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Journal articles on the topic 'Differential display polymerase chain reaction amplification'

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Author: Grafiati

Published: 4 June 2021

Last updated: 19 February 2023

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1

Kretzler, M., G. Fan, D. Rose, L. J. Arend, J. P. Briggs, and L. B. Holzman. "Novel mouse embryonic renal marker gene products differentially expressed during kidney development." American Journal of Physiology-Renal Physiology 271, no. 3 (September 1, 1996): F770—F777. http://dx.doi.org/10.1152/ajprenal.1996.271.3.f770.

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Investigators approaching the problem of renal organogenesis have been hampered by a paucity of suitable molecular markers that specify distinct developmental phenotypes. To identify such markers, differential display-polymerase chain reaction (DD-PCR) was used to survey the temporal pattern of gene expression in mouse kidney at 11.5, 13.5, 15.5, and 17.5 days after conception and in the adult kidney. Twenty-two differentially expressed amplification products were identified, isolated, and sequenced. Seventeen clones showed no significant similarity with previously reported nucleotide sequences: two were similar to two housekeeping gene products, and three were similar to human or rat expressed sequence tags. To confirm the differential expression patterns observed by DD-PCR, semiquantitative reverse transcription-PCR was performed using sequence-specific oligonucleotide primers. Nineteen of 22 clones were differentially expressed during kidney development [mouse embryonic renal marker (MERM) sequences 1-19]. The value of MERMs as developmental markers was further assessed in mouse metanephric organ culture, where the pattern of MERM transcript expression mimicked that observed in vivo. Therefore, the DD-PCR method permitted development of a panel of marker sequences that can be used to characterize renal developmental processes and that may allow the identification of novel, functionally relevant gene products.

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2

Liu, Yong-Gang, Yuan-Zhu Xiong, and Chang-Yan Deng. "Isolation, Sequence Analysis and Expression Profile of a Novel Swine Gene Differentially Expressed in the Longissimus Dorsi Muscle Tissues from Landrace×Large White Cross-combination." Acta Biochimica et Biophysica Sinica 37, no. 3 (March 1, 2005): 186–91. http://dx.doi.org/10.1093/abbs/37.3.186.

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Abstract The mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from Landrace×Large White cross-combination. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 260 amino acids that contains the putative conserved domain of the carbonic anhydrase, and this protein has high homology with the carbonic anhydrase III (CA-III) of four species-mouse (91%), horse (91%), rat (89%) and human (86%)–so that it can be defined as swine carbonic anhydrase III. The phylogenetic tree analysis revealed that the swine CA-III has a closer genetic relationship with the horse CA-III than with those of mouse, rat and human. The tissue expression analysis indicated that the swine CA-III gene is generally expressed in most tissues. Our experiment is the first to establish the primary foundation for further research on the swine CA-III gene.

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3

Selisana, S. M., M. J. Yanoria, B. Quime, C. Chaipanya, G. Lu, R. Opulencia, G. L. Wang, et al. "Avirulence (AVR) Gene-Based Diagnosis Complements Existing Pathogen Surveillance Tools for Effective Deployment of Resistance (R) Genes Against Rice Blast Disease." Phytopathology® 107, no. 6 (June 2017): 711–20. http://dx.doi.org/10.1094/phyto-12-16-0451-r.

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Avirulence (AVR) genes in Magnaporthe oryzae, the fungal pathogen that causes the devastating rice blast disease, have been documented to be major targets subject to mutations to avoid recognition by resistance (R) genes. In this study, an AVR-gene-based diagnosis tool for determining the virulence spectrum of a rice blast pathogen population was developed and validated. A set of 77 single-spore field isolates was subjected to pathotype analysis using differential lines, each containing a single R gene, and classified into 20 virulent pathotypes, except for 4 isolates that lost pathogenicity. In all, 10 differential lines showed low frequency (<24%) of resistance whereas 8 lines showed a high frequency (>95%), inferring the effectiveness of R genes present in the respective differential lines. In addition, the haplotypes of seven AVR genes were determined by polymerase chain reaction amplification and sequencing, if applicable. The calculated frequency of different AVR genes displayed significant variations in the population. AVRPiz-t and AVR-Pii were detected in 100 and 84.9% of the isolates, respectively. Five AVR genes such as AVR-Pik-D (20.5%) and AVR-Pik-E (1.4%), AVRPiz-t (2.7%), AVR-Pita (0%), AVR-Pia (0%), and AVR1-CO39 (0%) displayed low or even zero frequency. The frequency of AVR genes correlated almost perfectly with the resistance frequency of the cognate R genes in differential lines, except for International Rice Research Institute-bred blast-resistant lines IRBLzt-T, IRBLta-K1, and IRBLkp-K60. Both genetic analysis and molecular marker validation revealed an additional R gene, most likely Pi19 or its allele, in these three differential lines. This can explain the spuriously higher resistance frequency of each target R gene based on conventional pathotyping. This study demonstrates that AVR-gene-based diagnosis provides a precise, R-gene-specific, and differential line-free assessment method that can be used for determining the virulence spectrum of a rice blast pathogen population and for predicting the effectiveness of target R genes in rice varieties.

