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James Harris, David, and Catarina Rato. "Genetic variation within Saurodactylus and its phylogenetic relationships within the Gekkonoidea estimated from mitochondrial and nuclear DNA sequences." Amphibia-Reptilia 29, no. 1 (2008): 25–34. http://dx.doi.org/10.1163/156853808783431406.
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Abstract Phylogenetic relationships of the three morphological forms within the gecko genus Saurodactylus were estimated using mtDNA (12S rRNA and ND4) sequences. High between morphological forms variation (up to 25% with ND4), confirms that all three deserve specific status. Saurodactylus mauritanicus and Saurodactylus brosseti are strongly supported as sister taxa. Our results again highlight the extremely high mtDNA variability almost universally reported from within gecko species. The position of Saurodactylus within the Gekkonoidea was also investigated. Although considered as a member of the sphaerodactyl geckos, its taxonomic position is still highly uncertain. Evaluation of C-mos nuclear DNA sequences supports many of the recent taxonomic rearrangements within the Gekkonoidea. Using this marker, Saurodactylus is paraphyletic, with S. mauritanicus and S. brosseti sister taxa to Teratoscincus przewalskii rather than Saurodactylus fasciatus. This is supported by a further nuclear marker, RAG1, although for this gene region sampling is more limited. Based on this paraphyly, supported by two independent nuclear markers, we suggest it likely that Saurodactylus will need to be partitioned into two genera, pending further investigations.
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Tourbah, Ayman, Anne Gansmuller, and Madeleine Gumpel. "A Nuclear Marker for Mammalian Cells and Its Use with Intracerebral Transplants." Biotechnic & Histochemistry 66, no. 1 (1991): 29–34. http://dx.doi.org/10.3109/10520299109110546.
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Jin, Wei-Yin, Bing Liu, Shou-Zhou Zhang, Tao Wan, Chen Hou, and Yong Yang. "Gnetum chinense, a new species of Gnetaceae from southwestern China." PhytoKeys 148 (May 26, 2020): 105–17. http://dx.doi.org/10.3897/phytokeys.148.48510.
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Gnetum chinensesp. nov., a new lianoid species of Gnetaceae, is described from southwestern China. The new species is morphologically similar to G. montanum Markgr. in its oblong elliptic leaves and the ovoid to ellipsoid chlamydosperm, but differs from the latter by its shorter male spikes having fewer involucral collars (7–10 vs. 13–18 in G. montanum). We also did a new molecular analysis using one nuclear marker (i.e. nrITS) and four chloroplast markers (i.e. matK gene, rpoC1 intron, psbB-rps12 IGS, and trnF-trnV IGS). The result suggests that this specific clade is sister to a large clade consisting of all other known Chinese lianoid species of Gnetum except G. parvifolium (Warb.) W.C. Cheng.
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Meslet-Cladière, Laurence, and Olivier Vallon. "Novel Shuttle Markers for Nuclear Transformation of the Green Alga Chlamydomonas reinhardtii." Eukaryotic Cell 10, no. 12 (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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Wangiyana, I. Gde Adi Suryawan. "DNA BARCODING LIBRARY DATABASE OF AQUILARIA MEMBER AND GYRINOPS MEMBER." Jurnal Silva Samalas 3, no. 2 (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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Kijewska, Agnieszka, Artur Burzyński, and Roman Wenne. "Molecular identification of European flounder (Platichthys flesus) and its hybrids with European plaice (Pleuronectes platessa)." ICES Journal of Marine Science 66, no. 5 (2009): 902–6. http://dx.doi.org/10.1093/icesjms/fsp110.
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AbstractKijewska, A., Burzyński, A., and Wenne, R. 2009. Molecular identification of European flounder (Platichthys flesus) and its hybrids with European plaice (Pleuronectes platessa). – ICES Journal of Marine Science, 66: 902–906. European flounder (Platichthys flesus) and plaice (Pleuronectes platessa) are commercially important marine fish species inhabiting the continental shelf waters of Europe. Morphological similarity between the two makes it difficult to identify their hybrids, so species misclassification can generate errors in defining stocks in terms of their conservation and management. Flounder and plaice populations from the North Sea and the Baltic Sea were studied. Mitochondrial DNA (mtDNA) was used to confirm the morphological species identification. The set of molecular markers, two mitochondrial (cytochrome b and D-loop) and two nuclear (the ribosomal marker ITS and parathyroid hormone-related protein gene), was constructed to identify the two flatfish species and their hybrids. “Pure” flounder (P. flesus) were observed in the Bay of Gdańsk, Baltic Sea, and off the coast of Denmark in the North Sea. The fishing area near Bornholm in the Baltic is rich in P. flesus × P. platessa hybrids. The length difference of the amplified D-loop fragment was used for species identification. The characteristics of heteroplasmy in the control region (D-loop) can be useful as a population marker in the European flounder. Our studies demonstrate the utility of mtDNA polymorphism combined with nuclear molecular markers for correct identification of the morphologically similar and hybridized European flounder and plaice.
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Caramalho, Rita, Lisa Madl, Katharina Rosam, et al. "Evaluation of a Novel Mitochondrial Pan-Mucorales Marker for the Detection, Identification, Quantification, and Growth Stage Determination of Mucormycetes." Journal of Fungi 5, no. 4 (2019): 98. http://dx.doi.org/10.3390/jof5040098.
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Mucormycosis infections are infrequent yet aggressive and serious fungal infections. Early diagnosis of mucormycosis and its discrimination from other fungal infections is required for targeted treatment and more favorable patient outcomes. The majority of the molecular assays use 18 S rDNA. In the current study, we aimed to explore the potential of the mitochondrial rnl (encoding for large-subunit-ribosomal-RNA) gene as a novel molecular marker suitable for research and diagnostics. Rnl was evaluated as a marker for: (1) the Mucorales family, (2) species identification (Rhizopus arrhizus, R. microsporus, Mucor circinelloides, and Lichtheimia species complexes), (3) growth stage, and (4) quantification. Sensitivity, specificity, discriminatory power, the limit of detection (LoD), and cross-reactivity were evaluated. Assays were tested using pure cultures, spiked clinical samples, murine organs, and human paraffin-embedded-tissue (FFPE) samples. Mitochondrial markers were found to be superior to nuclear markers for degraded samples. Rnl outperformed the UMD universal® (Molyzm) marker in FFPE (71.5% positive samples versus 50%). Spiked blood samples highlighted the potential of rnl as a pan-Mucorales screening test. Fungal burden was reproducibly quantified in murine organs using standard curves. Identification of pure cultures gave a perfect (100%) correlation with the detected internal transcribed spacer (ITS) sequence. In conclusion, mitochondrial genes, such as rnl, provide an alternative to the nuclear 18 S rDNA genes and deserve further evaluation.
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Schoch, C. L., K. A. Seifert, S. Huhndorf, et al. "Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi." Proceedings of the National Academy of Sciences 109, no. 16 (2012): 6241–46. http://dx.doi.org/10.1073/pnas.1117018109.
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Gusel’nikova, V. V., and D. E. Korzhevskiy. "NeuN As a Neuronal Nuclear Antigen and Neuron Differentiation Marker." Acta Naturae 7, no. 2 (2015): 42–47. http://dx.doi.org/10.32607/20758251-2015-7-2-42-47.
