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Journal articles on the topic 'Nuclear markers'

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Published: 4 June 2021
Last updated: 10 March 2023

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1

Kathir, Pushpa, Matthew LaVoie, William J. Brazelton, Nancy A. Haas, Paul A. Lefebvre, and Carolyn D. Silflow. "Molecular Map of the Chlamydomonas reinhardtii Nuclear Genome." Eukaryotic Cell 2, no. 2 (April 2003): 362–79. http://dx.doi.org/10.1128/ec.2.2.362-379.2003.

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ABSTRACT We have prepared a molecular map of the Chlamydomonas reinhardtii genome anchored to the genetic map. The map consists of 264 markers, including sequence-tagged sites (STS), scored by use of PCR and agarose gel electrophoresis, and restriction fragment length polymorphism markers, scored by use of Southern blot hybridization. All molecular markers tested map to one of the 17 known linkage groups of C. reinhardtii. The map covers approximately 1,000 centimorgans (cM). Any position on the C. reinhardtii genetic map is, on average, within 2 cM of a mapped molecular marker. This molecular map, in combination with the ongoing mapping of bacterial artificial chromosome (BAC) clones and the forthcoming sequence of the C. reinhardtii nuclear genome, should greatly facilitate isolation of genes of interest by using positional cloning methods. In addition, the presence of easily assayed STS markers on each arm of each linkage group should be very useful in mapping new mutations in preparation for positional cloning.
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2

Dudu, Andreea, Radu Suciu, Marian Paraschiv, Sergiu Emil Georgescu, Marieta Costache, and Patrick Berrebi. "Nuclear Markers of Danube Sturgeons Hybridization." International Journal of Molecular Sciences 12, no. 10 (October 14, 2011): 6796–809. http://dx.doi.org/10.3390/ijms12106796.

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3

Bachmann, K. "Nuclear DNA markers in angiosperm taxonomy." Acta Botanica Neerlandica 41, no. 4 (December 1992): 369–84. http://dx.doi.org/10.1111/j.1438-8677.1992.tb00507.x.

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4

Amaral, A. R., M. C. Silva, L. M. Möller, L. B. Beheregaray, and M. M. Coelho. "Anonymous nuclear markers for cetacean species." Conservation Genetics 11, no. 3 (April 2, 2009): 1143–46. http://dx.doi.org/10.1007/s10592-009-9903-3.

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5

Davido, Tracy, and Robert H. Getzenberg. "Nuclear matrix proteins as cancer markers." Journal of Cellular Biochemistry 79, S35 (2000): 136–41. http://dx.doi.org/10.1002/1097-4644(2000)79:35+<136::aid-jcb1137>3.0.co;2-e.

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6

Sukhotu, Thitaporn, Osamu Kamijima, and Kazuyoshi Hosaka. "Nuclear and chloroplast DNA differentiation in Andean potatoes." Genome 47, no. 1 (January 1, 2004): 46–56. http://dx.doi.org/10.1139/g03-105.

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Over 3500 accessions of Andean landraces have been known in potato, classified into 7 cultivated species ranging from 2x to 5x (Hawkes 1990). Chloroplast DNA (ctDNA), distinguished into T, W, C, S, and A types, showed extensive overlaps in their frequencies among cultivated species and between cultivated and putative ancestral wild species. In this study, 76 accessions of cultivated and 19 accessions of wild species were evaluated for ctDNA types and examined by ctDNA high-resolution markers (ctDNA microsatellites and H3 marker) and nuclear DNA restriction fragment length polymorphisms (RFLPs). ctDNA high-resolution markers identified 25 different ctDNA haplotypes. The S- and A-type ctDNAs were discriminated as unique haplotypes from 12 haplotypes having C-type ctDNA and T-type ctDNA from 10 haplotypes having W-type ctDNA. Differences among ctDNA types were strongly correlated with those of ctDNA high-resolution markers (r = 0.822). Differentiation between W-type ctDNA and C-, S-, and A-type ctDNAs was supported by nDNA RFLPs in most species except for those of recent or immediate hybrid origin. However, differentiation among C-, S-, and A-type ctDNAs was not clearly supported by nDNA RFLPs, suggesting that frequent genetic exchange occurred among them and (or) they shared the same gene pool owing to common ancestry.Key words: potato, chloroplast DNA, microsatellite markers, nuclear DNA RFLPs.
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7

Meslet-Cladière, Laurence, and Olivier Vallon. "Novel Shuttle Markers for Nuclear Transformation of the Green Alga Chlamydomonas reinhardtii." Eukaryotic Cell 10, no. 12 (October 14, 2011): 1670–78. http://dx.doi.org/10.1128/ec.05043-11.

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ABSTRACTThe green algaChlamydomonas reinhardtiitoday is a premier model organism for the study of green algae and plants. Yet the efficient engineering of its nuclear genome requires development of new antibiotic resistance markers. We have recoded, based on codon usage in the nuclear genome, the AadA marker that has been used previously for chloroplast transformation. The recoded AadA gene, placed under the control of theHSP70A-RBCS2hybrid promoter and preceded by the RbcS2 chloroplast-targeting peptide, can be integrated into the nuclear genome by electroporation, conferring resistance to spectinomycin and streptomycin. Transformation efficiency is markedly increased when vector sequences are completely eliminated from the transforming DNA. Antibiotic resistance is stable for several months in the absence of selection pressure. Shuttle markers allowing selection in bothChlamydomonasandEscherichia coliwould also be a useful asset. By placing an artificial bacterial promoter and Shine-Dalgarno sequence in frame within the AadA coding sequence, we generated such a shuttle marker. To our surprise, we found that the classical AphVIII construct already functions as a shuttle marker. Finally, we developed a method to introduce the AadA and AphVIII markers into the vector part of the bacterial artificial chromosomes (BACs) of theChlamydomonasgenomic DNA library. Our aim was to facilitate complementation studies whenever the test gene cannot be selected for directly. After transformation of apetCmutant with a modified BAC carrying the AphVIII marker along with thePETCgene in the insert, almost half of the paromomycin-resistant transformants obtained showed restoration of phototrophy, indicating successful integration of the unselected test gene. With AadA, cotransformation was also observed, but with a lower efficiency.
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8

Ruņģis, Dainis, Anna Korica, Agnese Gailīte, Ilze Pušpure, and Ilze Veinberga. "Analysis of the Genetic Diversity and Population Structure of Latvian Ash (Fraxinus excelsior L.) Stands using Nuclear and Chloroplast SSR Markers." Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. 70, no. 3 (June 1, 2016): 101–8. http://dx.doi.org/10.1515/prolas-2016-0017.

