Journal of Applied Genetics最新文献

{"title":"Effect of miR-10a on the proliferation and differentiation of yak adipocyte precursors.","authors":"Quyangangmao Su, Zhanhong Gao, Fengshuo Zhang, Zhenling Wu, Qiurong Ji, Kaina Zhu, Linsheng Gui","doi":"10.1007/s13353-024-00932-6","DOIUrl":"https://doi.org/10.1007/s13353-024-00932-6","url":null,"abstract":"<p><p>The fat content of yak meat is significantly correlated with the meat quality, and an appropriate fat content helps to improve the texture of the meat. The involvement of miR-10a in regulating the differentiation and proliferation of various cell types has been reported. Therefore, in this study, the effects of miR-10a on lipid droplet accumulation were investigated by transfection of yak adipocyte precursors with an miR-10a inhibitor, followed by Oil Red O, BODIPY, EdU staining, and cell cycle analysis of the transfected and control cells. The relative expression of lipogenic marker genes was determined by RT-qPCR to clarify the effect of miR-10a on the differentiation and proliferation of yak adipocyte precursors. Mature adipocytes were collected for transcriptome analysis to identify differentially expressed target genes and the association of these genes with adipogenic pathways was investigated by GO and KEGG enrichment analyses. In addition, the phylogeny and expression profiles of miR-10a were analyzed in various yak tissues. The results showed that miR-10a could inhibit the differentiation and promote the proliferation of yak adipocyte precursors. Analysis of the RNA-Seq results showed that miR-10a inhibitor and inhibitor NC had six differentially expressed genes: FABP4, AKR1B7, IGF2, ROCK1, IFNB1, and PLA2G3. These genes were found to be involved in the regulation of adipogenesis, with IGF2 and IFNB1 being upregulated in the PI3K-Akt signaling pathway, which is activated upon stimulation by IGF2 and IFNB1 and inhibits the differentiation and promotes the proliferation of yak adipocytes precursor, which in turn affected adipogenesis. Moreover, phylogenetic analysis indicated that miR-10a evolved relatively recently in yak and sheep, while tissue expression profiles showed that miR-10a was highly expressed in yak lung tissues.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142882101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of quantitative trait loci for in vitro plant regeneration from leaf microexplants in cucumber (Cucumis sativus L.).","authors":"Renata Słomnicka, Magdalena Cieplak, Magda Antosiewicz, Alicja Sadłos, Aleksandra Galczak, Karolina Kaźmińska, Grzegorz Bartoszewski","doi":"10.1007/s13353-024-00927-3","DOIUrl":"https://doi.org/10.1007/s13353-024-00927-3","url":null,"abstract":"<p><p>Plant regeneration in tissue cultures is crucial for the application of biotechnological methods to plant breeding. However, the genetic basis of in vitro plant regeneration is not fully understood. For cucumber, regeneration protocols from different types of explants have been reported, but thus far, the molecular basis of regeneration from cotyledon explants has only been studied. The aim of this work was to identify quantitative trait loci (QTLs) for in vitro plant regeneration from cucumber leaf microexplants. Plant regeneration was evaluated using a population of recombinant inbred lines (RILs) developed from a cross between line B10, characterized by high regeneration efficiency, and the low regeneration efficiency line Gy14. All RILs were scored for frequency of callus formation, organogenesis, and shoot regeneration. RILs with regeneration efficiencies higher than that of line B10 have been observed. QTLs for the frequency of organogenesis and shoot regeneration were identified. All the QTLs were mapped on cucumber chromosome 6, explaining 11.9 to 20% of the phenotypic variance. The major-effect QTL for organogenesis or6.1 was located on the upper arm of chromosome 6. The QTLs for shoot regeneration frequency, sr6.1A and sr6.1B, were located on the lower arm of chromosome 6. Analysis of the genomic region corresponding to these QTLs combined with gene expression profiling revealed that CsARF6 and CsWOX9 are gene candidates underlying these QTLs. This study is a step toward identifying the genes controlling the ability of cucumber plant regeneration from leaf explants.