Journal Of Applied Genetics[JOURNAL]
Sun
200 papers
Exploring microRNA signatures in pediatric non-infectious uveitis: meta-analysis and molecular profiling of patient samples.
Wawrzyniak O, Wawrzyniak D, Smuszkiewicz M … +3 more , Głodowicz P, Gotz-Więckowska A, Rolle K
J Appl Genet · 2025 Sep · PMID 39695050 · Full text
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 juven...
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.
Computational analysis of MYC gene variants: structural and functional impact of non-synonymous SNPs.
Bhuyan P, Bharali V, Basumatary S … +3 more , Lego A, Sarma J, Borbora D
J Appl Genet · 2026 Feb · PMID 39673052 · Publisher ↗
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. Dy...
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.
Prevalence and comparative analysis of Y chromosome microdeletions in recurrent pregnancy loss.
Deepika MLN, Srilekha A, Pavani CL … +3 more , Gupta A, Nazneen R, Lakshmi BV
J Appl Genet · 2026 Feb · PMID 39673051 · Publisher ↗
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 ma...
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.
Modulatory effects of in ovo delivery of galactooligosaccharide and Lactiplantibacillus plantarum on antioxidant capacity, gene expression, and selected plasma metabolite parameters of broiler chickens.
Mangan M, Połtowicz K, Metges CC … +1 more , Siwek M
J Appl Genet · 2025 May · PMID 39666172 · Full text
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 deliv...
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 × 10/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.
Prognostic biomarker MICAL2 and associates with proliferation, migration and immune infiltration in pancreatic adenocarcinoma.
Yang H, Yu P, Gong J
J Appl Genet · 2025 Dec · PMID 39661267 · Publisher ↗
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...
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.
ADAR1 expression in different cancer cell lines and its change under heat shock.
Adamczak D, Fornalik M, Małkiewicz A … +4 more , Pestka J, Pławski A, Jagodziński PP, Słowikowski BK
J Appl Genet · 2025 Dec · PMID 39641903 · Full text
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 RN...
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.
Genetic and molecular mechanisms underlying the male sterility in rice.
Sohail A, Lu C, Xu P
J Appl Genet · 2025 May · PMID 39627604 · Publisher ↗
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 mal...
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.
Development of a novel gene expression panel for the characterization of MSCs for increased biological safety.
Różycka-Baczyńska AM, Stepaniec IM, Warzycha M … +4 more , Zdolińska-Malinowska I, Oldak T, Rozwadowska N, Kolanowski TJ
J Appl Genet · 2025 Sep · PMID 39621192 · Full text
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 als...
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.
Unraveling the genetic diversity, population structure, and stability for yield-related traits of rice genotypes in mid-hills of northeastern India.
Raj R, Kumar A, C B … +5 more , Kaur S, Verma VK, Rai M, Das SP, Mishra VK
J Appl Genet · 2025 Sep · PMID 39609356 · Publisher ↗
The cultivation of nearly 10,000 indigenous rice landraces in the North-Eastern Hill (NEH) region by various ethnic groups creates opportunities for the utilization of unique landraces through systematic evaluation of ge...
The cultivation of nearly 10,000 indigenous rice landraces in the North-Eastern Hill (NEH) region by various ethnic groups creates opportunities for the utilization of unique landraces through systematic evaluation of genetic variability. In the present study, a set of 102 rice landraces were assessed based on morphological and SSR markers, and five checks in augmented design vis-à-vis high-yielding rice genotypes with stable performance were identified. The presence of high estimates of heritability, genotypic coefficient of variation, and genetic advance over mean indicated the predominance of additive gene action, which necessitated the effectiveness of selection in augmenting productivity. A total of 83.73% of the total variation was accounted by the first five principal components. A total of 132 alleles were detected, with an average of 3 alleles per locus. The PIC values ranged from 0.01 to 0.70, with an average of 0.40. Based on F value (5.1%), significant differences between the genotypes of Arunachal Pradesh and Sikkim were observed. The percentage of variation among the population, among individuals within the population, and within individuals was 5.14, 75.66, and 19.2%, respectively. Both Nei's genetic distance and model-based clustering have differentiated the genotypes into five distinct clusters. Principal coordinate analysis illustrated that the genotypes of Manipur were scattered in all quadrants, showing that they are highly diverse, while the genotypes of Nagaland, Sikkim, and Meghalaya were found together, which represent the chance of mixing of the population at a certain point in time. Markers, namely RM 474, OSR 13, RM 413, and RM 259, were found to be associated with key traits for increasing yielding ability of plant. In a stability evaluation based on AMMI analysis and multi-trait genotype-ideoptype distance matrix (MGIDI), genotypes, namely Jyotrirmayie, RCPL 1-411, Tsamum firri, Ching Phouren, Rato Bhan Joha, MN-47, and Tara bali, were selected with higher yield potential.
