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Wahyuni DK, Indriati DT, Ilham M, Murtadlo AAA, Purnobasuki H, Junairiah, Purnama PR, Ikram NKK, Samian MZ, Subramaniam S. Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L. BRAZ J BIOL 2024; 84:e278393. [PMID: 38422290 DOI: 10.1590/1519-6984.278393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/06/2024] [Indexed: 03/02/2024] Open
Abstract
Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.
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Affiliation(s)
- D K Wahyuni
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - D T Indriati
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - M Ilham
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - A A A Murtadlo
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - H Purnobasuki
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - Junairiah
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - P R Purnama
- Chulalongkorn University, Faculty of Science, Graduate Program in Bioinformatics and Computational Biology, Bangkok, Thailand
| | - N K K Ikram
- Universiti Malaya, Faculty of Science, Institute of Biological Sciences, Kuala Lumpur, Malaysia
- Universiti Malaya, Centre for Research in Biotechnology for Agriculture - CEBAR, Kuala Lumpur, Malaysia
| | - M Z Samian
- Universiti Malaya, Faculty of Science, Institute of Biological Sciences, Kuala Lumpur, Malaysia
- Universiti Malaya, Centre for Research in Biotechnology for Agriculture - CEBAR, Kuala Lumpur, Malaysia
| | - S Subramaniam
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
- Universiti Sains Malaysia, School of Biological Science, Georgetown, Malaysia
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2
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Schactler SA, Scheuerman SJ, Lius A, Altemeier WA, An D, Matula TJ, Mikula M, Kulecka M, Denisenko O, Mar D, Bomsztyk K. CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis. BMC Genomics 2023; 24:446. [PMID: 37553584 PMCID: PMC10408117 DOI: 10.1186/s12864-023-09527-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Disease molecular complexity requires high throughput workflows to map disease pathways through analysis of vast tissue repositories. Great progress has been made in tissue multiomics analytical technologies. To match the high throughput of these advanced analytical platforms, we have previously developed a multipurpose 96-well microplate sonicator, PIXUL, that can be used in multiple workflows to extract analytes from cultured cells and tissue fragments for various downstream molecular assays. And yet, the sample preparation devices, such as PIXUL, along with the downstream multiomics analytical capabilities have not been fully exploited to interrogate tissues because storing and sampling of such biospecimens remain, in comparison, inefficient. RESULTS To mitigate this tissue interrogation bottleneck, we have developed a low-cost user-friendly system, CryoGrid, to catalog, cryostore and sample tissue fragments. TRIzol is widely used to isolate RNA but it is labor-intensive, hazardous, requires fume-hoods, and is an expensive reagent. Columns are also commonly used to extract RNA but they involve many steps, are prone to human errors, and are also expensive. Both TRIzol and column protocols use test tubes. We developed a microplate PIXUL-based TRIzol-free and column-free RNA isolation protocol that uses a buffer containing proteinase K (PK buffer). We have integrated the CryoGrid system with PIXUL-based PK buffer, TRIzol, and PureLink column methods to isolate RNA for gene-specific qPCR and genome-wide transcript analyses. CryoGrid-PIXUL, when integrated with either PK buffer, TRIzol or PureLink column RNA isolation protocols, yielded similar transcript profiles in frozen organs (brain, heart, kidney and liver) from a mouse model of sepsis. CONCLUSIONS RNA isolation using the CryoGrid-PIXUL system combined with the 96-well microplate PK buffer method offers an inexpensive user-friendly high throughput workflow to study transcriptional responses in tissues in health and disease as well as in therapeutic interventions.
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Affiliation(s)
- Scott A Schactler
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Stephen J Scheuerman
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Andrea Lius
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - William A Altemeier
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Center for Lung Biology, University of Washington, Seattle, WA, 98109, USA
| | - Dowon An
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Center for Lung Biology, University of Washington, Seattle, WA, 98109, USA
| | - Thomas J Matula
- Center for Industrial and Medical Ultrasound, Applied Physics Laboratory, University of Washington, Seattle, WA, 98195, USA
- Matchstick Technologies, Inc, Kirkland, WA, 98033, USA
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, 01-813, Warsaw, Poland
| | - Oleg Denisenko
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
| | - Daniel Mar
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA.
- Matchstick Technologies, Inc, Kirkland, WA, 98033, USA.
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Zago VHS, Scherrer DZ, Parra ES, Vieira IC, Marson FAL, de Faria EC. Effects of SNVs in ABCA1, ABCG1, ABCG5, ABCG8, and SCARB1 Genes on Plasma Lipids, Lipoproteins, and Adiposity Markers in a Brazilian Population. Biochem Genet 2021; 60:822-841. [PMID: 34505223 DOI: 10.1007/s10528-021-10131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
Several proteins are involved in cholesterol homeostasis, as scavenger receptor class B type I and ATP-binding cassette (ABC) transporters including ABCA1, ABCG1, ABCG5, and ABCG8. This study aimed to determine the effects of single nucleotide variants (SNVs) rs2275543 (ABCA1), rs1893590 (ABCG1), rs6720173 (ABCG5), rs6544718 (ABCG8), and rs5888 (SCARB1) on plasma lipids, lipoproteins, and adiposity markers in an asymptomatic population and its sex-specific effects. Volunteers (n = 590) were selected and plasma lipids, lipoproteins, and adiposity markers (waist-to-hip and waist-to-height ratios, lipid accumulation product and body adiposity index) were measured. Genomic DNA was isolated from peripheral blood cells according to the method adapted from Gross-Bellard. SNVs were detected in the TaqMan® OpenArray® Real-Time polymerase chain reaction platform and data analyses were performed using the TaqMan® Genotyper Software. The rs2275543*C point to an increase of high-density lipoprotein size in females while in males very-low-density lipoprotein, cholesterol, and triglycerides were statistically lower (P value < 0.05). The rs1893590*C was statistically associated with lower apolipoprotein A-I levels and higher activities of paraoxonase-1 and cholesteryl ester transfer protein (P value < 0.05). The rs6720173 was statistically associated with an increase in cholesterol and low-density lipoprotein cholesterol in males; moreover, rs6544718*T reduced adiposity markers in females (P value < 0.05). Regarding the rs5888, a decreased adiposity marker in the total population and in females occurred (P value < 0.05). Multivariate analysis of variance showed that SNVs could influence components of high-density lipoprotein metabolism, mainly through ABCG1 (P value < 0.05). The ABCA1 and ABCG5 variants showed sex-specific effects on lipids and lipoproteins, while SCARB1 and ABCG8 variants might influence adiposity markers in females. Our data indicate a possible role of ABCG1 on HDL metabolism.
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Affiliation(s)
- Vanessa Helena Souza Zago
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Daniel Zanetti Scherrer
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Eliane Soler Parra
- Department of Cardiology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Isabela Calanca Vieira
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil. .,Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil. .,Laboratory of Human and Medical Genetics and Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, Post Graduate Program in Health Science, São Francisco University, Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.
| | - Eliana Cotta de Faria
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil.
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Fischer S, Stanke F, Tümmler B. VJ Segment Usage of TCR-Beta Repertoire in Monozygotic Cystic Fibrosis Twins. Front Immunol 2021; 12:599133. [PMID: 33708199 PMCID: PMC7940196 DOI: 10.3389/fimmu.2021.599133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/28/2021] [Indexed: 11/26/2022] Open
Abstract
Sixteen monozygotic cystic fibrosis (CF) twin pairs of whom 14 pairs were homozygous for the most common p.Phe508del CFTR mutation were selected from the European Cystic Fibrosis Twin and Sibling Study Cohort. The monozygotic twins were examined in their T cell receptor (TCR) repertoire in peripheral blood by amplicon sequencing of the CDR3 variable region of the ß-chain. The recruitment of TCR J and V genes for recombination and selection in the thymus showed a strong genetic influence in the CF twin cohort as indicated by the shortest Jensen-Shannon distance to the twin individual. Exceptions were the clinically most discordant and/or most severely affected twin pairs where clonal expansion probably caused by recurrent pulmonary infections overshadowed the impact of the identical genomic blueprint. In general the Simpson clonality was low indicating that the population of TCRß clonotypes of the CF twins was dominated by the naïve T-cell repertoire. Intrapair sharing of clonotypes was significantly more frequent among monozygotic CF twins than among pairs of unrelated CF patients. Complete nucleotide sequence identity was observed in about 0.11% of CDR3 sequences which partially should represent persisting fetal clones derived from the same progenitor T cells. Complete amino acid sequence identity was noted in 0.59% of clonotypes. Of the nearly 40,000 frequent amino acid clonotypes shared by at least two twin siblings 99.8% were already known within the immuneACCESS database and only 73 had yet not been detected indicating that the CDR3ß repertoire of CF children and adolescents does not carry a disease-specific signature but rather shares public clones with that of the non-CF community. Clonotypes shared within twin pairs and between unrelated CF siblings were highly abundant among healthy non-CF people, less represented in individuals with infectious disease and uncommon in patients with cancer. This subset of shared CF clonotypes defines CDR3 amino acid sequences that are more common in health than in disease.
