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1
Szablowski, Jerzy O., Joon Pyung Seo, Sangsin Lee, et al. "Monitoring gene expression in the brain with synthetic serum markers." Journal of the Acoustical Society of America 155, no. 3_Supplement (2024): A22. http://dx.doi.org/10.1121/10.0026652.
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Blood tests are among the most common clinical tools due to their low cost, simplicity, and ability to observe many markers at once. However, currently, blood tests can only monitor a fraction of physiological processes that happen to have a serum marker. Here, we will present our work on the development of synthetic serum markers that can track gene expression in intact brain cells with a simple blood test. The synthetic marker approach has several advantages. First, detection of existing markers may be challenging due to their low levels in blood. With a synthetic marker, one can design a reporter that is easy to detect allowing for superior sensitivity. Second, there are large numbers of genes in each cell, but available brain imaging techniques can at most represent only a few signals (e.g., a few colors of fluorescent proteins, or types of MRI contrast). Synthetic serum markers use biochemical detection and can be designed to be massively multiplexed similarly to how thousands of proteins can be detected in blood simultaneously with mass spectrometry. Third, synthetic serum markers can surveil large brain regions, unlike invasive locally implanted devices. Finally, these markers have the potential for inexpensive and simple readout. We show applications of this concept with markers that can cross through an intact blood–brain barrier to report on gene expression and markers whose release from the brain relies on sonobiopsy to provide spatial selectivity.
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Lozano-Ramírez, Nerida, Susanne Dreisigacker, Carolina P. Sansaloni, et al. "Genome-Wide Association Study for Resistance to Tan Spot in Synthetic Hexaploid Wheat." Plants 11, no. 3 (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, et al. "Reconstruction of the Synthetic W7984 × Opata M85 wheat reference population." Genome 54, no. 11 (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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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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Zhao, Hao‐Qian, Wen‐Qing Wei, Chao Zhao, and Ze‐Xiong Xie. "Genomic markers on synthetic genomes." Engineering in Life Sciences 21, no. 12 (2021): 825–31. http://dx.doi.org/10.1002/elsc.202100030.
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Vadas, Evelin, Antonio J. López-Gambero, Antonio Vargas, et al. "Region-Specific Impact of Repeated Synthetic Cannabinoid Exposure and Withdrawal on Endocannabinoid Signaling, Gliosis, and Inflammatory Markers in the Prefrontal Cortex and Hippocampus." Biomolecules 15, no. 3 (2025): 417. https://doi.org/10.3390/biom15030417.
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Synthetic cannabinoid use raises concerns about its neuroinflammatory effects, including molecular adaptations of the endocannabinoid system (ECS) in the brain. This study investigates the pharmacological effects of 14-day repeated intraperitoneal administration, as well as 14-day administration followed by a 7-day withdrawal period of two synthetic cannabinoids: WIN55,212-2 and HU-210. The study assessed gene expression and protein markers related to the ECS, gliosis, and inflammation in two brain regions critical for cognitive processes and memory—key components of addiction pathways—the prefrontal cortex (PFC) and the hippocampus of rats. Our findings showed that repeated WIN55,212-2 administration induced adaptations in the ECS and reduced IBA1, a glial protein marker, along with inflammatory responses likely mediated through CB2 activity. Notably, regional differences emerged in the hippocampus, where repeated administration of WIN55,212-2 and HU-210 increased IBA1 and inflammatory markers, effects unrelated to CB2 activity. Withdrawal from WIN55,212-2 in the PFC, as well as from both compounds in the hippocampus, decreased IBA1 levels. This was associated with altered protein expression of cannabinoid-synthesizing and degrading enzymes, favoring acylethanolamide synthesis. These findings highlight region-specific effects of synthetic cannabinoids on cannabinoid signaling, gliosis, and inflammation. Further research is needed to elucidate the long-term neurobiological consequences of synthetic cannabinoid use and withdrawal.