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Abstract Common ash (Fraxinus excelsior L.) has a widespread distribution throughout Europe, and Latvia is almost at the north eastern edge of the distribution range. In Europe, ash is threatened by ash dieback, a disease caused by the introduced ascomycete Hymenoscyphus fraxineus. Chloroplast and nuclear DNA markers have been used to study the genetic diversity and population structure of ash both in a broader pan-European context as well as in more restricted regions. Some of the markers analysed in these previously published reports were also utilised in this study, enabling comparisons of the genetic parameters calculated from the nuclear SSR marker data and of the haplotypes identified with the chloroplast markers. Analysis of chloroplast markers revealed one dominant haplotype in Latvian stands, which corresponds to the haplotype previously found in Eastern Europe and Scandinavia. A second haplotype, corresponding to a previously reported central European haplotype was found in all individuals from the Ķemeri stand, indicating that this stand was naturally established from introduced germplasm, which was planted in a neighbouring park. The nuclear SSR markers revealed low levels of differentiation of Latvian F. excelsior stands, probably due efficient pollen flow between stands. The analysis of both chloroplast and nuclear DNA markers has revealed different aspects of the structure and provenance of Latvian F. excelsior populations.
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9

Koumakpayi, I. H., P. O. Gannon, C. Le Page, M. Alam-Fahmy, J. Madore, A. Mes-Masson, and F. Saad. "ErbB3, Cyclin D1 and Ki67 nuclear staining predicts biochemical recurrence in prostate cancer treated by radical prostatectomy." Journal of Clinical Oncology 24, no. 18_suppl (June 20, 2006): 10096. http://dx.doi.org/10.1200/jco.2006.24.18_suppl.10096.

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10096 Background: The nuclear accumulation of growth factor receptor was reported to be associated to increased cell proliferation. Cyclin D1 and Ki67 are nuclear markers of cell proliferation. Deregulation of Cyclin D1 and Ki67 expression play a role in tumorigenesis and metastasis. Recently, we observed that nuclear localization of ErbB3 was associated with prostate cancer progression. The objective of this study was to determine if the association of cell proliferation markers and nuclear localization of ErbB3 could predict biochemical recurrence (BCR) in patients with prostate cancer following radical prostatectomy. Methods: Using immunohistochemistry we analyzed a tissue microarray containing 386 cores from 64 formalin-fixed paraffin embedded specimens from prostate cancer patients who had undergone radical prostatectomy. No patient had received hormone therapy prior to surgery and prior to BCR. Antibodies against Cyclin D1, ErbB3 and Ki67 proteins were used. Results: Nuclear staining was 60%, 67% and 86% for Cyclin D1, ErbB3 and Ki67 respectively. In our cohort, 29 of 64 PCa patients (45%) had a BCR after a median 3 years of follow-up. Thirty seven (37) percent of patients had positive nuclear staining for all three markers. BCR free survival probability at 3 years was not significant for each marker individually, except for ErbB3 in positive surgical margin patients. When all three markers were combined for nuclear staining Kaplan-Meier analysis BCR free was 0.4 and 0.1 for positive and negative nuclear staining respectively (p=0.0068). Univariate COX regression analysis shows a 2.98 fold (95% CI: 1.29 - 6.86, p=0.01) higher rate of BCR in patients positive for these three markers. In addition, in a multivariate model, including pre-operative PSA (p=0.19), pathologic stage (p=0.29), Gleason grade (p=0.40) and specimens that had positive nuclear staining for the 3 markers were associated with a 3.97 fold higher rate of BCR (95% CI: 1.54 - 10.25, p=0.0068). Conclusion: These results suggest that the association of cell proliferation markers and nuclear localization of ErbB3 could be useful in predicting recurrence following radical prostatectomy and guide therapeutic decisions. Large scale trials are needed to confirm these results. No significant financial relationships to disclose.
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10

Zhang, De-Xing, and Godfrey M. Hewitt. "Nuclear integrations: challenges for mitochondrial DNA markers." Trends in Ecology & Evolution 11, no. 6 (June 1996): 247–51. http://dx.doi.org/10.1016/0169-5347(96)10031-8.

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11

Sancho, Rubén, Ana Guillem-Amat, Elena López-Errasquín, Lucas Sánchez, Félix Ortego, and Pedro Hernández-Crespo. "Genetic analysis of medfly populations in an area of sterile insect technique applications." Journal of Pest Science 94, no. 4 (February 10, 2021): 1277–90. http://dx.doi.org/10.1007/s10340-021-01337-8.

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AbstractThe sterile insect technique (SIT) is widely used in integrated pest management programs for the control of the Mediterranean fruit fly (medfly), Ceratitis capitata. The genetic interactions between the released individuals from the genetic sexing strains (GSS), used for SIT applications worldwide, and wild individuals have not been studied. Under the hypothesis that a number of Vienna GSS individuals released to the field might not be completely sterile and may produce viable offspring, we have analyzed medfly Spanish field populations to evaluate the presence of Vienna strain genetic markers. To this goal, we have used contrasted nuclear and mitochondrial genetic markers, and two novel sets of nuclear polymorphisms with the potential to be markers to discriminate between Vienna and wild individuals. Nuclear Vienna markers located on the 5th chromosome of Vienna males have been found in 2.2% (19 from 875) of the Spanish wild medfly females captured at the area where SIT is applied. In addition, a female-inherited mitochondrial Vienna marker has been found in two from the 19 females showing nuclear Vienna markers. The detection of several of these markers in single individuals represents evidence of the introgression of Vienna strain into natural populations. However, alternative explanations as their presence at low frequency in wild populations in the studied areas cannot be fully discarded. The undesired release of non-fully sterile irradiated GSS individuals into the field and their interactions with wild flies, and the potential environmental implications should be taken into account in the application of the SIT.
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12

Jones, R. G., J. H. Barth, and H. Mitchell. "Tumour Markers: Same Marker, Different Assay, Different Result." Clinical Oncology 11, no. 4 (August 1999): 221–22. http://dx.doi.org/10.1053/clon.1999.9052.

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13

Gazendam, Inge, Maria M. Greyling, and Sunette M. Laurie. "The Application of Molecular Markers to Accelerate the Recovery of Cytoplasmic and Nuclear Male Sterility in South African Onion (Allium cepa L.) Hybrid Parental Lines." Journal of Agricultural Science 10, no. 7 (June 8, 2018): 95. http://dx.doi.org/10.5539/jas.v10n7p95.