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Affiliation(s)
- Sebastian Fischer
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Frauke Stanke
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
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5
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Discussion of the protein characterization techniques used in the identification of membrane protein targets corresponding to tumor cell aptamers. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.11.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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6
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Wu Y, Pan X, Jin X. Haplotype-based association study between PRCP gene polymorphisms and essential hypertension in Hani minority group from a remote region of China. J Renin Angiotensin Aldosterone Syst 2020; 21:1470320320981316. [PMID: 33319614 PMCID: PMC7745576 DOI: 10.1177/1470320320981316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objective: Prolylcarboxypeptidase (PRCP) is both involved in the Kallikrein-Kinin system (KKS) and renin-angiotensin-aldosterone system (RAAS). This study aimed to determine the genetic impact of PRCP gene polymorphisms on essential hypertension (EH) in an isolated population from a remote region of China. Methods: A haplotype-based study was investigated in 346 EH patients and 346 normal subjects and all samples were Hani minority residents in Southwest China. A total of 11 tag single nucleotide polymorphisms (SNPs) in PRCP gene were tested by polymerase chain reaction-restriction fragment length polymorphism method. Results: Single site analysis found that PRCP gene 3′UTR SNP rs3750931 was associated with EH. The minor allele G of rs3750931 was more prevalent in the EH patients compared to control subjects after Bonferroni correction (p < 0.05). Moreover, the rs3750931 G allele carriers showed higher average blood pressure (BP) level among the subjects. The H2 (GAGCACTAACA) haplotype without rs3750931 G allele showed the protective effect for EH (OR = 0.68, 95 CI 0.54–0.85, p = 0.001). Conclusion: The present study indicated PRCP gene rs3750931 was associated with the risk of EH. This SNP G allele could be considered as one of risk markers for EH in Hani population.
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Affiliation(s)
- Yanrui Wu
- School of Basic Medical Sciences, Kunming Medical University, Kunming, Yunnan Province, P. R. China
| | - Xingming Pan
- Human Resources Department of Kunming Medical University, Kunming, Yunnan Province, P. R. China
| | - Xiaoxiao Jin
- School of Basic Medical Sciences, Kunming Medical University, Kunming, Yunnan Province, P. R. China
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7
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Rahim M, Mas Haris MRH, Saqib NU. An overview of polymeric nano-biocomposites as targeted and controlled-release devices. Biophys Rev 2020; 12:1223-1231. [PMID: 32901426 DOI: 10.1007/s12551-020-00750-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
In recent years, controlled drug delivery has become an important area of research. Nano-biocomposites can fulfil the necessary requirements of a targeted drug delivery device. This review describes use of polymeric nano-biocomposites in controlled drug delivery devices. Selection of suitable biopolymer and methods of preparation are discussed.
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Affiliation(s)
- Muhammad Rahim
- School of Chemical Sciences, Universiti Sains Malaysia, 11800 Pulau Penang, Malaysia.
| | | | - Najm Us Saqib
- Department of Zoology, University of Buner, Buner, KP, Pakistan
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8
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Genetic Association of rs2237572 Cyclin-Dependent Kinase 6 Gene with Breast Cancer in Iraq. Indian J Clin Biochem 2020; 36:304-311. [PMID: 34220005 DOI: 10.1007/s12291-020-00895-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
Abstract
This case-control study is aimed to evaluate serum concentration of Cyclin-Dependent Kinase 6 (CDK6) and the genetic association between rs2237572 CDK6 gene and breast cancer (BC) in Iraq. To attain this goal, 80 patients with BC as cases and 80 healthy individuals as controls were included. Further, BC patients were sorted according to the molecular classification into four subtypes of Luminal A, Luminal B, Her2/neu enriched and TPN. Serum concentration of CDK6 enzyme, allelic and genotypic frequencies of rs2237572 CDK6, and the occurrence of BC phenotype and its subtypes in the studied population were investigated. ELISA technique was used to perform the biochemical testing, while the molecular analysis was achieved by real-time PCR, high resolution melting analysis, conventional PCR, as well as sequencing analysis. The results revealed no significant difference in serum concentration of CDK6 enzyme between patients and healthy controls (p > 0.05). Also, no significant differences were shown between BC patients subtypes (p > 0.05). The rs2237572 CDK6 genotypes were associated with the BC and affirmed that allele C was inherited as a recessive risk factor. Moreover, a highly significant difference between patients' subtypes in the genotypic frequency of rs2237572 (p < 0.01) was noted. Furthermore, the association of rs2237572 genotypes and CDK6 serum concentration in BC patients showed a considered significant difference between C/C and T/T, C/C and T/C and the CDK6 level (p < 0.05). Nevertheless, T/T and T/C did not show any significant difference with the CDK6 level. Hence, it was concluded that the rs2237572 of CDK6 gene is significantly correlated with BC.
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9
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Wu Y, Yang H, Xiao C. Genetic association study of prolylcarboxypeptidase polymorphisms with susceptibility to essential hypertension in the Yi minority of China: A case-control study based on an isolated population. J Renin Angiotensin Aldosterone Syst 2020; 21:1470320320919586. [PMID: 32448049 PMCID: PMC7249571 DOI: 10.1177/1470320320919586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Objective: Prolylcarboxypeptidase (PRCP) is a negative regulator of the pressor actions of the renin–angiotensin–aldosterone system. It is also involved in the kallikrein–kinin system. This gene has an important role in blood pressure (BP) regulation. Methods: A case–control study was performed for 615 Yi participants (303 cases and 312 controls) from a remote mountainous area in Yunnan Province of China. For the PRCP gene, 11 tag single-nucleotide polymorphisms were genotyped using the polymerase chain reaction-restriction fragment length polymorphism method. Results: The PRCP gene rs12290550 was associated with the occurrence of essential hypertension (EH) and BP traits. Logistic regression analysis indicated that the rs12290550 T allele was significantly linked to the risk of EH (odds ratio (OR) = 1.85, 95% confidence interval (CI) 1.44–2.39, p = 0.2 × 10−5). Under Bonferroni correction, the H7 TAGCACTAACA haplotype containing the risk allele rs12290550 T increased the risk of EH (OR = 4.53, 95% CI 2.29–8.93, p = 0.2×10−5). Conclusions: The findings of this study demonstrate the strong association of the PRCP gene with EH. rs12290550 may be a useful genetic predictor of EH in the Yi minority.
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Affiliation(s)
- Yanrui Wu
- Cell Biology and Genetics Department, Kunming Medical University, China.,School of Medicine, Yunnan University, China
| | - Hongju Yang
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, China
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10
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Zago VHS, Parra ES, Virgínio VWM, Vendrame F, Gomes ÉIL, Scherrer DZ, Marson FAL, de Faria EC. Lipase C, Hepatic Type -250A/G (rs2070895) Variant Enhances Carotid Atherosclerosis in Normolipidemic and Asymptomatic Individuals from Brazil. Lipids 2020; 55:225-237. [PMID: 32196671 DOI: 10.1002/lipd.12232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 02/20/2020] [Accepted: 02/27/2020] [Indexed: 11/08/2022]
Abstract
The common genetic variant in the promoter region of the hepatic lipase gene [LIPC -250G/A(rs2070895)] has an ambiguous association with cardiovascular disease. In this context, our study was performed to identify the relationships between the rs2070895 with carotid atherosclerosis, plasma lipids, and parameters of reverse cholesterol transport. A total of 285 normolipidemic and asymptomatic participants from an initial sample of 598,288 individuals (inclusion criteria: LDL-C ≤130 mg/dL and triglycerides ≤150 mg/dL; age: 20-75 years, both genders; confirmation of clinical, anthropometric and laboratory data; attended all visits; DNA was achieved to perform genetic analysis) were enrolled and the rs2070895 variant was genotyped by TaqMan® OpenArray® Plataform. Carotid intima-media thickness and the screening of atherosclerotic plaques were determined by B-mode ultrasonography. The rs2070895 genotype frequencies were 0.44, 0.41, and 0.15 (GG, GA, and AA, respectively). Logistic regression analysis showed that the risk of having plaques was increased in participants carrying the AA or AG genotypes (OR = 3.90; 95% CI = 1.54-10.33), despite an increase in high-density lipoprotein cholesterol levels, HDL diameter and apolipoprotein A-I, as compared to the GG genotype. Hepatic lipase and endogenous lecithin cholesterol acyl transferase activities were reduced (38% and 19%, respectively) and lipoprotein lipase was increased by 30% (AA vs GG). Our results provide evidence that the AA or AG genotypes of the rs2070895 were associated with carotid atherosclerosis in apparently healthy participants, probably as a consequence of reduced reverse cholesterol transport and accumulation of HDL subfraction 2 rich in triglycerides and depleted in cholesteryl esters that could become dysfunctional.
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Affiliation(s)
- Vanessa H S Zago
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Eliane S Parra
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Vítor W M Virgínio
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Felipe Vendrame
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Érica I L Gomes
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Daniel Z Scherrer
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Fernando A L Marson
- Department of Pediatric, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil.,Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil.,Laboratory of Human and Medical Genetics, Post Graduate Program in Health Science, São Francisco University, São Francisco de Assis Av, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil
| | - Eliana C de Faria
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
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11
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Peñafiel N, Flores DM, Rivero De Aguilar J, Guayasamin JM, Bonaccorso E. A cost-effective protocol for total DNA isolation from animal tissue. NEOTROPICAL BIODIVERSITY 2020. [DOI: 10.1080/23766808.2019.1706387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Nicolás Peñafiel
- Department of Biology, Memorial University of Newfoundland, St. John’s, Canada
| | - Diana M. Flores
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Juan Rivero De Aguilar
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Juan M. Guayasamin
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Universidad Tecnológica Indoamérica, Quito, Ecuador
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, and Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Elisa Bonaccorso
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Universidad Tecnológica Indoamérica, Quito, Ecuador
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, and Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
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12
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Zhou D, Chen Y, Wu J, Shen J, Shang Y, Zheng L, Xie X. Association between chymase gene polymorphisms and atrial fibrillation in Chinese Han population. BMC Cardiovasc Disord 2019; 19:321. [PMID: 31888494 PMCID: PMC6936049 DOI: 10.1186/s12872-019-01300-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 12/05/2019] [Indexed: 12/18/2022] Open
Abstract
Background Chymase is the major angiotensin II (Ang II)-forming enzyme in cardiovascular tissue, with an important role in atrial remodeling. This study aimed to examine the association between chymase 1 gene (CMA1) polymorphisms and atrial fibrillation (AF) in a Chinese Han population. Methods This case-control study enrolled 126 patients with lone AF and 120 age- and sex-matched healthy controls, all from a Chinese Han population. Five CMA1 polymorphisms were genotyped. Results The CMA1 polymorphism rs1800875 (G-1903A) was associated with AF. The frequency of the GG genotype was significantly higher in AF patients compared with controls (p = 0.009). Haplotype analysis further demonstrated an increased risk of AF associated with the rs1800875-G haplotype (Hap8 TGTTG, odds ratio (OR) = 1.668, 95% CI 1.132–2.458, p = 0.009), and a decreased risk for the rs1800875-A haplotype (Hap5 TATTG, OR = 0.178, 95% CI 0.042–0.749, p = 0.008). Conclusions CMA1 polymorphisms may be associated with AF, and the rs1800875 GG genotype might be a susceptibility factor for AF in the Chinese Han population.
