Journal articles on the topic 'Synthetic markers'
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Lozano-Ramírez, Nerida, Susanne Dreisigacker, Carolina P. Sansaloni, Xinyao He, Sergio Sandoval Islas, Paulino Pérez-Rodríguez, Aquiles Carballo Carballo, Cristian Nava-Díaz, Masahiro Kishii, and Pawan K. Singh. "Genome-Wide Association Study for Resistance to Tan Spot in Synthetic Hexaploid Wheat." Plants 11, no. 3 (February 5, 2022): 433. http://dx.doi.org/10.3390/plants11030433.
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Synthetic hexaploid wheat (SHW) has shown effective resistance to a diversity of diseases and insects, including tan spot, which is caused by Pyrenophora tritici-repentis, being an important foliar disease that can attack all types of wheat and several grasses. In this study, 443 SHW plants were evaluated for their resistance to tan spot under controlled environmental conditions. Additionally, a genome-wide association study was conducted by genotyping all entries with the DArTSeq technology to identify marker-trait associations for tan spot resistance. Of the 443 SHW plants, 233 showed resistant and 183 moderately resistant reactions, and only 27 were moderately susceptible or susceptible to tan spot. Durum wheat (DW) parents of the SHW showed moderately susceptible to susceptible reactions. A total of 30 significant marker-trait associations were found on chromosomes 1B (4 markers), 1D (1 marker), 2A (1 marker), 2D (2 markers), 3A (4 markers), 3D (3 markers), 4B (1 marker), 5A (4 markers), 6A (6 markers), 6B (1 marker) and 7D (3 markers). Increased resistance in the SHW in comparison to the DW parents, along with the significant association of resistance with the A and B genome, supported the concept of activating epistasis interaction across the three wheat genomes. Candidate genes coding for F-box and cytochrome P450 proteins that play significant roles in biotic stress resistance were identified for the significant markers. The identified resistant SHW lines can be deployed in wheat breeding for tan spot resistance.
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Sorrells, Mark E., J. Perry Gustafson, Daryl Somers, Shiaoman Chao, David Benscher, Gina Guedira-Brown, Eric Huttner, et al. "Reconstruction of the Synthetic W7984 × Opata M85 wheat reference population." Genome 54, no. 11 (November 2011): 875–82. http://dx.doi.org/10.1139/g11-054.
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Reference populations are valuable resources in genetics studies for determining marker order, marker selection, trait mapping, construction of large-insert libraries, cross-referencing marker platforms, and genome sequencing. Reference populations can be propagated indefinitely, they are polymorphic and have normal segregation. Described are two new reference populations who share the same parents of the original wheat reference population Synthetic W7984 (Altar84/ Aegilops tauschii (219) CIGM86.940) × Opata M85, an F1-derived doubled haploid population (SynOpDH) of 215 inbred lines and a recombinant inbred population (SynOpRIL) of 2039 F6 lines derived by single-plant self-pollinations. A linkage map was constructed for the SynOpDH population using 1446 markers. In addition, a core set of 42 SSR markers was genotyped on SynOpRIL. A new approach to identifying a core set of markers used a step-wise selection protocol based on polymorphism, uniform chromosome distribution, and reliability to create nested sets starting with one marker per chromosome, followed by two, four, and six. It is suggested that researchers use these markers as anchors for all future mapping projects to facilitate cross-referencing markers and chromosome locations. To enhance this public resource, researchers are strongly urged to validate line identities and deposit their data in GrainGenes so that others can benefit from the accumulated information.
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Zhao, Hao‐Qian, Wen‐Qing Wei, Chao Zhao, and Ze‐Xiong Xie. "Genomic markers on synthetic genomes." Engineering in Life Sciences 21, no. 12 (November 10, 2021): 825–31. http://dx.doi.org/10.1002/elsc.202100030.
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Chimsook, Thitiphan. "Synthesis and Properties of Barakol Tailored for Fluorescent Biodiesel Marker." Applied Mechanics and Materials 490-491 (January 2014): 168–71. http://dx.doi.org/10.4028/www.scientific.net/amm.490-491.168.
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This work reports the synthesis and evaluation of barakol tailored to become biodiesel fluorescent markers. Fluorescent markers for biodiesel fuels were synthesized from the reaction between barakol, which was obtained from the leaves and flowers ofCassia siameLamk., with acid chloride in the presence of triethylamine. These synthetic fluorescent markers were 7-lauroyloxy-5-acetonyl-2-methylchromone, 7-butyryloxy-5-acetonyl-2-methylchromone and 7-(2-ethyl)-hexanoyloxy-5-acetonyl-2-methylchromone. These synthetic fluorescent markers were invisible color in biodiesel fuels when they were added into biodiesel and quantitative measurement was carried out using spectrofluorometer. All compounds gave fluorescence at 612 nm when they were excited at 464 nm. The testing results of fuel properties using the ASTM test methods revealed that the physical properties of the marked biodiesel fuels were similar to those of the unmarked biodiesel fuels. Moreover, those synthetic fluorescent markers were found to be stable in diesel fuels for at least three months at a concentration of 4 ppm.
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Farrakh, Sumaira, Sumbul Khalid, Ayesha Rafique, Naveeda Riaz, and Abdul Mujeeb-Kazi. "Identification of stripe rust resistant genes in resistant synthetic hexaploid wheat accessions using linked markers." Plant Genetic Resources 14, no. 3 (August 14, 2015): 219–25. http://dx.doi.org/10.1017/s1479262115000283.
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Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases affecting wheat. In this study, seven gene-linked markers were used to identify the presence of stripe rust resistant genes in 51 accessions of synthetic hexaploid of wheat which were found to be resistant at seedling plant stage. Molecular marker-based gene identification showed the presence of Yr5, Yr10 and Yr15 in three accessions, Yr36 in three accessions, Yr48 in seven accessions, YrR61 in four accessions, and YrTP1 in ten accessions of resistant hexaploid of wheat. These gene-linked markers were also used for the detection of genetic diversity. A total of 68 alleles were detected by these seven gene-linked markers. The mean number of allele was 11.3 alleles per locus. Genetic diversity values ranged from 0.34 to 0.93, with highest genetic diversity value of 0.93 detected for marker Xwm477. The lowest genetic diversity value was observed for marker Xbarc167. The polymorphic information content value ranged from 0.33 to 0.92 with an average of 0.54. The highest number of alleles (n= 24) were detected for marker Xwmc477. The evidence in this study on the basis of genetic diversity and presence of Yr genes in synthetic hexaploid wheat accessions will be useful in further breeding programmes.
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Kyle, Patrick B., and Jaswinder Kaur. "Evaluating Novel Markers for Specimen Validity Testing." Archives of Pathology & Laboratory Medicine 144, no. 2 (November 22, 2019): 168–71. http://dx.doi.org/10.5858/arpa.2019-0197-oa.
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Context.— Synthetic urine products are commercially marketed for the purpose of specimen substitution for urine drug screens. These products are widely popular because they yield negative drug screen results, meet criteria for specimen validity testing, and are easily accessible and affordable. Current specimen validity criteria are ineffective for detecting these synthetic products, and new markers of specimen validity are required. Objective.— To develop and evaluate a multicomponent liquid chromatography tandem mass spectrometry (LC-MS/MS) assay for urine specimen validity testing. Design.— A quantitative LC-MS/MS assay was developed for caffeine, cotinine, theobromine, and urobilin in urine. The assay was applied to known synthetic urine products (n = 10) as well as human specimens received for pre-employment testing (n = 500), for-cause workplace testing (n = 100), and medical pain management monitoring (n = 200). Specimens devoid of all 4 validity markers were subjected to follow-up testing that involved microscopic urinalysis and comprehensive gas chromatography mass spectrometry for drugs, pharmaceuticals, hormones, and lipids. Results.— Of the experimental groups, 10 of 10 synthetic urine products (100%), 12 of 500 pre-employment specimens (2.4%), and 4 of 200 pain management specimens (2.0%) failed the experimental LC-MS/MS assay. Follow-up testing indicated that each of the failed specimens was nonphysiologic in nature. Conclusions.— Simultaneous application of the 4 experimental validity markers appeared to be a robust method for detecting nonphysiologic specimens. New markers of specimen validity must be developed in order to identify commercially available synthetic urine products.
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Desai, Sonal, and Pratima Tatke. "Phytochemical Markers: Classification, Applications and Isolation." Current Pharmaceutical Design 25, no. 22 (September 27, 2019): 2491–98. http://dx.doi.org/10.2174/1381612825666190709203239.
