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In sheep, the woolly or hairy fleece type shows variation within and between breeds and populations. Recently, the woolly allele was shown to result from the insertion of an antisens retrogene into the 3'UTR of the ovine IRF2BP2 gene. The purpose of this study was to examine this InDel polymorphism within the IRF2BP2 gene using a specific PCR genotyping in 17 North African (Algeria and Tunisia) and Iranian sheep breeds showing various fleece types. The genotyping of the overall animals (n=908) showed the segregation of the two alleles insertion (I) and deletion (D), and the three genotypes (II, ID and DD) with various frequencies. Ouled Djellal, Rembi and Tâadmit known as woolly breeds had 100%, 94% and 94% of II homozygous animals, respectively. In contrast, Ifilène and Sidaou known as hairy breeds had 100% and 99% of DD homozygous animals. Other breeds showed the segregation of the I allele with a frequency from 3% to 91%. An association analysis, carried out only for the Algerian sheep breeds, revealed that this polymorphism was significantly associated with the fleece type trait (P<0.05). Thus, the current work meets previous results to further confirm the genetic effect of the insertion occurring into the 3' UTR of the IRF2BP2 gene on the fleece type trait of sheep breeds. [ABSTRACT FROM AUTHOR]

Background and Objectives: Amphotericin B is a broad-spectrum antifungal agent commonly used to treat Candida haemulonii infection. C. haemulonii was isolated from patients reported to be intrinsically resistant to amphotericin B, encoded by the ERG2 and ERG11 genes. However, there have been limited studies concerning amphotericin B-resistant C. haemulonii in Indonesia. The objective of this study is to explore the phenotypic and genotypic characteristics (ERG2 and ERG11) of C. haemulonii isolated from the ICU of a referral hospital in Indonesia. Materials and Methods: Identification and susceptibility tests were conducted using VITEK2. Thereafter, DNA was extracted and amplified using conventional PCR followed by DNA sequencing (Sanger method). Results: The results of the phenotypic susceptibility test showed that all C. haemulonii were resistant to amphotericin B. ERG2 and ERG11 sequences showed the same amino acid sequence and corresponded to references that are resistant to amphotericin B. Conclusion: The resistant properties of C. haemulonii against amphotericin B found in this study require further exploration, including comparing resistant and sensitive C. haemulonii to amphotericin B. In addition, it is necessary to analyze other genes besides ERG2 and ERG11. [ABSTRACT FROM AUTHOR]

In case of a nuclear accident, individuals with high-dose radiation exposure (>1–2 Gy) should be rapidly identified. While ferredoxin reductase (FDXR) was recently suggested as a radiation-responsive gene, the use of a single gene biomarker limits radiation dose assessment. To overcome this limitation, we sought to identify reliable radiation-responsive gene biomarkers. Peripheral blood mononuclear cells (PBMCs) were isolated from mice after total body irradiation, and gene expression was analyzed using a microarray approach to identify radiation-responsive genes. In light of the essential role of the immune response following radiation exposure, we selected several immune-related candidate genes upregulated by radiation exposure in both mouse and human PBMCs. In particular, the expression of ACOD1 and CXCL10 increased in a radiation dose-dependent manner, while remaining unchanged following lipopolysaccharide (LPS) stimulation in human PBMCs. The expression of both genes was further evaluated in the blood of cancer patients before and after radiotherapy. CXCL10 expression exhibited a distinct increase after radiotherapy and was positively correlated with FDXR expression. CXCL10 expression in irradiated PBMCs represents a potential biomarker for radiation exposure. [ABSTRACT FROM AUTHOR]

Background: Neurometabolic diseases are the results of genetic changes that lead to an imbalance in energy utilization and metabolism. Aim: Our aim was to explore the update in treatment and diagnosis of neurometabolic disease. Methods: PubMed, Scopus, Google scholar, and the web of science were searched for studies reported in the last 20 years (1997-30/10/2020). The data was searched and archived by keywords like "Neurometabolic", "neurogenesis", and "role of neuro-degeneration in neurometabolic disease" without narrowing or limiting search items. Only abstracts of searched publications were reviewed. A total of 389 publications were found in the initial research, in which 62 publications were considered for the study and the remaining were excluded because of their specificity to the subject. Study update: The neurometabolic disease affects one in 500 newborns, causing a major burden of illness and infant mortality. However, the cause of the disease is unclear in up to 50% of neurologicallike cases. Thus, we ask why are they referred to as neurometabolic disorders (NMD), despite extensive genetic and biochemistry investigations? Treatment is possible for some metabolic diseases. For instance, the devastating neurological effects of phenylketonuria have been recognized for many years. Except for some notable exceptions, treatment remains largely unsatisfactory. Therefore, research efforts concentrate on corrective genetic approaches applicable after early detection by newborn screening or before fertilization. We considered recent studies on treating neurometabolic diseases. We focused on the most common neurometabolic diseases and the associated clinical advancements in their therapy. [ABSTRACT FROM AUTHOR]

Purpose: This study aimed to analyze the genetic results of inherited retinal diseases (IRDs) and evaluate the diagnostic usefulness of whole genome sequencing (WGS) in the Korean National Project of Bio Big Data. Methods: As part of the Korean National Project of Bio Big Data, WGS was performed on 32 individuals with IRDs with no identified pathogenic variants through whole or targeted exome sequencing. Results: Individuals with retinitis pigmentosa (n = 23), cone dystrophy (n = 2), cone-rod dystrophy (n = 2), familial exudative vitreoretinopathy (n = 2), pigmented paravenous chorioretinal atrophy (n = 1), North Carolina macular dystrophy (n = 1), and bull's-eye macular dystrophy (n = 1) were included. WGS revealed genetic mutations in the IQCB1, PRPF31, USH2A, and GUCY2D genes in five cases (15.6%). Two large structural variations and an intronic variant were newly detected in three cases. Two individuals had biallelic missense mutations that were not identified in previous exome sequencing. Conclusion: With WGS, the causative variants in 15.6% of unsolved IRDs from the Korean National Project of Bio Big Data were identified. Further research with a larger cohort might unveil the diagnostic usefulness of WGS in IRDs and other diseases. [ABSTRACT FROM AUTHOR]

Genetic variations in the human cytochrome P450 family 2 subfamily C member 9 (CYP2C9) and cytochrome P450 family 2 subfamily D member 6 (CYP2D6) genes may affect drug metabolism and lead to alterations in phenotypes. Genetic variations are associated with toxicity, adverse drug reactions, inefficient treatment. Various in silico tools were combined to investigate the deleterious effects of missense non-synonymous single nucleotide polymorphisms (nsSNPs) of the human CYP2C9 and CYP2D6. The structural and functional effects of the high-risk non-synonymous SNPs in the human CYP2C9 and CYP2D6 were predicted by numerous computational mutation analysis methods. Out of 24 pathogenic missense SNPs in the CYP2C9, 22 nsSNPs had a decreasing effect on protein stability and 13 SNPs were showed to be located at conserved positions. Out of 27 high-risk deleterious non-synonymous SNPs in the human CYP2D6, 21 SNPs decreased protein stability and 16 nsSNPs were predicted to be positioned at conserved regions. Our present study suggests that the identified functional SNPs may affect drug metabolism associated with CYP2C9 and CYP2D6 enzymes. [ABSTRACT FROM AUTHOR]

A gene library is a collection of different DNA sequences from an organism, which has been cloned into vectors for ease of purification, storage, and analysis. There are two types of gene libraries based on the availability of a source of DNA used. The genomic library contains DNA fragments that represent the entire genome of an organism, whereas CDNA libraries will contain only the complementary DNA molecules synthesized from the mRNA molecules in a cell. For the construction of gene libraries, we have to know the size of the gene and insert size or capacity of vectors. Vectors used for gene library construction are plasmid, lambda phage, Cosmid, bacterial artificial chromosome, and yeast artificial chromosome. The most commonly used vector type is lambda, but most genomic libraries are constructed using BAC and YAC vectors. For the construction of gene libraries, the steps followed are the isolation of bacteria followed by cloning and sequencing DNA. The main use of genetic libraries is to increase the likelihood that a particular portion of a DNA source will be found within the collection. It is used to collect and store information as a set of DNA molecules. Gene libraries are stored inside bacterial cells. Bacterial colonies have the ability to store different genes, similar to how books are stored in a library. [ABSTRACT FROM AUTHOR]

