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Yang B, Zhao Z, Pan Y, Xie J, Zhou B, Li Y, Dong Y, Liu D. Shear-Thinning and Designable Responsive Supramolecular DNA Hydrogels Based on Chemically Branched DNA. ACS Appl Mater Interfaces 2021; 13:48414-48422. [PMID: 34633793 DOI: 10.1021/acsami.1c15494] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A novel supramolecular DNA hydrogel system was designed based on a directly synthesized chemically branched DNA. For the hydrogel formation, a self-dimer DNA with two sticky ends was designed as the linker to induce the gelation of B-Y. By programing the linker sequence, thermal and metal-ion responsiveness could be introduced into this hydrogel system. This supramolecular DNA hydrogel shows shear-thinning, designable responsiveness, and good biocompatibility, which will simplify the hydrogel composition and preparation process of the supramolecular DNA hydrogel and accelerate its biomedical applications.
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Affiliation(s)
- Bo Yang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhihan Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yufan Pan
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiayin Xie
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Bini Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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Tao Z, Wei L, Wu S, Duan N, Li X, Wang Z. A colorimetric aptamer-based method for detection of cadmium using the enhanced peroxidase-like activity of Au-MoS 2 nanocomposites. Anal Biochem 2020; 608:113844. [PMID: 32763304 DOI: 10.1016/j.ab.2020.113844] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022]
Abstract
In this work, a colorimetric aptamer-based method for detection of cadmium using gold nanoparticles modified MoS2 nanocomposites as enzyme mimic is established. In short, biotinylated Cd2+ aptamers are immobilized by biotin-avidin binding on the bottoms of the microplate, the complementary strands of Cd2+ aptamers are connected to the Au-MoS2 nanocomposites which have the function of enhanced peroxidase-like activity. The csDNA-Au-MoS2 signal probe and target Cd2+ compete for binding Cd2+ aptamer, the color change can be observed by addition of chromogenic substrate, thereby realizing visual detection of Cd2+. The absorbance of the solution at 450 nm has a clear linear relationship with the Cd2+ concentration. The linear range is 1-500 ng/mL, and the limit of detection is 0.7 ng/mL. The assay was used to test white wine samples, the results are consistent with those of atomic absorption spectrometry; which prove that this method can be used for detection of Cd2+ in real samples.
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Affiliation(s)
- Zui Tao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Liting Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Shijia Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Xiang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China; Collaborative Innovation Center of Food Safety and Quality Control of Jiangsu Province, Jiangnan University, Wuxi, 214122, China.
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Abstract
Viroids are noncoding RNA pathogens inducing severe to mild disease symptoms on agriculturally important crop plants. Viroid replication is entirely dependent on host transcription machinery, and their replication/accumulation in the infected cells can activate RNA silencing-a host defense mechanism that targets the viroid itself. RNA silencing produces in the cell large amounts of viroid-specific small RNAs of 21-24-nucleotides by cleaving (or "dicing") entire molecules of viroid RNA. However, viroid replication is resistant to the effects of RNA silencing and disrupts the normal regulation of host gene expression, finally resulting in the development of disease symptoms on infected plant. The molecular mechanisms of biological processes involving RNA silencing and underlying various aspects of viroid-host interaction, such as symptom expression, are of special interests to both basic and applied areas of viroid research. Here we present a method to create infectious viroid cDNA clones and RNA transcripts, the starting material for such analyses, using Hop stunt viroid as an example. Next we describe methods for the preparation and analysis of viroid-specific small RNAs by deep sequencing using tomato plants infected with Potato spindle tuber viroid as an example. Finally we introduce bioinformatics tools and methods necessary to process, analyze, and characterize these viroid-specific small RNAs. These bioinformatic methods provide a powerful new tool for the detection and discovery of both known and new viroid species.
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Affiliation(s)
- Charith Raj Adkar-Purushothama
- RNA group, Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
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Lovato A, Faoro F, Gambino G, Maffi D, Bracale M, Polverari A, Santi L. Construction of a synthetic infectious cDNA clone of Grapevine Algerian latent virus (GALV-Nf) and its biological activity in Nicotiana benthamiana and grapevine plants. Virol J 2014; 11:186. [PMID: 25367743 PMCID: PMC4289286 DOI: 10.1186/1743-422x-11-186] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/08/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Grapevine Algerian latent virus (GALV) is a tombusvirus first isolated in 1989 from an Algerian grapevine (Vitis spp.) plant and more recently from water samples and commercial nipplefruit and statice plants. No further reports of natural GALV infections in grapevine have been published in the last two decades, and artificial inoculations of grapevine plants have not been reported. We developed and tested a synthetic GALV construct for the inoculation of Nicotiana benthamiana plants and different grapevine genotypes to investigate the ability of this virus to infect and spread systemically in different hosts. METHODS We carried out a phylogenetic analysis of all known GALV sequences and an epidemiological survey of grapevine samples to detect the virus. A GALV-Nf clone under the control of the T7 promoter was chemically synthesized based on the full-length sequence of the nipplefruit isolate GALV-Nf, the only available sequence at the time the project was conceived, and the infectious transcripts were tested in N. benthamiana plants. A GALV-Nf-based binary vector was then developed for the agroinoculation of N. benthamiana and grapevine plants. Infections were confirmed by serological and molecular analysis and the resulting ultrastructural changes were investigated in both species. RESULTS Sequence analysis showed that the GALV coat protein is highly conserved among diverse isolates. The first epidemiological survey of cDNAs collected from 152 grapevine plants with virus-like symptoms did not reveal the presence of GALV in any of the samples. The agroinoculation of N. benthamiana and grapevine plants with the GALV-Nf binary vector promoted efficient infections, as revealed by serological and molecular analysis. The GALV-Nf infection of grapevine plants was characterized in more detail by inoculating different cultivars, revealing distinct patterns of symptom development. Ultrastructural changes induced by GALV-Nf in N. benthamiana were similar to those induced by tombusviruses in other hosts, but the cytopathological alterations in grapevine plants were less severe. CONCLUSIONS This is the first report describing the development of a synthetic GALV-Nf cDNA clone, its artificial transmission to grapevine plants and the resulting symptoms and cytopathological alterations.
