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Journal articles on the topic '378 bp DNA fragment'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

WU, Z., I. NAGANO, E. POZIO, and Y. TAKAHASHI. "Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) for the identification of Trichinella isolates." Parasitology 118, no. 2 (1999): 211–18. http://dx.doi.org/10.1017/s0031182098003679.

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In the present study, polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis was developed to identify 5 species (Trichinella spiralis, Trichinella britovi, Trichinella nativa, Trichinella nelsoni and Trichinella pseudospiralis) and 3 phenotypes of uncertain taxonomic status (Trichinella T5, T6, and T8). Eleven restriction endonucleases were used to restrict 3 DNA fragments (1) a 2800 bp fragment of the 43 kDa excretory–secretory (E–S) protein gene, (2) a 1250 bp fragment amplified with the primer pair SB147A and (3) a 372 bp fragment amplified with the primer p

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2

Abdel-Rahman, S. M., A. M. Elmaghraby, and A. S. Haggag. "Identification and differentiation among chicken’s, duck’s, quail’s, rabbit’s and turkey's meat using PCR-RFLP technique." Biotehnologija u stocarstvu 31, no. 1 (2015): 101–8. http://dx.doi.org/10.2298/bah1501101a.

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PCR-RFLP technique was developed for identification and differentiation among chicken?s, duck?s, quail?s, rabbit?s and turkey's meat. DNA from small amount of muscles (0.05 g) was extracted and a region of mitochondrial DNA (cytochrome-b gene) in chicken, duck, quail, rabbit and turkey was amplified by PCR. Fragment length of the PCR product was 371 bp in chicken, 374 bp in duck and rabbit and 377 bp in both quail and turkey. Six nucleotides different makes it difficult to differentiate among these five species-specific meat. For differentiation, three different restriction enzymes (DdeI, MspI

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3

Hawa, N. S., J. L. H. O'Riordan, and S. M. Farrow. "Binding of 1,25-dihydroxyvitamin D3 receptors to the 5′-flanking region of the bovine parathyroid hormone gene." Journal of Endocrinology 142, no. 1 (1994): 53–60. http://dx.doi.org/10.1677/joe.0.1420053.

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Abstract To further define the binding site for receptors for 1,25(OH)2D3 (VDR) in the bovine PTH gene and to study the interactions of transcription factors with VDR, Southwestern and gel shift assays were used. Data from the former indicated binding of VDR to DNA fragments spanning the regions −451 to −348 bp and −668 to −452 bp. Studies using gel shift assays confirmed binding to the −451 to −348 bp fragment and specificity was shown by using excess concentrations of unlabelled −451 to −348 bp fragment to compete for binding, whereas excess unlabelled −347 to +50 bp did not compete. Binding

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4

Chang, S., ME Reid, J. Conboy, YW Kan, and N. Mohandas. "Molecular characterization of erythrocyte glycophorin C variants." Blood 77, no. 3 (1991): 644–48. http://dx.doi.org/10.1182/blood.v77.3.644.644.

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Abstract Human erythrocyte glycophorin C plays a functionally important role in maintaining erythrocyte shape and regulating membrane mechanical stability. Immunochemical and serologic studies have identified a number of glycophorin C variants that include the Yus, Gerbich, and Webb phenotypes. We report here the molecular characterization of these variants. Amplification of glycophorin C mRNA from the Yus phenotype, using two oligonucleotide primers that span the coding domain, generated a 338-bp fragment compared with a 395-bp fragment generated by amplification of normal glycophorin C mRNA.

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5

Chang, S., ME Reid, J. Conboy, YW Kan, and N. Mohandas. "Molecular characterization of erythrocyte glycophorin C variants." Blood 77, no. 3 (1991): 644–48. http://dx.doi.org/10.1182/blood.v77.3.644.bloodjournal773644.

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Human erythrocyte glycophorin C plays a functionally important role in maintaining erythrocyte shape and regulating membrane mechanical stability. Immunochemical and serologic studies have identified a number of glycophorin C variants that include the Yus, Gerbich, and Webb phenotypes. We report here the molecular characterization of these variants. Amplification of glycophorin C mRNA from the Yus phenotype, using two oligonucleotide primers that span the coding domain, generated a 338-bp fragment compared with a 395-bp fragment generated by amplification of normal glycophorin C mRNA. Sequenci

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6

Demeke, T., A. Laroche, and D. A. Gaudet. "A DNA marker for the Bt-10 common bunt resistance gene in wheat." Genome 39, no. 1 (1996): 51–55. http://dx.doi.org/10.1139/g96-007.

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The Bt-10 bunt gene confers resistance to most races of the common bunt fungi, Tilletia tritici and T. laevis. The RAPD technique, employing a total of 965 decamer primers, was used to identify polymorphic markers between resistant (BW553) and susceptible ('Neepawa') near-isogenic lines. Primer 196 (5′ CTC CTC CCC C 3′) produced a 590 base pair (bp) reproducible fragment only in the resistant near-isogenic line. The 590-bp DNA fragment was present in all the 22 wheat cultivars known to carry the Bt-10 resistance gene and also in 15 resistant F2 lines obtained from a cross between the resistant

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7

Luo, Chao-Xi, Kerik D. Cox, Achour Amiri, and Guido Schnabel. "Occurrence and Detection of the DMI Resistance-Associated Genetic Element ‘Mona’ in Monilinia fructicola." Plant Disease 92, no. 7 (2008): 1099–103. http://dx.doi.org/10.1094/pdis-92-7-1099.

