitive to motesanib. Conclusions: We established a novel glycolysis-related gene signature for AML prognosis, enabling effective risk classification. Combined with immune microenvironment analysis and drug sensitivity analysis, we screened metabolic characteristics and identified an immune signature to provide deeper insight into AML. Our findings may assist in identifying new therapeutic targets and more effective personalized treatment regimes. Full article

Domain-specific O-fucosylation is an unusual type of glycosylation, where the fucose is directly attached to the serine or threonine residues in specific protein domains via an O-linkage. O-fucosylated proteins play critical roles in a wide variety of biological events and hold important therapeutic values, with the most studied being the Notch receptors and ADAMTS proteins. O-fucose glycans modulate the function of the proteins they modify and are closely associated with various diseases including cancer. In mammals, alongside the well-documented protein O-fucosyltransferase (POFUT) 1-mediated O-fucosylation of epidermal growth factor-like (EGF) repeats and POFUT2-mediated O-fucosylation of thrombospondin type 1 repeats (TSRs), a new type of O-fucosylation was recently identified on elastin microfibril interface (EMI) domains, mediated by POFUT3 and POFUT4 (formerly FUT10 and FUT11). In this review, we present an overview of our current knowledge of O-fucosylation, integrating the latest findings and with a particular focus on its biological functions and molecular mechanisms. Full article

During urban development, significant contrasts between urban villages and their surrounding areas lead to the emergence of fragmented urban spaces, dysfunctionalities, cultural barriers, and, ultimately, to the formation of fractured urban textures centered on urban villages (FUT-UVs). The fractured urban textures of an FUT-UV create a disconnect from the surrounding urban area, isolating it from the city. This separation significantly impacts the daily lives and interactions of its residents. To address this and support more sustainable urban development, a thorough and multi-dimensional understanding of FUT-UVs is of crucial importance. This study examines Nanhao Village in Baotou City, conducting a quantitative analysis of key indicators related to buildings, roads, and functional facilities. Using overlay analysis, it explores the characteristics of the FUT-UV, the interactions between these indicators, and opportunities for improvement. From these findings, strategies for reconnecting an FUT-UV with its surroundings are proposed. The results indicate that: (1) FUT-UVs are mainly characterized by low-rise, high-density developments with limited open space. Their road networks are narrow and congested, while accessibility remains low. Low-end businesses are concentrated in a single area within the village, showing minimal functional diversity; (2) FUT-UVs can increase construction intensity by raising the number of floors in buildings, and have higher building densities in the most accessible areas. This increase in density can effectively enhance functional diversity; and (3) improving road accessibility in FUT-UVs will allow for a smoother influx of external activity, enhancing functional diversity. Additionally, increasing the number of building floors intensifies construction, raises the density of functional facilities, and boosts urban vitality. Based on these characteristics of fragmentation and interactive mechanisms, this study suggests stitching strategies related to transportation, architecture, and functionality. This study introduces a new framework for analyzing urban texture, offering a detailed multi-faceted analysis of FUT-UV fragmentation and clarifying the interaction between FUT-UVs and surrounding urban forms. This study reinforces the coherence of the spatial form and the development of the functional economy of urban villages within the modern urban environment. It supports the sustainable development of urban areas and promotes balanced growth between urban villages and their surrounding regions. Full article