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4

Mahalingam, Ramamurthy, Gejiao Wang, and Halina T. Knap. "Polygalacturonase and Polygalacturonase Inhibitor Protein: Gene Isolation and Transcription in Glycine max - Heterodera glycines Interactions." Molecular Plant-Microbe Interactions® 12, no. 6 (June 1999): 490–98. http://dx.doi.org/10.1094/mpmi.1999.12.6.490.

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The cell wall acts as the first line of defense during pathogen invasion. Polygalacturonases (PGs) are a class of cell-wall-modifying enzymes with precise temporal and organ-specific expression. A 350-bp fragment with high homology to PGs was identified by differential display (DD) analysis of soybean cyst nematode (SCN) race 3 resistant PI 437654 and susceptible cultivar Essex. The fragment was strongly expressed in Essex, 2 days after inoculation (DAI). Complete coding sequences of two PG cDNAs, PG1 and PG2, were isolated by 3′ and 5′ rapid amplification of cDNA ends polymerase chain reaction (RACE PCR). PI 437654 and Essex had identical PG1 and PG2 sequences. A transversion from A to C created a PstI restriction site in the PG2 cDNA that was used to distinguish the two PG cDNAs by cleaved amplified polymorphic sequence (CAPS) analysis. A cDNA encoding a polygalacturonase-inhibitor protein (PGIP) that is 89% identical to the Phaseolus vulgaris PGIP was isolated from soybean roots by reverse transcription (RT)-PCR. Steady-state levels of PG and PGIP were investigated by RNA gel blot analysis in roots 1 to 5 DAI and in hypocotyls and leaves. Differences in the constitutive levels of PG mRNAs were observed in roots of different soybean genotypes. Steady-state levels of PG mRNAs were enhanced during compatible interactions with SCN and reduced in incompatible interactions and in mechanically wounded roots. Enhanced PGIP transcription was observed in response to mechanical wounding in both PI 437654 and Essex, but only in compatible interactions with SCN, suggesting uncoupling of PGIP functions in developmental and stress cues. Constitutive expression in incompatible interactions shows PGIP is not a factor in SCN resistance. Thus, the up-regulation of endogenous PG transcription in soybean roots early after SCN infection could facilitate successful parasitism by SCN.

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5

Reysenbach, A. L., L. J. Giver, G. S. Wickham, and N. R. Pace. "Differential amplification of rRNA genes by polymerase chain reaction." Applied and Environmental Microbiology 58, no. 10 (1992): 3417–18. http://dx.doi.org/10.1128/aem.58.10.3417-3418.1992.

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6

Jay, Venita, Sue MacNeill, and Maria Zielenska. "MYCN Amplification in Pediatric Brain Tumors: Detection by Differential Polymerase Chain Reaction." Journal of Histotechnology 20, no. 2 (June 1997): 115–18. http://dx.doi.org/10.1179/his.1997.20.2.115.

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7

Bombeccari, G. P., G. P. Guzzi, F. Pallotti, and F. Spadari. "Focal Epithelial Hyperplasia: Polymerase Chain Reaction Amplification as a Differential Diagnosis Tool." American Journal of Dermatopathology 31, no. 1 (February 2009): 98–100. http://dx.doi.org/10.1097/dad.0b013e31818ffc04.

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8

Wang, Chao, Fan Meng, Yanping Huang, Nongyue He, and Zhu Chen. "Design and Implementation of Polymerase Chain Reaction Device for Aptamers Selection of Tumor Cells." Journal of Nanoscience and Nanotechnology 20, no. 3 (March 1, 2020): 1332–40. http://dx.doi.org/10.1166/jnn.2020.17356.

