Journal of Applied Genetics最新文献

{"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":"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}

{"title":"Antibiotic resistance and its correlation with biofilm formation and virulence genes in Klebsiella pneumoniae isolated from wounds.","authors":"Mohammed Allami, Eman Jassim Mohammed, Zainab Alnaji, Salsabil A Jassim","doi":"10.1007/s13353-024-00893-w","DOIUrl":"10.1007/s13353-024-00893-w","url":null,"abstract":"<p><p>Klebsiella pneumoniae is the most important species of the Klebsiella genus and often causes hospital infections. These bacteria have a high resistance to most of the available drugs, which has caused concern all over the world. In this study, we investigated the antibiotic resistance profile and the ability to produce extended-spectrum beta-lactamase (ESBL) among K. pneumoniae isolates, and then we investigated the relationship between these two factors with biofilm formation and the prevalence of different virulence genes. In this study, 130 isolates of K. pneumoniae isolated from wounds were investigated. The antibiotic resistance of the isolates was evaluated by the disk diffusion method. The microtiter plate method was used to measure biofilm formation. The prevalence of virulence genes was detected by multiplex PCR. Among the examined isolates, 85.3% showed multidrug resistance. 87.6% of the isolates were ESBL-positive. Imipenem, meropenem, and fosfomycin were the most effective drugs. The ability of the isolates to produce biofilm was strong (80%), moderate (12.3%), and weak (7.6%), respectively. fimH, mrKD, entB, and tolC virulence genes were observed in all isolates. High prevalence of antibiotic resistance (especially multidrug resistance), high prevalence of ESBL-producing isolates, the ability of all isolates to biofilm formation, and the presence of fimH, mrKD, entB, and tolC virulence genes in all isolates show the importance of these factors in the pathogenesis of K. pneumoniae isolates in Iraq.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"925-935"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141731206","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 diversity and population structure of Uganda cassava germplasm.","authors":"Karoline Leonard Sichalwe, Ismail Kayondo, Richard Edema, Isaac O Dramadri, Emmanuel AAdjei, Heneriko Kulembeka, Wilson Kimani, Doreen Mgonja, Patrick Rubahaiyo, Edward Kanju","doi":"10.1007/s13353-024-00892-x","DOIUrl":"10.1007/s13353-024-00892-x","url":null,"abstract":"<p><p>Cassava (Manihot esculenta Crantz) holds significant economic importance globally. Evaluating a diverse range of germplasm based on molecular characteristics not only enhances its preservation but also supports its utilization in breeding programs. In this study, we assessed genetic diversity and population structure among 155 cassava genotypes from Uganda using 5247 single nucleotide polymorphism (SNP) markers. Genotyping by sequencing (GBS) was employed for SNP discovery and to evaluate genetic diversity and population structure using the ADMIXTURE software. The cassava accessions comprised two populations: 49 accessions from Ugandan lines and 106 accessions resulting from crosses between South American and Ugandan lines. The average call rate of 96% was utilized to assess marker polymorphism. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was moderately high. The principal component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of molecular variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"683-691"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141619927","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":"Genotype-environment interaction for grain yield in maize (Zea mays L.) using the additive main effects and multiplicative interaction (AMMI) model.","authors":"Jan Bocianowski, Kamila Nowosad, Dariusz Rejek","doi":"10.1007/s13353-024-00899-4","DOIUrl":"10.1007/s13353-024-00899-4","url":null,"abstract":"<p><p>Genotype-environment interaction consists of the different response of individual genotypes resulting from changing environmental conditions. Its significance is a phenomenon that makes the breeding process very difficult. On the one hand, the breeder expects stable genotypes, i.e., yielding similarly regardless of environmental conditions. On the other hand, selecting the best genotypes for each region is one of the key challenges for breeders and farmers. The aim of this study was to evaluate genotype-by-environment interaction for grain yield in new maize hybrids developed by Plant Breeding Smolice Co. Ltd., utilizing the additive main effects and multiplicative interaction (AMMI) model. The investigation involved 69 maize (Zea mays L.) hybrids, tested across five locations in a randomized complete block design with three replications. Grain yield varied from 8.76 t ha^-1 (SMH_16417 in Smolice) to 16.89 t ha^-1 (SMH_16043 in Płaczkowo), with a mean yield of 13.16 t ha^-1. AMMI analysis identified significant effects of genotype, environment, and their interaction on grain yield. Analysis of variance indicated that 25.12% of the total variation in grain yield was due to environment factor, 35.20% to genotypic differences, and 21.18% to genotype by environmental interactions. Hybrids SMH_1706 and SMH_1707 are recommended for further breeding programs due to their high stability and superior average grain yield.