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The NeuN protein is localized in nuclei and perinuclear cytoplasm of most of the neurons in the central nervous system of mammals. Monoclonal antibodies to the NeuN protein have been actively used in the immunohistochemical research of neuronal differentiation to assess the functional state of neurons in norm and pathology for more than 20 years. Recently, NeuN antibodies have begun to be applied in the differential morphological diagnosis of cancer. However, the structure of the protein, which can be revealed by antibodies to NeuN, remained unknown until recently, and the functions of the protein are still not fully clear. In the present mini-review, data on NeuN accumulated so far are summarized and analyzed. Data on the structure and properties of the protein, its isoforms, intracellular localization, and hypothesized functions are reported. The application field of immunocytochemical detection of NeuN in scientific and clinical studies, as well as the difficulties in the interpretation of the obtained experimental data and their possible causes, is described in details.
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MATTIUCCI, S., V. ACERRA, M. PAOLETTI, et al. "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 (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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Setiawan, Edwin, Nicole J. De Voogd, John N. A. Hooper, Gert Wörheide, and Dirk Erpenbeck. "The lysidyl aminoacyl transfer RNA synthetase intron, a new marker for demosponge phylogeographics – case study on Neopetrosia." Journal of the Marine Biological Association of the United Kingdom 96, no. 2 (2015): 333–39. http://dx.doi.org/10.1017/s0025315415001721.
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Suitable genetic markers for population studies in sponges are necessary to further our understanding of biodiversity and dispersal patterns, and contribute to conservation efforts. Due to the slow mitochondrial substitution rates in demosponges, nuclear introns are among the preferable markers for phylogeographic studies, but so far only the second intron of the ATP synthetase beta subunit-gene (ATPSβ) has been successfully established. In the present study, we analyse the intron of the Lysidyl Aminoacyl Transfer RNA Synthetase (LTRS), another potential marker to study demosponge intraspecific relationships, on samples of Neopetrosia chaliniformis from various locations in the Indo-Pacific and compare its variation with a mitochondrial marker (CO2). LTRS recovers several reciprocal monophyletic groups among the Indo-Pacific N. chaliniformis and provides a potential alternative to ATPSβ.
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Matumba, Tshifhiwa G., Jody Oliver, Nigel P. Barker, Christopher D. McQuaid, and Peter R. Teske. "Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA." F1000Research 9 (May 7, 2020): 339. http://dx.doi.org/10.12688/f1000research.23635.1.
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Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. To our knowledge, this is the first study to use nuclear rRNA at this taxonomic level, presumably because this marker is assumed to evolve so slowly that it is only suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolves effectively clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.
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Matumba, Tshifhiwa G., Jody Oliver, Nigel P. Barker, Christopher D. McQuaid, and Peter R. Teske. "Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA." F1000Research 9 (August 28, 2020): 339. http://dx.doi.org/10.12688/f1000research.23635.2.
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Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics. Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.
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Urruticoechea, Ander, Ian E. Smith, and Mitch Dowsett. "Proliferation Marker Ki-67 in Early Breast Cancer." Journal of Clinical Oncology 23, no. 28 (2005): 7212–20. http://dx.doi.org/10.1200/jco.2005.07.501.
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Molecular markers have been extensively investigated with a view to providing early and accurate information on long-term outcome and prediction of response to treatment of early breast cancer. Proliferation is a key feature of the progression of tumors and is now widely estimated by the immunohistochemical assessment of the nuclear antigen Ki-67. The expression of Ki-67 correlates with other measurements of proliferation, including S-phase and bromodeoxyuridine uptake. High Ki-67 is a sign of poor prognosis associated with a good chance of clinical response to chemotherapy, but its independent significance is modest and does not merit measurements in most routine clinical scenarios. However, its application as a pharmacodynamic intermediate marker of the effectiveness of medical therapy holds great promise for rapid evaluation of new drugs.
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Ha, Mihyang, Ji-Young Kim, Myoung-Eun Han, et al. "TMEM18: A Novel Prognostic Marker in Acute Myeloid Leukemia." Acta Haematologica 140, no. 2 (2018): 71–76. http://dx.doi.org/10.1159/000492742.
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Background: Certain nuclear envelope proteins are associated with important cancer cell characteristics, including migration and proliferation. Abnormal expression of and genetic changes in nuclear envelope proteins have been reported in acute myeloid leukemia (AML) patients. Transmembrane protein 18 (TMEM18), a nuclear envelope protein, is involved in neural stem cell migration and tumorigenicity. Methods: To examine the prognostic significance of TMEM18 in AML patients, we analyzed an AML cohort from The Cancer Genome Atlas (TCGA, n = 142). Results: Kaplan-Meier survival analysis revealed that TMEM18 overexpression was associated with a better AML prognosis with good discrimination (p = 0.019). Interestingly, this ability to predict the prognosis was significant in male AML patients, but not in female ones. C-index and area-under-the-curve analyses further supported this discriminative ability and multivariate analysis confirmed its prognostic significance (p = 0.00347). Correlation analysis revealed that TMEM18 had a statistically significant positive correlation with nuclear envelop protein 133 (NUP133), NUP35, NUP54, NUP62, and NUP88. Conclusion: Because the current AML prognostic factors do not take mRNA expression into consideration unlike other cancers, the development of mRNA-based prognostic factors would be beneficial for accurate prediction of the survival of AML patients. Therefore, TMEM18 gene is a potential biomarker for AML.
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Manokar, Jaganathan, Subramani Paranthaman Balasubramani, and Padma Venkatasubramanian. "Nuclear ribosomal DNA – ITS region based molecular marker to distinguish Gmelina arborea Roxb. Ex Sm. from its substitutes and adulterants." Journal of Ayurveda and Integrative Medicine 9, no. 4 (2018): 290–93. http://dx.doi.org/10.1016/j.jaim.2017.10.001.
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Sliwinska, Elwira. "Nuclear DNA replication and seed quality." Seed Science Research 19, no. 1 (2009): 15–25. http://dx.doi.org/10.1017/s0960258508186275.
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AbstractThe quality of a seed (germination and vigour) is established during its development and maturation, but can be improved by post-harvest processing and pre-sowing treatments. During commercial seed production, maturity is usually estimated visually, relying on experience of the growers, but seed researchers are working to find molecular markers that can be applied easily to help in establishing optimal harvest time. One marker is cell cycle activity expressed as DNA replication in the seeds, analysed by flow cytometry. This fast and accurate method for the estimation of DNA content in plant nuclei allows detection of nuclei at different replication stages in different seed tissues and thus makes it possible to follow changes in the physiological state of a seed. DNA replication, as a late event during germination, can also be used to mark completion of germination and transition to early seedling growth. This information can be useful in the evaluation of seed quality and for following the advancement of priming. Flow cytometric analysis of ploidy can be also used as a basis for control of purity of some polyploid species seed lots.
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Joensuu, R. P. J., R. E. Sepponen, A. E. Lamminen, and C. G. M. Standertskjöld-Nordenstam. "Interventional Mr imaging." Acta Radiologica 38, no. 1 (1997): 43–46. http://dx.doi.org/10.1080/02841859709171240.
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Purpose: The poor localization facility of interventional instruments in MR imaging has been one of the major obstacles to the popularization of interventional MR imaging. It has been suggested that the Overhauser enhancement be used to generate markers of small size and high visibility. This article studies the feasibility of a localization marker based on this method. Material and Methods: A small Overhauser marker was constructed on the tip of a coaxial cable and comparative images were taken by a 0.23 T imager with and without electron spin irradiation. Results: During irradiation an enhanced signal intensity from the marker was observed. The signal from the marker also exceeded the signal from a 0.25 mmol MnCl2 reference phantom. Conclusion: Its small size and high signal-to-noise ratio, together with immunity to most system nonlinearities and imaging errors, makes the Overhauser marker a promising localization method for the accurate positioning of interventional devices. The method may be applied at any field strength, and markers are visible in images obtained with any practical imaging sequence.