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Affiliation(s)
- Arianna Lovato
- />Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Franco Faoro
- />Department of Agricultural and Environmental Sciences (DiSAA), University of Milan, via Celoria 2, 20133 Milan, Italy
- />Institute for Sustainable Plant Protection, National Research Council, Grugliasco Unit, Largo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Giorgio Gambino
- />Institute for Sustainable Plant Protection, National Research Council, Grugliasco Unit, Largo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Dario Maffi
- />Department of Agricultural and Environmental Sciences (DiSAA), University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Marcella Bracale
- />Department of Environment, Health and Safety, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| | - Annalisa Polverari
- />Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Luca Santi
- />Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), University of Tuscia, Via San Camillo de Lellis snc, 01100 Viterbo, Italy
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Varshney S, Bhadada SK, Saikia UN, Sachdeva N, Behera A, Arya AK, Sharma S, Bhansali A, Mithal A, Rao SD. Simultaneous expression analysis of vitamin D receptor, calcium-sensing receptor, cyclin D1, and PTH in symptomatic primary hyperparathyroidism in Asian Indians. Eur J Endocrinol 2013; 169:109-16. [PMID: 23660642 DOI: 10.1530/eje-13-0085] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND To explore underlying molecular mechanisms in the pathogenesis of symptomatic sporadic primary hyperparathyroidism (PHPT). MATERIALS AND METHODS Forty-one parathyroid adenomas from patients with symptomatic PHPT and ten normal parathyroid glands either from patients with PHPT (n=3) or from euthyroid patients without PHPT during thyroid surgery (n=7) were analyzed for vitamin D receptor (VDR), calcium-sensing receptor (CASR), cyclin D1 (CD1), and parathyroid hormone (PTH) expressions. The protein expressions were assessed semiquantitatively by immunohistochemistry, based on percentage of positive cells and staining intensity, and confirmed by quantitative real-time PCR. RESULTS Immunohistochemistry revealed significant reductions in VDR (both nuclear and cytoplasmic) and CASR expressions and significant increases in CD1 and PTH expressions in adenomatous compared with normal parathyroid tissue. Consistent with immunohistochemistry findings, both VDR and CASR mRNAs were reduced by 0.36- and 0.45-fold change (P<0.001) and CD1 and PTH mRNAs were increased by 9.4- and 17.4-fold change respectively (P<0.001) in adenomatous parathyroid tissue. PTH mRNA correlated with plasma PTH (r=0.864; P<0.001), but not with adenoma weight, while CD1 mRNA correlated with adenoma weight (r=0.715; P<0.001). There were no correlations between VDR and CASR mRNA levels and serum Ca, plasma intact PTH, or 25-hydroxyvitamin D levels. In addition, there was no relationship between the decreases in VDR and CASR mRNA expressions and the increases in PTH and CD1 mRNA expressions. CONCLUSIONS The expression of both VDR and CASR are reduced in symptomatic PHPT in Asian Indians. In addition, CD1 expression was greatly increased and correlated with adenoma weight, implying a potential role for CD1 in adenoma growth and differential clinical expression of PHPT.
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Affiliation(s)
- Shweta Varshney
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research, 4th Floor, F-Block, Room No. 2, Chandigarh 160012, India
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Abstract
The ability to profile bacterial gene expression has markedly advanced the capacity to understand the molecular mechanisms of pathogenesis, epidemiology, and therapeutics. This advance has been coupled with the development of techniques that enable investigators to identify bacterial specifically expressed genes and promise to open new avenues of functional genomics by allowing researchers to focus on the identified differentially expressed genes. During the past two decades, a number of approaches have been developed to investigate bacterial genes differentially expressed in response to the changing environment, particularly during interaction with their hosts. The most commonly used techniques include in vivo expression technology, signature-tagged mutagenesis, differential fluorescence induction, and cDNA microarrays, which fall into two broad classes: mutagenesis-based technologies and hybridization-based technologies. Selective capture of transcribed sequences, a recently emerging method, is a hybridization-based technique. This technique is powerful in analyzing differential gene expression of the bacteria, with the superb ability to investigate the bacterial species with unknown genomic information. Herein, we describe the application of this technique in a comparative study of the gene expression between two closely related bacteria induced or repressed under a variety of conditions.
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Affiliation(s)
- Ruisheng An
- Department of Entomology, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691, USA.
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Abstract
Pituitary tumor transforming gene is an important gene which is involved in many cellular functions including cell division, DNA repair, organ development, expression, and secretion of various angiogenic and metastatic factors. Overexpression of this gene has also been reported in many cancers. Understanding the molecular pathways induced by this oncogene is therefore important not only to understand the development of the disease but also for proper diagnosis and treatment. Gene profiling is an excellent tool to identify the genetic mechanisms, networks, and pathways associated with a particular disease. Oligo-nucleotide microarrays can be everybody's choice as a first step to identify the global expression of genes involved in the study of interest. Each technique has its own limitation. Therefore, further confirmation of the results with a different technique is always necessary. Quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) is one of the widely used and best described techniques to confirm the microarray data. Here, we describe the qRT-PCR techniques for gene profiling studies and the methods used for the analysis of the output data for further studies.
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Affiliation(s)
- Siva Kumar Panguluri
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 500 S Preston Street, HSC A-Tower, Room 1001, Louisville, KY 40202, USA
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8
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Abstract
Earthworms (Eisenia fetida) were used to study the impact of low-dose cadmium in treated artificial soil (0, 0.6, 3, 6, 15, 30 mg/kg) and contaminated natural soil (1.46 mg/kg). The changes of earthworms' physiological related gene expressions of metallothionein (MT), annetocin, calreticulin and antimicrobial peptides were detected using real-time PCR after a 70-day incubation period. The results showed that low doses of cadmium could up regulate earthworms' MT and down regulate annetocin gene expression and show a significant positive and negative correlation respectively. The expression of two other genes, calreticulin and anti-microbial peptides, was induced at low doses of cadmium (highest gene expression at 0.6 mg/kg for calreticulin and 6 mg/kg for anti-microbial peptides) and inhibited at high doses. No significant correlation was found for these two genes. This study shows that MT and annetocin genes expression found in earthworms in contaminated soil have the potential to be developed as biomarkers of soil cadmium pollution.
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Affiliation(s)
- Xiaohui Mo
- Department of Ecology Science and Engineering, China Agricultural University, Beijing 100193, China.
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9
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Abstract
In the past decade, the advent of microarray technologies has allowed functional genomic studies of male germ cell development, resulting in the identification of genes governing various processes. A major limitation with conventional gene expression microarray is that results obtained are biased due to gene probe design. The gene probes for expression microarrays are usually represented by a small number of probes located at the 3' end of a transcript. Tiling microarrays eliminate such issue by interrogating the genome in an unbiased fashion through probes tiled across the entire genome. These arrays provide higher genomic resolution and allow the identification of novel transcripts. To reveal the complexity of the genomic landscape of developing male germ cells, we applied tiling microarray to evaluate the transcriptome in spermatogonial cells. Over 50% of all known mouse genes are expressed during testicular development. More than 47% of the transcripts are uncharacterized. The results suggested that the transcription machinery in spermaotogonial cells is more complex than previously envisioned.
