首页 > 最新文献

International journal of biochemistry and molecular biology最新文献

英文 中文
Methylation of the JMJD2B epigenetic regulator differentially affects its ability to coactivate the ETV1 and JUN transcription factors. JMJD2B表观遗传调节因子的甲基化会不同程度地影响其协同激活ETV1和JUN转录因子的能力。
Pub Date : 2023-12-15 eCollection Date: 2023-01-01
Tae-Dong Kim, Ruicai Gu, Ralf Janknecht

Objectives: Jumonji C domain-containing (JMJD) 2B (JMJD2B) is a transcriptional cofactor and histone demethylase that is involved in prostate cancer formation. However, how its function is regulated by posttranslational modification has remained elusive. Hence, we examined if JMJD2B would be regulated by lysine methylation.

Methods: Through in vitro methylation assays and Western blotting with methyl-lysine specific antibodies, we analyzed lysine methylation within JMJD2B. Identified methylated lysine residues were mutated to arginine residues and the respective impact on JMJD2B transcriptional activity measured with a reporter gene assay in human LNCaP prostate cancer cells.

Results: We discovered that JMJD2B is methylated on up to six different lysine residues. Further, we identified the suppressor of variegation 3-9/enhancer of zeste/trithorax (SET) domain-containing protein 7/9 (SET7/9) as the methyltransferase being responsible for this posttranslational modification. Mutating the methylation sites in JMJD2B to arginine residues led to diminished coactivation of the Ju-nana (JUN) transcription factor, which is a known oncogenic protein in prostate tumors. In contrast, methylation of JMJD2B had no impact on its ability to coactivate another transcription factor associated with prostate cancer, the DNA-binding protein E26 transformation-specific (ETS) variant 1 (ETV1). Consistent with a potential joint action of JMJD2B, SET7/9 and JUN in prostate cancer, the expression of JMJD2B in human prostate tumors was positively correlated with both SET7/9 and JUN levels.

Conclusions: The identified SET7/9-mediated methylation of JMJD2B appears to impact its cooperation with selected interacting transcription factors in prostate cancer cells. Given the implicated roles of JMJD2B beyond prostate tumorigenesis, SET7/9-mediated methylation of JMJD2B possibly also influences the development of other cancers, while its impairment might have relevance for obesity or a global developmental delay that can be elicited by reduced JMJD2B activity.

研究目的含 Jumonji C 结构域(JMJD)的 2B(JMJD2B)是一种转录辅因子和组蛋白去甲基化酶,参与了前列腺癌的形成。然而,它的功能如何受翻译后修饰的调控一直是个谜。因此,我们研究了 JMJD2B 是否会受到赖氨酸甲基化的调控:方法:通过体外甲基化测定和使用甲基赖氨酸特异性抗体进行 Western 印迹,我们分析了 JMJD2B 中的赖氨酸甲基化。将鉴定出的甲基化赖氨酸残基突变为精氨酸残基,并在人 LNCaP 前列腺癌细胞中用报告基因检测法测定其对 JMJD2B 转录活性的影响:结果:我们发现 JMJD2B 有多达六个不同的赖氨酸残基被甲基化。结果:我们发现 JMJD2B 在多达六个不同的赖氨酸残基上被甲基化。此外,我们还发现变异抑制因子 3-9/Ehancer of zeste/trithorax (SET) domain-containing protein 7/9 (SET7/9) 是负责这种翻译后修饰的甲基转移酶。将 JMJD2B 中的甲基化位点突变为精氨酸残基会导致 Ju-nana (JUN) 转录因子的共激活作用减弱,而 JUN 是前列腺肿瘤中的一种已知致癌蛋白。与此相反,JMJD2B 的甲基化对其协同激活另一种与前列腺癌相关的转录因子--DNA 结合蛋白 E26 转化特异性(ETS)变体 1(ETV1)的能力没有影响。与JMJD2B、SET7/9和JUN在前列腺癌中的潜在联合作用相一致,JMJD2B在人类前列腺肿瘤中的表达与SET7/9和JUN的水平呈正相关:结论:已发现的 SET7/9 介导的 JMJD2B 甲基化似乎会影响其与前列腺癌细胞中某些相互作用转录因子的合作。鉴于 JMJD2B 在前列腺肿瘤发生之外的作用,SET7/9 介导的 JMJD2B 甲基化可能也会影响其他癌症的发展,而其损伤可能与肥胖或 JMJD2B 活性降低引起的整体发育延迟有关。
{"title":"Methylation of the JMJD2B epigenetic regulator differentially affects its ability to coactivate the ETV1 and JUN transcription factors.","authors":"Tae-Dong Kim, Ruicai Gu, Ralf Janknecht","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Objectives: </strong>Jumonji C domain-containing (JMJD) 2B (JMJD2B) is a transcriptional cofactor and histone demethylase that is involved in prostate cancer formation. However, how its function is regulated by posttranslational modification has remained elusive. Hence, we examined if JMJD2B would be regulated by lysine methylation.</p><p><strong>Methods: </strong>Through in vitro methylation assays and Western blotting with methyl-lysine specific antibodies, we analyzed lysine methylation within JMJD2B. Identified methylated lysine residues were mutated to arginine residues and the respective impact on JMJD2B transcriptional activity measured with a reporter gene assay in human LNCaP prostate cancer cells.</p><p><strong>Results: </strong>We discovered that JMJD2B is methylated on up to six different lysine residues. Further, we identified the suppressor of variegation 3-9/enhancer of zeste/trithorax (SET) domain-containing protein 7/9 (SET7/9) as the methyltransferase being responsible for this posttranslational modification. Mutating the methylation sites in JMJD2B to arginine residues led to diminished coactivation of the Ju-nana (JUN) transcription factor, which is a known oncogenic protein in prostate tumors. In contrast, methylation of JMJD2B had no impact on its ability to coactivate another transcription factor associated with prostate cancer, the DNA-binding protein E26 transformation-specific (ETS) variant 1 (ETV1). Consistent with a potential joint action of JMJD2B, SET7/9 and JUN in prostate cancer, the expression of JMJD2B in human prostate tumors was positively correlated with both SET7/9 and JUN levels.</p><p><strong>Conclusions: </strong>The identified SET7/9-mediated methylation of JMJD2B appears to impact its cooperation with selected interacting transcription factors in prostate cancer cells. Given the implicated roles of JMJD2B beyond prostate tumorigenesis, SET7/9-mediated methylation of JMJD2B possibly also influences the development of other cancers, while its impairment might have relevance for obesity or a global developmental delay that can be elicited by reduced JMJD2B activity.</p>","PeriodicalId":94044,"journal":{"name":"International journal of biochemistry and molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10776875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139428099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Changes in phospholipid profiles in early larval stages of the marine mussel Mytilus galloprovincialis indicate a role of ceramides in bivalve development. 海洋贻贝(Mytilus galloprovincialis)早期幼虫期磷脂谱的变化表明神经酰胺在双壳类发育中的作用。
Pub Date : 2023-10-15 eCollection Date: 2023-01-01
Teresa Balbi, Francesco Trenti, Graziano Guella, Angelica Miglioli, Kristina Sepčić, Caterina Ciacci, Laura Canesi