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Affiliation(s)
- Dongchen Zhou
- Department of Cardiology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuewei Chen
- Department of Cardiology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiaxin Wu
- Department of Cardiology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiabo Shen
- Department of Cardiology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yushan Shang
- Department of Cardiology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Liangrong Zheng
- Department of Cardiology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xudong Xie
- Department of Cardiology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
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13
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Wang J, Zheng J, Zhang S, Du J, Chen Y, Liu X, Zhang H, Jiang X, Chen W. High-throughput blood sample preparation for single nucleotide polymorphism genotyping in less than 25 min. Talanta 2019; 191:119-125. [PMID: 30262040 DOI: 10.1016/j.talanta.2018.08.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/13/2018] [Accepted: 08/18/2018] [Indexed: 11/17/2022]
Abstract
Straightforward, rapid and high-throughput pretreatment for single nucleotide polymorphisms (SNP) genotyping is critically needed in clinical practice. However, all existing SNP genotyping methods require DNA purification step, which is labor-intensive and time-consuming. We develop a protocol for SNP genotyping by combining whole blood lysis (WBL) with qPCR and justify the practicality of our method in blood samples from 140 donors, including 40 samples from healthy donors, and 100 samples from donors with either low white blood cell counts, high level of serum uric acid or triglyceride. When compared with Sanger sequencing, the gold standard for SNP genotyping, our method exhibits a 100% consistency in the aspect of sensitivity and specificity. In addition, our method can obtain amplifiable DNA within 25 mins (which is the fastest to the best of our knowledge) from 48 samples. The blood samples, even with low white blood cell counts, high level of serum uric acid or triglyceride could not affect the sensitivity and specificity of our method. Our study demonstrates that the combination of WBL and qPCR genotyping can serve as a high-throughput and robust approach for routine clinical SNP genotyping.
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Affiliation(s)
- Jidong Wang
- Central Laboratory, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Jiaying Zheng
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Shaohua Zhang
- Department of Breast Cancer, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, PR China
| | - Jihui Du
- Central Laboratory, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Yongxin Chen
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Xiaolei Liu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Huisheng Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Xingyu Jiang
- Beijing Engineering Research Center for BioNanotechnology & Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing 100190, PR China.
| | - Wenwen Chen
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China.
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14
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Jauset-Rubio M, Tomaso H, El-Shahawi MS, Bashammakh AS, Al-Youbi AO, O'Sullivan CK. Duplex Lateral Flow Assay for the Simultaneous Detection of Yersinia pestis and Francisella tularensis. Anal Chem 2018; 90:12745-12751. [PMID: 30296053 DOI: 10.1021/acs.analchem.8b03105] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High-risk pathogens such as Francisella tularensis and Yersinia pestis are categorized as highly hazardous organisms that can be used as biological weapons. Given the extreme infectivity of these potential biowarfare agents, a rapid, sensitive, cost-effective, and specific method for their detection is required. Here, we report the multiplexed amplification detection of genomic DNA from Francisella tularensis and Yersinia pestis. Amplification was achieved using isothermal recombinase polymerase amplification, exploiting tailed primers, followed by detection using a nucleic-acid lateral flow assay. Excess primers were removed using a novel fishing strategy, avoiding the use of postamplification purification that requires centrifugation and infers additional assay cost. The entire assay is completed in less than 1 h, achieving limits of detection of 243 fg (1.21 × 102 genome equivalent) and 4 fg (0.85 genome equivalent) for Francisella tularensis and Yersinia pestis, respectively.
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Affiliation(s)
- Miriam Jauset-Rubio
- INTERFIBIO Consolidated Research Group, Department of Chemical Engineering , Universitat Rovira I Virgili , 43007 Tarragona , Spain
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses , Naumburger Strasse 96a , 07743 Jena , Germany
| | - Mohammad S El-Shahawi
- Department of Chemistry, Faculty of Science , King Abdulaziz University , P.O. Box 80203, Jeddah 21589 , Kingdom of Saudi Arabia
| | - Abdulaziz S Bashammakh
- Department of Chemistry, Faculty of Science , King Abdulaziz University , P.O. Box 80203, Jeddah 21589 , Kingdom of Saudi Arabia
| | - Abdulrahman O Al-Youbi
- Department of Chemistry, Faculty of Science , King Abdulaziz University , P.O. Box 80203, Jeddah 21589 , Kingdom of Saudi Arabia
| | - Ciara K O'Sullivan
- INTERFIBIO Consolidated Research Group, Department of Chemical Engineering , Universitat Rovira I Virgili , 43007 Tarragona , Spain.,Institució Catalana de Recerca I Estudis Avancats , Passeig Lluís Companys 23 , 08010 Barcelona , Spain
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15
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Basolo F, Elliott J, Russo J. Transfection of Human Breast Epithelial Cells with Foreign Dna Using Different Transfecting Techniques. TUMORI JOURNAL 2018; 76:455-60. [PMID: 2256190 DOI: 10.1177/030089169007600507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The introduction of DNA into eukaryotic cells is a powerful technique for the study of gene regulation. This requires both a technique by which genes can efficiently be introduced into cells and a recipient cell representative of the tissue under study. We have utilized a spontaneously immortalized human breast epithelial cell line, CMF-10, which is phenotypically normal for introducing a neomycin-resistant gene contained in the plasmid Homer 6 (pHo6). Three different transfection methods were tested: calcium phosphate, with and without glycerol shock, using as control NIH/3T3 cells, and strontium phosphate and electroporation. In MCF-10 cells the efficiency of calcium phosphate mediated DNA transfection, which was measured as the number of colonies growing in neomycin-containing medium, was 21 and 140 fold higher than in MCF-10 cells transfected by electroporation and strontium phosphate methods, respectively. Glycerol shock enhanced three fold transfection efficiencies. NIH/3T3 transfected cells by calcium phosphate method showed a transfection efficiency similar to that of MCF-10 cells, however, glycerol shock did not improve the efficiency. These studies revealed that calcium phosphate combined with glycerol shock is the most efficient technique for transfection of genomic DNA into human breast epithelial cells.
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Affiliation(s)
- F Basolo
- Istituto di Anatomia ed Istologia Patologica, Università di Pisa, Italy
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16
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Koebe H, Wick M, Cramer U, Lange V, Schildberg F. Collagen Gel Immobilisation Provides a Suitable Cell Matrix for Long Term Human Hepatocyte Cultures in Hybrid Reactors. Int J Artif Organs 2018. [DOI: 10.1177/039139889401700207] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
An easy to apply culture technique is presented that protects a monolayer configuration of liver cells within an extracellular matrix. The Immobilising Gel (IG)-Technique not only preserves hepatocyte morphology and supports a variety of differentiated cell functions over long term periods, but also offers higher resistance of IG-culture systems against shear forces of fluids in a hybrid reactor device, as compared to other culture techniques. Human hepatocyte cultures in IG-Technique: DNA-normalised levels for the total production of cholinesterase, albumin, urea and lactate remained high throughout the investigational period (50 days). Glutamic-Pyruvic-Transaminase (GPT) release decreased after peak values during early culture adaptation. Electron Microscopic (EM) findings after the shear forces experiment revealed undisturbed subcellular structures and a preserved intercellular morphology, including bile canaliculi and desmosomes. We conclude that the IG-technique is of considerable advantage as compared to other culture systems, especially in the field of dynamic applications, e.g. hybrid reactors for artificial organ development.
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Affiliation(s)
- H.G. Koebe
- Department of Surgery, Klinikum Grosshadern, L.M. University of Munich, Muenchen - Germany
| | - M. Wick
- Department of Surgery, Klinikum Grosshadern, L.M. University of Munich, Muenchen - Germany
| | - U. Cramer
- Department of Surgery, Klinikum Grosshadern, L.M. University of Munich, Muenchen - Germany
| | - V. Lange
- Department of Surgery, Klinikum Grosshadern, L.M. University of Munich, Muenchen - Germany
| | - F.W. Schildberg
- Department of Surgery, Klinikum Grosshadern, L.M. University of Munich, Muenchen - Germany
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17
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Wick M, Koebe H, Schildberg F. Extracorporeal Artificial Liver: The Influence of a Second Cell Layer on the Morphology and Function of Immobilized Human Hepatocytes. Int J Artif Organs 2018. [DOI: 10.1177/039139889601900707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hepatocytes in long-term cultures represent a promising approach to preserve liver function under standard culture conditions. Hepatocyte cultures as the key components in an extracorporeal artificial liver (EAL) in the treatment of hepatic insufficiency, would be a great advantage. However, one of the numerous unsolved problems is the limitation of the surface area of a future EAL. To decrease the dimensions of same, we modified the cell immobilization technique by placing a second layer of immobilized human hepatocytes onto a layer of pre-immobilized hepatocytes creating a “sandwich immobilization” (SI) system. Immobilization and sandwich immobilization were compared over an investigation period of 30 days: functional performance mirrored by cholinesterase (CHE) and albumin secretion showed remarkable differences only in the course of the first week, whereas we found almost no differences from day 8 on. The total DNA-values on days 0, 1, 7, 14, 21 and 30 varied strongly after the first week but were very similar up to day 30. Finally, it appears disadvantageous to enlarge number/cm2 of (human) hepatocytes in long-term cultures or for application in an EAL by means of sandwich immobilization.