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Zhan, Li, and Xu. "Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Ciliophora, Spirotrichea)." Microorganisms 7, no. 11 (2019): 493. http://dx.doi.org/10.3390/microorganisms7110493.
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Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence.
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Vigliani, M. Claudia, Adriano Chiò, Tiziana Pezzulo, Riccardo Soffietti, Maria T. Giordana, and Davide Schiffer. "Proliferating Cell Nuclear Antigen (PCNA) in Low-Grade Astrocytomas: Its Prognostic Significance." Tumori Journal 80, no. 4 (1994): 295–300. http://dx.doi.org/10.1177/030089169408000411.
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Aims and background A clear line cannot be drawn between well-differentiated and anaplastic astrocytomas, and a subset of low-grade tumors, histologically indistinguishable from the others, behaves similarly to anaplastic astrocytomas. The proliferative index could aid in the identification of this subgroup, for which a different therapeutic approach would be indicated. Methods We immunohistochemically evaluated the proliferating ceil nuclear antigen (PCNA) expression in 77 well-differentiated astrocytomas, since PCNA has been considered a good proliferation marker. The prognostic significance of PCNA labeling index (LI) was assessed in univariate and multivariate analysis, taking into consideration some clinical and histologic factors known to affect prognosis. Results PCNA immunostaining identified a subgroup of tumors, characterized by a LI > 5%, with a median survival close to that observed in anaplastic astrocytomas. The survival table of such a group was significantly different from that of the group with a lower LI (p = 0.0009). Multivariate analysis confirmed that PCNA-LI is an independent prognostic factor (p = 0.001). Conclusion These data suggest that PCNA immunostaining can be a useful tool to define the prognosis of low-grade astrocytomas on routine biopsy material.
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Juhlin, C. C., A. Villablanca, K. Sandelin, et al. "Parafibromin immunoreactivity: its use as an additional diagnostic marker for parathyroid tumor classification." Endocrine-Related Cancer 14, no. 2 (2007): 501–12. http://dx.doi.org/10.1677/erc-07-0021.
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Parafibromin is a protein product derived from the hyperparathyroidism 2(HRPT2) tumor suppressor geneand its inactivation has been coupled to familial and sporadic forms of parathyroid malignancy. In this study, we have conducted immunohistochemistry on 33 parathyroid carcinomas (22 unequivocal and 11 equivocal) using four parafibromin antibodies directed to different parts of the protein. Furthermore, for a fraction of cases, the immunohistochemical results were compared with known HRPT2 mutational status. Our findings show that 68% (15 out of 22) of the unequivocal carcinomas exhibited reduced expression of parafibromin while the 25 sporadic adenomas used as controls were entirely positive for parafibromin expression. Additionally, three out of the six carcinomas with known HRPT2 mutations showed reduced expression of parafibromin. Using all four antibodies, comparable results were obtained on the cellular level in individual tumors suggesting that there exists no epitope of choice in parafibromin immunohistochemistry. The results agree with the demonstration of a ~60 kDa product preferentially in the nuclear fraction by western blot analysis. We conclude that parafibromin immunohistochemistry could be used as an additional marker for parathyroid tumor classification, where positive samples have low risk of malignancy, whereas samples with reduced expression could be either carcinomas or rare cases of adenomas likely carrying an HRPT2 mutation.
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Herrera, Juan C., Marie C. Combes, Hernando Cortina, and Philippe Lashermes. "Factors influencing gene introgression into the allotetraploid Coffea arabica L. from its diploid relatives." Genome 47, no. 6 (2004): 1053–60. http://dx.doi.org/10.1139/g04-048.
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Factors controlling gene introgression into cultivated arabica coffee (Coffea arabica L.) were investigated. Interspecific triploid hybrid plants between the tetraploid species C. arabica (2n = 44) and a diploid species (2n = 22), either Coffea canephora or Coffea eugenioides, were backcrossed to C. arabica (male parent). Flow cytometric analysis of the nuclear DNA content revealed that most of the BC1 individuals derived from triploid hybrids involving C. eugenioides were tetraploid or nearly tetraploid. Among the gametes produced by the interspecific triploid hybrids, those possessing approximately 22 chromosomes appeared strongly favored. The amount of introgression in BC1 individuals (21 and 43 for the BC1 progenies involving C. canephora and C. eugenioides, respectively) was estimated using species-specific microsatellite markers. A large number of introgressed markers was observed in all BC1 individuals. Nevertheless, while the frequency of introgressed markers seemed as expected, assuming random chromosome segregation and diploid gamete formation, in the BC1 derived from triploid hybrids involving C. canephora, this frequency appeared significantly lower in the BC1 derived from triploid hybrids involving C. eugenioides. Furthermore, the comparison of reciprocal progenies between C. arabica and triploid interspecific hybrids (C. arabica × C. canephora) used as male or female parent revealed a very strong effect of the backcross direction.Key words: irregular meiosis, coffee, reciprocal crosses, molecular marker, triploid hybrids.
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Froufe, Elsa, Duarte V. Gonçalves, José Carlos Brito, and David James Harris. "Nuclear and mitochondrial markers reveal the existence of several geographically concordant lineages within a Sahelian gecko species, Ptyodactylus ragazzii." Amphibia-Reptilia 34, no. 1 (2013): 85–93. http://dx.doi.org/10.1163/15685381-00002873.
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The genetic diversity within Ptyodactylus ragazzii was analysed for the first time across the Western part of its range. We have used two mitochondrial (12s rRNA and 16s rRNA) and one nuclear (Cmos) marker to compare results directly with other related Ptyodactylus species, P. oudrii and P. hasselquistii. Results show high levels of intraspecific variability, with at least three divergent mtDNA lineages that have different haplotypes for Cmos and that are geographically concordant. P. ragazzii from Mauritania is probably a distinct species and possibly other lineages too, such as those from the Aïr Mountains in Niger, although more nuclear markers are needed to confirm this. All analysed Ptyodactylus species appear to be cryptic species complexes containing multiple deeply divergent forms, highlighting the need for a careful reassessment of the taxonomy of the whole genus.
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Rochette, Luc, Alexandre Meloux, Eve Rigal, Marianne Zeller, Yves Cottin, and Catherine Vergely. "The Role of Osteoprotegerin and Its Ligands in Vascular Function." International Journal of Molecular Sciences 20, no. 3 (2019): 705. http://dx.doi.org/10.3390/ijms20030705.
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The superfamily of tumor necrosis factor (TNF) receptors includes osteoprotegerin (OPG) and its ligands, which are receptor activators of nuclear factor kappa-B ligand (RANKL) and TNF-related apoptosis-inducing ligand (TRAIL). The OPG/RANKL/RANK system plays an active role in pathological angiogenesis and inflammation as well as cell survival. It has been demonstrated that there is crosstalk between endothelial cells and osteoblasts during osteogenesis, thus establishing a connection between angiogenesis and osteogenesis. This OPG/RANKL/RANK/TRAIL system acts on specific cell surface receptors, which are then able to transmit their signals to other intracellular components and modify gene expression. Cytokine production and activation of their receptors induce mechanisms to recruit monocytes and neutrophils as well as endothelial cells. Data support the role of an increased OPG/RANKL ratio as a possible marker of progression of endothelial dysfunction in metabolic disorders in relationship with inflammatory marker levels. We review the role of the OPG/RANKL/RANK triad in vascular function as well as molecular mechanisms related to the etiology of vascular diseases. The potential therapeutic strategies may be very promising in the future.