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Sterol demethylation inhibitor (DMI) fungicide resistance in isolates of Monilinia fructicola from Georgia has been linked to overexpression of the MfCYP51 gene and a corresponding 65-bp genetic element ‘Mona’ inserted in the upstream region of MfCYP51. In this study, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to detect the Mona element. Fourteen DMI fungicide-resistant (DMI-R) and six DMI fungicide-sensitive (DMI-S) isolates from Georgia, six DMI-R and 11 DMI-S isolates from South Carolina, seven DMI-R and nine DMI-S isolates from New

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8

Voevodin, A., E. Samilchuk, J. Allan, J. Rogers, and S. Broussard. "Simian T-lymphotropic virus type 1 (STLV-1) infection in wild yellow baboons (Papio hamadryas cynocephalus) from Mikumi National Park, Tanzania." Virology 228, no. 2 (1997): 350–59. https://doi.org/10.5281/zenodo.13533307.

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(Uploaded by Plazi for the Bat Literature Project) Serum and peripheral blood leukocytes from wild yellow baboons (Papio hamadryas cynocephalus) were tested for the presence of STLV-1-specific antibodies and proviral DNA. Fourteen of 30 sera tested positive by radioimmunoprecipitation assay (RIPA) with HTLV-1. Among 36 DNA samples tested by PCR 15 were positive by double nested PCR for a fragment of the STLV-1 env gene, the most sensitive assay among PCR tests employed. Of 30 animals that were tested both serologically and by PCR in only 1 case were the results discordant (PCR-positive, antibo

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9

Voevodin, A., E. Samilchuk, J. Allan, J. Rogers, and S. Broussard. "Simian T-lymphotropic virus type 1 (STLV-1) infection in wild yellow baboons (Papio hamadryas cynocephalus) from Mikumi National Park, Tanzania." Virology 228, no. 2 (1997): 350–59. https://doi.org/10.5281/zenodo.13533307.

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(Uploaded by Plazi for the Bat Literature Project) Serum and peripheral blood leukocytes from wild yellow baboons (Papio hamadryas cynocephalus) were tested for the presence of STLV-1-specific antibodies and proviral DNA. Fourteen of 30 sera tested positive by radioimmunoprecipitation assay (RIPA) with HTLV-1. Among 36 DNA samples tested by PCR 15 were positive by double nested PCR for a fragment of the STLV-1 env gene, the most sensitive assay among PCR tests employed. Of 30 animals that were tested both serologically and by PCR in only 1 case were the results discordant (PCR-positive, antibo

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10

Harju, Susanna, та Kenneth R. Peterson. "In Vivo and In Vitro Analysis of an Aγ-Globin Gene Silencer in Human β-Yac Transgenic Mice." Blood 104, № 11 (2004): 1220. http://dx.doi.org/10.1182/blood.v104.11.1220.1220.

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Abstract Autonomous silencing of gene expression is one mechanism operative in the control of human β-like globin gene switching and is best exemplified by the ε-globin gene. Experiments using variously truncated Aγ-globin genes linked to LCR sequences suggested that a region of the Aγ-globin gene between −730 to −378 relative to the mRNA CAP site may function as an adult stage-specific silencer element. A 5.4 Kb marked Aγ-globin gene (Aγm) inserted between LCR 5′HS1 and the ε-globin gene in a β-YAC (Aγm 5′ ε β-YAC) was silenced in transgenic mice during adult definitive erythropoiesis, even i

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11

Juliandri, Ria Reinnata, Shelly Zairina, Elhah Nailul Khasna, Dahlia ., and Dwi Listyorini. "Isolation 3’-end Fragment of Pun1 gene from Capsicum frutescens L. cultivar Cakra Hijau." KnE Life Sciences 3, no. 4 (2017): 194. http://dx.doi.org/10.18502/kls.v3i4.704.

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<p><em>Pun1 </em>gene <a href="file:///C:/Users/Mohamad%20Mostafa/Desktop/Knowledge%20E/In%20Press%20Conferences/ICBS-2015/Source%20files/ICBS-2015/Soure%20papers-ICBS-2015/25.%20Ria%20Reinnata-080117_Roy.doc#_msocom_1">[A1]</a> is the one of candidate gene that responsible to determine pungency in Capsicum. In previous researches, 1 310 bp fragment of 1 671 bp <em>Pun1 </em>gene from<em> Capsicum frutescens </em>L. cv. Cakra Hijau had been isolated. The purpose of this research was to isolate of 3’-<em>end</em> fragment and get

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12

Li, F., X. N. Liu, Y. Zhu, J. Ma, N. Liu, and J. H. Yang. "Identification of the 2-tridecanone responsive region in the promoter of cytochrome P450 CYP6B6 of the cotton bollworm, Helicoverpa armigera (Lepidoptera: Noctuidae)." Bulletin of Entomological Research 104, no. 6 (2014): 801–8. http://dx.doi.org/10.1017/s0007485314000698.

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AbstractEukaryote transcription is controlled by regulatory DNA sequences and transcription factors, so transcriptional control of gene plays a pivotal role in gene expression. In this study, we identified the region of the CYP6B6 gene promoter of Helicoverpa armigera which responds to the plant secondary toxicant 2-tridecanone. Transient transfection assay results from five of stepwise deletion fragments linked to the luciferase reporter gene revealed that the promoter activity of each CYP6B6 fragment was significantly higher than that of their basal activity after the Sf9 cells were treated

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13

Sangthong, Danai, Songmeung Suwannarat, Sompid Samipak, and Pradit Sangthong. "Multiplex PCR assay for species identification of meat and dairy products from buffalo (Bubalus bubalis), cattle (Bos indicus and Bos taurus), goat (Capra hircus), and sheep (Ovis aries)." International Food Research Journal 28, no. 4 (2021): 716–25. http://dx.doi.org/10.47836/ifrj.28.4.08.

