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Weiland-Bräuer N, Saleh L, Schmitz RA. Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds. Methods Mol Biol 2023; 2555:23-49. [PMID: 36306077 DOI: 10.1007/978-1-0716-2795-2_3] [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] [Indexed: 06/16/2023]
Abstract
The marine ecosystem covers more than 70% of the world's surface, and oceans represent a source of varied types of organisms due to the diversified environment. Consequently, the marine environment is an exceptional depot of novel bioactive natural products, with structural and chemical features generally not found in terrestrial habitats. Here, in particular, microbes represent a vast source of unknown and probably new physiological characteristics. They have evolved during extended evolutionary processes of physiological adaptations under various environmental conditions and selection pressures. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. Thus, metagenomic tools are required to exploit the untapped marine microbial diversity and their bioactive compounds. This chapter focuses on function-based marine metagenomics to screen for bioactive molecules of value for biotechnology. Functional metagenomic strategies are described, including sampling in the marine environment, constructing marine metagenomic large-insert libraries, and examples on function-based screens for quorum quenching and anti-biofilm activities.
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Affiliation(s)
- Nancy Weiland-Bräuer
- Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany
| | - Livía Saleh
- Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrechts University Kiel, Kiel, Germany.
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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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Emamjomeh A, Zahiri J, Asadian M, Behmanesh M, Fakheri BA, Mahdevar G. Identification, Prediction and Data Analysis of Noncoding RNAs: A Review. Med Chem 2019; 15:216-230. [PMID: 30484409 DOI: 10.2174/1573406414666181015151610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 06/03/2018] [Accepted: 09/30/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs) which play an important role in various cellular processes are important in medicine as well as in drug design strategies. Different studies have shown that ncRNAs are dis-regulated in cancer cells and play an important role in human tumorigenesis. Therefore, it is important to identify and predict such molecules by experimental and computational methods, respectively. However, to avoid expensive experimental methods, computational algorithms have been developed for accurately and fast prediction of ncRNAs. OBJECTIVE The aim of this review was to introduce the experimental and computational methods to identify and predict ncRNAs structure. Also, we explained the ncRNA's roles in cellular processes and drugs design, briefly. METHOD In this survey, we will introduce ncRNAs and their roles in biological and medicinal processes. Then, some important laboratory techniques will be studied to identify ncRNAs. Finally, the state-of-the-art models and algorithms will be introduced along with important tools and databases. RESULTS The results showed that the integration of experimental and computational approaches improves to identify ncRNAs. Moreover, the high accurate databases, algorithms and tools were compared to predict the ncRNAs. CONCLUSION ncRNAs prediction is an exciting research field, but there are different difficulties. It requires accurate and reliable algorithms and tools. Also, it should be mentioned that computational costs of such algorithm including running time and usage memory are very important. Finally, some suggestions were presented to improve computational methods of ncRNAs gene and structural prediction.
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Affiliation(s)
- Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Asadian
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Barat A Fakheri
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Ghasem Mahdevar
- Department of Mathematics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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Serum profile of cytokines and their genetic variants in metabolic syndrome and healthy subjects: a comparative study. Biosci Rep 2019; 39:BSR20181202. [PMID: 30635365 PMCID: PMC6356053 DOI: 10.1042/bsr20181202] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/19/2018] [Accepted: 01/01/2019] [Indexed: 12/18/2022] Open
Abstract
AIM To identify genetic variants in promoter areas of IL-6 -174 G>C and TNF-α -308 G>A in metabolic syndrome (Met S) and controls and associate them with Met S and serum cytokine levels.It was a cross-sectional study, including 224 cases of Met S and 200 controls. A fasting blood sample was taken and biochemical parameters including serum glucose, insulin, lipid profile, interleukin-6 (IL-6) and tumor necrosis factor α (TNF-α) were measured. Restriction fragment length polymorphism was used to identify the genetic variants of IL-6 and TNF-α. Serum levels of IL-6 and TNF-α and insulin resistance were significantly higher in cases than the controls. IL-6 showed significant positive correlation with HOMA-IR and TNF-α. CC genotype of IL-6 was associated with the increased risk of Met S (P=0.016, OR for CC vs GC+GG = 2.33, CI: 1.15-4.71). There was no significant difference of TNF-α genotypes between the cases and the controls. Serum TNF-α and IL-6 levels were significantly higher in AA and CC genotypes of TNF-α (-308 G>A) and IL-6 (-174 G>C) as compared with the GG (P=0.00 and P=0.001). Significant correlation of IL-6 with TNF-α and insulin resistance was observed that may provide us a therapeutic target for preventing metabolic derangements from insulin resistance.