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring microRNA signatures in pediatric non-infectious uveitis: meta-analysis and molecular profiling of patient samples.","authors":"Olga Wawrzyniak, Dariusz Wawrzyniak, Michał Smuszkiewicz, Paweł Głodowicz, Anna Gotz-Więckowska, Katarzyna Rolle","doi":"10.1007/s13353-024-00922-8","DOIUrl":"https://doi.org/10.1007/s13353-024-00922-8","url":null,"abstract":"<p><p>To find a distinct non-coding RNA characteristic for idiopathic uveitis in the pediatric population. To explore the autoimmune-related miRNA expression profile in pediatric patients with idiopathic uveitis (IU) and juvenile idiopathic arthritis-associated uveitis (JIA-AU) and find a common molecular background for idiopathic uveitis and other autoimmune diseases. The expression levels of miRNAs were analyzed by quantitative real-time PCR using serum samples from patients with idiopathic uveitis (n = 8), juvenile idiopathic arthritis-associated uveitis (n = 7), and healthy controls. We selected the most promising miRNAs from the original research papers: miR-16-5p, miR-26a-5p, miR-145-5p, and miR-451a as markers for juvenile idiopathic arthritis; miR-23a-3p, miR-29a-3p, miR-140-5p, miR-193a-5p, and miR-491-5p for uveitis in the adult population; and miR-125a-5p, miR-146a-5p, miR-155-5p, miR-223-5p, and miR-223-3p characteristic for both diseases and confirm their expression changes in serum from children with idiopathic uveitis. We comprehensively reviewed the literature enrolling the papers that met the inclusion criteria (miRNA and non-infectious uveitis/juvenile idiopathic arthritis) and performed target prediction analysis of appoint miRNAs. It additionally confirmed that altered miRNAs target the immunologically involved genes. Immunological-involved miRNAs such as miR-146a-5p and miR-155-5p show diverse expression levels in different patients as they interact with multiple targets. miR-204-5p is downregulated in both patient groups compared to healthy controls. miR-204-5p and miR-155-5p are candidates for molecular markers of autoimmune uveitis. We did not identify the miRNAs specific only to idiopathic uveitis, but for the first time in the pediatric population, we confirmed that this disease entity shares a molecular basis with other autoimmune diseases. Further studies are required to elucidate the molecular interactions among miRNAs, cytokines, and transcription factors within the intricate immune response, particularly in the eye.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational analysis of MYC gene variants: structural and functional impact of non-synonymous SNPs.","authors":"Plabita Bhuyan, Varshabi Bharali, Sangju Basumatary, Aido Lego, Juman Sarma, Debasish Borbora","doi":"10.1007/s13353-024-00929-1","DOIUrl":"https://doi.org/10.1007/s13353-024-00929-1","url":null,"abstract":"<p><p>The MYC proto-oncogene encodes a basic helix-loop-helix leucine zipper (HLH-LZ) transcription factor, acting as a master regulator of genes involved in cellular proliferation, differentiation, and immune surveillance. Dysregulation of MYC is implicated in over 70% of human cancers, driving oncogenic processes through altered gene expression and disrupted cellular functions. Non-synonymous single nucleotide polymorphisms (nsSNPs) within coding regions can significantly impact protein structure and function, leading to abnormal cellular behaviours. This study employed 29 in silico tools to systematically evaluate the deleteriousness of nsSNPs within the MYC gene. These tools assessed the variants' effects on protein structure, disease association, functional domains, and post-translational modification sites. This study investigated if these variants may disrupt protein-protein interactions, critical for MYC's oncogenic roles and normal cellular functions. Our analysis identified 21 nsSNPs that were predicted to be deleterious and pathogenic. These variants correspond to residues D63H, D63Y, P74L, P75L, N375D, N375I, E378K, E378Q, E378A, E378G, E378V, R379P, R381K, R381T, R382W, L392P, R393C, R393H, R393P, L411H, and L411P. Stability assessments indicated that these variants could destabilise the MYC protein. None of the variants affected post-translational modifications. Protein-protein interaction and docking analysis revealed that variants within bHLH and LZ domains may disrupt MYC/MAX binding, potentially impacting MYC's oncogenic activity and transcriptional regulation. This computational assessment enhances our understanding of genetic variations within the MYC gene and prioritises candidate nsSNPs for experimental validation and therapeutic exploration.