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Cases of fraudulent meat and dairy products have increased worldwide, especially in developing countries. To determine the misrepresented animal species, appropriate tools in routine monitoring should be available for food inspections. In the present work, a multiplex polymerase chain reaction assay for species identification of products from ruminants including buffalo, cattle, goat, and sheep was developed. The primer set KUMUT_cFarmSp1 was composed of five species-specific primers and a pair of positive-control primers. The primer set amplified 106-, 163-, 232-, and 308-bp specific fragment

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14

Fajardo, Violeta, Isabel González, Inés López-Calleja, et al. "Analysis of Mitochondrial DNA for Authentication of Meats from Chamois (Rupicapra rupicapra), Pyrenean Ibex (Capra pyrenaica), and Mouflon (Ovis ammon) by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism." Journal of AOAC INTERNATIONAL 90, no. 1 (2007): 179–86. http://dx.doi.org/10.1093/jaoac/90.1.179.

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Abstract The prevention of fraudulent labeling of game meat constitutes an important part of food regulatory control and quality assurance systems. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis based on mitochondrial deoxyribonucleic acid (DNA) was developed for authentication of meats from chamois (Rupicapra rupicapra), pyrenean ibex (Capra pyrenaica), and mouflon (Ovis ammon). Amplification and restriction site analysis of a DNA fragment about 720 base pairs (bp) from the mitochondrial 12S rRNA gene of all analyzed species permitted the selection of

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15

Ouardani, M., L. Wilson, R. Jetté, C. Montpetit, and S. Dea. "Multiplex PCR for Detection and Typing of Porcine Circoviruses." Journal of Clinical Microbiology 37, no. 12 (1999): 3917–24. http://dx.doi.org/10.1128/jcm.37.12.3917-3924.1999.

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Sets of oligonucleotide primers were designed according to the sequences of the open reading frames (ORFs) ORF1 and ORF2 of the prototype nonpathogenic PK-15 strain of porcine circovirus (PCV) type 1 (PCV-1). By the PCR performed with the various primer sets, genomic DNA or RNA from other bacterial or viral pathogens of the respiratory tracts of pigs could not be amplified. A positive amplification reaction could be visualized with DNA extracted from a viral suspension containing as few as 10 viral particles per ml. No DNA fragment could be amplified from lysates of continuous porcine cell lin

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16

Densmore, Llewellyn D., John W. Wright, and Wesley M. Brown. "LENGTH VARIATION AND HETEROPLASMY ARE FREQUENT IN MITOCHONDRIAL DNA FROM PARTHENOGENETIC AND BISEXUAL LIZARDS (GENUS CNEMIDOPHORUS)." Genetics 110, no. 4 (1985): 689–707. http://dx.doi.org/10.1093/genetics/110.4.689.

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ABSTRACT Samples of mtDNA isolated from each of 92 lizards representing all color pattern classes of Cnemidophorus tesselatus and two populations of C. tigris marmoratus were digested with the restriction endonucleases MboI, TaqI, RsaI and MspI. The mtDNA fragment sizes were compared after radioactive labeling and gel electrophoresis. Three features were notable in the comparisons: (1) there was little variation due to gain or loss of cleavage sites, (2) two fragments varied noticeably in length among the samples, one by a variable amount up to a maximum difference of ∼370 base pairs (bp) and

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17

Ray, R., and D. M. Miller. "Cloning and characterization of a human c-myc promoter-binding protein." Molecular and Cellular Biology 11, no. 4 (1991): 2154–61. http://dx.doi.org/10.1128/mcb.11.4.2154-2161.1991.

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A human cDNA clone encoding a c-myc promoter-binding protein was detected by screening a HeLa cell lambda phage expression cDNA library. The library was screened by using an XhoI-NaeI human c-myc P2 promoter fragment as a probe. The recombinant phage encoded a fusion protein, myc-binding protein 1 (MBP-1), which had an apparent molecular size of 40 kDa. A corresponding protein with a molecular size of 35 kDa was present in a HeLa cell extract. Sequence analysis of the cloned gene reveals an open reading frame of 1,038 bp with a 3' untranslated region of 378 bp. The predicted protein sequence c

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18

Ray, R., and D. M. Miller. "Cloning and characterization of a human c-myc promoter-binding protein." Molecular and Cellular Biology 11, no. 4 (1991): 2154–61. http://dx.doi.org/10.1128/mcb.11.4.2154.

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A human cDNA clone encoding a c-myc promoter-binding protein was detected by screening a HeLa cell lambda phage expression cDNA library. The library was screened by using an XhoI-NaeI human c-myc P2 promoter fragment as a probe. The recombinant phage encoded a fusion protein, myc-binding protein 1 (MBP-1), which had an apparent molecular size of 40 kDa. A corresponding protein with a molecular size of 35 kDa was present in a HeLa cell extract. Sequence analysis of the cloned gene reveals an open reading frame of 1,038 bp with a 3' untranslated region of 378 bp. The predicted protein sequence c

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19

Shelley, C. S., E. Remold-O'Donnell, F. S. Rosen, and A. S. Whitehead. "Structure of the human sialophorin (CD43) gene. Identification of features atypical of genes encoding integral membrane proteins." Biochemical Journal 270, no. 3 (1990): 569–76. http://dx.doi.org/10.1042/bj2700569.

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A human sialophorin (CD43) specific genomic clone was isolated, and a 6.5 kb fragment containing the 4.6 kb sialophorin gene was sequenced. The promoter region contains no TATA or CAAT boxes, but is highly enriched in G and C nucleotides and contains short repeat sequences similar to those found in the promoters of ‘housekeeping’ genes. S1-nuclease protection and primer-extension experiments established that the sialophorin gene has two major transcription initiation sites. There is a single intron of 378 bp that interrupts the sequence specifying the mRNA 5′ untranslated region. The gene is t

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20

Burnett, A., N. Lalancette, and K. McFarland. "First Report of the Peach Brown Rot Fungus Monilinia fructicola Resistant to Demethylation Inhibitor Fungicides in New Jersey." Plant Disease 94, no. 1 (2010): 126. http://dx.doi.org/10.1094/pdis-94-1-0126a.