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Techniques and strategies employing engineered transcription factors. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Vitale L, Caracausi M, Casadei R, Pelleri MC, Piovesan A. Difficulty in obtaining the complete mRNA coding sequence at 5' region (5' end mRNA artifact): Causes, consequences in biology and medicine and possible solutions for obtaining the actual amino acid sequence of proteins (Review). Int J Mol Med 2017; 39:1063-1071. [PMID: 28393177 DOI: 10.3892/ijmm.2017.2942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/16/2017] [Indexed: 11/06/2022] Open
Abstract
The known difficulty in obtaining the actual full length, complete sequence of a messenger RNA (mRNA) may lead to the erroneous determination of its coding sequence at the 5' region (5' end mRNA artifact), and consequently to the wrong assignment of the translation start codon, leading to the inaccurate prediction of the encoded polypeptide at its amino terminus. Among the known human genes whose study was affected by this artifact, we can include disco interacting protein 2 homolog A (DIP2A; KIAA0184), Down syndrome critical region 1 (DSCR1), SON DNA binding protein (SON), trefoil factor 3 (TFF3) and URB1 ribosome biogenesis 1 homolog (URB1; KIAA0539) on chromosome 21, as well as receptor for activated C kinase 1 (RACK1, also known as GNB2L1), glutaminyl‑tRNA synthetase (QARS) and tyrosyl-DNA phosphodiesterase 2 (TDP2) along with another 474 loci, including interleukin 16 (IL16). In this review, we discuss the causes of this issue, its quantitative incidence in biomedical research, the consequences in biology and medicine, and the possible solutions for obtaining the actual amino acid sequence of proteins in the post-genomics era.
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Affiliation(s)
- Lorenza Vitale
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Maria Caracausi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Raffaella Casadei
- Department for Life Quality Studies, University of Bologna, I‑47921 Rimini, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
| | - Allison Piovesan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, I‑40126 Bologna, Italy
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Bian S, Zhou Y, Hu Y, Cheng J, Chen X, Xu Y, Liu P. High-throughput in situ cell electroporation microsystem for parallel delivery of single guide RNAs into mammalian cells. Sci Rep 2017; 7:42512. [PMID: 28211892 PMCID: PMC5304186 DOI: 10.1038/srep42512] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/13/2017] [Indexed: 02/06/2023] Open
Abstract
Arrayed genetic screens mediated by the CRISPR/Cas9 technology with single guide RNA (sgRNA) libraries demand a high-throughput platform capable of transfecting diverse cell types at a high efficiency in a genome-wide scale for detection and analysis of sophisticated cellular phenotypes. Here we developed a high-throughput in situ cell electroporation (HiCEP) microsystem which leveraged the superhydrophobic feature of the microwell array to achieve individually controlled conditions in each microwell and coupled an interdigital electrode array chip with the microwells in a modular-based scheme for highly efficient delivery of exogenous molecules into cells. Two plasmids encoding enhanced green and red fluorescent proteins (EGFP and ERFP), respectively, were successfully electroporated into attached HeLa cells on a 169-microwell array chip with transfection efficiencies of 71.6 ± 11.4% and 62.9 ± 2.7%, and a cell viability above 95%. We also successfully conducted selective electroporation of sgRNA into 293T cells expressing the Cas9 nuclease in a high-throughput manner and observed the four-fold increase of the GFP intensities due to the repair of the protein coding sequences mediated by the CRISPR/Cas9 system. This study proved that this HiCEP system has the great potential to be used for arrayed functional screens with genome-wide CRISPR libraries on hard-to-transfect cells in the future.