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Male sterility is important to prevent self-pollination and loss of the onion hybrid genotype. Classic methods require 4-8 years of progeny testing before the cytoplasm type can be determined. An accurate and time-saving method was needed. Various types of markers were tested for application to South African onion parental lines of hybrid cultivars, and which could determine male sterility and maintainer genotypes accurately and easily with large numbers of samples. Five cytoplasmic (5’cob, orfA501, orf725, IGS and cob-type 2) and four nuclear markers (jnurf13, isotig34671_610, isotig30856_1351 and isotig29186_1830) were sourced. Genomic DNA was isolated from onion seedlings and young leaves growing from bulbs in the Agricultural Research Council (ARC) research field. PCR marker amplification products were separated by agarose or denaturing polyacrylamide gel electrophoresis (PAGE) gels. Real-time polymerase chain reaction (PCR) was performed with custom TaqMan® SNP genotyping assays containing primer/probe pairs designed to detect single nucleotide polymorphisms (SNPs) linked to the nuclear Ms locus. OrfA501 proved useful as a presence/absence marker for cytoplasmic male sterility, while TaqMan® SNP genotyping assays were superior to the jnurf13 nuclear marker in terms of rapid throughput. PCR molecular markers and custom TaqMan® SNP genotyping assays were efficient in screening the onion lines rapidly and accurately for their cytoplasmic and nuclear male sterility genotype. These methods reduced the time to identify the correct genotype of male sterile and maintainer lines, gave accurate genotypic information and proved to be useful on a larger scale. These molecular marker methods will facilitate the production of the correct seed for commercialization of onion lines worldwide.
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14

Strand, A. E., J. Leebens‐Mack, and B. G. Milligan. "Nuclear DNA‐based markers for plant evolutionary biology." Molecular Ecology 6, no. 2 (February 1997): 113–18. http://dx.doi.org/10.1046/j.1365-294x.1997.00153.x.

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15

NOONAN, BRICE P., and ANNE D. YODER. "Anonymous nuclear markers for Malagasy plated lizards (Zonosaurus)." Molecular Ecology Resources 9, no. 1 (January 2009): 402–4. http://dx.doi.org/10.1111/j.1755-0998.2008.02250.x.

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16

Hughes, M., M. Möller, D. U. Bellstedt, T. J. Edwards, and M. Woodhead. "EST and random genomic nuclear microsatellite markers forStreptocarpus." Molecular Ecology Notes 4, no. 1 (January 6, 2004): 36–38. http://dx.doi.org/10.1046/j.1471-8286.2003.00561.x.

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17

Du, J., P. Gouras, H. Kjeldbye, R. Kwun, and R. Lopez. "Monitoring photoreceptor transplants with nuclear and cytoplasmic markers." Experimental Neurology 115, no. 1 (January 1992): 79–86. http://dx.doi.org/10.1016/0014-4886(92)90226-g.

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18

Calonje, Miriam, Santiago Martín-Bravo, Christoph Dobeš, Wei Gong, Ingrid Jordon-Thaden, Christiane Kiefer, Markus Kiefer, Juraj Paule, Roswitha Schmickl, and Marcus A. Koch. "Non-coding nuclear DNA markers in phylogenetic reconstruction." Plant Systematics and Evolution 282, no. 3-4 (May 21, 2008): 257–80. http://dx.doi.org/10.1007/s00606-008-0031-1.

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19

Recanzone, Gregg, and William A. Harris. "Demonstration of neural induction using nuclear markers inXenopus." Wilhelm Roux's Archives of Developmental Biology 194, no. 6 (1985): 344–54. http://dx.doi.org/10.1007/bf00877372.

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20

Gokce, Ali Fuat, and Michael J. Havey. "069 Molecular-facilitated Selection of Maintainer Lines in Edible Onion (Allium cepa L.)." HortScience 34, no. 3 (June 1999): 453B—453. http://dx.doi.org/10.21273/hortsci.34.3.453b.

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Cytoplasmic-genic male sterility (CMS) is used to produce hybrid onion seed. For the most widely used source of CMS in onion, male sterility is conditioned by the interaction of sterile (S) cytoplasm and the homozygous recessive genotype at a single nuclear male-fertility restoration locus (Ms). Maintainer lines used to seed-propagate male-sterile lines possess normal fertile (N) cytoplasm and the homozyous recessive genotype at the Ms locus. Presently, it takes 4 to 8 years to establish if maintainer lines can be extracted from an uncharacterized population or family. We previously developed a PCR marker useful to distinguish N and S cytoplasms of onion. To tag the nuclear male-fertility restoration locus (Ms), we evaluated segregation at Ms over at least three environments. Segregations of AFLPs, RAPDs, and RFLPs revealed molecular markers flanking the Ms locus. We are working to convert these linked molecular markers to nonradioactive PCR-based detection. The organellar and nuclear markers were used to select plants from open-pollinated onion populations and determine if the number of test-crosses required to identify maintaining genotypes.
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21

Orive, Maria E., and Nicholas H. Barton. "Associations Between Cytoplasmic and Nuclear Loci in Hybridizing Populations." Genetics 162, no. 3 (November 1, 2002): 1469–85. http://dx.doi.org/10.1093/genetics/162.3.1469.

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Abstract We extend current multilocus models to describe the effects of migration, recombination, selection, and nonrandom mating on sets of genes in diploids with varied modes of inheritance, allowing us to consider the patterns of nuclear and cytonuclear associations (disequilibria) under various models of migration. We show the relationship between the multilocus notation recently presented by Kirkpatrick, Johnson, and Barton (developed from previous work by Barton and Turelli) and the cytonuclear parameterization of Asmussen, Arnold, and Avise and extend this notation to describe associations between cytoplasmic elements and multiple nuclear genes. Under models with sexual symmetry, both nuclear-nuclear and cytonuclear disequilibria are equivalent. They differ, however, in cases involving some type of sexual asymmetry, which is then reflected in the asymmetric inheritance of cytoplasmic markers. An example given is the case of different migration rates in males and females; simulations using 2, 3, 4, or 5 unlinked autosomal markers with a maternally inherited cytoplasmic marker illustrate how nuclear-nuclear and cytonuclear associations can be used to separately estimate female and male migration rates. The general framework developed here allows us to investigate conditions where associations between loci with different modes of inheritance are not equivalent and to use this nonequivalence to test for deviations from simple models of admixture.
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22

Gaffney, Patrick M. "Molecular tools for understanding population structure in Antarctic species." Antarctic Science 12, no. 3 (September 2000): 288–96. http://dx.doi.org/10.1017/s0954102000000353.