Background: Phospholipids are highly diverse molecules with pleiotropic biological roles, from membrane components and signaling molecules, whose composition can change in response to both endogenous and external stimuli. Recent lipidomic studies on edible bivalve mollusks were focused on lipid nutritional value and growth requirements. However, no data are available on phospholipid profiles during bivalve larval development. In the model marine bivalve Mytilus galloprovincialis, early larvae (up to 48 hours post fertilization-hpf) undergo dramatic molecular and functional changes, including shell biogenesis and neurogenesis, that are sustained by egg lipid reserves. Changes in phospholipid composition may also occur participating in the complex processes of early development.

Objective: The lipidome of M. galloprovincialis eggs and early larval stages (24 and 48 hpf) was investigated in order to identify possible changes in phospholipid classes and related metabolic pathways that may play a role in key steps of development.

Materials and methods: Lipidomic analysis were performed by NMR spectroscopy and liquid chromatography-mass spectrometry (LC-MS), with focus on phospholipids. Shifts in relative species composition of phosphatidylcholine, phosphatidylethanolamine, plasmalogen, and ceramide aminoethylphosphonate-CAEP, the bivalve analogue of the main mammalian ceramide sphingomyelin, were observed. Expression of genes involved in ceramide homeostasis was also modulated from eggs to early larval stages.

Results: The results represent the first data on changes in phospholipid composition in bivalve larvae and suggest a functional role of phospholipids in mussel early development.

Conclusion: The results underline the importance of lipidomic studies in bivalve larvae, in both physiological conditions and in response to environmental stress.