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Background: There has been aroused demand for herbal drugs/products worldwide because of their fewer side effects as compared to synthetic drugs. The major obstacle in the global acceptance of herbal products is the lack of proper standardization technique. Methods: Various test procedures have been used for authentication and quality control of botanicals among which marker based standardization has attained more attention. The major challenge faced by phytochemist is to select appropriate phytochemical marker for quality control of herbal drugs. Phytochemical markers used for standardization must be of known purity. Phytochemical markers which are not commercially available have to be isolated from respective medicinal plants. Various chromatographic techniques are reported for the purification of phytomarkers from plants. A comprehensive report on different purification techniques of isolation of phytochemical markers through in-depth review of scientific literature is required. Conclusion: This article highlights various classifications of phytochemical markers along with their applications in standardization of herbal drugs and various classical and modern analytical techniques for their isolation.
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Gálico, Diogo A., Jeffrey S. Ovens, and Muralee Murugesu. "NIR-to-NIR emission on a water-soluble {Er6} and {Er3Yb3} nanosized molecular wheel." Nanoscale 12, no. 21 (2020): 11435–39. http://dx.doi.org/10.1039/d0nr02236e.
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Lanthanide molecular clusters as near-infrared markers are highly tunable owing to the bottom-up synthetic approach. Facile synthesis, high crystallinity, water stability are all highly desirable attributes of clusters for biological and telecommunications technology.
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Čejka, Jan, Fabio Bruno, Dimitrios Skarlatos, and Fotis Liarokapis. "Detecting Square Markers in Underwater Environments." Remote Sensing 11, no. 4 (February 23, 2019): 459. http://dx.doi.org/10.3390/rs11040459.
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Augmented reality can be deployed in various application domains, such as enhancing human vision, manufacturing, medicine, military, entertainment, and archeology. One of the least explored areas is the underwater environment. The main benefit of augmented reality in these environments is that it can help divers navigate to points of interest or present interesting information about archaeological and touristic sites (e.g., ruins of buildings, shipwrecks). However, the harsh sea environment affects computer vision algorithms and complicates the detection of objects, which is essential for augmented reality. This paper presents a new algorithm for the detection of fiducial markers that is tailored to underwater environments. It also proposes a method that generates synthetic images with such markers in these environments. This new detector is compared with existing solutions using synthetic images and images taken in the real world, showing that it performs better than other detectors: it finds more markers than faster algorithms and runs faster than robust algorithms that detect the same amount of markers.
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Micklem, Kingsley J. "Novel leukaemia markers." Bioscience Reports 15, no. 6 (December 1, 1995): 463–68. http://dx.doi.org/10.1007/bf01204349.
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Using synthetic peptide or recombinant protein as immunising antigens we have produced monoclonal antibodies and polyclonal antisera directed against targets of particular interest in leukaemia diagnosis. In this way we have prepared reagents which recognise all T or all B lymphocytes in routinely fixed paraffin sections which are unique in this respect. We have also produced monoclonal antibodies to molecules potentially involved in specific neoplastic transformations, implicated by virtue of the involvement of their genes in chromosomal defects in these neoplasms. In particular, we have produced antibodies recognising bcl-2, involved in follicular lymphoma, tal-1, involved in T-cell acute leukaemias and HRX involved in a variety of hematologic disorders. The application of these reagents to diagnosis has so far proved useful. In addition their use outside the field of leukaemia diagnosis has proved to be even more important in some cases.
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Lee, Jeong Hee, Seok Tae Choi, and Young Jin Kang. "Kahweol, a Diterpenoid Molecule, Inhibits CTGF-Dependent Synthetic Phenotype Switching and Migration in Vascular Smooth Muscle Cells." Molecules 26, no. 3 (January 26, 2021): 640. http://dx.doi.org/10.3390/molecules26030640.
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Vascular smooth muscle cell (VSMC) phenotype switching from contractile to synthetic is essential for proliferation and migration in vascular pathophysiology. Connective tissue growth factor (CTGF) is a matricellular protein involved in cell adhesion, migration, and proliferation. Kahweol, a diterpene molecule in arabica coffee beans, has been reported to have anti-inflammatory, antiproliferative, and apoptotic effects in many cells. However, in VSMCs, the effects of kahweol on CTGF activities have not been investigated. Thus, in this study, the effects and associated mechanisms of kahweol in CTGF-dependent phenotype switching and migration in VSMCs were examined. Experiments were performed on primary rat aortic smooth muscle cells and a rat VSMC line, A7r5. Western blot analysis was used to determine the protein levels. The mRNA levels of synthetic markers were measured by qRT-PCR. Migration of VSMCs was evaluated by wound healing and transwell assays. Kahweol reduced the angiotensin II (Ang II)-induced CTGF expression. Further, kahweol inhibited expressions of synthetic phenotype markers of VSMC. The kahweol-reduced synthetic marker protein levels were reversed by the administration of rCTGF. However, expressions of contractile phenotype markers of VSMC were not affected. Kahweol suppressed Ang II-stimulated VSMC migration. Moreover, kahweol downregulated Ang II-induced p-FAK, p-Erk, and Yes-associated protein (YAP) protein expressions. Taken together, in Ang II-stimulated VSMCs, kahweol inhibited CTGF-dependent synthetic phenotype switching and migration, with focal adhesion kinase (FAK), Erk, and YAP involved in the underlying mechanisms of the kahweol effects. These results suggest that kahweol has a potential as a therapeutic agent to inhibit CTGF, which is a molecular target in sclerogenic vascular disease.
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Kim, Gyu-Tae, Ulrike Waizmann, and Siegmar Roth. "Simple efficient coordinate markers for investigating synthetic nanofibers." Applied Physics Letters 79, no. 21 (November 19, 2001): 3497–99. http://dx.doi.org/10.1063/1.1419054.
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Kent, Jack W. "Rare variants, common markers: synthetic association and beyond." Genetic Epidemiology 35, S1 (2011): S80—S84. http://dx.doi.org/10.1002/gepi.20655.
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Lin, Chin-Sheng, Po-Shiuan Hsieh, Ling-Ling Hwang, Yen-Hsien Lee, Shih-Hung Tsai, Yun-Chin Tu, Yao-Wen Hung, et al. "The CCL5/CCR5 Axis Promotes Vascular Smooth Muscle Cell Proliferation and Atherogenic Phenotype Switching." Cellular Physiology and Biochemistry 47, no. 2 (2018): 707–20. http://dx.doi.org/10.1159/000490024.
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Background/Aims: Hyperlipidemia induces dysfunction in the smooth muscle cells (SMCs) of the blood vessels, and the vascular remodeling that ensues is a key proatherogenic factor contributing to cardiovascular events. Chemokines and chemokine receptors play crucial roles in vascular remodeling. Here, we examined whether the hyperlipidemia-derived chemokine CCL5 and its receptor CCR5 influence vascular SMC proliferation, phenotypic switching, and explored the underlying mechanisms. Methods: Thoracoabdominal aorta were isolated from wild-type, CCL5 and CCR5 double-knockout mice (CCL5–/–CCR5–/–) fed a high-fat diet (HFD) for 12 weeks. Expression of the contractile, synthetic, and proliferation markers were assayed using immunohistochemical and western blotting. The effects of CCL5 and palmitic acid on cultured SMC proliferation and phenotypic modulation were evaluated using flow cytometry, bromodeoxyuridine (BrdU), and western blotting. Results: Wild-type mice fed an HFD showed markedly increased total cholesterol, triglyceride, and CCL5 serum levels, as well as significantly increased CCL5 and CCR5 expression in the thoracoabdominal aorta vs. normal-diet-fed controls. HFD-fed CCL5-/-CCR5-/- mice showed significantly decreased expression of the synthetic phenotype marker osteopontin and the proliferation marker proliferating cell nuclear antigen, and increased expression of the contractile phenotype marker smooth muscle α-actin in the thoracoabdominal aorta vs. wild-type HFD-fed mice. Human aorta-derived SMCs stimulated with palmitic acid showed significantly increased expression of CCL5, CCR5, and synthetic phenotype markers, as well as increased proliferation. CCL5-treated SMCs showed increased cell cycle regulatory protein expression, paralleling increased synthetic and decreased contractile phenotype marker expression. Inhibition of CCR5 activity by the specific antagonist maraviroc or its expression using small interfering RNA significantly inhibited human aortic SMC proliferation and synthetic phenotype formation. Therefore, CCL5 induces SMC proliferation and phenotypic switching from a contractile to synthetic phenotype via CCR5. CCL5-mediated SMC stimulation activated ERK1/2, Akt/p70S6K, p38 MAPK, and NF-κB signaling. NF-κB inhibition significantly reduced CCR5 expression along with CCR5-induced SMC proliferation and synthetic phenotype formation. Conclusions: Hyperlipidemia-induced CCL5/CCR5 axis activation serves as a pivotal mediator of vascular remodeling, indicating that CCL5 and CCR5 are key chemokine-related factors in atherogenesis. SMC proliferation and synthetic phenotype transformation attenuation by CCR5 pharmacological inhibition may offer a new approach to treatment or prevention of atherosclerotic diseases associated with hyperlipidemia.