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Reduced sensitivity and resistance of Monilinia fructicola to demethylation inhibitors (DMIs; fungicide group 3) have been previously found in stone fruit orchards in Georgia, South Carolina, Ohio, and New York (2). Resistance development is a major concern because of the importance of DMIs for brown rot management. Eleven single-spore isolates, originally collected during 2006 from separate commercial peach (Prunus persica) orchards in southern New Jersey, were removed from cold storage (5°C) in early 2008 and examined in vitro for resistance to the DMI propiconazole (Orbit 3.6EC; Syngenta Cr

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21

Zhuravlev, Aleksandr V., Gennadii A. Zakharov, Ekaterina V. Anufrieva, Anna V. Medvedeva, Ekaterina A. Nikitina, and Elena V. Savvateeva-Popova. "Chromatin Structure and “DNA Sequence View”: The Role of Satellite DNA in Ectopic Pairing of the Drosophila X Polytene Chromosome." International Journal of Molecular Sciences 22, no. 16 (2021): 8713. http://dx.doi.org/10.3390/ijms22168713.

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Chromatin 3D structure plays a crucial role in regulation of gene activity. Previous studies have envisioned spatial contact formations between chromatin domains with different epigenetic properties, protein compositions and transcription activity. This leaves specific DNA sequences that affect chromosome interactions. The Drosophila melanogaster polytene chromosomes are involved in non-allelic ectopic pairing. The mutant strain agnts3, a Drosophila model for Williams–Beuren syndrome, has an increased frequency of ectopic contacts (FEC) compared to the wild-type strain Canton-S (CS). Ectopic p

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22

Fernández, M., M. L. Ruiz, C. Linares, A. Fominaya, and M. Pérez de la Vega. "5S rDNA genome regions of Lens species." Genome 48, no. 5 (2005): 937–42. http://dx.doi.org/10.1139/g05-052.

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The length variability of the nontranscribed spacer (NTS) of the 5S rDNA repeats was analyzed in species of the genus Lens by means of PCR amplification. The NTS ranged from ~227 to ~952 bp. The polymorphism detected was higher than previous NTS polymorphisms described in this genus. Three NTS length variants from Lens culinaris subsp. culinaris and 2 from Lens culinaris subsp. orientalis were sequenced. The culinaris NTS fragment lengths were 239, 371, and 838 bp, whereas the orientalis ones were 472 bp and 506 bp, respectively. As a result of sequence similarities, 2 families of sequences we

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Tian, Ping, Dajun Du, Li Yang, Nan Zhou, and Ling Tao. "SP3-induced Timeless transcription contributes to cell growth of lung adenocarcinoma cells." PLOS ONE 19, no. 2 (2024): e0298295. http://dx.doi.org/10.1371/journal.pone.0298295.

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Background Timeless is well-known for its key role in replication checkpoints. Recent studies reveal the involvement of Timeless and specificity protein (SP) 1 in human malignancies. However, no evidence proved the interaction between SP3 and Timeless in lung adenocarcinoma (LUAD). Methods The expression and clinical significance of Timeless were analyzed using the LUAD dataset downloaded from the Cancer Genome Atlas (TCGA). Lentivirus-mediated Timeless knockdown in A549 cells was used to examine the role of Timeless in cell proliferation and pemetrexed (PEM) resistance. Transcription factors

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24

Tesfaye, Mesfin, and F. Brian Holl. "Group-specific differentiation of Rhizobium from clover species by PCR amplification of 23S rDNA sequences." Canadian Journal of Microbiology 44, no. 11 (1998): 1102–5. http://dx.doi.org/10.1139/w98-114.

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Two 20-bp primers that provide group-specific detection of Rhizobium spp. by polymerase chain reaction (PCR) have been used to differentiate strains that belong to different effectiveness groups within the Rhizobium-Trifolium cross-inoculation group. The target for DNA amplification was a 370-bp fragment of the 23S rDNA region. Analysis of additional root-nodule forming, as well as root-associated bacterial species by PCR-primer assay revealed that variability within this 20-bp segment of the 23S rDNA region may be widespread and provide an effective identification tool. Our data suggest that

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25

Ohst, Torsten, Wolfgang Böhme, Robert Schreiber, and Jörg Plötner. "Divergence in mitochondrial DNA of Near Eastern water frogs with special reference to the systematic status of Cypriote and Anatolian populations (Anura, Ranidae)." Amphibia-Reptilia 22, no. 4 (2001): 397–412. http://dx.doi.org/10.1163/15685380152770363.

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AbstractWater frogs from Anatolia, Syria, Jordan, and central Asia (Turkmenistan, Uzbekistan, Kazakhstan) were compared on the basis of the complete mitochondrial (mt) ND3 gene (340 bp), two flanking mt t-RNA gene fragments (26 bp), and a 374 bp fragment of the mt 12S rRNA gene. A total of 27 haplotypes were found among the investigated individuals. Anatolian water frogs differed from Syrian and Jordanian Rana bedriagae by 2.2-3.4% of the analysed sites. The observed divergence (2.8-4.1%) between the Cypriote water frogs and frogs from the surrounding mainland (southern Turkey, west Syria) was

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Zebua, Nistiarni, Ixchel F. Mandagi, K. W. A. Masengi, et al. "Study of e-DNA Quality at Fishing Ground of Manado Bay, North Sulawesi Province." Jurnal Ilmiah Platax 13, no. 1 (2025): 124–35. https://doi.org/10.35800/jip.v13i1.57404.

