Pub Date : 2024-07-05DOI: 10.1007/s12041-024-01476-8
Francisco Javier Cotrina-Vinagre, María Elena Rodríguez-García, Lucía Del Pozo-Filíu, Pilar Quijada-Fraile, Francisco Martínez-Azorín
We report the case of a Spanish pediatric patient with developmental delay, hypotonia, feeding difficulties, visual problems, and hyperkinetic movements. Whole-exome sequencing uncovered a new heterozygous de novo Synaptotagmin 1 (SYT1) missense variant, NM_005639.3:c.930T>A (p.Asp310Glu), in a female proband. This gene encodes the synaptotagmin-1 (SYT1) protein, which is a component of a protein complex involved in the fusion of synaptic vesicles with the presynaptic membrane. Pathogenic SYT1 variants have been associated with Baker–Gordon syndrome (BAGOS), an autosomal dominant neurodevelopmental disorder. Although up to 30 cases have been identified worldwide, to the best of our knowledge, this is the first patient described with mitochondrial respiratory chain deficiencies and rod–cone dysfunction. In conclusion, our data expand both the genetic and phenotypic spectrum associated with SYT1 variants.
{"title":"Expanding the genetic and phenotypic spectrum of Baker–Gordon syndrome: a new de novo SYT1 variant","authors":"Francisco Javier Cotrina-Vinagre, María Elena Rodríguez-García, Lucía Del Pozo-Filíu, Pilar Quijada-Fraile, Francisco Martínez-Azorín","doi":"10.1007/s12041-024-01476-8","DOIUrl":"https://doi.org/10.1007/s12041-024-01476-8","url":null,"abstract":"<p>We report the case of a Spanish pediatric patient with developmental delay, hypotonia, feeding difficulties, visual problems, and hyperkinetic movements. Whole-exome sequencing uncovered a new heterozygous <i>de novo</i> Synaptotagmin 1 (<i>SYT1</i>) missense variant, NM_005639.3:c.930T>A (p.Asp310Glu), in a female proband. This gene encodes the synaptotagmin-1 (SYT1) protein, which is a component of a protein complex involved in the fusion of synaptic vesicles with the presynaptic membrane. Pathogenic <i>SYT1</i> variants have been associated with Baker–Gordon syndrome (BAGOS), an autosomal dominant neurodevelopmental disorder. Although up to 30 cases have been identified worldwide, to the best of our knowledge, this is the first patient described with mitochondrial respiratory chain deficiencies and rod–cone dysfunction. In conclusion, our data expand both the genetic and phenotypic spectrum associated with <i>SYT1</i> variants.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"4 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141546691","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}
Colorectal cancer (CRC) is known to develop due to the accumulation of both genetic and epigenetic alterations, resulting in the conversion of intestinal epithelial cells to malignant adenocarcinoma cells. Caudal type homeobox 1 (CDX1) gene is a homeobox transcription factor and a selective tumour suppressor gene that is an important factor for the development of intestinal cells. This gene plays a role in the differentiation of intestinal epithelial cells, and its expression decreases in a number of cell lines derived from CRC, which suggests that a lack of CDX1 expression is a risk factor for the development of colorectal carcinoma. Therefore, the methylated DNA amounts of CDX1 gene in stool samples were investigated as a noninvasive method for the detection of CRC. In the present study, the methylation of CDX1 gene promoter region was assessed in stool samples of 50 CRC patients and 50 healthy individuals by MethyLight PCR using two primers and a Taq Man probe, which was completely specifically designed for fully methylated DNA of the gene promoter region. The percentage of methylated reference (PMR) of the studied gene in all samples was calculated similarly to previous studies. Statistical analysis was performed using SPSS 16. The PMR medians were 3.25 (95% CI: 0.1–100) and 0.1 (95% CI: 0.07–1) in the stool samples of CRC patients and healthy individuals, respectively. The results showed a significant difference in CDX1 gene PMR between stool samples of CRC patients and controls (P-value <0.001). According to the results of this study, it can be argued that measurement of CDX1 gene DNA in stool samples using the MethyLight PCR has acceptable sensitivity and specificity, and is adequately potential to be used as a noninvasive complementary method for the diagnosis of CRC, along with colonoscopy as the gold standard to this end. This study is the first report on CDX1 methylation in stool samples of CRC patients. Therefore, further research should be carried out with a larger sample size to evaluate its efficacy as a diagnostic biomarker in clinical laboratories.