Sex-controlled sperm combined with artificial insemination allows animals to reproduce offspring according to the desired sex, accelerates the process of animal genetics and breeding and promotes the development of animal husbandry. However, the molecular markers for sexual sperm sorting are unusual. To identify the molecular markers of boar sperm sorting, proteomics and metabolomics techniques were applied to analyze the differences in proteins and metabolism between X and Y sperm. Label-free quantitative proteomics identified 254 differentially expressed proteins (DEPs) in the X and Y sperm of boars, including 106 proteins that were highly expressed in X sperm and 148 proteins that were highly expressed in Y sperm. Among the differential proteins, COX6A1, COX1, CYTB, FUT8, GSTK1 and PFK1 were selected as potential biological markers for X and Y sperm sorting. Moreover, 760 metabolites from X and Y sperm were detected. There were 439 positive ion mode metabolites and 321 negative ion mode metabolites identified. The various metabolites were phosphoenolpyruvate, phytosphingosine, L-arginine, N-acetylputrescine, cytidine-5′-diphosphate and deoxyuridine. These metabolites were mainly involved in the TCA cycle, oxidative phosphorylation pathway, glycolysis pathway, lipid metabolism pathway, amino acid metabolism pathway, pentose phosphate pathway and nucleic acid metabolism pathway. The differential proteins and differential metabolites obtained by the combined proteomics and metabolomics analysis were projected simultaneously to the KEGG pathway, and a total of five pathways were enriched, namely oxidative phosphorylation pathway, purine metabolism, unsaturated fatty acid biosynthesis, ABC transporters and peroxisomes. In summary, COX6A1 and CYTB were identified as potential biomarkers for boar X and Y sperm sorting. Full article

Head and neck cancers (HNCs) are the sixth most commonly diagnosed cancer and the eighth leading cause of cancer-related mortality worldwide, with squamous cell carcinoma being the most prevalent type. The global incidence of HNCs is steadily increasing, projected to rise by approximately 30% per year by 2030, a trend observed in both developed and undeveloped countries. This study involved serum proteomic profiling to identify predictive clinical biomarkers in cancer patients undergoing chemoradiotherapy (CRT). Fifteen HNC patients at Tikur Anbessa Specialized Hospital, Radiotherapy (RT) center in Addis Ababa were enrolled. Serum samples were collected before and after RT, and patients were classified as responders (R) or non-responders (NR). Protein concentrations in the serum were determined using the Bradford assay, followed by nano-HPLC–MS/MS for protein profiling. Progenesis QI for proteomics identified 55 differentially expressed proteins (DEPs) between R and NR, with a significance of p < 0.05 and a fold-change (FC) ≥ 1.5. The top five-up-regulated proteins included MAD1L1, PSMC2, TRIM29, C5, and SERPING1, while the top five-down-regulated proteins were RYR1, HEY2, HIF1A, TF, and CNN3. Notably, about 16.4% of the DEPs were involved in cellular responses to DNA damage from cancer treatments, encompassing proteins related to deoxyribonucleic acid (DNA) damage sensing, checkpoint activation, DNA repair, and apoptosis/cell cycle regulation. The analysis of the relative abundance of ten proteins with high confidence scores identified three DEPs: ADIPOQ, HEY2, and FUT10 as potential predictive biomarkers for treatment response. This study highlighted the identification of three potential predictive biomarkers—ADIPOQ, HEY2, and FUT10—through serum proteomic profiling in HNC patients undergoing RT, emphasizing their significance in predicting treatment response. Full article

Lvliang black goat (LBG) is an excellent local breed resource in China that is known for its black fur, excellent meat quality, and strong adaptability. Studying the genetic mechanism and germplasm characteristics of LBG can provide theoretical and practical basis for the protection of the genetic resources of this breed and help implement conservation and breeding. In this study, the genetic diversity of the LBG population was evaluated using whole-genome SNP data. It was found that the LBG population had a high genetic diversity and a low degree of inbreeding. According to the clustering results of male goats and the relationship between individuals, the LBG population was divided into 13 families. Then, through population structure analysis, it was found that LBG had a close genetic relationship with the Nanjiang goat and Qinggoda goat populations, and they may have the same ancestors. The LBG population has retained some ancient genetic characteristics and is a special population that integrates local genetic characteristics and foreign gene flow. Through four selection signal analyses, we detected multiple candidate genes related to economic traits (CFL2, SCD, NLRP14, etc.) and adaptability (C4BPA, FUT8, PRNP, etc.) in the LBG population. In addition, in a comparative analysis with three commercial breeds (Saanen goat, Boer goat and Angora goat) we also found multiple genes related to physical characteristics (ERG, NRG3, EDN3, etc.). Finally, we performed functional enrichment analysis on these genes and explored their genetic mechanisms. This study provides important data support for the protection and breeding of LBG and provides a new perspective for enriching the genetic diversity of goat populations. Full article