The MYB gene family exerts significant influence over various biological processes and stress responses in plants. Despite this, a comprehensive analysis of this gene family in pumpkin remains absent. In this study, the MYB genes of Cucurbita moschata were identified and clustered into 33 groups (C1-33), with members of each group being highly conserved in terms of their motif composition. Furthermore, the distribution of 175 CmoMYB genes across all 20 chromosomes was found to be non-uniform. Examination of the promoter regions of these genes revealed the presence of cis-acting elements associated with phytohormone responses and abiotic/ biotic stress. Utilizing quantitative real-time polymerase chain reaction (qRT-PCR), the expression patterns of 13 selected CmoMYB genes were validated, particularly in response to exogenous phytohormone exposure and various abiotic stressors, including ABA, SA, MeJA, and drought treatments. Expression analysis in different tissues showed that CmoMYB genes are expressed at different levels in different tissues, suggesting that they are functionally divergent in regulating growth and abiotic stresses. These results provide a basis for future studies to characterize the function of the MYB gene family under abiotic stresses in pumpkins. [ABSTRACT FROM AUTHOR]

Clematis tomentella 2001 (Ranunculaceae) is a typical drought-tolerant sand-fixing plant in desert ecosystem in northwest China. To elucidate the phylogenetic status of C. tomentella and its related species, we determined the complete chloroplast (cp) genome and analyzed their interspecific relationships. The result showed that the cp genome of C. tomentella was 159 816 bp in length, including two inverted repeats of 31 045 bp, a large single copy region of 79 535 bp, and a small single copy region of 18 191 bp. 136 genes were annotated across the whole cp genome, including 92 protein-coding genes, 8 rRNA genes, and 36 tRNA genes, as well as the GC content accounted for 38%. Crucially, we found that the regions of psbE-petL, trnG_UCC-atpA, ndhF-rpl32, and rps8-infA were highly divergent, which could be marked as DNA barcodes for the identification of C. tomentella in Ranunculaceae. A maximum likelihood phylogenetic tree revealed that C. tomentella was closely related to C. fruticosa. Our results provide the references and implications for the phylogenetic study of Clematis in Ranunculaceae in the future. [ABSTRACT FROM AUTHOR]

Background: The Wnt/β-catenin pathway plays a critical role in the tumorigenesis and maintenance of glioma stem cells. This study aimed to evaluate significant genes associated with the Wnt/β-catenin pathway involved in mortality and disease progression in patients with grade II and III glioma, using the Cancer Genome Atlas (TCGA) database. Methods: We obtained clinicopathological information and mRNA expression data from 515 patients with grade II and III gliomas from the TCGA database. We performed a multivariate Cox regression analysis to identify genes independently associated with glioma prognosis. Results: The analysis of 34 genes involved in Wnt/β-catenin signaling demonstrated that four genes (CER1, FRAT1, FSTL1, and RPSA) related to the Wnt/β-catenin pathway were significantly associated with mortality and disease progression in patients with grade II and III glioma. We also identified additional genes related to the four significant genes of the Wnt/β-catenin pathway mentioned above. The higher expression of BMP2, RPL18A, RPL19, and RPS12 is associated with better outcomes in patients with glioma. Conclusions: Using a large-scale open database, we identified significant genes related to the Wnt/β-catenin signaling pathway associated with mortality and disease progression in patients with grade II and III gliomas. [ABSTRACT FROM AUTHOR]

Copyright of Revista Foco (Interdisciplinary Studies Journal) is the property of Revista Foco and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of China Tropical Medicine is the property of China Tropical Medicine Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

BACKGROUND: In recent years, the treatment of anterior cruciate ligament injury has become more and more mature. However, there are still disputes about the timing of surgery, the choice of surgical methods, the choice of grafts, and the methods to promote graft healing after anterior cruciate ligament injury. OBJECTIVE: To summarize the latest research progress of surgical timing, surgical methods, graft selection and methods to promote graft healing after anterior cruciate ligament injury, and to find new treatment directions for anterior cruciate ligament injury. METHODS: Relevant articles concerning anterior cruciate ligament injury were retrieved from PubMed, CNKI, WanFang Date, VIP, SinoMed, ScienceDirect, Springer and Cochrane Library. After the screening, 72 related articles were finally included. RESULTS AND CONCLUSION: (1) Surgical timing: Compared with delayed anterior cruciate ligament reconstruction, early reconstruction can reduce meniscus injury, elevate quality of life, and improve functional recovery. However, it is still uncertain whether the different operation timing will accelerate cartilage injury. (2) Surgical methods: Arthroscopic anterior cruciate ligament reconstruction is a common surgical method for anterior cruciate ligament injury. Dynamic internal stabilization repair of anterior cruciate ligament can bring similar results to traditional anterior cruciate ligament reconstruction in short-term and long-term effects. (3) Graft selection: Autogenous hamstring tendon is the first choice of anterior cruciate ligament graft, while bone-patellar tendon-bone grafts and allografts are the secondary choices. (4) Among the methods to promote graft healing, suture band strengthening can increase knee joint stability and ensure graft healing. Stem cells promote the tendon-bone healing of grafts through anti-inflammatory action, angiogenesis, inhibition of osteolysis and promotion of chondrocyte differentiation. Preserving the residual end of the anterior cruciate ligament can maintain the stability of the knee joint, promote the recovery of proprioception, and provide a prerequisite for the healing of the graft. The effectiveness of platelet-rich plasma in promoting graft healing remains to be discussed. However, biomaterials, gene therapy, stem cell application and other methods to promote tendon healing remain in the stage of molecular and animal researches. Clinical transformation is also needed in the future. [ABSTRACT FROM AUTHOR]

Simple Summary: Salivary duct carcinomas (SDC) can present with distinct immunologic profiles similar to breast cancer, such as androgen receptor (AR) and HER-2/Neu-positivity, raising the hypothesis that these tumors may respond to hormonal signaling. No consensus exists on how to best manage this entity. The data evaluating the use of targeted therapies, such as androgen deprivation therapy and HER-2 receptor inhibitors, in the front-line setting when treating curatively is limited. We studied patients with AR+ SDC, demonstrating high rates of control and survival using an aggressive approach to treatment. Immunoprofiles were highly variable, highlighting the potential for future treatment individualization. We hope that this may allow for personalization of treatment in the future, using molecular profiling to determine whether the addition of biological agents in the definitive setting against specific targets, such as AR and HER-2/Neu, will further improve outcomes for these patients. Background: Salivary duct carcinomas (SDC) are a rare and aggressive subtype of salivary gland neoplasm. They can present with distinct immunoprofiles, such as androgen receptor (AR) and HER-2/Neu-positivity. To date, no consensus exists on how to best manage this entity. Methods: All patients diagnosed with nonmetastatic AR+ SDC of the parotid from 2013 to 2019 treated with curative intent were included. Immunologic tumor profiling was conducted using 24 distinct markers. Kaplan–Meier analyses were used to estimate locoregional recurrence (LRR), distant control, and overall survival (OS). Results: Fifteen patients were included. Nine (60%) patients presented with T4 disease and eight (53%) had positive ipsilateral cervical lymphadenopathy. Ten (67%) patients underwent trimodality therapy, including surgery followed by adjuvant radiation and concurrent systemic therapy. The median follow-up was 5.5 years (interquartile range, 4.8–6.1). The estimated 5-year rates of LRR, distant progression, and OS were 6%, 13%, and 87%, respectively. Conclusion: Despite only including AR+ SDC of the parotid, immunoprofiles, such as expression of HER-2, were highly variable, highlighting the potential to tailor systemic regimens based on individual histologic profiles in the future. Studies with larger patient numbers using tumor-specific molecular profiling and tumor heterogeneity analyses are justified to better understand the biology of these tumors. Molecularly informed treatment approaches, including the potential use of AR- and HER-2/Neu-directed therapies upfront in the definitive setting, may hold future promise to further improve outcomes for these patients. [ABSTRACT FROM AUTHOR]

