Journal of Genetics最新文献

{"title":"miR-7160 inhibits gastric cancer cell proliferation and metastasis by silencing <i>SIX1</i>.","authors":"Meng Meng, Guoxin Guan, Xingming Liu, Wei Sun, Xinye Cui, Saiya Fu, Fuwen Luo","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Upregulation of homeoprotein <i>SIX1</i> in gastric cancer (GC) is related to tumour proliferation and invasion. MicroRNA-7160 (miR-7160) is a homeoprotein <i>SIX1</i>-targeting miRNA that downregulates miR-7160, leading to cancer development. Total gastric cancer samples were collected from six patients, and relative expression levels of <i>SIX1</i> mRNA and miRNAs were analysed by qRT-PCR. To evaluate the regulation of <i>SIX1</i> by miR-7160, pGL3-SIX1-mut, pGL3-SIX1, and miR-7160 mimics transfected into cells using lipofectamine 2000. After transfection, proliferation and apoptosis in cultured cells were assessed using the nuclear TUNEL staining and CCK8 reagent, respectively. We demonstrated that the downregulation of miR-7160 in human gastric cancer cells is related to the upregulation of <i>SIX1</i> mRNA. In gastric cancer cell lines, miR-7160 overexpression could downregulate the expression and inhibit cancer cell proliferation and growth in vitro. However, overexpression of miR-7160 did not increase gastric cancer cell apoptosis. In vitro downregulation of <i>SIX1</i> decreased vimentin, N-cadherin, and other EMT-related gene expression and increased E-cadherin expression. In brief, miR-7160, by targeting <i>SIX1</i>, inhibits gastric cancer proliferation and cell growth <i>in vitro</i>, which provides an idea for introducing a new treatment option for gastric cancer.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142120013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple mutations in <i>BADH2</i> gene reveal the novel fragrance allele in indica rice (<i>Oryza sativa L.</i>).","authors":"Sonali Chandanshive, Sarika Mathure, Altafhusain Nadaf","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The aroma in rice is the most appreciable quality trait, controlled by the loss of function of the betaine aldehyde dehydrogenase 2 (<i>BADH2</i>) gene. In the present study, <i>indica</i> rice cultivars (basmati, nonbasmati aromatic, and nonaromatic) were screened to explore allelic differences in the <i>BADH2</i> gene using two functional markers (<i>badh2-p-5'UTR</i> and <i>FMbadh2-E7</i>). Notably, the results of the present mutational analysis showed that both markers confirmed a different mutation in indica rice cultivars than earlier reported <i>japonica</i> accessions. It was found that there is 250-bp deletion in the promoter region of aromatic Kagesali and Kalakrishna as compared to nonaromatic Kolamb. The results of <i>FMbadh2-E7</i> showed 8-bp deletion and six SNPs in exon 7 of the Kalakrishna cultivar. Interestingly, the nonbasmati aromatic Lalbhat rice cultivar did not harbour any reported mutation and showed a novel <i>BADH2</i> allele carrying 1-bp deletion in exon 7. Among the selected aromatic rice cultivars, eight cultivars showed mutation in the 5' UTR region and interestingly 23 rice cultivars carried the mutation in both 5' UTR and exon 7 of a <i>BADH2</i> gene. The 2-acetyl-1-pyrroline (2AP) biosynthesis related metabolites, enzyme assay and gene expression supported mutation in <i>BADH2</i> gene and expression of 2AP in aromatic rice cultivars under study.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140335937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of VDR gene polymorphisms and vitamin D levels in normal and overweight patients with PCOS.","authors":"Zümrüt Mine Işik Saǧlam, Vuslat Lale Bakir, Merve Nur Ataş, H Arzu Ergen","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Polycystic ovary syndrome (PCOS) is one of the most common endocrine diseases in women. In recent years, the effects of vitamin D receptor (VDR) gene variants and VitD3 levels on clinical features of PCOS have been frequently described. In this study, we aimed to determine the relationship between VDR <i>ApaI</i>, <i>TaqI</i> and <i>Cdx2</i> gene variants and VitD3 levels in PCOS patients. Patients were divided into two groups: BMI<25 and BMI>=25. VDR genotypes were determined by real-time polymerase chain reaction (PCR) and serum VitD3 levels were examined by ELISA. We observed that frequencies of the <i>Apa1</i> AC genotype, C allele and <i>Cdx2</i> T allele are increased in the BMI>=25 group compared to BMI<25 group. Also, the <i>ApaI</i> C allele, <i>Taq1</i> AA genotype and A allele, <i>Cdx2</i> CC genotype and C allele are associated with increased triglyceride, total cholesterol, LDL-cholesterol levels in patients with BMI>=25. When examining the relationship between VitD3 levels and clinical profiles in all PCOS patients, regardless of BMI distinction, it is determined that there is a positive correlation between LDL-cholesterol and ftestosterone levels. The present findings suggest that VDR variants are one of the most important risk factors for PCOS, especially for patients with BMI>=25.