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Affiliation(s)
- M. Wick
- Department of Surgery, Berufsgenossenschaftliche Kliniken Bergmannsheil, Ruhr University of Bochum, Bochum
| | - H.G. Koebe
- Department of Surgery, Klinikum Großhadern, L.M. University of Munich, München - Germany
| | - F.W. Schildberg
- Department of Surgery, Klinikum Großhadern, L.M. University of Munich, München - Germany
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Gueli Alletti G, Carstens EB, Weihrauch B, Jehle JA. Agrotis segetum nucleopolyhedrovirus but not Agrotis segetum granulovirus replicate in AiE1611T cell line of Agrotisipsilon. J Invertebr Pathol 2018; 151:7-13. [DOI: 10.1016/j.jip.2017.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023]
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19
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Kim H, Padmakshan D, Li Y, Rencoret J, Hatfield RD, Ralph J. Characterization and Elimination of Undesirable Protein Residues in Plant Cell Wall Materials for Enhancing Lignin Analysis by Solution-State Nuclear Magnetic Resonance Spectroscopy. Biomacromolecules 2017; 18:4184-4195. [DOI: 10.1021/acs.biomac.7b01223] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hoon Kim
- Department
of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726, United States
| | - Dharshana Padmakshan
- Department
of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726, United States
| | - Yanding Li
- Department
of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726, United States
- Department
of Biological System Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53726, United States
| | - Jorge Rencoret
- Instituto
de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, 41012 Seville, Spain
| | - Ronald D. Hatfield
- USDA-ARS Dairy Forage Research Center, 1925 Linden Drive West, Madison, Wisconsin 53706, United States
| | - John Ralph
- Department
of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department
of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726, United States
- Department
of Biological System Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53726, United States
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20
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Redondo MJ, Grant SFA, Davis A, Greenbaum C. Dissecting heterogeneity in paediatric Type 1 diabetes: association of TCF7L2 rs7903146 TT and low-risk human leukocyte antigen (HLA) genotypes. Diabet Med 2017; 34:286-290. [PMID: 27027642 DOI: 10.1111/dme.13123] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2016] [Indexed: 01/02/2023]
Abstract
AIMS To test the hypothesis that non-obese individuals with childhood-onset Type 1 diabetes and the rs7903146 TT genotype would be less likely to have high-risk human leukocyte antigen (HLA) genotypes and alleles. METHODS We studied a cohort of 105 non-obese participants in the T1D Exchange Biobank Residual Insulin Study who had childhood-onset Type 1 diabetes [mean (sd) age at onset and recruitment, respectively, 9.9 (4.15) and 14.4 (4.13) years; 84.8% non-Hispanic white]. We analysed islet autoantibodies (glutamic acid decarboxylase 65, islet cell autoantigen 512/islet antigen-2 and zinc transporter 8), non-fasting random C-peptide levels, HLA type and TCF7L2 single nucleotide polymorphism rs7903146 in this cohort. RESULTS None of the 13 individuals with the rs7903146 TT genotype carried the highest Type 1 diabetes risk HLA genotype, i.e. DRB1*03:01/DR4 (DRB1*0401, *04:05 or *04:02), compared with 29.4% (27/92) of those without it (P=0.023). The DRB1*03:01 allele was present in 15.4% (2/13) of individuals with the single nucleotide polymorphism, compared with 59.8% (55/92) of those without it (P=0.003). Analyses restricted to autoantibody-positive individuals (n=80) yielded similar results. The HLA DRB1*15:01 allele, which affords dominant protection against Type 1 diabetes, was found in one participant, who had multiple islet autoantibodies and carried the rs7903146 TT genotype. CONCLUSIONS These findings further support the hypothesis that TCF7L2 gene variation contributes to diabetogenesis in a subset of young people with Type 1 diabetes, opening possible new pathways for therapy and prevention.
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Affiliation(s)
- M J Redondo
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - S F A Grant
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - A Davis
- Diabetes Clinical Research Program, Benaroya Research Institute, Seattle, WA, USA
| | - C Greenbaum
- Diabetes Clinical Research Program, Benaroya Research Institute, Seattle, WA, USA
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21
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Lomonosova E, Tavis JE. In Vitro Enzymatic and Cell Culture-Based Assays for Measuring Activity of HBV RNaseH Inhibitors. Methods Mol Biol 2017; 1540:179-192. [PMID: 27975316 PMCID: PMC10591453 DOI: 10.1007/978-1-4939-6700-1_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
HBV is a small, enveloped DNA virus that replicates by reverse transcription via an RNA intermediate. Current anti-HBV treatment regiments that include interferon α and nucleos(t)ide analogs have insufficient efficiency, are of long duration and can be accompanied by systemic side effects. Though HBV RNaseH is essential for viral replication, it is unexploited as a drug target against HBV. RNaseH inhibitors that actively block viral replication would represent an important addition to the potential new drugs for treating HBV infection. Here we describe two methods to measure the activity of RNaseH inhibitors. DNA oligonucleotide-directed RNA cleavage assay allows low-throughput screening of compounds for potential anti-HBV RNaseH activity in vitro. Analysis of preferential inhibition of plus-polarity DNA strand synthesis by HBV RNaseH inhibitors in a cell culture model of HBV replication can be used to validate the efficiency of these compounds to block viral replication.
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Affiliation(s)
- Elena Lomonosova
- Department of Molecular Microbiology and Immunology, Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., Saint Louis, MO, 63104, USA
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., Saint Louis, MO, 63104, USA.
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22
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Lee HJ, Kim JY, Park JE, Yoon YD, Tsang BK, Kim JM. Induction of Fas-Mediated Apoptosis by Interferon-γ is Dependent on Granulosa Cell Differentiation and Follicular Maturation in the Rat Ovary. Dev Reprod 2016; 20:315-329. [PMID: 28144637 PMCID: PMC5270607 DOI: 10.12717/dr.2016.20.4.315] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/20/2016] [Accepted: 12/13/2016] [Indexed: 11/17/2022]
Abstract
Fas ligand (FasL) and its receptor Fas have been implicated in granulosa cell apoptosis during follicular atresia. Although interferon-gamma (IFN-γ) is believed to be involved in the regulation Fas expression in differentiated granulosa or granulosa-luteal cells, the expression of this cytokine and its role in the regulation of the granulosa cell Fas/FasL system and apoptosis during follicular maturation have not been thoroughly investigated. In the present study, we have examined the presence of IFN-γ in ovarian follicles at different stage of development by immunohistochemistry and related their relative intensities with follicular expression of Fas and FasL, and with differences in granulosa cell sensitivity to Fas activation by exogenous agonistic Anti-Fas monoclonal antibody (Fas mAb). Although IFN-γ immunostaining was detectable in oocyte and granulosa cells in antral follicles, most intense immunoreactivity for the cytokine was observed in these cells of preantral follicles. Intense immunoreactivity for IFN-γ was most evident in granulosa cells of atretic early antral follicles where increased Fas and FasL expression and apoptosis were also observed. Whereas low concentrations of IFN-γ (10-100 U/mL) significantly increased Fas expression in undifferentiated granulosa cells (from preantral or very early antral follicles) in vitro, very higher concentrations (≥ 1,000 U/mL) were required to up-regulate of Fas in differentiated cells isolated from eCG-primed (antral) follicles. Addition of agonistic Fas mAb to cultures of granulosa cells at the two stages of differentiation and pretreated with IFN-γ (100 U/mL) elicited morphological and biochemical apoptotic features which were more prominent in cells not previously exposed to the gonadotropin in vivo. These findings suggested that IFN-γ is an important physiologic intra-ovarian regulator of follicular atresia and plays a pivotal role in regulation of expression of Fas receptor and subsequent apoptotic response in undifferentiated (or poorly differentiated) granulosa cells at an early (penultimate) stage of follicular development.
