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Kim YY, Kim SW, Kim E, Kim YJ, Kang BC, Ku SY. Transcriptomic Profiling of Reproductive Age Marmoset Monkey Ovaries. Reprod Sci 2024; 31:81-95. [PMID: 37710086 DOI: 10.1007/s43032-023-01342-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023]
Abstract
The decline in ovarian reserve and the aging of the ovaries is a significant concern for women, particularly in the context of delayed reproduction. However, there are ethical limitations and challenges associated with conducting long-term studies to understand and manipulate the mechanisms that regulate ovarian aging in human. The marmoset monkey offers several advantages as a reproductive model, including a shorter gestation period and similar reproductive physiology to that of human. Additionally, they have a relatively long lifespan compared to other mammals, making them suitable for long-term studies. In this study, we focused on analyzing the structural characteristics of the marmoset ovary and studying the mRNA expression of 244 genes associated with ovarian aging. We obtained ovaries from marmosets at three different reproductive stages: pre-pubertal (1.5 months), reproductive (82 months), and menopausal (106 months) ovaries. The structural analyses revealed the presence of numerous mitochondria and lipid droplets in the marmoset ovaries. Many of the genes expressed in the ovaries were involved in multicellular organism development and transcriptional regulation. Additionally, we identified the expression of protein-binding genes. Within the expressed genes, VEGFA and MMP9 were found to be critical for regulating ovarian reserve. An intriguing finding of the study was the strong correlation between genes associated with female infertility and genes related to fibrosis and wound healing. The authors suggest that this correlation might be a result of the repeated rupture and subsequent healing processes occurring in the ovary due to the menstrual cycle, potentially leading to the indirect onset of fibrosis. The expression profile of ovarian aging-related gene set in the marmoset monkey ovaries highlight the need for further studies to explore the relationship between fibrosis, wound healing, and ovarian aging.
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Affiliation(s)
- Yoon Young Kim
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Daehak-ro 101, Jongno-gu, Seoul, 03080, South Korea
- Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University, Seoul, South Korea
| | - Sung Woo Kim
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Daehak-ro 101, Jongno-gu, Seoul, 03080, South Korea
| | - Eunjin Kim
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Daehak-ro 101, Jongno-gu, Seoul, 03080, South Korea
| | - Yong Jin Kim
- Department of Obstetrics and Gynecology, Korea University College of Medicine, Seoul, South Korea
| | - Byeong-Cheol Kang
- Department of Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Seung-Yup Ku
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Daehak-ro 101, Jongno-gu, Seoul, 03080, South Korea.
- Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University, Seoul, South Korea.
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Zhang H, Liu C, Zhu D, Zhang Q, Li J. Medicinal Chemistry Strategies for the Development of Inhibitors Disrupting β-Catenin's Interactions with Its Nuclear Partners. J Med Chem 2023; 66:1-31. [PMID: 36583662 DOI: 10.1021/acs.jmedchem.2c01016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dysregulation of the Wnt/β-catenin signaling pathway is strongly associated with various aspects of cancer, including tumor initiation, proliferation, and metastasis as well as antitumor immunity, and presents a promising opportunity for cancer therapy. Wnt/β-catenin signaling activation increases nuclear dephosphorylated β-catenin levels, resulting in β-catenin binding to TCF and additional cotranscription factors, such as BCL9, CBP, and p300. Therefore, directly disrupting β-catenin's interactions with these nuclear partners holds promise for the effective and selective suppression of the aberrant activation of Wnt/β-catenin signaling. Herein, we summarize recent advances in biochemical techniques and medicinal chemistry strategies used to identify potent peptide-based and small-molecule inhibitors that directly disrupt β-catenin's interactions with its nuclear binding partners. We discuss the challenges involved in developing drug-like inhibitors that target the interactions of β-catenin and its nuclear binding partner into therapeutic agents.