{"title":"Detection of caudal type homeobox 1 (CDX1) gene methylated DNA, as a stool-based diagnostic biomarker in colorectal cancer","authors":"Sarina Almasi, Lida Haghnazari, Seyedeh Ozra Hosseini, Nayebali Rezvani","doi":"10.1007/s12041-024-01473-x","DOIUrl":"https://doi.org/10.1007/s12041-024-01473-x","url":null,"abstract":"<p>Colorectal cancer (CRC) is known to develop due to the accumulation of both genetic and epigenetic alterations, resulting in the conversion of intestinal epithelial cells to malignant adenocarcinoma cells. Caudal type homeobox 1 (<i>CDX1</i>) gene is a homeobox transcription factor and a selective tumour suppressor gene that is an important factor for the development of intestinal cells. This gene plays a role in the differentiation of intestinal epithelial cells, and its expression decreases in a number of cell lines derived from CRC, which suggests that a lack of <i>CDX1</i> expression is a risk factor for the development of colorectal carcinoma. Therefore, the methylated DNA amounts of <i>CDX1</i> gene in stool samples were investigated as a noninvasive method for the detection of CRC. In the present study, the methylation of <i>CDX1</i> gene promoter region was assessed in stool samples of 50 CRC patients and 50 healthy individuals by MethyLight PCR using two primers and a Taq Man probe, which was completely specifically designed for fully methylated DNA of the gene promoter region. The percentage of methylated reference (PMR) of the studied gene in all samples was calculated similarly to previous studies. Statistical analysis was performed using SPSS 16. The PMR medians were 3.25 (95% CI: 0.1–100) and 0.1 (95% CI: 0.07–1) in the stool samples of CRC patients and healthy individuals, respectively. The results showed a significant difference in <i>CDX1</i> gene PMR between stool samples of CRC patients and controls (<i>P</i>-value <0.001). According to the results of this study, it can be argued that measurement of <i>CDX1</i> gene DNA in stool samples using the MethyLight PCR has acceptable sensitivity and specificity, and is adequately potential to be used as a noninvasive complementary method for the diagnosis of CRC, along with colonoscopy as the gold standard to this end. This study is the first report on <i>CDX1</i> methylation in stool samples of CRC patients. Therefore, further research should be carried out with a larger sample size to evaluate its efficacy as a diagnostic biomarker in clinical laboratories.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"31 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141511349","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}
Pub Date : 2024-06-18DOI: 10.1007/s12041-024-01474-w
LAURA L. VALDEZ-VELAZQUEZ, HÉCTOR OCHOA-DÍAZ-LÓPEZ, IVÁN DELGADO-ENCISO, HÉCTOR RANGEL-VILLALOBOS, IRÁM P. RODRÍGUEZ-SÁNCHEZ, ROSARIO GARCÍA-MIRANDA, DOIREYNER DANIEL VELÁZQUEZ-RAMÍREZ, NANCY A. REYES-MÉNDEZ, CARLOS EDUARDO BARAJAS-SAUCEDO, MARGARITA L. MARTÍNEZ-FIERRO
Trachoma, caused by Chlamydia trachomatis, is the most common infectious blindness in the world and is present in indigenous Mayan from Chiapas (Mexico). Inflammatory genes are activated when suffering from trachoma, thus some polymorphisms could increase the susceptibility to develop irreversible blindness. This study aimed to evaluate the genetic risk of developing late-stage trachoma in Mayan ethnic groups. In a case–control study (n = 51 vs n = 102, respectively), the following single-nucleotide polymorphisms (SNPs) in genes related to inflammation were analysed: HSD11B1 (rs11807619), HSD11B1 (rs932335), ABCG2 (rs2231142), SLCO1B1 (rs4149056), IL-10 (rs1800890), TNF (rs1800629), MMP2 (rs243865) and ACE. Three SNPs were associated with late-stage trachoma risk: (i) the T allele of rs11807619, (ii) the C allele of rs932335, which are linked to the HSD11B1 gene (OR = 22.5–27.3), particularly in men when adjusts for gender (OR = 16–16.7); and (iii) D allele of rs4340 in the ACE gene (OR = 5.2–5.3). In fact, significant linkage disequilibrium demonstrated association between ACE gene and HSD11B1 SNPs (r = 0.17–0.179; P = 0.0048–0.0073). Two SNPs HSD11B1 gene (P = 0.013 vs 0.0039) and HSD11B1–ACE haplotypes showed association with late-stage trachoma in Mayan ethnic groups.