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During the last decade, methods for detecting DNA polymorphisms have proliferated at a bewildering pace. Today the investigator must choose among various types of genetic markers as well as between a variety of methods for discovering and screening polymorphisms. Polymorphisms useful for the analysis of population structure are found in both mitochondrial and nuclear genomes. Marker development may proceed along two routes: 1) discovery of species–specific markers, and 2) application of universal methods. Species-specific markers are based on sequence data from the target species or close relatives, whereas universal markers are based on the use of polymerase chain reaction (PCR) primers targeted to regions highly conserved across diverse taxa. Markers commonly employed include mitochondrial DNA polymorphisms, microsatellites, anonymous nuclear loci and known genes (both coding and noncoding regions). Methods for detecting polymorphisms range from technically simple (RFLP analysis) to more sophisticated mutation scanning methods. We review the application of these approaches to several key Antarctic species (the Patagonian toothfish Dissostichus eleginoides, the mackerel icefish Champsocephalus gunnari, and the squid Martialia hyadesi Rochebrune & Mabille, 1889) and present preliminary data on genetic polymorphisms in toothfish and icefish.
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23

Wangiyana, I. Gde Adi Suryawan. "DNA BARCODING LIBRARY DATABASE OF AQUILARIA MEMBER AND GYRINOPS MEMBER." Jurnal Silva Samalas 3, no. 2 (December 29, 2020): 68. http://dx.doi.org/10.33394/jss.v3i2.3693.

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Aquilaria and Gyrinops are the primary agarwood producer on international trade. For authentication and standardization purposes, it is essential to carry DNA barcoding studies of these genera. DNA barcoding studies on plants need a database of several regions on the plant genome that could act as a barcoding marker. These DNA barcoding markers could be divided into Chloroplasts barcoding and Nuclear barcoding. Several markers have been used for DNA barcoding study of agarwood producer species, including trnL-trnF, matK, rbcL, rpoC1, ycf1 (Chloroplast barcoding), and ITS (Nuclear barcoding). This review breakdown the availability of those DNA barcoding markers on the online genebank database for Aquilaria and Gyrinops. Aquilaria genus has 12 species members, while Gyrinops genus has six species members. The sequence of region trnL-trnF is the only barcoding marker covering all 12 species members of Aquilaria and six species members of Gyrinops. Both ITS and matK have covered nine species among 12 total species members of Aquilaria. The rbcL, rpoC1, and ycf1, respectively, have covered eight, five, and four species members of Aquilaria. Most of the barcoding markers have covered three species members of Gyrinops except for ITS (5 species) and rpoC1 (1 species). However, Gyrinops members have no ycf1 sequence on genebank database. Based on sequence availability on the genebank database, it could be concluded that the trnL-trnF region is the most promising DNA barcoding marker for the Aquilaria and Gyrinops members especially for the phylogenetic analysis purpose.
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24

Shao, Wanting, Christina Kuhn, Doris Mayr, Nina Ditsch, Magdalena Kailuweit, Verena Wolf, Nadia Harbeck, et al. "Cytoplasmic and Nuclear Forms of Thyroid Hormone Receptor β1 Are Inversely Associated with Survival in Primary Breast Cancer." International Journal of Molecular Sciences 21, no. 1 (January 3, 2020): 330. http://dx.doi.org/10.3390/ijms21010330.

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The aim of this study was to investigate the expression of thyroid hormone receptor β1 (THRβ1) by immunohistochemistry in breast cancer (BC) tissues and to correlate the results with clinico-biological parameters. In a well-characterized cohort of 274 primary BC patients, THRβ1 was widely expressed with a predominant nuclear location, although cytoplasmic staining was also frequently observed. Both nuclear and cytoplasmic THRβ1 were correlated with high-risk BC markers such as human epidermal growth factor receptor 2 (HER2), Ki67 (also known as MKI67), prominin-1 (CD133), and N-cadherin. Overall survival analysis demonstrated that cytoplasmic THRβ1 was correlated with favourable survival (p = 0.015), whereas nuclear THRβ1 had a statistically significant correlation with poor outcome (p = 0.038). Interestingly, in our cohort, nuclear and cytoplasmic THRβ1 appeared to be independent markers either for poor (p = 0.0004) or for good (p = 0.048) prognosis, respectively. Altogether, these data indicate that the subcellular expression of THRβ1 may play an important role in oncogenesis. Moreover, the expression of nuclear THRβ1 is a negative outcome marker, which may help to identify high-risk BC subgroups.
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Salava, J., Y. Wang, B. Krška, J. Polák, P. Komínek, R. W. Miller, W. M. Dowler, G. L. Reighard, and A. G. Abbott. "Molecular genetic mapping in apricot." Czech Journal of Genetics and Plant Breeding 38, No. 2 (July 30, 2012): 65–68. http://dx.doi.org/10.17221/6113-cjgpb.

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A genetic linkage map for apricot (Prunus armeniaca L.) has been constructed using amplified fragment length polymorphism (AFLP) markers in 80 BC1&nbsp;individuals derived from a cross LE-3246 &times; Vestar. From 26 different primer combinations, a total of 248 AFLP markers were scored, of which, 40 were assigned to 8 linkage groups covering 315.8 cM of the apricot nuclear genome. The average interval between these markers was 7.7 cM. One gene (PPVres1) involved in resistance to PPV (Plum pox virus) was mapped. Two AFLP markers (EAA/MCAG8 and EAG/MCAT14) were found to be closely associated with the PPVres1 locus (4.6 cM resp. 4.7 cM). These markers are being characterized and they will be studied for utilization in apricot breeding with marker-assisted selection (MAS).
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Yu, Yun, Meiyu Wu, Nan Zhang, Hua Yin, Bin Shu, and Weigang Duan. "A pilot study on searching for peri-nuclear NeuN-positive cells." PeerJ 8 (January 7, 2020): e8254. http://dx.doi.org/10.7717/peerj.8254.

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The aim of this study was to find out neuron (-like) cells in peripheral organs by cell markers in rats. Adult male Sprague-Dawley rats were anaesthetized. Their organs including brain, heart, lung, liver, kidney, stomach, duodenum, and ileum were harvested. The mRNA and protein in these organs were extracted. RNA sequencing (RNA-Seq) was carried out, and NeuN, a “specific” marker for neuronal soma, was assayed with Western blotting. The sections of the aforementioned organs were obtained after a routine fixation (4% methanal)-dehydration (ethanol)-embedding (paraffin) process. NeuN in the sections and seven non-neuronal cell lines was analyzed by immunofluorescence (IF) or immunohistochemistry (IHC). Neuronal markers, such as Eno2, NeuN (Rbfox3), choline acetyltransferase (Chat), as well as tyrosine hydroxylase (Th), and neuronal-glial markers, e.g., glial fibrillary acidic protein (Gfap), S100b, 2′, 3′-cyclic nucleotide 3′-phosphodiesterase (Cnp), and other related markers, were positively expressed in all the organs at mRNA level. NeuN was further analyzed by Western blotting. The IF and IHC assays showed that NeuN-positive cells were distributed in all the peripheral tissues (mainly peri-nuclear NeuN-positive cells) though with different patterns from that in brain (nuclear NeuN-positive cells), and a NeuN-negative tissue could not be found. Especially, NeuN and Myl3 co-expressed in the cytoplasm of myocardial cells, suggesting that NeuN could possess other functions than neuronal differentiation. Also, the protein was positively expressed in seven non-neuronal cell lines. Our findings suggested that NeuN-positive cells exist widely, and without identification of its distribution pattern, the specificity of NeuN for neurons could be limited.
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27

Iwaizumi, M. G., A. Watanabe, and K. Isoda. "Primer Note: Development of Highly Polymorphic Nuclear Microsatellite Markers for Hinoki (Chamaecyparis obtusa)." Silvae Genetica 60, no. 1-6 (December 1, 2011): 62–65. http://dx.doi.org/10.1515/sg-2011-0008.