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Affiliation(s)
- Shengtai Bian
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China
| | - Yicen Zhou
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China
| | - Yawei Hu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China
| | - Jing Cheng
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China
| | - Xiaofang Chen
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Youchun Xu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China
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Gong Y, Desveaux D, Guttman DS, Lewis JD. A Practical Guide to Quantitative Interactor Screening with Next-Generation Sequencing (QIS-Seq). Methods Mol Biol 2017; 1613:1-20. [PMID: 28849555 DOI: 10.1007/978-1-4939-7027-8_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Yeast two-hybrid screens are a powerful approach to identify protein-protein interactions; however, they are typically limited in the number of interactions identified, and lack quantitative values to ascribe confidence scores to the interactions that are obtained. We have developed a high-throughput, quantitative, yeast two-hybrid screening approach coupled with next-generation sequencing. This strategy allows the identification of interacting proteins that are preferentially associated with a bait of interest, and helps eliminate nonspecific interacting proteins. The method is high-throughput, allowing many more baits to be tested and many more candidate interacting proteins to be identified. Quantitative data allows the interactors to be ascribed confidence scores based on their enrichment with particular baits, and can identify both common and rare interacting proteins.
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Affiliation(s)
- Yunchen Gong
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada, M5S 3B2
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada, M5S 3B2
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada, M5S 3B2
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada, M5S 3B2
| | - David S Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada, M5S 3B2
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada, M5S 3B2
| | - Jennifer D Lewis
- Plant Gene Expression Center, United States Department of Agriculture, 800 Buchanan St., Albany, CA, 94710, USA.
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
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Harbers M. Shift-Western Blotting: Separate Analysis of Protein and DNA from Protein-DNA Complexes. Methods Mol Biol 2015; 1312:355-73. [PMID: 26044017 DOI: 10.1007/978-1-4939-2694-7_36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The electrophoretic mobility shift assay (EMSA) is the most frequently used experiment for studying protein-DNA interactions and to identify DNA-binding proteins. Protein-DNA complexes formed during EMSA experiments can be further analyzed by shift-western blotting, where the protein and DNA components contained in a polyacrylamide gel are transferred to stacked membranes: First a nitrocellulose membrane retains the proteins while double-stranded DNA passes through the nitrocellulose membrane and binds only to a charged membrane placed below. Immobilized proteins can then be stained with specific antibodies while the DNA can be detected by a radioactive label or a nonradioactive detection system. Shift-western blotting can overcome many limitations of supershift experiments and allows for the analysis of complex protein-DNA complexes containing multiple protein factors. Moreover, proteins and/or DNA may be recovered from membranes after the blotting step for further analysis by other means.
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Affiliation(s)
- Matthias Harbers
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan,
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Archer SK, Shirokikh NE, Preiss T. Probe-Directed Degradation (PDD) for Flexible Removal of Unwanted cDNA Sequences from RNA-Seq Libraries. ACTA ACUST UNITED AC 2015; 85:11.15.1-11.15.36. [PMID: 25827346 DOI: 10.1002/0471142905.hg1115s85] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Most applications for RNA-seq require the depletion of abundant transcripts to gain greater coverage of the underlying transcriptome. The sequences to be targeted for depletion depend on application and species and in many cases may not be supported by commercial depletion kits. This unit describes a method for generating RNA-seq libraries that incorporates probe-directed degradation (PDD), which can deplete any unwanted sequence set, with the low-bias split-adapter method of library generation (although many other library generation methods are in principle compatible). The overall strategy is suitable for applications requiring customized sequence depletion or where faithful representation of fragment ends and lack of sequence bias is paramount. We provide guidelines to rapidly design specific probes against the target sequence, and a detailed protocol for library generation using the split-adapter method including several strategies for streamlining the technique and reducing adapter dimer content.