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Nucleic acid aptamers are a kind of one-dimensional biological nanomaterials and have found many applications. This paper designed and implemented a polymerase chain reaction (PCR) amplification device with a reaction volume of 500 μL, which can be used for the amplification of nucleic acid aptamers of tumor cells in the aptamer selection. This device mainly includes a control module, a temperature measuring module, a PCR amplification tube, a metal tank module, a liquid crystal display (LCD) and operation module and a cooling module. The new PCR amplification chamber is matched with the designed metal tank to ensure the temperature uniformity of the PCR amplification solution. The control module based on the STM32F103RCT6 manages the workflow of the entire device. The PCR amplification chamber and PT100 sensors on the metal tank formed a closed-loop feedback system, and the incremental proportional-integral-derivative (PID) algorithm was used to achieve the precise temperature control. In addition, we introduced the Smith predictive compensation algorithm to solve the temperature hysteresis problem of the PCR amplification chamber. The experimental results showed that the PCR device can meet the requirements for the nucleic acid aptamer selection of tumor cells. The device can also be used in other experiments with large-volume PCR amplification.

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9

Chen, Yihua, Bin Wang, Song Weining, and Grant Daggard. "Anchor primer associated problems in differential display reverse transcription polymerase chain reaction." Analytical Biochemistry 329, no. 1 (June 2004): 145–47. http://dx.doi.org/10.1016/j.ab.2004.02.030.

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10

Gramlich, Terry L., Christine R. Fritsch, David Maurer, Mary Eberle, and Ted S. Gansler. "Differential Polymerase Chain Reaction Assay of Cyclin Dl Gene Amplification in Esophageal Carcinoma." Diagnostic Molecular Pathology 3, no. 4 (December 1994): 255–59. http://dx.doi.org/10.1097/00019606-199412000-00007.

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11

Suzuki, Hiroaki, Jun Moriya, Atsuko Nakahata, Yasunori Fujioka, Kazuaki Inoue, and Kazuo Nagashima. "Cyclin D1 gene amplification in esophageal carcinosarcoma shown by differential polymerase chain reaction." Human Pathology 29, no. 7 (July 1998): 662–67. http://dx.doi.org/10.1016/s0046-8177(98)90273-8.

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12

Gilbert, J., M. D. Norris, M. Haber, M. Kavallaris, G. M. Marshall, and B. W. Stewart. "Determination of N-myc gene amplification in neuroblastoma by differential polymerase chain reaction." Molecular and Cellular Probes 7, no. 3 (June 1993): 227–34. http://dx.doi.org/10.1006/mcpr.1993.1033.

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13

Passadore, M., N. Bianchi, G. Feriotto, C. Mischiati, P. Giacomini, R. Piva, and R. Gambari. "Differential effects of distamycin analogues on amplification of human gene sequences by polymerase-chain reaction." Biochemical Journal 308, no. 2 (June 1, 1995): 513–19. http://dx.doi.org/10.1042/bj3080513.

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In this report we analyse the effects of distamycin and five distamycin analogues on amplification by polymerase-chain reaction (PCR) of two gene sequences displaying a different A+T/G+C content. The first was a 5′ region of the human oestrogen receptor (ER) gene, containing a (TA)26 stretch; the second was a CG-rich sequence of the human Ha-ras oncogene. The results obtained unequivocally demonstrate that the addition of one pyrrole ring significantly improves the ability of distamycin derivatives to interfere with PCR-mediated amplification of the human ER genomic region carrying a (TA)26 stretch. The distamycin analogues analysed differ in the number of pyrrole rings and in the presence of an N-formyl, an N-formimidoyl or a retroamide group at position X1. Among compounds carrying the same number of pyrrole rings, those carrying an N-formyl or an N-formimidoyl group retain a similar inhibitory activity. The retroamide analogues, on the contrary, are much less efficient in inhibiting PCR-mediated amplification of the 5′ER region. With respect to sequence selectivity both distamycin and distamycin analogues exhibit a sequence preference, since they do not inhibit PCR amplification of Ha-ras CG-rich gene regions, with the exception of a distamycin analogue carrying four pyrrole rings.

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14

Tsai, J. P., and W. Shi. "Analysis of gene expression in Treponema denticola with differential display polymerase chain reaction." Oral Microbiology and Immunology 15, no. 5 (October 2000): 305–8. http://dx.doi.org/10.1034/j.1399-302x.2000.150506.x.

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15

Liang, P., and A. Pardee. "Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction." Science 257, no. 5072 (August 14, 1992): 967–71. http://dx.doi.org/10.1126/science.1354393.

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16

Jörgensen, Marianne, Maja Bévort, Thuri S. Kledal, Brian V. Hansen, Marlene Dalgaard, and Henrik Leffers. "Differential display competitive polymerase chain reaction: An optimal tool for assaying gene expression." Electrophoresis 20, no. 2 (February 1, 1999): 230–40. http://dx.doi.org/10.1002/(sici)1522-2683(19990201)20:2<230::aid-elps230>3.0.co;2-i.