磷脂是一种高度多样化的分子,具有多种生物学作用,从膜组分到信号分子,其组成可以响应内源性和外源性刺激而改变。近年来食用双壳类软体动物的脂质组学研究主要集中在脂质营养价值和生长需求方面。然而,没有关于双壳类幼虫发育过程中磷脂谱的数据。在海洋双壳贝(Mytilus galloprovincialis)模型中,早期幼虫(受精后48小时)经历了剧烈的分子和功能变化,包括壳生物发生和神经发生,这些变化是由卵脂储备维持的。磷脂组成的变化也可能参与早期发育的复杂过程。目的:研究加洛省扁扁螨卵和幼虫早期(24和48 hpf)的脂质组,以确定可能在发育关键步骤中发挥作用的磷脂类和相关代谢途径的变化。材料和方法:脂质学分析采用核磁共振波谱和液相色谱-质谱(LC-MS),重点研究磷脂。研究人员观察到磷脂酰胆碱、磷脂酰乙醇胺、浆磷脂原和神经酰胺氨基乙基磷酸酯- caep(主要哺乳动物神经酰胺鞘磷脂的双壳类类似物)相对物种组成的变化。参与神经酰胺稳态的基因的表达也从卵到早期幼虫阶段被调节。结果:研究结果首次揭示了双壳类动物幼虫体内磷脂成分的变化,并提示磷脂在贻贝早期发育过程中具有一定的功能作用。结论:本研究结果强调了双壳类动物幼虫脂质组学研究在生理条件和环境胁迫下的重要性。
{"title":"Changes in phospholipid profiles in early larval stages of the marine mussel <i>Mytilus galloprovincialis</i> indicate a role of ceramides in bivalve development.","authors":"Teresa Balbi, Francesco Trenti, Graziano Guella, Angelica Miglioli, Kristina Sepčić, Caterina Ciacci, Laura Canesi","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>Phospholipids are highly diverse molecules with pleiotropic biological roles, from membrane components and signaling molecules, whose composition can change in response to both endogenous and external stimuli. Recent lipidomic studies on edible bivalve mollusks were focused on lipid nutritional value and growth requirements. However, no data are available on phospholipid profiles during bivalve larval development. In the model marine bivalve <i>Mytilus galloprovincialis</i>, early larvae (up to 48 hours post fertilization-hpf) undergo dramatic molecular and functional changes, including shell biogenesis and neurogenesis, that are sustained by egg lipid reserves. Changes in phospholipid composition may also occur participating in the complex processes of early development.</p><p><strong>Objective: </strong>The lipidome of <i>M. galloprovincialis</i> eggs and early larval stages (24 and 48 hpf) was investigated in order to identify possible changes in phospholipid classes and related metabolic pathways that may play a role in key steps of development.</p><p><strong>Materials and methods: </strong>Lipidomic analysis were performed by NMR spectroscopy and liquid chromatography-mass spectrometry (LC-MS), with focus on phospholipids. Shifts in relative species composition of phosphatidylcholine, phosphatidylethanolamine, plasmalogen, and ceramide aminoethylphosphonate-CAEP, the bivalve analogue of the main mammalian ceramide sphingomyelin, were observed. Expression of genes involved in ceramide homeostasis was also modulated from eggs to early larval stages.</p><p><strong>Results: </strong>The results represent the first data on changes in phospholipid composition in bivalve larvae and suggest a functional role of phospholipids in mussel early development.</p><p><strong>Conclusion: </strong>The results underline the importance of lipidomic studies in bivalve larvae, in both physiological conditions and in response to environmental stress.</p>","PeriodicalId":94044,"journal":{"name":"International journal of biochemistry and molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10658153/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138465211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Periplasmic β-glucosidase BglX from E. coli demonstrates greater activity towards galactose-containing substrates. 来自大肠杆菌的周浆β-葡萄糖苷酶BglX对含有半乳糖的底物表现出更大的活性。
Pub Date : 2023-08-15 eCollection Date: 2023-01-01
Lorna Ngo, Joshua Weimer, Li Sui, Tara Pickens, Nina V Stourman

Background: The diverse nature of carbohydrate structures and linkages requires a variety of enzymes responsible for sugar degradation. The E. coli periplasmic protein encoded by the bglX gene has been assigned to glycoside hydrolase family 3 and is predicted to function as a β-glucosidase.

Objectives: We investigated the catalytic properties of the E. coli protein BglX and identified two functionally important amino acid residues.

Methods: The bglX gene was cloned into a pET20b(+) vector, and three mutants, D111N, D287G, and E293Q, were generated using site-directed mutagenesis. Kinetic studies were performed on the wild-type and mutant enzymes.

Results: Substrate specificity tests indicated that the BglX enzyme hydrolyzes β-glycosidic bonds in nitrophenyl-β-glycosides and demonstrates greater activity towards galactose-containing substrates compared to glucose derivatives. Monomeric glucose and galactose inhibit enzyme activity to a different degree in a substrate-dependent manner. In addition, BglX can hydrolyze lactose but not cellobiose, maltose, or laminarin. Subsequently, E. coli cells overexpressing active BglX have a growth advantage on minimal media supplemented with lactose as a carbon source. Mutation of D287 or D111 residues negatively affected the activity of BglX indicating their involvement in catalysis. Overexpression of BglX by E. coli cells did not increase biofilm formation.

Conclusions: The low activity towards glucose-containing substrates and significantly elevated activity towards galactosides suggests that β-glucosidase activity may not be the primary function of the BglX enzyme.