Molecular characterization of doublesex and Mab-3 (DMRT) gene family in Ctenopharyngodon idella (grass carp).
Parveen S, Khan MF, Sultana M … +2 more , Rehman SU, Shafique L
J Appl Genet · 2025 May · PMID 39607661 · Publisher ↗
Doublesex and Mab-3 (DMRT) gene family is a diverse group of transcriptional factors crucially involved in sex differentiation and biological processes such as body growth and differentiation in vertebrates. In this stud...
Doublesex and Mab-3 (DMRT) gene family is a diverse group of transcriptional factors crucially involved in sex differentiation and biological processes such as body growth and differentiation in vertebrates. In this study, we analyzed DMRT genes structural characterization and physiochemical properties, and elucidated their functional role as a ligand of different gonadal receptors including androgen (AR), estrogen β (ER-β), estrogen γ (ER-γ), and progesterone (PR). All six genes of the DMRT gene family in grass carp (Ctenopharyngodon Idella Valenciennes, 1844) exhibited an acidic nature. These DMRT genes are primarily localized in the nucleus, where they play a role in DNA binding via doublesex DNA binding motif. All the DMRT gene pairs are under strong purifying selection with two segmental duplications envisaged about 18.30 (DMRT3a/DMRTA2) and 24.90 (DMRT2b/DMRT2a) million years ago (MYA). Recombination analysis revealed six potential recombinant breakpoints posing substantial evolutionary pressure for diverse cellular functioning of DMRT isoforms. Moreover, the DMRTA1 protein had a highest binding affinity of - 270.42 and - 267.16 for androgen receptors (AR) and progesterone receptors (PR), whereas, for estrogen receptors ER-β and ER-γ, the maximum binding affinity was observed with DMRT2a and DMRT2b proteins showing a docking score of - 254.22 and - 261.71, respectively. First time we studied the binding scores and interface residues of the DMRT genes as a ligand of gonadal receptors that play a crucial role in fish growth, sex development and differentiation, and spermatogenesis and oocyte maturation. The present study provides a molecular basis for DMRT genes in grass carp that may serve as a reference for in-depth phylogenomic study in other species.
Identification of trait-associated microRNA modules in liver transcriptome of pig fed with PUFAs-enriched supplementary diet.
Pareek CS, Sachajko M, Kalra G … +19 more , Sultana S, Szostak A, Chalaskiewicz K, Kepka-Borkowska K, Poławska E, Ogłuszka M, Pierzchała D, Starzyński R, Taniguchi H, Juszczuk-Kubiak E, Lepczyński A, Ślaska B, Kozera W, Czarnik U, Wysocki P, Kadarmideen HN, Te Pas MFW, Szyda J, Pierzchała M
J Appl Genet · 2025 May · PMID 39546271 · Full text
Dietary lipids provide energy, are cellular structural components, and are involved in physiological processes. Lipids are the dietary source in supplementary diet experiments in pigs. This study aims to investigate the...