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Sood, Meemansa, Ulrike Suenkel, Anna-Katharina von Thaler, et al. "Bayesian network modeling of risk and prodromal markers of Parkinson’s disease." PLOS ONE 18, no. 2 (2023): e0280609. http://dx.doi.org/10.1371/journal.pone.0280609.
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Parkinson’s disease (PD) is characterized by a long prodromal phase with a multitude of markers indicating an increased PD risk prior to clinical diagnosis based on motor symptoms. Current PD prediction models do not consider interdependencies of single predictors, lack differentiation by subtypes of prodromal PD, and may be limited and potentially biased by confounding factors, unspecific assessment methods and restricted access to comprehensive marker data of prospective cohorts. We used prospective data of 18 established risk and prodromal markers of PD in 1178 healthy, PD-free individuals and 24 incident PD cases collected longitudinally in the Tübingen evaluation of Risk factors for Early detection of NeuroDegeneration (TREND) study at 4 visits over up to 10 years. We employed artificial intelligence (AI) to learn and quantify PD marker interdependencies via a Bayesian network (BN) with probabilistic confidence estimation using bootstrapping. The BN was employed to generate a synthetic cohort and individual marker profiles. Robust interdependencies were observed for BN edges from age to subthreshold parkinsonism and urinary dysfunction, sex to substantia nigra hyperechogenicity, depression, non-smoking and to constipation; depression to symptomatic hypotension and excessive daytime somnolence; solvent exposure to cognitive deficits and to physical inactivity; and non-smoking to physical inactivity. Conversion to PD was interdependent with prior subthreshold parkinsonism, sex and substantia nigra hyperechogenicity. Several additional interdependencies with lower probabilistic confidence were identified. Synthetic subjects generated via the BN based representation of the TREND study were realistic as assessed through multiple comparison approaches of real and synthetic data. Altogether our work demonstrates the potential of modern AI approaches (specifically BNs) both for modelling and understanding interdependencies between PD risk and prodromal markers, which are so far not accounted for in PD prediction models, as well as for generating realistic synthetic data.
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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 (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 (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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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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Desai, Sonal, and Pratima Tatke. "Phytochemical Markers: Classification, Applications and Isolation." Current Pharmaceutical Design 25, no. 22 (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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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 (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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Lin, Chin-Sheng, Po-Shiuan Hsieh, Ling-Ling Hwang, 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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Čejka, Jan, Fabio Bruno, Dimitrios Skarlatos, and Fotis Liarokapis. "Detecting Square Markers in Underwater Environments." Remote Sensing 11, no. 4 (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 (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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Kim, Gyu-Tae, Ulrike Waizmann, and Siegmar Roth. "Simple efficient coordinate markers for investigating synthetic nanofibers." Applied Physics Letters 79, no. 21 (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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Ondrašovič, Milan, and Peter Tarábek. "Homography Ranking Based on Multiple Groups of Point Correspondences." Sensors 21, no. 17 (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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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 (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, et al. "Two Main Stripe Rust Resistance Genes Identified in Synthetic-Derived Wheat Line Soru#1." Phytopathology® 109, no. 1 (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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Dosoky, Noura S., Ambika Poudel, and Prabodh Satyal. "Authentication and Market Survey of Sweet Birch (Betula lenta L.) Essential Oil." Plants 11, no. 16 (2022): 2132. http://dx.doi.org/10.3390/plants11162132.