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We used the Nansen Bottle Sampler to collect water samples in the deepsea area, ranging from 150 meters to 175 meters in six water points around Manado Bay, to test the quality of e-DNA water samples to detect target species in the fishing area. Therefore, the basis of the case study method with a sampling technique was carried out on July 29 2023 using Power Water Sterivex Kits, water samples were then stored at -250C and were then taken to TBRC, University of the Ryukyus for further laboratory works, such as; eDNA extract, eDNA quality testing, 1st and 2nd PCR and Electrophoresis eDNA analys

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27

SINGH, PALLAVI, M. K. SINGH, P. K. ROUT, and M. S. DIGE. "Association of growth hormone gene receptor polymorphism with production traits in Jamunapari goat." Indian Journal of Animal Sciences 88, no. 8 (2018): 932–37. http://dx.doi.org/10.56093/ijans.v88i8.82954.

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Genetic polymorphism for GHR gene was carried out in Jamunapari kids by Polymerase Chain Reaction- Restriction Fragment Length Polymorphism (PCR-RFLP). Blood samples were collected from 200 kids for isolation of genomic DNA. The exon 1A (210 bp fragment), exon 10 (342 bp fragment) and 5’ non-coding region (318 bp fragment) of GHR gene were amplified and digested with MspI, AluI and NsiI restriction endonuclease, respectively. PCR-RFLP analysis for 5’ non-coding region revealed monomorphic pattern while exon 1A and exon 10 of GHR were polymorphic. The frequency of A and T alleles was 0.54 and 0

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28

Mauricio-Castillo, J. A., G. R. Argüello-Astorga, A. G. Alpuche-Solís, C. T. Monreal-Vargas, O. Díaz-Gómez, and R. De La Torre-Almaraz. "First Report of Tomato severe leaf curl virus in México." Plant Disease 90, no. 8 (2006): 1116. http://dx.doi.org/10.1094/pd-90-1116a.

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San Luis Potosí and Morelos are states situated in the north-central and south-central regions of Mexico, respectively, where a considerable area of agricultural land is occupied by tomato crops. In the summer of 2005, stunting and leaf curling/crumpling symptoms were observed in several tomato (Lycopersicon esculentum L.) fields in Rioverde, San Luis Potosí (Rioverde-SLP). These symptoms and the existence of large populations of whiteflies (Bemisia tabaci Gennadius) in the affected fields suggested a viral etiology. Symptomatic tomato leaves collected during July and September of 2005 from se

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RUBIO, J. M., P. J. BERZOSA, and A. BENITO. "Amplified fragment length polymorphism (AFLP) protocol for genotyping the malarial parasite Plasmodium falciparum." Parasitology 123, no. 4 (2001): 331–36. http://dx.doi.org/10.1017/s0031182001008563.

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We have established an amplified fragment length polymorphism (AFLP) protocol for identifying anonymous polymorphic loci of the malarial parasite, Plasmodium falciparum. The method consists of the following steps (i) digestion and ligation in one reaction; (ii) selective fluorescence forward primers labelled; (iii) PCR products resolved in polyacrylamide gels using the ABIPRISMTM 377 XL DNA sequencer and, (iv) the use of GenescanTM software to size the fragments. This standardized protocol distinguished between 2 standard reference clones of P. falciparum from West African and Southeast Asian

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Cohen, Michael F., and John C. Meeks. "A Hormogonium Regulating Locus, hrmUA, of the Cyanobacterium Nostoc punctiforme Strain ATCC 29133 and its Response to an Extract of a Symbiotic Plant Partner Anthoceros punctatus." Molecular Plant-Microbe Interactions® 10, no. 2 (1997): 280–89. http://dx.doi.org/10.1094/mpmi.1997.10.2.280.

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Transposon-generated mutant strain UCD 328 of Nostoc punctiforme strain ATCC 29133 has a phenotype of an increased sensitivity to a hormogonium-inducing factor exuded by a symbiotic plant partner, Anthoceros punctatus, and an initial increased hormogonium-dependent infection of the plant. Sequence analysis showed that the transposition site in strain UCD 328 lies within a 1,251-bp open reading frame (ORF), designated hrmA, that displays no significant similarity to known database sequences. A second, 837-bp ORF (hrmU) ends 2 bp 5′ from the start of hrmA and has the signature sequences belongin

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Pieterse, Reneé, Svetoslav D. Todorov, and Leon M. T. Dicks. "Bacteriocin ST91KM, produced by Streptococcus gallolyticus subsp. macedonicus ST91KM, is a narrow-spectrum peptide active against bacteria associated with mastitis in dairy cattle." Canadian Journal of Microbiology 54, no. 7 (2008): 525–31. http://dx.doi.org/10.1139/w08-040.

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Streptococcus gallolyticus subsp. macedonicus ST91KM produces a bacteriocin (macedocin ST91KM) active against Streptococcus agalactiae , Streptococcus dysgalactiae subsp. dysgalactiae , Streptococcus uberis , Staphylococcus aureus , and Staphylococcus epidermidis . Macedocin ST91KM is, according to tricine-SDS PAGE, between 2.0 and 2.5 kDa in size. Antimicrobial activity remained unchanged after 2 h of incubation at pH 2.0–10.0 and after 100 min at 100 °C. The peptide was inactivated after 20 min at 121 °C and when treated with proteolytic enzymes. Treatment with α-amylase had no effect on act

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Mirandola, Prisco, Paola Menegazzi, Stefania Merighi, Tullia Ravaioli, Enzo Cassai, and Dario Di Luca. "Temporal Mapping of Transcripts in Herpesvirus 6 Variants." Journal of Virology 72, no. 5 (1998): 3837–44. http://dx.doi.org/10.1128/jvi.72.5.3837-3844.1998.