由沙眼衣原体引起的沙眼是世界上最常见的传染性失明,在恰帕斯州(墨西哥)的玛雅原住民中也有发生。患沙眼时,炎症基因会被激活,因此某些多态性会增加患上不可逆失明的易感性。本研究旨在评估玛雅人患晚期沙眼的遗传风险。在一项病例对照研究中(n = 51 对 n = 102),分析了与炎症有关的基因中的以下单核苷酸多态性(SNPs):HSD11B1(rs11807619)、HSD11B1(rs932335)、ABCG2(rs2231142)、SLCO1B1(rs4149056)、IL-10(rs1800890)、TNF(rs1800629)、MMP2(rs243865)和 ACE。有三个 SNP 与晚期沙眼风险有关:(i) rs11807619 的 T 等位基因,(ii) rs932335 的 C 等位基因,它们与 HSD11B1 基因有关(OR = 22.5-27.3),尤其是男性,如果调整性别(OR = 16-16.7);(iii) ACE 基因中 rs4340 的 D 等位基因(OR = 5.2-5.3)。事实上,ACE 基因与 HSD11B1 SNPs 之间存在明显的连锁不平衡关系(r = 0.17-0.179;P = 0.0048-0.0073)。两个 SNP HSD11B1 基因(P = 0.013 vs 0.0039)和 HSD11B1-ACE 单倍型与玛雅族晚期沙眼有关。
{"title":"Association of polymorphisms of HSD11B1 and ACE genes with trachoma disease","authors":"LAURA L. VALDEZ-VELAZQUEZ, HÉCTOR OCHOA-DÍAZ-LÓPEZ, IVÁN DELGADO-ENCISO, HÉCTOR RANGEL-VILLALOBOS, IRÁM P. RODRÍGUEZ-SÁNCHEZ, ROSARIO GARCÍA-MIRANDA, DOIREYNER DANIEL VELÁZQUEZ-RAMÍREZ, NANCY A. REYES-MÉNDEZ, CARLOS EDUARDO BARAJAS-SAUCEDO, MARGARITA L. MARTÍNEZ-FIERRO","doi":"10.1007/s12041-024-01474-w","DOIUrl":"https://doi.org/10.1007/s12041-024-01474-w","url":null,"abstract":"<p>Trachoma, caused by <i>Chlamydia trachomatis</i>, is the most common infectious blindness in the world and is present in indigenous Mayan from Chiapas (Mexico). Inflammatory genes are activated when suffering from trachoma, thus some polymorphisms could increase the susceptibility to develop irreversible blindness. This study aimed to evaluate the genetic risk of developing late-stage trachoma in Mayan ethnic groups. In a case–control study (<i>n</i> = 51 vs <i>n</i> = 102, respectively), the following single-nucleotide polymorphisms (SNPs) in genes related to inflammation were analysed: <i>HSD11B1</i> (rs11807619), <i>HSD11B1</i> (rs932335), ABCG2 (rs2231142), SLCO1B1 (rs4149056), IL-10 (rs1800890), TNF (rs1800629), MMP2 (rs243865) and <i>ACE</i>. Three SNPs were associated with late-stage trachoma risk: (i) the T allele of rs11807619, (ii) the C allele of rs932335, which are linked to the <i>HSD11B1</i> gene (OR = 22.5–27.3), particularly in men when adjusts for gender (OR = 16–16.7); and (iii) D allele of rs4340 in the <i>ACE</i> gene (OR = 5.2–5.3). In fact, significant linkage disequilibrium demonstrated association between <i>ACE</i> gene and <i>HSD11B1</i> SNPs (r = 0.17–0.179; <i>P</i> = 0.0048–0.0073). Two SNPs <i>HSD11B1</i> gene (<i>P</i> = 0.013 vs 0.0039) and <i>HSD11B1</i>–<i>ACE</i> haplotypes showed association with late-stage trachoma in Mayan ethnic groups.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"42 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141530271","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}
Pub Date : 2024-05-28DOI: 10.1007/s12041-024-01468-8
Wei-Liang Liu, Fang Li, Lu Liu, Rong Ai
In the past, there were no easily distinct and recognizable features as a guide for precise clinical and genetic diagnosis of cases with chromosome microdeletions involving 15q26 including CHD2. The present study analysed the clinical data and collected venous blood samples from a pediatric patient and his healthy family members for DNA testing. The whole-exome sequencing was performed by the next-generation sequencing (NGS). Chromosomal copy-number variations were tested based on NGS. We present a review of all cases with chromosome microdeletions affecting CHD2. A novel de novo 5.82-Mb deletion at 15q25.3-15q26.1 including CHD2 was identified in our patient who is an 11.6-year-old boy. We first found surprising efficacy of lamotrigine in controlling intractable drop seizures in the individual. These cases have development delay, behavioural problems, epilepsy, variable multiple anomalies, etc. Phenotypes of individuals with deletions involving 15q26 including CHD2 are highly variable with regard to facial features and multiple developmental anomalies. We first found the special clinical entity of development delay, behavioural problems, epilepsy, variable skeletal and muscular anomalies, abnormalities of variable multiple systems and characteristic craniofacial phenotypes in patients with chromosome microdeletions involving CHD2. The larger deletions involving 15q26 including CHD2 tend to cause the classical phenotype. A distinctive craniofacial appearance of the classical phenotype is midface hypoplasia and perifacial protrusion.
