International journal of biochemistry and molecular biology最新文献

{"title":"Role of BRCA1 and BRCA2 gene mutations in epithelial ovarian cancer in Indian population: a pilot study.","authors":"Shikha Sharma,&nbsp;Shalini Rajaram,&nbsp;Tusha Sharma,&nbsp;Neerja Goel,&nbsp;Sarla Agarwal,&nbsp;Basu Dev Banerjee","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Ovarian cancer is a silent killer as most patients have non-specific symptoms and usually present in advanced stage of the disease. It occurs due to certain genetic alterations and mutations namely founder mutations, 187delAG and 5385insC in BRCA1 and 6174delT in BRCA2 which are associated with specific family histories. These highly penetrant susceptibility genes responsible for approximately half of families containing 2 or more ovarian cancer cases account for less than 40% of the familial excess malignancy risk. The remaining risk may be due to single nucleotide polymorphisms (SNPs) which are single base change in a DNA sequence with usual alternatives of two possible nucleotides at a given position. Preliminary study involving 30 women with histologically proven epithelial ovarian cancer was conducted and their detailed genetic analysis was carried out. Regions of founder mutations on BRCA1 and BRCA2 were amplified and sequenced using primers designed based on 200 bp upstream and downstream regions of the mutation sites. Five sequence variants in BRCA1 were identified of which three novel sequence variants were found in 23 patients while in BRCA2, one novel sequence variant was found. The three founder mutations 187delAG, 5385insC in BRCA1 and 6174delT in BRCA2 were not seen in any of the subjects. </p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"5 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2014-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058959/pdf/ijbmb0005-0001.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32445777","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}

{"title":"Gene environment interaction in preterm delivery with special reference to organochlorine pesticide: a case control study.","authors":"Tusha Sharma,&nbsp;Basu Dev Banerjee,&nbsp;Md Mustafa,&nbsp;Kiran Guleria,&nbsp;Rafat S Ahmed,&nbsp;Ashok K Tripathi","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Objectives: </strong>To assess the Gene-Environmental interaction between maternal organochlorine pesticides (OCPs) level and CYP17 gene polymorphism with the risk of preterm delivery (PTD).</p><p><strong>Materials and methods: </strong>Maternal blood samples of hundred cases (n = 100) of PTD and of equal number of healthy controls were collected at the time of delivery. OCPs levels were estimated by Gas chromatography system equipped with electron capture detector and PCR-RFLP was used for polymorphic analysis of CYP17 gene.</p><p><strong>Results: </strong>Significantly (p < 0.05) higher levels of α-HCH, β-HCH, and γ-HCH were found in maternal blood samples of PTD cases as compared to controls. We did not found any significant difference in the frequency genotype distribution CYP17 gene in PTD cases as compared to controls. When gene environmental interaction between the CYP17 gene polymorphism and OCPs level was considered, a significant interaction was observed between ≥ 50th percentile of γ-HCH and CYP17 A1A1 (wild type) genotype.</p><p><strong>Conclusions: </strong>Higher levels of OCPs along with wild type state of CYP17 gene (A1A1) in women may be considered as an important etiological factor in 'idiopathic' PTD. The present study provides evidence that genetic variation and its interaction with the environmental exposure may increase the risk of PTD.</p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"4 4","pages":"209-14"},"PeriodicalIF":0.0,"publicationDate":"2013-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867707/pdf/ijbmb0004-0209.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31991207","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}