Carrot is an important vegetable with roots as the edible organ. A complex regulatory network controls root growth, in which auxin is one of the key players. To clarify the molecular mechanism on auxin regulating carrot root expansion, the growth process and the indole-3-acetic acid (IAA) content in the roots were measured in this experiment. It was found that the rapid expansion period of the root was from 34 to 41 days after sowing and the IAA content was the highest during this period. The root growth then slowed down and the IAA levels decreased. Using the transcriptome sequencing database, we analyzed the expression of IAA-metabolism-related genes and found that the expression of most of the IAA synthesis genes, catabolism genes, and genes related to signal transduction was consistent with the changes in IAA content during root expansion. Among them, a total of 31 differentially expressed genes (DEGs) were identified, including 10 IAA synthesis genes, 8 degradation genes, and 13 genes related to signal transduction. Analysis of the correlations between the DEGs and IAA levels showed that the following genes were closely related to root development: three synthesis genes, YUCCA10 (DCAR_012429), TAR2 (DCAR_026162), and AMI1 (DCAR_003244); two degradation genes, LPD1 (DCAR_023341) and AACT1 (DCAR_010070); and five genes related to signal transduction, IAA22 (DCAR_012516), IAA13 (DCAR_012591), IAA27 (DCAR_023070), IAA14 (DCAR_027269), and IAA7 (DCAR_030713). These results provide a reference for future studies on the mechanism of root expansion in carrots. [ABSTRACT FROM AUTHOR]

Background: Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry. Multi-omics approaches enable the comprehensive investigation of the complex interactions between multiple layers of information to provide a more holistic view of disease pathogenesis. Therefore, this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data (mRNA and lncRNA), small RNA sequencing data (miRNA) and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus chromogenes. Results: Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis, provided further insights into subclinical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical mastitis. The abundant genomic and epigenomic signatures with significant alterations related to subclinical mastitis were observed, including 30,846, 2552, 1276 and 57 differential methylation haplotype blocks (dMHBs), differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs), respectively. Next, 5 factors presenting the principal variation of differential multi-omics signatures were identified. The important roles of Factor 1 (DEG, DEM and DEL) and Factor 2 (dMHB and DEM), in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were revealed. Each of the omics within Factors 1 and 2 explained about 20% of the source of variation in subclinical mastitis. Also, networks of important functional gene sets with the involvement of multi-omics signatures were demonstrated, which contributed to a comprehensive view of the possible regulatory mechanisms underlying subclinical mastitis. Furthermore, multi-omics integration enabled the association of the epigenomic regulatory factors (dMHBs, DELs and DEMs) of altered genes in important pathways, such as 'Staphylococcus aureus infection pathway' and 'natural killer cell mediated cytotoxicity pathway', etc., which provides further insights into mastitis regulatory mechanisms. Moreover, few multi-omics signatures (14 dMHBs, 25 DEGs, 18 DELs and 5 DEMs) were identified as candidate discriminant signatures with capacity of distinguishing subclinical mastitis cows from healthy cows. Conclusion: The integration of genomic and epigenomic data by multi-omics approaches in this study provided a better understanding of the molecular mechanisms underlying subclinical mastitis and identified multi-omics candidate discriminant signatures for subclinical mastitis, which may ultimately lead to the development of more effective mastitis control and management strategies. [ABSTRACT FROM AUTHOR]

Copyright of SPORMETRE: The Journal of Physical Education & Sport Sciences / Beden Eğitimi ve Spor Bilimleri Dergisi is the property of SPORMETRE: The Journal of Physical Education & Sport Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Previous observational studies have investigated the association between sleep-related traits and male fertility; however, conclusive evidence of a causal connection is lacking. This study aimed to explore the causal relationship between sleep and male fertility using Mendelian randomisation. Methods: Eight sleep-related traits (chronotype, sleep duration, insomnia, snoring, dozing, daytime nap, oversleeping, and undersleeping) and three descriptors representing male fertility (male infertility, abnormal sperm, and bioavailable testosterone levels) were selected from published Genome-Wide Association Studies. The causal relationship between sleep-related traits and male fertility was evaluated using multiple methods, including inverse variance weighting (IVW), weighted median, Mendelian randomisation-Egger, weighted model, and simple model through two-sample Mendelian randomisation analysis. Mendelian randomisation-Egger regression was used to assess pleiotropy, Cochrane's Q test was employed to detect heterogeneity, and a leave-one-out sensitivity analysis was conducted. Results: Genetically-predicted chronotype (IVW, OR = 1.07; 95%CL = 1.04-1.12; p = 0.0002) was suggestively associated with bioavailable testosterone levels. However, using the IVW method, we found no evidence of a causal association between other sleep traits and male fertility. Conclusion: This study found that chronotype affects testosterone secretion levels. However, further studies are needed to explain this mechanism. [ABSTRACT FROM AUTHOR]

Background: Recently, genetic predisposition to injury has become a popular area of research and the association between a few single nucleotide polymorphisms (SNPs) and the susceptibility to develop musculoskeletal injuries has been shown. This pilot study aimed to investigate the combined effect of common gene polymorphisms previously associated with muscle injuries in Italian soccer players. Results: A total of 64 Italian male top football players (age 23.1 ± 5.5 years; stature 180.2 ± 7.4 cm; weight 73.0 ± 7.9 kg) were genotyped for four gene polymorphisms [ACE I/D (rs4341), ACTN3 c.1729C > T (rs1815739), COL5A1 C > T (rs2722) and MCT1 c.1470A > T (rs1049434)]. Muscle injuries were gathered for 10 years (2009–2019). Buccal swabs were used to obtain genomic DNA, and the PCR method was used to genotype the samples. The combined influence of the four polymorphisms studied was calculated using a total genotype score (TGS: from 0 to 100 arbitrary units; a.u.). A genotype score (GS) of 2 was assigned to the "protective" genotype for injuries, a GS of 1 was assigned to the heterozygous genotype while a GS of 0 was assigned to the "worst" genotype. The distribution of genotype frequencies in the ACE I/D (rs4341), ACTN3 c.1729C > T (rs1815739) and MCT1 c.1470A > T (rs1049434) polymorphisms was different between non-injured and injured football players (p = 0.001; p = 0.016 and p = 0.005, respectively). The incidence of muscle injuries was significantly different among the ACE I/D (rs4341), ACTN3 c.1729C > T (rs1815739) and COL5A1 C > T (rs2722) genotype groups, showing a lower incidence of injuries in the "protective" genotype than "worse" genotype (ACE, p < 0.001; ACTN3, p = 0.005) or intermediate genotype (COL5A1, p = 0.029). The mean TGS in non-injured football players (63.7 ± 13.0 a.u.) was different from that of injured football players (42.5 ± 12.5 a.u., p < 0.001). There was a TGS cut-off point (56.2 a.u.) to discriminate non-injured from injured football players. Players with a TGS beyond this cut-off had an odds ratio of 3.5 (95%CI 1.8–6.8; p < 0.001) to suffer an injury when compared with players with lower TGS. Conclusions: These preliminary data suggest that carrying a high number of "protective" gene variants could influence an individual's susceptibility to developing muscle injuries in football. Adapting the training load parameters to the athletes' genetic profile represents today the new frontier of the methodology of training. Key Points: The ACE I/D (rs4341), ACTN3 c.1729C>T (rs1815739), COL5A1 C>T (rs2722) and MCT1 c.1470A>T (rs1049434) polymorphisms (and their interaction) are associated with muscle injury in football players. The ACE D allele, the ACTN3 C allele, the COL5A1 C allele, and the MCT1 T allele seem to protect football players from developing muscle injuries. The Total Genotype Score was associated with the incidence of muscle injuries in Italian top-level footballers, and this result needs replication in a larger independent cohort. [ABSTRACT FROM AUTHOR]