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Melnikova, Nataliya V., Fedor A. Konovalov, and Alexander M. Kudryavtsev. "Long terminal repeat retrotransposon Jeli provides multiple genetic markers for common wheat (Triticum aestivum)." Plant Genetic Resources 9, no. 2 (March 25, 2011): 163–65. http://dx.doi.org/10.1017/s1479262111000487.
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The recombinant inbred line mapping population Opata85 × Synthetic W7984 was used to map Jeli long terminal repeat retrotransposon insertion sites in the hexaploid wheat genome. Sequence-specific amplified polymorphism technique was applied to reveal Jeli insertions. Jeli was found to provide multiple genetic markers for common wheat. Our marker system revealed A-genome Jeli insertions, and therefore can be used for targeted analysis of the A genome.
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Zhang, Ruiqi, Ravi P. Singh, Morten Lillemo, Xinyao He, Mandeep S. Randhawa, Julio Huerta-Espino, Pawan K. Singh, Zhikang Li, and Caixia Lan. "Two Main Stripe Rust Resistance Genes Identified in Synthetic-Derived Wheat Line Soru#1." Phytopathology® 109, no. 1 (January 2019): 120–26. http://dx.doi.org/10.1094/phyto-04-18-0141-r.
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Stripe rust is a major disease constraint of wheat production worldwide. Resistance to stripe rust was analyzed using 131 F6 recombinant inbred lines (RILs) derived from a cross between synthetic derived wheat line Soru#1 and wheat cultivar Naxos. The phenotype was evaluated in Mexico and Norway at both seedling and adult plant stages. Linkage groups were constructed based on 90K single-nucleotide polymorphism (SNP), sequence-tagged site, and simple sequence repeat markers. Two major resistance loci conferred by Soru#1 were detected and located on chromosomes 1BL and 4DS. The 1BL quantitative trait loci explained 15.8 to 40.2 and 51.1% of the phenotypic variation at adult plant and seedling stages, respectively. This locus was identified as Yr24/Yr26 based on the flanking markers and infection types. Locus 4DS was flanked by molecular markers D_GB5Y7FA02JMPQ0_238 and BS00108770_51. It explained 8.4 to 27.8 and 5.5% of stripe rust variation at the adult plant and seedling stages, respectively. The 4DS locus may correspond to known resistance gene Yr28 based on the resistance source. All RILs that combine Yr24/Yr26 and Yr28 showed significantly reduced stripe rust severity in all four environments compared with the lines with only one of the genes. SNP marker BS00108770_51 was converted into a breeder-friendly kompetitive allele-specific polymerase chain reaction marker that will be useful to accelerate Yr28 deployment in wheat breeding programs.
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Ondrašovič, Milan, and Peter Tarábek. "Homography Ranking Based on Multiple Groups of Point Correspondences." Sensors 21, no. 17 (August 26, 2021): 5752. http://dx.doi.org/10.3390/s21175752.
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Homography mapping is often exploited to remove perspective distortion in images and can be estimated using point correspondences of a known object (marker). We focus on scenarios with multiple markers placed on the same plane if their relative positions in the world are unknown, causing an indeterminate point correspondence. Existing approaches may only estimate an isolated homography for each marker and cannot determine which homography achieves the best reprojection over the entire image. We thus propose a method to rank isolated homographies obtained from multiple distinct markers to select the best homography. This method extends existing approaches in the post-processing stage, provided that the point correspondences are available and that the markers differ only by similarity transformation after rectification. We demonstrate the robustness of our method using a synthetic dataset and show an approximately 60% relative improvement over the random selection strategy based on the homography estimation from the OpenCV library.
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Ignjatovic-Micic, Dragana, Ksenija Markovic, and Vesna Lazic-Jancic. "Application of molecular markers in bulk segragant analysis of yield in maize (Zea mays L) synthetic populations." Genetika 38, no. 1 (2006): 59–66. http://dx.doi.org/10.2298/gensr0601059i.
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Chromosome regions which carry potential QTLs for high grain yield in two synthetic maize populations - B73xMol7 and LlxMol7, were identified by bulk segregant analysis (BSA). Yield was evaluated on F2 testcross families in field trials using a Nested design. Based on yield data, p3 families with the corresponding highest and lowest testcross yields were selected for BSA. Genome analysis of F3 families was carried out with 58 RFLP markers. Allele frequency differences were detected at four RFLP loci n chromosomes 1, 2, 6 and 10 (B73xMol7), i.e. four RFLP loci on chromosomes 1, 2, 6 and 9 (LlxMo17). Only one region, at chromosome 6, was identified in both populations, but with two different RFLP markers. In B73xMol7 it was umc65 and in LlxMol7 umc2l RFLP marker. Bulk segregant analysis was shown to be a quick and informative method for identification of chromosome regions which determine high yield expression in maize, i.e. for identification of RFLP markers closely linked to potential genes involved in expression of the trait.
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McIntyre, C. L., A. Rattey, A. Kilian, M. F. Dreccer, and R. Shorter. "Preferential retention of chromosome regions in derived synthetic wheat lines: a source of novel alleles for wheat improvement." Crop and Pasture Science 65, no. 2 (2014): 125. http://dx.doi.org/10.1071/cp13153.
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Synthetic hexaploid wheats (SHWs) and their synthetic derivative lines (SDLs) are being used as a means of introducing novel genetic variation into bread wheat (BW). Phenotypic information for days to flowering, height, grain weight and grain yield was collected from multiple environments for three SDL families, each with ~50 lines, and their elite BW parents. In general, the SDLs were earlier flowering and taller with larger grain size, but similar grain yield to the BWs. The three SDL families and their SHW and BW parents were genotyped using mapped DArT (diversity arrays technology) markers. Within each SDL family, SHW-specific DArT markers were used to identify SHW-derived chromosomal regions that appeared to be preferentially retained in the SDL families, as determined by retention at frequencies >0.25, the expected frequency for Mendelian segregation. Regions on chromosomes 2BS and 7BL appeared to be preferentially retained in all three SDL families, while regions on chromosomes 1AL, 1BS, 3BS, 5AS, 5BL, and 7AS were preferentially retained in two of the three SDL families. Other regions were preferentially retained in single families only, including some regions located on the D genome. Single-marker regression analysis was performed using the preferentially retained markers and identified markers and regions that were significantly associated with one or more of the four traits measured. Comparative mapping also indicates that these preferentially retained markers and chromosome regions may co-locate with previously identified QTLs for anthesis, height, grain weight and/or grain yield. Therefore, SHWs may contain novel alleles at these loci in these regions for these traits, which may provide a selective advantage to the SDLs. This approach could provide a useful method for identifying chromosomal regions of interest with potentially novel alleles for introgression for further BW improvement.
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McGrath, J. Mitchell, and Carlos F. Quiros. "Generation of alien chromosome addition lines from synthetic Brassica napus: morphology, cytology, fertility, and chromosome transmission." Genome 33, no. 3 (June 1, 1990): 374–83. http://dx.doi.org/10.1139/g90-057.
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The chromosome complement of Brassica oleracea (2n = 18) was dissected by means of alien chromosome addition lines generated by successive backcrosses of either of two B. campestris accessions (2n = 20) to the resynthesized B. napus 'Hakuran' (2n = 38). Alien chromosome addition lines were characterized by chromosome counts, morphology, pollen and seed fertility, and transmission of chromosome-specific markers. Mean chromosome number in the first backcross generation was approximately 23.5 and was little influenced by the B. campestris accession. Fertility and isozyme marker transmission were also not affected by choice of B. campestris accession. Transmission of chromosome-specific markers to the BC2 was more variable than to the BC1, and appeared to be affected by the B. campestris recurrent accession. Twenty-five monosomic addition lines (2n = 21) were recovered in the second backcross generation, representing 7 of the 9 B. oleracea synteny groups. One monosomic alien chromosome decreased seed fertility but not pollen fertility. Only one monosomic addition could be reliably identified morphologically.Key words: chromosome markers, aneuploidy, restriction fragment length polymorphism, isoymes.
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Siegel, Jeff, Benedikt Szmrecsanyi, and Bernd Kortmann. "Measuring analyticity and syntheticity in creoles." Journal of Pidgin and Creole Languages 29, no. 1 (February 7, 2014): 49–85. http://dx.doi.org/10.1075/jpcl.29.1.02sie.