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Affiliation(s)
- Tin-Lap Lee
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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10
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Marques MC, Perez-Amador MA. Construction and analysis of full-length and normalized cDNA libraries from citrus. Methods Mol Biol 2012; 815:51-65. [PMID: 22130983 DOI: 10.1007/978-1-61779-424-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have developed an integrated method to generate a normalized cDNA collection enriched in full-length and rare transcripts from citrus, using different species and multiple tissues and developmental stages. Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. In this regard, the availability of full-length cDNA clones facilitates functional analysis of the corresponding genes enabling manipulation of their expression and the generation of a variety of tagged versions of the native protein. The development of full-length cDNA sequences has the power to improve the quality of genome annotation, as well as provide tools for functional characterization of genes.
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Affiliation(s)
- M Carmen Marques
- Instituto de Biología Molecular y Celular de Plantas-IBMCP, Universidad Politécnica de Valencia-UPV and Consejo Superior de Investigaciones Científicas-CSIC, CPI 8E, Ingeniero Fausto Elio s/n, Valencia 46022, Spain
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Abstract
Small RNAs (sRNAs) have emerged as one of the most important regulators of gene expression in eukaryotes. sRNAs are intermediate molecules as well as end products in the antiviral defense pathway called RNA interference in plants and animals. Profiling of sRNAs using next-generation sequencing technologies has identified a number of plant viruses that have never been reported previously, and has provided a deeper view of virus populations in a plant that cannot be achieved by conventional methods like PCR and ELISA. In this chapter, we describe the methodology of deep sequencing of sRNAs. The high-throughput and highly sensitive method will revolutionize the identification of plant viruses and the study of molecular plant-virus interactions.
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Affiliation(s)
- Kashmir Singh
- Center for Grapevine Biotechnology, William H. Darr School of Agriculture, Missouri State University, Mountain Grove, MO, USA.
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Fedchenko VI, Kaloshin AA, Medvedev AE. [A novel vector for construction of a cDNA library]. Biomed Khim 2010; 56:329-341. [PMID: 20695212 DOI: 10.18097/pbmc20105603329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A new original vector pEM-(dT)40(f+) has been prepared. It can be used for cDNA library construction from polyadenylated mRNA, isolated from various sources. The pGEM-(dT)40f(+) is initially transformed into single stranded and then into a linear form and its (dT)40 tail at 3'-end is used as the vector-primer for synthesis of the first strand cDNA. The use of a synthetic oligonucleotide complementary to the vector and recombinant DNA results in vector cyclization and synthesis of the second strand cDNA. This approach significantly simplifies cDNA library construction, it does not require PCR reaction (which can induce artifact mutations in cDNA sequences) and restrictase treatment.
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Qi G, Li JT, Ruan QP, Yang J, Su ZX. An optimised, small-scale preparation of high-quality RNA from dry seeds of Davidia involucrata. Phytochem Anal 2009; 20:139-142. [PMID: 19140111 DOI: 10.1002/pca.1108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
INTRODUCTION The dormancy of Davidia involucrata seeds normally lasts for an extended period of time and because of this unique property the species is an excellent model for studying the molecular mechanisms of plant dormancy. The use of minimal plant material is desirable for RNA extraction since D. involucrata is a rare plant and it is relatively difficult to collect large amounts of seeds in order to perform molecular biology studies. OBJECTIVE To improve the quality of RNA obtained from seeds of D. involucrata by eliminating the oxidation of polyphenols during extraction and by preventing polysaccharides and other impurities from being extracted. METHODS A previously described method was modified by the addition of 4% (w/v) poly(N-vinyl-2-pyrrolidone) to the dry seeds during grinding and by adding 5% (v/v) beta-mercaptoethanol and 28% (v/v) ethanol to the extraction buffer. Two further centrifugation steps (5000 and 8000 rpm) were utilised and one-seventh volume of ethanol was incubated with the supernatant at 4 degrees C for 2-3 h prior to the precipitation of RNA. RESULTS Following these modifications, an effective method was established for total RNA extraction from a small amount of dry seeds of D. involucrata. The isolated RNA was shown to have high purity and integrity by gel electrophoresis and spectrophotometry, and was confirmed to be suitable for RT-PCR and the construction of cDNA libraries. CONCLUSION The modified method reduced the amount of seeds required for extraction of total DNA and was beneficial for preserving the endangered species.
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Affiliation(s)
- G Qi
- Sichuan Provincial key Laboratory of Environmental Science and Biological Diversity Conservation, China West Normal University, Nanchong, Sichuan, People's Republic of China
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14
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Abstract
The 5' ends of transcripts provide important information about transcription initiation sites and the approximate locations of local cis-acting enhancer elements; it is therefore important to establish the 5' ends with some precision. RACE (rapid amplification of cDNA ends) PCR is useful for quickly obtaining full length cDNAs for mRNAs for which only part of the sequence is known and to identify alternative 5' or 3' ends of fully sequenced genes. The method consists of using PCR to amplify, from complex mixtures of cellular mRNA, the regions between the known parts of the sequence and non-specific tags appended to the ends of the cDNA. Whereas the poly(A) tail serves to provide such a tag at the 3' end of the mRNA, an artificial one needs to be generated at the 5' end, and various approaches have been described to address this step. The classical scheme for 5' RACE described here is simple, suffices in many instances in which RACE is needed and can be performed in 1-3 days.
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Affiliation(s)
- Elizabeth Scotto-Lavino
- Graduate Program in Molecular & Cellular Pharmacology, Stony Brook University, Stony Brook, New York 11794, USA
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15
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Abstract
Having knowledge of the entire 3' sequence of a cDNA is often important because the non-coding terminal region can contain signals that regulate the stability or subcellular localization of the mRNA. Also, some messages use alternative genomic sites for cleavage and polyadenylation that can alter the above properties, or change the encoded protein. Full-length cDNAs can be obtained from complex mixtures of cellular mRNA using rapid amplification of cDNA ends (RACE) PCR as long as part of the mRNA sequence is known; adding non-specific tags to the ends of the cDNA allows the regions between the known parts of the sequence and the ends to be amplified. In 3' RACE, the poly(A) tail functions as a non-specific tag at the 3' end of the mRNA. cDNA ends can be obtained in 1-3 days using this protocol.