背景:碳水化合物结构和连接的多样性需要多种负责糖降解的酶。由bglX基因编码的大肠杆菌周质蛋白已被归属于糖苷水解酶家族3,并被预测为β-葡糖苷酶。目的:我们研究了大肠杆菌蛋白bglX的催化特性,并鉴定了两个具有重要功能的氨基酸残基。方法:将bglX基因克隆到pET20b(+)载体中,通过定点诱变产生三个突变体D111N、D287G和E293Q。对野生型和突变型酶进行了动力学研究。结果:底物特异性测试表明,与葡萄糖衍生物相比,BglX酶水解硝基苯基-β-糖苷中的β-糖苷键,并对含半乳糖的底物表现出更大的活性。单体葡萄糖和半乳糖以底物依赖的方式在不同程度上抑制酶活性。此外,BglX可以水解乳糖,但不能水解纤维二糖、麦芽糖或昆布蛋白。随后,过表达活性BglX的大肠杆菌细胞在补充有乳糖作为碳源的最小培养基上具有生长优势。D287或D111残基的突变对BglX的活性产生负面影响,表明它们参与了催化作用。大肠杆菌细胞过表达BglX不会增加生物膜的形成。结论:对含葡萄糖底物的活性较低,对半乳糖苷的活性显著升高,这表明β-葡萄糖苷酶活性可能不是BglX酶的主要功能。
{"title":"Periplasmic β-glucosidase BglX from <i>E. coli</i> demonstrates greater activity towards galactose-containing substrates.","authors":"Lorna Ngo,&nbsp;Joshua Weimer,&nbsp;Li Sui,&nbsp;Tara Pickens,&nbsp;Nina V Stourman","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>The diverse nature of carbohydrate structures and linkages requires a variety of enzymes responsible for sugar degradation. The <i>E. coli</i> periplasmic protein encoded by the <i>bglX</i> gene has been assigned to glycoside hydrolase family 3 and is predicted to function as a β-glucosidase.</p><p><strong>Objectives: </strong>We investigated the catalytic properties of the <i>E. coli</i> protein BglX and identified two functionally important amino acid residues.</p><p><strong>Methods: </strong>The <i>bglX</i> gene was cloned into a pET20b(+) vector, and three mutants, D111N, D287G, and E293Q, were generated using site-directed mutagenesis. Kinetic studies were performed on the wild-type and mutant enzymes.</p><p><strong>Results: </strong>Substrate specificity tests indicated that the BglX enzyme hydrolyzes β-glycosidic bonds in nitrophenyl-β-glycosides and demonstrates greater activity towards galactose-containing substrates compared to glucose derivatives. Monomeric glucose and galactose inhibit enzyme activity to a different degree in a substrate-dependent manner. In addition, BglX can hydrolyze lactose but not cellobiose, maltose, or laminarin. Subsequently, <i>E. coli</i> cells overexpressing active BglX have a growth advantage on minimal media supplemented with lactose as a carbon source. Mutation of D287 or D111 residues negatively affected the activity of BglX indicating their involvement in catalysis. Overexpression of BglX by <i>E. coli</i> cells did not increase biofilm formation.</p><p><strong>Conclusions: </strong>The low activity towards glucose-containing substrates and significantly elevated activity towards galactosides suggests that β-glucosidase activity may not be the primary function of the BglX enzyme.</p>","PeriodicalId":94044,"journal":{"name":"International journal of biochemistry and molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10509532/pdf/ijbmb0014-0076.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41151064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Association of eating disorders with glycaemic control and insulin resistance in patients of type 2 diabetes mellitus. 2型糖尿病患者饮食失调与血糖控制和胰岛素抵抗的关系。
Pub Date : 2023-08-15 eCollection Date: 2023-01-01
Akshay Kumar, Sana Alam, Shazia Bano, Rashmi Prakash, Vineet Jain

Background: There is insufficient data on the prevalence and consequences of eating disorders in Type 2 diabetic patients.

Objective: To evaluate the presence of eating disorders (ED) and their association with glycaemic control and metabolic parameters in adult patients with type 2 diabetes mellitus (T2DM).

Materials and methods: A cross-sectional study on 145 patients was conducted in the medicine outpatient unit of HAHC Hospital, Jamia Hamdard tertiary care center. The Eating Attitudes Test (EAT-26) was used to screen for ED in adults with T2DM. The Score of less than 20 and more than 30 on EAT-26 questionnaire was defined as control for participants and relevant medical details like duration of treatment, glycaemic control, complications were recorded.

Results: A total of 145 diabetic individuals participated in this study. Out of these, 17.3% of individuals with T2DM screened positive for ED on EAT-26 scale and had a significant positive correlation in <20 groups and a significant negative correlation in >30 groups.

Conclusion: Our study reveals that eating disorders are not very common in our clinical population of T2DM, the prevalence rates of eating disorders are lower in patients with T2DM than those reported from developed western countries.