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Affiliation(s)
- Hao Zhang
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Chenglong Liu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Di Zhu
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Department of Pharmacology, School of Basic Medical Science, Fudan University, Shanghai 201100, China
| | - Qingwei Zhang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Jianqi Li
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
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Mikhailov VF, Shulenina LV. Regulation of Gene Activity Is One of the Mechanisms for Changing Radiosensitivity. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022110140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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Bioinformatics and System Biological Approaches for the Identification of Genetic Risk Factors in the Progression of Cardiovascular Disease. Cardiovasc Ther 2022; 2022:9034996. [PMID: 36035865 PMCID: PMC9381297 DOI: 10.1155/2022/9034996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/17/2022] [Accepted: 07/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Cardiovascular disease (CVD) is the combination of coronary heart disease, myocardial infarction, rheumatic heart disease, and peripheral vascular disease of the heart and blood vessels. It is one of the leading deadly diseases that causes one-third of the deaths yearly in the globe. Additionally, the risk factors associated with it make the situation more complex for cardiovascular patients, which lead them towards mortality, but the genetic association between CVD and its risk factors is not clearly explored in the global literature. We addressed this issue and explored the linkage between CVD and its risk factors. Methods We developed an analytical approach to reveal the risk factors and their linkages with CVD. We used GEO microarray datasets for the CVD and other risk factors in this study. We performed several analyses including gene expression analysis, diseasome analysis, protein-protein interaction (PPI) analysis, and pathway analysis for discovering the relationship between CVD and its risk factors. We also examined the validation of our study using gold benchmark databases OMIM, dbGAP, and DisGeNET. Results We observed that the number of 32, 17, 53, 70, and 89 differentially expressed genes (DEGs) is overlapped between CVD and its risk factors of hypertension (HTN), type 2 diabetes (T2D), hypercholesterolemia (HCL), obesity, and aging, respectively. We identified 10 major hub proteins (FPR2, TNF, CXCL8, CXCL1, IL1B, VEGFA, CYBB, PTGS2, ITGAX, and CCR5), 12 significant functional pathways, and 11 gene ontological pathways that are associated with CVD. We also found the connection of CVD with its risk factors in the gold benchmark databases. Our experimental outcomes indicate a strong association of CVD with its risk factors of HTN, T2D, HCL, obesity, and aging. Conclusions Our computational approach explored the genetic association of CVD with its risk factors by identifying the significant DEGs, hub proteins, and signaling and ontological pathways. The outcomes of this study may be further used in the lab-based analysis for developing the effective treatment strategies of CVD.
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Expression profiling of TaARGOS homoeologous drought responsive genes in bread wheat. Sci Rep 2022; 12:3595. [PMID: 35246579 PMCID: PMC8897478 DOI: 10.1038/s41598-022-07637-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Drought tolerant germplasm is needed to increase crop production, since water scarcity is a critical bottleneck in crop productivity worldwide. Auxin Regulated Gene involved in Organ Size (ARGOS) is a large protein family of transcription factors that plays a vital role in organ size, plant growth, development, and abiotic stress responses in plants. Although, the ARGOS gene family has been discovered and functionalized in a variety of crop plants, but a comprehensive and systematic investigation of ARGOS genes in locally used commercial wheat cultivars is still yet to be reported. The relative expression of three highly conserved TaARGOS homoeologous genes (TaARGOS-A, TaARGOS-B, TaARGOS-D) was studied in three drought-tolerant (Pakistan-2013, NARC-2009 and NR-499) and three sensitive (Borlaug-2016, NR-514 and NR-516) wheat genotypes under osmotic stress, induced by PEG-6000 at 0 (exogenous control), 2, 4, 6, and 12 h. The normalization of target genes was done using β-actin as endogenous control, whereas DREB3, as a marker gene was also transcribed, reinforcing the prevalence of dehydration in all stress treatments. Real-time quantitative PCR revealed that osmotic stress induced expression of the three TaARGOS transcripts in different wheat seedlings at distinct timepoints. Overall, all genes exhibited significantly higher expression in the drought-tolerant genotypes as compared to the sensitive ones. For instance, the expression profile of TaARGOS-A and TaARGOS-D showed more than threefold increase at 2 h and six to sevenfold increase after 4 h of osmotic stress. However, after 6 h of osmotic stress these genes started to downregulate, and the lowest gene expression was noticed after 12 h of osmotic stress. Among all the homoeologous genes, TaARGOS-D, in particular, had a more significant influence on controlling plant growth and drought tolerance as it showed the highest expression. Altogether, TaARGOSs are involved in seedling establishment and overall plant growth. In addition, the tolerant group of genotypes had a much greater relative fold expression than the sensitive genotypes. Ultimately, Pakistan-2013 showed the highest relative expression of the studied genes than other genotypes which shows its proficiency to mitigate osmotic stress. Therefore, it could be cultivated in arid and semi-arid regions under moisture-deficient regimes. These findings advocated the molecular mechanism and regulatory roles of TaARGOS genes in plant growth and osmotic stress tolerance in contrasting groups of wheat genotypes, accompanied by the genetic nature of identified genotypes in terms of their potential for drought tolerance.