The FUT2 gene encodes an enzyme called α-1,2-fucosyltransferase, which is involved in the formation of blood group antigens AB0(H) and is also involved in the processes of vitamin B12 absorption and its transport between cells. FUT2 gene polymorphisms are associated with vitamin B12 levels in the body. Vitamin B12 deficiency associated with hyperhomocysteinemia is a major risk factor for cardiovascular diseases (CVDs), which are one of the main causes of death in patients after kidney transplantation. The aim of our study was to determine the impact of the rs602662 (G>A) polymorphism of the FUT2 gene on the functionality of transplanted kidneys and the risk of CVD in patients after kidney transplantation. The study included 402 patients treated with immunosuppression (183 patients taking cyclosporine (CsA) and 219 patients taking tacrolimus (TAC)). The analysis of the FUT2 rs602662 (G>A) polymorphism was performed using real-time PCR. Patients with CsA were more likely to be underweight (1.64% vs. 0.91%) and obese (27.87% vs. 15.98%), while those taking TAC were more likely to be of normal weight (39.27%) or overweight (43.84%). No statistically significant differences were observed comparing the mean blood pressure, both systolic and diastolic. The renal profile showed a higher median urea nitrogen concentration in patients with CsA (26.45 mg/dL (20.60–35.40) vs. 22.95 mg/dL (17.60–33.30), p = 0.004). The observed frequency of rs602662 alleles of the FUT2 gene was similar in the analyzed groups. The A allele was present in 43.7% of patients with CsA and 41.1% of those taking TAC (OR = 0.898; 95% CI: 0.678–1.189; p = 0.453). In the group with CsA, the GG genotype was present in 32.2% of patients, the GA in 48.1% and the AA in 19.7%. A similar distribution was obtained in the TAC group: GG—33.8%, GA—50.2%, and AA—16.0%. An association of genotypes containing the G allele with a higher incidence of hypertension was observed. The G allele was present in 65% of people with hypertension and in 56% of patients with normal blood pressure (p = 0.036). Moreover, the evaluation of the renal parameters showed no effect of the FUT2 polymorphism on the risk of organ rejection because the levels of creatinine, eGFR, potassium, and urea nitrogen were prognostic of successful transplantation. Our results suggest that the rs6022662 FUT2 polymorphism may influence the risk of cardiovascular diseases. Full article