The applications of centrality measures in protein-protein interaction (PPI) network analysis are diverse and encompass fundamental biological insights; cancer disease-related discoveries, and practical implications for drug development. This multidimensional approach in PPI network analysis provides a comprehensive understanding of the pivotal elements and their impact on biological systems. Analyzing centrality measures in PPI networks enables the identification of essential proteins, hub and bottleneck proteins that occupy strategic positions within the PPI network structure. Essential proteins in PPI networks are significant elements that indicate their importance in maintaining PPI network integrity and functionality. Studying centrality measures can reveal hidden patterns and relationships within these PPI networks. This paper identifes PPI networks with a high degree of connectivity ("hubs") and proteins with high betweenness centrality (bottlenecks), along with closeness centrality and clustering coefficient. This measure's significance in PPI networks has implications for various felds. The proposed approach successfully identifed and characterized infuential proteins and found the top 20 essential proteins. These proteins likely hold significant functional importance through hubs and bottlenecks and serve as potential targets for further investigation. This approach has the potential to identify essential proteins involved in cancer diseases. Leveraging centrality measures in the analysis of PPI networks ofers a multifaceted approach to understanding cancer biology and its implications for personalized medicine, drug design, and the development of innovative cancer therapies. [ABSTRACT FROM AUTHOR]

Background and objectives: Colorectal mucinous adenocarcinoma (MAC) is a particular pathological type that has yet to be thoroughly studied. This study aims to investigate the characteristics of colorectal MAC-related genes in colorectal cancer (CRC), explore the role of MAC-related genes in accurately classifying CRC, and further construct a prognostic signature. Methods: CRC samples were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). MAC-related differentially expressed genes (DEGs) were analyzed in TCGA samples. Based on colorectal MAC-related genes, TCGA CRC samples were molecularly typed by the non-negative matrix factorization (NMF). According to the molecular subtype characteristics, the RiskScore signature was constructed through univariate Cox, the least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses. Clinical significance in CRC of the RiskScore signature was analyzed. A nomogram was further built based on the RiskScore signature. Results: From the colorectal MAC-related genes, three distinct molecular subtypes were identified. A RiskScore signature composed of six CRC subtype-related genes (CALB1, MMP1, HOXC6, ZIC2, SFTA2, and HYAL1) was constructed. Patients with high-RiskScores had the worse prognoses. RiskScores led to differences in gene mutation characteristics, antitumor drug sensitivity, and tumor microenvironment of CRC. A nomogram based on the signature was developed to predict the one-, three-, and five-year survival of CRC patients. Conclusion: MAC-related genes were able to classify CRC. A RiskScore signature based on the colorectal MAC-related molecular subtype was constructed, which had important clinical significance for guiding the accurate stratification of CRC patients. [ABSTRACT FROM AUTHOR]

Hypertrophic cardiomyopathy (HCM) is among the most common forms of cardiomyopathies, with a prevalence of 1:200 to 1:500 people. HCM is caused by variants in genes encoding cardiac sarcomeric proteins, of which a majority reside in MYH7, MYBPC3, and TNNT2. Up to 40% of the HCM cases do not have any known HCM variant. Genotype–phenotype associations in HCM remain incompletely understood. This study involved two visits of 46 adult patients with a confirmed diagnosis of HCM. In total, 174 genes were analyzed on the Next-Generation Sequencing platform, and transthoracic echocardiography was performed. Gene-specific discriminative echocardiogram findings were identified using the computer vision library Fast AI. This was accomplished with the generation of deep learning models for the classification of ultrasonic images based on the underlying genotype and a later analysis of the most decisive image regions. Gene-specific echocardiogram findings were identified: for variants in the MYH7 gene (vs. variant not detected), the most discriminative structures were the septum, left ventricular outflow tract (LVOT) segment, anterior wall, apex, right ventricle, and mitral apparatus; for variants in MYBPC3 gene (vs. variant not detected) these were the septum, left ventricle, and left ventricle/chamber; while for variants in the TNNT2 gene (vs. variant not detected), the most discriminative structures were the septum and right ventricle. [ABSTRACT FROM AUTHOR]

Objective: This study aimed to identify glycopeptide resistance genes and virulence factors in vancomycin-resistant Enterococcus species and to investigate the influence of the microbiota and hospital environment on glycopeptide resistance. Materials and Methods: A total of 107 enterococcal isolates were collected from patients' rectal swab cultures and environmental samples taken for surveillance purposes. Multiplex Polymerase Chain Reaction (PCR) analysis was conducted to investigate specific virulence genes (esp, hyl, asa1, cyl, and galE) and glycopeptide resistance genes (vanA, vanB, van C1-C2, van D, vanE, and vanG). Additionally, perirectal swab cultures were obtained from patients without vancomycin-resistant enterococcal colonization to investigate the presence of glycopeptide resistance genes in their microbiota. Results: Seven isolates (6.5%) were identified as infectious agents. The most common vancomycin resistance genes were vanA (23.3%), followed by vanA + vanB (14%) and vanB + vanD (14%), respectively. The Random Amplified Polymorphic DNA Polymerase Chain Reaction (RAPD-PCR) method showed that patient surveillance and environmental isolates were clonally related. Moreover, microbiota analysis of patients without vancomycin-resistant enterococcal colonization revealed Clostridium spp. in two patients and Lactobacillus spp. in one patient, with the vanG gene found in the microbiota of only one (2.5%) patient. Conclusion: The detection of genes responsible for dissemination indicates that colonized isolates also have the potential for infection, and the hospital environment plays a primary role in the acquisition of vancomycin-resistant enterococci. [ABSTRACT FROM AUTHOR]

Background: Poultry is one of the most prominent sources of Campylobacter jejuni, which is also a major means of transmission to people. Campylobacter jejuni contamination in chicken meat comes from chicken feces because it naturally exists in the intestines of chickens. Aim: The purpose of this study is to identify the antibiotic resistance patterns and genes of C. jejuni, which was found in chickens in Pasuruan, Indonesia. Methods: The samples used in this study were 200 contents of the small intestine of broiler chickens from 40 farms in Pasuruan Regency. The enriched sample was streaked on the selective media of modified charcoal cefoperazone deoxycholate agar containing the CCDA selective supplement. Antimicrobial susceptibility test utilizing the Kirby-Bauer diffusion test method in accordance with Clinical and Laboratory Standards Institute standards. The polymerase chain reaction (PCR) method was used to detect the (hipO), which encodes the C. jejuni strain, fluoroquinolone resistance (gyrA), beta-lactam resistance (blaOXA-61), and tetracycline resistance (tetO) genes. Results: The findings revealed a 14% (28/200) prevalence of C. jejuni in the small intestine of broiler chickens. These isolates showed high resistance to enrofloxacin (92.9%). All isolates (100%) were susceptible to amoxicillinclavulanate. The PCR results showed all C. jejuni isolates (100%) detected the gyrA gene, 96.4% detected the blaOXA-61 gene, and 50% detected the tetO gene. Conclusion: The findings of antimicrobial resistance at a high level from the small intestine of broiler chickens illustrate the potential threat to human health. To lessen the effects now and in the future, coordinated and suitable action is needed, as well as steps to guarantee the poultry industry's economic survival and public health insurance. [ABSTRACT FROM AUTHOR]

In a nuclear or radiological incident, first responders must quickly and accurately measure radiation exposure among civilians as medical countermeasures are radiation dose-dependent and time-sensitive. Although several approaches have been explored to measure absorbed radiation dose, there is an important need to develop point-of-care (POC) bioassay devices that can be used immediately to triage thousands of individuals potentially exposed to radiation. Here we present a proof-of-concept study showing the use of a paper-based vertical flow immunoassay (VFI) to detect radiation dosimetry genes. Using labeled primers during amplification and a multiplex membrane, our results showed that the nucleic acid VFI can simultaneously detect two biodosimetry genes, CDKN1A and DDB2, as well as one housekeeping gene MRPS5. The assay demonstrated good linearity and precision with an inter- and intra-assay coefficient of variance <20% and <10%, respectively. Moreover, the assay showed its ability to discriminate non-irradiated controls (0 Gy) from irradiated samples (1 + 2 Gy) with an overall sensitivity of 62.5% and specificity of 100% (AUC = 0.8672, 95% CI: 0.723–1.000; p = 0.004). Interestingly, the gene combination also showed a dose-dependent response for 0, 1, and 2 Gy, similar to data obtained by real-time PCR benchmark. These preliminary results suggest that a VFI platform can be used to detect simultaneously multiple genes that can be then quantified, thus offering a new approach for a POC biodosimetry assay that could be rapidly deployed on-site to test a large population and help triage and medical management after radiological event. [ABSTRACT FROM AUTHOR]