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Martin-Richard, Marta, Ariadna Tibau, Malena Ferre, et al. "MEK/ERK pathway characterization and its prognostic implication in gastric cancer (GC)." Journal of Clinical Oncology 30, no. 15_suppl (2012): e14552-e14552. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.e14552.
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e14552 Background: MEK/ERK pathway is considered one of the main controllers of cell proliferation and survival and its deregulation has been involved in several tumors. Different mechanisms have been described leading to ERK activation and nuclear translocation including mutations on genes encoding pathway constituents', or upstream factors overexpression. Little is known about the status of this pathway in GC. The aim of our study was to evaluate the expression of different factors of this pathway in GC and their correlation with patient outcome. Methods: Fifty-eight patients with localized stage Ib-III GC who underwent radical surgery followed by adjuvant chemoradiotherapy were selected. ERK and its activated form (pERK) expression were analyzed by IHC, and KRAS and BRAF mutations were determined by PCR. Additionally, expression of upstream factors such as EGFR, HER2, VEGFR and downstream factor such as MST2 was evaluated by IHC. Finally, EGFR and HER2 copy number alterations were analyzed by FISH. Association of these markers to overall survival was assessed using the log rank test, and survival curves were plotted with Kaplan-Meier methodology. Results: Among the 58 tumors analyzed, 7% arose from the cardias and 33% corresponded to signet ring cell carcinomas. ERK and pERK expression was observed in the majority of tumors (86 and 64%, respectively, p=0.002). Cytoplasmic pERK expression did not show any association with the clinico-pathological characteristics. Notably, nuclear pERK (pERKnc) expression was observed in 12% of the cases and it showed a significant correlation with patient survival (p=0.05), conferring a worse prognosis. Moreover, EGFR overexpression (p=0.03) correlated with pERKnc. Finally, multivariate Cox analysis for survival confirmed that stage (HR 0.31, p=0.01) and pERKnc (HR 2.7, p=0.04) are unique independent prognostic factors. Conclusions: MEK/ERK pathway is commonly activated in localized GC, backed up by ERK and pERK being highly expressed in these tumors. Moreover, EGFR expression correlates with nuclear ERK expression, suggesting that ERK translocation to the nucleus could be mediated by this factor. More importantly, nuclear ERK has appeared as an independent marker of poor prognosis.
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Górniak, Marcin, Anna Jakubska-Busse, and Marek S. Ziętara. "Genetic History of the Remnant Population of the Rare Orchid Cypripedium calceolus Based on Plastid and Nuclear rDNA." Genes 12, no. 6 (2021): 940. http://dx.doi.org/10.3390/genes12060940.
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The lady’s slipper orchid (Cypripedium calceolus), which inhabits shady deciduous and mixed forests and meadows, is now threatened with extinction in many European countries, and its natural populations have been dramatically declining in recent years. Knowledge of its evolutionary history, genetic variability, and processes in small populations are therefore crucial for the species’ protection. Nowadays, in south-west Poland, it is only distributed in seven small remnant and isolated populations, which we examined. One nuclear (ITS rDNA) and two plastid (accD-psa1, trnL-F) markers were analyzed and compared globally in this study. Based on the nuclear marker, the most common ancestor of C. calceolus and Cypripedium shanxiense existed about 2 million years ago (95% HPD: 5.33–0.44) in Asia. The division of the C. calceolus population into the European and Asian lineages indicated by C/T polymorphism started about 0.5 million years ago (95% HPD: 1.8–0.01). The observed variation of plastid DNA, which arose during the Pleistocene glacial–interglacial cycles, is still diffuse in Poland. Its distribution is explained by the result of fragmentation or habitat loss due to human impact on the environment.
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Wolf, Diana E., Jessica A. Satkoski, Kara White, and Loren H. Rieseberg. "Sex Determination in the Androdioecious Plant Datisca glomerata and Its Dioecious Sister Species D. cannabina." Genetics 159, no. 3 (2001): 1243–57. http://dx.doi.org/10.1093/genetics/159.3.1243.
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Abstract Datisca glomerata is an androdioecious plant species containing male and hermaphroditic individuals. Molecular markers and crossing data suggest that, in both D. glomerata and its dioecious sister species D. cannabina, sex is determined by a single nuclear locus, at which maleness is dominant. Supporting this conclusion, an amplified fragment length polymorphism (AFLP) is heterozygous in males and homozygous recessive in hermaphrodites in three populations of the androdioecious species. Additionally, hermaphrodite × male crosses produced 1:1 sex ratios, while hermaphrodite × hermaphrodite crosses produced almost entirely hermaphroditic offspring. No perfectly sex-linked marker was found in the dioecious species, but all markers associated with sex mapped to a single linkage group and were heterozygous in the male parent. There was no sex-ratio heterogeneity among crosses within D. cannabina collections, but males from one collection produced highly biased sex ratios (94% females), suggesting that there may be sex-linked meiotic drive or a cytoplasmic sex-ratio factor. Interspecific crosses produced only male and female offspring, but no hermaphrodites, suggesting that hermaphroditism is recessive to femaleness. This comparative approach suggests that the hermaphrodite form arose in a dioecious population from a recessive mutation that allowed females to produce pollen.
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ISHIGAMI, Akihito, Setsuko HANDA, Naoki MARUYAMA, and Prakash C. SUPAKAR. "Nuclear Localization of Senescence Marker Protein-30, SMP30, in Cultured Mouse Hepatocytes and Its Similarity to RNA Polymerase." Bioscience, Biotechnology, and Biochemistry 67, no. 1 (2003): 158–60. http://dx.doi.org/10.1271/bbb.67.158.
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Liu, Ji-Long, Zheng'an Wu, Zehra Nizami, et al. "Coilin Is Essential for Cajal Body Organization in Drosophila melanogaster." Molecular Biology of the Cell 20, no. 6 (2009): 1661–70. http://dx.doi.org/10.1091/mbc.e08-05-0525.
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Cajal bodies (CBs) are nuclear organelles that occur in a variety of organisms, including vertebrates, insects, and plants. They are most often identified with antibodies against the marker protein coilin. Because the amino acid sequence of coilin is not strongly conserved evolutionarily, coilin orthologues have been difficult to recognize by homology search. Here, we report the identification of Drosophila melanogaster coilin and describe its distribution in tissues of the fly. Surprisingly, we found coilin not only in CBs but also in histone locus bodies (HLBs), calling into question the use of coilin as an exclusive marker for CBs. We analyzed two null mutants in the coilin gene and a piggyBac insertion mutant, which leads to specific loss of coilin from the germline. All three mutants are homozygous viable and fertile. Cells that lack coilin also lack distinct foci of other CB markers, including fibrillarin, the survival motor neuron (SMN) protein, U2 small nuclear RNA (snRNA), U5 snRNA, and the small CB-specific (sca) RNA U85. However, HLBs are not obviously affected in coilin-null flies. Thus, coilin is required for normal CB organization in Drosophila but is not essential for viability or production of functional gametes.