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Atout S, Shurrab S, Loveridge C. Evaluation of the Suitability of RNAscope as a Technique to Measure Gene Expression in Clinical Diagnostics: A Systematic Review. Mol Diagn Ther 2021; 26:19-37. [PMID: 34957535 PMCID: PMC8710359 DOI: 10.1007/s40291-021-00570-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2021] [Indexed: 01/01/2023]
Abstract
Objective To evaluate the application of RNAscope in the clinical diagnostic field compared to the current ‘gold standard’ methods employed for testing gene expression levels, including immunohistochemistry (IHC), quantitative real time PCR (qPCR), and quantitative reverse transcriptase PCR (qRT-PCR), and to detect genes, including DNA in situ hybridisation (DNA ISH). Methods This systematic review searched CINAHL, Medline, Embase and Web of Science databases for studies that were conducted after 2012 and that compared RNAscope with one or more of the ‘gold standard’ techniques in human samples. QUADAS-2 test was used for the evaluation of the articles’ risk of bias. The results were reviewed narratively and analysed qualitatively. Results A total of 27 articles (all retrospective studies) were obtained and reviewed. The 27 articles showed a range of low to middle risk of bias scores, as assessed by QUADAS-2 test. 26 articles studied RNAscope within cancer samples. RNAscope was compared to different techniques throughout the included studies (IHC, qPCR, qRT-PCR and DNA ISH). The results confirmed that RNAscope is a highly sensitive and specific method that has a high concordance rate (CR) with qPCR, qRT-PCR, and DNA ISH (81.8–100%). However, the CR with IHC was lower than expected (58.7–95.3%), which is mostly due to the different products that each technique measures (RNA vs. protein). Discussion This is the first systematic review to be conducted on the use of RNAscope in the clinical diagnostic field. RNAscope was found to be a reliable and robust method that could complement gold standard techniques currently used in clinical diagnostics to measure gene expression levels or for gene detection. However, there were not enough data to suggest that RNAscope could stand alone in the clinical diagnostic setting, indicating further prospective studies to validate diagnostic accuracy values, in keeping with relevant regulations, followed by cost evaluation are required. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-021-00570-2.
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Affiliation(s)
- Sameeha Atout
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Room 202, Sir James Black Building, Glasgow, G128QQ, UK
| | - Shaymaa Shurrab
- Division of Biochemical Diseases, Department of Paediatrics, School of Medicine, BC Children's Hospital, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Carolyn Loveridge
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Room 202, Sir James Black Building, Glasgow, G128QQ, UK.
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Abstract
We developed a new label-free biosensor technique for the detection of messenger ribonucleic acid (mRNA) that can be used in the prognosis and diagnosis of certain diseases. We observed a dependence of the negative dielectrophoresis (DEP) force applied to polystyrene microspheres (PMs) in conjugation with different types of mRNA and the frequency of the electric field produced by interdigitated microelectrodes. Since the frequency dependence of the negative DEP force is an effective transduction mechanism for the detection of mRNA, this sensing technology has the potential to be used in the diagnosis and identification of gene expression that is associated with various human disease.
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Weiberg A, Karlovsky P. Components of variance in transcriptomics based on electrophoretic separation of cDNA fragments (cDNA-AFLP). Electrophoresis 2009; 30:2549-57. [PMID: 19588459 PMCID: PMC2909398 DOI: 10.1002/elps.200800756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The sources of variance and errors in transcriptomics based on the electrophoretic separation of amplified cDNA fragments were investigated using cDNA-amplified fragment length polymorphism (AFLP). Transcriptome profiles of the plant-pathogenic fungus Verticillium longisporum were generated by a standard cDNA-AFLP protocol followed by electrophoretic separation of amplified DNA fragments in flatbed polyacrylamide gels with fluorescence detection as well as by capillary electrophoresis (DNA sequencer). The total variance was partitioned into contributions of cDNA synthesis, adapter ligation, preamplification, amplification, and electrophoresis. Parameters of computer-aided peak recognition and matching were investigated and strategies improving matching success based on double passage with different signal intensity thresholds were developed. The overall quality of data was similar for cDNA-AFLP and microarray hybridization. Variance of cDNA-AFLP was independent of signal intensity, whereas microarray data showed higher variance for low-intensity signals. Capillary electrophoresis significantly reduced the number of wrongly matched and unmatched signals as compared with flatbed gels. These results are also likely to apply to related electrophoresis-based transcriptome analysis techniques such as mRNA differential display.