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Creoles (here including expanded pidgins) are commonly viewed as being more analytic than their lexifiers and other languages in terms of grammatical marking. The purpose of the study reported in this article was to examine the validity of this view by measuring the frequency of analytic (and synthetic) markers in corpora of two different English-lexified creoles — Tok Pisin and Hawai‘i Creole — and comparing the quantitative results with those for other language varieties. To measure token frequency, 1,000 randomly selected words in each creole corpus were tagged with regard to word class, and categorized as being analytic, synthetic, both analytic and synthetic, or purely lexical. On this basis, an Analyticity Index and a Syntheticity Index were calculated. These were first compared to indices for other languages and then to L1 varieties of English (e.g. standard British and American English and British dialects) and L2 varieties (e.g. Singapore English and Hong Kong English). Type frequency was determined by the size of the inventories of analytic and synthetic markers used in the corpora, and similar comparisons were made. The results show that in terms of both token and type frequency of grammatical markers, the creoles are not more analytic than the other varieties. However, they are significantly less synthetic, resulting in much higher ratios of analytic to synthetic marking. An explanation for this finding relates to the particular strategy for grammatical expansion used by individuals when the creoles were developing.
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Adhikari, Tika B., Joseph M. Anderson, and Stephen B. Goodwin. "Identification and Molecular Mapping of a Gene in Wheat Conferring Resistance to Mycosphaerella graminicola." Phytopathology® 93, no. 9 (September 2003): 1158–64. http://dx.doi.org/10.1094/phyto.2003.93.9.1158.
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Septoria tritici leaf blotch (STB), caused by the ascomycete Mycosphaerella graminicola (anamorph Septoria tritici), is an economically important disease of wheat. Breeding for resistance to STB is the most effective means to control this disease and can be facilitated through the use of molecular markers. However, molecular markers linked to most genes for resistance to STB are not yet available. This study was conducted to test for resistance in the parents of a standard wheat mapping population and to map any resistance genes identified. The population consisted of 130 F10 recombinant-inbred lines (RILs) from a cross between the synthetic hexaploid wheat W7984 and cv. Opata 85. Genetic analysis indicated that a single major gene controls resistance to M. graminicola in this population. This putative resistance gene is now designated Stb8 and was mapped with respect to amplified fragment length polymorphism (AFLP) and microsatellite markers. An AFLP marker, EcoRI-ACG/MseI-CAG5, was linked in repulsion with the resistance gene at a distance of approximately 5.3 centimorgans (cM). Two flanking microsatellite markers, Xgwm146 and Xgwm577, were linked to the Stb8 gene on the long arm of wheat chromosome 7B at distances of 3.5 and 5.3 cM, respectively. The microsatellite markers identified in this study have potential for use in marker-assisted selection in breeding programs and for pyramiding of Stb8 with other genes for resistance to M. graminicola in wheat.
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Ito, Shosuke, Sandra Del Bino, Tomohisa Hirobe, and Kazumasa Wakamatsu. "Improved HPLC Conditions to Determine Eumelanin and Pheomelanin Contents in Biological Samples Using an Ion Pair Reagent." International Journal of Molecular Sciences 21, no. 14 (July 20, 2020): 5134. http://dx.doi.org/10.3390/ijms21145134.
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Alkaline hydrogen peroxide oxidation (AHPO) of eumelanin and pheomelanin, two major classes of melanin pigments, affords pyrrole-2,3,5-tricarboxylic acid (PTCA), pyrrole-2,3-dicarboxylic acid (PDCA) and pyrrole-2,3,4,5-tetracarboxylic acid (PTeCA) from eumelanin and thiazole-2,4,5-tricarboxylic acid (TTCA) and thiazole-4,5-dicarboxylic acid (TDCA) from pheomelanin. Quantification of these five markers by HPLC provides useful information on the quantity and structural diversity of melanins in various biological samples. HPLC analysis of these markers using the original method of 0.1 M potassium phosphate buffer (pH 2.1):methanol = 99:1 (85:15 for PTeCA) on a reversed-phase column had some problems, including the short lifetime of the column and, except for the major eumelanin marker PTCA, other markers were occasionally overlapped by interfering peaks in samples containing only trace levels of these markers. These problems can be overcome by the addition of an ion pair reagent for anions, such as tetra-n-butylammonium bromide (1 mM), to retard the elution of di-, tri- and tetra-carboxylic acids. The methanol concentration was increased to 17% (30% for PTeCA) and the linearity, reproducibility, and recovery of the markers with this improved method is good to excellent. This improved HPLC method was compared to the original method using synthetic melanins, mouse hair, human hair, and human epidermal samples. In addition to PTCA, TTCA, a major marker for pheomelanin, showed excellent correlations between both HPLC methods. The other markers showed an attenuation of the interfering peaks with the improved method. We recommend this improved HPLC method for the quantitative analysis of melanin markers following AHPO because of its simplicity, accuracy, and reproducibility.
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Zwart, R. S., J. P. Thompson, and I. D. Godwin. "Identification of quantitative trait loci for resistance to two species of root-lesion nematode (Pratylenchus thornei and P. neglectus) in wheat." Australian Journal of Agricultural Research 56, no. 4 (2005): 345. http://dx.doi.org/10.1071/ar04223.
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Pratylenchus thornei and P. neglectus are two species of root-lesion nematode that cause substantial yield losses in wheat. No commercially available wheat variety has resistance to both species. A doubled-haploid population developed from a cross between the synthetic hexaploid wheat line CPI133872 and the bread wheat Janz was used to locate and tag quantitative trait loci (QTLs) associated with resistance to both P. thornei and P. neglectus. Wheat plants were inoculated with both species of nematode in independent replicated glasshouse trials repeated over 2 years. Known locations of wheat microsatellite markers were used to construct a framework map. After an initial single-marker analysis to detect marker-trait linkages, chromosome regions associated with putative QTLs were targetted with microsatellite markers to increase map density in the chromosome regions of interest. In total, 148 wheat microsatellite markers and 21 amplified fragment length polymorphism markers were mapped. The codominant microsatellite marker Xbarc183 on the distal end of chromosome 6DS was allelic for resistance to both P. thornei and P. neglectus. The QTL were designated QRlnt.lrc-6D.1 and QRlnn.lrc-6D.1, for the 2 traits, respectively. The allele inherited from CPI133872 explained 22.0–24.2% of the phenotypic variation for P. thornei resistance, and the allele inherited from Janz accounted for 11.3–14.0% of the phenotypic variation for P. neglectus resistance. Composite interval mapping identified markers that flank a second major QTL on chromosome 6DL (QRlnt.lrc-6D.2) that explained 8.3–13.4% of the phenotypic variation for P. thornei resistance. An additional major QTL associated with P. neglectus resistance was detected on chromosome 4DS (QRlnn.lrc-4D.1) and explained a further 10.3–15.4% of the phenotypic variation. The identification and tagging of nematode resistance genes with molecular markers will allow appropriate allele combinations to be selected, which will aid the successful breeding of wheat with dual nematode resistance.
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Freudenberg, Robert A., Luisa Wittemeier, Alexander Einhaus, Thomas Baier, and Olaf Kruse. "The Spermidine Synthase Gene SPD1: A Novel Auxotrophic Marker for Chlamydomonas reinhardtii Designed by Enhanced CRISPR/Cas9 Gene Editing." Cells 11, no. 5 (February 28, 2022): 837. http://dx.doi.org/10.3390/cells11050837.
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Biotechnological application of the green microalga Chlamydomonas reinhardtii hinges on the availability of selectable markers for effective expression of multiple transgenes. However, biological safety concerns limit the establishment of new antibiotic resistance genes and until today, only a few auxotrophic markers exist for C. reinhardtii. The recent improvements in gene editing via CRISPR/Cas allow directed exploration of new endogenous selectable markers. Since editing frequencies remain comparably low, a Cas9-sgRNA ribonucleoprotein (RNP) delivery protocol was strategically optimized by applying nitrogen starvation to the pre-culture, which improved successful gene edits from 10% to 66% after pre-selection. Probing the essential polyamine biosynthesis pathway, the spermidine synthase gene (SPD1) is shown to be a potent selectable marker with versatile biotechnological applicability. Very low levels of spermidine (0.75 mg/L) were required to maintain normal mixotrophic and phototrophic growth in newly designed spermidine auxotrophic strains. Complementation of these strains with a synthetic SPD1 gene was achieved when the mature protein was expressed in the cytosol or targeted to the chloroplast. This work highlights the potential of new selectable markers for biotechnology as well as basic research and proposes an effective pipeline for the identification of new auxotrophies in C. reinhardtii.