背景:关于2型糖尿病患者饮食失调的患病率和后果的数据不足。目的:评估成年2型糖尿病(T2DM)患者饮食障碍(ED)的存在及其与血糖控制和代谢参数的关系。材料和方法:在Jamia Hamdard三级护理中心HAHC医院的内科门诊部对145名患者进行了横断面研究。饮食态度测试(EAT-26)用于筛查成人T2DM患者的ED。EAT-26问卷的得分小于20和大于30被定义为参与者的对照,并记录相关的医疗细节,如治疗时间、血糖控制、并发症。结果:共有145名糖尿病患者参与了这项研究。其中,17.3%的T2DM患者在EAT-26量表上ED筛查呈阳性,在30组中呈显著正相关。结论:我们的研究表明,饮食障碍在我国T2DM临床人群中并不常见,T2DM患者的饮食障碍患病率低于西方发达国家。
{"title":"Association of eating disorders with glycaemic control and insulin resistance in patients of type 2 diabetes mellitus.","authors":"Akshay Kumar,&nbsp;Sana Alam,&nbsp;Shazia Bano,&nbsp;Rashmi Prakash,&nbsp;Vineet Jain","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>There is insufficient data on the prevalence and consequences of eating disorders in Type 2 diabetic patients.</p><p><strong>Objective: </strong>To evaluate the presence of eating disorders (ED) and their association with glycaemic control and metabolic parameters in adult patients with type 2 diabetes mellitus (T2DM).</p><p><strong>Materials and methods: </strong>A cross-sectional study on 145 patients was conducted in the medicine outpatient unit of HAHC Hospital, Jamia Hamdard tertiary care center. The Eating Attitudes Test (EAT-26) was used to screen for ED in adults with T2DM. The Score of less than 20 and more than 30 on EAT-26 questionnaire was defined as control for participants and relevant medical details like duration of treatment, glycaemic control, complications were recorded.</p><p><strong>Results: </strong>A total of 145 diabetic individuals participated in this study. Out of these, 17.3% of individuals with T2DM screened positive for ED on EAT-26 scale and had a significant positive correlation in <20 groups and a significant negative correlation in >30 groups.</p><p><strong>Conclusion: </strong>Our study reveals that eating disorders are not very common in our clinical population of T2DM, the prevalence rates of eating disorders are lower in patients with T2DM than those reported from developed western countries.</p>","PeriodicalId":94044,"journal":{"name":"International journal of biochemistry and molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10509534/pdf/ijbmb0014-0040.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41180731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Assessing the impact of meta-genomic tools on current cutting-edge genome engineering and technology. 评估元基因组工具对当前尖端基因组工程和技术的影响。
Pub Date : 2023-08-15 eCollection Date: 2023-01-01
Tuward J Dweh, Subhashree Pattnaik, Jyoti Prakash Sahoo
<p><p>Metagenomics is defined as the study of the genome of the total microbiota found in nature and is often referred to as microbial environmental genomics because it entails the examination of a group of genetic components (genomes) from a diverse community of organisms in a particular setting. It is a sub-branch of omics technology that encompasses Deoxyribonucleic Acid (DNA), Ribonucleic acid (DNA), proteins, and various components associated with comprehensive analysis of all aspects of biological molecules in a system-wide manner. Clustered regularly interspaced palindromic repeats and its endonuclease, CRISPR-associated protein which forms a complex called CRISPR-cas9 technology, though it is a different technique used to make precise changes to the genome of an organism, it can be used in conjunction with metagenomic approaches to give a better, rapid, and more accurate description of genomes and sequence reads. There have been ongoing improvements in sequencing that have deepened our understanding of microbial genomes forever. From the time when only a small amount of gene could be sequenced using traditional methods (e.g., "the plus and minus" method developed by Allan and Sanger and the "chemical cleavage" method that is known for its use in the sequencing the phiX174 bacteriophage genome via radio-labeled DNA polymerase-primer in a polymerization reaction aided by polyacrylamide gel) to the era of total genomes sequencing which includes "sequencing-by-ligation" and the "sequencing-by-synthesis" that detects hydrogen ions when new DNA is synthesized (Second Generation) and then Next Generation Sequencing technologies (NGS). With these technologies, the Human Genome Project (HGP) was made possible. The study looks at recent advancements in metagenomics in plants and animals by examining findings from randomly selected research papers. All selected case studies examined the functional and taxonomical analysis of different microbial communities using high-throughput sequencing to generate different sequence reads. In animals, five studies indicated how Zebrafish, Livestock, Poultry, cattle, niches, and the human microbiome were exploited using environmental samples, such as soil and water, to identify microbial communities and their functions. It has also been used to study the microbiome of humans and other organisms, including gut microbiomes. Recent studies demonstrated how these technologies have allowed for faster and more accurate identification of pathogens, leading to improved disease diagnostics. They have also enabled the development of personalized medicine by allowing for the identification of genetic variations that can impact drug efficacy and toxicity. Continued advancements in sequencing techniques and the refinement of CRISPR-Cas9 tools offer even greater potential for transformative breakthroughs in scientific research and applications. On the other hand, metagenomic data are always large and uneasy to handle. The compl