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Affiliation(s)
- Elizabeth Scotto-Lavino
- Graduate Program in Molecular & Cellular Pharmacology, Stony Brook University, Stony Brook, New York 11794, USA
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16
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Abstract
Single-cell gene expression analysis holds great promise for studying diverse biological systems, but methodology to process these precious samples in a reproducible, quantitative, and parallel fashion remains challenging. Here, we utilize microfluidics to isolate picogram and subpicogram mRNA templates, as well as to synthesize cDNA from these templates. We demonstrate single-cell mRNA isolation and cDNA synthesis, provide quantitative calibrations for each step in the process, and measure gene expression in individual cells. The techniques presented here form the foundation for highly parallel single-cell gene expression studies.
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Affiliation(s)
- Joshua S Marcus
- Biochemistry and Molecular Biophysics, California Institute of Technology, MS 128-95, Pasadena, California 91125, USA
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17
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Abstract
'New RACE' (rapid amplification of cDNA ends) PCR is a method for obtaining full-length cDNA for mRNA for which only part of the sequence is known. Starting with cellular mRNA, PCR is used to amplify regions between the known parts of the sequence and nonspecific tags at the ends of the cDNA. In 'new RACE', an anchor is ligated to the 5' end of the mRNA before reverse transcription, resulting in the selective production of full-length 5' cDNA ends. Although 'new RACE' can also be used to amplify 3' ends, only the protocol for obtaining 5' ends is presented here. This protocol can be completed in 1-3 days.
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Affiliation(s)
- Elizabeth Scotto-Lavino
- Graduate Program in Molecular & Cellular Pharmacology, Stony Brook University, Stony Brook, New York 11794, USA
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18
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Abstract
The sedimentation of an mRNA in sucrose gradients is highly affected by its ribosomal association. Sedimentation analysis has therefore become routine for studying changes in ribosomal association of mRNAs of interest. DNA microarray technology has been combined with sedimentation analysis to characterize changes in ribosomal association for thousands of mRNAs in parallel. Such analyses revealed mRNAs that are translationally regulated and have provided new insights into the translation process. In this chapter, we describe possible experimental designs for analyzing genome-wide changes in ribosomal association, and discuss some of their advantages and disadvantages. We then provide a detailed protocol for analysis of polysomal fractions using spotted DNA microarrays.
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Affiliation(s)
- Daniel Melamed
- Department of Biology, Technion--Israel Institute of Technology, Haifa, Israel
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19
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Chen L, Cao L, Zhou L, Jing Y, Chen Z, Deng C, Shen Y, Chen L. Trehalose as a good candidate for enriching full-length cDNAs in cDNA library construction. J Biotechnol 2007; 127:402-7. [PMID: 16950532 DOI: 10.1016/j.jbiotec.2006.07.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 07/09/2006] [Accepted: 07/27/2006] [Indexed: 11/20/2022]
Abstract
It has been reported that the disaccharide trehalose is capable of increasing the thermostability and thermoactivity of reverse transcriptase, and therefore improving the length of cDNA synthesis. However, no test has been done on how the disaccharide trehalose performs in the context of the entire cDNA synthesis processes, or whether it can seamlessly integrate into the commercially available cDNA synthesis kit. In this report, we optimized a protocol to incorporate trehalose in the Stratagene's cDNA library construction kit in order to demonstrate great improvement in cDNA's length (average length of 1.8 kb in the trehalose group versus 1.0 kb in the control). Sequence analysis of the cDNA clones showed that the addition of trehalose did not increase the error rate of the RT products but greatly increase the quantity of full-length in cDNA library.
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Affiliation(s)
- Lei Chen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100080, China
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20
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Dai ZM, Zhu XJ, Chen Q, Yang WJ. PCR-suppression effect: kinetic analysis and application to representative or long-molecule biased PCR-based amplification of complex samples. J Biotechnol 2006; 128:435-43. [PMID: 17194496 DOI: 10.1016/j.jbiotec.2006.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2006] [Revised: 10/18/2006] [Accepted: 10/26/2006] [Indexed: 10/23/2022]
Abstract
In the present study, we analyzed the kinetics of the PCR-suppression effect (PS-effect) and firstly demonstrate that lower annealing temperature enhances PS-effect. Furthermore, we controlled the average size of complex PCR products over a wide range, and simultaneously amplified targets from 0.25 to 10kb by regulating the degree of suppression in a single-primer PCR. In addition, we describe an improved template-switching full-length cDNA synthesis method that greatly reduces truncated cDNA. This study provides a general guide for the design of PS-effect related PCR and is useful for representative or long-transcript enriched cDNA library construction, especially when only a small amount of total RNA is available.
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Affiliation(s)
- Zhong-Min Dai
- Institute of Cell Biology and Genetics, 317, College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang 310058, China
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21
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Asada K. [Analysis of the parameter influencing efficiency of RNA interference and analytic prediction of siRNA effect]. Hokkaido Igaku Zasshi 2006; 81:197-210. [PMID: 16768151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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22
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Gunnarsson GH, Gudmundsson B, Thormar HG, Alfredsson A, Jonsson JJ. Two-dimensional strandness-dependent electrophoresis: A method to characterize single-stranded DNA, double-stranded DNA, and RNA–DNA hybrids in complex samples. Anal Biochem 2006; 350:120-7. [PMID: 16455036 DOI: 10.1016/j.ab.2005.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 12/02/2005] [Accepted: 12/06/2005] [Indexed: 12/11/2022]
Abstract
We describe two-dimensional strandness-dependent electrophoresis (2D-SDE) for quantification and length distribution analysis of single-stranded (ss) DNA fragments, double-stranded (ds) DNA fragments, RNA-DNA hybrids, and nicked DNA fragments in complex samples. In the first dimension nucleic acid molecules are separated based on strandness and length in the presence of 7 M urea. After the first-dimension electrophoresis all nucleic acid fragments are heat denatured in the gel. During the second-dimension electrophoresis all nucleic acid fragments are single-stranded and migrate according to length. 2D-SDE takes about 90 min and requires only basic skills and equipment. We show that 2D-SDE has many applications in analyzing complex nucleic acid samples including (1) estimation of renaturation efficiency and kinetics, (2) monitoring cDNA synthesis, (3) detection of nicked DNA fragments, and (4) estimation of quality and in vitro damage of nucleic acid samples. Results from 2D-SDE should be useful to validate techniques such as complex polymerase chain reaction, subtractive hybridization, cDNA synthesis, cDNA normalization, and microarray analysis. 2D-SDE could also be used, e.g., to characterize biological nucleic acid samples. Information obtained with 2D-SDE cannot be readily obtained with other methods. 2D-SDE can be used for preparative isolation of ssDNA fragments, dsDNA fragments, and RNA-DNA hybrids.