Dietary lipids provide energy, are cellular structural components, and are involved in physiological processes. Lipids are the dietary source in supplementary diet experiments in pigs. This study aims to investigate the dietary effects of PUFAs on the hepatic transcriptome and physiological pathways of two diets on two pig breeds. Polish Landrace (PL: n = 6) and six PLxDuroc (PLxD: n = 6) pigs were fed with a normal diet (n = 3) or PUFAs-enriched healthy diet (n = 3), and the hepatic miRNA profiles were studied for weighted gene co-expression network analysis biological interactions between gene networks and metabolic pathways of DE miRNA genes. The study identified trait-associated modules that were significantly associated with four phenotypic traits in the dietary groups of PL and PLxD: meat colour (a*), shoulder subcutaneous fat thickness, conductivity 24 h post-mortem (PE24), and ashes. Trait-wise, a large set of co-expressed miRNAs of porcine liver were identified in these trait-associated significant modules (9, 7, 2, and 8) in PL and PLxD. Each module is represented by a module eigengene (ME). Forty-four miRNAs out of 94 miRNAs interacted with 6719 statistically significant target genes with a target score > 90. The GO/pathway analysis showed association with pathways including regulation of metallopeptidase activity, sebaceous gland development, collagen fibril organization, WNT signalling, epithelial tube morphogenesis, etc. The study showed the differences in miRNA expression between the dietary groups of PL and PLxD breeds. Hub genes of discovered miRNA clusters can be considered predicted miRNA genes associated with PE24, meat colour, shoulder subcutaneous fat thickness, and ashes. Discovered target genes for miRNA clusters play significant roles in biological functions such as (i) muscle and body growth development, (ii) different cellular processes and developments, (iii) system development, and (iv) metabolic processes.
Association of pedigree indexes and genomic breeding values with the performance of Polish Holstein-Friesian cows.
Strabel T
J Appl Genet · 2025 Feb · PMID 39546270 · Full text
Pedigree indices (PI) and genomically enhanced breeding values (GBV) of Polish Holstein-Friesian heifers were compared with their future performance. Phenotypes of 15,794 cows from 294 herds were analyzed. The traits eva...
Pedigree indices (PI) and genomically enhanced breeding values (GBV) of Polish Holstein-Friesian heifers were compared with their future performance. Phenotypes of 15,794 cows from 294 herds were analyzed. The traits evaluated included milk, fat and protein yield, somatic cell score (SCC), stature, overall udder and feet and legs score, heifer conception rate, and longevity. PI and GBV were from official evaluation systems, and performance records were adjusted for non-genetic effects. Correlations between breeding values and adjusted phenotypes were analyzed. Additionally, cows within each herd were divided into quartiles based on their breeding values, and the performance of cows from the top and bottom quartiles was compared. For production traits, similar analyses were conducted separately for high and low milk-producing herds to check for possible genotype by environment interaction. The analyses confirmed the significant correlation between breeding values and cow performance. Incorporating genomic information into PI significantly improved the predictive accuracy for milk, fat, and protein yields, as well as for SCC and stature, with increases ranging from 34 to 64%. Comparisons of cows' performance from the top and bottom quartiles supported these observations for all these traits except protein yield, with differences in performance being 43-92% greater when cows were ranked by GBV instead of PI. In a more productive environment, greater differences in performance were found between the top and bottom quartiles. These findings suggest that Polish breeders can enhance the outcomes of their breeding decisions by using GBV instead of PI. This change offers particular benefits in improving the predictability of future performance for the most economically important traits such as milk yield, fat yield, protein yield, somatic cell score, and stature.
Giardia fibrillarin: a bioinformatics exploration of sequence and structure.
Lagunas-Rangel FA
J Appl Genet · 2025 Feb · PMID 39527366 · Full text
Fibrillarin is a key nucleolar S-adenosyl-L-methionine (SAM)-dependent methyltransferase, highly conserved among species in both sequence and function. It is actively involved in numerous cellular processes, particularly...
Fibrillarin is a key nucleolar S-adenosyl-L-methionine (SAM)-dependent methyltransferase, highly conserved among species in both sequence and function. It is actively involved in numerous cellular processes, particularly in the early stages of pre-ribosomal RNA processing. Although a fibrillarin orthologue has been identified in Giardia, an intestinal protozoan parasite responsible for numerous infections worldwide, its functional and structural features in this parasite remain largely unexplored. In this study, bioinformatics tools were used to analyze the sequence and structure of Giardia fibrillarin to provide insights that could aid future experimental and therapeutic investigations. Taking advantage of the protein sequence of Giardia fibrillarin, multiple bioinformatics tools were employed to estimate its domains, nuclear and nucleolar localization signals (NLS and NoLS), post-translational modifications, phylogeny, and three-dimensional structure. The analysis revealed significant conservation of Giardia fibrillarin, showing close relationships with archaeal and parasitic amoeba orthologs. It retains essential features such as the SAM-dependent methyltransferase domain, a glycine- and arginine-rich domain, and both NLS and NoLS. While the core region of the protein is structurally conserved, the N-terminal region exhibits notable divergence. The potential for inhibition of Giardia fibrillarin by SAM competitors suggests that it could be a promising target for drug development, particularly for strains resistant to current treatments.