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Abstract We developed 32 microsatellite markers from an enriched genomic DNA library of hinoki (Chamaecyparis obtusa), one of the most important Japanese forestry conifer species. From a total of 1,056 cloned plasmids, 96 sequence-specific primer pairs were designed from 110 candidate clones. We selected 32 primers that showed successful amplification and marked polymorphism and evaluated their characteristics using DNA from 38 C. obtusa elite trees planted in the Forest Tree Breeding Center. The markers were highly polymorphic, with the number of alleles ranging from 8 to 32 (mean: 20.09), and expected heterozygosity ranging from 0.811 to 0.958 (mean: 0.901). Progress in breeding projects and studies of the ecological genetics of this species can be expected through the use of this enlarged marker pool.
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28

Bongiovanni, Laura, Francesca Caposano, Mariarita Romanucci, Valeria Grieco, Daniela Malatesta, Chiara Brachelente, Marcella Massimini, Cinzia Benazzi, Rachel E. Thomas, and Leonardo Della Salda. "Survivin and Sox9: Potential Stem Cell Markers in Canine Normal, Hyperplastic, and Neoplastic Canine Prostate." Veterinary Pathology 56, no. 2 (August 21, 2018): 200–207. http://dx.doi.org/10.1177/0300985818794161.

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Canine prostatic carcinoma is a relevant model for human prostatic carcinoma. Survivin is proposed as a biomarker of malignancy in human prostatic cancer. Sox9 is a stem cell marker required for prostate development and expressed in several adult tissues. The aims of the present study were to evaluate the patterns and expression levels of 2 putative stem cell markers, survivin and Sox9, in canine benign prostatic hyperplasia (BPH) and prostatic carcinoma to investigate their potential as stem cell markers. Immunohistochemistry with specific antibodies was performed on 3 samples of normal prostate gland, 18 samples of canine BPH, and 16 samples of prostatic carcinoma. The basal cell layer of normal and hyperplastic prostatic lobules had nuclear Sox9 immunolabeling and nuclear and rarely cytoplasmic survivin immunostaining, identifying them as potential stem cell markers. Significantly more frequent survivin and Sox9 expression (≥10% of nuclei) was observed in prostatic carcinoma as compared with BPH. The potential coexpression of survivin with Sox9, androgen receptor, and p63 was also investigated in selected BPH and prostatic carcinoma cases with immunofluorescence, and a partial colocalization was observed. Results indicate that Sox9 and survivin could be considered markers of stemness in canine prostate cells. Given its role in proliferation, cells in the basal cell layer with nuclear survivin expression are likely to be transit-amplifying cells that maintain some stem cell proprieties.
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Lee, Christine, Chenyun Zhou, Brenda Hyde, Pengfei Song, and Nicholas Hangiandreou. "Techniques for Improving Ultrasound Visualization of Biopsy Markers in Axillary Lymph Nodes." Journal of Clinical Imaging Science 10 (April 18, 2020): 21. http://dx.doi.org/10.25259/jcis_9_2020.

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Objective: Biopsy markers are often placed into biopsy-proven metastatic axillary lymph nodes to ensure later accurate node excision. Ultrasound is the preferred imaging modality in the axilla. However, sonographic identification of biopsy markers after neoadjuvant therapy can be challenging. This is due to poor conspicuity relative to surrounding parenchymal interfaces, treatment-related alteration of malignant morphology during neoadjuvant chemotherapy, or extrusion of the marker from the target. To the authors’ knowledge, the literature provides no recommendations for ultrasound scanning parameters that improve the detection of biopsy markers. The purpose of this manuscript is 3-fold: (1) To determine scanning parameters that improve sonographic conspicuity of biopsy markers in a phantom and cadaver model; (2) to implement these scanning parameters in the clinical setting; and (3) to provide strategies that might increase the likelihood of successful ultrasound detection of biopsy markers in breast imaging practices. Materials and Methods: An ex vivo study was performed using a phantom designed to simulate the heterogeneity of normal mammary or axillary soft tissues. A selection of available biopsy markers was deployed into this phantom and ultrasound (GE LOGIQ E9) was performed. Scanning parameters were adjusted to optimize marker conspicuity. For the cadaver study, the biopsy markers were deployed using ultrasound guidance into axillary lymph nodes of a female cadaver. Adjustments in transducer frequency, dynamic range, cross-beam (spatial compound imaging), beam steering, speckle reduction imaging, harmonic imaging, colorization, and speed of sound were evaluated. Settings that improved marker detection were used clinically for a year. Results: Sonographic scanning settings that improved biopsy marker conspicuity included increasing transducer frequency, decreasing dynamic range, setting cross-beam to medium hybrid, turning on beam steering, and setting speckle reduction imaging in the mid-range. There was no appreciable improvement with harmonic imaging, colorization, or speed of sound. Conclusion: On a currently available clinical ultrasound scanning system, ultrasound scanning parameters can be adjusted to improve the conspicuity of biopsy markers. Overall, optimization requires a balance between techniques that clinically increase contrast (dynamic range, harmonic imaging, and steering) and those that minimize graininess (spatial compound imaging, speckle reduction imaging, and steering). Additional scanning and procedural strategies have been provided to improve the confidence of sonographic detection of biopsy markers closely associated with the intended target.
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Cesar, Aline S. M., Fernando H. Biase, Paula Ripamonte, Albino Luchiari Filho, Giovana K. Merighe, and Flávio V. Meirelles. "Nuclear and mitochondrial DNA markers in traceability of retail beef samples." Pesquisa Veterinária Brasileira 30, no. 9 (September 2010): 783–86. http://dx.doi.org/10.1590/s0100-736x2010000900012.