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence and comparative analysis of Y chromosome microdeletions in recurrent pregnancy loss.","authors":"M L N Deepika, Avvari Srilekha, C Lalitha Pavani, Aryan Gupta, Ridah Nazneen, B Vijaya Lakshmi","doi":"10.1007/s13353-024-00928-2","DOIUrl":"https://doi.org/10.1007/s13353-024-00928-2","url":null,"abstract":"<p><p>Recurrent pregnancy loss (RPL) is defined as the spontaneous loss of two or more pregnancies before reaching viability. Diagnosis for couples with RPL usually involves only the female partner. However, it is seen that male partners contribute equally to the occurrence of spontaneous abortions as the Y chromosome harbors several genes that control spermatogenesis and the quality of sperms. Three non-overlapping regions (AZFa, AZFb, AZFc) in the distal half of Y chromosome have been reported to be associated with spermatogenesis in males with normal karyotype. Microdeletions in these three regions have been identified in many male partners with repeated abortions. The STS regions of the Y chromosome are prone to self-recombination, making it susceptible to deletions, thereby leading to poor sperm quality and fetal implantation failure. The present study aimed to identify the frequency and type of microdeletions among male partners of RPL women. Analysis revealed nearly 76% of cases revealed microdeletions, whereas no deletions were observed among controls in Y chromosome, suggesting a strong link between RPL and microdeletion in the AZF regions of the Y chromosome in the male partner.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142821808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modulatory effects of in ovo delivery of galactooligosaccharide and Lactiplantibacillus plantarum on antioxidant capacity, gene expression, and selected plasma metabolite parameters of broiler chickens.","authors":"Modou Mangan, Katarzyna Połtowicz, Cornelia C Metges, Maria Siwek","doi":"10.1007/s13353-024-00931-7","DOIUrl":"https://doi.org/10.1007/s13353-024-00931-7","url":null,"abstract":"<p><p>A stable gut microbiota promotes a healthy gut and enhances immune function, antioxidant status, and metabolic activities in chickens. The present research work aimed to investigate the modulatory impacts of in ovo delivery of prebiotic and probiotic on oxidative stress, the intestinal transcriptome, and various plasma metabolites in chickens. Fertilized Ross 308 eggs were administered in ovo either with galactooligosaccharide (GOS) (3.5 mg/egg or Lactiplantibacillus plantarum (LP) 1 × 10⁶/egg on the 12th day of egg incubation. Three hundred viable Ross 308 broiler hatching eggs in total were randomly assigned to four groups, namely, the negative control not injected group, the group receiving physiological saline injections as the positive control, GOS, and LP. The analysis of genes associated with immune functions, antioxidants, barrier functions, and free fatty acid receptors were determined via qPCR. The analysis of the selected plasma blood metabolites was performed automatically with Pentra C 400. The antioxidant capacity of the chickens' liver, breast muscle, and spleen was enhanced by the in ovo injection of GOS and LP. The immune-related gene expression levels were upregulated after in ovo stimulation with either GOS or LP which improved the gut health of broiler chickens. In addition, several genes related to gut barrier functions were upregulated, thus ensuring epithelial integrity. As for blood plasma metabolites, no adverse effects were observed. In summary, we report that in ovo stimulation with either GOS or LP stimulates the immune system and improves the antioxidant status and gut health of chickens with no negative impact on plasma blood metabolite indices.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prognostic biomarker MICAL2 and associates with proliferation, migration and immune infiltration in pancreatic adenocarcinoma.","authors":"Huachao Yang, Pingping Yu, Jianping Gong","doi":"10.1007/s13353-024-00919-3","DOIUrl":"https://doi.org/10.1007/s13353-024-00919-3","url":null,"abstract":"<p><p>To elucidate the crucial function of MICAL2 as a potential immunotherapeutic target and a predictive biomarker in PAAD. The expression of MICAL2 in pan-cancer was investigated using public database, and the expression of MICAL2 in PAAD was validated using tissue samples. The diagnostic and prognostic significance of MICAL2 in PAAD was assessed through the application of ROC curves and Kaplan-Meier curves. The correlation between MICAL2 and infiltrating immune cells and immune checkpoints in PAAD was researched using the TIMER and TCGA databases. In vitro studies involved the evaluation of the biological functions of MICAL2 in human PAAD cells through the knockdown of MICAL2 expression using shRNA. Compared to corresponding normal tissues, the expression of MICAL2 exhibits significant differences in various cancers. Specifically, the level of MICAL2 expression is significantly increased in PAAD. Moreover, MICAL2 demonstrates considerable diagnostic potential in PAAD patients, and its elevated expression is indicative of an unfavorable prognosis. The differential expression of MICAL2 is related to infiltrating immune cells, immune cell markers, and immune checkpoints in PAAD. In ASPC-1 and PANC-1 cells, when MICAL2 was knocked down, there was a notable suppression of proliferation, migration, and invasion. MICAL2 functions as a significant predictor and promising immunotherapeutic target for prognosis assessment in PAAD. It has a pivotal function in fostering the growth and migration of PAAD cells.