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Sweet Birch (Betula lenta) has several economic and medicinal uses. Very little is known about the chemical composition of B. lenta. In this study, the volatile compositions of the bark of B. lenta from authentic and commercial sources were assessed by gas chromatography-mass spectrometry (GC–MS) and gas chromatography–flame ionization detection (GC–FID). Overall, more than 60 compounds were identified in natural sweet birch EO obtained by hydro-distillation. The oil was dominated by methyl salicylate (93.24–99.84%). A good approach to distinguishing wintergreen and birch oils would be biomarker-based analysis. The biomarkers are selected based upon three main criteria: (1) the marker should be commercially unavailable or too expensive which renders the adulteration process very costly, (2) The marker should be detected consistently in all the tested authentic EO samples, and (3) A birch EO marker should be found exclusively in birch EO, not in wintergreen and vice versa. The minor components o-guaiacol, veratrole, 2-E-4-Z-decadienal, and 2-E-4-E-decadienal were identified as natural marker compounds for authentic sweet birch oil. Surprisingly, none of the tested 27 commercial samples contained any of the identified birch markers. The detection of wintergreen markers such as vitispirane and β-dehydroelsholtzia ketone, the synthetic marker dimethyl-2-hydroxyterephthalate, and ricenalidic acid lactone suggest the addition of wintergreen, synthetic methyl salicylate, and castor oil, respectively. This is the first report to identify birch biomarkers to the best of our knowledge.
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Lozano-Ramirez, Nerida, Susanne Dreisigacker, Carolina P. Sansaloni, et al. "Genome-Wide Association Study for Spot Blotch Resistance in Synthetic Hexaploid Wheat." Genes 13, no. 8 (2022): 1387. http://dx.doi.org/10.3390/genes13081387.
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Spot blotch (SB) caused by Bipolaris sorokiniana (Sacc.) Shoem is a destructive fungal disease affecting wheat and many other crops. Synthetic hexaploid wheat (SHW) offers opportunities to explore new resistance genes for SB for introgression into elite bread wheat. The objectives of our study were to evaluate a collection of 441 SHWs for resistance to SB and to identify potential new genomic regions associated with the disease. The panel exhibited high SB resistance, with 250 accessions showing resistance and 161 showing moderate resistance reactions. A genome-wide association study (GWAS) revealed a total of 41 significant marker–trait associations for resistance to SB, being located on chromosomes 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4D, 5A, 5D, 6D, 7A, and 7D; yet none of them exhibited a major phenotypic effect. In addition, a partial least squares regression was conducted to validate the marker–trait associations, and 15 markers were found to be most important for SB resistance in the panel. To our knowledge, this is the first GWAS to investigate SB resistance in SHW that identified markers and resistant SHW lines to be utilized in wheat breeding.
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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 (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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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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Sankar, Muthu, Binod Kumar, Haranahally Vasanthachar Manjunathachar, et al. "Genetic Diversity of Rhipicephalus (Boophilus) microplus for a Global Scenario: A Comprehensive Review." Pathogens 13, no. 6 (2024): 516. http://dx.doi.org/10.3390/pathogens13060516.
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Rhipicephalus microplus poses a substantial threat to livestock health and agricultural economies worldwide. Its remarkable adaptability to diverse environments and hosts is a testament to its extensive genetic diversity. This review delves into the genetic diversity of R. microplus, employing three pivotal genetic markers: the cytochrome c oxidase I (COX1) gene, ribosomal genes, and microsatellites. The COX1 gene, a crucial tool for genetic characterization and phylogenetic clustering, provides insights into the adaptability of ticks. Ribosomal genes, such as internal transcribed spacer regions (ITS-1 and2) as well as 18S and 28S, are routinely utilized for species differentiation. However, their use is limited due to indels (insertions and deletions). Microsatellites and minisatellites, known for their high polymorphism, have been successfully employed to study populations and genetic diversity across various tick species. Despite their effectiveness, challenges such as null alleles and marker variations warrant careful consideration. Bm86, a well-studied vaccine candidate, exhibits substantial genetic diversity. This diversity directly influences vaccine efficacy, posing challenges for developing a universally effective Bm86-based vaccine. Moreover, the review emphasizes the prevalence of genes associated with synthetic pyrethroid resistance. Identifying single nucleotide polymorphisms in the acaricide-resistant genes of R. microplus has facilitated the development of molecular markers for detecting and monitoring resistance against synthetic pyrethroids. However, mutations in sodium channels, the target site for synthetic pyrethroid, correlate well with the resistance status of R. microplus, which is not the case with other acaricide target genes. This study underscores the importance of understanding genetic diversity in developing effective tick management strategies. The choice of genetic marker should be tailored based on the level of taxonomic resolution and the group of ticks under investigation. A holistic approach combining multiple markers and integrating additional molecular and morphological data may offer a more comprehensive understanding of tick diversity and relationships. This research has far-reaching implications in formulating breeding programs and the development of vaccine against ticks and tick-borne diseases (TTBDs) as well as strategies for the management of resistant ticks.