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Affiliation(s)
- Stuart K Archer
- Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton, Canberra, Australian Capital Territory, Australia.,Present address: Monash Bioinformatics Platform, Monash University, Clayton, Victoria, Australia.,These authors contributed equally to this work
| | - Nikolay E Shirokikh
- Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton, Canberra, Australian Capital Territory, Australia.,Present address: Moscow Regional State Institute of Humanities and Social Studies, Ministry of Education of Moscow Region, Kolomna, Moscow Region, Russia.,These authors contributed equally to this work
| | - Thomas Preiss
- Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton, Canberra, Australian Capital Territory, Australia.,Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales, Australia
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11
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Harbers M. Wheat germ systems for cell-free protein expression. FEBS Lett 2014; 588:2762-73. [PMID: 24931374 DOI: 10.1016/j.febslet.2014.05.061] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/25/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Cell-free protein expression plays an important role in biochemical research. However, only recent developments led to new methods to rapidly synthesize preparative amounts of protein that make cell-free protein expression an attractive alternative to cell-based methods. In particular the wheat germ system provides the highest translation efficiency among eukaryotic cell-free protein expression approaches and has a very high success rate for the expression of soluble proteins of good quality. As an open in vitro method, the wheat germ system is a preferable choice for many applications in protein research including options for protein labeling and the expression of difficult-to-express proteins like membrane proteins and multiple protein complexes. Here I describe wheat germ cell-free protein expression systems and give examples how they have been used in genome-wide expression studies, preparation of labeled proteins for structural genomics and protein mass spectroscopy, automated protein synthesis, and screening of enzymatic activities. Future directions for the use of cell-free expression methods are discussed.
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Affiliation(s)
- Matthias Harbers
- RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan; CellFree Sciences Co., Ltd., 75-1, Ono-cho, Leading Venture Plaza 201, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan.
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12
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Cipriani F, Ricci G, Leoni MC, Capra L, Baviera G, Longo G, Maiello N, Galli E. Autoimmunity in atopic dermatitis: Biomarker or simply epiphenomenon? J Dermatol 2014; 41:569-76. [DOI: 10.1111/1346-8138.12464] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 01/31/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Francesca Cipriani
- Pediatric Unit; Department of Medical and Surgical Sciences; University of Bologna; Bologna Italy
| | - Giampaolo Ricci
- Pediatric Unit; Department of Medical and Surgical Sciences; University of Bologna; Bologna Italy
| | - Maria Chiara Leoni
- Pediatric Unit; Department of Clinical-Surgical, Diagnostic and Pediatric Sciences; University of Pavia; Pavia Italy
| | - Lucetta Capra
- Department of Reproduction and Pediatrics; University Hospital S. Anna; Ferrara Italy
| | | | | | - Nunzia Maiello
- Department of Woman, Child and General and Specialized Surgery; Second University of Naples; Naples Italy
| | - Elena Galli
- Pediatric Allergy Unit; Research Center; San Pietro Hospital - Fatebenefratelli; Rome Italy
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Silva CC, Mantello CC, Campos T, Souza LM, Gonçalves PS, Souza AP. Leaf-, panel- and latex-expressed sequenced tags from the rubber tree ( Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:1035-1053. [PMID: 25242886 PMCID: PMC4162974 DOI: 10.1007/s11032-014-0095-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/17/2014] [Indexed: 05/10/2023]
Abstract
Hevea brasiliensis is a native species of the Amazon Basin of South America and the primary source of natural rubber worldwide. Due to the occurrence of South American Leaf Blight disease in this area, rubber plantations have been extended to suboptimal regions. Rubber tree breeding is time-consuming and expensive, but molecular markers can serve as a tool for early evaluation, thus reducing time and costs. In this work, we constructed six different cDNA libraries with the aim of developing gene-targeted molecular markers for the rubber tree. A total of 8,263 reads were assembled, generating 5,025 unigenes that were analyzed; 912 expressed sequence tags (ESTs) represented new transcripts, and two sequences were highly up-regulated by cold stress. These unigenes were scanned for microsatellite (SSR) regions and single nucleotide polymorphisms (SNPs). In total, 169 novel EST-SSR markers were developed; 138 loci were polymorphic in the rubber tree, and 98 % presented transferability to six other Hevea species. Locus duplication was observed in H. brasiliensis and other species. Additionally, 43 SNP markers in 13 sequences that showed similarity to proteins involved in stress response, latex biosynthesis and developmental processes were characterized. cDNA libraries are a rich source of SSR and SNP markers and enable the identification of new transcripts. The new markers developed here will be a valuable resource for linkage mapping, QTL identification and other studies in the rubber tree and can also be used to evaluate the genetic variability of other Hevea species, which are valuable assets in rubber tree breeding.