What, how, and why? - anti-EHEC phages and their application potential in medicine and food industry.
Necel A, Dydecka A, Topka-Bielecka G … +4 more , Wesołowski W, Lewandowska N, Bloch S, Nejman-Faleńczyk B
J Appl Genet · 2025 Feb · PMID 39527365 · Full text
Enterohemorrhagic Escherichia coli (EHEC) are pathogens that, only in the United States, cause more than 250,000 foodborne infections a year. Since antibiotics or other antidiarrheal agents may increase the hemolytic-ure...
Enterohemorrhagic Escherichia coli (EHEC) are pathogens that, only in the United States, cause more than 250,000 foodborne infections a year. Since antibiotics or other antidiarrheal agents may increase the hemolytic-uremic syndrome (HUS) development risk, currently only supportive therapy, including hydration, is used. Therefore, many methods to fight EHEC bacteria focus on their use in food processing to prevent human infection. One of the proposed anti-EHEC agents is bacteriophages, known for their bactericidal effect, host specificity, and lack of cross-resistance with antibiotics. In this review article, we provide an overview of the characteristics like source of isolation, morphology, kinetics of life cycle, and treatment potential of over 130 bacteriophages able to infect EHEC strains. Based on the reviewed literature, we conclude that bacteriophages may play a highly significant role in regulating EHEC propagation. In addition, we also point out the phage features that should be taken into account not only when using bacteriophages but also when examining their properties. This may contribute to accelerating the pace of work on the preventive use of bacteriophages, which is extremely needed in the modern world of the food industry, but also stimulate interest in phages and accelerate regulatory work that would enable the use of bacteriophages also in medicine, to fight the drug-resistant strains.
Polymorphic insertions of DcSto miniature inverted-repeat transposable elements reveal genetic diversity structure within the cultivated carrot.
Hadagali S, Stelmach-Wityk K, Macko-Podgórni A … +2 more , Cholin S, Grzebelus D
J Appl Genet · 2025 May · PMID 39466592 · Full text
Miniature inverted-repeat transposable elements (MITEs) are a potent source of polymorphisms in plant genomes. A genotyping system, named DcS-ILP, based on polymorphic insertions of Stowaway MITEs (DcStos) localized in i...
Miniature inverted-repeat transposable elements (MITEs) are a potent source of polymorphisms in plant genomes. A genotyping system, named DcS-ILP, based on polymorphic insertions of Stowaway MITEs (DcStos) localized in introns and identified in the reference genome DH1, has been developed for carrot. Here, we report an extension of the DcS-ILP genotyping system by incorporation of non-reference insertions identified in resequenced genomes representing the eastern gene pool. We genotyped 52 carrot accessions representing the eastern and western carrot gene pools with 92 markers developed previously (western DcS-ILP panel) together with 84 newly developed markers (eastern DcS-ILP panel). Overall, the DcS-ILP markers revealed a highly structured genetic diversity separating the eastern and the western carrot accessions at K = 2 and differentiating Indian breeding lines from the eastern accessions at K = 3. The eastern DcS-ILP panel proved to be more robust with respect to the eastern carrot gene pool, while it provided little information on the western accessions, as many of the DcSto insertions present in the eastern gene pool were absent in the western gene pool. As the western carrot accessions represent improved cultivars, DcSto insertional polymorphisms allowed detection of a selection-driven bottleneck at the improvement stage. Selection in the course of the improvement stage generally operated on standing variation, as the subset of DcSto insertions present in the western carrot likely originated from transposition events preceding the separation of both gene pools. However, occasional frequency shifts in the opposite direction were also revealed, possibly indicating selection for favorable variants associated with DcSto insertions.
Cannabidiol (CBD) modulates the transcriptional profile of ethanol-exposed human dermal fibroblast cells.
Gurgul A, Żurowski J, Szmatoła T … +4 more , Kucharski M, Sawicki S, Semik-Gurgul E, Ocłoń E
J Appl Genet · 2024 Dec · PMID 39466591 · Full text
Cannabidiol (CBD) is abundant in the Cannabis sativa plant and exhibits complex immunomodulatory, anxiolytic, antioxidant, and antiepileptic properties. Several studies suggest that CBD could be used for different purpos...