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17

Jorgensen, Marianne, Maja Bévort, Thuri S. Kledal, Brian V. Hansen, Marlene Dalgaard, and Henrik Leffers. "Differential display competitive polymerase chain reaction: An optimal tool for assaying gene expression." Electrophoresis 20, no. 2 (February 1, 1999): 230. http://dx.doi.org/10.1002/1522-2683(19990201)20:2<230::aid-elps230>3.0.co;2-i.

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18

Chervoneva, Inna, Boris Freydin, Terry Hyslop, and Scott A. Waldman. "Modeling qRT-PCR dynamics with application to cancer biomarker quantification." Statistical Methods in Medical Research 27, no. 9 (May 14, 2017): 2581–95. http://dx.doi.org/10.1177/0962280216683204.

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Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

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19

Gramlich, Terry L., Cynthia Cohen, Christine Fritsch, Patricia B. Derose, and Ted Gansler. "Evaluation of c-erbB-2 Amplification in Breast Carcinoma by Differential Polymerase Chain Reaction." American Journal of Clinical Pathology 101, no. 4 (April 1, 1994): 493–99. http://dx.doi.org/10.1093/ajcp/101.4.493.

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20

Islam, Aminul, Bruce Harrison, Brian F. Cheetham, Timothy J. Mahony, Peter L. Young, and Stephen W. Walkden-Brown. "Differential amplification and quantitation of Marek’s disease viruses using real-time polymerase chain reaction." Journal of Virological Methods 119, no. 2 (August 2004): 103–13. http://dx.doi.org/10.1016/j.jviromet.2004.03.006.

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21

Weng, Wei-Chien, and Yu-Cheng Lin. "Development of Detection Equipment for a Polymerase Chain Reaction with a Loop-Mediated Isothermal Amplification Reaction." Journal of Nanomaterials 2021 (March 29, 2021): 1–9. http://dx.doi.org/10.1155/2021/5513772.

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In this research, low-cost detection equipment intended to carry out a polymerase chain reaction (PCR) through a loop-mediated isothermal amplification (LAMP) reaction is presented. We designed the internal structure with SolidWorks and AutoCAD. The equipment comprised a Raspberry Pi development board, a temperature control module, and a fluorescent optical detection module. The main program, temperature control, florescent signal processing, signal analysis, and screen display were programmed with Java. We applied the digital temperature controller module to obtain precise temperature control of the equipment. The experimental results showed that the heating rate of the testing equipment could reach 65°C within 4 minutes and could be accurately controlled to within 1°C. The duration of the LAMP PCR experiment was found to be significantly shorter than that of the conventional PCR. The results also revealed that with LAMP PCR, the temperature could be accurately controlled within a specific range, and the designed heating tasks could be completed within 15 minutes to one hour, depending on the specimen. The equipment could also correctly read both the positive and negative reactions with fluorescent signals. Thus, the proposed LAMP PCR detection equipment is more sensitive, more stable, and more cost-effective than other conventional alternatives and can be used in numerous clinical applications.

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22

Hall, G. D., B. Smith, R. J. Weeks, P. J. Selby, J. Southgate, and J. D. Chester. "Novel Urothelium Specific Gene Expression Identified by Differential Display Reverse Transcriptase-Polymerase Chain Reaction." Journal of Urology 175, no. 1 (January 2006): 337???342. http://dx.doi.org/10.1097/00005392-200601000-00117.

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23

Hall, G. D., B. Smith, R. J. Weeks, P. J. Selby, J. Southgate, and J. D. Chester. "Novel Urothelium Specific Gene Expression Identified by Differential Display Reverse Transcriptase-Polymerase Chain Reaction." Journal of Urology 175, no. 1 (January 2006): 337–42. http://dx.doi.org/10.1016/s0022-5347(05)00006-6.

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24

Ranamukhaarachchi, Daya G., Mangalathu S. Rajeevan, Suzanne D. Vernon, and Elizabeth R. Unger. "Modifying Differential Display Polymerase Chain Reaction to Detect Relative Changes in Gene Expression Profiles." Analytical Biochemistry 306, no. 2 (July 2002): 343–46. http://dx.doi.org/10.1006/abio.2002.5679.

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25

Diener, Lara C., Patricia M. Schulte, D. George Dixon, and Bruce M. Greenberg. "Optimization of differential display polymerase chain reaction as a bioindicator for the cladoceranDaphnia magna." Environmental Toxicology 19, no. 3 (2004): 179–90. http://dx.doi.org/10.1002/tox.20010.