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Several characteristics are important in a traceability system of animal products, such as age at slaughter, breed composition, besides information of the productive chain. In general, the certification agent records information about the animals and the system which it came from, although cannot guarantee that the slaughtering, meat processing and distribution are error proof. Besides, there is a differential price, at least at the international market, based on sex and breed composition of the animals. Genetic markers allow identification of characteristics controlled in the beef cattle traceability program, as sex and breed composition, in order to correctly identify and appraise the final product for the consumer. The hypothesis of this study was that the majority beef samples retailed in the local market originate from female with a great participation of zebu breeds. Therefore, the objective of this work was to characterize retail beef samples with DNA markers that identify cattle sex and breed composition. Within 10 beef shops localized in Pirassununga, SP, Brazil, 61 samples were collected, all were genotyped as harboring Bos taurus mitochondrial DNA and 18 were positive for the Y chromosome amplification (male). For the marker sat1711b-Msp I the frequency of the allele A was 0.278 and for the marker Lhr-Hha I the frequency of the allele T was 0.417. The results of sat1711b-Msp I and Lhr-Hha I allelic frequencies are suggestive that the proportion of indicus genome compared with the taurine genome in the market meat is smaller than the observed in the Nellore breed. The procedure described in this study identified sex and subspecies characteristics of beef meat samples, with potential application in meat products certification in special as an auxiliary tool in beef cattle traceability programs.
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Lu, Zhen-Xiang, B. Sosinski, G. L. Reighard, W. V. Baird, and A. G. Abbott. "Construction of a genetic linkage map and identification of AFLP markers for resistance to root-knot nematodes in peach rootstocks." Genome 41, no. 2 (April 1, 1998): 199–207. http://dx.doi.org/10.1139/g98-008.

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A genetic linkage map for peach (Prunus persica (L.) Batsch) rootstocks has been constructed using amplified fragment length polymorphism (AFLP) markers in 55 F2 individuals derived from the cross Lovell x Nemared. From 21 different primer combinations, a total of 169 AFLP markers were scored, of which, 153 were assigned to 15 linkage groups covering 1297 centimorgans (cM) of the peach nuclear genome. The average interval between these markers was 9.1 cM. Two genes (Mi and Mij) involved in resistance to root-knot nematodes (Meloidogyne incognita (Kofoid and White) Chitwood and Meloidogyne javanica (Treub) Chitwood) were mapped to a single linkage group (Group I). These two loci were separated by a 16.5-cM interval. One codominant AFLP marker (EAA/MCAT10) was tightly linked to the Mij locus (3.4 cM), and a dominant AFLP marker (EAT/MCAT2) was found to be closely associated with the Mi locus (6.0 cM). These markers are being studied for utilization in peach rootstock breeding with marker-assisted selection.Key words: peach rootstocks, root-knot nematodes, resistance, AFLP, mapping.
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Wang, Fei, James McD Stewart, and Jinfa Zhang. "Molecular markers linked to the Rf2 fertility restorer gene in cotton." Genome 50, no. 9 (September 2007): 818–24. http://dx.doi.org/10.1139/g07-061.

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Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants do not produce viable pollen. Fertility in plants with CMS can be recovered by nuclear restorer genes. Most restorer genes cloned so far are members of the pentatricopeptide repeat (PPR) protein family. The objective of our study was to use the CMS-D8 and restoration (Rf2) system of cotton ( Gossypium hirsutum L.) to develop more DNA markers for the Rf2 gene. In a backcross population with 112 plants, segregation of male fertility was 1 fertile : 1 sterile. Three new RAPD markers were identified for Rf2, one of which was converted to a CAPS marker. In addition, 2 AFLP markers and 1 SSR marker were identified to be linked to the fertility restorer gene (Rf2). PPR motif primers were designed based on the conserved PPR motifs and used in combination with AFLP primers to test the mapping population, and 1 PPR-AFLP marker was identified. A linkage map with 9 flanking markers including 1 from a previous study was constructed.
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Nuroniah, H. S., O. Gailing, and R. Finkeldey. "Development of SCAR Markers for Species Identification in the Genus Shorea (Dipterocarpaceae)." Silvae Genetica 59, no. 1-6 (December 1, 2010): 249–57. http://dx.doi.org/10.1515/sg-2010-0035.

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AbstractThe development of molecular markers unambiguously distinguishing groups at different taxonomic levels has numerous forensic applications. The identification of tropical timber is of particular interest in this context. We describe the development of SCAR (Sequence Characterized Amplified Region) markers for forensic applications taking the example of two closely related species of the tropical tree family Shorea (Dipterocarpaceae). Two AFLP (Amplified Fragment Length Polymorphism) fragments have been described earlier showing strong differentiation between S. leprosula and S. parvifolia. The AFLP markers were isolated from a gel, re-amplified, cloned and sequenced. Primer sets were designed from these sequences and AFLP fragments were converted into SCAR markers. The SCAR markers and PCR-RFLP markers of the chloroplast region trnLF digested with HinfI were used to screen in total 557 samples of S. parvifolia and S. leprosula from nineteen widely separated populations in Indonesia. Complete genetic differentiation between species was observed based on the putatively nuclear SCAR marker and the PCR-RFLP of the cpDNA region. We found a good agreement between leaf morphological variation and species identification based on both marker types and no indication for interspecific hybridization.
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MATTIUCCI, S., V. ACERRA, M. PAOLETTI, P. CIPRIANI, A. LEVSEN, S. C. WEBB, D. CANESTRELLI, and G. NASCETTI. "No more time to stay ‘single’ in the detection of Anisakis pegreffii, A. simplex (s. s.) and hybridization events between them: a multi-marker nuclear genotyping approach." Parasitology 143, no. 8 (April 5, 2016): 998–1011. http://dx.doi.org/10.1017/s0031182016000330.

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SUMMARYA multi-marker nuclear genotyping approach was performed on larval and adult specimens of Anisakis spp. (N = 689) collected from fish and cetaceans in allopatric and sympatric areas of the two species Anisakis pegreffii and Anisakis simplex (s. s.), in order to: (1) identify specimens belonging to the parental taxa by using nuclear markers (allozymes loci) and sequence analysis of a new diagnostic nuclear DNA locus (i.e. partial sequence of the EF1 α−1 nDNA region) and (2) recognize hybrid categories. According to the Bayesian clustering algorithms, based on those markers, most of the individuals (N = 678) were identified as the parental species [i.e. A. pegreffii or A. simplex (s. s.)], whereas a smaller portion (N = 11) were recognized as F1 hybrids. Discordant results were obtained when using the polymerase chain reaction–restriction fragment length polymorphisms (PCR–RFLPs) of the internal transcribed spacer (ITS) ribosomal DNA (rDNA) on the same specimens, which indicated the occurrence of a large number of ‘hybrids’ both in sympatry and allopatry. These findings raise the question of possible misidentification of specimens belonging to the two parental Anisakis and their hybrid categories derived from the application of that single marker (i.e. PCR–RFLPs analysis of the ITS of rDNA). Finally, Bayesian clustering, using allozymes and EF1 α−1 nDNA markers, has demonstrated that hybridization between A. pegreffii and A. simplex (s. s.) is a contemporary phenomenon in sympatric areas, while no introgressive hybridization takes place between the two species.
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35

Hall, H. G. "Parental analysis of introgressive hybridization between African and European honeybees using nuclear DNA RFLPs." Genetics 125, no. 3 (July 1, 1990): 611–21. http://dx.doi.org/10.1093/genetics/125.3.611.