Cannabidiol (CBD) is abundant in the Cannabis sativa plant and exhibits complex immunomodulatory, anxiolytic, antioxidant, and antiepileptic properties. Several studies suggest that CBD could be used for different purposes in alcohol use disorder (AUD) and alcohol-related injuries to the brain and the liver. In this study, we focused on analyzing transcriptional alterations in human dermal fibroblasts (HDFs) cell line challenged simultaneously with ethanol and CBD as an ethanol-protective agent. We aimed to expose the genes and pathways responsible for at least some of the CBD effects in those cells that can be related to the AUD. Transcriptome analysis was performed using HDFs cell line that expresses both cannabinoid receptors and can metabolize ethanol through alcohol dehydrogenase activity. Fibroblasts are also responsible for the progression of liver fibrosis, a common comorbidity in AUD. With the use of a cellular test, we found that CBD at the lowest applied concentration (0.75 μM) was able to stimulate depressed metabolism and reduce the level of apoptosis of cells treated with different concentrations of ethanol to the level observed in the control cells. Similar observations were made at the transcriptome level, in which cells treated with ethanol and CBD had similar expression profiles to the control cells. CBD also affects several genes connected with extracellular matrix formation (especially its collagen constituent), which can have potential implications for, e.g., fibrosis process.
Experimental and in silico analysis of LINC01279 expression in tumor of patients with breast cancer.
Mokhtari N, Ahmadi N, Moradi S … +3 more , Farmani S, Kheyrani E, Dolatabadi NF
J Appl Genet · 2025 Dec · PMID 39465460 · Publisher ↗
Breast cancer (BC) is characterized by the increase of malignant cells in the breast. The malignant cells begin in the lining of the breast milk glands or ducts (ductal epithelium). BC is the most frequent cancer in wome...
Breast cancer (BC) is characterized by the increase of malignant cells in the breast. The malignant cells begin in the lining of the breast milk glands or ducts (ductal epithelium). BC is the most frequent cancer in women, but it may also occur in males. Long non-coding RNAs (lncRNA) have been demonstrated to control the development and incidence of cancer. However, some lncRNAs experience potential changes in BC, but their role has not been well studied. LINC01279 is known as a valuable biomarker in gastric cancer but has not yet been studied in BC. Changes in LINC01279 expression levels in BC samples were investigated by microarray. Q-PCR was also used to evaluate the expression of LINC01279 in the tumor and normal adjacent samples of 30 BC patients. The LINC01279 co-expressed gene module was discovered using weighted gene correlation network analysis (WGCNA) on the relevant dataset. The top ten hub genes were determined using gene ontology (GO) functional enrichments on the co-expressed gene module. The results of the bioinformatics study showed an increase in LINC01279 expression levels (log2FC = 3.228749561, adj.P.Val = 1.69E - 12) in tumor samples compared to normal marginal tissue. Q-PCR results also showed a significant increase in LINC01279 expression (P-value = 0.0005) in tumor samples. WGCNA analysis identified that the black module is the LINC01279 co-expressed module, and functional annotation analysis of black module genes enriched in significant cancer-related pathways and processes, including cell growth and/or maintenance, regulation of immune response, regulation of cell proliferation, and epithelial-to-mesenchymal transition (EMT). Regarding the real-time PCR results, the analysis of expression patterns has illuminated a distinct association between the heightened expression levels of LINC01279, and the stages of cancer progression as well as the metastatic potential of tumors. However, intriguingly, our observations have failed to reveal any statistically significant correlations between the relative expression of LINC01279 and tumor grade classification, or the presence of ER, PR, and HER2 biomarkers. The present study could provide a new perspective on the molecular regulatory. Processes associated with BC pathogenic mechanisms are linked to the LINC01279, although further research is needed on the possible role of this lncRNA in BC.
DNA methylation dysregulation patterns in the 1p36 region instability.
Swierkowska-Janc J, Kabza M, Rydzanicz M … +4 more , Giefing M, Ploski R, Shaffer LG, Gajecka M
J Appl Genet · 2025 Sep · PMID 39460848 · Full text
In the monosomy 1p36 deletion syndrome, the role of DNA methylation in the genomic stability of the 1p36 region remains elusive. We hypothesize that changes in the methylation pattern at the 1p36 breakpoint hotspot regio...