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ABSTRACT To define the molecular features characteristic of the early stages of infection of lymphocytes with human herpesvirus 6 (HHV-6) variant A or B, we studied the temporal regulation of expression of selected sets of viral genes. Thus, U42, U94, U89-U90, U73, and U39 are α genes since their transcripts (i) were made in the presence of inhibitors of protein synthesis and (ii) were detected 3 h after infection of untreated cells. U41, U53, U31, and U19 are β genes since their expression is inhibited by cycloheximide but not by phosphonoacetate, an inhibitor of DNA synthesis. U100 is a γ ge

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Nawaz, Muhammad Talha, Muhammad Talha Waheed, Kirsten Dennison, et al. "Abstract 5893: Feasibility of DNA analysis in peritoneal fluid from patients with peritoneal carcinomatosis." Cancer Research 85, no. 8_Supplement_1 (2025): 5893. https://doi.org/10.1158/1538-7445.am2025-5893.

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Abstract Introduction: Gastrointestinal (GI) cancers often metastasize to the peritoneum. Current diagnostic tools for peritoneal carcinomatosis (PC) show limited accuracy. Reliable biomarkers to detect and monitor treatment response for PC are urgently needed. While circulating tumor DNA in plasma is a promising cancer biomarker, contribution of tumor DNA from PC into blood is minimal. We hypothesize that peritoneal fluid tumor DNA (ptDNA) may be useful for PC detection and response monitoring. Currently, there are no established laboratory methods for ptDNA analysis. In this study, we evalua

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Rong, Haiqin, Hong Ji, Ylva Pernow, Ulrika Sjöstedt, and Elisabet Bucht. "Quantification of parathyroid hormone-related protein mRNA by competitive PCR and time-resolved lanthanide fluorometry." Clinical Chemistry 43, no. 12 (1997): 2268–73. http://dx.doi.org/10.1093/clinchem/43.12.2268.

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Abstract Using dissociation and enhancement time-resolved lanthanide fluorometry, we have developed a quantitative competitive (QC)-PCR for measuring parathyroid hormone-related protein (PTHrP) mRNA after reverse transcription. A cloned PTHrP cDNA target was also modified by deletion of 10 bp and insertion of 21 bp in the midregion of the fragment and cloned for use as a competitor (i.e., internal standard). Two primers spanning 362 bp of target and 373 bp of competitor were designed and one of the primers was biotinylated. Two oligonucleotide probes, one recognizing the target and the other h

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Andreotti, Patrícia Ferrari, Juliana Leal Monteiro da Silva, Elaine Cristina Teixeira, et al. "Identification of a gene encoding adaptin-like protein in the Paracoccidioides brasiliensis genome by random amplified polymorphic DNA analysis." Journal of Medical Microbiology 56, no. 7 (2007): 884–87. http://dx.doi.org/10.1099/jmm.0.47127-0.

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Paracoccidioides brasiliensis isolates are not homogeneous in their patterns of pathogenicity in animals and adhesion to epithelial cells. During this investigation, genotypic differences were observed between two samples of P. brasiliensis strain 18 yeast phase (Pb18) previously cultured many times, one taken before (Pb18a) and the other after (Pb18b) animal inoculation. Random amplified polymorphic DNA analysis using the primer OPJ4 distinguished Pb18b from Pb18a by one 308 bp DNA fragment, which after cloning and sequencing was shown to encode a polypeptide sequence homologous to the protei

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Tarnowski, Maciek, Magdalena Kucia, and Mariusz Z. Ratajczak. "Isolation and Functional Analysis of CXCR7 Promoter - a Novel Receptor for Stromal Derived Factor-1 (SDF-1): Different Regulation of Expression in Human Hematopoietic Cells Versus Pediatric Sarcomas." Blood 114, no. 22 (2009): 4583. http://dx.doi.org/10.1182/blood.v114.22.4583.4583.

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Abstract Abstract 4583 Stromal derived factor-1 (SDF-1) binds to seven transmembrane-span G-protein coupled receptor CXCR4 and directs homing of CXCR4+ hematopoietic stem cells to bone marrow (BM) as well as metastasis of CXCR4+ cancer cells. Recently, a new SDF-1 binding receptor has been identified and named CXCR7. With identification of this receptor a role of SDF-1 in directing chemotaxis of CXCR7+ hematopoietic cells as well as metastasis of CXCR7+ tumors become more complex. While CXCR7 is expressed at very low level on normal hematopoietic stem cells, its expression becomes high on leuk

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Farrell, John J., Richard M. Sherva, Zhi-yi Chen, et al. "A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression." Blood 117, no. 18 (2011): 4935–45. http://dx.doi.org/10.1182/blood-2010-11-317081.

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Abstract Fetal hemoglobin (HbF) is regulated as a multigenic trait. By genome-wide association study, we confirmed that HBS1L-MYB intergenic polymorphisms (HMIP) and BCL11A polymorphisms are highly associated with HbF in Chinese β-thalassemia heterozygotes. In this population, the variance in HbF resulting from the HMIP is 13.5%; that resulting from the BCL11A polymorphism is 6.4%. To identify the functional variant in HMIP, we used 1000 Genomes Project data, single nucleotide polymorphism imputation, comparisons of association results across populations, potential transcription factor binding

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Gallagher, Jeanne, John A. Finarelli, Jónas P. Jonasson, and Jens Carlsson. "Mitochondrial D-loop DNA analyses of Norway lobster (Nephrops norvegicus) reveals genetic isolation between Atlantic and East Mediterranean populations." Journal of the Marine Biological Association of the United Kingdom 99, no. 4 (2018): 933–40. http://dx.doi.org/10.1017/s0025315418000929.