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Abstract African honeybees, introduced into Brazil 33 years ago, have spread through most of South and Central America and have largely replaced the extant European bees. Due to a paucity of genetic markers, genetic interactions between European and African bees are not well understood. Three restriction fragment length polymorphisms (RFLPs), detected with random, nuclear DNA probes, are described. The polymorphisms are specific to bees of European descent, possibly specific to certain European races. Each European marker was found present at a high frequency in U.S. colonies but absent in South African bees. Previous mitochondrial DNA studies of neotropical bees have revealed negligible maternal gene flow from managed European apiaries into feral African populations. The findings reported here with nuclear DNA show paternal gene flow between the two but suggest asymmetries in levels of introgressive hybridization. Managed colonies in southern Mexico, derived from European maternal lines, showed diminished levels of the European nuclear markers, reflecting significant hybridization with African drones. The European alleles were present only at low frequencies in feral swarms from the same area. The swarms were of African maternal descent. In Venezuelan colonies, also derived from African maternal lines, the European markers were almost totally absent. The results point to limited paternal introgression from European colonies into the African honeybee populations. These findings dispute other views regarding modes of Africanization.
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36

Ozminkowski, Richard H., and Pablo Jourdan. "Comparing the Resynthesis of Brassica napus L. by Interspecific Somatic and Sexual Hybridization. II. Hybrid Morphology and Identifying Organelle Genomes." Journal of the American Society for Horticultural Science 119, no. 4 (July 1994): 816–23. http://dx.doi.org/10.21273/jashs.119.4.816.

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Brassica napus (genome aacc), a natural allotetraploid derived from hybridization between B. oleracea L. (genome cc) and B. rapa L. (genome aa), was resynthesized by somatic and sexual hybridization. Seventy-two interspecific somatic (R0) hybrids and 27 sexual (F1) hybrids were produced from the same parent plants. R0 and F1 hybrids displayed morphology that was intermediate to the species parents, but B. rapa characteristics tended to predominate. R0 hybrids with nuclear DNA content equivalent to natural B. napus were uniform for nuclear-encoded traits, whereas allotetraploid F1 hybrids were variable for traits such as morphology, flower color, and seed production. Chloroplast restriction fragment length polymorphisms (RFLPs) showed unequal segregation in the R0 population favoring the chloroplasts of B. rapa; two of the 58 R0 hybrids tested had only the B. oleracea marker and 10 contained markers of both parents. Mitochondrial RFLPs showed a similar bias among the 56 R0 hybrids tested; only four plants showed B. oleracea markers exclusively, and the remaining plants were evenly distributed between having only B. rapa markers or having combinations from both species. In contrast, sexual hybrids displayed only maternal organelle markers.
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Yu, Chiun-Chieh, Meng-Hsiang Chen, Cheng-Hsien Lu, Yung-Cheng Huang, Hsiu-Ling Chen, Nai-Wen Tsai, Hung-Chen Wang, I.-Hsiao Yang, Shau-Hsuan Li, and Wei-Che Lin. "Altered Striatocerebellar Metabolism and Systemic Inflammation in Parkinson’s Disease." Oxidative Medicine and Cellular Longevity 2016 (2016): 1–12. http://dx.doi.org/10.1155/2016/1810289.

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Parkinson’s disease (PD) is the most second common neurodegenerative movement disorder. Neuroinflammation due to systemic inflammation and elevated oxidative stress is considered a major factor promoting the pathogenesis of PD, but the relationship of structural brain imaging parameters to clinical inflammatory markers has not been well studied. Our aim was to evaluate the association of magnetic resonance spectroscopy (MRS) measures with inflammatory markers. Blood samples were collected from 33 patients with newly diagnosed PD and 30 healthy volunteers. MRS data including levels of N-acetylaspartate (NAA), creatine (Cre), and choline (Cho) were measured in the bilateral basal ganglia and cerebellum. Inflammatory markers included plasma nuclear DNA, plasma mitochondrial DNA, and apoptotic leukocyte levels. The Cho/Cre ratio in the dominant basal ganglion, the dominant basal ganglia to cerebellum ratios of two MRS parameters NAA/Cre and Cho/Cre, and levels of nuclear DNA, mitochondrial DNA, and apoptotic leukocytes were significantly different between PD patients and normal healthy volunteers. Significant positive correlations were noted between MRS measures and inflammatory marker levels. In conclusion, patients with PD seem to have abnormal levels of inflammatory markers in the peripheral circulation and deficits in MRS measures in the dominant basal ganglion and cerebellum.
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38

Guo, Rui, Yi Tian, Na Zhang, Hong Huang, Ying Huang, and Jun Yang. "Use of dual-marker staining to differentiate between lung squamous cell carcinoma and adenocarcinoma." Journal of International Medical Research 48, no. 4 (December 27, 2019): 030006051989386. http://dx.doi.org/10.1177/0300060519893867.

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Objective To assess the value of dual-marker immunostaining for detecting p40 and napsin A, and cytokeratin 5/6 (CK5/6) and thyroid transcription factor 1 (TTF1) in single sections of lung cancer tissue, for differentiating between lung squamous cell carcinoma and adenocarcinoma. Methods Lung cancer tissue sections from 58 patients were stained by dual-marker immunostaining using a mixtures of anti-p40 and anti-napsin A, and anti-CK5/6 and anti-TTF1 primary antibodies. Sections stained with single markers were used as controls. Nuclear or cytoplasmic staining was considered as indicating positive p40 or napsin A expression, respectively, and cytoplasmic or nuclear staining was considered as indicating positive CK5/6 or TTF1 expression, respectively. Results p40/napsin A and CK5/6/TTF1 dual-marker staining showed high sensitivity, specificity, positive predictive value, and negative predictive value for the diagnosis of squamous cell carcinoma and adenocarcinoma respectively. There were no differences in marker expression between dual-marker and single-marker staining. Conclusions Dual-marker immunostaining is a relatively easy, time- and cost-conserving staining method for detecting two markers in a single section using one procedure and one chromogen. p40 and napsin A, and CK5/6 and TTF1 dual-marker staining were suitable for the differential diagnosis of lung squamous cell carcinoma and adenocarcinoma.
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Kono, Tomohiro. "Influence of epigenetic changes during oocyte growth on nuclear reprogramming after nuclear transfer." Reproduction, Fertility and Development 10, no. 8 (1998): 593. http://dx.doi.org/10.1071/rd98056.