The biosynthesis and distribution of lignans in medicinal plants, particularly in Schisandra sphenanthera, hold significant pharmacological importance. This study bridges the knowledge gap in understanding the tissue-specific biosynthesis and distribution of these compounds, with a focus on Gomisin J. Our phytochemical analysis revealed a distinct accumulation pattern of Gomisin J, predominantly in the roots, contrasting with the distribution of Pregomisin and Dihydroguaiaretic acid. This finding highlights the roots' unique role in lignan storage and biosynthesis. Further, differential gene expression analysis across various tissues illuminated the biosynthetic pathways and regulatory mechanisms of these lignans. Utilizing Weighted Gene Co-expression Network Analysis (WGCNA), we identified the MEtan module as a key player, strongly correlated with Gomisin J levels. This module's in-depth examination revealed the crucial involvement of four cytochrome P450 (CYP) enzymes and eight transcription factors. Notably, the CYP genes DN6828 and DN2874-i3 exhibited up-regulation in roots across both male and female plants, while DN51746 was specifically up-regulated in male roots, indicating a potential gender-specific aspect in Gomisin J biosynthesis. Comparative analysis with functionally characterized CYP71A homologs suggests these CYP genes might be involved in distinct biosynthetic pathways, including terpenoids, alkaloids, and phenylpropanoids, and potentially in lignan biosynthesis. This hypothesis, supported by their more than 55% identity with CYP71As and strong correlation with Gomisin J concentration, opens avenues for novel discoveries in lignan biosynthesis, pending further functional characterization. Our research provides a comprehensive understanding of the genetic and metabolic mechanisms underlying the tissue-specific distribution of lignans in Schisandra sphenanthera, offering valuable insights for their pharmacological exploitation. [ABSTRACT FROM AUTHOR]

The aim of this study is twofold: (1) to identify differences in certain anaerobic parameters (10m sprint, 30m sprint, anaerobic power, and Illinois agility tests) between professional and amateur soccer players, and (2) to determine whether there is a difference in the ACTN3 gene polymorphism between professional and amateur soccer players. Ultimately, the goal is to reveal which parameters contribute to the differentiation in these two aspects. A total of 133 volunteer soccer players, including 71 professionals and 62 amateurs, participated in the research. DNA extraction from buccal epithelial cells was performed using a commercial kit to determine the genetic background of the athletes, and Real-Time PCR was conducted for genotyping. Statistical analysis of the findings obtained from the test results was performed using the SPSS 23 (SPSS Inc., Chicago, IL, USA) package program. The homogeneity of variance of the data was assessed using the Levene Test, and normal distribution analyses were conducted using the Shapiro-Wilk Test. Chi-square and Mann-Whitney U tests were employed for parameter analysis. The significance level was set at p<0.05. Evaluation of the data in our study revealed no statistically significant difference in ACTN3 rs1815739 gene polymorphism between the groups (p>0.05). However, there is a statistically significant difference in anaerobic parameters (10m sprint, 30m sprint, and anaerobic power) except for the Illinois test (p<0.05). In conclusion, our study found that gene polymorphism is not a differentiating factor between professional and amateur soccer players, but speed (10m and 30m) and anaerobic power parameters are differentiating factors. [ABSTRACT FROM AUTHOR]

The main aims of the present study were to explore the relationship of the OPRM1 gene rs1074287 polymorphism in alcohol-dependent women with their personality traits and to try to find out whether any specific features may influence alcohol cravings and be a prognostic for alcohol dependency and treatment in AUD women. Our study found a notable correlation between openness and the interaction of the ORIM1 gene and AUD. The alcohol use disorder subjects with genotype AG showed a higher level of openness compared to the control group with genotypes AG (p = 0.0001) and AA (p = 0.0125). The alcohol use disorder subjects with the AA genotype displayed higher levels of openness than the control group with genotype AG (p = 0.0271). However, the alcohol use disorder subjects with the AA genotype displayed lower levels of openness than the control group with genotype GG (p = 0.0212). Our study indicates that openness as a personality trait is correlated with the OPRM1 gene rs1074287 polymorphism in alcohol-dependent women. These are the first data and results exploring such a relationship between opioid and alcohol pathways and the mental construction of AUD women. Personality traits such as openness to experience and neuroticism might play major roles in the addiction mechanism, especially in genetically predisposed females, independent of the reward system involved in the emotional disturbances that coexist with anxiety and depression. [ABSTRACT FROM AUTHOR]

Background: Worldwide, atrial fibrillation (AF) is the most common arrhytmia in all subtypes of cardiomyopathies (CMP). Genetic testing of CMP genes is a standard aspect of clinical management in affected families. Aim: To determine the association of selected genetic markers of patients with cardiomyopathies and atrial fibrillation in the region of eastern Slovakia. Patients and methods: After signing informed consent, clinical data and a venous blood sample were obtained from all study participants for genetic analysis. After analyzing the genetic results, allele and genotype frequencies were calculated in the patient group and in the control group. Our case-control study was conducted in a group of 85 individuals from the region of eastern Slovakia, of which 43.53% were patients with CMP and AF with an average age of 62.65 ± 11.01 years. The group was dominated by men (64.71%) and there were more frequent patients with dilated CMP and at the same time with persistent AF. Results: Representation of potentially risky alleles associated with AF was higher in the case of rs13143308 and rs2220427 in patients with CMP and AF compared to the control group. The potentially risky T allele of the genetic variant rs3853445 dominated in the control group (73% vs. 68%). After evaluating the allelic and genotypic distributions, an analysis of associations of genetic models of variants rs13143308, rs2220427 and rs3853445 with location in the 4q25 locus in relation to cardiomyopathy associated with AF was carried out. None of these analyses confirmed a significant association of the respective genetic model in relation to CMP associated with AF. The p-value of the odds ratio (OR) calculations was higher than 0.05 in all cases Conclusion: By analyzing the selected genetic markers rs13143308, rs2220427 and rs3853445 located in the 4q25 locus, we failed to statistically confirm their association with cardiomyopathy and related atrial fibrillation. Thus, we can conclude that the basic limitation of our study was the size of the research sample. [ABSTRACT FROM AUTHOR]

The interaction of genetic, epigenetic, and environmental factors underlies the pathogenesis of allergic diseases. Allergic rhinitis and atopic bronchial asthma are closely related and often concurrent allergic airway diseases. The chronic recurrent course of these diseases establishes the importance of further and more profound studies of the mechanisms underlying the development of these pathologies. Histamine is one of the most significant inflammatory mediators secreted during allergic reactions. The aim of the research was to study the role of polymorphic variants of the AOC1, HRH2, HRH3, ALDH7A1, ADCYAP1, HNMT, PSAP, and SCG3 genes involved in the histamine metabolism in the development of different endophenotypes of the allergic airway diseases in individuals living in the Republic of Bashkortostan. DNA samples of 358 individuals with allergic airway diseases of different ethnicity (Russians—165, Tatars—143, Bashkirs—50) and 200 controls with unweighted heredity in allergic diseases (Russians—75, Tatars—83, Bashkirs—42). Genotyping of polymorphic variants was performed by real-time PCR and PCR-RFLP analysis. It was revealed that the rs104979793*CC genotype and the rs104979793*C allele of the AOC1 gene were associated with allergic airway diseases and asthma with concomitant allergic rhinitis in Russians. A significant increase in total IgE level was revealed in Russian patients with allergic airway diseases with the rs1049793*CC genotype of the AOC1 gene compared to carriers of the rs1049793*CG and rs1049793*GG genotypes. The association of the C allele of the rs17525472 polymorphic variant localized near the SCG3 gene with allergic rhinitis in Russians was established. The results revealed that AOC1 and SCG3 genes involved in the metabolism of histamine are related to the development of different endophenotypes of allergic airway tract diseases in children. [ABSTRACT FROM AUTHOR]