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Affiliation(s)
- Carla C. Silva
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, Campinas, SP CEP 13083-970 Brazil
| | - Camila C. Mantello
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, Campinas, SP CEP 13083-970 Brazil
| | - Tatiana Campos
- Centro de Pesquisa Agroflorestal do Acre (CPAFAC), Embrapa, Rodovia BR-364, km 14, CP 321, Rio Branco, AC CEP 69900-970 Brazil
| | - Livia M. Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, Campinas, SP CEP 13083-970 Brazil
| | - Paulo S. Gonçalves
- Instituto Agronômico de Campinas (IAC), CP 28, Campinas, SP CEP 13012-970 Brazil
| | - Anete P. Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, Campinas, SP CEP 13083-970 Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6109, Campinas, SP CEP 13083-970 Brazil
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Heinemann JA, Kurenbach B, Quist D. Molecular profiling--a tool for addressing emerging gaps in the comparative risk assessment of GMOs. ENVIRONMENT INTERNATIONAL 2011; 37:1285-93. [PMID: 21624662 DOI: 10.1016/j.envint.2011.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 04/15/2011] [Accepted: 05/05/2011] [Indexed: 05/20/2023]
Abstract
Assessing the risks of genetically modified organisms (GMOs) is required by both international agreement and domestic legislation. Many view the use of the "omics" tools for profiling classes of molecules as useful in risk assessment, but no consensus has formed on the need or value of these techniques for assessing the risks of all GMOs. In this and many other cases, experts support case-by-case use of molecular profiling techniques for risk assessment. We review the latest research on the applicability and usefulness of molecular profiling techniques for GMO risk assessment. As more and more kinds of GMOs and traits are developed, broader use of molecular profiling in a risk assessment may be required to supplement the comparative approach to risk assessment. The literature-based discussions on the use of profiling appear to have settled on two findings: 1. profiling techniques are reliable and relevant, at least no less so than other techniques used in risk assessment; and 2. although not required routinely, regulators should be aware of when they are needed. The dismissal of routine molecular profiling may be confusing to regulators who then lack guidance on when molecular profiling might be worthwhile. Molecular profiling is an important way to increase confidence in risk assessments if the profiles are properly designed to address relevant risks and are applied at the correct stage of the assessment.
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Affiliation(s)
- Jack A Heinemann
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
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15
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Wu H, Wang J, Deng R, Xing K, Xiong Y, Huang J, He X, Wang X. Benefits of random-priming: exhaustive survey of a cDNA library from lung tissue of a SARS patient. J Med Virol 2011; 83:574-86. [PMID: 21328370 PMCID: PMC7166665 DOI: 10.1002/jmv.22012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The severe acute respiratory syndrome (SARS) leads to severe injury in the lungs with multiple factors, though the pathogenesis is still largely unclear. This paper describes the particular analyses of the transcriptome of human lung tissue that was infected by SARS‐associated coronavirus (SARS‐CoV). Random primers were used to produce ESTs from total RNA samples of the lung tissue. The result showed a high diversity of the transcripts, covering much of the human genome, including loci which do not contain protein coding sequences. 10,801 ESTs were generated and assembled into 267 contigs plus 7,659 singletons. Sequences matching to SARS‐CoV RNAs and other pneumonia‐related microbes were found. The transcripts were well classified by functional annotation. Among the 7,872 assembled sequences that were identified as from human genome, 578 non‐coding genes were revealed by BLAST search. The transcripts were mapped to the human genome with the restriction of identity = 100%, which found a candidate pool of 448 novel transcriptional loci where EST transcriptional signal was never found before. Among these, 13 loci were never reported to be transcriptional by other detection methods such as gene chips, tiling arrays, and paired‐end ditags (PETs). The result showed that random‐priming cDNA library is valid for the investigation of transcript diversity in the virus‐infected tissue. The EST data could be a useful supplemental source for SARS pathology researches. J. Med. Virol. 83:574–586, 2011. © 2011 Wiley‐Liss, Inc.