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26

Gomes, Thiago dos Santos, Mariana Coimbra Garcia, Flavia de Souza Cunha, Heloisa Werneck de Macedo, José Mauro Peralta, and Regina Helena Saramago Peralta. "Differential Diagnosis ofEntamoebaspp. in Clinical Stool Samples Using SYBR Green Real-Time Polymerase Chain Reaction." Scientific World Journal 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/645084.

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Amoebiasis, a disease caused byEntamoeba histolytica, is usually diagnosed by microscopic examination, which does not differentiate the morphologically identical species of theE. histolytica/E. disparcomplex. Furthermore, morphologically similar species such asEntamoeba hartmannicontribute to misidentification. Therefore, there is a need for more sensitive and specific methods. This study standardized a multiplex real-time PCR system forE. histolyticaandE. disparand a single real-time PCR forE. hartmanni. The multiplex protocol detected up to 0.0143 pg ofE. histolyticaDNA and 0.5156 pg ofE. disparDNA, and the average melting temperature (Tm) was 73°C and 70°C, respectively. ForE. hartmanni, theTmwas 73°C and the amplification was successful down to 0.03 fg of plasmid DNA. Negative controls and other intestinal parasites presented no amplification. Among the 48 samples tested,E. disparDNA was detected in 37; none exhibitedE. histolyticaDNA and 11 were negative in the multiplex protocol. In 4 of these 11 samples, however,E. hartmanniDNA was amplified. SYBR Green is demonstrated to be an interesting option and these combined PCR reactions can improve laboratory diagnosis of amoebiasis in developing countries.

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27

Ji, Feng. "Study of differential polymerase chain reaction of C-erbB-2 oncogene amplification in gastric cancer." World Journal of Gastroenterology 5, no. 2 (1999): 152. http://dx.doi.org/10.3748/wjg.v5.i2.152.

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28

Birek, C., E. Lui, R. C. K. Jordan, and I. Dardick. "Analysis of c-erbB-2 amplification in salivary gland tumours by differential polymerase chain reaction." European Journal of Cancer Part B: Oral Oncology 30, no. 1 (January 1994): 47–50. http://dx.doi.org/10.1016/0964-1955(94)90050-7.

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29

Salilew-Wondim, D., M. Hoelker, U. Besenfelder, V. Havlicek, F. Rings, D. Gagné, E. Fournier, et al. "199 IN VITRO-DEVELOPED BOVINE BLASTOCYSTS ARE MARKED WITH ABERRANT HYPER- AND HYPO-METHYLATED GENOMIC REGIONS." Reproduction, Fertility and Development 27, no. 1 (2015): 190. http://dx.doi.org/10.1071/rdv27n1ab199.

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Most often, in vitro produced embryos display poor quality and altered gene expression patterns compared to their in vivo counterparts. Aberrant DNA methylation occurring during in vitro embryo development is believed to be one of the multifaceted factors which may cause altered gene expression and poor embryo quality. Here, we investigated the genome-wide DNA methylation patterns of in vitro derived embryos using the recently developed Bovine EmbryoGENE Methylation Platform (BEGMP) array (Shojaei Saadi et al. BMC Genomics 2014 15, 451. doi: 10.1186/1471-2164-15-451) to unravel the aberrantly methylated genomic region in in vitro developed embryos. For this, in vitro and in vivo produced blastocysts were produced and used for genome-wide DNA methylation analysis. In vitro blastocysts were produced from oocytes retrieved from ovaries collected from the local abattoir and matured, fertilized, and cultured in vitro using SOF media. The in vivo blastocysts were produced by superovulation and AI of Simmental heifers followed by uterine flushing. Genomic DNA (gDNA) was then isolated from four replicates (each 10 blastocysts) of in vivo and in vitro derived blastocysts using Allprep DNA/RNA micro kit (Qiagen, Valencia, CA, USA) and the gDNA was then fragmented using the MseI enzyme. Following this, MseLig21 and MseLig were ligated to the MseI-digested genomic fragments in the presence of Ligase enzyme. Methyl-sensitive enzymes, HpaII, AciI, and Hinp1I, were used to cleave unmethlayted genomic regions within the MseI-MseI region of the fragmented DNA. The gDNA was subjected to two rounds of ligation-mediated polymerase chain reaction (LM-PCR) amplification. After removal of the adapters, the amplified gDNA samples from in vivo or in vitro groups were labelled either Cy-3 or Cy-5 dyes in dye-swap design using ULS Fluorescent gDNA labelling kit (Kreatech Biotechnology BV, Amsterdam, The Netherlands). Hybridization was performed for 40 h at 65°C. Slides were scanned using Agilent's High-Resolution C Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) and features were extracted with Agilent's Feature Extraction software (Agilent Technologies Inc.). The results have shown that from a total of 414 566 probes harboured by the BEGMP array, 248 453 and 253 147 probes were detected in in vitro and in vivo derived blastocysts, respectively. Data analysis using the linear modelling for microarray (LIMMA) package and R software (The R Project for Statistical Computing, Vienna, Austria) revealed a total of 3434 differentially methylated regions (DMRs; Fold change ≥1.5, P-value <0.05), of which 42 and 58% were hyper- and hypo-methylated, respectively, in in vitro derived blastocysts compared to their in vivo counterparts. The DMRs were found to be localised in the intronic, exonic, promoter, proximal promoter, and distal promoter, and some of the probes did not have nearby genes. In addition, 10.8% of the DMRs were found to be stretched in short, long, or intermediate CpG islands. Thus, this study demonstrated genome-wide dysregulation in the epigenome landscape of in vitro-derived embryos by the time they reach to the blastocysts stage.