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Affiliation(s)
- Hye-Jeong Lee
- Department of Pharmacology, College of Medicine, Dong-A University, Busan 602-714, Korea
| | - Ji Young Kim
- Division of Medical Oncology, Department of Internal Medicine, Korea University College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Ji Eun Park
- Department of Anatomy and Cell Biology, College of Medicine, Dong-A University, Busan 602-714, Korea
| | - Yong-Dal Yoon
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133-791, Korea
| | - Benjamin K Tsang
- Department of Obstetrics and Gynecology and Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1Y 4E9
| | - Jong-Min Kim
- Department of Anatomy and Cell Biology, College of Medicine, Dong-A University, Busan 602-714, Korea
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Qi LP, Chen LF, Dang AM, Li LY, Fang Q, Yan XW. Association between the ABCA1-565C/T gene promoter polymorphism and coronary heart disease severity and cholesterol efflux in the Chinese Han population. Genet Test Mol Biomarkers 2015; 19:347-52. [PMID: 26090796 DOI: 10.1089/gtmb.2015.0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND ABCA1 -565C/T gene promoter variants have been associated with the severity of coronary artery disease in Western populations. The purpose of our study was to investigate the association between the -565C/T gene polymorphism and coronary artery disease severity and cholesterol efflux in the Chinese Han population. METHODS A cohort of 298 acute coronary syndrome (ACS) patients and 541 healthy controls was genotyped using the highly sensitive ligase detection reaction. ABCA1 -565C/T genotype was correlated with the clinical features of 164 acute myocardial infarction (AMI) patients. Monocytes from patients with various -565C/T gene polymorphisms were isolated and differentiated into foam cells by coincubation with [(3)H]-labeled acetyl-low-density lipoprotein cholesterol. ABCA1 mRNA and protein expression levels were evaluated, as well as cellular cholesterol efflux. RESULTS The frequency of the TT genotype in the -565C/T polymorphism of ACS patients was significantly increased when compared with controls (0.211 vs. 0.162, p<0.05). The TT genotype, but not the CT or CC genotypes, in the -565C/T gene polymorphism correlated with the severity of the coronary lesion observed in AMI patients. Patients with the TT homozygote genotype also exhibited significantly lower cellular cholesterol efflux (TT [6.37%±0.554%]) levels than controls and also had the lowest levels of ABCA1 mRNA and protein expression among the group of variants. In contrast, cholesterol efflux levels in AMI patients with CT [11.35%±3.975%] and CC ([15.32%±6.293%]) genotypes were not significantly different from controls. CONCLUSIONS Impaired ABCA1-mediated cholesterol efflux in macrophages may be associated with the severity of the coronary lesions in AMI patients with the TT genotype at the -565C/T gene polymorphism.
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Affiliation(s)
- Li-Ping Qi
- 1 Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College , Chinese Academy of Medicine Science, Beijing, China
- 2 Department of Second Geriatric Cardiology, The People's Liberation Army General Hospital , Beijing, China
| | - Lian-Feng Chen
- 1 Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College , Chinese Academy of Medicine Science, Beijing, China
| | - Ai-Min Dang
- 3 Department of Cardiology, FuWai Cardiovascular Disease Hospital, Peking Union Medical College , Chinese Academy of Medicine Science, Beijing, China
| | - Li-Yun Li
- 1 Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College , Chinese Academy of Medicine Science, Beijing, China
| | - Quan Fang
- 1 Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College , Chinese Academy of Medicine Science, Beijing, China
| | - Xiao-Wei Yan
- 1 Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College , Chinese Academy of Medicine Science, Beijing, China
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Association between ABCG1 polymorphism rs1893590 and high-density lipoprotein (HDL) in an asymptomatic Brazilian population. Mol Biol Rep 2014; 42:745-54. [PMID: 25398214 DOI: 10.1007/s11033-014-3823-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 11/08/2014] [Indexed: 10/24/2022]
Abstract
ATP binding cassette transporter G1 (ABCG1) promotes lipidation of nascent high-density lipoprotein (HDL) particles, acting as an intracellular transporter. SNP rs1893590 (c.-204A > C) of ABCG1 gene has been previously studied and reported as functional over plasma HDL-C and lipoprotein lipase activity. This study aimed to investigate the relationships of SNP rs1893590 with plasma lipids and lipoproteins in a large Brazilian population. Were selected 654 asymptomatic and normolipidemic volunteers from both genders. Clinical and anthropometrical data were taken and blood samples were drawn after 12 h fasting. Plasma lipids and lipoproteins, as well as HDL particle size and volume were determined. Genomic DNA was isolated for SNP rs1893590 detection by TaqMan(®) OpenArray(®) Real-Time PCR Plataform (Applied Biosystems). Mann-Whitney U, Chi square and two-way ANOVA were the used statistical tests. No significant differences were found in the comparison analyses between the allele groups for all studied parameters. Conversely, significant interactions were observed between SNP and age over plasma HDL-C, were volunteers under 60 years with AA genotype had increased HDL-C (p = 0.048). Similar results were observed in the group with body mass index (BMI) < 25 kg/m(2), where volunteers with AA genotype had higher HDL-C levels (p = 0.0034), plus an increased HDL particle size (p = 0.01). These findings indicate that SNP rs1893590 of ABCG1 has a significant impact over HDL-C under asymptomatic clinical conditions in an age and BMI dependent way.
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ROY DEBASISH, CALAF GLORIAM. Mutation of β-catenin in a radiation and estrogen breast cancer model. Int J Oncol 2014; 46:153-60. [DOI: 10.3892/ijo.2014.2722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/17/2014] [Indexed: 11/06/2022] Open
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Roy D, Calaf GM. Allelic loss at chromosome 11q13 alters FGF3 gene expression in a human breast cancer progression model. Oncol Rep 2014; 32:2445-52. [PMID: 25333703 DOI: 10.3892/or.2014.3502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 08/26/2014] [Indexed: 11/06/2022] Open
Abstract
Identification of markers with the potential to predict tumorigenic behavior is important in breast cancer, due to the variability in clinical disease progression. Genetic alterations during neoplastic progression may appear as changes in total DNA content, single genes, or gene expression. Oncogenic alterations are thought to be prognostic indices for patients with breast cancer. Breast cancer deregulation can occur in the normal cellular process and can be measured by microsatellite instability (MSI)/loss of heterozygosity (LOH). Chromosome 11 is unique in this respect, as three regions of MSI/LOH have been identified (11p15-p15.5, 11q13-q13.3 and 11q23-q24). There are many important families of genes, such as FGF, CCND1, FADD, BAD and GAD2, that are located on chromosome 11 and these play a crucial role in breast cancer progression. Among them, different members of the fibroblast growth factor (FGF) family of genes are clustered around human chromosome 11q13 amplicon, which are constantly altering during breast cancer progression. Therefore, in this study, locus 11q13 and FGF3 gene (11q13) function were investigated in a radiation and estrogen breast cancer model induced by high-LET (α-particle) radiation and estrogen exposure. To assess the effect of ionizing radiation and estrogen at chromosome 11q13 loci and the subsequent role of FGF3 gene expression, various microsatellite markers were chosen in this region, and allelic loses (~20-45%) were identified by PCR-SSCP analysis. Results showed an increase in FGF3 protein expression and a 6- to 8-fold change in gene expression of FGF3 and associated genes. These deregulations could be utilized as an appropriate target for therapeutic intervention in breast cancer.
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Affiliation(s)
- Debasish Roy
- Department of Natural Sciences, Hostos College of the City University of New York, Bronx, NY, USA
| | - Gloria M Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
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Lehane AM, Ridgway MC, Baker E, Kirk K. Diverse chemotypes disrupt ion homeostasis in the Malaria parasite. Mol Microbiol 2014; 94:327-39. [PMID: 25145582 DOI: 10.1111/mmi.12765] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2014] [Indexed: 01/09/2023]
Abstract
The antimalarial spiroindolones disrupt Plasmodium falciparum Na(+) regulation and induce an alkalinization of the parasite cytosol. It has been proposed that they do so by inhibiting PfATP4, a parasite plasma membrane P-type ATPase postulated to export Na(+) and import H(+) equivalents. Here, we screened the 400 antiplasmodial compounds of the open access 'Malaria Box' for their effects on parasite ion regulation. Twenty eight compounds affected parasite Na(+) and pH regulation in a manner consistent with PfATP4 inhibition. Six of these, with chemically diverse structures, were selected for further analysis. All six showed reduced antiplasmodial activity against spiroindolone-resistant parasites carrying mutations in pfatp4. We exposed parasites to incrementally increasing concentrations of two of the six compounds and in both cases obtained resistant parasites with mutations in pfatp4. The finding that diverse chemotypes have an apparently similar mechanism of action indicates that PfATP4 may be a significant Achilles' heel for the parasite.
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Affiliation(s)
- Adele M Lehane
- Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia
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Luviano A, Aguiñiga-Sánchez I, Demare P, Tiburcio R, Ledesma-Martínez E, Santiago-Osorio E, Regla I. Antineoplastic activity of rinvanil and phenylacetylrinvanil in leukaemia cell lines. Oncol Lett 2014; 7:1651-1656. [PMID: 24765194 PMCID: PMC3997731 DOI: 10.3892/ol.2014.1958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 01/07/2014] [Indexed: 11/06/2022] Open
Abstract
In the search for novel chemotherapeutic agents for cancer treatment, capsaicin has been shown to inhibit proliferation and induce apoptosis in various types of cancer cell line, including leukaemia cell lines. The capsaicin analogues, rinvanil and phenylacetylrinvanil (PhAR), share a binding affinity for vanilloid receptors and may have biological activities similar to capsaicin; however, their anticancer potential has not yet been reported. This study analyses the antineoplastic activities of rinvanil and PhAR in leukaemia versus normal cells. P388, J774 and WEHI-3 leukaemia cell lines, as well as mouse bone marrow mononuclear cells, were cultured with varying concentrations of rinvanil and PhAR. Following this, proliferation and apoptosis were determined by the sulforhodamine B (SRB) assay and DNA ladder. Cultured leukaemia cell lines and mouse bone marrow mononuclear cells demonstrated a dose-dependent inhibition of proliferation, while non-diseased cells were less sensitive to the cytotoxic effect of capsaicin, rinvanil and PhAR. Rinvanil and PhAR also induced apoptosis in leukaemia cell lines but not in bone marrow. Given the lower IC50 values for apoptosis induction in leukaemia cells compared with that of normal cells, PhAR is a promising selective anticancer agent.