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Affiliation(s)
- Hongkai Wu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Xingangxi Road, Guangzhou, People's Republic of China
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Yang W, Ying D, Lau YL. In-depth cDNA library sequencing provides quantitative gene expression profiling in cancer biomarker discovery. GENOMICS PROTEOMICS & BIOINFORMATICS 2009; 7:1-12. [PMID: 19591787 DOI: 10.1016/s1672-0229(09)00003-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Quantitative gene expression analysis plays an important role in identifying differentially expressed genes in various pathological states, gene expression regulation and co-regulation, shedding light on gene functions. Although microarray is widely used as a powerful tool in this regard, it is suboptimal quantitatively and unable to detect unknown gene variants. Here we demonstrated effective detection of differential expression and co-regulation of certain genes by expressed sequence tag analysis using a selected subset of cDNA libraries. We discussed the issues of sequencing depth and library preparation, and propose that increased sequencing depth and improved preparation procedures may allow detection of many expression features for less abundant gene variants. With the reduction of sequencing cost and the emerging of new generation sequencing technology, in-depth sequencing of cDNA pools or libraries may represent a better and powerful tool in gene expression profiling and cancer biomarker detection. We also propose using sequence-specific subtraction to remove hundreds of the most abundant housekeeping genes to increase sequencing depth without affecting relative expression ratio of other genes, as transcripts from as few as 300 most abundantly expressed genes constitute about 20% of the total transcriptome. In-depth sequencing also represents a unique advantage of detecting unknown forms of transcripts, such as alternative splicing variants, fusion genes, and regulatory RNAs, as well as detecting mutations and polymorphisms that may play important roles in disease pathogenesis.
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Affiliation(s)
- Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, China.
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Zeller S, Rhyner C, Meyer N, Schmid-Grendelmeier P, Akdis CA, Crameri R. Exploring the repertoire of IgE-binding self-antigens associated with atopic eczema. J Allergy Clin Immunol 2009; 124:278-85, 285.e1-7. [PMID: 19541355 DOI: 10.1016/j.jaci.2009.05.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 05/11/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
Abstract
BACKGROUND Atopic eczema (AE) is the most common chronic inflammatory skin disease. Recent data demonstrate the presence of autoreactive serum IgE antibodies correlating with the severity of the disease. OBJECTIVE Although several IgE-binding self-antigens have been reported, the whole repertoire of IgE-binding self-antigens is unknown. We aimed to estimate the repertoire size of autoreactive proteins related to AE and clone, produce, and characterize humoral and T-cell responses against novel self-antigens. METHODS Phage surface-displayed human cDNA libraries were enriched for clones binding to serum IgE from patients with AE and screened by using high-throughput technology. Selected clones were used to produce the encoded proteins, to test their IgE-binding ability in Western blots and ELISAs, and their ability to induce mediator release from basophils of sensitized individuals. RESULTS One hundred forty sequences encoding potential IgE-binding self-antigens associated with AE were identified. Sixteen sequences encoded already described self-antigens. Three new sequences showed homology with environmental allergens, 86 encoded known human proteins, 7 predicted proteins, and 28 showed sequence identity with genomic contigs. Immunoblotting and ELISA experiments demonstrated the presence of IgE antibodies in sera from patients with AE to 5 selected recombinant self-antigens and their ability to induce mediator release from basophils of patients with AE who have self-antigen-specific IgE antibodies. CONCLUSION These data demonstrate a broad spectrum of at least 140 IgE-binding self-antigens associated with AE. By binding IgE antibodies or activating specific T cells, they might promote, perpetuate, or both existing skin inflammation.