宏基因组学被定义为对自然界中发现的总微生物群基因组的研究,通常被称为微生物环境基因组学,因为它需要检查特定环境中来自不同生物群落的一组遗传成分(基因组)。它是组学技术的一个分支,包括脱氧核糖核酸(DNA)、核糖核酸(脱氧核糖核酸)、蛋白质和各种成分,以全系统的方式对生物分子的各个方面进行综合分析。聚集的规则间隔的回文重复序列及其核酸内切酶,CRISPR相关蛋白,形成了一种称为CRISPR-cas9技术的复合物,尽管这是一种用于对生物体基因组进行精确改变的不同技术,但它可以与宏基因组方法相结合,对基因组和序列读取进行更好、快速、更准确的描述。测序技术的不断进步,永远加深了我们对微生物基因组的理解。从使用传统方法只能对少量基因进行测序的时代(例如,Allan和Sanger开发的“正负”方法,以及以在聚丙烯酰胺凝胶辅助的聚合反应中通过放射性标记的DNA聚合酶引物对phiX174噬菌体基因组进行测序而闻名的“化学切割”方法)到全基因组时代测序,包括“连接测序”和“合成测序”,在合成新DNA时检测氢离子(第二代),然后是下一代测序技术(NGS)。有了这些技术,人类基因组计划(HGP)成为可能。这项研究通过检查随机选择的研究论文的发现,着眼于植物和动物宏基因组学的最新进展。所有选定的案例研究都使用高通量测序来产生不同的序列读数,检查了不同微生物群落的功能和分类分析。在动物方面,五项研究表明,斑马鱼、牲畜、家禽、牛、生态位和人类微生物组是如何利用土壤和水等环境样本来识别微生物群落及其功能的。它还被用于研究人类和其他生物的微生物组,包括肠道微生物组。最近的研究表明,这些技术可以更快、更准确地识别病原体,从而改善疾病诊断。他们还通过识别可能影响药物疗效和毒性的基因变异,促进了个性化药物的发展。测序技术的持续进步和CRISPR-Cas9工具的改进为科学研究和应用的变革性突破提供了更大的潜力。另一方面,宏基因组数据总是庞大且难以处理。分类谱、功能注释和复杂相互作用机制的复杂性仍然需要更好的生物信息学工具。目前的综述集中在更好的(例如,人工智能驱动的算法)工具上,这些工具可以预测代谢途径和相互作用,并操纵复杂的数据来解决准确解释的潜在偏差。
{"title":"Assessing the impact of meta-genomic tools on current cutting-edge genome engineering and technology.","authors":"Tuward J Dweh, Subhashree Pattnaik, Jyoti Prakash Sahoo","doi":"","DOIUrl":"","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Metagenomics is defined as the study of the genome of the total microbiota found in nature and is often referred to as microbial environmental genomics because it entails the examination of a group of genetic components (genomes) from a diverse community of organisms in a particular setting. It is a sub-branch of omics technology that encompasses Deoxyribonucleic Acid (DNA), Ribonucleic acid (DNA), proteins, and various components associated with comprehensive analysis of all aspects of biological molecules in a system-wide manner. Clustered regularly interspaced palindromic repeats and its endonuclease, CRISPR-associated protein which forms a complex called CRISPR-cas9 technology, though it is a different technique used to make precise changes to the genome of an organism, it can be used in conjunction with metagenomic approaches to give a better, rapid, and more accurate description of genomes and sequence reads. There have been ongoing improvements in sequencing that have deepened our understanding of microbial genomes forever. From the time when only a small amount of gene could be sequenced using traditional methods (e.g., \"the plus and minus\" method developed by Allan and Sanger and the \"chemical cleavage\" method that is known for its use in the sequencing the phiX174 bacteriophage genome via radio-labeled DNA polymerase-primer in a polymerization reaction aided by polyacrylamide gel) to the era of total genomes sequencing which includes \"sequencing-by-ligation\" and the \"sequencing-by-synthesis\" that detects hydrogen ions when new DNA is synthesized (Second Generation) and then Next Generation Sequencing technologies (NGS). With these technologies, the Human Genome Project (HGP) was made possible. The study looks at recent advancements in metagenomics in plants and animals by examining findings from randomly selected research papers. All selected case studies examined the functional and taxonomical analysis of different microbial communities using high-throughput sequencing to generate different sequence reads. In animals, five studies indicated how Zebrafish, Livestock, Poultry, cattle, niches, and the human microbiome were exploited using environmental samples, such as soil and water, to identify microbial communities and their functions. It has also been used to study the microbiome of humans and other organisms, including gut microbiomes. Recent studies demonstrated how these technologies have allowed for faster and more accurate identification of pathogens, leading to improved disease diagnostics. They have also enabled the development of personalized medicine by allowing for the identification of genetic variations that can impact drug efficacy and toxicity. Continued advancements in sequencing techniques and the refinement of CRISPR-Cas9 tools offer even greater potential for transformative breakthroughs in scientific research and applications. On the other hand, metagenomic data are always large and uneasy to handle. The compl","PeriodicalId":94044,"journal":{"name":"International journal of biochemistry and molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10509535/pdf/ijbmb0014-0062.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41165201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Apolipoprotein M gene polymorphisms in childhood-onset type 1 diabetes in southern Brazil. 巴西南部儿童期1型糖尿病患者载脂蛋白M基因多态性。
Pub Date : 2023-08-15 eCollection Date: 2023-01-01
Susan Webber de Souza, Mateus Santana Lopes, Bruna Rodrigues Martins, Manoella Abrão da Costa, Suzana Nesi-França, Graciele Cristiane More Manica, Angelica Beate Winter Boldt, Alexessander Couto Alves, Vivian Rotuno Moure, Glaucio Valdameri, Geraldo Picheth, Fabiane Gomes de Moraes Rego