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Affiliation(s)
- Axel Luviano
- Laboratory of Drug Synthesis, L9-PA, Research Unit on Cell Differentiation and Cancer, L8-PB, Campus II, UMIEZ FES-Zaragoza, UNAM, Iztapalapa, Mexico City 09230, Mexico
| | - Itzen Aguiñiga-Sánchez
- Hematopoiesis and Leukaemia Laboratory, Research Unit on Cell Differentiation and Cancer, L8-PB, Campus II, UMIEZ FES-Zaragoza, UNAM, Iztapalapa, Mexico City 09230, Mexico
| | - Patricia Demare
- Laboratory of Drug Synthesis, L9-PA, Research Unit on Cell Differentiation and Cancer, L8-PB, Campus II, UMIEZ FES-Zaragoza, UNAM, Iztapalapa, Mexico City 09230, Mexico
| | - Reynaldo Tiburcio
- Hematopoiesis and Leukaemia Laboratory, Research Unit on Cell Differentiation and Cancer, L8-PB, Campus II, UMIEZ FES-Zaragoza, UNAM, Iztapalapa, Mexico City 09230, Mexico
| | - Edgar Ledesma-Martínez
- Hematopoiesis and Leukaemia Laboratory, Research Unit on Cell Differentiation and Cancer, L8-PB, Campus II, UMIEZ FES-Zaragoza, UNAM, Iztapalapa, Mexico City 09230, Mexico
| | - Edelmiro Santiago-Osorio
- Hematopoiesis and Leukaemia Laboratory, Research Unit on Cell Differentiation and Cancer, L8-PB, Campus II, UMIEZ FES-Zaragoza, UNAM, Iztapalapa, Mexico City 09230, Mexico
| | - Ignacio Regla
- Hematopoiesis and Leukaemia Laboratory, Research Unit on Cell Differentiation and Cancer, L8-PB, Campus II, UMIEZ FES-Zaragoza, UNAM, Iztapalapa, Mexico City 09230, Mexico
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Sharma D, Hussain SA, Akhter N, Singh A, Trivedi SS, Bhatttacharjee J. Endothelial nitric oxide synthase (eNOS) gene Glu298Asp polymorphism and expression in North Indian preeclamptic women. Pregnancy Hypertens 2013; 4:65-9. [PMID: 26104257 DOI: 10.1016/j.preghy.2013.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 10/03/2013] [Accepted: 11/07/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Pathophysiological processes in preeclampsia (PE) are influenced by genetic factors, nitric oxide synthases seem to play important roles, although their expression in and their role is still unclear. To better characterize the host genetic factors determining the susceptibility to PE, we evaluated the influence of polymorphisms (Glu298Asp) in the endothelial nitric oxide synthase (eNOS) gene on the risk of developing PE by checking the expression level. METHODS We conducted a hospital-based case-control study including 300 women with preeclampsia and 200 healthy pregnant women. Their blood samples were analyzed for levels of nitric oxide, eNOS gene polymorphism and expression. eNOS mRNA levels were determined using RT-PCR and expressed as arbitrary units after correction with control β-Actin gene mRNA levels. RESULTS The mRNA expression of eNOS gene was found to be significantly lower in blood (P<0.05) from women with PE compared to that from normal pregnancies. The total nitric oxide levels (P<0.001) were decreased in study Group as compared to healthy pregnant patients. The intergenotypic variation of nitric oxide levels in preeclamptic women was found to be significant (P<0.001). CONCLUSIONS These results indicate the relationship between reduced nitric oxide levels and eNOS gene polymorphism leading to its altered expression in preeclamptic women.
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Affiliation(s)
- D Sharma
- Department of Biochemistry, Lady Hardinge Medical College, New Delhi 110001, India.
| | - S A Hussain
- Department of Bioscience, Jamia Milia Islamia, New Delhi 110025, India.
| | - N Akhter
- Department of Bioscience, Jamia Milia Islamia, New Delhi 110025, India.
| | - A Singh
- Department of Biochemistry, Lady Hardinge Medical College, New Delhi 110001, India
| | - S S Trivedi
- Department of Obstetrics and Gynecology, Lady Hardinge Medical College, New Delhi 110001, India
| | - J Bhatttacharjee
- Department of Biochemistry, Lady Hardinge Medical College, New Delhi 110001, India.
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Lemieux C, Turmel M, Lee RW. Characterization of chloroplast DNA in Chlamydomonas eugametos and C. moewusii and its inheritance in hybrid progeny. Curr Genet 2013; 2:139-47. [PMID: 24189805 DOI: 10.1007/bf00420626] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/1980] [Indexed: 10/26/2022]
Abstract
The density, molecular weight, and cellular repetition of DNA molecules associated with the β-DNA satellite of the interfertile algae Chlamydomonas eugametos and C. moewusii are reported. The similarities between these values and those for the chloroplast DNA (cpDNA) in the related alga Chlamydomonas reinhardtii indicate that these satellites represent cpDNA. The buoyant densities of C. eugametos and C. moewusii cpDNAs are indistinguishable from one another, as are those of their respective nuclear DNAs. These densities differ slightly from the densities of the homologous components of C. reinhardtii whole cell DNA. All three species differ with respect to additional minor satellite DNAs and low molecular weight DNAs of unknown cellular location.Differences in the Aval and Smal restriction endonuclease fragmentation patterns of C. eugametos and C. moewusii cpDNAs were employed to study the inheritance of cpDNA in an F1 hybrid which had inherited a non-Mendelian streptomycin resistance marker (sr-2) from the C. eugametos mating-type plus (mt (+)) parent and in two homoplasmic mitotic segregants from a B 1 hybrid (F1 × C. moewusii) which had been initially heteroplasmic for the resistance marker. Although the cpDNA patterns in the F1 hybrid were similar to those of the C. eugametos ml (1) parent, important differences were noted which suggest that recombination between C. eugametos and C. moewusii cpDNA had occurred. Homoplasmic streptomycin resistant and sensitive mitotic segregants recovered from the B1 hybrid product reveal Aval restriction patterns similar to those of the respective resistant and sensitive parents. These data are consistent with the hypothesis that the sr-2 marker is located in cpDNA and that C. eugametos and C. moewusii cpDNA sequences can coexist in the same chloroplast and, at least sometimes, segregate without extensive recombination. The transmission of low molecular weight DNAs characteristic of C. moewusii but of unknown cellular origin shows no direct correlation with the transmission of the sr-2 marker.
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Affiliation(s)
- C Lemieux
- Department of Biology, Dalhousie University, B3H 4J1, Halifax, Nova Scotia, Canada
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31
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Dispersive labelling of Chlamydomonas chloroplast DNA in (15)N- (14)N density transfer experiments. Curr Genet 2013; 4:91-7. [PMID: 24185954 DOI: 10.1007/bf00365687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/1981] [Indexed: 10/26/2022]
Abstract
(15)N-(14)N density transfer experiments with synchronized vegetative cultures of Chlamydomonas reinhardtii revealed a dispersive labelling of chloroplast DNA (cpDNA) while the labelling of nuclear DNA was consistent with semiconservative replication. The dispersive labelling of cpDNA was progressive and extensive as after less than two net doublings of this DNA in (14)N-medium no significant amount of fully heavy, (15)N-strands could be detected in denatured cpDNA preparations; the average size of DNA in these preparations corresponded to 6% of the intact chloroplast genome or about 12 kbp. The density shifts of native cpDNA samples were found to be consistent with the net amounts of cpDNA synthesized. This observation indicates that essentially all (15)N atoms incorporated prior to the transfer were conserved and that metabolic turnover of cpDNA was probably absent. Our results are best explained by the exchange of homologous single-stranded segments between cpDNA molecules to form heteroduplex regions and by each DNA molecule undergoing several rounds of heteroduplex formation.
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Peña-Llopis S, Brugarolas J. Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications. Nat Protoc 2013; 8:2240-55. [PMID: 24136348 DOI: 10.1038/nprot.2013.141] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genomic technologies have revolutionized our understanding of complex Mendelian diseases and cancer. Solid tumors present several challenges for genomic analyses, such as tumor heterogeneity and tumor contamination with surrounding stroma and infiltrating lymphocytes. We developed a protocol to (i) select tissues of high cellular purity on the basis of histological analyses of immediately flanking sections and (ii) simultaneously extract genomic DNA (gDNA), mRNA, noncoding RNA (ncRNA; enriched in miRNA) and protein from the same tissues. After tissue selection, about 12-16 extractions of DNA, RNA or protein can be obtained per day. Compared with other similar approaches, this fast and reliable methodology allowed us to identify mutations in tumors with remarkable sensitivity and to perform integrative analyses of whole-genome and exome data sets, DNA copy numbers (by single-nucleotide polymorphism (SNP) arrays), gene expression data (by transcriptome profiling and quantitative PCR (qPCR)) and protein levels (by western blotting and immunohistochemical analysis) from the same samples. Although we focused on renal cell carcinoma, this protocol may be adapted with minor changes to any human or animal tissue to obtain high-quality and high-yield nucleic acids and proteins.