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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 (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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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 (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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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 (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 (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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Upadhyay, Sweta, Sanjay Gupta, Vijay Kumar, and Anjali Uniyal. "In vitro propagation, synthetic seeds production and clonal fidelity assessment of regenerants of endangered herb Rheum emodi." Research Journal of Biotechnology 19, no. 12 (2024): 70–78. https://doi.org/10.25303/1912rjbt070078.
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Rheum emodi, pharmaceutically important medicinal plant is mainly found in northern Himalayas. This herb has therapeutic properties such as anticancerous, antimicrobial, behaves like astringent and improves gastro related problems. All these factors contribute in immense decline of this herb in its natural habitat as it is excessively used by local people for medicinal as well as common eating purpose. We have optimized the efficient in vitro plant regeneration system through the callus from leaf explant and synthetic seed production for this herb. The culture medium used was Murashige and Skoog (MS) basal medium with the different concentration of phytohormones. Highest percentage of callus formation (84.44±0.27%) was observed in MS medium perforated with 2,4-D in combination with BAP. The maximum number of shoots (3.67±0.27) per explant was attained on MS medium with BAP (35.5 μM) and Kn (11.61 μM). For synthetic seed production, encapsulation was done in 3% of sodium alginate+ 50mM CaCl2. The highest survival and germination frequency of somatic embryos without storage period were observed as 78.9±1.33 and 66.7±0.58 respectively. The survival and germination rate of encapsulated embryos at 4 ͦC were significantly reduced as compared to non-stored somatic embryos. For ascertaining the clonal fidelity, 20 ISSR markers and 15 RAPD markers were assayed and employed to validate the true-to-type regenerants of Rheum emodi. Out of 15 RAPD and 20 ISSR markers, 7 markers and 15 markers produced distinct, clear and scorable bands. All the markers produced the monomorphic bands and no variation was detected among the micropropagated plants. Thus, the analysis of ISSR and RAPD patterns revealed that the bands were shared by both the in vitro raised plants and parent clump confirming the genetic stability. These markers proved to be a model tool for routine analysis of clonal fidelity of micropropagated plants prior to commercialization. These protocols could be beneficial in the future for rapid and mass multiplication or propagation of Rheum emodi and dissemination of synthetic or artificial seeds.
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Capetti, Francesca, Arianna Marengo, Cecilia Cagliero, et al. "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 (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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Koshy, Anish. "Re-evaluating Affixes and Clitics in Munda Multi-verb Constructions." Indian Journal of Language and Linguistics 5, no. 3 (2024): 62–75. http://dx.doi.org/10.54392/ijll2436.
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Languages from the same genetic lineage often exhibit differences in certain parameters, but significant variation in their morphological typology is uncommon. Austroasiatic languages present a notable paradox, where Munda languages are categorized as polysynthetic, while Mon-Khmer languages are considered isolating. This contrast within the same linguistic family, with both sub-branches occupying opposite ends of the synthesis continuum, is particularly intriguing. This paper aims to explore whether the morphological disparity between Munda and Mon-Khmer languages can be reconciled by examining specific bound elements in Munda languages that contribute to their synthetic characteristics. The study conducts a detailed analysis of numerous bound elements in Munda languages, comparing these to similar structures in Mon-Khmer languages. The focus is on understanding whether these bound markers are better classified as clitics rather than affixes, especially in the context of multi-verb constructions. The analysis suggests that many bound elements in Munda languages are more likely to be clitics rather than affixes. The study specifically investigates phrase-level affixation involving multi-verbs, concluding that when these markers attach at the phrase level, they should be considered clitics. This study sheds light on the synthetic nature of Munda languages within the Austroasiatic family, arguing for a reclassification of certain bound markers as clitics rather than affixes, particularly in multi-verb constructions. This reclassification could help reconcile the typological differences observed between Munda and Mon-Khmer languages.