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Affiliation(s)
- Gudmundur H Gunnarsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Reykjavik
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23
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Abstract
BACKGROUND Current gene expression analysis relies on the assumption that the isolated RNA represents all species of mRNA in proportions equal to those in the original materials. No system is available for absolute quantification of mRNA. METHODS We applied whole blood to 96-well filterplates to trap leukocytes. Lysis buffer containing cocktails of specific reverse primers and known concentrations of synthetic external control RNA (RNA34) was added to filterplates, and cell lysates were transferred to oligo(dT)-immobilized microplates for hybridization. We then synthesized the cDNA in the oligo(dT)-immobilized microplates from these primer sites and used the cDNA for real-time PCR. RNA34 acted as a universal control, and gene amplification results were converted to quantities of mRNA per microliter of whole blood after the recovery of RNA34 in each sample was determined. RESULTS Under fully optimized conditions, both added RNA34 and native mRNA species exhibited approximately 10% recovery from whole blood to real-time PCR. When whole blood was stimulated ex vivo, changes in gene expression as low as 30%-40% were detected with statistical significance, and the experimental CVs were low (10%-20%). CONCLUSION This new system to estimate mRNA copies per microliter of whole blood may allow standardization of gene-expression-based molecular diagnostics.
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24
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Abstract
Microarray chips produced by commercial vendors and academic laboratories are mostly generic in nature to facilitate wide applicability. With the sequencing of the human, mouse, and rat genomes, the thrust is to expand clone and oligonucleotide sets and increase the number of genes represented on a particular array. This is appropriate for discovery based investigations where microarray technology has been successfully utilized. However, array technology can also be employed to perform hypothesis based studies if optimized chips can be produced with relevant content. Existing array technology available at core facilities can be effectively utilized to produce a custom microarrays with genes that are most relevant to the research interests of individual investigators or research groups for use as a standard molecular tool. The power of this technology can be harnessed to further our understanding of specific biological problems without involvement in extensive data mining and analysis. The custom microarray approach is presented with procedural details for design and production in the context of neurobiological investigations.
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Affiliation(s)
- Samuel S Newton
- Division of Molecular Psychiatry, Yale University School of Medicine, New Haven, CT 06508, USA.
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25
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Degenkolbe T, Hannah MA, Freund S, Hincha DK, Heyer AG, Köhl KI. A quality-controlled microarray method for gene expression profiling. Anal Biochem 2005; 346:217-24. [PMID: 16213454 DOI: 10.1016/j.ab.2005.08.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 08/18/2005] [Accepted: 08/23/2005] [Indexed: 10/25/2022]
Abstract
Gene expression profiling on microarrays is widely used to measure the expression of large numbers of genes in a single experiment. Because of the high cost of this method, feasible numbers of replicates are limited, thus impairing the power of statistical analysis. As a step toward reducing technically induced variation, we developed a procedure of sample preparation and analysis that minimizes the number of sample manipulation steps, introduces quality control before array hybridization, and allows recovery of the prepared mRNA for independent validation of results. Sample preparation is based on mRNA separation using oligo(dT) magnetic beads, which are subsequently used for first-strand cDNA synthesis on the beads. cDNA covalently bound to the magnetic beads is used as template for second-strand cDNA synthesis, leaving the intact mRNA in solution for further analysis. The quality of the synthesized cDNA can be assessed by quantitative polymerase chain reaction using 3'- and 5'-specific primer pairs for housekeeping genes such as glyceraldehyde-3-phosphate dehydrogenase. Second-strand cDNA is chemically labeled with fluorescent dyes to avoid dye bias in enzymatic labeling reactions. After hybridization of two differently labeled samples to microarray slides, arrays are scanned and images analyzed automatically with high reproducibility. Quantile-normalized data from five biological replica display a coefficient of variation 45% for 90% of profiled genes, allowing detection of twofold changes with false positive and false negative rates of 10% each. We demonstrate successful application of the procedure for expression profiling in plant leaf tissue. However, the method could be easily adapted for samples from animal including human or from microbial origin.
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Affiliation(s)
- Thomas Degenkolbe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14424 Potsdam, Germany
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26
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Schindler H, Wiese A, Auer J, Burtscher H. cRNA target preparation for microarrays: Comparison of gene expression profiles generated with different amplification procedures. Anal Biochem 2005; 344:92-101. [PMID: 16038869 DOI: 10.1016/j.ab.2005.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 06/02/2005] [Accepted: 06/02/2005] [Indexed: 10/25/2022]
Abstract
Microarray technology has become a standard tool for generation of gene expression profiles to explore human disease processes. Being able to start from minute amounts of RNA extends the fields of application to core needle biopsies, laser capture microdissected cells, and flow-sorted cells. Several RNA amplification methods have been developed, but no extensive comparability and concordance studies of gene expression profiles are available. Different amplification methods may produce differences in gene expression patterns. Therefore, we compared profiles processed by a standard microarray protocol with three different types of RNA amplification: (i) two rounds of linear target amplification, (ii) random amplification, and (iii) amplification based on a template switching mechanism. The latter two methods accomplish target amplification in a nonlinear way using PCR technology. Starting from as little as 50 ng of total RNA, the yield of labeled cRNA was sufficient for hybridization to Affymetrix HG-U133A GeneChip array using the respective methods. Replicate experiments were highly reproducible for each method. In comparison with the standard protocol, all three approaches are less sensitive and introduced a minor but clearly detectable bias of the detection call. In conclusion, the three amplification protocols used are applicable for GeneChip analysis of small tissue samples.