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"653-664"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11560994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genome analysis of endophytic Bacillus amyloliquefaciens MR4: a potential biocontrol agent isolated from wild medicinal plant root tissue.","authors":"Kaiying Yang, Xianxing Dai, Zulihumar Maitikadir, Huijiang Zhang, Haiting Hao, Chengcai Yan","doi":"10.1007/s13353-024-00905-9","DOIUrl":"10.1007/s13353-024-00905-9","url":null,"abstract":"<p><p>In this investigation, 396 endophytic bacterial strains from six indigenous medicinal plant species within the Xinjiang Tumor Peak National Nature Reserve were subjected to screening. The strain MR4 emerged as a noteworthy contender, demonstrating pronounced biocontrol capabilities coupled with exceptional cold tolerance. Through morphological scrutiny and comprehensive genomic sequencing, MR4 was identified as Bacillus amyloliquefaciens. Antagonistic assays revealed MR4's efficacy in suppressing the causative agents of cotton wilt and verticillium wilt, achieving inhibition rates surpassing 50%. Analyses, underpinned by PCR methodologies, indicated MR4's capacity to biosynthesize a minimum of eight distinct antimicrobial agents. The whole-genome sequencing data indicated that B. amyloliquefaciens MR4 had the genome size and GC content of 4,017,872 bp and 47.14%, respectively, and 4191 coding genes were identified. The genome consists of a single chromosome and one plasmid. Moreover, it was augmented by annotations from various databases, including GO, KEGG, and COG. The pathogenicity of MR4 undergoes evaluation, while predictions concerning MR4's secondary metabolites have disclosed gene clusters for 13 varieties of these compounds, with particular emphasis on surfactins and fengycin. Comparative analyses with four paradigmatic strains shed light on MR4's genomic composition and its phylogenetic lineage within the Bacillus genus. The genomic data pertaining to MR4 have been duly submitted to the NCBI GenBank, bearing the accession numbers CP146236 (Chr1) and CP146237 (plas1). This study endeavors to furnish potent microbial resources for the biocontrol and enhancement of plant growth, thereby providing a theoretical groundwork for MR4's agronomic utilization.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"907-923"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Importance and variability of the paternal component in sow reproductive traits.","authors":"G Cieleń, E Sell-Kubiak","doi":"10.1007/s13353-024-00910-y","DOIUrl":"10.1007/s13353-024-00910-y","url":null,"abstract":"<p><p>Reproductive traits are an integral part of the goals of the breeding programs that contribute to the economic success of production. Reproductive phenotypes such as litter size, number of piglets born alive, or litter weight at birth are mainly attributed to females. Thus, the maternal components can be found by default in quantitative genetics' animal models. Still, paternal contribution to variance components should not be discarded. In this review, we indicate the importance of paternal effects in pig breeding by describing both the biology and genetics of boars' traits, the use of (non-)genetic service sire effects in quantitative genetic models for traits measured on females, and genes involved in male reproduction. We start by describing the important biological traits of boars that have the most important effect on their reproductive abilities, i.e., sexual maturity, sperm quality, and testes parameters. Then we move to the possible environmental effects that could affect those traits of boars (e.g., feed, temperature). The main part of the review in detail describes the genetics of boars' reproductive traits (i.e., heritability) and their direct effect on reproductive traits of females (i.e., genetic correlations). We then move to the use of both genetic and non-genetic service sire effects in quantitative models estimated as their percentage in the total variance of traits, which vary depending on the breed from 1 to 4.5% or from 1 to 2%, respectively. Finally, we focus on the description of candidate genes and confirmed mutations affecting male reproduction success: IGF2, Tgm8, ESR1, ZSWIM7, and ELMO1. In conclusion, the observed variance of paternal effects in female reproduction traits might come from various attributes of boars including biological and genetic aspects. Those attributes of boars should not be neglected as they contribute to the success of female reproductive traits.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"853-866"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142465956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcript level of telomerase reverse-transcriptase (TERT) gene in the rainbow trout (Oncorhynchus mykiss) eggs with different developmental competence for gynogenesis.","authors":"Konrad Ocalewicz, Marcin Kuciński, Igor Jasielczuk, Artur Gurgul, Mirosław Kucharski, Stefan Dobosz","doi":"10.1007/s13353-024-00887-8","DOIUrl":"10.1007/s13353-024-00887-8","url":null,"abstract":"<p><p>Expression of the telomerase reverse-transcriptase (TERT) gene and activity of telomerase have been reported in the somatic tissues and gonads in fish irrespective of their age and size. Nevertheless, little is known about TERT expression in the fish eggs. In the current study, the presence of the TERT transcripts was confirmed in the rainbow trout ovulated eggs before and after activation with nonirradiated and UV-irradiated (gynogenesis) sperm. Eggs originating from eight females had high and comparable quality