Abiotic stresses are major limiting factors for maize growth. Therefore, exploration of the mechanisms underlying the response to abiotic stress in maize is of great interest. Toward this end, we performed integration of the feature selection method into the meta-analysis of microarray gene expression. Following extraction of raw data, normalization, and batch effect removal, the data were merged into one expression profile. Differentially expressed genes (DEGs) between control and abiotic conditions were used for the feature selection algorithm to find the minimum features for high-performance classification. Feature selection was performed using a correlation-based feature selection (CFS) algorithm, considering features with a coefficient of 0.7 to 1. Different algorithms of Bayes, Functions, Lazy, Meta, Rules, and Trees were then tested in order to classify the samples and find the best performance classifier in each group. Moreover, the biological pathways and promoter motif analysis of selected genes were identified. The superior and overall performance of classification using all features (DEGs) were 98.86% (Multilayer Perceptron) and 81.25%, respectively. Classification based on feature selection resulted in an average accuracy of 94.69% and 93.56% with 33 and 12 features, respectively. Subsequently, gene ontology and promoter analysis were performed for the 12 selected biomarker genes. Five of them were downregulated and 7 were upregulated. ABRE, unnamed-1, G-box, and G-Box are motifs related to genes involved in several abiotic stress responses and are located upstream of at least nine probes in our study. This study revealed key genes associated with tolerance to abiotic stress in maize. [ABSTRACT FROM AUTHOR]

Background: Changes in gut microbiota abundance have been linked to prostate cancer development. However, the causality of the gut-prostate axis remains unclear. Methods: The genome-wide association study (GWAS) data for gut microbiota sourced from MiBioGen (n = 14,306), alongside prostate cancer summary data from PRACTICAL (n = 140,254) and FinnGen Consortium (n = 133,164). Inverse-variance-weighted (IVW) was mainly used to compute odds ratios (OR) and 95% confidence intervals (Cl), after diligently scrutinizing potential sources of heterogeneity and horizontal pleiotropy via the rigorous utilization of Cochran's Q test, the MR-PRESSO method, and MR-Egger. We used meta-analysis methods in random effects to combine the Mendelian randomization (MR) estimates from the two sources. Results: The pooled analyses of MR results show that genus Eubacterium fissicatena (OR = 1.07, 95% CI 1.01 to 1.13, P = 0.011) and genus Odoribacter (OR = 1.14, 95% CI 1.01 to 1.27, P = 0.025) were positively associated with prostate cancer. However, genus Adlercreutzia (OR = 0.89, 95% CI 0.83 to 0.96, P = 0.002), Roseburia (OR = 0.90, 95% CI 0.83 to 0.99, P = 0.03), Holdemania (OR = 0.92, 95% CI 0.86 to 0.97, P = 0.005), Flavonifractor (OR = 0.85, 95% CI 0.74 to 0.98, P = 0.024) and Allisonella (OR = 0.93, 95% CI 0.89 to 0.98, P = 0.011) seems to be a protective factor for prostate cancer. Sensitivity analysis found no significant heterogeneity, horizontal pleiotropy, or reverse causal links in all causal associations. Conclusion: This MR study lends support to a causal relationship between genetically predicted gut microbiota and prostate cancer. Research on the gut-prostate axis, along with further multi-omics analyses, holds significant implications for the prevention and treatment of prostate cancer. [ABSTRACT FROM AUTHOR]

The gene B4GALNT2, with 12 Exons, is located on chromosome 11. This gene is associated with the production of the B4GALNT2 protein, which functions as a transferase in the final step of synthesizing the Sda antigen. In the Lacaune breed, a mutation known as FecLL (g.36938224T>A) in intron 7 of this gene has been found to have a positive effect on fertility and multiple births. Considering the effect of multiple births in the small ruminant industry, an investigation was conducted to explore the presence of the FecLl mutation and other potential mutation near its location in part of the intron 7 of B4GALNT2 gene. Two groups of multiple birth and single birth, each containing 20 shal ewes were selected for blood collection, DNA extraction and sanger sequencing, based on their reproductive histories of last 5 year of lambing records and the current breeding season. The sequence analysis revealed the absence of the FecLL mutation in the samples. However, three other mutations were identified: g.37129493 T>C, g.37129812 C>A, and g.37130289 T>A. No significant differences were observed between the two study groups regarding these mutations (P > 0.05). Based on these findings, it appears that the FecLL mutation may not be present in the Shal breed. However, due to the occurrence of the mutations in the intron and their potential low impact on the final protein, further investigation of the gene network and a larger sample size is recommended to explore other phenotypic associations and detect additional mutation. [ABSTRACT FROM AUTHOR]

Metabolic syndrome (MetS) is common among schizophrenia patients, and one of MetS's causes may be an imbalance in nitric oxide regulation. In this study, we examined associations of three polymorphic variants of the nitric oxide synthase 1 adapter protein (NOS1AP) gene with MetS in schizophrenia. NOS1AP regulates neuronal nitric oxide synthase, which controls intracellular calcium levels and may influence insulin secretion. The aim of the investigation was to study polymorphic variants of the NOS1AP gene as possible markers of MetS in patients with schizophrenia. A total of 489 Caucasian patients with schizophrenia (ICD-10) from Siberia (Russia) were included in the study, and 131 (26.8%) patients had MetS (IDF classification, 2007). The participants were genotyped for three single-nucleotide polymorphisms in NOS1AP (rs12143842, rs10494366, and rs12029454). Logistic regression was used for association analysis. Single-nucleotide polymorphisms, sex, and age served as covariates; the dependent variable was the coded parameter of the presence/absence of MetS. Polymorphisms rs12143842 and rs10494366 showed a stable association even after Bonferroni's correction for multiple comparisons (p = 0.005 and 0.002, respectively), indicating a statistically significant contribution of these polymorphic variants to the pathogenesis of MetS. Our results suggest that in patients with schizophrenia, NOS1AP may be involved in MetS pathophysiology. [ABSTRACT FROM AUTHOR]

Background/Aim: The tumor protein 53 (TP53) tumor suppressor protein (17p13.1) acts as a significant regulator for the cell cycle normal function. The gene is frequently mutated in colorectal adenocarcinoma (CRC) patients and is associated to poor prognosis and low response rates to chemo-targeted therapy. Our purpose was to correlate TP53 expression with Mouse Double Minute 2 Homolog (MDM2), a proto-oncogene (12q14.3) and a major negative regulator in the TP53-MDM2 auto-regulatory pathway. Materials and Methods: A total of forty (n=40) colorectal adenocarcinoma (CRC) cases were included in this study. An immunohistochemistry-based assay was implemented by using anti-TP53 and anti-MDM2 antibodies in the corresponding tissue sections. Additionally, a digital image analysis assay was implemented for objectively measuring TP53/MDM2 immunostaining intensity levels. Results: TP53 protein overexpression was detected in 27/40 (67.5%), whereas MDM2 overexpression in 28/40 (70%) cases. Interestingly, in 21/40 (52.5%) cases, a combined TP53/MDM2 co-expression was detected, whereas in 6/40 (15%), a combined loss of expression was identified (overall co-expression: p=0.119). p53 overexpression was significantly correlated to grade of the examined cases (p=0.001), whereas MDM2 to stage and max diameter of the malignancies (p=0.001 and 0.024, respectively). Conclusion: TP53/MDM2 over expression is a frequent and significant genetic event in CRCs associated with an aggressive biological behavior, as a result of increased dedifferentiation grade and advanced stage/elevated tumor volume, respectively. MDM2 oncogene overactivation combined with mutated and overexpressed TP53 is observed in sub-groups of patients leading to specific gene/protein signatures - targets for personalized chemotherapeutic approaches. [ABSTRACT FROM AUTHOR]