{"title":"Special clinical entity with 15q26 deletion: a novel case report","authors":"Wei-Liang Liu, Fang Li, Lu Liu, Rong Ai","doi":"10.1007/s12041-024-01468-8","DOIUrl":"https://doi.org/10.1007/s12041-024-01468-8","url":null,"abstract":"<p>In the past, there were no easily distinct and recognizable features as a guide for precise clinical and genetic diagnosis of cases with chromosome microdeletions involving 15q26 including <i>CHD2</i>. The present study analysed the clinical data and collected venous blood samples from a pediatric patient and his healthy family members for DNA testing. The whole-exome sequencing was performed by the next-generation sequencing (NGS). Chromosomal copy-number variations were tested based on NGS. We present a review of all cases with chromosome microdeletions affecting <i>CHD2</i>. A novel <i>de novo</i> 5.82-Mb deletion at 15q25.3-15q26.1 including <i>CHD2</i> was identified in our patient who is an 11.6-year-old boy. We first found surprising efficacy of lamotrigine in controlling intractable drop seizures in the individual. These cases have development delay, behavioural problems, epilepsy, variable multiple anomalies, etc. Phenotypes of individuals with deletions involving 15q26 including <i>CHD2</i> are highly variable with regard to facial features and multiple developmental anomalies. We first found the special clinical entity of development delay, behavioural problems, epilepsy, variable skeletal and muscular anomalies, abnormalities of variable multiple systems and characteristic craniofacial phenotypes in patients with chromosome microdeletions involving <i>CHD2</i>. The larger deletions involving 15q26 including <i>CHD2</i> tend to cause the classical phenotype. A distinctive craniofacial appearance of the classical phenotype is midface hypoplasia and perifacial protrusion.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"21 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141166152","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}
Genomic studies make it possible to breakthrough in many fields such as biochemistry, physiology, phylogenetics, etc., though they are unworkable without sequences of genomic DNA of an organism. The terrestrial mollusks’ genomes would benefit gastropod biology investigations, that are unavailable so far due to problems in DNA integrity and quality after the isolation procedures. Here we describe a fast and handy protocol for genomic DNA extraction from the tissues of Helix lucorum, which allows to yield high-quality samples applicable for downstream analysis such as high-throughput DNA sequencing. Troubleshooting revealed the nuclease activity of snail tissue lysate, which may be avoided by heating the lysate and decreasing the incubation time.