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AbstractNephrops norvegicus is a commercially valuable demersal fisheries species. Relatively little is understood about this species’ population dynamics across its distribution with previous mitochondrial and microsatellite studies failing to identify significant population-level differentiation. In this study, sequence variation in the mitochondrial (mtDNA) D-loop was analysed from samples across the distribution range, and compared with COI sequences for this species retrieved from GenBank. Analysis of a 375 bp fragment of the D-loop revealed significant genetic differentiation between sam

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Rebijith, K. B., R. Asokan, N. K. Krishna Kumar, V. Krishna, B. N. Chaitanya, and V. V. Ramamurthy. "DNA barcoding and elucidation of cryptic aphid species (Hemiptera: Aphididae) in India." Bulletin of Entomological Research 103, no. 5 (2013): 601–10. http://dx.doi.org/10.1017/s0007485313000278.

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AbstractRapid, precise and timely identification of invasive pest insects such as aphids is important and a challenge worldwide due to their complex life cycles, parthenogenetic reproduction, sex and colour morphs. In this respect, DNA barcoding employing a 658 bp fragment of 5′ region of the mitochondrial cytochrome oxidase I (CO-I) gene is an effective tool in addressing the above. In the present study, we employed CO-I for discriminating 142 individuals representing 32 species of aphids from India. Sequence analyses revealed that the intraspecific and interspecific distances ranged from zer

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Yang, Ze Xiao, Bo Wang, Qiu Mei Xu, et al. "Design and Evaluation of the Primers for Rift Valley Fever (RVF) Virus RT-PCR Detection." Advanced Materials Research 989-994 (July 2014): 1115–19. http://dx.doi.org/10.4028/www.scientific.net/amr.989-994.1115.

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Rift Valley Fever (RVF) is a notifiable multiple species diseases in the OIE list, and causes human and agricultural losses in endemic regions. To develop the rapid method for detecting of RVF, 2 specific primers for reverse transcriptase polymerase chain reaction (RT-PCR) and 7 overlapping oligo primers were designed according to the nucleotide sequence information of RVFV published in GenBank, and a DNA fragment about 318 bp of the segment S was synthesized in vitro by overlap extension PCR to construct the recombinant plasmid pMD19-T-RVFVS. Then, the 2 specific primers were evaluated via a

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Mauricio-Castillo, J. A., G. R. Argüello-Astorga, S. Ambriz-Granados, A. G. Alpuche-Solís, and C. T. Monreal-Vargas. "First Report of Tomato golden mottle virus on Lycopersicon esculentum and Solanum rostratum in Mexico." Plant Disease 91, no. 11 (2007): 1513. http://dx.doi.org/10.1094/pdis-91-11-1513b.

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The Rioverde Valley is an important farming area of the San Luis Potosi State in the north-central region of Mexico, where a variety of horticultural crops (i.e., tomato, pepper, cucumber, and watermelon) are annually cultivated. In the summer of 2005, a number of plants exhibiting a variety of symptoms, including leaf yellowing, curling, and stunted growth, were observed in several tomato (Lycopersicon esculentum L.) fields. The presence of whiteflies (Bemisia tabaci Genn.) and symptoms seemed to suggest a begomoviral etiology. Leaves of 12 symptomatic tomato plants and seven plants of the we

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DABERT, MIROSŁAWA, AGATA BIGOŚ, and WOJCIECH WITALIŃSKI. "DNA barcoding reveals andropolymorphism in Aclerogamasus species (Acari: Parasitidae) MIROSŁAWA DABERT, AGATA BIGOŚ & WOJCIECH WITALIŃSKI (Poland)." Zootaxa 3015, no. 1 (2011): 13. http://dx.doi.org/10.11646/zootaxa.3015.1.2.

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Andropolymorphism, defined as discontinuous morphological variability in males, can lead to taxonomic confusion when different male morphs are determined and described as separate species. This study addresses this issue in two occasionally sympatric mite species Aclerogamasus similis (Willmann, 1953) and A. holzmannae (Micherdziński, 1969) collected in Poland. The females of these two taxa are morphologically indistinguishable but males are quite different, and could be either separate species or one species with two male morphs. We address this question by performing molecular assays, testin

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Rungrojn, Artharee, Kittipong Chaisiri, Yossapong Paladsing, et al. "Prevalence and Molecular Characterization of Rickettsia spp. from Wild Small Mammals in Public Parks and Urban Areas of Bangkok Metropolitan, Thailand." Tropical Medicine and Infectious Disease 6, no. 4 (2021): 199. http://dx.doi.org/10.3390/tropicalmed6040199.

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Rural areas usually show a higher prevalence of rickettsial infection than urban areas. However, information on the rickettsial infection status in urban settings (e.g., built-up areas and city parks) is still limited, particularly in the Bangkok metropolitan area. In this study, we performed a molecular rickettsial survey of spleen samples of small mammals caught in public parks and built-up areas of Bangkok. Out of 198 samples, the Rattus rattus complex was found to be most prevalent. The amplification of rickettsial gltA fragment gene (338 bp) by nested PCR assay revealed positive results i

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Preston, R. A., M. F. Manolson, K. Becherer, et al. "Isolation and characterization of PEP3, a gene required for vacuolar biogenesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 12 (1991): 5801–12. http://dx.doi.org/10.1128/mcb.11.12.5801-5812.1991.