Introduction: Malaria still remains the most frequent parasitic disease on the world with, in 2022, 249 million cases and 608,000 deaths worldwide. Malaria control is compromised by the spread of the parasite's resistance to available antimalarials. The objective of our study is to characterize the Plasmodium falciparum resistance genes to common antimalarial drugs in semi-urban areas of Burkina Faso. Materials and Methods: This is a prospective cross-sectional study whose collection took place from June to October 2021 and from June to October 2022 in five health facilities in Burkina Faso. The molecular analysis based on PCR–RFLP took place from January to June 2023 at Centre National de Recherche et de Formation (CNRFP) to determine resistance genes such as Pfcrt, Pfmdr1, Pfdhps, and Pfdhfr. Results: A total of 150 samples were analyzed giving a prevalence of 46.67, 1.33, 0.67, 20, 82, and 4.67%, for Pfcrt 76 T, Pfmdr1 86Y, Pfdhps 437G, Pfdhfr 51I, Pfdhfr 59R, and Pfdhfr 108N mutations, respectively. There are no mutations observed Pfdhps 540E and Pfdhfr 164L positions. However, mutation on Pfdhfr 59R position was the most common. In addition, triple mutation (Pfdhps 437G + Pfdhfr 59R + Pfdhfr 108N) was found with a low frequency which is 0.67%. Conclusion: Surveillance of Plasmodium falciparum resistance markers to antimalarial drugs, remains one of the priorities in the context of the control or malaria elimination. [ABSTRACT FROM AUTHOR]

Lead (Pb), a widespread heavy metal, causes severe toxicity in human and animal organs (e.g., bone marrow), whereas the mechanisms of the bone marrow toxicity induced by Pb exposure are unclear. Hence, this study was designed to reveal the hub genes involved in Pb-induced bone marrow toxicity. GSE59894 dataset obtained from Gene Expression Omnibus (GEO) was composed of lead acetate (PbAc2)-treated and control bone marrow samples. Totally 120 and 85 differentially expressed genes (DEGs) were identified on the 1st day, while 153 and 157 DEGs on the 3rd day in the bone marrow treated with 200 and 600 mg/kg of PbAc2, respectively. Notably, a total of 28 and 32 overlapping DEGs were identified in the bone marrow on the 1st and 3rd day treated with PbAc2, respectively. Biological process analysis suggested that the common DEGs were primarily participated in cell differentiation, the response to drug, xenobiotic stimulus, and organic cyclic compound. Pathway analysis demonstrated that the overlapping DEGs were primarily linked to PI3K-Akt, TGF-β, MAPK, and osteoclast differentiation signaling pathways. Moreover, the hub genes, including PLD2, DAPK1, ALB, TNF, FOS, CDKN1A, and TGFB3, might contribute to PbAc2-induced bone marrow toxicity. Overall, our study offers an important insight into the molecular mechanisms of Pb-induced bone marrow toxicity. [ABSTRACT FROM AUTHOR]

Amoebiasis is a widespread parasitic disease caused by Entamoeba histolytica (E. histolytica), affecting various hosts, such as humans, birds, and pigs. This study aimed to investigate Entamoeba spp. in monkeys (Macaca spp.) diagnose them using molecular methods. A total of 33 fecal samples were collected from monkeys (Macaca spp.) aged 3-5 years in Babylon province to investigate a common and zoonotic parasitic disease. Initially, microscopic examination was conducted on all samples, and those yielding positive results were preserved for molecular study. The DNA was extracted, and conventional PCR was carried out with a pair of primers to detect the 857 bp fragment of E. histolytica SSU rRNA gene. PCR results for 19 fecal samples, previously identified as positive by the direct smear method, from monkeys in the reserves of Babylon province indicated that the presence of the SSUrRNA gene with an 857 bp was 45% in only 15 samples. Sequencing of the SSUrRNA gene revealed 98-100% similarity with E.histolytica sequences deposited in International GenBank, which have the sequence numbers OP522013, OP522014, OP522015, OP522016, OP522017, Op626161, Op626162, Op626163, Op626164, and Op626165. [ABSTRACT FROM AUTHOR]

Fowlpox is an infectious viral disease affecting domestic and wild birds. The current study was conducted using PCR-based molecular detection to determine the avian pox virus (APV) and its genetic sequence. A total of 40 pigeons and 40 chickens suspected of APV were obtained from different bird markets. Following euthanasia, tissue samples were taken from the vents, eyes, wings, and beaks for molecular analysis. DNA extraction was focused on the core protein gene region (pb4). PCR results confirmed the presence of APV in all samples, generating specific cDNA bands of 329 bp. Four GenBank accession codes (OR670580, OR670581, OR670582, and OR670583) represented pigeon pox samples, whereas two GenBank accession numbers (OR619724 and OR619725) represented samples of fowlpox. A significant similarity of 99% was found by genetic analysis between the reference target sequences and the sequenced samples. In viral samples of fowlpox and avipoxvirus, nucleic acid variants (205 C > G and 204 T > C) were found with missense and silent effects on particular proteins (p.101Leu>Val and p.108Pro). Phylogenetic analysis organized the samples into clades representing fowlpox and pigeon pox viruses, showing close relationships with strains from different geographical regions. This study unequivocally demonstrates the susceptibility of both domestic and wild birds to avian pox, highlighting the pivotal role of phylogenetic analysis and molecular detection in elucidating novel perspectives on the genetic landscape of these viruses. [ABSTRACT FROM AUTHOR]

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Bipolar disorder is a chronic disorder characterized by fluctuations in mood state and energy and recurrent episodes of mania/hypomania and depression. Bipolar disorder may be regarded as a neuro-progressive disorder in which repeated mood episodes may lead to cognitive decline and dementia development. In the current review, we employed genome-wide association studies to comprehensively investigate the genetic variants associated with bipolar disorder and dementia. Thirty-nine published manuscripts were identified: 20 on bipolar disorder and 19 on dementia. The results showed that the genes CACNA1C, GABBR2, SCN2A, CTSH, MSRA, and SH3PXD2A were overlapping between patients with bipolar disorder and dementia. In conclusion, the genes CACNA1C, GABBR2, SCN2A, CTSH, MSRA, and SH3PXD2A may be associated with the neuro-progression of bipolar disorder to dementia. Further genetic studies are needed to comprehensively clarify the role of genes in cognitive decline and the development of dementia in patients with bipolar disorder.

Soybean (Glycine max [L.] Merr) plays a crucial role in the advancement of agriculture in Kazakhstan, serving as a promising food crop and feed source. The primary challenge in boosting soybean production in Northern Kazakhstan lies in the absence of soybean cultivars suited to the region's conditions. As such, the foremost focus of breeding initiatives should be on creating soybean varieties that possess both early maturity and satisfactory yield potential. The objective of this research was to assess the impact of maturity time (MT) on both the yield formation and the adaptive characteristics of soybean varieties from different origins. This evaluation was conducted by analyzing the outcomes of their testing under diverse cultivation conditions in the northern region of Kazakhstan. The soybean cultivars that were examined, originating from various sources, were classified into three primary groups. These groups varied in terms of their growing season duration as well as their yield levels. The way the alleles of the E1–E4 flowering genes were spread out in the identified clusters showed that for soybean varieties where recessive alleles of the E1–E4 genes build up, the growing season usually shorter. Cultivars of Chinese, Russian, and domestic selections isolated as a result of the research were good initial material for use in local breeding programs. Within the framework of the clusters, an environmental assessment of soybean accessions was carried out, which made it possible to determine their degree of plasticity and, in general, their adaptive potential in the conditions of Northern Kazakhstan. The best cultivars were the Chinese selection ‘Dongnong 63’ and the Russian selection ‘SIBNIIK 315’. Hence, the present study successfully discovered soybean cultivars that possess exceptional adaptability and flexibility. These cultivars hold significant potential for cultivation and practical use in the specific environmental circumstances of northern Kazakhstan.