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Genomic imprinting is the epigenetic mechanism that distinguishes whether the loci that are inherited from the maternal or paternal genome lead to parent-specific gene expression. The mechanism also regulates development in mammalian embryos. Genomic imprinting is established after implantation according to the specific markers that are imposed on the genome during gametogenesis; the allele-specific gene expression is then maintained throughout embryogenesis. The genomic imprinting markers are erased and renewed on an own-sex basis only in cells that differentiate into germline cells. This report shows that the epigenetic modifications that occur during oogenesis perform the crucial function of establishing the allele-specific expression of imprinted genes, and also suggests that the epigenetic DNA modification is related to the reprogramming and aberrant development seen in manipulated embryos.
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40

Schroeder, Hilke, and Birgit Kersten. "A Small Set of Nuclear Markers for Reliable Differentiation of the Two Closely Related Oak Species Quercus Robur and Q. Petraea." Plants 12, no. 3 (January 26, 2023): 566. http://dx.doi.org/10.3390/plants12030566.

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Quercus robur and Q. petraea are, in addition to Fagus sylvatica, the main economically used deciduous tree species in Europe. Identification of these two species is crucial because they differ in their ecological demands. Because of a changing climate, foresters must know more than ever which species will perform better under given environmental conditions. The search for differentiating molecular markers between these two species has already lasted for decades. Until now, differentiation has only been possible in approaches with a combination of several molecular markers and a subsequent statistical analysis to calculate the probability of being one or the other species. Here, we used MiSeq Illumina data from pools of Q. robur and Q. petraea specimens and identified nuclear SNPs and small InDels versus the Q. robur reference genome. Selected sequence variants with 100% allele frequency difference between the two pools were further validated in an extended set of Q. robur and Q. petraea specimens, and then the number of markers was deliberately reduced to the smallest possible set for species differentiation. A combination of six markers from four nuclear regions is enough to identify Q. robur, Q. petraea or hybrids between these two species quite well and represents a marker set that is cost-efficient and useable in every laboratory.
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Böckelmann, Jörg, David Wieser, Karin Tremetsberger, Kateřina Šumberová, and Karl‐Georg Bernhardt. "Isolation of nuclear microsatellite markers for Cyperus fuscus (Cyperaceae)." Applications in Plant Sciences 3, no. 11 (November 2015): 1500071. http://dx.doi.org/10.3732/apps.1500071.

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42

Ju Han, Hang Chang, K. Andarawewa, P. Yaswen, M. H. Barcellos-Hoff, and B. Parvin. "Multidimensional Profiling of Cell Surface Proteins and Nuclear Markers." IEEE/ACM Transactions on Computational Biology and Bioinformatics 7, no. 1 (January 2010): 80–90. http://dx.doi.org/10.1109/tcbb.2008.134.

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Ganjei, Parvin, Manijeh Moezzi, Merce Jorda, and Mehrdad Nadji. "IMMUNOHISTOCHEMICAL EVALUATION OF NUCLEAR PROLIFERATING MARKERS IN OVARIAN CARCINOMA." Southern Medical Journal 85, Supplement (September 1992): 3S—82. http://dx.doi.org/10.1097/00007611-199209001-00231.

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44

de Bruyn, Mark, Wendy Grail, Axel Barlow, and Gary R. Carvalho. "Anonymous nuclear markers for SouthEast Asian halfbeak fishes (Dermogenys)." Conservation Genetics Resources 2, S1 (April 27, 2010): 325–27. http://dx.doi.org/10.1007/s12686-010-9228-z.

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Sebastiani, F., F. Pinzauti, S. T. Kujala, S. C. González-Martínez, and G. G. Vendramin. "Novel polymorphic nuclear microsatellite markers for Pinus sylvestris L." Conservation Genetics Resources 4, no. 2 (September 9, 2011): 231–34. http://dx.doi.org/10.1007/s12686-011-9513-5.

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Pakull, Birte, Lasse Schindler, Malte Mader, Birgit Kersten, Celine Blanc-Jolivet, Maike Paulini, Maristerra R. Lemes, et al. "Development of nuclear SNP markers for Mahogany (Swietenia spp.)." Conservation Genetics Resources 12, no. 4 (August 12, 2020): 585–87. http://dx.doi.org/10.1007/s12686-020-01162-8.

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Abstract Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™ genotyping. These markers can be used for population genetic studies and timber tracking purposes.
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Rothfels, Carl J., Anders Larsson, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Dylan O. Burge, Markus Ruhsam, et al. "Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns." PLoS ONE 8, no. 10 (October 8, 2013): e76957. http://dx.doi.org/10.1371/journal.pone.0076957.

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López, Carlos, Marylène Lejeune, María Teresa Salvadó, Patricia Escrivà, Ramón Bosch, Lluis E. Pons, Tomás Álvaro, et al. "Automated quantification of nuclear immunohistochemical markers with different complexity." Histochemistry and Cell Biology 129, no. 3 (January 3, 2008): 379–87. http://dx.doi.org/10.1007/s00418-007-0368-5.

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Donald Chapman, J., R. H. Schneider, C. C. Stobbe, E. Kim, E. L. Engelhardt, and L. Coia. "33 Nuclear medicine markers of tumor oxygenation and radioresistance." International Journal of Radiation Oncology*Biology*Physics 36, no. 1 (January 1996): 175. http://dx.doi.org/10.1016/s0360-3016(97)85375-8.

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50

Orive, Maria E., and Marjorie A. Asmussen. "The Effects of Pollen and Seed Migration on Nuclear-Dicytoplasmic Systems. II. A New Method for Estimating Plant Gene Flow From Joint Nuclear-Cytoplasmic Data." Genetics 155, no. 2 (June 1, 2000): 833–54. http://dx.doi.org/10.1093/genetics/155.2.833.

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Abstract A new maximum-likelihood method is developed for estimating unidirectional pollen and seed flow in mixed-mating plant populations from counts of joint nuclear-cytoplasmic genotypes. Data may include multiple unlinked nuclear markers with a single maternally or paternally inherited cytoplasmic marker, or with two cytoplasmic markers inherited through opposite parents, as in many conifer species. Migration rate estimates are based on fitting the equilibrium genotype frequencies under continent-island models of plant gene flow to the data. Detailed analysis of their equilibrium structures indicates when each of the three nuclear-cytoplasmic systems allows gene flow estimation and shows that, in general, it is easier to estimate seed than pollen migration. Three-locus nuclear-dicytoplasmic data only increase the conditions allowing seed migration estimates; however, the additional dicytonuclear disequilibria allow more accurate estimates of both forms of gene flow. Estimates and their confidence limits for simulated data sets confirm that two-locus data with paternal cytoplasmic inheritance provide better estimates than those with maternal inheritance, while three-locus dicytonuclear data with three modes of inheritance generally provide the most reliable estimates for both types of gene flow. Similar results are obtained for hybrid zones receiving pollen and seed flow from two source populations. An estimation program is available upon request.
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