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The Saccharomyces cerevisiae PEP3 gene was cloned from a wild-type genomic library by complementation of the carboxypeptidase Y deficiency in a pep3-12 strain. Subclone complementation results localized the PEP3 gene to a 3.8-kb DNA fragment. The DNA sequence of the fragment was determined; a 2,754-bp open reading frame predicts that the PEP3 gene product is a hydrophilic, 107-kDa protein that has no significant similarity to any known protein. The PEP3 predicted protein has a zinc finger (CX2CX13CX2C) near its C terminus that has spacing and slight sequence similarity to the adenovirus E1a zi

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Preston, R. A., M. F. Manolson, K. Becherer, et al. "Isolation and characterization of PEP3, a gene required for vacuolar biogenesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 12 (1991): 5801–12. http://dx.doi.org/10.1128/mcb.11.12.5801.

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The Saccharomyces cerevisiae PEP3 gene was cloned from a wild-type genomic library by complementation of the carboxypeptidase Y deficiency in a pep3-12 strain. Subclone complementation results localized the PEP3 gene to a 3.8-kb DNA fragment. The DNA sequence of the fragment was determined; a 2,754-bp open reading frame predicts that the PEP3 gene product is a hydrophilic, 107-kDa protein that has no significant similarity to any known protein. The PEP3 predicted protein has a zinc finger (CX2CX13CX2C) near its C terminus that has spacing and slight sequence similarity to the adenovirus E1a zi

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Prévot, J., S. Dubrou, and J. Maréchal. "Detection of Human Hepatitis a Virus in Environmental Water by an Antigen-Capture Polymerase Chain Reaction Method." Water Science and Technology 27, no. 3-4 (1993): 227–33. http://dx.doi.org/10.2166/wst.1993.0351.

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To detect hepatitis A virus (HAV) in environmental water samples, sensitive and specific methods are needed. An hemi-nested enzymatic amplification procedure was developed. When it was associated with an immuno-capture (IC) step, specificity and sensitivity were increased. The presence of a specific DNA fragment of 318 bp was detected by the analysis of the electrophoresis of the PGR products and confirmed on the autoradiogram of the Southern blot of the gel, using a labeled oligoprobe PAl selected in a very highly conserved region of the genome coding for the capsid protein VPl. The IC/PCR de

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Parenrengi, Andi, Alimuddin Alimuddin, Sukenda Sukenda, Komar Sumantadinata, Muhammad Yamin, and Andi Tenriulo. "CLONING OF ProAV PROMOTER ISOLATED FROM TIGER PRAWN Penaeus monodon." Indonesian Aquaculture Journal 4, no. 1 (2009): 1. http://dx.doi.org/10.15578/iaj.4.1.2009.1-7.

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Promoter is a specific DNA sequence involved in the transcription of a particular gene. It is usually located in the upstream of the gene they regulate. Isolation and characterization of promoter is essentially needed in order to establish the sequence analysis and transcription factor that are used in the regulation of gene expression. The research was conducted to analyze the characteristics of Penaeus monodon anti viral gene promoter (ProAV) towards generation of auto-transgenic tiger prawn, P. monodon. ProAV promoter was isolated by PCR (Polymerase Chain Reaction) method and the purified D

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Solodenko, Anzhella. "DNA Marker-Based High-Throughput Identification of Downy Mildew Infected and Non-Infected Sunflower Plants." Helia 42, no. 70 (2019): 37–43. http://dx.doi.org/10.1515/helia-2018-0017.

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AbstractDeveloping hybrids, resistant to causal pathogen of Downy mildew (Plasmopara halstedii (Farl.) Berl. & de Toni), is one of the critical tasks in sunflower breeding. Molecular markers have advanced breeding practice in the past decades, however there are still unmet needs for reliable high-throughput (HT) selection of the pathogen resistant starting material and differentiation of the plants infected by different pathogens. In this study, we tested the known DNA marker (308 bp fragment from ribosomal DNA of P. halstedii) for detection of pathogen in different tissues of sunflower pl

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Olanrewaju, B. M., E. B. Oghate, A. J. Adetunb, O. OlawaleJ, and A. C. Chineke. "ASSOCIATON OF KAPPA-CASEIN GENOTYPE AND THE LINEAR PARAMETER IN TWO INDIGENIOUS BOS INDICUS AND BOS TAURUS CATTLE IN NIGERIA." Open Journal of Agricultural Science (ISSN: 2734-214X) 1, no. 1 (2020): 12–22. http://dx.doi.org/10.52417/ojas.v1i1.89.

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Kappa-casein as a mammalian milk protein is involved in a several important physiological processes and it’s about 80% of the total protein in cow milk. This study aimed at genotyping bovine Kappa casein (CSN3) in two indigenous Nigerian cattle populations and to determine the frequency distribution of Kappa casein variants as detected across the animals examined and their association with the body measurement. DNA was extracted from 100 blood samples of 50 White Fulani and 50 N’dama cattle for identification and genotyping of kappa-casein gene by polymerase chain reaction restriction fragment

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Manna, Adhar, and Ambrose L. Cheung. "Characterization of sarR, a Modulator ofsar Expression in Staphylococcus aureus." Infection and Immunity 69, no. 2 (2001): 885–96. http://dx.doi.org/10.1128/iai.69.2.885-896.2001.

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ABSTRACT The expression of virulence determinants in Staphylococcus aureus is controlled by global regulatory loci (e.g.,sar and agr). The sar locus is composed of three overlapping transcripts (sar P1, P3, and P2 transcripts from P1, P3, and P2 promoters, respectively), all encoding the 372-bp sarA gene. The level of SarA, the major regulatory protein, is partially controlled by the differential activation of sar promoters. We previously partially purified a ∼12 kDa protein with a DNA-specific column containing asar P2 promoter fragment. In this study, the putative gene, designated sarR, was

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