Type 1 diabetes mellitus (T1DM), associated with autoimmune destruction of pancreatic β cells, is observed in children and adolescents.

Objective: We investigated the potential association of the apolipoprotein M (APOM) polymorphisms rs707921, rs805264, rs805296, rs805297, and rs9404941 in childhood-onset T1DM (n = 144) and compared them to those in healthy (mostly Euro-Brazilian) children (n = 168).

Methods: This project was approved by the Ethics Committee of the Federal University of Parana (CAAE 24676613.6.0000.0102). Genotyping was performed using PCR-restriction fragment length polymorphisms (rs805296 and rs9404941) and TaqMan probes (rs707921, rs805264, and rs805297).

Results: All polymorphisms were in Hardy-Weinberg equilibrium. In the codominant model, no significant differences (P > 0.05) were observed in genotype and allele frequencies between healthy controls and children with T1DM. The minor allele frequencies (95% CI) for healthy subjects were rs707921 (A, 10.7%; 7-14%), rs805264 (A, 6.5%; 4-9%), rs805296 (C, 3.6%; 2-6%), rs805297 (A, 22.6%; 22-31%), and rs9404941 (C, 2.7%; 1-4%). The frequencies of the rs805297 A allele and rs805296 C allele were similar to those of other Caucasian populations; both the rs707921 and rs805264 A alleles were similar to American and Latin American populations, whereas that of the rs9404941 C allele was lower than that observed in the Caucasian and Asian populations.

Conclusions: Haplotype analysis suggests that rs805297-C, rs9404941-T, rs805296-T, rs805264-G, and rs707921-C conferred risk (OR: 4.25; 95% CI: 1.81-10.1) to childhood-onset T1DM in the Euro-Brazilian population.

在儿童和青少年中观察到1型糖尿病(T1DM)与胰腺β细胞的自身免疫破坏有关。目的:探讨载脂蛋白M(APOM)基因多态性rs707921、rs805264、rs805296、rs806297、,和rs9404941,并将其与健康(主要是欧洲-巴西)儿童(n=168)进行比较(rs707921、rs805264和rs805297)。结果:所有多态性均处于Hardy-Weinberg平衡。在共显性模型中,健康对照组和T1DM儿童的基因型和等位基因频率没有显著差异(P>0.05)。健康受试者的次要等位基因频率(95%CI)为rs707921(A,10.7%;7-14%)、rs805264(A,6.5%;4-9%)、rs806296(C,3.6%;2-6%)、rs803297(A,22.6%;22-31%)和rs9404941(C,2.7%;1-4%)。rs805297 A等位基因和rs805296 C等位基因的频率与其他高加索人群相似;rs707921和rs805264A等位基因均与美洲和拉丁美洲人群相似,而rs9404941C等位基因的等位基因低于高加索和亚洲人群。结论:单倍型分析表明,在欧洲-巴西人群中,rs805297-C、rs9404941-T、rs805296-T、rs805264-G和rs707921-C赋予儿童期发作性T1DM的风险(OR:4.25;95%CI:1.81-10.1)。
{"title":"Apolipoprotein M gene polymorphisms in childhood-onset type 1 diabetes in southern Brazil.","authors":"Susan Webber de Souza, Mateus Santana Lopes, Bruna Rodrigues Martins, Manoella Abrão da Costa, Suzana Nesi-França, Graciele Cristiane More Manica, Angelica Beate Winter Boldt, Alexessander Couto Alves, Vivian Rotuno Moure, Glaucio Valdameri, Geraldo Picheth, Fabiane Gomes de Moraes Rego","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Type 1 diabetes mellitus (T1DM), associated with autoimmune destruction of pancreatic β cells, is observed in children and adolescents.</p><p><strong>Objective: </strong>We investigated the potential association of the apolipoprotein M (<i>APOM</i>) polymorphisms rs707921, rs805264, rs805296, rs805297, and rs9404941 in childhood-onset T1DM (<i>n</i> = 144) and compared them to those in healthy (mostly Euro-Brazilian) children (<i>n</i> = 168).</p><p><strong>Methods: </strong>This project was approved by the Ethics Committee of the Federal University of Parana (CAAE 24676613.6.0000.0102). Genotyping was performed using PCR-restriction fragment length polymorphisms (rs805296 and rs9404941) and TaqMan probes (rs707921, rs805264, and rs805297).</p><p><strong>Results: </strong>All polymorphisms were in Hardy-Weinberg equilibrium. In the codominant model, no significant differences (<i>P</i> > 0.05) were observed in genotype and allele frequencies between healthy controls and children with T1DM. The minor allele frequencies (95% CI) for healthy subjects were rs707921 (A, 10.7%; 7-14%), rs805264 (A, 6.5%; 4-9%), rs805296 (C, 3.6%; 2-6%), rs805297 (A, 22.6%; 22-31%), and rs9404941 (C, 2.7%; 1-4%). The frequencies of the rs805297 A allele and rs805296 C allele were similar to those of other Caucasian populations; both the rs707921 and rs805264 A alleles were similar to American and Latin American populations, whereas that of the rs9404941 C allele was lower than that observed in the Caucasian and Asian populations.</p><p><strong>Conclusions: </strong>Haplotype analysis suggests that rs805297-C, rs9404941-T, rs805296-T, rs805264-G, and rs707921-C conferred risk (OR: 4.25; 95% CI: 1.81-10.1) to childhood-onset T1DM in the Euro-Brazilian population.</p>","PeriodicalId":94044,"journal":{"name":"International journal of biochemistry and molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10509533/pdf/ijbmb0014-0051.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41158688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effect of methanolic crude extract of Aframomum melegueta (A.m) seeds on selected lactogenic hormones of Albino rats. Aframomum melegueta(A.m.)种子甲醇粗提取物对白化大鼠某些泌乳激素的影响
Pub Date : 2019-06-15 eCollection Date: 2019-01-01
Hyacinth Ibekwe