The aim of this study was to identify effective genetic markers for the Antigen Processing Associated Transporter 1 (TAP1), α (1,2) Fucosyltransferase 1 (FUT1), Natural Resistance Associated Macrophage Protein 1 (NRAMP1), Mucin 4 (MUC4) and Mucin 13 (MUC13) diarrhea-resistance genes in the local pig breeds, namely Shanghai white pigs, Fengjing pigs, Shawutou pigs, Meishan pigs and Pudong white pigs, to provide a reference for the characterization of local pig breed resources in Shanghai. Polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLR) and sequence sequencing were applied to analyze the polymorphisms of the above genes and to explore the effects on the immunity of Shanghai local pig breeds in conjunction with some immunity factors. The results showed that both TAP1 and MUC4 genes had antidiarrheal genotype GG in the five pig breeds, AG and GG genotypes of the FUT1 gene were detected in Pudong white pigs, AA antidiarrheal genes of the NRAMP1 gene were detected in Meishan pigs, the AB type of the NRAMP1 gene was detected in Pudong white pigs, and antidiarrheal genotype GG of the MUC13 gene was only detected in Shanghai white pigs. The MUC13 antidiarrhea genotype GG was only detected in Shanghai white pigs. The TAP1 gene was moderately polymorphic in Shanghai white pigs, Fengjing pigs, Shawutou pigs, Meishan pigs and Pudong white pigs, among which TAP1 in Shanghai white pigs and Shawutou pigs did not satisfy the Hardy–Weinberg equilibrium. The FUT1 gene of Pudong white pigs was in a state of low polymorphism. NRAMP1 of Meishan pigs and Pudong white pigs was in a state of moderate polymorphism, which did not satisfy the Hardy–Weinberg equilibrium. The MUC4 genes of Shanghai white pigs and Pudong white pigs were in a state of low polymorphism, and the MUC4 genes of Fengjing pigs and Shawutou pigs were in a state of moderate polymorphism, and the MUC4 genes of Fengjing pigs and Pudong white pigs did not satisfy the Hardy–Weinberg equilibrium. The MUC13 gene of Shanghai white pigs and Pudong white pigs was in a state of moderate polymorphism. Meishan pigs had higher levels of IL-2, IL-10, IgG and TNF-α, and Pudong white pigs had higher levels of IL-12 than the other pigs. The level of interleukin 12 (IL-12) was significantly higher in the AA genotype of the MUC13 gene of Shanghai white pigs than in the AG genotype. The indicator of tumor necrosis factor alpha (TNF-α) in the AA genotype of the TAP1 gene of Fengjing pigs was significantly higher than that of the GG and AG genotypes. The indicator of IL-12 in the AG genotype of the Shawutou pig TAP1 gene was significantly higher than that of the GG genotype. The level of TNF-α in the AA genotype of the NRAMP1 gene of Meishan pigs was markedly higher than that of the AB genotype. The IL-2 level of the AG type of the FUT1 gene was obviously higher than that of the GG type of Pudong white pigs, the IL-2 level of the AA type of the MUC4 gene was dramatically higher than that of the AG type, and the IgG level of the GG type of the MUC13 gene was apparently higher than that of the AG type. The results of this study are of great significance in guiding the antidiarrhea breeding and molecular selection of Shanghai white pigs, Fengjing pigs, Shawutou pigs, Meishan pigs and Pudong white pigs and laying the foundation for future antidiarrhea breeding of various local pig breeds in Shanghai. Full article

The ABO blood groups, Lewis antigens, and secretor systems are important components of transfusion medicine. These interconnected systems have been also shown to be associated with differing susceptibility to bacterial and viral infections, likely as the result of selection over the course of evolution and the constant tug of war between humans and infectious microbes. This comprehensive narrative review aimed to explore the literature and to present the current state of knowledge on reported associations of the ABO, Lewis, and secretor blood groups with SARS-CoV-2 infection and COVID-19 severity. Our main finding was that the A blood group may be associated with increased susceptibility to SARS-CoV-2 infection, and possibly also with increased disease severity and overall mortality. The proposed pathophysiological pathways explaining this potential association include antibody-mediated mechanisms and increased thrombotic risk amongst blood group A individuals, in addition to altered inflammatory cytokine expression profiles. Preliminary evidence does not support the association between ABO blood groups and COVID-19 vaccine response, or the risk of developing long COVID. Even though the emergency state of the pandemic is over, further research is needed especially in this area since tens of millions of people worldwide suffer from lingering COVID-19 symptoms. Full article

The infant non-secretor histoblood group antigen phenotype is associated with reduced risk of symptomatic rotavirus diarrhea, one of the leading global causes of severe pediatric diarrheal disease and mortality. However, little is known regarding the role of secretor status in asymptomatic rotavirus infections. Therefore, we performed a nested case–control study within a birth cohort study previously conducted in Dhaka, Bangladesh, to determine the association between infant secretor phenotype and the odds of asymptomatic rotavirus infection, in addition to the risk of rotavirus diarrhea, in unvaccinated infants. In the parent cohort, infants were enrolled in the first week of life and followed through the first two years of life with multiple clinic visits and active surveillance for diarrheal illness. Secretor phenotyping was performed on saliva. Eleven surveillance stools collected over the first year of life were tested for rotavirus by real-time RT-PCR, followed by conventional PCR and amplicon sequencing to identify the infecting P-type of positive specimens. Similar to findings for symptomatic diarrhea, infant non-secretors experienced significantly fewer primary episodes of asymptomatic rotavirus infection through the first year of life in a likely rotavirus P-genotype-dependent manner. These data suggest that non-secretors experienced reduced risk from rotavirus due to decreased susceptibility to infection rather than reduced infection severity. Full article