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Capetti, Francesca, Arianna Marengo, Cecilia Cagliero, Erica Liberto, Carlo Bicchi, Patrizia Rubiolo, and Barbara Sgorbini. "Adulteration of Essential Oils: A Multitask Issue for Quality Control. Three Case Studies: Lavandula angustifolia Mill., Citrus limon (L.) Osbeck and Melaleuca alternifolia (Maiden & Betche) Cheel." Molecules 26, no. 18 (September 16, 2021): 5610. http://dx.doi.org/10.3390/molecules26185610.
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The quality control of essential oils (EO) principally aims at revealing the presence of adulterations and at quantifying compounds that are limited by law by evaluating EO chemical compositions, usually in terms of the normalised relative abundance of selected markers, for comparison to reference values reported in pharmacopoeias and/or international norms. Common adulterations of EO consist of the addition of cheaper EO or synthetic materials. This adulteration can be detected by calculating the percent normalised areas of selected markers or the enantiomeric composition of chiral components. The dilution of the EO with vegetable oils is another type of adulteration. This adulteration is quite devious, as it modifies neither the qualitative composition of the resulting EO nor the marker’s normalised percentage abundance, which is no longer diagnostic, and an absolute quantitative analysis is required. This study aims at verifying the application of the two above approaches (i.e., normalised relative abundance and absolute quantitation) to detect EO adulterations, with examples involving selected commercial EO (lavender, bergamot and tea tree) adulterated with synthetic components, EO of different origin and lower economical values and heavy vegetable oils. The results show that absolute quantitation is necessary to highlight adulteration with heavy vegetable oils, providing that a reference quantitative profile is available.
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Longinotti, Gloria, Gabriel Ybarra, Susana Vighi, Claudia Perandones, Javier Montserrat, Juan Sebastian Yakisich, Mariano Grasselli, and Martin Radrizzani. "One Step Histological Detection and Staining of the PTEN Tumor Suppressor Protein by a Single Strand DNA." Diagnostics 11, no. 2 (January 26, 2021): 171. http://dx.doi.org/10.3390/diagnostics11020171.
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Antibodies are the most used technological tool in histochemistry. However, even with monoclonal antibodies, their standardization is difficult due to variation of biological systems as well as to variability due to the affinity and amplification of the signal arising from secondary peroxidase detection systems. In this article we combined two synthetic molecules to facilitate the standardization of a detection protocol of protein markers in histological sections. The first molecule was an aptamer, a 50-base single-stranded DNA fragment, which recognizes a PTEN tumor suppressor. The second molecule used was also another single stranded 18-base aptamer DNA fragment, which forms a quadruplex structure guanine box. This G-quadruplex recognizes and attaches a molecule of hemin, increasing the catalytic capacity for the hydrogen peroxide. Our results show how the correct structural design of DNA combining an aptamer together with the peroxidase-like DNAzyme allows to detect proteins in histological sections. This tool offers the standardization of the detection of prognostic markers in cancer, in quality and quantity, due to its synthetic nature and its 1:1 antigen:enzyme ratio. This is the first time that reproducible results have been presented in histological sections staining a cancer marker using a single-stranded DNA molecule with dual function.
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Southwood, O. I., S. Hoste, T. H. Short, A. J. Mileham, and D. Cuthbert-Heavens. "Evaluation of genetic markers for litter size in Meishan synthetic and Large White pigs." Proceedings of the British Society of Animal Science 1996 (March 1996): 18. http://dx.doi.org/10.1017/s0308229600029937.
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A significant relationship between the oestrogen receptor gene (ESR) and litter size has been detected in USA populations of Large White and a synthetic comprising 50% Meishan (Rothschild et al., 1995). Animals carrying two copies of the favourable allele (B) had an extra pig born per litter than those that did not have the allele. This paper reports on results observed in a UK 50% Meishan synthetic and four UK Large White lines.Litter size data from 50% Meishan synthetic (L93) full-sib females where more than one ESR genotype was segregating. Data were analysed using a mixed model with full relationships and including the fixed effects of season of farrowing, parity, ESR genotype (AA, AB or BB) and service type (AI or natural service). Heritiability and permanent environmental effects for litter size were assumed as 0.09 and 0.11, repectively. A total of 27 full-sib families were represented and included 62 sows and 139 litter records. Hypothesis testing used the option in PEST under a mixed model (Groeneveld et al., 1991).
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Southwood, O. I., S. Hoste, T. H. Short, A. J. Mileham, and D. Cuthbert-Heavens. "Evaluation of genetic markers for litter size in Meishan synthetic and Large White pigs." Proceedings of the British Society of Animal Science 1996 (March 1996): 18. http://dx.doi.org/10.1017/s1752756200592229.
Full textAbstract:
A significant relationship between the oestrogen receptor gene (ESR) and litter size has been detected in USA populations of Large White and a synthetic comprising 50% Meishan (Rothschild et al., 1995). Animals carrying two copies of the favourable allele (B) had an extra pig born per litter than those that did not have the allele. This paper reports on results observed in a UK 50% Meishan synthetic and four UK Large White lines.Litter size data from 50% Meishan synthetic (L93) full-sib females where more than one ESR genotype was segregating. Data were analysed using a mixed model with full relationships and including the fixed effects of season of farrowing, parity, ESR genotype (AA, AB or BB) and service type (AI or natural service). Heritiability and permanent environmental effects for litter size were assumed as 0.09 and 0.11, repectively. A total of 27 full-sib families were represented and included 62 sows and 139 litter records. Hypothesis testing used the option in PEST under a mixed model (Groeneveld et al., 1991).
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CHEN, Guo-yue, and Li-hui LI. "Detection of Genetic Diversity in Synthetic Hexaploid Wheats Using Microsatellite Markers." Agricultural Sciences in China 6, no. 12 (December 2007): 1403–10. http://dx.doi.org/10.1016/s1671-2927(08)60001-2.
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Khalid, Maria, Alvina Gul, Rabia Amir, Mohsin Ali, Fakiha Afzal, Umar Masood Quraishi, Zubair Ahmed, and Awais Rasheed. "QTL mapping for seedling morphology under drought stress in wheat cross synthetic (W7984)/Opata." Plant Genetic Resources: Characterization and Utilization 16, no. 4 (March 13, 2018): 359–66. http://dx.doi.org/10.1017/s1479262118000023.
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AbstractDrought stress ‘particularly at seedling stage’ causes morpho-physiological differences in wheat which are crucial for its survival and adaptability. In the present study, 209 recombinant inbred lines (RILs) from synthetic wheat (W7984)× ‘Opata’ (also known as SynOpRIL) population were investigated under well-watered and water-limited conditions to identify quantitative trait loci (QTL) for morphological traits at seedling stage. Analysis of variance revealed significant differences (P < 0.01) among RILs, and water treatments for all traits with moderate to high broad sense heritability. Pearson's coefficient of correlation revealed positive correlation among all traits except dry root weight that showed poor correlation with fresh shoot weight (FSW) under water-limited conditions. A high-density linkage map was constructed with 2639 genotyping-by-sequencing markers and covering 5047 cM with an average marker density of 2 markers/cM. Composite interval mapping identified 16 QTL distributed over nine chromosomes, of which six were identified under well-watered and 10 in water-limited conditions. These QTL explained from 4 to 59% of the phenotypic variance. Six QTL were identified on chromosome 7B; three for shoot length under water-limited conditions (QSL.nust-7B) at 64, 104 and 221 cM, two for fresh root weight (QFRW.nust-7B) at 124 and 128 cM, and one for root length (QRL.nust-7B) at 122 cM positions. QFSW.nust-7B appeared to be the most significant QTL explaining 59% of the phenotypic variance and also associated with FSW at well-watered conditions. These QTL could serve as target regions for candidate gene discovery and marker-assisted selection in wheat breeding.
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Jani, Mehul, and Rajeev K. Azad. "IslandCafe: Compositional Anomaly and Feature Enrichment Assessment for Delineation of Genomic Islands." G3: Genes|Genomes|Genetics 9, no. 10 (August 6, 2019): 3273–85. http://dx.doi.org/10.1534/g3.119.400562.
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One of the evolutionary forces driving bacterial genome evolution is the acquisition of clusters of genes through horizontal gene transfer (HGT). These genomic islands may confer adaptive advantages to the recipient bacteria, such as, the ability to thwart antibiotics, become virulent or hypervirulent, or acquire novel metabolic traits. Methods for detecting genomic islands either search for markers or features typical of islands or examine anomaly in oligonucleotide composition against the genome background. The former tends to underestimate, missing islands that have the markers either lost or degraded, while the latter tends to overestimate, due to their inability to discriminate compositional atypicality arising because of HGT from those that are a consequence of other biological factors. We propose here a framework that exploits the strengths of both these approaches while bypassing the pitfalls of either. Genomic islands lacking markers are identified by their association with genomic islands with markers. This was made possible by performing marker enrichment and phyletic pattern analyses within an integrated framework of recursive segmentation and clustering. The proposed method, IslandCafe, compared favorably with frequently used methods for genomic island detection on synthetic test datasets and on a test-set of known islands from 15 well-characterized bacterial species. Furthermore, IslandCafe identified novel islands with imprints of likely horizontal acquisition.
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Maisak, Timur. "Endoclitics in Andi." Folia Linguistica 55, no. 1 (January 12, 2021): 1–34. http://dx.doi.org/10.1515/flin-2020-2069.
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Abstract The paper provides evidence for the existence of endoclitics in Andi, a Nakh-Daghestanian language of the Avar-Andic branch spoken in the Republic of Daghestan, Russia. In Andi, the additive marker (‘also’) and the intensifying marker (‘even, at all’) behave as enclitics on various types of hosts and as endoclitics when they occur on negative verb forms. In the latter case, the additive and intensifying markers break up the word form and appear before the negation marker. I argue that both the additive and the intensifier are clitics, especially in view of their highly promiscuous attachment. I also show that negative verb forms are morphologically synthetic, so the additive and the intensifier are genuine endoclitics, i.e. clitics that occur inside morphological words. In addition I provide a few parallels for the unusual morphosyntactic behaviour of additive and intensifying clitics in some other Nakh-Daghestanian languages as well as in some languages of Northern Eurasia. Although in these cases the corresponding markers do not qualify as endoclitics proper, the available data hint at a cross-linguistic tendency towards word-internal placement of morphemes with meanings like ‘also’, ‘even’ or ‘only’.
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Lu, Zhen-Xiang, G. L. Reighard, W. V. Baird, A. G. Abbott, and S. Rajapakse. "Identification of Peach Rootstock Cultivars by RAPD Markers." HortScience 31, no. 1 (February 1996): 127–29. http://dx.doi.org/10.21273/hortsci.31.1.127.
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Eighteen peach rootstock cultivars, most of Prunus persica (L.) Batsch, were screened for diagnostic random amplified polymorphic DNA (RAPD) markers using synthetic decamer oligonucleotide primers. Twenty of the 80 primers were informative, and 40 amplified DNA bands from the informative primers were selected as RAPD markers. Based on combined banding patterns, all 18 rootstock cultivars were identified with only six of the 20 informative primers. Cluster analysis of the 18 peach rootstock cultivars using 40 RAPD markers produced a dendrogram of genetic relatedness in good agreement with their putative pedigrees. The first major bifurcation in the dendrogram divided these rootstock cultivars into two groups according to their resistance or susceptibility to root-knot nematodes [Meloidogyne incognita (Kofoid and White) Chitwood and M. javanica (Treub) Chitwood].
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Nerusheva, Olga, Natalia Dorogova, and Leonid Omelyanchuk. "GFP markers for studying D. melanogaster spermatogenesis." Open Life Sciences 4, no. 4 (December 1, 2009): 452–60. http://dx.doi.org/10.2478/s11535-009-0052-y.
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AbstractLocalization of a set of chimeric GFP proteins in D. melanogaster spermatogenesis has been studied. In the collection used, the proteins with detectable germ-line expression frequently occur to be involved in mRNA maturation. According to the cellular localization, proteins fall into three groups, namely, the protein Rtc1, involved in splicing, displays an exclusively nuclear localization; the proteins Squid (splicing and mRNA transport), Pabp2 (polyadenylation), and Hrb98DE (splicing and mRNA transport) change their localization during germ-line development; and the protein Imp (mRNA localization) is located exclusively in the cytoplasm. The distribution of Rtc1, Squid and Hrb98DE in the spermatocyte nuclei is morphologically similar to the distribution of splicing bodies, the so-called splicing factor compartments. The proteins Imp and Hrb98DE at the stage of elongation are localized to a specialized structure in the caudal region of cyst; this region corresponds to the site of the highest synthetic activity in the cyst cells at this developmental stage.
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Yamada, Yohko, Mari Maeda, Mohamed Mahdi Alshahni, Michel Monod, Peter Staib, and Tsuyoshi Yamada. "Flippase (FLP) recombinase-mediated marker recycling in the dermatophyte Arthroderma vanbreuseghemii." Microbiology 160, no. 10 (October 1, 2014): 2122–35. http://dx.doi.org/10.1099/mic.0.076562-0.
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Biological processes can be elucidated by investigating complex networks of relevant factors and genes. However, this is not possible in species for which dominant selectable markers for genetic studies are unavailable. To overcome the limitation in selectable markers for the dermatophyte Arthroderma vanbreuseghemii (anamorph: Trichophyton mentagrophytes), we adapted the flippase (FLP) recombinase-recombination target (FRT) site-specific recombination system from the yeast Saccharomyces cerevisiae as a selectable marker recycling system for this fungus. Taking into account practical applicability, we designed FLP/FRT modules carrying two FRT sequences as well as the flp gene adapted to the pathogenic yeast Candida albicans (caflp) or a synthetic codon-optimized flp (avflp) gene with neomycin resistance (nptII) cassette for one-step marker excision. Both flp genes were under control of the Trichophyton rubrum copper-repressible promoter (PCTR4 ). Molecular analyses of resultant transformants showed that only the avflp-harbouring module was functional in A. vanbreuseghemii. Applying this system, we successfully produced the Ku80 recessive mutant strain devoid of any selectable markers. This strain was subsequently used as the recipient for sequential multiple disruptions of secreted metalloprotease (fungalysin) (MEP) or serine protease (SUB) genes, producing mutant strains with double MEP or triple SUB gene deletions. These results confirmed the feasibility of this system for broad-scale genetic manipulation of dermatophytes, advancing our understanding of functions and networks of individual genes in these fungi.
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Furmanik, Malgorzata, Martijn Chatrou, Rick van Gorp, Asim Akbulut, Brecht Willems, Harald Schmidt, Guillaume van Eys, et al. "Reactive Oxygen-Forming Nox5 Links Vascular Smooth Muscle Cell Phenotypic Switching and Extracellular Vesicle-Mediated Vascular Calcification." Circulation Research 127, no. 7 (September 11, 2020): 911–27. http://dx.doi.org/10.1161/circresaha.119.316159.
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Rationale: Vascular calcification, the formation of calcium phosphate crystals in the vessel wall, is mediated by vascular smooth muscle cells (VSMCs). However, the underlying molecular mechanisms remain elusive, precluding mechanism-based therapies. Objective: Phenotypic switching denotes a loss of contractile proteins and an increase in migration and proliferation, whereby VSMCs are termed synthetic. We examined how VSMC phenotypic switching influences vascular calcification and the possible role of the uniquely calcium-dependent reactive oxygen species (ROS)-forming Nox5 (NADPH oxidase 5). Methods and Results: In vitro cultures of synthetic VSMCs showed decreased expression of contractile markers CNN-1 (calponin 1), α-SMA (α-smooth muscle actin), and SM22-α (smooth muscle protein 22α) and an increase in synthetic marker S100A4 (S100 calcium binding protein A4) compared with contractile VSMCs. This was associated with increased calcification of synthetic cells in response to high extracellular Ca 2+ . Phenotypic switching was accompanied by increased levels of ROS and Ca 2+ -dependent Nox5 in synthetic VSMCs. Nox5 itself regulated VSMC phenotype as siRNA knockdown of Nox5 increased contractile marker expression and decreased calcification, while overexpression of Nox5 decreased contractile marker expression. ROS production in synthetic VSMCs was cytosolic Ca 2+ -dependent, in line with it being mediated by Nox5. Treatment of VSMCs with Ca 2+ loaded extracellular vesicles (EVs) lead to an increase in cytosolic Ca 2+ . Inhibiting EV endocytosis with dynasore blocked the increase in cytosolic Ca 2+ and VSMC calcification. Increased ROS production resulted in increased EV release and decreased phagocytosis by VSMCs. Conclusions: We show here that contractile VSMCs are resistant to calcification and identify Nox5 as a key regulator of VSMC phenotypic switching. Additionally, we describe a new mechanism of Ca 2+ uptake via EVs and show that Ca 2+ induces ROS production in VSMCs via Nox5. ROS production is required for release of EVs, which promote calcification. Identifying molecular pathways that control Nox5 and VSMC-derived EVs provides potential targets to modulate vascular remodeling and calcification in the context of mineral imbalance. Graphic Abstract: A graphic abstract is available for this article.
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Farman, M. L., and S. A. Leong. "Genetic and physical mapping of telomeres in the rice blast fungus, Magnaporthe grisea." Genetics 140, no. 2 (June 1, 1995): 479–92. http://dx.doi.org/10.1093/genetics/140.2.479.
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Abstract Telomeric restriction fragments were genetically mapped to a previously described linkage map of Magnaporthe grisea, using RFLPs identified by a synthetic probe. (TTAGGG)3. Frequent rearrangement of telomeric sequences was observed in progeny isolates creating a potential for misinterpretation of data. Therefore a consensus segregation data set used to minimize mapping errors. TWelve of the 14 telomeres were found to be genetically linked to existing RFLP markers. Second-dimensional electrophoresis of restricted chromosomes confirmed these linkage assignments and revealed the chromosomal location of the two unlinked telomeres. We were thus able to assign all 14 M. grisea telomeres to their respective chromosome ends. The Achilles' cleavage (AC) technique was employed to determine that chromosome 1 markers 11 and CH5-120H were approximately 1.8 Mb and 1.28 Mb, respectively, from their nearest telomeres. RecA-AC was also used to determine that unlinked telomere 6 was approximately 530 kb from marker CH5-176H in strain 2539 and 580 kb in Guy11. These experiments indicated that large portions of some chromosome ends are unrepresented by genetic markers and provided estimates of the relationship of genetic to physical distance in these regions of the genome.
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Iwagaki, Hiromi, Akio Hizuta, Kenta Kobashi, Hiroshi Isozaki, Norihisa Takakura, and Noriaki Tanaka. "Clinical Value of Neopterin In Infectious Complications." Pteridines 10, no. 1 (February 1999): 20–23. http://dx.doi.org/10.1515/pteridines.1999.10.1.20.
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Neopterin, a pteridine intermediate metabolite in the biopterine synthetic pathway, is synthesized and secreted by monocyte/macrophages upon stimulation, mainly by gamma-interferon by activated T cells. C-reactive protein (CRP) is one of the major acute phase reactants and its release is thought to be mediated by interleukin-6. Soluble IL-2 receptor (sIL-2R) is released by activated T cells. Plasma concentrations of neopterin, CRP and sIL-2R were synchronously analyzed in 25 determinations of 5 patients with severe infectious complications. A marked increase in neopterin, CRP and sIL-2R levels was observed. The increase in neopterin was significantly correlated to that of neopterin which is a marker of macrophage activity. These results suggest that macrophages are involved in the stimulation of sIL-2R release. In contrast, the increase in neopterin was not correlated to that of CRP and the lack of correlation between neopterin and CRP indicated that independent mechanisms control the synthesis of these two markers.
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Molfetta, Matteo Gianluca, Maria Francesca Bruno, Luigi Pratola, Antonio Rinaldi, Alberto Morea, Giovanni Preziosa, Davide Pasquali, Marcello Di Risio, and Michele Mossa. "A Sterescopic System to Measure Water Waves in Laboratories." Remote Sensing 12, no. 14 (July 16, 2020): 2288. http://dx.doi.org/10.3390/rs12142288.
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A new system for estimating the synthetic parameters of sea states during physical investigations has been implemented. The technique proposed herein is based on stereographic analysis of digital images acquired with optical sensors. A series of ad hoc floating markers has been made and properly moored to the bottom of a large wave tank to estimate the synthetic parameters of generated waves. The implemented acquisition system and the proposed algorithm provide automatic recognition of all markers by a pair of optical sensors that synchronously captures their instantaneous location and tracks their movements over time. After transformation from the image to the real-world coordinates, water surface elevation time series have been obtained. Several experimental tests have been carried out to assess the feasibility and reliability of the proposed approach. The estimated wave synthetic parameters have been then compared with those obtained by employing standard resistive probes. The deviation were found to be equal to ~6% for the significant wave height and 1% for peak, mean, and significant wave periods.
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Gupta, Arvind K., Deepak Pardasani, Hemendra K. Gupta, and Devendra K. Dubey. "N,N′-Dichlorobis(2,4,6-trichlorophenyl)urea (CC-2): an Efficient Reagent for the Synthesis of Chemical Weapons Convention-Related Dialkyl-N,N-dialkylphosphoramidates from Dialkylphosphites." Australian Journal of Chemistry 60, no. 11 (2007): 879. http://dx.doi.org/10.1071/ch07081.
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The present paper describes the one-pot synthesis of dialkyl N,N-dialkylphosphoramidates (DADAP) from dialkylphosphites and dialkylamines using N,N′-dichlorobis(2,4,6-trichlorophenyl)urea (CC-2) as chlorinating reagent. DADAP belong to the schedule 2.B.6 category of the Chemical Weapons Convention (CWC), as they are the important markers of the chemical warfare agent tabun and its analogues. The study was undertaken to develop the spectral database of DADAP for verification of CWC. The reported synthetic strategy can be adopted to rapidly synthesize several analogues of DADAP during official proficiency tests.
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Mikic, Sanja, Ankica Kondic-Spika, Ljiljana Brbaklic, Dusan Stanisavljevic, Dragana Trkulja, Marina Ceran, and Bojan Mitrovic. "Association analysis of agronomic traits with microsatellites in maize inbred lines." Genetika 50, no. 2 (2018): 379–94. http://dx.doi.org/10.2298/gensr1802379m.
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Association analysis or linkage disequilibrium mapping is a method for identification of quantitative trait loci (QTLs) in a panel of divergent unrelated individuals based on historical recombinations during a crop?s domestication and selection. It should account for the population structure, which can be the result of adaptation to local conditions or selection, to reduce the possibility of declaring false-positive associations. The aim of this study was to determine potentially significant and consistent associations between markers and agronomic important maize (Zea mays L.) traits using association analysis in a diverse breeding material that can be ultimately implemented in maize selection. To this end, 96 maize inbred lines were evaluated in field trials at three locations in Serbia for eleven agronomic traits and analysed with microsatellite markers. Twenty five microsatellites were used to assess the population structure using Bayesian model-based clustering method and to test the significance of associations between the markers and the traits with general (GLM) and mixed linear (MLM) models. The cluster analysis divided maize inbred lines in four subpopulations, corresponding to the BSSS (Iowa Stiff Stalk Synthetic), LSC (Lancaster Sure Crop), Iodent heterotic groups and exotic and independent germplasm. The models identified associations between twenty five microsatellite markers and eleven agronomic traits, resulting in 133 and 71 associations across the environments for GLM and MLM, respectively. Some of the identified marker-trait associations were significant and consistent in several environments. The associations stable in several environments were identified between the markers bnlg1067 and two flowering traits; nc005 and bnlg434 and plant height, bnlg434 and ear height; bnlg1643 and umc1127 and leaf number, bnlg1360 and ear diameter; umc1019 and umc1506 and number of rows per ear; bnlg2305 and bnlg1451 and ear length, and between bnlg1175 and thousand-kernel weight. The results of this study indicate that these microsatellites could be used in marker-assisted selection of inbred lines, after validation of the marker-trait associations and testing combining abilities of the inbreds during hybrid development.
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Lanham, Patrick G., Sarah Fennell, J. P. Moss, and W. Powell. "Detection of polymorphic loci in Arachis germplasm using random amplified polymorphic DNAs." Genome 35, no. 5 (October 1, 1992): 885–89. http://dx.doi.org/10.1139/g92-134.
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The development of easily scoreable genetic markers in Arachis will facilitate the introgression of desirable traits from wild species into adapted germplasm. We have used random amplified polymorphic DNAs (RAPDs) to identify polymorphic molecular markers in a range of wild and cultivated Arachis species. From a total of sixty 10-mer oligonucleotide primers, 49 polymorphic loci were identified between a cultivated A. hypogaea type (TMV-2) and a synthetic amphidiploid (B × C)2 created from a A. batizocoi and A. chacoense cross. The inheritance of polymorphic markers, both in the amphidiploid and in the F1 progeny in a TMV-2 × (B × C)2 cross, has also been demonstrated. The potential exploitation of RAPD markers in groundnut improvement programs is discussed.Key words: groundnut, Arachis species, RAPDs, amphidiploid.
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Ruel, Katia, Vincent Burlat, and Jean-Paul Joseleau. "Relationship Between Ultrastructural Topochemistry of Lignin and Wood Properties." IAWA Journal 20, no. 2 (1999): 203–11. http://dx.doi.org/10.1163/22941932-90000681.
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The main subunits of lignin could be visualized by transmission electron microscopy (TEM) with antibodies raised against synthetic lignin model polymers. Thus, immunological probes against p-hydroxyphenyl propane, guaiacyl and mixed guaiacyl-syringyl units allowed to specifically localize the qualitative distribution of lignins in plant cell tissues . Depending on the mode of preparation of the synthetic lignin antigens , the corresponding antibodies showed specificity for condensed or noncondensed interunits linkages . This specificity is illustrated with the different labellings provided by the antibodies when applied to various wood and nonwoody materials . The results c1early show the heterogeneity of lignification between tissues but also demonstrate the microheterogeneity of lignin deposition within a a single wood cell wall. Our immunological markers were successfully applied to transgenic plants in which lignin synthesis pathways had been modified, to tissues from reaction wood, as well as to materials degraded by ligninolytic fungi.
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Wendt, Anke S., Monzurul Alam, and Joao Paulo Castagnoli. "Sand injectite mapping using a resistivity-velocity transform function." Leading Edge 40, no. 3 (March 2021): 202–7. http://dx.doi.org/10.1190/tle40030202.1.
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Lack of resolution in the distribution of sand injectites in hydrocarbon fields is common and makes it difficult to predict drilling challenges and plan for optimum production. A practical workflow was developed that enables the distinction of shale and sand bodies by using a combination of low-resolution seismic data and high-resolution resistivity log data. Measured resistivity logs were used to predict synthetic velocity logs, which accurately match shale velocities and over- or underestimate velocities of other rock types. The synthetic velocity logs were spatially distributed in a 3D cube in order to predict synthetic velocities in between and away from the well locations. The 3D cube was representative of a field. It covered the interval from the seabed to below the reservoir. The spatial distribution was based on a geostatistical approach guided by measured seismic interval velocities. A residual velocity cube was calculated from the measured and synthetic velocities. The residual velocity cube produced near-zero velocities for shaly materials and velocity over- or underestimates for other rock types. Interpretation of the residual velocity cube required the identification of strong stratigraphic markers. The markers were removed from the residual cube by setting their specific layer velocities to 0 m/s. The final information stored in the residual velocity cube was then related to the over- or underestimated velocities in sand bodies.
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Linkhart, S. G., T. A. Linkhart, A. K. Taylor, J. E. Wergedal, P. Bettica, and D. J. Baylink. "Synthetic peptide-based immunoassay for amino-terminal propeptide of type I procollagen: application for evaluation of bone formation." Clinical Chemistry 39, no. 11 (November 1, 1993): 2254–58. http://dx.doi.org/10.1093/clinchem/39.11.2254.
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Abstract Serum biochemical markers are powerful tools for the evaluation of bone turnover. In this study, we developed a radioimmunoassay, using a synthetic peptide for the N-terminal fragment of human type I [alpha 1(I)] procollagen (N-PCP). A 14-amino acid peptide was synthesized from the amino terminus and used to generate antibodies in rabbits. The synthetic peptide was used as standard and tracer in the assay. Both native type I amino procollagen (PINP), which was purified from skin fibroblasts, and human serum displaced tracer binding in parallel with the synthetic peptide. The range for measurement of N-PCP in serum was 0.7 to 30 micrograms/L (0.21-9.18 nmol/L). In a sample of 17 normal adults and 13 children (ages 9-16 years) there was a strong correlation between serum N-PCP determined by this assay and both skeletal alkaline phosphatase isoenzyme and osteocalcin, markers of bone formation. Serum concentrations of N-PCP in a group of normal children were eightfold higher than concentrations in normal adults, with no overlap between the two groups. N-PCP also correlated with C-terminal type I procollagen determined with a commercially available kit (r = 0.92).
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Zhang, Lin, Yanyan Zhang, Ying Wu, Jingjing Yu, Yimin Zhang, Fanxing Zeng, and Lijun Shi. "Role of the Balance of Akt and MAPK Pathways in the Exercise-Regulated Phenotype Switching in Spontaneously Hypertensive Rats." International Journal of Molecular Sciences 20, no. 22 (November 13, 2019): 5690. http://dx.doi.org/10.3390/ijms20225690.
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The mechanisms regulating vascular smooth muscle cell (VSMC) phenotype switching and the critical signal modulation affecting the VSMCs remain controversial. Physical exercise acts as an effective drug in preventing elevated blood pressure and improving vascular function. This study was designed to explore the influence of aerobic exercise on the suppression of VSMC phenotype switching by balancing of the Akt, also known as PKB (protein kinase B) and mitogen-activated protein kinase (MAPK) signaling pathways. Spontaneously hypertensive rats (SHRs) and normotensive rats were subjected to exercise treatment before measuring the vascular morphological and structural performances. Exercise induced reverse expression of VSMC protein markers (α-SM-actin, calponin, and osteopontin (OPN)) in spontaneously hypertensive rats. It is noteworthy that the low expression of phosphorylated Akt significantly decreased the expression of VSMC contractile phenotype markers (α-SM-actin and calponin) and increased the expression of the VSMC synthetic phenotype marker (OPN). However, the MAPK signal pathway exerts an opposite effect. VSMCs and whole vessels were treated by inhibitors, namely the p-Akt inhibitor, p-ERK inhibitor, and p-p38 MAPK inhibitors. VSMC phenotype markers were reversed. It is important to note that a significant reverse regulatory relationship was observed between the expression levels of MAPK and the contractile markers in both normotensive and spontaneously hypertensive rats. We demonstrate that aerobic exercise regulates the VSMC phenotype switching by balancing the Akt and MAPK signaling pathways in SHRs.
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Zwart, R. S., J. P. Thompson, J. G. Sheedy, and J. C. Nelson. "Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population." Australian Journal of Agricultural Research 57, no. 5 (2006): 525. http://dx.doi.org/10.1071/ar05177.
Full textAbstract:
Root-lesion nematode (Pratylenchus thornei) is a serious pathogen of wheat in many countries. The International Triticeae Mapping Initiative (ITMI) population of recombinant inbred lines (RILs) was assessed for resistance to P. thornei to determine the chromosome locations of the resistance genes. The ITMI population is derived from a cross between the resistant synthetic hexaploid wheat W-7984 and a susceptible bread wheat cultivar Opata 85. Two years of phenotypic data for resistance to P. thornei were obtained in replicated glasshouse trials. Quantitative trait locus (QTL) analysis was performed using available segregation and map data for 114 RILs. A QTL on chromosome 6DS showed consistent effects for reduced nematode numbers (partial resistance) across years and accounted for 11% and 23% of the phenotypic variation. A second QTL for P. thornei resistance on chromosome 2BS accounted for an additional 19% and 5%. Restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers associated with the QTLs are physically located in regions rich in major genes at the distal ends of the short chromosome arms of 6D and 2B. SSR markers with potential for marker-assisted selection of P. thornei resistance effective in different genetic backgrounds have been identified.
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Nishijima, Ryo, Kentaro Yoshida, Kohei Sakaguchi, Shin-ichi Yoshimura, Kazuhiro Sato, and Shigeo Takumi. "RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat." International Journal of Molecular Sciences 19, no. 12 (November 26, 2018): 3749. http://dx.doi.org/10.3390/ijms19123749.
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Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome.
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Gorafi, Yasir S. A., Takayoshi Ishii, June-Sik Kim, Awad Ahmed Elawad Elbashir, and Hisashi Tsujimoto. "Genetic variation and association mapping of grain iron and zinc contents in synthetic hexaploid wheat germplasm." Plant Genetic Resources: Characterization and Utilization 16, no. 1 (August 12, 2016): 9–17. http://dx.doi.org/10.1017/s1479262116000265.
Full textAbstract:
AbstractFe and Zn deficiency are widespread worldwide. As wheat is the primary food for the majority of the world people, producing wheat grains with high mineral content can ameliorate the problem of mineral hunger. However, the genetic variation available for breeders is limited. The aim of this study was to assess the genetic variation in grain Fe and Zn contents in 47 synthetic hexaploid wheats and to identify marker loci associated with Fe and Zn contents. We measured the grain Fe and Zn contents using inductively coupled plasma atomic emission spectroscopy and performed genotyping using SSR markers. The results showed considerable genetic variation for these minerals. We identified three lines with high Fe and Zn contents and six quantitative trait loci of which three were associated with Fe content and the other three with Zn content. The minerals showed positive phenotypic and genotypic correlation and high heritability (>60%). The ratio of the σ2g to the σ2g×e was ≥1 for the two mineral contents indicating that breeding for increasing mineral content within the synthetic lines is possible. The synthetic wheat lines identified in this study are valuable genetic resources, and can be utilized for breeding wheat cultivars with high mineral content.