{"title":"Caenorhabditis elegans neuron degeneration and mitochondrial suppression caused by selected environmental chemicals.","authors":"Shaoyu Zhou,&nbsp;Zemin Wang,&nbsp;James E Klaunig","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Mitochondrial alterations have been documented for many years in the brains of Parkinson's disease (PD), a disorder that is characterized by the selective loss of dopamine neurons. Recent studies have demonstrated that Parkinson's disease-associated proteins are either present in mitochondria or translocated into mitochondria in response to stress, further reinforcing the importance of the mitochondrial function in the pathogenesis of Parkinson's disease. Exposure to environmental chemicals such as pesticides and heavy metals has been suggested as risk factors in the development of Parkinson's disease. It has been reported that a number of environmental agents including tobacco smoke and perfluorinated compounds, pesticides, as well as metals (Mn(2+) and Pb(2+)) modulate mitochondrial function. However the exact mechanism of mitochondrial alteration has not been defined in the context of the development and progression of Parkinson's disease. The complexity of the mammalian system has made it difficult to dissect the molecular components involved in the pathogenesis of Parkinson's disease. In the present study we used the nematode Caenorhabditis elegans (C. elegans) model of neuron degeneration and investigated the effect of environmental chemicals on mitochondrial biogenesis and mitochondrial gene regulation. Chronic exposure to low concentration (2 or 4 μM) of pesticide rotenone, resulted in significant loss of dopamine neuron in C. elegans, a classic feature of Parkinson's disease. We then determined if the rotenone-induced neuron degeneration is accompanied by a change in mitochondria biogenesis. Analysis of mitochondrial genomic replication by quantitative PCR showed a dramatic decrease in mitochondrial DNA (mtDNA) copies of rotenone-treated C. elegans compared to control. This decreased mitochondrial biogenesis occurred prior to the development of loss of dopamine neurons, and was persistent. The inhibition of mtDNA replication was also found in C. elegans exposed to another neuron toxicant Mn(2+) at the concentration 50 or 100 mM. We further examined the mitochondrial gene expression and found significant lower level of mitochondrial complex IV subunits COI and COII in C. elegans exposed to rotenone. These results demonstrate that environmental chemicals cause persistent suppression of mitochondrial biogenesis and mitochondrial gene expression, and suggest a critical role of modifying mitochondrial biogenesis in toxicants-induced neuron degeneration in C. elegans model. </p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"4 4","pages":"191-200"},"PeriodicalIF":0.0,"publicationDate":"2013-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867705/pdf/ijbmb0004-0191.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31991251","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}

{"title":"Structure of chitinase D from Serratia proteamaculans reveals the structural basis of its dual action of hydrolysis and transglycosylation.","authors":"Jogi Madhuprakash,&nbsp;Avinash Singh,&nbsp;Sanjit Kumar,&nbsp;Mau Sinha,&nbsp;Punit Kaur,&nbsp;Sujata Sharma,&nbsp;Appa R Podile,&nbsp;Tej P Singh","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Chitinases are known to hydrolyze chitin polymers into smaller chitooligosaccharides. Chitinase from bacterium Serratia proteamaculans (SpChiD) is found to exhibit both hydrolysis and transglycosylation activities. SpChiD belongs to family 18 of glycosyl hydrolases (GH-18). The recombinant SpChiD was crystallized and its three-dimensional structure was determined at 1.49 Å resolution. The structure was refined to an R-factor of 16.2%. SpChiD consists of 406 amino acid residues. The polypeptide chain of SpChiD adopts a (β/α)8 triosephosphate isomerase (TIM) barrel structure. SpChiD contains three acidic residues, Asp149, Asp151 and Glu153 as part of its catalytic scheme. While both Asp149 and Glu153 adopt single conformations, Asp151 is observed in two conformations. The substrate binding cleft is partially obstructed by a protruding loop, Asn30 - Asp42 causing a considerable reduction in the number of available subsites in the substrate binding site. The positioning of loop, Asn30 - Asp42 appears to be responsible for the transglycosylation activity. The structure determination indicated the presence of sulfone Met89 (SMet89). The sulfone methionine residue is located on the surface of the protein at a site where extra domain is attached in other chitinases. This is the first structure of a single domain chitinase with hydrolytic and transglycosylation activities. </p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"4 4","pages":"166-78"},"PeriodicalIF":0.0,"publicationDate":"2013-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867703/pdf/ijbmb0004-0166.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31991249","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}