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ADAR1 expression in different cancer cell lines and its change under heat shock.","authors":"Dominika Adamczak, Michał Fornalik, Anna Małkiewicz, Julia Pestka, Andrzej Pławski, Paweł Piotr Jagodziński, Bartosz Kazimierz Słowikowski","doi":"10.1007/s13353-024-00926-4","DOIUrl":"https://doi.org/10.1007/s13353-024-00926-4","url":null,"abstract":"<p><p>Adenosine deaminase acting on RNA 1 (ADAR1) plays an essential role in the development of malignancies by modifying the expression of different oncogenes. ADAR1 presents three distinct activities: adenosine-to-inosine RNA editing, modulating IFN pathways, and response to cellular stress factors. Following stressors such as heat shock, ADAR1p110 isoform relocates from the nucleus to the cytoplasm, where it suppresses RNA degradation which leads to the arrest of apoptosis and cell survival. In this study, we assessed the expression of ADAR1 across different cancer cell lines. We revealed that the presence of ADAR1 varies between cells of different origins and that a high transcript level does not reflect protein abundance. Additionally, we subjected cells to a heat shock in order to evaluate how cellular stress factors affect the expression of ADAR1. Our results indicate that ADAR1 transcript and protein levels are relatively stable and do not change under heat shock in examined cell lines. This research lays a groundwork for future directions on ADAR1-related studies suggesting in which types of cancer ADAR1 may be a promising target for novel therapeutic approaches.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic and molecular mechanisms underlying the male sterility in rice.","authors":"Amir Sohail, Chengkai Lu, Peng Xu","doi":"10.1007/s13353-024-00923-7","DOIUrl":"https://doi.org/10.1007/s13353-024-00923-7","url":null,"abstract":"<p><p>Male reproductive development is a complex and highly ordered phenomenon which demands comprehensive understandings of underlying molecular mechanisms to expand its scope for crop improvement. Genetic manipulation of male fertility/sterility is critical for crop hybrid breeding. Although male sterility is not a good trait for the plant itself, its wider application in hybrid rice breeding has made it valuable. The currently widely used male sterile line breeding systems mainly include the following: three-line hybrid rice based on cytoplasmic male sterility and two-line hybrid rice based on environmentally sensitive gene male sterility. The study of male sterility is an excellent thoroughfare to critically understand the regulatory mechanisms essential for the complicated male reproductive developmental process. The unique trait of male sterility also provides valuable resources and convenience for the genetic improvement of rice hybrids. Therefore, deeper and broader understandings about the genetic causes of male sterility are necessary for both basic studies and rice genetic improvement.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a novel gene expression panel for the characterization of MSCs for increased biological safety.","authors":"Anna M Różycka-Baczyńska, Igor M Stepaniec, Marta Warzycha, Izabela Zdolińska-Malinowska, Tomasz Oldak, Natalia Rozwadowska, Tomasz J Kolanowski","doi":"10.1007/s13353-024-00917-5","DOIUrl":"https://doi.org/10.1007/s13353-024-00917-5","url":null,"abstract":"<p><p>Mesenchymal stromal cells (MSCs) have a wide range of therapeutic applications due to their multipotency, immunomodulatory, and anti-inflammatory properties. Their ability to migrate and recolonize damaged tissues is also remarkable. However, the controversial occurrence of spontaneous tumorigenesis or malignant transformation of MSCs raises concerns about proposed cell-based therapies for patients that researchers must address. There are several in vitro and in vivo strategies for MSC safety approval, but there is still no described coherent scheme that allows the assessment of MSC oncogenic potential in a simple, robust, and reproducible manner. Here, we have developed a diagnostic panel of molecular markers that allows for the accurate verification of the quality and safety of MSCs. Moreover, presented in this article diagnostic panel that can define the origin and tumorigenicity of MSCs can be easily introduced into the routine quality control processes of MSC-based product manufacturing which will improve further clinical applications of MSCs.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}