基因组研究使生物化学、生理学、系统发育学等许多领域的研究取得突破成为可能,但如果没有生物体的基因组DNA序列,这些研究是无法进行的。陆生软体动物的基因组将有利于腹足类生物学研究,但由于分离程序后 DNA 的完整性和质量问题,迄今为止还无法获得陆生软体动物的基因组。在此,我们介绍了一种快速、简便的方法,用于从螺旋藻组织中提取基因组DNA,从而获得高质量的样本,用于下游分析,如高通量DNA测序。故障排除显示蜗牛组织裂解液具有核酸酶活性,这可以通过加热裂解液和缩短孵育时间来避免。
{"title":"Extraction of genomic DNA for sequencing from snail Helix lucorum","authors":"Dmitry Panteleev, Anastasia Sadova, Galina Pavlova","doi":"10.1007/s12041-024-01472-y","DOIUrl":"https://doi.org/10.1007/s12041-024-01472-y","url":null,"abstract":"<p>Genomic studies make it possible to breakthrough in many fields such as biochemistry, physiology, phylogenetics, etc., though they are unworkable without sequences of genomic DNA of an organism. The terrestrial mollusks’ genomes would benefit gastropod biology investigations, that are unavailable so far due to problems in DNA integrity and quality after the isolation procedures. Here we describe a fast and handy protocol for genomic DNA extraction from the tissues of <i>Helix lucorum,</i> which allows to yield high-quality samples applicable for downstream analysis such as high-throughput DNA sequencing. Troubleshooting revealed the nuclease activity of snail tissue lysate, which may be avoided by heating the lysate and decreasing the incubation time.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"57 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141061784","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}
Pub Date : 2024-05-18DOI: 10.1007/s12041-024-01471-z
Maheshkumar Prakash Patil, Young-Ryun Kim, Shinya Nakashita, Jong-Oh Kim, Kyunghoi Kim
The mitogenome is an important tool for taxonomic and evolutionary investigation. Here, a few complete mitogenomes of red algae have been reported. We have reported the complete mitogenome sequences of Grateloupia cornea Okamura, 1913 (Rhodophyta, Halymeniales). The genome is 30,595 bp in circumference, and has a strongly biased [AT] = 66.9%. Like most other Grateloupia species, it has a group II intron in the cox1 gene. Maximum likelihood and maximum parsimony analyses showed that G. cornea is more closely related to G. asiatica. This shows that the group II intron in the cox1 ORF present in most species of Grateloupia was present in their common ancestor, and uniquely lost in G. asiatica. The seven Grateloupia species with known mitogenome sequences remain monophyletic, with the genus Polyopes as sister taxon. The complete mitochondrial genome data will be valuable for future research on comparative mitochondrial genome analysis, an extensive understanding of gene content and organization, evolution of the cox1 intron in Rhodophyta as well as phylogenetic analysis.
有丝分裂基因组是分类和进化研究的重要工具。目前,已有一些完整的红藻有丝分裂基因组被报道。我们报告了冈村藻(Grateloupia cornea Okamura, 1913)(红藻门,Halymeniales)的完整有丝分裂基因组序列。该基因组周长为 30,595 bp,具有强偏倚 [AT] = 66.9%。与其他大多数 Grateloupia 物种一样,它的 cox1 基因中有一个 II 组内含子。最大似然法和最大拟合分析表明,G. cornea 与 G. asiatica 的亲缘关系更近。这表明,大多数 Grateloupia 种类的 cox1 ORF 中的 II 组内含子存在于它们的共同祖先中,而在 G. asiatica 中丢失了。具有已知有丝分裂基因组序列的 7 个 Grateloupia 物种仍为单系,与 Polyopes 属为姐妹类群。完整的线粒体基因组数据对今后的线粒体基因组比较分析研究、广泛了解基因内容和组织、红叶植物中 cox1 内含子的进化以及系统发育分析都很有价值。
{"title":"Mitogenome features and phylogenetic analysis of red algae, Grateloupia cornea (Rhodophyta, Halymeniales)","authors":"Maheshkumar Prakash Patil, Young-Ryun Kim, Shinya Nakashita, Jong-Oh Kim, Kyunghoi Kim","doi":"10.1007/s12041-024-01471-z","DOIUrl":"https://doi.org/10.1007/s12041-024-01471-z","url":null,"abstract":"<p>The mitogenome is an important tool for taxonomic and evolutionary investigation. Here, a few complete mitogenomes of red algae have been reported. We have reported the complete mitogenome sequences of <i>Grateloupia cornea</i> Okamura, 1913 (Rhodophyta, Halymeniales). The genome is 30,595 bp in circumference, and has a strongly biased [AT] = 66.9%. Like most other <i>Grateloupia</i> species, it has a group II intron in the <i>cox1</i> gene. Maximum likelihood and maximum parsimony analyses showed that <i>G. cornea</i> is more closely related to <i>G. asiatica</i>. This shows that the group II intron in the <i>cox1</i> ORF present in most species of <i>Grateloupia</i> was present in their common ancestor, and uniquely lost in <i>G. asiatica</i>. The seven <i>Grateloupia</i> species with known mitogenome sequences remain monophyletic, with the genus <i>Polyopes</i> as sister taxon. The complete mitochondrial genome data will be valuable for future research on comparative mitochondrial genome analysis, an extensive understanding of gene content and organization, evolution of the <i>cox1</i> intron in Rhodophyta as well as phylogenetic analysis.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"29 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141061738","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}
Pub Date : 2024-05-03DOI: 10.1007/s12041-024-01469-7
Mohd Hairul Mohd Salleh, Yuzine Esa
We present here the complete mitochondrial sequence of the critically endangered Malaysian giant turtle, Orlitia borneensis. The assembled mitochondrial genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (rRNAs), and one control region. This mitochondrial genome has been archived in the NCBI GenBank with accession number OQ808845. The Batagur control region is relatively smaller than O. borneensis and closer to Aldabrachelys gigantea, which suggests potentially that O. borneensis has undergone an expansion in the control region.