{"title":"Insert sequence length determines transfection efficiency and gene expression levels in bicistronic mammalian expression vectors.","authors":"Andrew J Payne,&nbsp;Bryan C Gerdes,&nbsp;Simon Kaja,&nbsp;Peter Koulen","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Bicistronic expression vectors have been widely used for co-expression studies since the initial discovery of the internal ribosome entry site (IRES) about 25 years ago. IRES sequences allow the 5' cap-independent initiation of translation of multiple genes on a single messenger RNA strand. Using a commercially available mammalian expression vector containing an IRES sequence with a 3' green fluorescent protein fluorescent marker, we found that sequence length of the gene of interest expressed 5' of the IRES site influences both expression of the 3' fluorescent marker and overall transfection efficiency of the vector construct. Furthermore, we generated a novel construct expressing two distinct fluorescent markers and found that high expression of one gene can lower expression of the other. Observations from this study indicate that caution is warranted in the design of experiments utilizing an IRES system with a short 5' gene of interest sequence (<300 bp), selection of single cells based on the expression profile of the 3' optogenetic fluorescent marker, and assumptions made during data analysis. </p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"4 4","pages":"201-8"},"PeriodicalIF":0.0,"publicationDate":"2013-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867706/pdf/ijbmb0004-0201.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31991252","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}

{"title":"Functions of the Hsp90 chaperone system: lifting client proteins to new heights.","authors":"Julia M Eckl,&nbsp;Klaus Richter","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The molecular chaperone Hsp90 is an essential protein in eukaryotic organisms and is highly conserved throughout all kingdoms of life. It serves as a platform for the folding and maturation of many client proteins including protein kinases and steroid hormone receptors. To fulfill this task Hsp90 performs conformational changes driven by the hydrolysis of ATP. Further, it can resort to a broad set of co-chaperones, which fit the Hsp90 machinery to the needs of specific client proteins. During the last years the number of identified co-chaperones has been consistently rising, implying that the client spectrum of Hsp90 may be much more diverse and larger than currently known. Many cofactors contain a TPR-domain for interactions at the C-terminus of Hsp90 and in many cases their functions and client sets remain to be uncovered. Hsp90 is also a putative target to interfere with cancerous and infectious diseases. Thus the knowledge on more of its cellular functions would provide also more therapeutic options for the future. In this review we compile the current knowledge on the Hsp90 ATPase mechanism, cofactor regulation and prospects of Hsp90 inhibition. </p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"4 4","pages":"157-65"},"PeriodicalIF":0.0,"publicationDate":"2013-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867702/pdf/ijbmb0004-0157.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31991248","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}

{"title":"Modulation of formation of the 3'-end of the human argininosuccinate synthetase mRNA by GT-repeat polymorphism.","authors":"Shih-Heng Tseng,&nbsp;Cheng-Yi Cheng,&nbsp;Miao-Zeng Huang,&nbsp;Ming-Yi Chung,&nbsp;Tsung-Sheng Su","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Microsatellites are abundant in the human genome and may acquire context-dependent functions. A highly polymorphic GT microsatellite is located downstream of the poly(A) signal of the human argininosuccinate synthetase (ASS1) gene. The ASS1 participates in urea and nitric oxide production and is a rate-limiting enzyme in arginine biosynthesis. To examine possible involvement of the GT microsatellite in ASS1 mRNA 3'-end formation, ASS1 minigene constructs were used in transient transfection for assessment of poly(A) site usage by S1 nuclease mapping. Synthesis of the major human ASS1 mRNA is found to be controlled by two consecutive non-canonical poly(A) signals, UAUAAA and AUUAAA, located 7 nucleotides apart where a U-rich sequence and the GU microsatellite serve as their respective downstream GU/U-rich elements. Moreover, AUUAAA utilization is affected by the GU-repeat number possibly leading to differential regulation of ASS1 polyadenylation in individuals with different repeat numbers. Interestingly, the less efficient UAUAAA motif is noted to be the major ASS1 poly(A) signal possibly as a result of an indispensable downstream U-rich element and restricted utilization of the AUUAAA motif by the presence of extended GU-repeats. The UAUAAA motif and the GT microsatellite are conserved only in primates whereas AUUAAA motif is present in all mammals analyzed. The suboptimal UAUAAA motif and the utilization of the polymorphic GT microsatellite as polyadenylation signal of the ASS1 gene may be used as a strategy in primates to modulate ASS1 level in response to interactions of genetic and environmental factors. </p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"4 4","pages":"179-90"},"PeriodicalIF":0.0,"publicationDate":"2013-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867704/pdf/ijbmb0004-0179.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31991250","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}