Chronic insomnia (CI) is a complex disease involving multiple factors including genetics, gut microbiota, and brain structure and function. However, there lacks a unified framework to elucidate how these factors interact in CI. By combining data of clinical assessment, sleep behavior recording, cognitive test, multimodal MRI (structural, functional, and perfusion), gene, and gut microbiota, this study demonstrated that enhanced cerebral blood flow (CBF) similarities of the somatomotor network (SMN) acted as a key mediator to link multiple factors in CI. Specifically, we first demonstrated that only CBF but not morphological or functional networks exhibited alterations in patients with CI, characterized by increases within the SMN and between the SMN and higher-order associative networks. Moreover, these findings were highly reproducible and the CBF similarity method was test-retest reliable. Further, we showed that transcriptional profiles explained 60.4 % variance of the pattern of the increased CBF similarities with the most correlated genes enriched in regulation of cellular and protein localization and material transport, and gut microbiota explained 69.7 % inter-individual variance in the increased CBF similarities with the most contributions from Negativicutes and Lactobacillales. Finally, we found that the increased CBF similarities were correlated with clinical variables, accounted for sleep behaviors and cognitive deficits, and contributed the most to the patient-control classification (accuracy = 84.4 %). Altogether, our findings have important implications for understanding the neuropathology of CI and may inform ways of developing new therapeutic strategies for the disease.

Background: Mitophagy is the selective degradation of mitochondria by autophagy. It becomes increasingly clear that mitophagy pathways are important for cancer cells to adapt to their high-energy needs. However, which genes associated with mitophagy could be used to prognosis cancer is unknown. Methods: We created a clinical prognostic model using mitophagy-related genes (MRGs) in lung adenocarcinoma (LUAD) patients for the first time, and we employed bioinformatics methods to search for biomarkers that affect the progression and prognosis of LUAD. Transcriptome data for LUAD were obtained from The Cancer Genome Atlas (TCGA) database, and additional expression data from LUAD patients were sourced from the Gene Expression Omnibus (GEO) database. Furthermore, 25 complete MRGs were identified based on annotations from the MSigDB database. Results: A comparison of the mitophagy scores between the groups with high and low scores was done using receiver operating characteristic (ROC) curves, which also revealed the differential gene expression patterns between the two groups. Using Kaplan-Meier analysis, two prognostic MRGs from the groups with high and low mitophagy scores were identified: TOMM40 and VDAC1. Using univariate and multivariate Cox regression, the relationship between the expression levels of these two genes and prognostic clinical features of LUAD was examined further.The prognosis of LUAD patients was shown to be significantly correlated (P

The relationship between brain entropy (BEN) and early brain development has been established through animal studies. However, it remains unclear whether the BEN can be used to identify age-dependent functional changes in human neonatal brains and the genetic underpinning of the new neuroimaging marker remains to be elucidated. In this study, we analyzed resting-state fMRI data from the Developing Human Connectome Project, including 280 infants who were scanned at 37.5–43.5 weeks postmenstrual age. The BEN maps were calculated for each subject, and a voxel-wise analysis was conducted using a general linear model to examine the effects of age, sex, and preterm birth on BEN. Additionally, we evaluated the correlation between regional BEN and gene expression levels. Our results demonstrated that the BEN in the sensorimotor-auditory and association cortices, along the ‘S-A’ axis, was significantly positively correlated with postnatal age (PNA), and negatively correlated with gestational age (GA), respectively. Meanwhile, the BEN in the right rolandic operculum correlated significantly with both GA and PNA. Preterm-born infants exhibited increased BEN values in widespread cortical areas, particularly in the visual-motor cortex, when compared to term-born infants. Moreover, we identified five BEN-related genes (DNAJC12, FIG4, STX12, CETN2, and IRF2BP2), which were involved in protein folding, synaptic vesicle transportation and cell division. These findings suggest that the fMRI-based BEN can serve as an indicator of age-dependent brain functional development in human neonates, which may be influenced by specific genes.

Pearl millet (Pennisetum glaucum, also known as Cenchrus americanus) is a cereal crop that has a C4 photosynthesis system and that can grow and develop seeds even under stressed conditions including drought-stressed, high temperature-stressed and nutrient-poor conditions. In previous studies, transcriptomes of pearl millet were studied by RNA sequencing (RNA-Seq) to understand mechanisms regulating its development and tolerance to such stressed conditions. Here, RNA-Seq reads from 565 pearl millet samples from 25 projects in the NCBI (National Center for Biotechnology Information) BioProject database were collected and mapped to the pearl millet reference genome to obtain read counts and transcripts per million (TPM) for each pearl millet gene. The count and TPM data for all the 565 samples as well as the attributes of those samples and projects were deposited in the figshare repository (https://doi.org/10.6084/m9.figshare.24902100).

Objective Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occurrence and progression of lung adenocarcinoma but also have the potential to serve as biomarkers for clinical diagnosis, prognosis evaluation and treatment guidance. Methods Differentially expressed genes (DEGs) were identified using comprehensive GSE1987 and GSE18842 gene expression databases. A comprehensive bioinformatics analysis of these DEGs was conducted to explore enriched functions and pathways, relative expression levels, and interaction networks. Random Forest and LASSO regression analysis techniques were used to identify the three most significant target genes. The TCGA database and quantitative polymerase chain reaction (qPCR) experiments were used to verify the expression levels and receiver operating characteristic (ROC) curves of these three target genes. Furthermore, immune invasiveness, pan-cancer, and mRNA-miRNA interaction network analyses were performed. Results Eighty-nine genes showed increased expression and 190 genes showed decreased expression. Notably, the upregulated DEGs were predominantly associated with organelle fission and nuclear division, whereas the downregulated DEGs were mainly associated with genitourinary system development and cell-substrate adhesion. The construction of the DEG protein-protein interaction network revealed 32 and 19 hub genes with the highest moderate values among the upregulated and downregulated genes, respectively. Using random forest and LASSO regression analyses, the hub genes were employed to identify three most significant target genes.TCGA database and qPCR experiments were used to verify the expression levels and ROC curves of these three target genes, and immunoinvasive analysis, pan-cancer analysis and mRNA-miRNA interaction network analysis were performed. Conclusion Three target genes identified by machine learning: BUB1B, CENPF, and PLK1 play key roles in LUAD development of lung adenocarcinoma.

A 33-year-old patient presented with a chief complaint of patent ductus arteriosus (PDA) persisting for over 30 years. Physical examination revealed bilateral facial angiofibromas, multiple nail fibromas, intraoral fibromas, and a ’shagreen patch’ on the left lumbar region. Genetic testing was performed using a peripheral venous blood sample, which confirmed the diagnosis of Tuberous Sclerosis Type 2 (TSC2). Subsequently, the patient underwent cardiac color Doppler ultrasound and chest computed tomography angiography, which confirmed the presence of PDA. Tuberous sclerosis complex (TSC) is associated with cardiovascular diseases. The initial clinical manifestation of TSC is usually cardiac rhabdomyoma in children, and it is rarely reported in adults with PDA. In this case, the patient was diagnosed with PDA when he was young, and the genetic test showed heterozygous variation of TSC2 gene. The purpose of this article is to explore the correlation between TSC and PDA at the gene level through literature review.

Soybean is one of the world’s most economically significant crops and is widely utilized as an essential source of vegetable protein and edible oil. Cultivated soybean is domesticated from its annual counterpart, wild soybean, which is considered valuable germplasm for soybean breeding. However, wild soybean accessions generally produce seeds with impermeable coats, a trait known as hard seededness (HS), which is beneficial for long-term seed survival but is undesirable for the uniform water absorption and germination of seeds, thus limiting the utilization of wild soybeans in breeding. In addition, moderate HS can isolate the embryo from the surrounding environment and is thus beneficial for long-term seed storage and germplasm preservation. The HS trait is primarily associated with the structure and chemical composition of the seed coat. Moreover, its development is also influenced by various environmental conditions, such as water and temperature. Genetic analysis has revealed that HS of soybean is a complex quantitative trait controlled by multiple genes or minor quantitative trait loci (QTL), with many QTLs and several causal genes currently identified. Investigating the physiological and molecular mechanisms underlying this trait is crucial for soybean breeding, production, and food processing. For this article, the literature was reviewed and condensed to create a well-rounded picture of the current understanding of internal and external factors, QTLs, causal genes, and the regulatory mechanisms related to the HS of soybean, with the aim of providing reference for future research and utilization of this trait.