我们在此发表了极度濒危的马来西亚巨龟 Orlitia borneensis 的完整线粒体序列。该线粒体基因组包括 13 个蛋白质编码基因(PCGs)、22 个转运核糖核酸(tRNA)基因、两个核糖体核糖核酸基因(rRNAs)和一个控制区。该线粒体基因组已存档于 NCBI GenBank,登录号为 OQ808845。Batagur 的控制区比 O. borneensis 小,更接近 Aldabrachelys gigantea,这可能表明 O. borneensis 的控制区发生了扩展。
{"title":"The first complete mitochondrial genome of the critically endangered Malaysian giant turtle, Orlitia borneensis (Testudines: Geoemydidae)","authors":"Mohd Hairul Mohd Salleh, Yuzine Esa","doi":"10.1007/s12041-024-01469-7","DOIUrl":"https://doi.org/10.1007/s12041-024-01469-7","url":null,"abstract":"<p>We present here the complete mitochondrial sequence of the critically endangered Malaysian giant turtle, <i>Orlitia borneensis</i>. The assembled mitochondrial genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (rRNAs), and one control region. This mitochondrial genome has been archived in the NCBI GenBank with accession number OQ808845. The <i>Batagur</i> control region is relatively smaller than <i>O. borneensis</i> and closer to <i>Aldabrachelys gigantea</i>, which suggests potentially that <i>O. borneensis</i> has undergone an expansion in the control region.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"162 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140889897","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}
Pub Date : 2024-04-17DOI: 10.1007/s12041-024-01466-w
Mohammad Nurul Matin, Kyung Eun Lee, Sang Gu Kang
Phenotypic mutants are valuable resources for elucidating the function of genes responsible for their expression. This study examined mutant rice strains expressing three traits: spotted leaf 6 (spl6), lax panicle (lax), and liguleless (lg). In the mutant, the spl6 phenotype was a genetically programmed lesion-mimicking mutation (LMM) that displayed spontaneously scattered spots across the leaf surface. In the lg trait, the plant lacked a collar region, and there were no auricles and ligules at the junction of the leaf blade and leaf sheath. The lax panicle trait manifested as sparely arranged spikelets resulting from the terminal spikelet with no lateral spikelets, which caused a drastic reduction of the total seed number in the mutant. All three mutant genes were genetically recessive and had nuclear gene regulation. The dihybrid segregation of the lg gene was classified independently according to the Mendelian 9:3:3:1 dihybrid segregation ratio in the F2 generation, suggesting that the lg gene is not linked to the same chromosome as the lax and spl6 genes. On the other hand, spl6 and lax were not assorted independently, indicating that they are closely linked on chromosome 1 in rice. Additional linkage analysis from the recombination of spl6 and lax genes reconfirmed that the two genes were ~9.4 cM away from each other. The individual single-gene mutant plant from one plant with a three-gene mutation (spl6, lax, and lg) was isolated and characterized, which will be a crucial resource for the gene cloning and molecular characterization of these genes.