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De Block, Petra, Franck Rakotonasolo, Sylvain G. Razafimandimbison, Aaron P. Davis, and Steven B. Janssens. "Tarennella, a new Pavetteae (Rubiaceae) genus from eastern Madagascar." Plant Ecology and Evolution 154, no. 1 (2021): 87–110. http://dx.doi.org/10.5091/plecevo.2021.1756.
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Background – This contribution is part of an ongoing study on the taxonomy and the phylogenetic relationships of the Malagasy representatives of the tribe Pavetteae (Rubiaceae).Material and methods – Taxonomic methods follow normal practice of herbarium taxonomy. A molecular study using the plastid markers rps16, trnT-F, petD, and accD-psa1, the nuclear ribosomal marker ITS and the nuclear MADS-box gene marker PI was executed.Key results – Five new species are described from littoral, lowland, or mid-elevation humid forests in eastern Madagascar. They are characterized by compact inflorescences with small, sessile flowers, a densely pubescent style, large placentas with 2–3 immersed ovules, seeds with a small, superficial hilum not surrounded by a thickened annulus, and pollen grains with supratectal elements. The phylogenetic tree, which included three of the five new species, showed an unresolved backbone but high support for distal nodes grouping species. The new species form a distinct monophyletic clade among the other Malagasy Pavetteae genera and are recognised at genus level under the name Tarennella. Provisional IUCN Red List assessments show that Tarennella homolleana is Vulnerable, T. cordatifolia and T. sanguinea are Endangered, T. puberula is Critically Endangered, and T. coronata is Critically Endangered (Possibly Extinct).
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HARPKE, DÖRTE, HELMUT KERNDORFF, ERICH PASCHE, and LORENZO PERUZZI. "Neotypification of the name Crocus biflorus Mill. (Iridaceae) and its consequences in the taxonomy of the genus." Phytotaxa 260, no. 2 (2016): 131. http://dx.doi.org/10.11646/phytotaxa.260.2.3.
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Recent phylogenetic investigations on the genus Crocus proved several infra-generic units predominantly within section Nudiscapus to be para- or polyphyletic even at infra-specific level. In particular, the 23 “subspecies” of C. biflorus Mill. turned out to be a polyphyletic assemblage grouping in very different clades and sub-groups. In addition, they were established under the binomial Crocus biflorus, not yet typified. As first step, we neotypified this name. Then, through a phylogeny based on the ETS region of the nuclear ribosomal (nr) DNA as an additional nuclear marker to the already available nrITS region, we further demonstrated that all the “subspecies” represent independent evolutionary lineages. Therefore, all these taxa are treated here at species level. To achieve this, 10 new combinations are proposed.
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Semerikova, Svetlana A., Martin Lascoux, and Vladimir L. Semerikov. "Nuclear and cytoplasmic genetic diversity reveals long-term population decline in Abies semenovii, an endemic fir of central Asia." Canadian Journal of Forest Research 42, no. 12 (2012): 2142–52. http://dx.doi.org/10.1139/cjfr-2012-0158.
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The genus Abies is one of the largest conifer genera and many of the marginal species remain poorly characterized. Abies semenovii B. Fedtsch. is a rare mountain fir species from central Asia, and its species status is still disputed. We used both nuclear (allozymes and AFLP) and chloroplastic (cpSSR) markers to show that A. semenovii deserves to be considered as a species and that its low genetic diversity justifies more a proactive conservation policy. First, A. semenovii was significantly differentiated from the Siberian fir Abies sibirica Ledeb. and we did not detect gene flow between the two species. Second, A. semenovii has a very low nuclear genetic diversity, suggesting a prolonged restricted effective population size. Abies semenovii had low cpSSR diversity too but the identification of seven closely related haplotypes suggests that these mutations accumulated recently during a phase of population expansion. This agrees well with the palynological record and is in contrast with the situation observed in another rare Eurasian fir endemic to Kamchatka, Abies gracilis Kom., which was devoid of variation in cpSSRs but that also had a more substantial nuclear marker diversity than A. semenovii, thereby suggesting a more recent but less severe population bottleneck.
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Asakura, Nobuaki, Chiharu Nakamura, and Ichiro Ohtsuka. "Homoeoallelic gene Ncc-tmp of Triticum timopheevii conferring compatibility with the cytoplasm of Aegilops squarrosa in the tetraploid wheat nuclear background." Genome 43, no. 3 (2000): 503–11. http://dx.doi.org/10.1139/g00-009.
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A nuclear gene, Ncc-tmp1A, of Triticum timopheevii is required for the nucleus-cytoplasm (NC) compatibility in tetraploid NC hybrids with the cytoplasm of Aegilops squarrosa. A euploid NC hybrid of T. durum was previously produced by introgressing the gene from chromosome 1A of T. timopheevii. To examine the possible presence of a functional homoeoallele in the G genome of T. timopheevii, segregation of seed viability was studied as a marker phenotype in BC1s involving the two types of NC hybrids, (Ae. squarrosa) - T. timopheevii and (Ae. squarrosa) - T. turgidum. The result of these test crosses suggested that the G genome possesses a functional homoeoallele Ncc-tmp1G. Segregation of two RAPD (random amplified polymorphic DNA) markers that were closely linked to Ncc-tmp1A was further studied among the viable BC1s obtained from a test cross of (Ae. squarrosa) - T. timopheevii × T. turgidum. Some viable BC1 segregants without the markers were obtained, suggesting a limited degree of transmission of chromosome 1G carrying Ncc-tmp1G. However, a similar RAPD analysis of BC1s obtained after backcrosses of reciprocal F1s of T. timopheevii / T. turgidum with T. turgidum showed random marker segregation. Thus, it was concluded that Ncc-tmp1A is not required for compatibility with its own cytoplasm. Southern blot analysis of the euploid NC hybrid using RFLP (restriction fragment length polymorphism) markers on the homoeologous group 1 chromosomes showed that Ncc-tmp1A locates in the centromeric region.Key words: nucleus-cytoplasm (NC) compatibility, Ncc genes, Aegilops squarrosa, Triticum timopheevii, durum wheat.
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Conn, B. J., N. Streiber, E. A. Brown, M. J. Henwood, and R. G. Olmstead. "Infrageneric phylogeny of Chloantheae (Lamiaceae) based on chloroplast ndhF and nuclear ITS sequence data." Australian Systematic Botany 22, no. 4 (2009): 243. http://dx.doi.org/10.1071/sb09011.
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The tribe Chloantheae (Prostantheroideae, Lamiaceae) currently consists of over 100 species in nine genera, all of which are endemic to Australia. Generic delimitations were assessed using chloroplast 3′ndhF and nuclear ITS nucleotide sequence data for up to seventy species. Analyses of the two datasets, independently and in combination, used maximum parsimony and Bayesian phylogenetic inference methods. Topologies derived from each marker were broadly congruent, but better resolution and stronger branch support was achieved by combining the datasets. The monophyly of the Chloantheae was confirmed. Brachysola is sister to the rest of the tribe and Chloanthes, Cyanostegia and Dicrastylis (including Mallophora) are monophyletic. Although the species within Dicrastylis were only partially resolved, it appears likely that the current sectional classification of this genus will require revision. A clade containing Newcastelia, Physopsis and Lachnostachys (=Physopsideae) was recovered, but the topology indicates that the current generic circumscriptions need further investigation. A close relationship between Hemiphora elderi, Pityrodia bartlingii and P. uncinata was resolved and reflects their palynological and carpological similarities. The relationship between remaining species of Pityrodia was incompletely resolved.