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Affiliation(s)
- Arne Weiberg
- Molecular Phytopathology and Mycotoxin Research Unit, University of Goettingen, Goettingen, Germany
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Martínez-Fernández M, Bernatchez L, Rolán-Alvarez E, Quesada H. Semi-quantitative differences in gene transcription profiles between sexes of a marine snail by a new variant of cDNA-AFLP analysis. Mol Ecol Resour 2009; 10:324-30. [PMID: 21565027 DOI: 10.1111/j.1755-0998.2009.02762.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A variant of the cDNA-AFLP method coupled to an automated sequencer was used to quantify transcripts differentially expressed between sexes of the marine snail Littorina saxatilis. First, we conducted a validation study of the technique using known concentrations of a commercial marker. Second, we analysed six replicates of males and females from a population showing no apparent sexual dimorphism. The results confirm that the method can be properly used within the range of DNA concentrations utilized. In addition, we detected a small percentage of spots (1.8%) differentially expressed between sexes, as expected from a low to moderately sexual dimorphic species.
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Affiliation(s)
- M Martínez-Fernández
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Campus As Lagoas-Marcosende Universidad de Vigo, 36310 Vigo, Spain Department of Biology, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Université Laval, Québec, QC, Canada G1V 0A6
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Hammerling U, Tallsjö A, Grafström R, Ilbäck NG. Comparative Hazard Characterization in Food Toxicology. Crit Rev Food Sci Nutr 2009; 49:626-69. [DOI: 10.1080/10408390802145617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Weiberg A, Pöhler D, Morgenstern B, Karlovsky P. Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA. BMC Genomics 2008; 9:480. [PMID: 18851732 PMCID: PMC2577664 DOI: 10.1186/1471-2164-9-480] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 10/13/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND cDNA-AFLP is a transcriptomics technique which does not require prior sequence information and can therefore be used as a gene discovery tool. The method is based on selective amplification of cDNA fragments generated by restriction endonucleases, electrophoretic separation of the products and comparison of the band patterns between treated samples and controls. Unequal distribution of restriction sites used to generate cDNA fragments negatively affects the performance of cDNA-AFLP. Some transcripts are represented by more than one fragment while other escape detection, causing redundancy and reducing the coverage of the analysis, respectively. RESULTS With the goal of improving the coverage of cDNA-AFLP without increasing its redundancy, we designed a modified cDNA-AFLP protocol. Immobilized cDNA is sequentially digested with several restriction endonucleases and the released DNA fragments are collected in mutually exclusive pools. To investigate the performance of the protocol, software tool MECS (Multiple Enzyme cDNA-AFLP Simulation) was written in Perl. cDNA-AFLP protocols described in the literature and the new sequential digestion protocol were simulated on sets of cDNA sequences from mouse, human and Arabidopsis thaliana. The redundancy and coverage, the total number of PCR reactions, and the average fragment length were calculated for each protocol and cDNA set. CONCLUSION Simulation revealed that sequential digestion of immobilized cDNA followed by the partitioning of released fragments into mutually exclusive pools outperformed other cDNA-AFLP protocols in terms of coverage, redundancy, fragment length, and the total number of PCRs. Primers generating 30 to 70 amplicons per PCR provided the highest fraction of electrophoretically distinguishable fragments suitable for normalization. For A. thaliana, human and mice transcriptome, the use of two marking enzymes and three sequentially applied releasing enzymes for each of the marking enzymes is recommended.
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Affiliation(s)
- Arne Weiberg
- Molecular Phytopathology and Mycotoxin Research Division, University of Goettingen, Goettingen, Germany.
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Kadota K, Araki R, Nakai Y, Abe M. GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data. Algorithms Mol Biol 2007; 2:5. [PMID: 17535446 PMCID: PMC1904450 DOI: 10.1186/1748-7188-2-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 05/30/2007] [Indexed: 11/28/2022] Open
Abstract
Background One-dimensional (1-D) electrophoretic data obtained using the cDNA-AFLP method have attracted great interest for the identification of differentially expressed transcript-derived fragments (TDFs). However, high-throughput analysis of the cDNA-AFLP data is currently limited by the need for labor-intensive visual evaluation of multiple electropherograms. We would like to have high-throughput ways of identifying such TDFs. Results We describe a method, GOGOT, which automatically detects the differentially expressed TDFs in a set of time-course electropherograms. Analysis by GOGOT is conducted as follows: correction of fragment lengths of TDFs, alignment of identical TDFs across different electropherograms, normalization of peak heights, and identification of differentially expressed TDFs using a special statistic. The output of the analysis is a highly reduced list of differentially expressed TDFs. Visual evaluation confirmed that the peak alignment was performed perfectly for the TDFs by virtue of the correction of peak fragment lengths before alignment in step 1. The validity of the automated ranking of TDFs by the special statistic was confirmed by the visual evaluation of a third party. Conclusion GOGOT is useful for the automated detection of differentially expressed TDFs from cDNA-AFLP temporal electrophoretic data. The current algorithm may be applied to other electrophoretic data and temporal microarray data.