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Affiliation(s)
- Samuel Peña-Llopis
- 1] Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA. [2] Department of Developmental Biology, UT Southwestern Medical Center, Dallas, Texas, USA. [3] Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas, USA
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Hennekens CM, Cooper ES, Cotton RW, Grgicak CM. The Effects of Differential Extraction Conditions on the Premature Lysis of Spermatozoa,. J Forensic Sci 2013; 58:744-52. [DOI: 10.1111/1556-4029.12098] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 01/10/2012] [Accepted: 04/03/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Catherine M. Hennekens
- Biomedical Forensic Sciences; Boston University School of Medicine; 72 East Concord Street; Boston; MA; 02118
| | - Elyse S. Cooper
- Biomedical Forensic Sciences; Boston University School of Medicine; 72 East Concord Street; Boston; MA; 02118
| | - Robin W. Cotton
- Biomedical Forensic Sciences; Boston University School of Medicine; 72 East Concord Street; Boston; MA; 02118
| | - Catherine M. Grgicak
- Biomedical Forensic Sciences; Boston University School of Medicine; 72 East Concord Street; Boston; MA; 02118
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34
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Ohnaka S, Soga E, Inouye K. Deletion of the κ genes from mouse hybridomas established with NS-1 myelomas. Cytotechnology 2012; 24:213-8. [PMID: 22358764 DOI: 10.1023/a:1007910831550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Monoclonal antibodies (mAbs) of the IgG class produced by mouse hybridomas raised with NS-1 myelomas have been shown to contain two types of immunoglobulin light (κ) chains derived from the myelomas and antigen-stimulated spleen lymphocytes, and the hybridomas produce three mAb species with light chain heterogeneity (Abe and Inouye, 1993). In the present study, 9 hybridoma lines secreting homogeneous mAbs have been isolated from 63 lines cloned from an established hybridoma line producing three mAbs. They secrete homogeneous mAbs containing light chains derived from either myeloma or spleen cells. They contain either κ gene derived from the respective cells, and the other gene was deleted during the cultivation. The deletion frequency of the κ gene of myelomas is 3 times higher than that of spleen cells, although 80-85% of hybridomas reach the stable state containing both κ genes.
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Sharma D, Trivedi SS, Bhattacharjee J. Intergenotypic Variation of Endothelial Dysfunction and Inflammatory Markers in Eclampsia. Hypertens Pregnancy 2012; 32:11-9. [DOI: 10.3109/10641955.2012.697949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Mörlein D, Lungershausen M, Steinke K, Sharifi AR, Knorr C. A single nucleotide polymorphism in the CYP2E1 gene promoter affects skatole content in backfat of boars of two commercial Duroc-sired crossbred populations. Meat Sci 2012; 92:739-44. [PMID: 22795630 DOI: 10.1016/j.meatsci.2012.06.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/15/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
Abstract
The prevention of unpleasant boar taint is the main reason for castration of male piglets. This study aimed to investigate how the malodorous compound skatole is affected by a single nucleotide polymorphism (g.2412 C>T at -586 ATG) in the porcine cytochrome p450 II E1 (CYP2E1) gene. 119 boars of two commercial Duroc-sired crossbred populations raised at different farms were investigated. Skatole and androstenone in backfat averaged 114±125 ng/g and 1206±895 ng/g melted fat, respectively. The frequency of the genotypes CC, CT, and TT was 25, 52, and 23%, respectively. CC boars had the highest average skatole levels (175 ng/g) compared to CT (92 ng/g) and TT (93 ng/g). Applying suggested sensory threshold levels for skatole (>150 ng/g) and androstenone (>2000 ng/g), 30% of the carcasses may be unacceptably tainted while the proportion of tainted carcasses is significantly higher within genotype CC (56.7%) compared to genotypes CT (24.3%) and TT (14.8%). Effective reduction of tainted carcasses appears feasible applying marker assisted selection.
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Affiliation(s)
- Daniel Mörlein
- Department of Animal Science, University of Göttingen, Göttingen, Germany
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Wu Y, Yang H, Yang B, Yang K, Xiao C. Association of polymorphisms in prolylcarboxypeptidase and chymase genes with essential hypertension in the Chinese Han population. J Renin Angiotensin Aldosterone Syst 2012; 14:263-70. [PMID: 22679278 DOI: 10.1177/1470320312448949] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION The prolylcarboxypeptidase (PRCP) gene encodes a membrane protein that acts on angiotensin II (Ang II) and kallikrein to release vasoactive peptides. The chymase (CMA1) gene is important for Ang II generation. Therefore, the two genes might be involved in the pathogenesis of essential hypertension (EH). MATERIALS AND METHODS Eleven tag single nucleotide polymorphisms (SNPs) in the PRCP gene and four tag SNPs and G-1903A (rs1800875) polymorphism in the CMA1 gene were genotyped in the Chinese Han population (n=1020) using a polymerase chain reaction-restriction fragment length polymorphism method. RESULTS In the PRCP gene, single site analyses indicated that the rs7104980 G allele was a susceptible factor for EH (adjusted odds ratio (OR)=1.98, 95% confidence interval (CI) 1.62-2.43, p=0.3×10(-10)). The protective effect of Hap3 GAGCACTAACA was observed without carrying the susceptible rs7104908 G allele (OR=0.67, 95% CI 0.56-0.81, p=0.3×10(-4)) by haplotype analyses. In the case of the CMA1 gene, no associations with EH were found through single site analyses. However, haplotype analyses showed that Hap16 TTTA significantly increased the risk of EH with OR=3.15 (p=0.0002) which may be driven by interaction with a nearby SNP combination. CONCLUSIONS The present results indicated PRCP rs7104980 can be considered as a marker for EH and Hap3 GAGCACTAACA (PRCP) and Hap16 TTTA (CMA1) might be associated with EH in Chinese Han population.
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Affiliation(s)
- Yanrui Wu
- Cell Biology and Genetics Department, Kunming Medical University, China
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38
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Godoi DF, Cardoso CR, Silva MJB, Ferraz DB, Provinciatto PR, Cunha FDQ, da Silva JS, Voltarelli JC. Reappraisal of total body irradiation followed by bone marrow transplantation as a therapy for inflammatory bowel disease. Immunobiology 2012; 218:317-24. [PMID: 22771114 DOI: 10.1016/j.imbio.2012.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 05/16/2012] [Indexed: 01/14/2023]
Abstract
The main current therapies for inflammatory bowel diseases (IBD) are aimed at controlling the exacerbated inflammation in the gut. Although these therapies have been successful, they are not curative and it is not possible to predict whether a beneficial response will occur or which patients will be refractory to the treatment. Total body irradiation (TBI) associated with chemotherapy is the first choice in the treatment of some hematological disorders and is an applicable option in the preparation of patients with hematologic diseases for hematopoietic stem cell transplantation. Then, in this study we investigated the association of TBI as immunosuppressive therapy and bone marrow cell (BMC) transplantation as a strategy to induce colitis recovery and immune reconstitution in the TNBS model of intestinal inflammation. TNBS mice treated with TBI associated with BMC transplantation presented elevated gain of weight and an overall better outcome of the disease when compared to those treated only with TBI. In addition, TBI associated or not with BMC reduced the frequency of inflammatory cells in the gut and restored the goblet cell counts. These results were accompanied by a down regulation in the production of inflammatory cytokines in the colon of mice treated with TBI alone or in association with BMC transplantation. The BMC infused were able to repopulate the ablated immune system and accumulate in the site of inflammation. However, although both treatments (TBI or TBI+BMC) were able to reduce gut inflammation, TBI alone was not enough to fully restore mice weight and these animals presented an extremely reduced survival rate when their immune system was not promptly reconstituted with BMC transplantation. Finally, these evidences suggest that the BMC transplantation is an efficient strategy to reduce the harmful effects of TBI in the colitis treatment, suggesting that radiotherapy may be an important immunosuppressive therapy in patients with IBD, by modulating the local inflammatory response.
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Affiliation(s)
- Dannielle Fernandes Godoi
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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Magwood AC, Mundia MM, Baker MD. High levels of wild-type BRCA2 suppress homologous recombination. J Mol Biol 2012; 421:38-53. [PMID: 22579622 DOI: 10.1016/j.jmb.2012.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 04/23/2012] [Accepted: 05/03/2012] [Indexed: 11/26/2022]
Abstract
Endogenous levels of the BRCA2 (breast cancer susceptibility 2) protein promote homologous recombination by regulating the essential strand exchange protein RAD51. To examine BRCA2 function in homologous recombination, we expressed human BRCA2 in control mouse hybridoma cells, as well as those that were depleted of endogenous Brca2 by small interfering RNA. With moderate human BRCA2 expression, homologous recombination was stimulated. Conversely, a higher level of BRCA2 reduced homologous recombination and DNA-damage-induced Rad51 foci formation. Cells expressing high levels of BRCA2 feature normal growth, increased sensitivity to mitomycin C, and increased illegitimate recombination. BRCA2-overexpressing cells are also characterized by suppression of p53 transcriptional regulation and a corresponding reduction in the expression of the p53-responsive genes Noxa and p21. Notably, in cells expressing high levels of BRCA2, small interfering RNA depletion of human BRCA2 or ectopic expression of Rad51 increases homologous recombination and decreases illegitimate recombination. Thus, high levels of wild-type BRCA2 perturb Rad51-mediated homologous recombination, and relatively normal recombination responses can be restored by rebalancing recombination factors.