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Gama, A., A. Alves, F. Gartner, and F. Schmitt. "p63: A Novel Myoepithelial Cell Marker in Canine Mammary Tissues." Veterinary Pathology 40, no. 4 (2003): 412–20. http://dx.doi.org/10.1354/vp.40-4-412.
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Several immunohistochemical markers have been used to demonstrate the presence of myoepithelial cells in order to determine their role in the histogenesis of mammary tumors. p63, a recently characterized p53 homologue, is consistently expressed in myoepithelial cells of the human breast; however, no assessment of its immunoreactivity has been reported so far in canine mammary tissues. We investigated p63 immunohistochemical expression, as a novel myoepithelial cell nuclear marker, in 81 samples of normal ( n = 2), hyperplastic ( n = 11), and neoplastic ( n = 68) canine mammary tissues. Myoepithelial phenotype was confirmed by using complementary monoclonal antibodies: alpha-smooth muscle actin, cytokeratin 14, cytokeratin AE1/AE3, and vimentin. p63 expression was observed in 91.4% (74/81) of the samples evaluated. Normal mammary glands, mammary hyperplasias, and benign tumors showed 100% immunoreactivity, with p63 expression restricted to myoepithelial cell nuclei. In general, benign mixed tumors showed a basal cell compartment immunoreactive to p63, with a gradual decrease of its expression during myoepithelial transformation. p63 expression was found in 72% of malignant tumors, allowing myoepithelial or basal cell identification in spindle-cell carcinomas (2/2), tubulopapillary carcinomas (8/9), solid carcinomas (7/10), and carcinosarcomas (1/3). The osteosarcoma analyzed was p63 negative. In our series, stromal components were consistently nonreactive to p63. In conclusion, the present study reveals p63 as a sensitive and highly specific marker of myoepithelial cells in canine mammary tissues, and the authors suggest p63 as an additional marker for defining myoepithelial histogenesis.
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Murata, Takayuki, Fumi Goshima, Tetsuo Koshizuka, Hiroki Takakuwa, and Yukihiro Nishiyama. "A Single Amino Acid Substitution in the ICP27 Protein of Herpes Simplex Virus Type 1 Is Responsible for Its Resistance to Leptomycin B." Journal of Virology 75, no. 2 (2001): 1039–43. http://dx.doi.org/10.1128/jvi.75.2.1039-1043.2001.
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ABSTRACT Leptomycin B (LMB) is a specific inhibitor of Crm1-dependent nuclear export of proteins. The replication of herpes simplex virus (HSV) is normally highly sensitive to LMB; a resistant HSV variant, however, was isolated by serial passages of the virus. Analysis of marker transfer and viral DNA sequences revealed that a single amino acid substitution within the ICP27 gene is responsible for conferring this resistance.
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Moreth, Ute, and Olaf Schmidt. "Identification of Indoor Rot Fungi by Taxon-Specific Priming Polymerase Chain Reaction." Holzforschung 54, no. 1 (2000): 1–8. http://dx.doi.org/10.1515/hf.2000.001.
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Summary The internal transcribed spacer (ITS) of the nuclear ribosomal DNA (rDNA) of the main fungal species causing wood rot damages in European buildings was amplified by the polymerase chain reaction (PCR). After sequencing the ITS, fungus-specific oligonucleotide primers were designed for taxon-specific priming PCR. These DNA marker molecules were suitable for the differential diagnosis of the Dry rot fungus, Serpula lacrymans, the Wild merulius, S. himantioides, the Oak polypore, Donkioporia expansa, the Brown cellar fungus, Coniophora puteana, the Broad-spored white polypore, Antrodia vaillantii, the Sap polypore, Tyromyces placenta, and the Yellow-red gill polypore, Gloeophyllum sepiarium. Each specific marker identified isolates of its respective target species. Cross reaction with ‘foreign’ fungi was the exception. Species detection from rot samples in buildings was possible, since DNA from contaminating organisms does not response to the marker molecules. The diagnosis was rapid, since preceding fungal pure cultures, special DNA extraction/purification and restriction by endonucleases are not required.
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Vanstapel, F., L. Hammaker, K. Pua, and N. Blanckaert. "Properties of membrane-bound bilirubin UDP-glucuronyltransferase in rough and smooth endoplasmic reticulum and in the nuclear envelope from rat liver." Biochemical Journal 259, no. 3 (1989): 659–63. http://dx.doi.org/10.1042/bj2590659.
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We examined regulatory properties of bilirubin UDP-glucuronyltransferase in sealed RER (rough endoplasmic reticulum)- and SER (smooth endoplasmic reticulum)-enriched microsomes (microsomal fractions), as well as in nuclear envelope from rat liver. Purity of membrane fractions was verified by electron microscopy and marker studies. Intactness of RER and SER vesicles was ascertained by a high degree of latency of the lumenal marker mannose-6-phosphatase. No major differences in the stimulation of UDP-glucuronyltransferase by detergent or by the presumed physiological activator, UDPGlcNAc, were observed between total microsomes and RER- or SER-enriched microsomes. Isolated nuclear envelopes were present as a partially disrupted membrane system, with approx. 50% loss of mannose-6-phosphatase latency. The nuclear transferase had lost its latency to a similar extent, and the enzyme failed to respond to UDPGlcNAc. Our results underscore the necessity to include data on the integrity of the membrane permeability barrier when reporting regulatory properties of UDP-glucuronyltransferase in different membrane preparations.
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Schanzer, Ivan A., Alina V. Fedorova, Olga V. Shelepova, and Guzyaliya F. Suleymanova. "Molecular Phylogeny and Phylogeography of Potentilla multifida L. agg. (Rosaceae) in Northern Eurasia with Special Focus on Two Rare and Critically Endangered Endemic Species, P. volgarica and P. eversmanniana." Plants 9, no. 12 (2020): 1798. http://dx.doi.org/10.3390/plants9121798.
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The results of a molecular genetic study of Potentilla multifida agg. using two plastid markers (ndhC-trnV and psbA-trnH) and a nuclear ITS marker suggested that this group comprises a number of relatively young and incompletely differentiated species widely distributed in Northern Eurasia. The sequences were analyzed using tree-based (maximum likelihood) and network-based (statistical parsimony network) approaches. The plastid data suggested incomplete lineage sorting, characteristic of the group as a whole. The nuclear ITS results demonstrated quite a different pattern, with mostly conspecific accessions shaping monophyletic clades. The majority of the Potentilla sect. Multifidae species studied possess few, usually closely related plastid haplotypes, or are even monomorphic. In contrast, P. volgarica, a narrow endemic from the Volga River valley, presents plastid haplotypes belonging to two distantly related groups. Such a pattern of genetic diversity in P. volgarica may be explained by a long persistence of the species within an extremely small distribution range, on the right bank of the Volga River, most likely representing a contemporary refugium. The genealogy of plastid markers in P. volgarica suggests that this species is ancestral to P.eversmanniana, another narrow endemic from the S Urals.
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Ikhena, Deborah E., Shimeng Liu, Stacy Kujawa, et al. "RANKL/RANK Pathway and Its Inhibitor RANK-Fc in Uterine Leiomyoma Growth." Journal of Clinical Endocrinology & Metabolism 103, no. 5 (2018): 1842–49. http://dx.doi.org/10.1210/jc.2017-01585.