{"title":"Redundancy or specificity? The role of the CDK Pho85 in cell cycle control.","authors":"Javier Jiménez,&nbsp;Natalia Ricco,&nbsp;Carmen Grijota-Martínez,&nbsp;Rut Fadó,&nbsp;Josep Clotet","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>It is generally accepted that progression through the eukaryotic cell cycle is driven by cyclin-dependent kinases (CDKs), which are regulated by interaction with oscillatory expressed proteins called cyclins. CDKs may be separated into 2 categories: essential and non-essential. Understandably, more attention has been focused on essential CDKs because they are shown to control cell cycle progression to a greater degree. After clearly determining the basic and \"core\" mechanisms of essential CDKs, several questions arise. What role do non-essential CDKs play? Are these CDKs functionally redundant and do they serve as a mere backup? Or might they be responsible for some accessory tasks in cell cycle progression or control? In the present review we will try to answer these questions based on recent findings on the involvement of non-essential CDKs in cell cycle progression. We will analyse the most recent information with regard to these questions in the yeast Saccharomyces cerevisiae, a well-established eukaryotic model, and in its unique non-essential CDK involved in the cell cycle, Pho85. We will also briefly extend our discussion to higher eukaryotic systems. </p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"4 3","pages":"140-9"},"PeriodicalIF":0.0,"publicationDate":"2013-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776146/pdf/ijbmb0004-0140.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31744400","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}

{"title":"The role of calcium, NF-κB and NFAT in the regulation of CXCL8 and IL-6 expression in Jurkat T-cells.","authors":"Hazem Khalaf,&nbsp;Jana Jass,&nbsp;Per-Erik Olsson","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>T-cells play an important role in host immunity against invading pathogens. Determining the underlying regulatory mechanisms will provide a better understanding of T-cell-derived immune responses. In this study, we have shown the differential regulation of IL-6 and CXCL8 by NF-κB and NFAT in Jurkat T-cells, in response to PMA, heat killed Escherichia coli and calcium. CXCL8 was closely associated with the activation pattern of NFAT, while IL-6 expression was associated with NF-κB. Furthermore, increasing the intracellular Ca(2+) concentration by calcium ionophore treatment of the cells resulted in NFAT induction without affecting the NF-κB activity. Interestingly, NF-κB activation by heat killed E. coli, as well as CXCL8 and IL-6 expression was significantly suppressed following addition of the calcium ionophore. This indicates that calcium plays an important role in regulating protein trafficking and T-cell signalling, and the subsequent inflammatory gene expression infers an involvement of NFAT in CXCL8 regulation.Understanding these regulatory patterns provide clarification of conditions that involve altered intracellular signalling leading to T-cell-derived cytokine expression. </p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"4 3","pages":"150-6"},"PeriodicalIF":0.0,"publicationDate":"2013-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776147/pdf/ijbmb0004-0150.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31744401","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}

{"title":"Lactoperoxidase: structural insights into the function,ligand binding and inhibition.","authors":"Sujata Sharma,&nbsp;Amit Kumar Singh,&nbsp;Sanket Kaushik,&nbsp;Mau Sinha,&nbsp;Rashmi Prabha Singh,&nbsp;Pradeep Sharma,&nbsp;Harshverdhan Sirohi,&nbsp;Punit Kaur,&nbsp;Tej P Singh","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Lactoperoxidase (LPO) is a member of a large group of mammalian heme peroxidases that include myeloperoxidase (MPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). The LPO is found in exocrine secretions including milk. It is responsible for the inactivation of a wide range of micro-organisms and hence, is an important component of defense mechanism in the body. With the help of hydrogen peroxide, it catalyzes the oxidation of halides, pseudohalides and organic aromatic molecules. Historically, LPO was isolated in 1943, nearly seventy years ago but its three-dimensional crystal structure has been elucidated only recently. This review provides various details of this protein from its discovery to understanding its structure, function and applications. In order to highlight species dependent variations in the structure and function of LPO, a detailed comparison of sequence, structure and function of LPO from various species have been made. The structural basis of ligand binding and distinctions in the modes of binding of substrates and inhibitors have been analyzed extensively. </p>","PeriodicalId":13891,"journal":{"name":"International journal of biochemistry and molecular biology","volume":"4 3","pages":"108-28"},"PeriodicalIF":0.0,"publicationDate":"2013-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776144/pdf/ijbmb0004-0108.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31744479","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}