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30

Assmann, Eliana Maria, Laura Maria Mariscal Ottoboni, Andre Ferraz, Jaime Rodriguez, and Maricilda Palandi de Mello. "Iron-responsive genes of Phanerochaete chrysosporium isolated by differential display reverse transcription polymerase chain reaction." Environmental Microbiology 5, no. 9 (September 2003): 777–86. http://dx.doi.org/10.1046/j.1462-2920.2003.00475.x.

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31

An, Han-Xiang, Dieter Niederacher, Matthias W. Beckmann, Uwe-Jochen Göhring, Anton Scharl, Frauke Picard, Claudiavan van Roeyen, Hans-Georg Schnürch, and Hans G. Bender. "ERBB2 gene amplification detected by fluorescent differential polymerase chain reaction in paraffin-embedded breast carcinoma tissues." International Journal of Cancer 64, no. 5 (October 20, 1995): 291–97. http://dx.doi.org/10.1002/ijc.2910640502.

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32

El Awady, M. K., N. M. Abdalla, A. M. Salem, S. Samir, and A. M. Nour. "Differential display analysis of mRNAs in chronic myelogenous leukaemia." Eastern Mediterranean Health Journal 7, no. 4-5 (September 15, 2001): 707–15. http://dx.doi.org/10.26719/2001.7.4-5.707.

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Analysis of expressed mRNAs with differential display-polymerase chain reaction [DD-PCR] is a powerful tool for the characterization of genes involved in malignant pathways and might identify markers for different phases of chronic myelogenous leukaemia [CML]. We examined the presence of BCR-ABL transcripts in 25 CML patients in either the chronic phase or blast crisis. We then analysed the expression of leukocytic RNA transcripts in CML phases. DD-PCR technique was used to examine CML cases with BCR-ABL in comparison with CML cases lacking detectable BCR-ABL transcripts. Our results support the use of differential display not only for characterization of the CML differentially expressed genes but also to locate patterns that can be implemented as valuable fingerprints for each phase of CML.

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33

Liu, Gui-qiong, Jin-jin Zhu, Zhi-yue Wang, and Xun-ping Jiang. "Search for Specific Expressed Genes in Chicken Sperm Storage Tubules by differential Display Polymerase Chain Reaction." Avian Biology Research 2, no. 3 (August 2009): 151–56. http://dx.doi.org/10.3184/175815509x12474776260634.

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The objective of this study was to find the specific expressed genes in chicken sperm storage tubules. One hundred and fifty dual-purpose hens at 30 weeks of age were inseminated with 1 × 108spermatozoa on two consecutive days. Eggs were collected and set daily during the 24 days following the latter of two inseminations. Five hens with fertility below 60% were inseminated with fresh semen. Fifteen hens with fertility above 80% were divided into three groups. Fresh semen, frozen dead semen and 0.9% NaCl, respectively, were injected into the vagina of five hens in each group. RNA from the utero-vaginal junction (UVJ) of the hens was reverse transcribed and differentially displayed. Four bands of interest which were expressed in UVJ from hens inseminated with fresh semen or frozen semen but not from hens inseminated with saline were selected, re-amplified, cloned and sequenced. BLAST search showed that band A is similar to part of chromosome 3 (the homology is 9–8%) and the nearest gene to the fragment is 1,722 base pairs up-stream whose product is mitogen- activated kinase. Band B is similar to phosphatidyl inositol glycan anchor biosynthesis gene (PIGK) and the homology is 98%. PIGK is a subunit of glycosylphosphatidylinositol transamidase (GPI8). GPI-linked proteins participate in the release of membrane proteins. Band F is similar to a hypothetical protein gene and the homology is 9–7%. This hypothetical protein belongs to chicken neurexophilin. Band G is similar to fat3 and the homology is 97%. Neurexophilin and fat3 are proteins that function in the nervous system. Taken together these data indicate that hens may regulate sperm storage in UVJ through the nervous system and may release sperm from the UVJ through GPI8.