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Affiliation(s)
- Alissa C Magwood
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Minas K, McEwan NR, Newbold CJ, Scott KP. Optimization of a high-throughput CTAB-based protocol for the extraction of qPCR-grade DNA from rumen fluid, plant and bacterial pure cultures. FEMS Microbiol Lett 2011; 325:162-9. [DOI: 10.1111/j.1574-6968.2011.02424.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Konstantinos Minas
- Institute for Innovation Design and Sustainability; Robert Gordon University; Aberdeen; UK
| | - Neil R. McEwan
- Institute of Biological Environmental and Rural Sciences; Aberystwyth University; Aberystwyth; UK
| | - Charles Jamie Newbold
- Institute of Biological Environmental and Rural Sciences; Aberystwyth University; Aberystwyth; UK
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Sommer C, Hertel TC, Schmelzer CEH, Pietzsch M. Investigations on the activation of recombinant microbial pro-transglutaminase: in contrast to proteinase K, dispase removes the histidine-tag. Amino Acids 2011; 42:997-1006. [DOI: 10.1007/s00726-011-1016-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 06/13/2011] [Indexed: 11/24/2022]
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Intergenotypic variation of nitric oxide and inflammatory markers in preeclampsia: A pilot study in a North Indian population. Hum Immunol 2011; 72:436-9. [DOI: 10.1016/j.humimm.2011.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 02/04/2011] [Accepted: 02/22/2011] [Indexed: 10/18/2022]
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Sharma D, Trivedi SS, Bhattacharjee J. Oxidative stress and eNOS (Glu298Asp) gene polymorphism in preeclampsia in Indian population. Mol Cell Biochem 2011; 353:189-93. [PMID: 21424903 DOI: 10.1007/s11010-011-0786-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Accepted: 03/07/2011] [Indexed: 10/18/2022]
Abstract
Oxidative stress causing widespread endothelial dysfunction has been proposed as a key factor involved in the development of preeclampsia (PE). With this background our objective was to study oxidative stress biomarkers like nitric oxide and malondialdehyde (MDA) and to correlate these markers with endothelial nitric oxide synthase (eNOS) (Glu298Asp) gene polymorphism. This cross-sectional study included 300 pregnant women diagnosed with PE and 200 women with normal pregnancy. Plasma NO and MDA levels were analyzed using student's t test and eNOS gene polymorphism was studied by performing polymerase chain reaction amplification and restriction length polymorphism and frequencies were distributed by using χ(2) analysis. The mean plasma levels of NO were significantly lower in study group while MDA levels were significantly higher in study group (P < 0.001). Genotypic and allelic frequency of eNOS gene in both groups was found to be significant (P < 0.05). The intergenotypic variation of NO and MDA levels was found to be significant (P < 0.001). We concluded that the plasma levels of NO are decreased while MDA levels are increased in subjects with PE and that might contribute to the pathophysiology of PE. As observed in this study Glu298Asp eNOS gene polymorphism showed significant association with PE.
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Affiliation(s)
- Deepika Sharma
- Department of Biochemistry, Lady Hardinge Medical College and Associated Hospitals, New Delhi 110001, India.
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Zacharin M, Bajpai A, Chow CW, Catto-Smith A, Stratakis C, Wong MW, Scott R. Gastrointestinal polyps in McCune Albright syndrome. J Med Genet 2011; 48:458-61. [PMID: 21357941 DOI: 10.1136/jmg.2010.086330] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND McCune Albright syndrome (MAS), a disorder caused by somatic activating mutations in the GNAS gene, usually presents with cutaneous, skeletal, and endocrine manifestations. While focal lesions involving multiple tissues have been identified in MAS, almost nothing is known about gastrointestinal lesions in this disease. METHODS Two MAS patients with perioral freckling, resembling Peutz-Jeghers syndrome (PJS), and two MAS patients without similar pigmentation underwent gastrointestinal endoscopy to establish if they had coexisting hamartomatous polyposis. Three of 4 subjects had documented GNAS mutations in peripheral blood. Genetic testing for STK11 and PRKAR1A genes was performed to exclude presence of coexistent PJS and Carney complex. Genetic testing of biopsy material was also performed. RESULTS Hamartomatous gastrointestinal polyps with histological features similar to those in PJS were observed in all 4 subjects, only in the stomach and/or upper duodenum. Activating GNAS mutations were found in the polyps or adjacent mucosa in 3 of 4 subjects. One patient each had mutation only in the blood or tissue, while 2 patients had both. No subject harboured any detectable PRKARIA or STK11 mutation as determined by direct DNA sequencing and copy number variation analysis. CONCLUSIONS These findings confirm that gastrointestinal polyps are a common manifestation of MAS, indicate an overlap between MAS and PJS, and point towards a putative interaction between the GNAS and STK11 genes in the pathogenesis of these two disorders. The findings suggest a need for routine gastrointestinal endoscopy in patients with MAS, to establish the true incidence of polyps in these patients.
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Affiliation(s)
- Margaret Zacharin
- Department of Endocrinology and Diabetes, Royal Children's Hospital, Flemington Road, Parkville, Melbourne, Victoria 3052, Australia.
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Kuzin BA, Modestova EA, Vorontsova YE, Zatsepina OG, Mikaelyan AS, Slezinger MV, Simonova OB. Interaction of the ss and CG5017 genes in the regulation of morphogensis of limbs in Drosophila melanogaster. Russ J Dev Biol 2010. [DOI: 10.1134/s1062360410050061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chen XH, Li XQ, Chen Y, Feng YM. Risk of aggressive breast cancer in women of Han nationality carrying TGFB1 rs1982073 C allele and FGFR2 rs1219648 G allele in North China. Breast Cancer Res Treat 2010; 125:575-82. [DOI: 10.1007/s10549-010-1032-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 06/30/2010] [Indexed: 11/28/2022]
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Cashmore AR. Structure and expression of a pea nuclear gene encoding a chlorophyll a/b-binding polypeptide. Proc Natl Acad Sci U S A 2010; 81:2960-4. [PMID: 16593461 PMCID: PMC345200 DOI: 10.1073/pnas.81.10.2960] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A nuclear gene AB80 has been isolated from a phage lambda Charon 4 library of pea DNA. The sequence of the gene has been determined and it has been shown to contain an uninterrupted reading frame of 269 amino acids, corresponding to a precursor to a constituent polypeptide of the light-harvesting chlorophyll a/b-protein complex. Primer extension and S1 nuclease studies defined a cap site for AB80. The first methionine codon 3' from this site is 69 nucleotides away and is the initiating codon of the open reading frame. A "TATA" sequence occurs 31 nucleotides 5' from the cap site. A second TATA sequence is found 7 nucleotides on the 5' side of the initiating methionine codon and the sequences surrounding this TATA sequence are strikingly similar to those surrounding the first TATA sequence. The mature polypeptide encoded by AB80 differs by 5 amino acids from the polypeptide corresponding to a previously characterized cDNA sequence pAB96. This result is indicative of heterogeneity within the constituent polypeptides of the light-harvesting chlorophyll a/b-protein complex. The sequence Arg-Lys-Ser-Ala-Thr-Thr-Lys-Lys occurs at, or near, the NH(2)-terminus of the mature polypeptide encoded by AB80. This basic peptide is of interest because of its apparent involvement in changes in excitation-energy distribution in chloroplast membranes. Some general similarities, but no extensive sequence homology, is found on comparing the transit sequence for the precursor to the chlorophyll a/b-binding polypeptide with the transit sequences previously determined for the precursors to the small subunit of ribulose-1,5-bisphosphate carboxylase.
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Affiliation(s)
- A R Cashmore
- Laboratory of Cell Biology, The Rockefeller University, New York, NY 10021
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Wu Y, Cun Y, Dong J, Shao J, Luo S, Nie S, Yu H, Zheng B, Wang Q, Xiao C. Polymorphisms in PPARD, PPARG and APM1 associated with four types of traditional Chinese medicine constitutions. J Genet Genomics 2010; 37:371-9. [PMID: 20621019 DOI: 10.1016/s1673-8527(09)60055-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 04/30/2010] [Accepted: 05/10/2010] [Indexed: 11/19/2022]
Abstract
Based on the theory of constitution of Traditional Chinese Medicine (TCM), the human population is divided into nine constitutions including one balanced constitution (Normality) and eight unbalanced constitutions (Yang-deficiency, Yin-deficiency, Phlegm-wetness, Qi-deficiency, Wetness-heat, Blood stasis, Depressed constitution, and Inherited special constitution). Different constitutions have specific metabolic features and different susceptibility to certain diseases. However, whether a genetic basis accounts for such constitution classification is yet to be determined. Here we performed a genetic study to assess the association between genetic variations of metabolic genes including PPARD, PPARG and APM1 and the constitutions. A total of 233 individuals of the Han population in China were classified into four groups, Normality, Yang-deficiency, Yin-deficiency and Phlegm-wetness with whom 23 single nucleotide polymorphisms (SNPs) in the three genes were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Biased distribution of PPARD rs2267669 and rs2076167, APM1 rs7627128 and rs1063539 in Yang-deficiency, PPARG Pro12Ala in Yin-deficiency and PPARD rs2076167, APM1 rs266729 and rs7627128 in Phlegm-wetness were observed. The frequencies of Haplotype13 (Hap13) of PPARG in Yin-deficiency, Hap25 of APM1 in Yang-deficiency and Hap2 of PPARD and Hap14 of PPARG in Phlegm-wetness, were significantly different from those in Normality, suggesting those might be group-associated haplotypes. These results suggested that single SNP and haplotypes of PPARD, PPARG and APM1 may underlie the genetic basis of the constitutions classified in TCM.
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Affiliation(s)
- Yanrui Wu
- Human Genetics Center of Yunnan University, Kunming, China
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Ohno S, Taniguchi T. Structure of a chromosomal gene for human interferon beta. Proc Natl Acad Sci U S A 2010; 78:5305-9. [PMID: 16593086 PMCID: PMC348733 DOI: 10.1073/pnas.78.9.5305] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have cloned and analyzed a chromosomal DNA segment containing the human interferon beta(1) gene from a human gene library. The nucleotide sequence of the protein-coding and the noncoding regions of the chromosomal gene was identical to the cDNA sequence reported previously. In the region upstream from the putative transcription initiation site, significant nucleotide sequence homology was observed between interferon beta(1) and alpha(1) genes. This region thus may play a role in expression of the interferon genes. From the sequence data and the result of nuclease S1 mapping experiments, we conclude that, like the interferon alpha(1) gene, the interferon beta(1) gene is devoid of intervening sequences.
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Affiliation(s)
- S Ohno
- Department of Biochemistry, Cancer Institute, Japanese Foundation for Cancer Research, Toshima-ku, Tokyo 170, Japan
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