expressed by similar hatching rates. However, survival of the gynogenetic larvae that hatched from eggs activated with UV-irradiated sperm and further exposed to the high hydrostatic pressure (HHP) shock for duplication of the maternal chromosomes varied between females from 2.1 ± 0.4 to 40.5 ± 2.2%. Increased level of TERT transcripts was observed in eggs originating from two females, and gametes from only one of them showed improved competence for gynogenesis (27.3 ± 1.9%). In turn, eggs from the female that exhibited the highest survival after gynogenetic activation were characterized by the lowest expression of the TERT gene. Telomerase in rainbow trout eggs may compensate erosion of the telomeres during early embryonic development; however, its upregulation does not assure better development after gynogenetic activation.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"897-905"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11560991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Peptidylprolyl isomerase D circular RNA sensitizes breast cancer to trastuzumab through remodeling HER2 N4-acetylcytidine modification.","authors":"Shengting Wang, Qian Li, Yufang Wang, Xiaoming Li, Xinghua Feng, Yuxuan Wei, Jiaman Wang, Xin Zhou","doi":"10.1007/s13353-024-00840-9","DOIUrl":"10.1007/s13353-024-00840-9","url":null,"abstract":"<p><p>Human epidermal growth factor receptor 2 (HER2) overexpression and activation are crucial for trastuzumab resistance in HER2-positive breast cancer; however, the potential regulatory mechanism of HER2 is still largely undetermined. In this study, a novel circular RNA derived from peptidylprolyl isomerase D (PPID) is identified as a negative regulator of trastuzumab resistance. Circ-PPID is highly stable and significantly downregulated in trastuzumab-resistant cells and tissues. Restoration of circ-PPID markedly enhances HER2-positive breast cell sensitivity to trastuzumab in vitro and in vivo. Circ-PPID directly binds to N-acetyltransferase 10 (NAT10) in the nucleus and blocks the interaction between NAT10 and HER2 mRNA, reducing N4-acetylcytidine (ac4C) modification on HER2 exon 25, leading to HER2 mRNA decay. Intriguingly, the subcellular localization of circ-PPID differs between trastuzumab-sensitive and -resistant cells. Circ-PPID in trastuzumab-resistant cells is located more in the cytoplasm, mainly due to the upregulation of Exportin 4 (XPO4), which results in the loss of spatial conditions for circ-PPID to bind to nuclear NAT10. Taken together, our data suggest that circ-PPID is a previously unappreciated ac4C-dependent HER2 epigenetic regulator, providing a promising therapeutic direction for overcoming trastuzumab resistance in clinical setting.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"797-807"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716122","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":"Gene-edited cells: novel allogeneic gene/cell therapy for epidermolysis bullosa.","authors":"Fatemeh Gila, Vahab Alamdari-Palangi, Maedeh Rafiee, Arezoo Jokar, Sajad Ehtiaty, Aria Dianatinasab, Seyyed Hossein Khatami, Mortaza Taheri-Anganeh, Ahmad Movahedpour, Jafar Fallahi","doi":"10.1007/s13353-024-00839-2","DOIUrl":"10.1007/s13353-024-00839-2","url":null,"abstract":"<p><p>Epidermolysis bullosa (EB) is a group of rare genetic skin fragility disorders, which are hereditary. These disorders are associated with mutations in at least 16 genes that encode components of the epidermal adhesion complex. Currently, there are no effective treatments for this disorder. All current treatment approaches focus on topical treatments to prevent complications and infections. In recent years, significant progress has been achieved in the treatment of the severe genetic skin blistering condition known as EB through preclinical and clinical advancements. Promising developments have emerged in the areas of protein and cell therapies, such as allogeneic stem cell transplantation; in addition, RNA-based therapies and gene therapy approaches have also become a reality. Stem cells obtained from embryonic or adult tissues, including the skin, are undifferentiated cells with the ability to generate, maintain, and replace fully developed cells and tissues. Recent advancements in preclinical and clinical research have significantly enhanced stem cell therapy, presenting a promising treatment option for various diseases that are not effectively addressed by current medical treatments. Different types of stem cells such as primarily hematopoietic and mesenchymal, obtained from the patient or from a donor, have been utilized to treat severe forms of diseases, each with some beneficial effects. In addition, extensive research has shown that gene transfer methods targeting allogeneic and autologous epidermal stem cells to replace or correct the defective gene are promising. These methods can regenerate and restore the adhesion of primary keratinocytes in EB patients. The long-term treatment of skin lesions in a small number of patients has shown promising results through the transplantation of skin grafts produced from gene-corrected autologous epidermal stem cells. This article attempts to summarize the current situation, potential development prospects, and some of the challenges related to the cell therapy approach for EB treatment.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"705-726"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140065205","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}