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139521122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transferability of <i>Nikita</i> and <i>Sukkula</i> retrotransposons in domestic goose (<i>Anser anser domesticus</i>) genome.","authors":"Levent Mercan, Cihat Erdem Bülbül, Fatih Bilgi, Sevgi Marakli","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This article aimed to detect the existence of barley-specific <i>Nikita</i> and <i>Sukkula</i> retrotransposons in domestic geese samples and to evaluate the evolutionary relationships between these and other transposons belonging to the family Anatidae. Inter-retrotransposonamplified polymorphism-polymerase chain reaction (IRAP-PCR) method was performed for these retrotransposons movements in three diverse domestic goose populations (Chinese x Embden crossbred, Turkish White, and Turkish Multicolor). Polymorphism ratios were between 0 and 33% in all samples for <i>Nikita</i> and 0-73% in all samples for <i>Sukkula</i>. In addition, intrapopulation genetic polymorphism rates were also 0-15% in Chinese x Embden crossbred, 0-25% in Turkish White, 0-25% in Turkish Multicolor for <i>Nikita</i>; while 0-27% in Chinese x Embden, and 0-50% in Turkish Multicolor for <i>Sukkula</i>. There was no polymorphism for <i>Sukkula</i> among Turkish White samples. Moreover, the neighbour-joining method was used for phylogenetic tree construction using 38 sequences of different ducks, geese, and swans. In <i>silico</i> analyses supported the transitions of retrotransposons in the family Anatidae. It is concluded that transposon mobility among the phylogenetically distant species may lead to understanding evolutionary relationships. This report is one of the first studies investigating retrotransposon movements in domestic geese, revealing a new perspective on the goose genome regarding mobile genetic elements.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139521123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characters of the <i>MOCA</i> family in wheat and <i>TaMOCA1</i> function in salt stress tolerance.","authors":"Yuxiang Qin, Ping Cui, Bao Zhang, Yuning Wang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p><i>MOCA1</i> encodes the last key glucuronosyltransferase for ionic stress sensor glycosyl inositol phosphoryl-ceramide (GIPCs) biosynthesis in <i>Arabidopsis</i>, which indicates that the <i>MOCA</i> gene family play important role in plant tolerance to salt stress. However, the isolation and function of <i>MOCAs</i> in staple crops have not been reported and the downstream targets of <i>MOCAs</i> in salt stress tolerance signalling pathway are not clear. In this study, we identified 110 <i>MOCA</i> genes in wheat which were classified into five clades and they differed in gene structure, protein length, conserved motifs and expression profiles in different tissues and under salt stress. <i>TaMOCA1</i> was selected for further functional study in response to salt stress. <i>TaMOCA1</i> was rapidly induced by NaCl treatment. The 35S::<i>TaMOCA1-GFP</i> construction showed the cell nucleus and cytoplasm location in wheat protoplast. <i>TaMOCA1</i> over-expressing <i>Arabidopsis</i> seedlings formed longer primary roots and more lateral roots than the wild type ones under 50 mM NaCl treatment. The over-expressing <i>Arabidopsis</i> had higher expression levels of <i>HKT1</i>, but lower expression levels of <i>NHX1</i> and <i>SOS</i> genes than the wild type. Also, the transgenic plants had higher SOD activity and lower MDA content than the wild <i>Arabidopsis</i> seedling under salt stress. These results may indicate that <i>TaMOCA1</i> increases salt stress tolerance through decreasing Na⁺ loading from the xylem parenchyma cells to the xylem via <i>SOS1</i> and <i>HKT1</i>, hence lowering root-to-shoot delivery of Na? and superior antioxidant ability. All these results lay a foundation for further functional study of <i>MOCAs</i> in wheat.