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Affiliation(s)
- Heike Schindler
- Roche Diagnostics, Pharma Research, Nonnenwald 2, D-82372 Penzberg, Germany
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27
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Abstract
The fluorinated olefinic peptide nucleic acid (F-OPA) system was designed as a peptide nucleic acid (PNA) analogue in which the base carrying amide moiety was replaced by an isostructural and isoelectrostatic fluorinated C-C double bond, locking the nucleobases in one of the two possible rotameric forms. By comparison of the base-pairing properties of this analogue with its nonfluorinated analogue OPA and PNA, we aimed at a closer understanding of the role of this amide function in complementary DNA recognition. Here we present the synthesis of the F-OPA monomer building blocks containing the nucleobases A, T, and G according to the MMTr/Acyl protecting group scheme. Key steps are a selective desymmetrization of the double bond in the monomer precursor via lactonization as well as a highly regioselective Mitsunobu reaction for the introduction of the bases. PNA decamers containing single F-OPA mutations and fully modified F-OPA decamers and pentadecamers containing the bases A and T were synthesized by solid-phase peptide chemistry, and their hybridization properties with complementary parallel and antiparallel DNA were assessed by UV melting curves and CD spectroscopic methods. The stability of the duplexes formed by the decamers containing single (Z)-F-OPA modifications with parallel and antiparallel DNA was found to be strongly dependent on their position in the sequence with T(m) values ranging from +2.4 to -8.1 degrees C/modification as compared to PNA. Fully modified F-OPA decamers and pentadecamers were found to form parallel duplexes with complementary DNA with reduced stability compared to PNA or OPA. An asymmetric F-OPA pentadecamer was found to form a stable self-complex (T(m) approximately 65 degrees C) of unknown structure. The generally reduced affinity to DNA may therefore be due to an increased propensity for self-aggregation.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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28
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Stockhausen MT, Sjölund J, Manetopoulos C, Axelson H. Effects of the histone deacetylase inhibitor valproic acid on Notch signalling in human neuroblastoma cells. Br J Cancer 2005; 92:751-9. [PMID: 15685243 PMCID: PMC2361888 DOI: 10.1038/sj.bjc.6602309] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Neuroblastoma (NB), a sympathetically derived childhood tumour, shows characteristics of neuronal precursor cells, suggesting a halted differentiation process. We have previously shown that the Notch signalling cascade, a key player during normal neurogenesis, also might be involved in NB differentiation. Valproic acid (VPA), a well-tolerated antiepileptic drug, has been shown to induce differentiation and cell death of NB cells, possibly associated with its recently described HDAC inhibiting activity. Stimulation of NB cells with VPA led to increased cell death and phenotypic changes associated with differentiation, that is, neurite extension and upregulation of neuronal markers. VPA treatment also led to an activated Notch signalling cascade as shown by increased levels of intracellular Notch-1 and Hes-1, mimicking the initial phase of induced differentiation. These results reinforce that VPA potentially could be used in differentiation therapy of NB and that the effects in part could be a consequence of interference with the Notch signalling cascade.
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Affiliation(s)
- M-T Stockhausen
- Department of Laboratory Medicine, Division of Molecular Medicine, Lund University, University Hospital MAS, S-205 02 Malmö, Sweden
| | - J Sjölund
- Department of Laboratory Medicine, Division of Molecular Medicine, Lund University, University Hospital MAS, S-205 02 Malmö, Sweden
| | - C Manetopoulos
- Department of Laboratory Medicine, Division of Molecular Medicine, Lund University, University Hospital MAS, S-205 02 Malmö, Sweden
| | - H Axelson
- Department of Laboratory Medicine, Division of Molecular Medicine, Lund University, University Hospital MAS, S-205 02 Malmö, Sweden
- Department of Laboratory Medicine, Division of Molecular Medicine, Lund University, University Hospital MAS, S-205 02 Malmö, Sweden. E-mail:
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29
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Iwahashi F, Fujisaki K, Kaido M, Okuno T, Mise K. Synthesis of infectious in vitro transcripts from Cassia yellow blotch bromovirus cDNA clones and a reassortment analysis with other bromoviruses in protoplasts. Arch Virol 2005; 150:1301-14. [PMID: 15770356 DOI: 10.1007/s00705-005-0500-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Accepted: 01/14/2005] [Indexed: 11/28/2022]
Abstract
Cassia yellow blotch virus (CYBV), genus Bromovirus, was isolated from the Australian native legume, Cassia pleurocarpa, in western Queensland, and its host range was found to be distinct from other bromoviruses. In this study, CYBV was shown to infect systemically and efficiently a model plant species, Arabidopsis thaliana, as we recently reported for another bromovirus, Spring beauty latent virus (SBLV). We constructed full-length cDNA clones of CYBV genomic RNAs from which infectious in vitro transcripts can be transcribed, and determined their complete nucleotide sequences. CYBV RNA3 contains the box B motif in the intercistronic region, but lacks the subgenomic promoter-like sequence in the 5' noncoding region, as does Brome mosaic virus (BMV). To understand relationships among bromoviruses, we generated reassortants between CYBV and three other bromoviruses, BMV, SBLV and Cowpea chlorotic mottle virus. We found that all reassortants between BMV and CYBV accumulated viral RNAs to detectable levels in protoplasts of Nicotiana benthamiana, even when RNAs 1 and 2, which encode the replication proteins 1a and 2a, respectively, were heterologous. Sequence comparison and reassortment experiments of CYBV and other bromoviruses demonstrated that CYBV is closely related to BMV.
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Affiliation(s)
- F Iwahashi
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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30
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Rollin J, Iochmann S, Bléchet C, Hubé F, Régina S, Guyétant S, Lemarié E, Reverdiau P, Gruel Y. Expression and methylation status of tissue factor pathway inhibitor-2 gene in non-small-cell lung cancer. Br J Cancer 2005; 92:775-83. [PMID: 15685245 PMCID: PMC2361876 DOI: 10.1038/sj.bjc.6602298] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Revised: 10/27/2004] [Accepted: 11/02/2004] [Indexed: 01/22/2023] Open
Abstract
Tissue factor pathway inhibitor-2 (TFPI-2) is a Kunitz-type serine proteinase inhibitor that inhibits plasmin-dependent activation of several metalloproteinases. Downregulation of TFPI-2 could thus enhance the invasive potential of neoplastic cells in several cancers, including lung cancer. In this study, TFPI-2 mRNA was measured using a real-time PCR method in tumours of 59 patients with non-small-cell lung cancer (NSCLC). Tumour TFPI-2 mRNA levels appeared well correlated with protein expression evaluated by immunohistochemistry and were 4-120 times lower compared to those of nonaffected lung tissue in 22 cases (37%). Hypermethylation of the TFPI-2 gene promoter was demonstrated by restriction enzyme-polymerase chain reaction in 12 of 40 cases of NSCLC (30%), including nine of 17 for whom tumour TFPI-2 gene expression was lower than in noncancerous tissue. In contrast, this epigenetic modification was shown in only three of 23 tumours in which no decrease in TFPI-2 synthesis was found (P=0.016). Decreased TFPI-2 gene expression and hypermethylation were more frequently associated with stages III or IV NSCLC (eight out of 10, P=0.02) and the TFPI-2 gene promoter was more frequently hypermethylated in patients with lymph node metastases (eight out of 16, P=0.02). These results suggest that silencing of the TFPI-2 gene by hypermethylation might contribute to tumour progression in NSCLC.
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Affiliation(s)
- J Rollin
- INSERM U 618 ‘Protéases et Vectorisation Pulmonaires’ and IFR 135 Faculté de Médecine, 2 bis Bd Tonnellé, 37032 Tours Cedex, France
| | - S Iochmann
- INSERM U 618 ‘Protéases et Vectorisation Pulmonaires’ and IFR 135 Faculté de Médecine, 2 bis Bd Tonnellé, 37032 Tours Cedex, France
| | - C Bléchet
- INSERM U 618 ‘Protéases et Vectorisation Pulmonaires’ and IFR 135 Faculté de Médecine, 2 bis Bd Tonnellé, 37032 Tours Cedex, France
| | - F Hubé
- INSERM U 618 ‘Protéases et Vectorisation Pulmonaires’ and IFR 135 Faculté de Médecine, 2 bis Bd Tonnellé, 37032 Tours Cedex, France
| | - S Régina
- INSERM U 618 ‘Protéases et Vectorisation Pulmonaires’ and IFR 135 Faculté de Médecine, 2 bis Bd Tonnellé, 37032 Tours Cedex, France
| | - S Guyétant
- INSERM U 618 ‘Protéases et Vectorisation Pulmonaires’ and IFR 135 Faculté de Médecine, 2 bis Bd Tonnellé, 37032 Tours Cedex, France
| | - E Lemarié
- INSERM U 618 ‘Protéases et Vectorisation Pulmonaires’ and IFR 135 Faculté de Médecine, 2 bis Bd Tonnellé, 37032 Tours Cedex, France
| | - P Reverdiau
- INSERM U 618 ‘Protéases et Vectorisation Pulmonaires’ and IFR 135 Faculté de Médecine, 2 bis Bd Tonnellé, 37032 Tours Cedex, France
| | - Y Gruel
- INSERM U 618 ‘Protéases et Vectorisation Pulmonaires’ and IFR 135 Faculté de Médecine, 2 bis Bd Tonnellé, 37032 Tours Cedex, France
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31
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Abstract
RNA extraction still relies almost exclusively on the use of fresh or frozen tissue, limiting the number of samples that can be analyzed, and there is a growing need for means of global mRNA analysis of archived formalin-fixed paraffin-embedded tissue (FFPET). Previous reports of RNA extraction and amplification from FFPET are limited and do not enable global cDNA amplification. This study used polyA PCR to generate globally amplified cDNA from RNA extracted from formalin-fixed paraffin-embedded samples. RNA was extracted from nine routinely processed archival FFPET samples (lymph node, nasopharynx, prostate, lung and bone marrow) using an Ambion Paraffin Block RNA Isolation Kit. Global cDNA was generated by polyA RT-PCR and used in GAPDH specific PCR and PCR for CD33, c-myb, and SNF2. PolyA cDNA was reamplified by polyA PCR and the reamplified cDNA also used in GAPDH PCR. RNA was extracted from all nine samples, but was degraded. PolyA RT-PCR generated cDNA from all samples and was positive for GAPDH PCR in seven. PCR for CD33, c-myb, and SNF2 was positive in all samples tested. Following reamplification, the polyA cDNA remained positive for GAPDH by PCR. The results demonstrate the feasibility of globally amplifying RNA isolated from archival FFPET samples using polyA RT-PCR, which generates a renewable cDNA pool that can be probed for any cDNA species and reamplified as necessary.
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Affiliation(s)
- Richard Byers
- Laboratory Medicine Academic Group, Faculty of Medicine, Dentistry, Nursing, and Pharmacy, University of Manchester, England.
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32
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Venkataraman T, Dancausse E, King ML. PCR-based cloning and differential screening of RNAs from Xenopus primordial germ cells: cloning uniquely expressed RNAs from rare cells. Methods Mol Biol 2004; 254:67-78. [PMID: 15041756 DOI: 10.1385/1-59259-741-6:067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
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33
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Bovin LF, Rieneck K, Workman C, Nielsen H, Sørensen SF, Skjødt H, Florescu A, Brunak S, Bendtzen K. Blood cell gene expression profiling in rheumatoid arthritis. Immunol Lett 2004; 93:217-26. [PMID: 15158620 DOI: 10.1016/j.imlet.2004.03.018] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2004] [Revised: 03/26/2004] [Accepted: 03/29/2004] [Indexed: 11/18/2022]
Abstract
UNLABELLED To study the pathogenic importance of the rheumatoid factor (RF) in rheumatoid arthritis (RA) and to identify genes differentially expressed in patients and healthy individuals, total RNA was isolated from peripheral blood mononuclear cells (PBMC) from eight RF-positive and six RF-negative RA patients, and seven healthy controls. Gene expression of about 10,000 genes were examined using oligonucleotide-based DNA chip microarrays. The analyses showed no significant differences in PBMC expression patterns from RF-positive and RF-negative patients. However, comparisons of gene expression patterns from all fourteen RA patients and healthy controls identified a subset of discriminative genes. These results were validated by real time reverse transcription polymerase chain reaction (RT-PCR) on another group of RA patients and healthy controls. This confirmed that the following genes had a significantly higher expression in RA patients than in healthy controls: CD14 antigen, defensin alpha-1 and alpha-3 (DEFA), fatty-acid-Coenzyme A ligase, long-chain 2 (FACL), ribonuclease 2 (RNASE2), S100 calcium-binding protein A8 and A12 (S100A8 and S100A12). In contrast, the expression of MHC class II, DQ beta1 (HLA-DQB1) was significantly reduced in RA patients compared to healthy controls. CONCLUSIONS With the analytical procedure employed, we did not find any indication that RF-positive and RF-negative RA are two fundamentally different diseases. Most of the genes discriminative between RA patients and healthy individuals are known to be involved in immunoinflammatory responses, especially those related to altered phagocytic functions.
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Affiliation(s)
- Lone Frier Bovin
- Institute for Inflammation Research IIR 7521, Rigshospitalet National University Hospital, Blegdamsvej 9, DK-2100, Copenhagen, Denmark
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34
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Hemberger M. cDNA subtraction and cloning in the field of trophoblast/placental development. Methods Mol Biol 2004; 254:49-66. [PMID: 15041755 DOI: 10.1385/1-59259-741-6:049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- Myriam Hemberger
- Department of Biochemistry and Molecular Biology, Genes and Development Research Group, University of Calgary, Alberta, Canada
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35
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Camacho A, Korn K, Damond M, Cajot JF, Litborn E, Liao B, Thyberg P, Winter H, Honegger A, Gardellin P, Rigler R. Direct quantification of mRNA expression levels using single molecule detection. J Biotechnol 2004; 107:107-14. [PMID: 14711494 DOI: 10.1016/j.jbiotec.2003.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Determination of the gene expression by direct quantification of mRNA is becoming increasingly important in basic, pharmaceutical and clinical research. We present a novel approach for gene quantification based on direct hybridization of gene-specific probes to target mRNA sequences in solution at temperatures ensuring absolute specificity of the probe-target complex. No enzymatic steps like reverse transcription or amplification by PCR are involved within the quantification process. In order to increase specificity as well as sensitivity, two probes emitting fluorescence light in different colors are used for our homogeneous assay using fluorescence cross-correlation. We relate to the single molecule sensitivity of excitation and detection in confocal cavities avoiding the amplification of the detected signal. The analysis of the expression level of high, medium and low abundant genes is described in two different cell lines, whereby the genes are quantified in absolute numbers.