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Affiliation(s)
- Sabine Zeller
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
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Yang W, Ying D, Lau YL. In-depth cDNA Library Sequencing Provides Quantitative Gene Expression Profiling in Cancer Biomarker Discovery. GENOMICS, PROTEOMICS & BIOINFORMATICS 2009. [PMID: 19591787 PMCID: PMC5054226 DOI: 10.1016/s1672-0229(08)60028-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Quantitative gene expression analysis plays an important role in identifying differentially expressed genes in various pathological states, gene expression regulation and co-regulation, shedding light on gene functions. Although microarray is widely used as a powerful tool in this regard, it is suboptimal quantitatively and unable to detect unknown gene variants. Here we demonstrated effective detection of differential expression and co-regulation of certain genes by expressed sequence tag analysis using a selected subset of cDNA libraries. We discussed the issues of sequencing depth and library preparation, and propose that increased sequencing depth and improved preparation procedures may allow detection of many expression features for less abundant gene variants. With the reduction of sequencing cost and the emerging of new generation sequencing technology, in-depth sequencing of cDNA pools or libraries may represent a better and powerful tool in gene expression profiling and cancer biomarker detection. We also propose using sequence-specific subtraction to remove hundreds of the most abundant housekeeping genes to increase sequencing depth without affecting relative expression ratio of other genes, as transcripts from as few as 300 most abundantly expressed genes constitute about 20% of the total transcriptome. In-depth sequencing also represents a unique advantage of detecting unknown forms of transcripts, such as alternative splicing variants, fusion genes, and regulatory RNAs, as well as detecting mutations and polymorphisms that may play important roles in disease pathogenesis.
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Sarropoulou E, Sepulcre P, Poisa-Beiro L, Mulero V, Meseguer J, Figueras A, Novoa B, Terzoglou V, Reinhardt R, Magoulas A, Kotoulas G. Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax. BMC Genomics 2009; 10:157. [PMID: 19361338 PMCID: PMC2674461 DOI: 10.1186/1471-2164-10-157] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2008] [Accepted: 04/10/2009] [Indexed: 11/10/2022] Open
Abstract
Background The European seabass (Dicentrarchus labrax), one of the most extensively cultured species in European aquaculture productions, is, along with the gilthead sea bream (Sparus aurata), a prospective model species for the Perciformes which includes several other commercially important species. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Revealing transcripts involved in immune response and studying their relative expression enhances the understanding of the immune response mechanism and consequently also the creation of vaccines. The analysis of expressed sequence tags (EST) is an efficient and easy approach for gene discovery, comparative genomics and for examining gene expression in specific tissues in a qualitative and quantitative way. Results Here we describe the construction, analysis and comparison of a total of ten cDNA libraries, six from different tissues infected with V. anguillarum (liver, spleen, head kidney, gill, peritoneal exudates and intestine) and four cDNA libraries from different tissues infected with Nodavirus (liver, spleen, head kidney and brain). In total 9605 sequences representing 3075 (32%) unique sequences (set of sequences obtained after clustering) were obtained and analysed. Among the sequences several immune-related proteins were identified for the first time in the order of Perciformes as well as in Teleostei. Conclusion The present study provides new information to the Gene Index of seabass. It gives a unigene set that will make a significant contribution to functional genomic studies and to studies of differential gene expression in relation to the immune system. In addition some of the potentially interesting genes identified by in silico analysis and confirmed by real-time PCR are putative biomarkers for bacterial and viral infections in fish.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology and Genetics, Hellenic Center of Marine Research, Iraklio, Crete, Greece.
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