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34

Abts, Harry F., Kai Breuhahn, Gunter Michel, Karl Kohrer, Peter Esser, and Thomas Ruzicka. "Analysis of UVB-modulated Gene Expression in Human Keratinocytes by mRNA Differential Display Polymerase Chain Reaction." Photochemistry and Photobiology 66, no. 3 (September 1997): 363–67. http://dx.doi.org/10.1111/j.1751-1097.1997.tb03159.x.

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35

Bräuer, A. U., N. E. Savaskan, M. Plaschke, O. Ninnemann, and R. Nitsch. "Cholecystokinin expression after hippocampal deafferentiation: molecular evidence revealed by differential display-reverse transcription–polymerase chain reaction." Neuroscience 121, no. 1 (September 2003): 111–21. http://dx.doi.org/10.1016/s0306-4522(03)00336-1.

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Rhodes, Linda D., and Rebecca J. Van Beneden. "Application of differential display polymerase chain reaction to the study of neoplasms of feral marine bivalves." Marine Environmental Research 42, no. 1-4 (June 1996): 81–85. http://dx.doi.org/10.1016/0141-1136(95)00070-4.

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37

Mirmohammadsadegh, Alireza, Ulrike Tartler, Günter Michel, Annett Baer, Markus Walz, Ronald Wolf, Thomas Ruzicka, and Ulrich R. Hengge. "HAX-1, Identified by Differential Display Reverse Transcription Polymerase Chain Reaction, Is Overexpressed in Lesional Psoriasis." Journal of Investigative Dermatology 120, no. 6 (June 2003): 1045–51. http://dx.doi.org/10.1046/j.1523-1747.2003.12247.x.

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38

Wilkinson, Jack Q., Michael B. Lanahan, Timothy W. Conner, and Harry J. Klee. "Identification of mRNAs with enhanced expression in ripening strawberry fruit using polymerase chain reaction differential display." Plant Molecular Biology 27, no. 6 (March 1995): 1097–108. http://dx.doi.org/10.1007/bf00020883.

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39

Rockett, J. C., D. J. Esdaile, and G. G. Gibson. "Molecular profiling of non-genotoxic hepatocarcinogenesis using differential display reverse transcription-polymerase chain reaction (ddRT-PCR)." European Journal of Drug Metabolism and Pharmacokinetics 22, no. 4 (December 1997): 329–33. http://dx.doi.org/10.1007/bf03190966.

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40

Wu, Gen Sheng, Siddhartha Kar, and Brian I. Carr. "Identification op a human hepatocellular carcinoma-associated tumor suppressor gene by differential display polymerase chain reaction." Life Sciences 57, no. 11 (August 1995): 1077–85. http://dx.doi.org/10.1016/0024-3205(95)02053-l.

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41

Yong-Hua, Chen, Zhao Sen, Yan Qin-Quan, Li Yang-Sheng, Wu Xing-Rong, and Xiao Guo-Ying. "Tolerance of submergence in rice: gene studies using differential display technique." Chinese Journal of Agricultural Biotechnology 4, no. 2 (August 2007): 139–44. http://dx.doi.org/10.1017/s1479236207001428.

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AbstractGene expression profiles between submergence rice (Oryza sativa ssp. indica) varieties, tolerant FR13A and sensitive IR39595-503-2-1-2, under submergence stress were identified using differential display reverse transcriptase-polymerase chain reaction (DDRT-PCR). A total of 1428 bands were amplified with 40 pairs of primers, of which 102 were significantly different between the two lines. The differential display ratio was 7.1%. Among 42 differential display bands derived from the submergence tolerant variety, the expression of seven fragments was confirmed by Northern blot analysis. The analysis of their sequences indicated that four of them showed high homology with genes related to a water stress response: genes encoding ATP-binding protein, isocitrate dehydrogenase, NADH dehydrogenase and terminal acetyltransferase, respectively. The remaining three fragments were novel cDNA fragments.

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42

Beckmann, M. W., H. X. An, D. Niederacher, K. Kohrer, M. Finken-Eigen, W. Schroder, H. G. Schnurch, and H. G. Bender. "Oncogene amplification in archival ovarian carcinoma detected by fluorescent differential polymerase chain reaction - a routine analytical approach." International Journal of Gynecological Cancer 6, no. 4 (July 1996): 291–97. http://dx.doi.org/10.1046/j.1525-1438.1996.06040291.x.