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139912763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient assembly of a synthetic attenuated SARS-CoV-2 genome in <i>Saccharomyces cerevisiae</i> using multi-copy yeast vectors.","authors":"Abhishek Kumar Singh, Harsh Goar, Nikita Vashist, Prakash Sinha, Anand Kumar Bachhawat","doi":"","DOIUrl":"","url":null,"abstract":"<p><p><i>Saccharomyces cerevisiae</i> has been demonstrated to be an excellent platform for the multi-fragment assembly of large DNA constructs through its powerful homologous recombination ability. These assemblies have invariably used the stable centromeric single copy vectors. However, many applications of these assembled genomes would benefit from assembly in a higher copy number vector for improved downstream extraction of intact genomes from the yeast. A review of the literature revealed that large multi-fragment assemblies did not appear to have been attempted in multicopy vectors. Therefore, we devised a toolkit that would enable one to seamlessly transition with the same assembling fragments between a single copy and a multicopy vector. We evaluated the assembly of a 28 kb attenuated SARSCoV- 2 genome (lacking the N gene) from 10 fragments in both single copy and multicopy vector systems. Our results reveal that assembly was comparably efficient in the two vector systems. The findings should add to the synthetic biology toolkit of <i>S. cerevisiae</i> and should enable researchers to utilize any of these vector systems depending on their downstream applications.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139912764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Foetal haemoglobin elevation, unfavourable prognosis, and protective role of genetic variants <i>HBG2</i> rs7482144, <i>HBS1L-MYB</i> rs9399137 and <i>BCL11A</i> rs4671393 in children with ALL.","authors":"Francisco Javier Borrayo-LóPez, Bertha Ibarra-Cortés, FranciscoJavier Perea-Díaz, Abril Ixchel MuñOz-Zúñiga, Héctor Montoya-Fuentes, Janeth Margarita Soto-Padilla, Lourdes Del Carmen Rizo-De La Torre","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In acute lymphoblastic leukaemia (ALL), elevated foetal haemoglobin (HbF) levels have been associated with the prognosis of patients. Genetic variants in HbF regulatory genes: BAF chromatin remodelling complex subunit (<i>BCL11A</i>), HBS1L-MYB transcriptional GTPase intergenic region (<i>HBS1L-MYB</i>), Krüppel-like factor 1 (<i>KLF1</i>), haemoglobin gamma subunit 2 (<i>HBG2</i>), haemoglobin gamma subunit 1 (HBG1), and haemoglobin subunit beta pseudogene 1 (<i>HBBP1</i>) are often associatedwith elevatedHbF concentration. This study investigated the association of genetic variants in HbF regulatory genes with HbF concentration, unfavourable prognosis, and outcome in children with ALL.We quantified HbF concentration and genotyped 17 genetic variants in 48 patients with ALL and 64 children without ALL as a reference group. HbF concentrationwas higher in patients than in the reference group (4.4%vs 1.4%), and 75%(<i>n</i> = 36) of thepatientshadHbF>2.5%.Unfavourable prognosis ALL was established in 68.8% (<i>n</i> = 33) of the patients. Variant HBG2 rs7482144 was associated with high HbF concentration (<i>P</i> = 0.015); while HBS1L-MYB rs9399137 (<i>P</i> = 0.001), HBG2 rs7482144 (<i>P</i> = 0.001) and the β-globin genes <i>HBG2</i>, <i>HBG1</i>, and <i>HBPP1</i> haplotypeTGC(P = 0.017) with unfavourable prognosisALL.Additionally, variantBCL11A rs4671393 showed a protective role (P = 0.0001). In conclusion, variants <i>HBG2</i> rs7482144, <i>HBS1L-MYB</i> rs9399137 and <i>BCL11A</i> rs4671393 may play a significant role in ALL.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extraction of genomic DNA for sequencing from snail <i>Helix lucorum</i>.","authors":"Dmitry Panteleev, Anastasia Sadova, Galina Pavlova","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Genomic studies make it possible to breakthrough in many fields such as biochemistry, physiology, phylogenetics, etc., though\u0000they are unworkable without sequences of genomic DNA of an organism. The terrestrial mollusks’ genomes would benefit gastropod\u0000biology investigations, that are unavailable so far due to problems in DNA integrity and quality after the isolation procedures. Here we\u0000describe a fast and handy protocol for genomic DNA extraction from the tissues of <i>Helix lucorum</i>, which allows to yield high-quality\u0000samples applicable for downstream analysis such as high-throughput DNA sequencing. Troubleshooting revealed the nuclease activity of\u0000snail tissue lysate, which may be avoided by heating the lysate and decreasing the incubation time.