In the monosomy 1p36 deletion syndrome, the role of DNA methylation in the genomic stability of the 1p36 region remains elusive. We hypothesize that changes in the methylation pattern at the 1p36 breakpoint hotspot region influenced the chromosomal breakage leading to terminal deletions. From the monosomy 1p36 material collection, four cases with 4.0 to 5.5 Mb terminal deletions and their parents were investigated. DNA samples were assessed by targeted bisulfite sequencing (NimbleGen SeqCap Epi) to examine DNA methylation status in the 1p36 hotspot region at single-base resolution as compared to the chromosomal hotspot regions, 9p22, 18q21.1, and 22q11.2. Additionally, in in silico assessment, the mean GC content of various classes of repeats in the genome and especially in the breakpoint regions was evaluated. A complex landscape of DNA methylation in the 1p36 breakpoint hotspot region was found. Changes in DNA methylation level in the vicinity of the breakpoint in the child's DNA when compared to parents' and control DNA were observed, with a shift from 15.1 to 70.8% spanning the breakpoint region. In the main classes of evaluated repeats, higher mean GC contents in the 1p36 breakpoint region (47.06%), 22q11.2 (48.47%), and 18q21.1 (44.21%) were found, compared to the rest of the genome (40.78%). The 9p22 region showed a lower GC content (39.42%) compared to the rest of the genome. Both dysregulation of DNA methylation and high GC content were found to be specific for the 1p36 breakpoint hotspot region suggesting that methylation abnormalities could contribute to aberrations at 1p36.
Experimental evaluation of effectiveness of genomic selection for resistance to northern corn leaf blight in maize.
Lohithaswa HC, Balasundara DC, Mallikarjuna MG … +5 more , Sowmya MS, Mallikarjuna N, Kulkarni RS, Pandravada AS, Bhatia BS
J Appl Genet · 2025 Sep · PMID 39446310 · Publisher ↗
Northern corn leaf blight (NLB) caused by Setosphaeria turcica (Luttrell) Leonard & Suggs is a severe foliar disease in maize. Resistance to NLB is complexly inherited and controlled by several quantitative trait loci (Q...
Northern corn leaf blight (NLB) caused by Setosphaeria turcica (Luttrell) Leonard & Suggs is a severe foliar disease in maize. Resistance to NLB is complexly inherited and controlled by several quantitative trait loci (QTL) distributed across the genome. Phenotype and DNA marker-based selection for resistance to NLB is expected to be effective. Hence, an investigation was carried out to predict the genetic value of selection candidates for resistance to NLB and compare the accuracies of genomic prediction in two F populations of two crosses (CM212 × MAI172; CM202 × SKV50) derived from contrasting parents. Linkage analysis using 297 polymorphic SNPs in population-1 and 290 polymorphic SNPs in population-2 revealed ten linkage groups spanning 3623.88 cM and 4261.92 cM with an average distance of 12.40 cM and 14.9 cM in population-1 and population-2, respectively. Location-wise and pooled data across locations identified common QTLs on linkage groups 1 and 6 in population-1 and 3 and 8 in population-2. The prediction accuracy of the QTL mapping (9.92 and 9.10 for population-1 and population-2, respectively) was based on only a few markers, which explained higher percent phenotypic variation. The prediction accuracies of the genomic estimated breeding values in the present investigation were relatively low in population-1 (0.24 to 0.26) and population-2 (0.29-0.32) compared to the expected accuracies. This could be due to fewer polymorphic markers and a small training/population size. Though the GS prediction accuracies were relatively low, they were significantly higher than QTL mapping, which promises better genetic gain per cycle. The resistant progenies from both populations were advanced to derive inbred lines and crossed with four different testers in line × tester mating design to test for their combining ability and effectiveness of genomic selection. High overall general combining ability was exhibited by 21 inbred lines. Among Fs, 48% were assigned high overall specific combining ability status. Out of the 136 single crosses, seven recorded significant positive standard heterosis over the best check for grain yield. Twenty-five inbreds with high GEBVs were crossed with four testers to obtain 100 Fs and evaluated for their response to NLB. The majority of hybrids displayed moderate to resistant reaction to NLB either in combination with susceptible or resistant testers indicating the effectiveness of selection based on high GEBVs.
Importance and variability of the paternal component in sow reproductive traits.
Cieleń G, Sell-Kubiak E
J Appl Genet · 2024 Dec · PMID 39422876 · Full text
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 w...
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.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe