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Zhang X, Guo J, Song B, Zhang F. Spatiotemporal Regulation of Metal Ions in the Polymerase Chain Reaction. ACS OMEGA 2022; 7:33530-33536. [PMID: 36157739 PMCID: PMC9494670 DOI: 10.1021/acsomega.2c04507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
The polymerase chain reaction (PCR) has been widely used in medical diagnosis and forensic identification due to its ultrahigh sensitivity and signal amplification. Metal ions (i.e., Cu2+, Zn2+) have been considered PCR inhibitors and rarely shown their positive roles in PCR amplification until our report, in which we discovered that metal ions can significantly improve the PCR specificity and the yield of target DNA sequences. For an in-depth investigation with taking copper ions as a typical model, here we found an interesting spatiotemporal regulation mechanism of metal ions in PCR. The ionic concentration window for improving PCR specificity not only was independent of annealing temperature but also can be well regulated by both the annealing time and extension time. Using the ionic concentration window as a measure, the time affects either the amount or the sequence length of nonspecific amplicons in the space. The mechanism proposed in this work will deepen our understanding of the unneglectable roles of metal ions in DNA replication and meanwhile provide a new strategy for designing regulation kits for PCR-based biomedical applications.
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Affiliation(s)
- Xianjing Zhang
- Key
Laboratory of Optical Technology and Instrument for Medicine, Ministry
of Education, School of Optical-Electrical Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Jun Guo
- Key
Laboratory of Optical Technology and Instrument for Medicine, Ministry
of Education, School of Optical-Electrical Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Bo Song
- Key
Laboratory of Optical Technology and Instrument for Medicine, Ministry
of Education, School of Optical-Electrical Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Feng Zhang
- Key
Laboratory of Optical Technology and Instrument for Medicine, Ministry
of Education, School of Optical-Electrical Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
- Quantum
Biophotonic Lab, Wenzhou Institute, University
of Chinese Academy of Sciences, Wenzhou 325001, China
- School
of Biomedical Engineering, Guangzhou Medical
University, Guangzhou 511436, China
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Liguori K, Keenum I, Davis BC, Calarco J, Milligan E, Harwood VJ, Pruden A. Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9149-9160. [PMID: 35732277 DOI: 10.1080/10643389.2021.2024739] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in the water environment that contribute to its evolution and spread. Environmental monitoring could provide vital information for mitigating the spread of AMR; this includes assessing antibiotic resistance genes (ARGs) circulating among human populations, identifying key hotspots for evolution and dissemination of resistance, informing epidemiological and human health risk assessment models, and quantifying removal efficiencies by domestic wastewater infrastructure. However, standardized methods for monitoring AMR in the water environment will be vital to producing the comparable data sets needed to address such questions. Here we sought to establish scientific consensus on a framework for such standardization, evaluating the state of the science and practice of AMR monitoring of wastewater, recycled water, and surface water, through a literature review, survey, and workshop leveraging the expertise of academic, governmental, consulting, and water utility professionals.
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Affiliation(s)
- Krista Liguori
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Ishi Keenum
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Benjamin C Davis
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Jeanette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Erin Milligan
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Amy Pruden
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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Abdul Rashid JI, Yusof NA, Abdullah J, Shomiad Shueb RH. Strategies for the preparation of non-amplified and amplified genomic dengue gene samples for electrochemical DNA biosensing applications. RSC Adv 2021; 12:1-10. [PMID: 35424522 PMCID: PMC8978653 DOI: 10.1039/d1ra06753b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/25/2021] [Indexed: 11/21/2022] Open
Abstract
The application of electrochemical DNA biosensors in real genomic sample detection is challenging due to the existence of complex structures and low genomic concentrations, resulting in inconsistent and low current signals. This work highlights strategies for the treatment of non-amplified and amplified genomic dengue virus gene samples based on real samples before they can be used directly in our DNA electrochemical sensing system, using methylene blue (MB) as a redox indicator. The main steps in this study for preparing non-amplified cDNA were cDNA conversion, heat denaturation, and sonication. To prepare amplified cDNA dengue virus genomic samples using an RT-PCR approach, we optimized a few parameters, such as the annealing temperature, sonication time, and reverse to forward (R/F) primer concentration ratio. We discovered that the generated methylene blue (MB) signals during the electrochemical sensing of non-amplified and amplified samples differ due to the different MB binding affinities based on the sequence length and base composition. The findings show that our developed electrochemical DNA biosensor successfully discriminates MB current signals in the presence and absence of the target genomic dengue virus, indicating that both samples were successfully treated. This work also provides interesting information about the critical factors in the preparation of genomic gene samples for developing miniaturized PCR-based electrochemical sensing applications in the future. We also discuss the limitations and provide suggestions related to using redox-indicator-based electrochemical biosensors to detect real genomic nucleic acid genes.
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Affiliation(s)
- Jahwarhar Izuan Abdul Rashid
- Department of Chemistry and Biology, Centre for Defence Foundation Studies, National Defence University of Malaysia Sungai Besi Camp 57000 Kuala Lumpur Malaysia
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Jaafar Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Rafidah Hanim Shomiad Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 16150 Kubang Kerian Kelantan Malaysia
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Alexandrov OS, Karlov GI. The Development of New Species-Specific Molecular Markers Based on 5S rDNA in Elaeagnus L. Species. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122713. [PMID: 34961186 PMCID: PMC8704621 DOI: 10.3390/plants10122713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
The Elaeagnus L. species are trees and bushes that mainly grow in temperate zones of Western Europe; Minor, Central, and Southeast Asia; the Far East; and North America. Some species are used as fruit or ornamental plants and have economic value. Problems with the identification of species in the Elaeagnus genus by molecular genetical methods arise in the study of populations, systematics, breeding, and other areas of plant science and practice. Recently, the polymorphism of 5S ribosomal DNA non-transcribed spacers (5S rDNA NTSs) in Elaeagnaceae Adans. has been described. The results were used in our study as a basis for development of new species-specific molecular markers for some members of the Elaeagnus genus. The author's method was applied for finding regions that were potentially applicable for species-specific primer design. As a result, some species-specific molecular markers were developed for Elaeagnus angustifolia L., E. commutata Bernh., E. pungens Thunb., and E. multiflora Thunb. These markers were tested in a range of samples and showed the presence of amplified fragments in lanes of the marked species only. Samples of other species showed no amplifications. Thus, the developed markers may be useful for the species identification of the studied Elaeagnus plants in botanical, dendrological, and genetic research (especially in a leafless period of year), as well as in breeding and hybridization experiments.
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Affiliation(s)
- Oleg S Alexandrov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia
| | - Gennady I Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia
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Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review. Molecules 2019; 24:molecules24010163. [PMID: 30609875 PMCID: PMC6337382 DOI: 10.3390/molecules24010163] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/28/2018] [Accepted: 12/29/2018] [Indexed: 12/12/2022] Open
Abstract
Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.
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Yang F, Yang N, Huo X, Xu S. Thermal sensing in fluid at the micro-nano-scales. BIOMICROFLUIDICS 2018; 12:041501. [PMID: 30867860 PMCID: PMC6404956 DOI: 10.1063/1.5037421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/19/2018] [Indexed: 06/09/2023]
Abstract
Temperature is one of the most fundamental parameters for the characterization of a physical system. With rapid development of lab-on-a-chip and biology at single cell level, a great demand has risen for the temperature sensors with high spatial, temporal, and thermal resolution. Nevertheless, measuring temperature in liquid environment is always a technical challenge. Various factors may affect the sensing results, such as the fabrication parameters of built-in sensors, thermal property of electrical insulating layer, and stability of fluorescent thermometers in liquid environment. In this review, we focused on different kinds of micro/nano-thermometers applied in the thermal sensing for microfluidic systems and cultured cells. We discussed the advantages and limitations of these thermometers in specific applications and the challenges and possible solutions for more accurate temperature measurements in further studies.
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Affiliation(s)
- Fan Yang
- Key Laboratory for the Physics and Chemistry of Nanodevices, Department of Electronics, Peking University, Beijing 100871, People's Republic of China
| | - Nana Yang
- Key Laboratory for the Physics and Chemistry of Nanodevices, Department of Electronics, Peking University, Beijing 100871, People's Republic of China
| | - Xiaoye Huo
- Faculty of Mechanical Engineering, Micro-and Nanofluidics Laboratory, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Shengyong Xu
- Key Laboratory for the Physics and Chemistry of Nanodevices, Department of Electronics, Peking University, Beijing 100871, People's Republic of China
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454-Pyrosequencing Analysis of Bacterial Communities from Autotrophic Nitrogen Removal Bioreactors Utilizing Universal Primers: Effect of Annealing Temperature. BIOMED RESEARCH INTERNATIONAL 2015; 2015:892013. [PMID: 26421306 PMCID: PMC4573432 DOI: 10.1155/2015/892013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/26/2015] [Indexed: 02/03/2023]
Abstract
Identification of anaerobic ammonium oxidizing (anammox) bacteria by molecular tools aimed at the evaluation of bacterial diversity in autotrophic nitrogen removal systems is limited by the difficulty to design universal primers for the Bacteria domain able to amplify the anammox 16S rRNA genes. A metagenomic analysis (pyrosequencing) of total bacterial diversity including anammox population in five autotrophic nitrogen removal technologies, two bench-scale models (MBR and Low Temperature CANON) and three full-scale bioreactors (anammox, CANON, and DEMON), was successfully carried out by optimization of primer selection and PCR conditions (annealing temperature). The universal primer 530F was identified as the best candidate for total bacteria and anammox bacteria diversity coverage. Salt-adjusted optimum annealing temperature of primer 530F was calculated (47°C) and hence a range of annealing temperatures of 44–49°C was tested. Pyrosequencing data showed that annealing temperature of 45°C yielded the best results in terms of species richness and diversity for all bioreactors analyzed.
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Alves-Costa FA, Wasko AP. DDRT-PCR approaches applied for preeminent results in the isolation of DETs from fish brain tissues. BRAZ J BIOL 2015; 75:224-8. [PMID: 25945641 DOI: 10.1590/1519-6984.12213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/20/2013] [Indexed: 11/21/2022] Open
Abstract
Differential Display (DD) is a technique widely used in studies of differential expression. Most of these analyses, especially those involving fish species, are restricted to species from North America and Europe or to commercial species, as salmonids. Studies related to South American fish species are underexplored. Thus, the present work aimed to describe DD technique modifications in order to improve outcomes related to the isolation of DETs (Differentially Expressed Transcripts), using Leporinus macrocephalus, a large commercially exploited South American species, as a fish design. Different DDRT-PCR approaches were applied to brain samples and the products of the reactions were analyzed on 6% polyacrylamide gels stained with 0.17% Silver Nitrate (AgNO3). The use of PCR reactions under high stringency conditions and longer oligonucleotides based on VNTR (Variable Number of Tandem Repeats) core sequences led to better results when compared to low stringency PCR conditions and the use of decamer oligonucleotides. The improved approach led to the isolation of differentially expressed transcripts on adult males and females of L. macrocephalus. This study indicates that some modifications on the DDRT-PCR method can ensure isolation of DETs from different fish tissues and the development of robust data related to this approach.
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Affiliation(s)
- F A Alves-Costa
- Instituto de Ciências da Saúde, Universidade Paulista, Bauru, SP, Brazil
| | - A P Wasko
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
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9
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Ward JA, Ponnala L, Weber CA. Strategies for transcriptome analysis in nonmodel plants. AMERICAN JOURNAL OF BOTANY 2012; 99:267-76. [PMID: 22301897 DOI: 10.3732/ajb.1100334] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Even with recent reductions in sequencing costs, most plants lack the genomic resources required for successful short-read transcriptome analyses as performed routinely in model species. Several approaches for the analysis of short-read transcriptome data are reviewed for nonmodel species for which the genome of a close relative is used as the reference genome. Two approaches using a data set from Phytophthora-challenged Rubus idaeus (red raspberry) are compared. Over 70000000 86-nt Illumina reads derived from R. idaeus roots were aligned to the Fragaria vesca genome using publicly available informatics tools (Bowtie/TopHat and Cufflinks). Alignment identified 16956 putatively expressed genes. De novo assembly was performed with the same data set and a publicly available transcriptome assembler (Trinity). A BLAST search with a maximum e-value threshold of 1.0 × 10(-3) revealed that over 36000 transcripts had matches to plants and over 500 to Phytophthora. Gene expression estimates from alignment to F. vesca and de novo assembly were compared for raspberry (Pearson's correlation = 0.730). Together, alignment to the genome of a close relative and de novo assembly constitute a powerful method of transcriptome analysis in nonmodel organisms. Alignment to the genome of a close relative provides a framework for differential expression testing if alignments are made to the predefined gene-space of a close relative and de novo assembly provides a more robust method of identifying unique sequences and sequences from other organisms in a system. These methods are considered experimental in nonmodel systems, but can be used to generate resources and specific testable hypotheses.
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Affiliation(s)
- Judson A Ward
- Department of Horticulture, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456, USA
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10
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Identification of sexually dimorphic gene expression in brain tissue of the fish Leporinus macrocephalus through mRNA differential display and real time PCR analyses. Genetica 2009; 138:321-31. [PMID: 19890727 DOI: 10.1007/s10709-009-9421-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 10/20/2009] [Indexed: 12/18/2022]
Abstract
Differentially expressed genes in males and females of vertebrate species generally have been investigated in gonads and, to a lesser extent, in other tissues. Therefore, we attempted to identify sexually dimorphic gene expression in the brains of adult males and females of Leporinus macrocephalus, a gonochoristic fish species that presents a ZZ/ZW sex determination system, throughout a comparative analysis using differential display reverse transcriptase-PCR and real-time PCR. Four cDNA fragments were characterized, representing candidate genes with differential expression between the samples. Two of these fragments presented no significant identity with previously reported gene sequences. The other two fragments, isolated from male specimens, were associated to the gene that codes for the protein APBA2 (amyloid beta (A4) precursor protein-binding, family A, member 2) and to the Rab 37 gene, a member of the Ras oncogene family. The overexpression of these genes has been associated to a greater production of the beta-amyloid protein which, in turns, is the major factor that leads to Alzheimer's disease, and to the development of brain-tumors, respectively. Quantitative RT-PCR analyses revealed a higher Apba2 gene expression in males, thus validating the previous data on differential display. L. macrocephalus may represent an interesting animal model to the understanding of the function of several vertebrate genes, including those involved in neurodegenerative and cancer diseases.
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Shin KS, Lee SM, Lim SH, Woo HJ, Cho HS, Lee KR, Lee MC, Kweon SJ, Suh SC. Molecular biological characteristics and analysis using the specific markers of leaf folder-resistant GM rice. ACTA ACUST UNITED AC 2009. [DOI: 10.5010/jpb.2009.36.2.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Rowe A, Yun K, Emery D, Sangster N. Haemonchus contortus: Development of a two-step, differential-display PCR to detect differential gene expression in nematodes from immune and naïve sheep. Exp Parasitol 2008; 119:207-16. [DOI: 10.1016/j.exppara.2008.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 01/17/2008] [Accepted: 01/23/2008] [Indexed: 02/02/2023]
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Wei T, Lu G, Clover G. Novel approaches to mitigate primer interaction and eliminate inhibitors in multiplex PCR, demonstrated using an assay for detection of three strawberry viruses. J Virol Methods 2008; 151:132-9. [PMID: 18453003 DOI: 10.1016/j.jviromet.2008.03.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 02/26/2008] [Accepted: 03/04/2008] [Indexed: 11/25/2022]
Abstract
Multiplex PCR is an important technique for detecting a variety of pathogens simultaneously in a single assay. Previous research has focused on optimising the factors affecting reliable multiplex PCR, including primer design, PCR components and conditions, and inhibitors in samples. In this study, the interaction of primers to form complex secondary structures including visible dimers and invisible "primer clusters", a novel form of primer secondary structure found during this research, were shown to be the most important factors affecting successful multiplex PCR. Approaches to mitigate primer interaction and eliminate inhibitors were tested, including: reduction of primer concentrations especially those with preferential amplification; decrease of PCR extension temperature; increase of extension time and PCR cycles; and addition of bovine serum albumin. Based on these approaches, a multiplex RT-PCR with sensitivity comparable to the simplex PCR for individual viruses was developed for the detection of Raspberry ringspot virus, Strawberry latent ringspot virus and Tomato bushy stunt virus. A plant internal amplification control was also included. These approaches may be useful as a guideline for the development of multiplex PCR protocols for the detection of other pathogens or organisms associated with plants, humans, animals and the environment.
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Affiliation(s)
- Ting Wei
- Plant Health and Environment Laboratory, Investigation and Diagnostic Centre, MAF Biosecurity New Zealand, P.O. Box 2095, Auckland 1140, New Zealand
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Abdel-latief M, Hilker M. Innate immunity: eggs of Manduca sexta are able to respond to parasitism by Trichogramma evanescens. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2008; 38:136-45. [PMID: 18207075 DOI: 10.1016/j.ibmb.2007.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 10/01/2007] [Accepted: 10/04/2007] [Indexed: 05/12/2023]
Abstract
So far, it was unknown whether immune responses of insect eggs are inducible or suppressed by parasitism. We investigated whether transcription of immune related genes in eggs of Manduca sexta changed in response to parasitism by Trichogramma evanescens. First, using DDRT-PCR, several cDNA elements known to represent immune related M. sexta genes inducible by bacterial challenge were isolated from eggs. In addition, two novel cDNAs were found: (a) immulectin-V (IML-V) suggested to be involved in recognition of foreign bodies, and (b) a new like-moricin protein with possible antimicrobial effects (L-Mor). Quantitative real time RT-PCR analyses revealed enhanced transcription in parasitized eggs compared to unparasitized ones for IML-V, prophenoloxidase (ProPO), prophenoloxidase activating protease I (PAP I), and proparalytic peptide (ProPP). No significant differences between parasitized and unparasitized eggs were detected for sequences encoding the antimicrobial peptides L-Mor, leureptin Leu, and attacin II Att II. Transcript levels of other antibacterial peptides were suppressed after parasitization for 3d (cecropin 6, Cec 6) and 2d (gloverin, Glov). While nearly 100% of the Manduca eggs contained Trichogramma specimens 1d after exposure to parasitoids, only 64% of the host eggs harbored parasitoid larvae 4d after parasitization. Our data demonstrate that the immune system of Manduca eggs shows differentiated responses to parasitization and suggest that insect eggs can defend against parasitization.
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Affiliation(s)
- M Abdel-latief
- Department of Applied Zoology/Animal Ecology, Institute of Biology, Freie Universität Berlin, 12163 Berlin, Germany
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Hu G, Yang Q, Cui X, Yue G, Azaro MA, Wang HY, Li H. A highly sensitive and specific system for large-scale gene expression profiling. BMC Genomics 2008; 9:9. [PMID: 18186939 PMCID: PMC2267712 DOI: 10.1186/1471-2164-9-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Accepted: 01/10/2008] [Indexed: 12/02/2022] Open
Abstract
Background Rapid progress in the field of gene expression-based molecular network integration has generated strong demand on enhancing the sensitivity and data accuracy of experimental systems. To meet the need, a high-throughput gene profiling system of high specificity and sensitivity has been developed. Results By using specially designed primers, the new system amplifies sequences in neighboring exons separated by big introns so that mRNA sequences may be effectively discriminated from other highly related sequences including their genes, unprocessed transcripts, pseudogenes and pseudogene transcripts. Probes used for microarray detection consist of sequences in the two neighboring exons amplified by the primers. In conjunction with a newly developed high-throughput multiplex amplification system and highly simplified experimental procedures, the system can be used to analyze >1,000 mRNA species in a single assay. It may also be used for gene expression profiling of very few (n = 100) or single cells. Highly reproducible results were obtained from duplicate samples with the same number of cells, and from those with a small number (100) and a large number (10,000) of cells. The specificity of the system was demonstrated by comparing results from a breast cancer cell line, MCF-7, and an ovarian cancer cell line, NCI/ADR-RES, and by using genomic DNA as starting material. Conclusion Our approach may greatly facilitate the analysis of combinatorial expression of known genes in many important applications, especially when the amount of RNA is limited.
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Affiliation(s)
- Guohong Hu
- Department of Molecular Genetics, Microbiology and Immunology/The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.
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16
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Lim SH, Kim NY, Lee SM, Woo HJ, Shin KS, Jin YM, Cho HS. Molecular Characterization and Event-Specific Marker Development of Insect Resistant Chinese Cabbage for Environmental Risk Assessment. ACTA ACUST UNITED AC 2007. [DOI: 10.5010/jpb.2007.34.4.347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Ray A, Macwana S, Ayoubi P, Hall LT, Prade R, Mort AJ. Negative subtraction hybridization: an efficient method to isolate large numbers of condition-specific cDNAs. BMC Genomics 2004; 5:22. [PMID: 15050035 PMCID: PMC400731 DOI: 10.1186/1471-2164-5-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Accepted: 03/29/2004] [Indexed: 11/17/2022] Open
Abstract
Background The construction of cDNA libraries is a useful tool to understand gene expression in organisms under different conditions, but random sequencing of unbiased cDNA collections is laborious and can give rise to redundant EST collections. We aimed to isolate cDNAs of messages induced by switching Aspergillus nidulans from growth on glucose to growth on selected polysaccharides. Approximately 4,700 contigs from 12,320 ESTs were already available from a cDNA library representing transcripts isolated from glucose-grown A. nidulans during asexual development. Our goals were to expand the cDNA collection without repeated sequencing of previously identified ESTs and to find as many transcripts as possible that are specifically induced in complex polysaccharide metabolism. Results We have devised a Negative Subtraction Hybridization (NSH) method and tested it in A. nidulans. NSH entails screening a plasmid library made from cDNAs prepared from cells grown under a selected physiological condition with labeled cDNA probes prepared from another physiological condition. Plasmids with inserts that failed to hybridize to cDNA probes through two rounds of screening (i.e. negatives) indicate that they are transcripts present at low concentration in the labeled probe pool. Thus, these transcripts will be predominantly condition-specific, along with some rare transcripts. In a screen for transcripts induced by switching the carbon source from glucose to 12 selected polysaccharides, 3,532 negatives were isolated from approximately 100,000 surveyed colonies using this method. Negative clones were end-sequenced and assembled into 2,039 contigs, of which 1,722 were not present in the previously characterized glucose-grown cDNA library. Single-channel microarray hybridization experiments confirmed that the majority of the negatives represented genes that were differentially induced by a switch from growth in glucose to one or more of the polysaccharides. Conclusions The Negative Subtraction Hybridization method described here has several practical benefits. This method can be used to screen any existing cDNA library, including full-length and pooled libraries, and does not rely on PCR or sequence information. In addition, NSH is a cost-effective method for the isolation of novel, full-length cDNAs for differentially expressed transcripts or enrichment of rare transcripts.
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Affiliation(s)
- Anamika Ray
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Sunita Macwana
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Patricia Ayoubi
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Leo T Hall
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
- Department of Chemistry, Eastern Oklahoma State College, Willburton, OK 74578, USA
| | - Rolf Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Andrew J Mort
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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18
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Bernal-Mizrachi E, Cras-Méneur C, Ohsugi M, Permutt MA. Gene expression profiling in islet biology and diabetes research. Diabetes Metab Res Rev 2003; 19:32-42. [PMID: 12592642 DOI: 10.1002/dmrr.331] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Following the sequencing of most of the human and mouse genomes, the next task for physicians and scientists will be to assess the relative levels of expression of these genes during development, following exposure to various nutritional and pharmacological conditions, and in disease states such as diabetes and related metabolic disorders. This review provides an overview of the various methodologies available for monitoring global gene expression. Use of cDNA libraries, Expressed Sequence Tag (EST) sequencing projects and databases, differential display (DD), serial analysis of gene expression (SAGE), subtractive cloning, and both cDNA and oligo microarrays are discussed, along with their merits and limitations. The Endocrine Pancreas Consortium http://www.cbil.upenn.edu/EPConDB/ has constructed mouse and human cDNA libraries from adult and various stages of embryonic development of endocrine pancreas. Over 100,000 ESTs have been deposited in public databases, and each clone is available through the IMAGE Consortium. A guide to Internet access is provided for future investigation.
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Affiliation(s)
- Ernesto Bernal-Mizrachi
- Washington University School of Medicine, Division of Endocrinology, Diabetes and Metabolism, St Louis, Missouri 63110, USA
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19
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Scheel J, Von Brevern MC, Hörlein A, Fischer A, Schneider A, Bach A. Yellow pages to the transcriptome. Pharmacogenomics 2002; 3:791-807. [PMID: 12437481 DOI: 10.1517/14622416.3.6.791] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Transcriptomics has become an important tool for the large-scale analysis of biological processes. This review aims to provide sufficient criteria to make an appropriate choice among the variety of 'closed' systems, represented by DNA microarrays, and 'open' systems like fragment display, tag sequencing and subtractive hybridization, depending on the biological system under investigation. The most important technologies currently available are presented, their strengths and weaknesses are discussed and companies active in the field are listed. The potential of transcriptomics in the pharmaceutical research and development process is highlighted by applications in oncology, research on neurological diseases, and predictive toxicology. Finally, a prognosis for future developments of the technologies is given.
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Affiliation(s)
- Julia Scheel
- Axaron Bioscience AG, Im Neuenheimer Feld 515, D-69120 Heidelberg, Germany.
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20
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Carré W, Bourneuf E, Douaire M, Diot C. Differential expression and genetic variation of hepatic messenger RNAs from genetically lean and fat chickens. Gene 2002; 299:235-43. [PMID: 12459271 DOI: 10.1016/s0378-1119(02)01077-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Although excessive adiposity has become a major drawback in meat type chicken production, few of the genes involved in this process have been characterized so far. In order to identify putative genes involved in adiposity, we performed differential display analysis of RNAs extracted from the liver of divergently selected lean and fat chickens. Twenty-six differential products were selected and purified by single strand conformation polymorphism gel electrophoresis before sequencing and Northern blot analyses. An orthologous sequence of a mammalian cytochrome P450 2C subfamily member was proven to be differentially expressed in the liver of lean and fat chickens and could play an important role in the regulation of adiposity. In mammals, these genes are involved in detoxification of xenobiotics and metabolism of some important biological compounds. Four other genes were found differentially expressed to a lower extent. Some unidentified products were shown to be lean or fat specific, with sequence polymorphism and liver specific expression, strongly suggesting that the related gene could be directly involved in adiposity. Our data indicate that differential display can evidence genes with differential expression and with sequence polymorphism, making this strategy more accurate for differential analysis of messenger RNAs.
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Affiliation(s)
- Wilfrid Carré
- Unité Mixte de Recherche INRA-ENSA de Génétique Animale, 65 rue de Saint-Brieuc, CS 84215, 35042 Rennes Cedex, France
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21
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Matin MM, Andrews PW, Hornby DP. Multidimensional differential display via ion-pair reversed-phase denaturing high-performance liquid chromatography. Anal Biochem 2002; 304:47-54. [PMID: 11969188 DOI: 10.1006/abio.2001.5563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Experimental approaches are now available for the analysis of whole transcriptome expression in cells and tissues. Since the introduction of such methods for the investigation of differences in mRNA populations, they have been applied successfully to many areas of biology and medicine including development, differentiation, physiology, pharmacology, and carcinogenesis. Here we describe an improved and automated approach based on the differential mRNA display method developed by Liang and Pardee (P. Liang and A. B. Pardee, 1992, Science 257, 967-971). We report the use of ion-pair reversed-phase denaturing high-performance liquid chromatography (IP RP DHPLC), for the first time, to produce a "fingerprint," after amplification of the cDNA corresponding to the mRNA populations, from two or more of the samples that are to be compared. By overlaying the chromatograms produced from the amplification of different samples derived from the same set of oligodeoxynucleotide primers, those genes that are differentially expressed can be selected and subsequently cloned and sequenced rapidly to establish a profile of differentially expressed genes. In addition, validation of the data obtained is readily achieved by this method using IP RP DHPLC and quantitative RT-PCR. In this study total RNA was prepared from NTERA2 cells before and after differentiation induced by retinoic acid and was reverse-transcribed into cDNA prior to amplification to produce fluorescently tagged products. This methodology facilitates multiple rounds of interrogation of RT-PCR products and we tentatively refer to this approach as Multidimensional Differential Display.
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Affiliation(s)
- Maryam M Matin
- The Transgenomic Research Laboratory, Department of Molecular Biology, Krebs Institute, Firth Court, Sheffield, S10 2TN, United Kingdom
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22
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Clipsham RC, McCabe ER. Single-tube gene-specific expression analysis by high primer density multiplex reverse transcription. Mol Genet Metab 2001; 74:435-48. [PMID: 11749049 DOI: 10.1006/mgme.2001.3261] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Molecular genetics is rapidly moving from simple identification of a gene of interest to characterization of gene products as components in complex networks. Critical tools for gene product analysis require a rapid method for evaluation of contextual expression. Here, we describe a robust, high primer density, single-tube, multiplex reverse transcription (HD-MRT) technique. This approach is capable of analyzing for the presence of numerous transcripts when polymerase chain reaction (PCR) is subsequently employed for individual gene-specific sequence amplification (HD-MRT-PCR). This assay substantially increases the total number of different cDNAs for amplification beyond previously published techniques. Our approach simultaneously eliminates RNA quality control issues for samples run in parallel while improving efficiency in the use of time and materials. This assay is designed for broad applicability and accessibility, employs modifications of commercially available components, and allows more than 25 independently selected gene-specific primers to be used simultaneously. Our protocol allows multiplexed primers to behave similarly to uniplex RT reactions, while avoiding potential interference between gene-specific and/or nonspecific primers during annealing and reverse transcription. Expression of putatively networked homologous transcripts was analyzed in multiple cell lines and tissues from mouse and human to validate the technique.
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Affiliation(s)
- R C Clipsham
- Molecular Biology Institute, UCLA, Los Angeles, California 90095-1752, USA
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23
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Fischer A. Restriction-mediated differential display (RMDD). CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2001; Chapter 25:Unit 25B.4. [PMID: 18265217 DOI: 10.1002/0471142727.mb25b04s56] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A variation on differential display, restriction-mediated differential display (RMDD) presents an alternative approach to the fragment display technologies. It touts high sensitivity (detection of mRNAs at a dilution of 1:100,000 and of regulation factors lower than two-fold), a strategy for avoiding false positives, nonradioactive detection, and universal applicability to any polyadenylated RNA.
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Affiliation(s)
- A Fischer
- F. Hoffmann-La Roche AG, Basel, Switzerland
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24
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Carré W, Diot C, Fillon V, Crooijmans RP, Lagarrigue S, Morrisson M, Vignal A, Groenen MA, Douaire M. Development of 112 unique expressed sequence tags from chicken liver using an arbitrarily primed reverse transcriptase-polymerase chain reaction and single strand conformation gel purification method. Anim Genet 2001; 32:289-97. [PMID: 11683716 DOI: 10.1046/j.1365-2052.2001.00792.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In order to provide information on chicken genome expression, expressed sequence tags (ESTs) were developed from chicken liver RNAs using a method based on arbitrarily primed reverse transcription-polymerase chain reaction (RT-PCR) of total RNAs. The method is similar to differential display, using one base anchored oligo-d(T) reverse-primers and 20-mer arbitrary forward-primers. A purification step by single strand conformation gel electrophoresis was added before sequencing. With a ratio of 112 unique sequences out of 155, we found this method to be highly effective when compared with EST production with randomly selected clones from non-subtracted, non-normalized libraries. A large proportion of the ESTs sequenced correspond to genes involved in transcriptional and post-transcriptional events. Cytogenetic mapping was performed for a subset of ESTs and four regions of conserved synteny between chicken and human were confirmed.
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Affiliation(s)
- W Carré
- Unité Mixte de Recherche INRA-ENSA de Génétique Animale, Rennes Cedex, France
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25
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Lorkowski S, Ellinghaus P, Galinski EA, Assmann G, Cullen P. Use of longer extension phases to improve yield of high molecular weight products in differential display PCR. Clin Chim Acta 2000; 299:199-204. [PMID: 10900305 DOI: 10.1016/s0009-8981(00)00292-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- S Lorkowski
- Institute of Arteriosclerosis Research, University of Münster, D-48149, Münster, Germany
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26
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Applications of differential-display reverse transcription-PCR to molecular pathogenesis and medical mycology. Clin Microbiol Rev 2000. [PMID: 10885984 DOI: 10.1128/cmr.13.3.408-427.2000] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The host-fungus interaction is characterized by changes in gene expression in both host and pathogen. Differential-display reverse transcription PCR (DDRT-PCR) is a PCR-based method that allows extensive analysis of gene expression among several cell populations. Several limitations and drawbacks to this procedure have now been addressed, including the large number of false-positive results and the difficulty in confirming differential expression. Modifications that simplify the reaction time, allow the use of minute quantities of RNA, or address unusual species- or gene-specific sequences have been reported. DDRT-PCR has been used to address biological questions in mammalian systems, including cell differentiation, cell activation, cell stress, and identification of drug targets. In microbial pathogenesis and plant pathogenesis, DDRT-PCR has allowed the identification of virulence factors, genes involved in cell death, and signaling genes. In Candida albicans, DDRT-PCR studies identified TIF-2, which may play a role in the upregulation of phospholipases, and the stress-related genes, CIP1 and CIP2. In Histoplasma capsulatum and C. albicans, genes involved in the host-pathogen interaction, including a member of the 100-kDa family in Histoplasma and an ALS and 14-3-3 gene in Candida, were potentially identified by DDRT-PCR. Although very few reports have been published in medical mycology, studies in mammalian, nonfungal microbial, and plant pathogen systems are easily applied to basic questions in fungal pathogenesis and antifungal therapeutics.
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27
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Sturtevant J. Applications of differential-display reverse transcription-PCR to molecular pathogenesis and medical mycology. Clin Microbiol Rev 2000; 13:408-27. [PMID: 10885984 PMCID: PMC88940 DOI: 10.1128/cmr.13.3.408] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The host-fungus interaction is characterized by changes in gene expression in both host and pathogen. Differential-display reverse transcription PCR (DDRT-PCR) is a PCR-based method that allows extensive analysis of gene expression among several cell populations. Several limitations and drawbacks to this procedure have now been addressed, including the large number of false-positive results and the difficulty in confirming differential expression. Modifications that simplify the reaction time, allow the use of minute quantities of RNA, or address unusual species- or gene-specific sequences have been reported. DDRT-PCR has been used to address biological questions in mammalian systems, including cell differentiation, cell activation, cell stress, and identification of drug targets. In microbial pathogenesis and plant pathogenesis, DDRT-PCR has allowed the identification of virulence factors, genes involved in cell death, and signaling genes. In Candida albicans, DDRT-PCR studies identified TIF-2, which may play a role in the upregulation of phospholipases, and the stress-related genes, CIP1 and CIP2. In Histoplasma capsulatum and C. albicans, genes involved in the host-pathogen interaction, including a member of the 100-kDa family in Histoplasma and an ALS and 14-3-3 gene in Candida, were potentially identified by DDRT-PCR. Although very few reports have been published in medical mycology, studies in mammalian, nonfungal microbial, and plant pathogen systems are easily applied to basic questions in fungal pathogenesis and antifungal therapeutics.
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Affiliation(s)
- J Sturtevant
- Department of Microbiology, Georgetown University Medical School, Washington, DC 20007, USA.
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28
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von der Kammer H, Albrecht C, Mayhaus M, Hoffmann B, Stanke G, Nitsch RM. Identification of genes regulated by muscarinic acetylcholine receptors: application of an improved and statistically comprehensive mRNA differential display technique. Nucleic Acids Res 1999; 27:2211-8. [PMID: 10219095 PMCID: PMC148442 DOI: 10.1093/nar/27.10.2211] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In order to identify genes that are regulated by muscarinic acetylcholine receptors, we developed an mRNA differential display technique (DD) approach. By increasing redundancy and by evaluating optimised reagents and conditions for reverse transcription of total RNA, PCR and separation of PCR products, we generated a DD protocol that yields highly consistent results. A set of 64 distinct random primers was specifically designed in order to approach a statistically comprehensive analysis of all mRNA species in a defined cell population. This modified DD protocol was applied to total RNA of HEK293 cells stably expressing muscarinic m1 acetylcholine receptors and cells stimulated with the receptor agonist carbachol were compared to identical but non-stimulated cells. In 81 of 192 possible PCR experiments, 38 differential bands were identified. Sequence analysis followed by northern blot analyses confirmed differentially expressed genes in 19 of 23 bands analysed. These represented 10 distinct immediate-early genes that were up-regulated by m1AChR activation: Egr-1, Egr-2, Egr-3, NGFi-B, ETR101, c- jun, jun -D, Gos-3 and hcyr61, as well as the unknown gene Gig-2. These data show that this improved DD protocol can be readily applied to reliably identify differentially expressed genes.
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Affiliation(s)
- H von der Kammer
- Center for Molecular Neurobiology Hamburg, University of Hamburg, Martinistrasse 52, D-20246 Hamburg, Germany.
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29
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Malhotra K, Luehrsen KR, Costello LL, Raich TJ, Sim K, Foltz L, Davidson S, Xu H, Chen A, Yamanishi DT, Lindemann GW, Cain CA, Madlansacay MR, Hashima SM, Pham TL, Mahoney W, Schueler PA. Identification of differentially expressed mRNAs in human fetal liver across gestation. Nucleic Acids Res 1999; 27:839-47. [PMID: 9889281 PMCID: PMC148255 DOI: 10.1093/nar/27.3.839] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Differential gene expression, with its precise start and stop times, is believed to be critical for the programmed development of new cells and tissues. Within the developing fetus, one tissue of particular interest is fetal liver. This organ undergoes rapid changes in the pathway toward liver development in utero since it is also the major site of hematopoiesis, until bone marrow hematopoiesis predominates. Believing that patterns would emerge from the bi-weekly large-scale inspection of expressed genes in the fetal liver, we employed differential display reverse transcription-polymerase chain reaction (DDRT-PCR) as ourprimary inspection tool. Using DDRT-PCR, we isolated cDNAs differentially expressed throughout fetal liver development and in adult liver. We displayed approximately 25 000 cDNAs from 10 and 24 week fetal liver and adult liver. From this initial screen, we determined that approximately 0.1-1% of the mRNA population undergoes expression changes. We extracted, purified and sequenced 25 differentially displayed cDNA bands. Fourteen cDNAs had similarities to known genes, while 11 cDNAs were not similar to any characterized gene. The differentially expressed cDNAs from known genes present in fetal liver include alpha-fetoprotein, stem cell factor, erythroid alpha-spectrin, 2,3-bisphosphoglycerate mutase, insulin-like growth factor-2, porphobilinogen deaminase and Mac30. The differentially expressed cDNAs present in adult liver but not in 10 week fetal liver were nicotinamide deaminase, human fibrinogen-related protein and alpha-acid glycoprotein. The majority of differentially expressed genes found during this effort appear to be turned on during organogenesis, however, some genes were found that are apparently turned off completely.
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Affiliation(s)
- K Malhotra
- Roche Diagnostics, Chief Technology Office, 2929 7th Street, Suite 100, Berkeley, CA 94710, USA
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