{"title":"Genetic characterization and linkage analysis of spotted leaf 6, liguleless and lax panicle traits in mutant rice","authors":"Mohammad Nurul Matin, Kyung Eun Lee, Sang Gu Kang","doi":"10.1007/s12041-024-01466-w","DOIUrl":"https://doi.org/10.1007/s12041-024-01466-w","url":null,"abstract":"<p>Phenotypic mutants are valuable resources for elucidating the function of genes responsible for their expression. This study examined mutant rice strains expressing three traits: spotted leaf 6 (<i>spl6</i>), lax panicle (<i>lax</i>), and liguleless (<i>lg</i>). In the mutant, the <i>spl6</i> phenotype was a genetically programmed lesion-mimicking mutation (LMM) that displayed spontaneously scattered spots across the leaf surface. In the <i>lg</i> trait, the plant lacked a collar region, and there were no auricles and ligules at the junction of the leaf blade and leaf sheath. The <i>lax</i> panicle trait manifested as sparely arranged spikelets resulting from the terminal spikelet with no lateral spikelets, which caused a drastic reduction of the total seed number in the mutant. All three mutant genes were genetically recessive and had nuclear gene regulation. The dihybrid segregation of the <i>lg</i> gene was classified independently according to the Mendelian 9:3:3:1 dihybrid segregation ratio in the F<sub>2</sub> generation, suggesting that the <i>lg</i> gene is not linked to the same chromosome as the <i>lax</i> and <i>spl6</i> genes. On the other hand, <i>spl6</i> and <i>lax</i> were not assorted independently, indicating that they are closely linked on chromosome 1 in rice. Additional linkage analysis from the recombination of <i>spl6</i> and <i>lax</i> genes reconfirmed that the two genes were ~9.4 cM away from each other. The individual single-gene mutant plant from one plant with a three-gene mutation (<i>spl6, lax</i>, and <i>lg</i>) was isolated and characterized, which will be a crucial resource for the gene cloning and molecular characterization of these genes.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"12 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140608763","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}
Pub Date : 2024-04-17DOI: 10.1007/s12041-024-01470-0
FRANCISCO JAVIER BORRAYO-LÓPEZ, BERTHA IBARRA-CORTÉS, FRANCISCO JAVIER PEREA-DÍAZ, ABRIL IXCHEL MUÑOZ-ZÚÑIGA, HÉCTOR MONTOYA-FUENTES, JANETH MARGARITA SOTO-PADILLA, LOURDES DEL CARMEN RIZO-DE LA TORRE
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 (BCL11A), HBS1L-MYB transcriptional GTPase intergenic region (HBS1L-MYB), Krüppel-like factor 1 (KLF1), haemoglobin gamma subunit 2 (HBG2), haemoglobin gamma subunit 1 (HBG1), and haemoglobin subunit beta pseudogene 1 (HBBP1) are often associated with elevated HbF 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 concentration was higher in patients than in the reference group (4.4% vs 1.4%), and 75% (n = 36) of the patients had HbF > 2.5%. Unfavourable prognosis ALL was established in 68.8% (n = 33) of the patients. Variant HBG2 rs7482144 was associated with high HbF concentration (P = 0.015); while HBS1L-MYB rs9399137 (P = 0.001), HBG2 rs7482144 (P = 0.001) and the β-globin genes HBG2, HBG1, and HBPP1 haplotype TGC (P = 0.017) with unfavourable prognosis ALL. Additionally, variant BCL11A rs4671393 showed a protective role (P = 0.0001). In conclusion, variants HBG2 rs7482144, HBS1L-MYB rs9399137 and BCL11A rs4671393 may play a significant role in ALL.