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Affiliation(s)
- Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryoko Araki
- Transcriptome Research Center, National Institute of Radiological Sciences (NIRS), 9-1, Anagawa-4-chome, Chiba-shi 263-8555, Japan
| | - Yuji Nakai
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masumi Abe
- Transcriptome Research Center, National Institute of Radiological Sciences (NIRS), 9-1, Anagawa-4-chome, Chiba-shi 263-8555, Japan
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Vähämaa H, Ojala P, Pahikkala T, Nevalainen OS, Lahesmaa R, Aittokallio T. Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments. Electrophoresis 2007; 28:879-93. [PMID: 17309051 DOI: 10.1002/elps.200600424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Modern multicapillary devices allow researchers to address increasingly complex biological questions involving comparisons of gene expression patterns across electrophoretic samples under various experimental conditions. As labor-intensive visual evaluation of the electrophoretic results is often the bottleneck of large-scale differential display (DD) studies, one way to further streamline this process is to focus only on a highly compressed list of the most potential patterns that are likely to provide reliable findings. To enable the identification of such candidate patterns, we present a computer-assisted method for objective ranking of multitrace peak patterns in DD experiments. The fundamental component of the multitrace pattern ranking method (MRANK) is the multiple alignment algorithm that allows for discovery of patterns involving sets of peak complexes from various electrophoretic samples. A score value is attached to each detected pattern which characterizes how accurately the pattern resembles the desired pattern query, freely defined by the researcher. The ranked pattern list produced by MRANK is validated against visual evaluation in terms of detecting and ranking a group of relevant patterns in a DD analysis of T-helper cell differentiation. We demonstrate high enrichment of the desired patterns on top of the score-ranked list (e.g., 90% of the visually selected patterns are discovered by looking through the first 3% of patterns in the ranked list of all patterns). The results suggest that a substantial amount of manual labor can be saved without compromising the accuracy of the findings by prioritizing the patterns according to MRANK output in the visual confirmation phase.
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Affiliation(s)
- Heidi Vähämaa
- Department of Information Technology, University of Turku, Turku, Finland
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Ventzki R, Stegemann J, Martinez L, de Marco A. Automated protein analysis by online detection of laser-induced fluorescence in slab gels and 3-D geometry gels. Electrophoresis 2006; 27:3338-48. [PMID: 16850506 DOI: 10.1002/elps.200600006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) still remains the most reliable and comprehensive analytical method for the evaluation of protein extracts. However, conventional SDS-PAGE is time-consuming and, thus, unpractical if several tens or hundreds of samples must be examined. We show that SDS-PAGE protein analysis can be automated using slab gel DNA sequencers and compare the instrument's performance with conventional SDS-PAGE in terms of resolution, sensitivity and sample capacity. Labeled protein bands are detected online by laser-induced fluorescence (LIF) and the acquired signals are electronically stored for further processing, avoiding gel staining and scanning. Appropriate software allows immediate display of recorded data and convenient evaluation. The method provides a higher sensitivity and dynamic range than conventional Coomassie-stained gels and the resolution of proteins with different masses is independent of the polyacrylamide concentration. Internal markers can also be used for direct quantification and assignment of the molecular masses. Additionally, we present a novel electrophoresis instrument for the simultaneous separation and online LIF detection of all samples of a microtiterplate in parallel lanes in a 3-D geometry gel cylinder. The specific gel thermostatting concept prevents irregular sample migration (smiling) and improves the reproducibility and comparability of individual separation patterns. In combination with the expected large capacity of 384 or 1,536 samples, this makes the instrument a valuable tool for high-throughput comparative screening applications.
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Affiliation(s)
- Robert Ventzki
- Scientific Core Facilities, Services & Technology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447519 DOI: 10.1002/cfg.420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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