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MESH Headings
- Calcium-Binding Proteins
- Calibration
- Chromatography, High Pressure Liquid
- Cytoskeletal Proteins/analysis
- DNA, Complementary/chemical synthesis
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Complementary/metabolism
- Fluorescent Dyes
- Gene Expression
- HL-60 Cells
- Humans
- K562 Cells
- Membrane Glycoproteins/analysis
- Nerve Tissue Proteins/analysis
- Phosphoglycerate Kinase/analysis
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Reproducibility of Results
- Rhodamines
- Sensitivity and Specificity
- Solutions
- Spectrometry, Fluorescence/methods
- Spectrophotometry, Ultraviolet
- Synaptotagmins
- Time Factors
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Affiliation(s)
- Agnès Camacho
- Gnothis SA, PSE-B, EPFL, CH-1015 Lausanne, Switzerland
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36
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Leonard MO, O'Reilly S, Comerford KM, Taylor CT. Identification of Cyclic AMP Response Element-Binding Protein-Dependent Transcriptional Responses in Hypoxia by Microarray Analysis. Methods Enzymol 2004; 381:511-24. [PMID: 15063695 DOI: 10.1016/s0076-6879(04)81033-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- Martin O Leonard
- The Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Ireland
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37
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Gregory P, Ziemiecki A, Zürcher G, Brodbeck U, Bütikofer P. Anti-Mouse GPI-PLD Antisera Highlight Structural Differences between Murine and Bovine GPI-PLDs. Biol Chem 2003; 384:1575-82. [PMID: 14719799 DOI: 10.1515/bc.2003.174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractDespite its well characterised biochemistry, the physiological role of glycosylphosphatidylinositolspecific phospholipase D (GPIPLD) is unknown. Most of the previous studies investigating the distribution of GPI-PLD have focused on the human and bovine forms of the enzyme. Studies on mouse GPI-PLD are rare, partly due to the lack of a specific antimouse GPI-PLD antibody, but also due to the apparent low reactivity of existing antibodies to rodent GPI-PLDs. Here we describe the isolation of a mouse liver cDNA, the construction and expression of a recombinant enzyme and the generation of an affinitypurified rabbit antimouse GPI-PLD antiserum. The antibody shows good reactivity to partially purified murine and purified bovine GPI-PLD. In contrast, a rat antibovine GPI-PLD antibody shows no reactivity with the mouse enzyme and the two antibodies recognise different proteolytic fragments of the bovine enzyme. Comparison between the rodent, bovine and human enzymes indicates that small changes in the amino acid sequence of a short peptide in the mouse and bovine GPI-PLDs may contribute to the different reactivities of the two antisera. We discuss the implications of these results and stress the importance of antibody selection while investigating GPI-PLD in the mouse.
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Affiliation(s)
- Patrick Gregory
- Institute of Biochemistry and Molecular Biology, University of Bern, Bühlstrasse 28, CH-3012 Bern, Switzerland
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38
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Affiliation(s)
- B C Delidow
- Department of Anatomy, University of Connecticut Health Center, Farmington, USA
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39
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Burrell MM. Construction of cDNA libraries. Methods Mol Biol 2003; 58:199-209. [PMID: 8713866 DOI: 10.1385/0-89603-402-x:199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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40
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Affiliation(s)
- C W Schweinfest
- Hollings Cancer Center, Medical University of South Carolina, Charleston, USA
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41
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Abstract
Real-time observation of DNA strand synthesis by using a supercritical angle fluorescence detection apparatus for surface-selective fluorescence detection is described. DNA template molecules were immobilized on a glass surface and the synthesis of the complementary strand was observed after addition of enzyme, dTTP, dATP, dGTP, and fluorescently labeled dCTP (d, deoxy; TP, triphosphate; T, A, G, and C, nucleobases). The fluorescence increase during the Klenow-fragment-catalyzed polymerization depends on the number of labeled dCTP nucleotides incorporated. The efficiency of this reaction is of the same order of magnitude as that of a bimolecular hybridization reaction.
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Affiliation(s)
- Alexander Krieg
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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42
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Affiliation(s)
- Iuri D Louro
- Department of Medicine, The University of Alabama at Birmingham, USA
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43
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Bugni JM, Drinkwater NR. Representational difference analysis of gene expression. Methods Mol Biol 2003; 222:385-97. [PMID: 12710700 DOI: 10.1385/1-59259-328-3:385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- James M Bugni
- McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, USA
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44
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Affiliation(s)
- Kathy Boon
- Duke University Medical Center, Durham, NC, USA
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45
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Biade S, Murphy ME. Differential display techniques to identify tumor suppressor gene pathways. Methods Mol Biol 2003; 222:481-90. [PMID: 12710706 DOI: 10.1385/1-59259-328-3:481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Siham Biade
- Department of Pharmacology, Fox Chase Cancer Center, Philadelphia, PA, USA
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46
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Affiliation(s)
- Zhaohui Wang
- Western Australia State Agricultural Biotechnology Center, Murdoch University, Perth, Australia
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47
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Asada M, Imamura T. Strategy for construction of a cDNA encoding a repetitive amino acid sequence. Methods Mol Biol 2003; 221:261-9. [PMID: 12703750 DOI: 10.1385/1-59259-359-3:261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Masahiro Asada
- Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
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48
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Affiliation(s)
- Mikhail V Matz
- Whitney Laboratory, University of Florida, St. Augustine, USA
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49
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Affiliation(s)
- Yutaka Suzuki
- Laboratory of Genome Structure Analysis, HGC, Institute of Medical Science, University of Tokyo, Japan
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50
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Ying SY, Lin SL. Subtractive cloning of differential genes using RNA-PCR. Methods Mol Biol 2003; 221:253-9. [PMID: 12703749 DOI: 10.1385/1-59259-359-3:253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Affiliation(s)
- Shao-Yao Ying
- Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, USA
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