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43

Friedrichs, Kay, Dietmar Lohmann, and Heinz Höfler. "Detection of HER-2 oncogene amplification in breast cancer by differential polymerase chain reaction from single cryosections." Virchows Archiv B Cell Pathology Including Molecular Pathology 64, no. 1 (December 1993): 209–12. http://dx.doi.org/10.1007/bf02915114.

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44

Nagpal, J. K., and B. R. Das. "Identification of differentially expressed genes in tobacco chewing-mediated oral cancer by differential display?polymerase chain reaction." European Journal of Clinical Investigation 37, no. 8 (August 2007): 658–64. http://dx.doi.org/10.1111/j.1365-2362.2007.01841.x.

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45

Tomita, Masafumi, Tsutomu Nohno, Toshiko Okuyama, Shin-ichiro Nishimatsu, and Junko Adachi. "Paraquat-induced gene expression in rat lung tissues using a differential display reverse transcription-polymerase chain reaction." Archives of Toxicology 76, no. 9 (September 1, 2002): 530–37. http://dx.doi.org/10.1007/s00204-002-0379-x.

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46

Deleu, C., M. Coustaut, M. ‐F Niogret, and F. Larher. "Three new osmotic stress‐regulated cDNAs identified by differential display polymerase chain reaction in rapeseed leaf discs." Plant, Cell & Environment 22, no. 8 (August 15, 1999): 979–88. http://dx.doi.org/10.1046/j.1365-3040.1999.00471.x.

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47

Fukusaki, Ei-ichiro, Takashi Oishi, Hozumi Tanaka, Shin-ichiro Kajiyama, and Akio Kobayashi. "Identification of Genes Induced by Taxol Application Using a Combination of Differential Display RT-PCR and DNA Microarray Analysis." Zeitschrift für Naturforschung C 56, no. 9-10 (October 1, 2001): 814–19. http://dx.doi.org/10.1515/znc-2001-9-1022.

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Abstract The differential display reverse transcriptional polymerase chain reaction (DD-RT-PCR) was used to hunt for cDNA fragments specifically expressed by taxol treatment of HeLa cells. Forty-eight cDNA clones were differentially displayed through the experiments. The cDNA fragments obtained were separately spotted onto glass slides to prepare a tailor-made DNA chip. The gene expression pattern of differentially displayed cDNA fragments were checked by DNA microarray analysis.

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Frels, J. S., C. M. Tebeau, S. Z. Doktor, and C. L. Jahn. "Differential replication and DNA elimination in the polytene chromosomes of Euplotes crassus." Molecular Biology of the Cell 7, no. 5 (May 1996): 755–68. http://dx.doi.org/10.1091/mbc.7.5.755.

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The transposon-like Tec elements of Euplotes crassus are precisely excised during formation of polytene chromosomes in the developing macronucleus. To determine whether all Tec elements exhibit identical developmental timing of excision, we used polymerase chain reaction to visualize amplification and diminution at numerous randomly selected Tec insertion sites. Two classes of sites are evident. Early replicating sites show one or more rounds of amplification and diminution (corresponding to excision) and frequently occur within macronuclear-destined sequences. Late replicating sites do not undergo diminution until chromosome fragmentation and are predominantly associated with eliminated sequences. We conclude that the previously described clustering of macro-nuclear-destined sequences in the micronuclear genome allows for their differential replication at the polytene stage and results in targeting of these sequences for transcriptional activation and highly specific deletion and chromosome fragmentation processes.

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Park, Joo Young, Dong Hwa Kim, Woon Seob Shin, Hee Seok Seo, Kyung Hoon Kim, Kyoung Ho Lee, Choon Myung Koh, and Jeong Pyo Bong. "Search for Genes Potentially Related to Germ Tube Formation inCandida albicansby Differential-Display Reverse Transcription Polymerase Chain Reaction." Yonsei Medical Journal 44, no. 1 (2003): 110. http://dx.doi.org/10.3349/ymj.2003.44.1.110.

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Chong, V. Z., W. Costain, J. Marriott, S. Sindwani, D. J. Knauer, J.-F. Wang, L. T. Young, D. MacCrimmon, and R. K. Mishra. "Differential display polymerase chain reaction reveals increased expression of striatal rat glia-derived nexin following chronic clozapine treatment." Pharmacogenomics Journal 4, no. 6 (September 7, 2004): 379–87. http://dx.doi.org/10.1038/sj.tpj.6500274.

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