FUT8, the sole glycosyltransferase responsible for N-glycan core fucosylation, plays a crucial role in tumorigenesis and development. Aberrant FUT8 expression disrupts the function of critical cellular components and triggers the abnormality of tumor signaling pathways, leading to malignant transformations such as proliferation, invasion, metastasis, and immunosuppression. The association between FUT8 and unfavorable outcomes in various tumors underscores its potential as a valuable diagnostic marker. Given the remarkable variation in biological functions and regulatory mechanisms of FUT8 across different tumor types, gaining a comprehensive understanding of its complexity is imperative. Here, we review how FUT8 plays roles in tumorigenesis and development, and how this outcome could be utilized to develop potential clinical therapies for tumors. Full article

Behçet’s disease (BD) is a complex, recurring inflammatory disorder with autoinflammatory and autoimmune components. This comprehensive review aims to explore BD’s pathogenesis, focusing on established genetic factors. Studies reveal that HLA-B*51 is the primary genetic risk factor, but non-HLA genes (ERAP1, IL-10, IL23R/IL-12RB2), as well as innate immunity genes (FUT2, MICA, TLRs), also contribute. Genome-wide studies emphasize the significance of ERAP1 and HLA-I epistasis. These variants influence antigen presentation, enzymatic activity, and HLA-I peptidomes, potentially leading to distinct autoimmune responses. We conducted a systematic review of the literature to identify studies exploring the association between HLA-B*51 and BD and further highlighted the roles of innate and adaptive immunity in BD. Dysregulations in Th1/Th2 and Th17/Th1 ratios, heightened clonal cytotoxic (CD8+) T cells, and reduced T regulatory cells characterize BD’s complex immune responses. Various immune cell types (neutrophils, γδ T cells, natural killer cells) further contribute by releasing cytokines (IL-17, IL-8, GM-CSF) that enhance neutrophil activation and mediate interactions between innate and adaptive immunity. In summary, this review advances our understanding of BD pathogenesis while acknowledging the research limitations. Further exploration of genetic interactions, immune dysregulation, and immune cell roles is crucial. Future studies may unveil novel diagnostic and therapeutic strategies, offering improved management for this complex disease. Full article

Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs—for group of traits withers height, rump height, body length, 2 SNPs—for withers height and rump height, 1 SNP—for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats. Full article

In this paper, a novel distributed optical fiber temperature sensor based on Raman anti-Stokes scattering light is proposed and experimentally demonstrated. The Raman anti-Stokes scattering light is sensitive to temperature parameters that are detected by the fiber under test conditions (FUT), and this allowed the temperature demodulation algorithm to be obtained through the relationship between the temperature and the power of the back-scattered Raman anti-Stokes light. In addition, we propose a new temperature calibration method to ensure accurate temperature measurement, which is greatly affected by the stability of a pulse laser. The experimental system is constructed with an optical fiber length of approximately 3.5 km. The proposed system obtains a 24 dB dynamic range with a pulse width of 20 ns and temperature testing ranges of 30.0 °C to 80.0 °C. The results demonstrate that the maximum temperature deviation range is −1.5 °C to +1.6 °C and the root mean square (RMS) error of the whole temperature range is 0.3 °C, which means it has the potential for practical engineering applications. More importantly, it avoids the walk-off effect that must be corrected in commonly used temperature demodulation schemes adopting both Raman Stokes light and anti-Stokes light. It also saves a signal channel, which is more suitable for the integration of hybrid distributed optical fiber sensing systems for multi-parameter monitoring. Full article