{"title":"Foetal haemoglobin elevation, unfavourable prognosis, and protective role of genetic variants HBG2 rs7482144, HBS1L-MYB rs9399137 and BCL11A rs4671393 in children with ALL","authors":"FRANCISCO JAVIER BORRAYO-LÓPEZ, BERTHA IBARRA-CORTÉS, FRANCISCO JAVIER PEREA-DÍAZ, ABRIL IXCHEL MUÑOZ-ZÚÑIGA, HÉCTOR MONTOYA-FUENTES, JANETH MARGARITA SOTO-PADILLA, LOURDES DEL CARMEN RIZO-DE LA TORRE","doi":"10.1007/s12041-024-01470-0","DOIUrl":"https://doi.org/10.1007/s12041-024-01470-0","url":null,"abstract":"<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 (<i>HBG1</i>), and haemoglobin subunit beta pseudogene 1 (<i>HBBP1</i>) are often associated with elevated HbF 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 concentration was higher in patients than in the reference group (4.4% vs 1.4%), and 75% (<i>n</i> = 36) of the patients had HbF > 2.5%. Unfavourable prognosis ALL was established in 68.8% (<i>n</i> = 33) of the patients. Variant <i>HBG2</i> rs7482144 was associated with high HbF concentration (<i>P</i> = 0.015); while <i>HBS1L</i>-<i>MYB</i> rs9399137 (<i>P</i> = 0.001), <i>HBG2</i> rs7482144 (<i>P</i> = 0.001) and the β-globin genes <i>HBG2</i>, <i>HBG1</i>, and <i>HBPP1</i> haplotype TGC (<i>P</i> = 0.017) with unfavourable prognosis ALL. Additionally, variant <i>BCL11A</i> rs4671393 showed a protective role (<i>P</i> = 0.0001). In conclusion, variants <i>HBG2</i> rs7482144, <i>HBS1L</i>-<i>MYB</i> rs9399137 and <i>BCL11A</i> rs4671393 may play a significant role in ALL.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"29 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140608701","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}
Pub Date : 2024-04-08DOI: 10.1007/s12041-024-01467-9
Oliver Mayo, Vidyanand Nanjundiah
A recent report by G. Clark points to a sustained persistence of social status in England that extends vertically across several generations and horizontally across many levels of kinship. We seek to put his findings in historical perspective. We do so by relating them to two lines of thinking related to biological inheritance. One predated the rediscovery of Mendel’s work and led to the field of quantitative genetics, which dealt on the whole with quasi-continuously varying traits. The other is based on the rediscovery itself and led to a reconciliation between quantitative genetics and discrete Mendelian elements of heredity. Both were enmeshed with the supposed need for, and societal consequences of, eugenics and assortative mating. Also on both issues, the significant ideas can be traced to R. A. Fisher, inspired in one case by F. Galton and in the other by J. A. Cobb, with strong support for Galton and Cobb coming from Karl Pearson. Clark’s findings point to societal stratification, and assortative mating for wealth is a straightforward hypothesis to account for it. However, it should be noted that the findings support, but do not prove, the hypothesis.
克拉克(G. Clark)最近的一份报告指出,英国的社会地位持续存在,纵向上跨越几代人,横向上跨越多个亲属层次。我们试图从历史的角度来看待他的发现。为此,我们将其与有关生物遗传的两种思路联系起来。一种是在重新发现孟德尔的工作之前,并导致了数量遗传学领域的出现,该领域总体上涉及准连续变化的性状。另一个领域则以孟德尔的重新发现为基础,导致了定量遗传学与孟德尔遗传学离散元素之间的调和。这两个问题都与优生学和异性交配的所谓必要性和社会后果有关。同样,在这两个问题上,重要的观点都可以追溯到 R. A. 费雪,一个是受 F. 高尔顿的启发,另一个是受 J. A. 柯布的启发,而卡尔-皮尔逊对高尔顿和柯布的大力支持。克拉克的研究结果表明了社会分层,而财富的同类交配则是解释这一现象的直接假设。不过,应该指出的是,研究结果支持了这一假设,但并没有证明这一假设。
{"title":"Reflections on assortative mating, social stratification, and genetics","authors":"Oliver Mayo, Vidyanand Nanjundiah","doi":"10.1007/s12041-024-01467-9","DOIUrl":"https://doi.org/10.1007/s12041-024-01467-9","url":null,"abstract":"<p>A recent report by G. Clark points to a sustained persistence of social status in England that extends vertically across several generations and horizontally across many levels of kinship. We seek to put his findings in historical perspective. We do so by relating them to two lines of thinking related to biological inheritance. One predated the rediscovery of Mendel’s work and led to the field of quantitative genetics, which dealt on the whole with quasi-continuously varying traits. The other is based on the rediscovery itself and led to a reconciliation between quantitative genetics and discrete Mendelian elements of heredity. Both were enmeshed with the supposed need for, and societal consequences of, eugenics and assortative mating. Also on both issues, the significant ideas can be traced to R. A. Fisher, inspired in one case by F. Galton and in the other by J. A. Cobb, with strong support for Galton and Cobb coming from Karl Pearson. Clark’s findings point to societal stratification, and assortative mating for wealth is a straightforward hypothesis to account for it. However, it should be noted that the findings support, but do not prove, the hypothesis.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"2 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140563334","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}