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Abstract Context Uterine leiomyomas are the most common type of gynecologic tumor in women. Objective To determine the role of the cytokine receptor activator of nuclear factor κ-Β ligand (RANKL); its receptor, receptor activator of nuclear factor κ-Β (RANK); and the RANKL/RANK pathway inhibitor RANK-Fc in leiomyoma growth. Design Messenger RNA (mRNA) or protein levels of RANKL, RANK, and proliferation markers cyclin D1 and Ki67 were assessed in various leiomyoma tissues and cell populations. Human xenograft experiments were performed to determine the effects of RANK-Fc on leiomyoma growth in vivo. Setting Research laboratory. Patients Twenty-four regularly cycling premenopausal women (age 28 to 49 years) who were not receiving hormone therapy. Interventions None. Main Outcome Measure Tumor growth in a murine xenograft model following targeting of the RANKL/RANK pathway with RANK-Fc. Results RANKL mRNA levels in leiomyoma were significantly higher than those in myometrial tissues. The highest RANK levels were found in the leiomyoma stem cell population, which is deficient in progesterone receptor (PR). Conversely, the highest RANKL levels were found in the PR-rich leiomyoma intermediate cell (LIC) population. R5020, a PR agonist, specifically increased RANKL expression in LICs. RANK-Fc blocked RANKL-induced expression of the proliferative gene cyclin D1. Treatment with RANK-Fc also significantly decreased tumor growth in vivo and diminished the expression of proliferation marker Ki67 in tumors (P < 0.01; n = 4). Conclusions Treatment with the RANKL/RANK pathway inhibitor RANK-Fc significantly decreased human leiomyoma cell proliferation and tumor growth. This suggests that the RANKL/RANK pathway could serve as a potential target for the prevention and treatment of uterine leiomyoma.
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Şen, Sinan, Christopher J. Lux, and Ralf Erber. "A Potential Role of Semaphorin 3A during Orthodontic Tooth Movement." International Journal of Molecular Sciences 22, no. 15 (2021): 8297. http://dx.doi.org/10.3390/ijms22158297.
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Background: Induced tooth movement during orthodontic therapy requires mechano-induced bone remodeling. Besides various cytokines and growth-factors, neuronal guidance molecules gained attention for their roles in bone homeostasis and thus, potential roles during tooth movement. Several neuronal guidance molecules have been implicated in the regulation of bone remodeling. Amongst them, Semaphorin 3A is particular interesting as it concurrently induces osteoblast differentiation and disturbs osteoclast differentiation. Methods: Mechano-regulation of Sema3A and its receptors PlexinA1 and Neuropilin (RT-qPCR, WB) was evaluated by applying compressive and tension forces to primary human periodontal fibroblasts (hPDLF) and alveolar bone osteoblasts (hOB). The association of the transcription factor Osterix (SP7) and SEMA3A was studied by RT-qPCR. Mechanisms involved in SEMA3A-mediated osteoblast differentiation were assessed by Rac1GTPase pull-downs, β-catenin expression analyses (RT-qPCR) and nuclear translocation assays (IF). Osteogenic markers were analyzed by RT-qPCR. Results: SEMA3A, PLXNA1 and NRP1 were differentially regulated by tension or compressive forces in hPDLF. Osterix (SP7) displayed the same pattern of regulation. Recombinant Sema3A induced the activation of Rac1GTPase, the nuclear translocation of β-catenin and the expression of osteogenic marker genes. Conclusion: Sema3A, its receptors and Osterix are regulated by mechanical forces in hPDLF. SEMA3A upregulation was associated with Osterix (SP7) modulation. Sema3A-enhanced osteogenic marker gene expression in hOB might be dependent on a pathway involving Rac1GTPase and β-catenin. Thus, Semaphorin 3A might contribute to bone remodeling during induced tooth movement.
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Boerkamp, Kim, Gerard Rutteman, Marja Kik, Jolle Kirpensteijn, Christoph Schulze, and Guy Grinwis. "Nuclear DNA-Content in Mesenchymal Lesions in Dogs: Its Value as Marker of Malignancy and Extent of Genomic Instability." Cancers 4, no. 4 (2012): 1300–1317. http://dx.doi.org/10.3390/cancers4041300.
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Turner, Kara J., Eleanor M. Watson, Benjamin M. Skinner, and Darren K. Griffin. "Telomere Distribution in Human Sperm Heads and Its Relation to Sperm Nuclear Morphology: A New Marker for Male Factor Infertility?" International Journal of Molecular Sciences 22, no. 14 (2021): 7599. http://dx.doi.org/10.3390/ijms22147599.
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Infertility is a problem affecting an increasing number of couples worldwide. Currently, marker tests for male factor infertility are complex, highly technical and relatively subjective. Up to 40% of cases of male factor infertility are currently diagnosed as idiopathic therefore, there is a clear need for further research into better ways of diagnosing it. Changes in sperm telomere length have been associated with infertility and closely linked to DNA damage and fragmentation, which are also known to be related to infertility. However, telomere distribution is a parameter thus far underexplored as an infertility marker. Here, we assessed morphological parameters of sperm nuclei in fertile control and male factor infertile cohorts. In addition, we used 2D and 3D fluorescence in situ hybridization (FISH) to compare telomere distribution between these two groups. Our findings indicate that the infertile cohort sperm nuclei were, on average, 2.9% larger in area and showed subtle differences in sperm head height and width. Telomeres were mainly distributed towards the periphery of the nuclei in the control cohort, with diminishing telomere signals towards the center of the nuclei. Sperm nuclei of infertile males, however, had more telomere signals towards the center of the nuclei, a finding supported by 3D imaging. We conclude that, with further development, both morphology and telomere distribution may prove useful investigative tools in the fertility clinic.
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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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Kim, Hye Ran, Eun-Jeong Won, Hyun-Jung Choi, et al. "Mitochondrial DNA Minisatellites Showed Higher Informativeness and Sensitivity Than the Nuclear DNA Markers for the Quantitative Determination of Chimerism After Allogeneic Stem Cell Transplantation,." Blood 118, no. 21 (2011): 4004. http://dx.doi.org/10.1182/blood.v118.21.4004.4004.
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Abstract Abstract 4004 Background: Mitochondrial DNA (mtDNA) is widely used in forensic identification and anthropologic studies on account of its abundance resulting in preferential amplification, sequencing and inherent variability. We developed mtDNA markers to monitor donor cell engraftment after allogeneic stem cell transplantation(SCT), then compared with nuclear short tandem repeat (STR) markers. Patients and methods: The mtDNA control regions and six mtDNA minisatellites (mtMS) (303 poly C, 16184 poly C, 514 (CA) repeat, 3566 poly C, 12385 poly C and 12418 poly A) from the total DNA samples of 215 cases (donor, recipient and after allogeneic SCT) were amplified using the designated specific primers and PCR. The results were compared with those from the six short tandem repeat (STR) markers (D12S391, D18S51, F13A1, HUM RENA-4, HUM FABP2 and Amelogenin). Results: Polymorphisms in the mtDNA control region identify an informative marker in 88% (189 cases) of all cases. Among the six mtMS markers, the informativeness of 303 poly C and 16184 poly C mtMS was 63% and 67% respectively. A combination of direct sequencing through the mtDNA control region, 303poly C and 16184 poly C mtMS could completely distinguish the donor cells from the recipient cells. The results from a typical mixing experiment to determine the sensitivity revealed a detection limit (DL) of the gene scan analysis in a mtDNA mixture to be visible at 1% heteroplasmy in 303 poly C mtMS marker. However, the DL from D12S391 in the same mixing experiment was 5–10% heteroplasmy. Conclusions: mtMS markers, especially 303 poly C and 16184 poly C markers, can provide a sensitive, accurate and quantitative determination of mixed chimerism after a SCT. Disclosures: No relevant conflicts of interest to declare.
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Bongiovanni, Laura, Francesca Caposano, Mariarita Romanucci, et al. "Survivin and Sox9: Potential Stem Cell Markers in Canine Normal, Hyperplastic, and Neoplastic Canine Prostate." Veterinary Pathology 56, no. 2 (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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Zhou, Hai-Jun, Archie Tamayo, Lan Pham, Yen-Chiu Lin-Lee, and Richard J. Ford. "From Signalosome to Enhanceosome: The Translocation of CD40 from Membrane to Nucleus Involves Multiple Mechanisms." Blood 112, no. 11 (2008): 3781. http://dx.doi.org/10.1182/blood.v112.11.3781.3781.
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Abstract CD40 plays important roles in the proliferation, survival and differentiation of lymphocytes. Constitutively active CD40 recruits TRAFs and IKKs within the lipid rafts to form a signalosome that mediates pivotal downstream proliferation and survival mechanisms involving NF-kB. Recently, we have reported that nuclear localization of CD40, through its interaction with c-Rel, promotes growth, cell cycle progression and survival in large B cell lymphoma. Our studies have opened a new paradigm in the functional role of CD40 in non-Hodgkin lymphomas of B cell origin (NHL-B). However, the mechanism about how CD40 enters nuclear still remains elusive. In this study, we show that CD40 ligation enhances its nuclear accumulation with activation of c-Rel in both normal B-lymphocytes and B cell lymphoma cells with cell fractionation assay and con-focal microscopy. Over-expression of c-Rel in B cell lymphoma cells drives CD40 into cell nucleus. We hypothesize that the route CD40 enters nucleus may involve endosome-endoplasmic reticulum-nuclear pore complex. Indeed, further studies show CD40 co-localizes with endosome marker-EEA1 and endoplasmic reticulum marker-Sec61. Furthermore, our co-immunoprecipitation assay has demonstrated CD40 interacts with Sec61. CD40 also co-localizes and immuno-precipitates with nuclear pore complex (NPC) proteins-NUP62 in normal B-lymphocytes and B lymphoma cells, which suggests NPC proteins may facilitate the nuclear translocation of CD40 protein. Overall, our study suggests that translocation of CD40 into cell nucleus involves multiple pathways. Blocking nuclear localization may modulate the function of CD40 in lymphoma cells; which could provide a new-targeted therapeutic approach for lymphoma therapy.
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Wanka, Giulia, Elisa Schmoeckel, Doris Mayr, et al. "LDOC1 as Negative Prognostic Marker for Vulvar Cancer Patients." International Journal of Molecular Sciences 21, no. 23 (2020): 9287. http://dx.doi.org/10.3390/ijms21239287.
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So far, studies about targeted therapies and predictive biomarkers for vulva carcinomas are rare. The leucine zipper downregulated in cancer 1 gene (LDOC1) has been identified in various carcinomas as a tumor-relevant protein influencing patients’ survival and prognosis. Due to the lack of information about LDOC1 and its exact functionality, this study focuses on the expression of LDOC1 in vulvar carcinoma cells and its surrounding immune cells as well as its correlation to clinicopathological characteristics and prognosis. Additionally, a possible regulation of LDOC1 in vulvar cancer cell lines via the NF-κB signaling pathway was analyzed. Vulvar carcinoma sections of 157 patients were immunohistochemically stained and examined regarding LDOC1 expression by using the immunoreactive score (IRS). To characterize LDOC1-positively stained immune cell subpopulations, immunofluorescence double staining was performed. The effect of the NF-κB inhibitor C-DIM 12 (3,3′-[(4-chlorophenyl)methylene]bis[1 H-indole]) on vulvar cancer cell lines A431 and SW 954 was measured according to MTT and BrdU assays. Baseline expression levels of LDOC1 in the vulvar cancer cell lines A431 and SW 954 was analyzed by real-time PCR. LDOC1 was expressed by about 90% of the cancer cells in the cytoplasm and about half of the cells in the nucleus. Cytoplasmatic expression of LDOC1 was associated with decreased ten-year overall survival of the patient, whereas nuclear staining showed a negative association with disease-free survival. Infiltrating immune cells were mainly macrophages followed by regulatory T cells. Incubation with C-DIM 12 decreased the cell viability and proliferation of vulvar cancer cell line A431, but not of cell line SW 954. LDOC1 expression on mRNA level was twice as high in the cell line A431 compared to the cell line SW 954. Overexpression of LDOC1 was associated with unfavorable overall and disease-free survival. Tumor growth could be inhibited by C-DIM 12 in vitro if the expressed LDOC1 level was high enough.
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Arafah, Maria A., Abderrahman Ouban, Omar Z. Ameer, and Ko Jin Quek. "KI-67 LI Expression in Triple-Negative Breast Cancer Patients and Its Significance." Breast Cancer: Basic and Clinical Research 15 (January 2021): 117822342110169. http://dx.doi.org/10.1177/11782234211016977.
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Purpose: Triple-negative breast cancer (TNBC) is a subset of breast cancer which is known to carry a poor prognosis because of lack of targets for hormonal therapy. Research efforts have focused in recent years on discovering biomarkers of management in TNBCs. KI-67 Labelling Index (LI) is a nuclear protein which has proven to play diagnostic and prognostic roles in many cancers. Materials and methods: We analysed the expression of KI-67 LI by immunohistochemistry in TNBC cases from the University hospital. This expression was cross-checked against clinical-pathological criteria of TNBC patients and against Vimentin expression in TNBC patients with significant KI-67 expression. Results: KI-67 LI was significantly expressed in the majority of TNBC cases. This expression was significantly correlated with lymph node metastases, tumour invasion, high tumour nuclear grade, clinical stage, adverse survival outcome, and failure to achieve pathological complete response. TNBCs’ KI-67 LI expression was also correlated with Vimentin expression, the mesenchymal chief marker of the EMT phenomenon. Conclusion: Collectively, our study presents a strong argument for the use of KI-67 LI as a biomarker of aggressive, metastatic TNBC disease with poor outcome. This study, along with mounting evidence in the scientific literature, presents a case for the use of this nuclear protein in diagnosis, prognosis, and follow-up of patients with this difficult diagnosis.
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Solokhina, M. P., N. S. Sergeeva, N. V. Marshutina, et al. "KIM-1 as a potential serological/urinological tumor-associated marker of renal cell carcinoma and chemotherapy nephrotoxicity." Cancer Urology 15, no. 3 (2019): 132–42. http://dx.doi.org/10.17650/1726-9776-2019-15-3-132-142.
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The last decades are characterized by an active search for highly sensitive and specific urinological and serological tumor-associated markers of renal cell carcinoma. This review analyses the results of studies of traditional serological tumor-associated markers and a potential new tumor-associated marker of renal cell carcinoma: kidney injury molecule-1, or KIM-1. The structure, sources and functions of KIM-1 in normal conditions and in damaged renal tubules, its potential role in carcinogenesis are described. The experience of using KIM-1 for specifying diagnosis of the most common histological types of renal cell carcinoma is analyzed. Data on KIM-1 expression in malignant tumors in other locations and non-oncological kidney disorders are presented. The role of KIM-1 in early diagnosis of nephrotoxic effect of antitumor drugs is described. The accumulated data is promising in regards to using KIM-1 in clinical oncology as a urinological and serological marker of renal cell carcinoma and chemotherapy nephrotoxicity.