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141237463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial control region sequences show high genetic connectivity in the brownstripe snapper, <i>Lutjanus vitta</i> (Quoy and Gaimard, 1824) from the east coast of Peninsular Malaysia.","authors":"Ahasan Habib, Nor Athirah Husna Ahmad, Nur Asma Ariffin, Ying Giat Seah, M M Mahbub Alam, Tun Nurul Aimi Mat Jaafar, Nur Fadli, Siti Azizah Mohd Nor, Md Moshiur Rahman","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The Brownstripe Snapper, <i>Lutjanus vitta</i> (Quoy and Gaimard, 1824) is a commercially important snapper extensively caught in Malaysia. We examined genetic diversity, population connectivity, and historical demographics of the <i>L. vitta</i>, off the eastern coast of peninsular Malaysia based on an 817 bp region of the mtDNA control region sequences. Maximum likelihood gene trees demonstrated that the populations under study had limited structuring and formed a single panmictic population that lacks support for internal clades. AMOVA and population pairwise Φ_ST values indicated high genetic exchange between the study areas. A high level of haplotype diversity (0.956-1.000) with low nucleotide diversity (0.008-0.014) indicates a recent expansion of <i>L. vitta</i> populations. However, both neutrality and goodness of fit tests revealed nonsignificant values. These data reflect a recent demographic expansion, which the Bayesian skyline plot estimates population expansion at 44 Kya. The absence of genetic differentiation can be attributed to spawning patterns, dispersal of egg and planktonic larvae, and the absence of physical barriers, which are typical of other <i>Lutjanus</i> species. The current findings could initiate efficient management strategies for <i>L. vitta</i> along Malaysia and other nearby nations that share the same waterways.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 specific molecular markers for medicinal peony (<i>Paeonia lactiflora</i>) with double flower.","authors":"Jinqiu Liao, Shuai Zhang, Qunqun Yang, Zhenge Han, Xuexue Deng, Ruiwu Yang, Yuanyuan Jiang, Li Zhang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In China, medicinal <i>Paeonia lactiflora</i> with double flowers (DFs) does not produce seeds, yet it possesses significantly higher paeoniflorin content compared with its single-flowered counterpart. The propagation of medicinal <i>P. lactiflora</i> with DFs relies solely on rhizomes. However, due to economic motivations, the rhizomes of medicinal <i>P. lactiflora</i> with single flowers (SFs) are often mixed with those of medicinal <i>P. lactiflora</i> with DFs. This practice results in a mixed population and a subsequent decline in quality. To ensure the quality of medicinal <i>P. lactiflora</i> with DFs, it is essential to develop specific molecular markers for its identification and breeding. The genetic diversity of 30 populations from six species in sect. <i>Paeonia</i> was studied using inter-simple sequence repeat (ISSR) analysis. Specific bands in medicinal <i>P. lactiflora</i> with DFs and medicinal <i>P. lactiflora</i> with SFs were cloned and utilized as distinctive molecular markers for their identification. A total of 244 polymorphic bands were identified from 18 primers. Among these primers, UBC844 displayed the highest genetic diversity (<i>N</i>_e = 1.37, <i>h</i> = 0.23, <i>I</i> = 0.36). Based on the UPGMA and PCA analyses, all species were classified into three clusters. Medicinal <i>P. lactiflora</i> with SFs showed closer proximity to the wild-type species of <i>Paeonia</i>, while it was further apart from medicinal <i>P. lactiflora</i> with DFs. The specific band amplified by UBC836-3 (~431 bp) was exclusive to medicinal <i>P. lactiflora</i> with DFs, while the band amplified by UBC842-7 (~341 bp) was specific to medicinal <i>P. lactiflora</i> with SFs. There are significant genomic disparities between medicinal <i>P. lactiflora</i> with SFs and DFs. Consequently, stable and specific sequence characterized amplified region markers (UBC836-3 and UBC842-7) have been established to effectively differentiate between the two types. This development will substantially enhance the quality and efficiency of medicinal <i>P. lactiflora</i>, thus supporting the growth of the industry. By utilizing these specific molecular markers, breeding experts can select parent plants and shorten the cultivation cycle for new medicinal peony varieties.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}