The search for alternative control of excessive milk secretion associated with exclusive breast feeding necessitated this study. This study was designed to investigate the effect of methanolic crude extract of Aframomum melegueta (A.m) seed by measuring serum concentrations of selected lactogenic (prolactin, estradiol and progesterone) hormones in lactating and non-lactating Albino rats. A total of 18 non-lactating and lactating rats each were assigned into three (3) treatments of 6 rats each. Treatment 1 and 2 (controls) received 0.11 mg/kg/day of reference drug (bromocriptine) and 100 mg/kg/day of Dimethylsulfoxide (Dmso) 1 ml:9 ml of normal saline which is referred to as normal control in this study. Treatment 3 received 100 mg/kg/day of A.m methanolic crude extract. Serum samples were collected and analyzed for prolactin, estradiol and progesterone by ELISA techniques. The result obtained showed a 21.13% and 25.12% significant (P<0.05) reduction in serum concentration of prolactin for both non-lactating (26.15±0.15 ng/ml) and lactating (14.90±1.16 ng/ml) rats relative to (33.23±1.82 and 19.90±1.16 ng/ml) normal control rats but a significant (P<0.05) increase (26.15±0.15 ng/ml; 14.90±1.16 ng/ml) in serum levels of the same hormone relative to (12.56±0.89 ng/ml; 10.56±0.29 ng/ml) reference control drug (bromocriptine) in both groups. Serum estradiol levels were significantly (P<0.05) reduced by methanol extract relative to normal control rats in both groups. There was however, no significant (P>0.05) changes in serum levels of estradiol relative to reference control drugs in both rats. Serum levels of progesterone were not significantly altered in both groups relative to normal control rats. The above findings confer on the extract antilactogenic capability and hence a good alternative to bromocriptine.

为了寻找控制纯母乳喂养引起的乳汁分泌过多的替代方法,有必要进行这项研究。本研究旨在通过测量哺乳期和非哺乳期白化大鼠血清中某些泌乳激素(催乳素、雌二醇和黄体酮)的浓度,研究 Aframomum melegueta(A.m.)种子甲醇粗提取物的作用。总共 18 只非哺乳期和哺乳期大鼠被分成三(3)个处理,每个处理 6 只大鼠。处理 1 和处理 2(对照组)接受 0.11 毫克/千克/天的参考药物(溴隐亭)和 100 毫克/千克/天的二甲基亚砜(Dmso),1 毫升:9 毫升生理盐水,即本研究中的正常对照组。处理 3 接受 100 毫克/千克/天的 A.m 甲醇粗提取物。收集血清样本并通过 ELISA 技术分析催乳素、雌二醇和孕酮。结果显示,与参考对照药物相比,两只大鼠血清中的雌二醇水平分别有 21.13% 和 25.12% 的显著变化(P0.05)。与正常对照组相比,两组大鼠血清中的孕酮水平均无明显变化。上述研究结果表明,该提取物具有抗泌乳能力,因此是溴隐亭的良好替代品。
{"title":"Effect of methanolic crude extract of Aframomum melegueta (A.m) seeds on selected lactogenic hormones of Albino rats.","authors":"Hyacinth Ibekwe","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The search for alternative control of excessive milk secretion associated with exclusive breast feeding necessitated this study. This study was designed to investigate the effect of methanolic crude extract of Aframomum melegueta (A.m) seed by measuring serum concentrations of selected lactogenic (prolactin, estradiol and progesterone) hormones in lactating and non-lactating Albino rats. A total of 18 non-lactating and lactating rats each were assigned into three (3) treatments of 6 rats each. Treatment 1 and 2 (controls) received 0.11 mg/kg/day of reference drug (bromocriptine) and 100 mg/kg/day of Dimethylsulfoxide (Dmso) 1 ml:9 ml of normal saline which is referred to as normal control in this study. Treatment 3 received 100 mg/kg/day of A.m methanolic crude extract. Serum samples were collected and analyzed for prolactin, estradiol and progesterone by ELISA techniques. The result obtained showed a 21.13% and 25.12% significant (P<0.05) reduction in serum concentration of prolactin for both non-lactating (26.15±0.15 ng/ml) and lactating (14.90±1.16 ng/ml) rats relative to (33.23±1.82 and 19.90±1.16 ng/ml) normal control rats but a significant (P<0.05) increase (26.15±0.15 ng/ml; 14.90±1.16 ng/ml) in serum levels of the same hormone relative to (12.56±0.89 ng/ml; 10.56±0.29 ng/ml) reference control drug (bromocriptine) in both groups. Serum estradiol levels were significantly (P<0.05) reduced by methanol extract relative to normal control rats in both groups. There was however, no significant (P>0.05) changes in serum levels of estradiol relative to reference control drugs in both rats. Serum levels of progesterone were not significantly altered in both groups relative to normal control rats. The above findings confer on the extract antilactogenic capability and hence a good alternative to bromocriptine.</p>","PeriodicalId":94044,"journal":{"name":"International journal of biochemistry and molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141636187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
International journal of biochemistry and molecular biology
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1