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Longinotti, Gloria, Gabriel Ybarra, Susana Vighi, et al. "One Step Histological Detection and Staining of the PTEN Tumor Suppressor Protein by a Single Strand DNA." Diagnostics 11, no. 2 (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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Wen, Juan, Baiyi Tang, Lan Guo, Wei Chen, and Xiaohong Tang. "miR-145 Alleviates Smooth Muscle Cell Phenotype Transition via ADAM17-Mediated ACE2 Shedding." International Journal of Hypertension 2023 (July 20, 2023): 1–14. http://dx.doi.org/10.1155/2023/9497716.
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It has been shown that miR-145 is involved in the differentiation of vascular smooth muscle cells (VSMCs) and may regulate vascular remodeling. However, the molecular mechanisms behind these pathological processes in hypertension are not fully elucidated. The present study was to examine whether miR-145 modulates phenotypic transformation of VSMCs under normal state and synthetic state and to explore the possible role of ADAM17-mediated ACE2 shedding and ACE2-Ang-(1–7)-Mas receptor axis. Wistar rats were fed with high-sucrose/high-fat diet for 30 weeks to establish a metabolic hypertension animal model. VSMCs were cultured and treated with Ang II with or without miR-145 mimics or miR-145 inhibitor. Results showed the expression of contractile markers α-SMA and SM22α, miR-145, ACE2, and Mas receptor reduced in the thoracic aorta of metabolic hypertensive rats (MHRs), while that of synthetic marker OPN increased as compared to the control group. In in vitro study, miR-145 inhibitor inhibited the expression of α-SMA, SM22α, ACE2, Mas receptor, and the Ang-(1–7) excretion and induced the expression of synthetic markers OPN, EREG, and MMP2. However, miR-145 mimic produced opposite effects on the VSMCs. In addition, in the synthetic VSMC induced by Ang II, miR-145 inhibitor partially reversed the induced expression of OPN, EREG, and MMP2 by Ang II, while further decreasing the expression of α-SMA and SM22α and ACE2-Ang-(1–7)-Mas receptor. Cotreatment with ADAM17 siRNA partially reversed the inducible effect of miR-145 inhibitor on the EREG and MMP2, induced Ang-(1–7) excretion, and upregulated ACE2 and Mas receptor expression. In conclusion, miR-145 alleviates phenotype transition from contractile to synthetic type via ADAM17-mediated ACE2 shedding in VSMCs and retains the activation of ACE2-Ang-(1–7)-Mas axis, which may benefit the vascular structural remodeling in the metabolic hypertension.
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Babayeva, M., A. Kerimov, S. Mamedova, and Z. Akperov. "Study of synthetic wheat genotypes based on prolamine protein markers." Science and Innovations 1, no. 12 (2024): 68–72. http://dx.doi.org/10.29235/1818-9857-2023-12-68-72.
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BAI, X. "A55 CHRONIC STRESS IMPAIRS THE INTESTINAL CRYPTAL STEM CELL CYCLE AND PANETH CELL PROLIFERATION." Journal of the Canadian Association of Gastroenterology 8, Supplement_1 (2025): i22—i23. https://doi.org/10.1093/jcag/gwae059.055.
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Abstract Background The small intestine’s epithelial barrier is essential for intestinal homeostasis and host defense. It consists of epithelial cells constantly renewed by crypt stem cells and their progeny, which have different functions in the gut. Chronic stress can impair the barrier by modulating the gut-brain axis, which involves the hypothalamic-pituitary-adrenal (HPA) axis, the vagus nerve, and the immune system. Chronic stress can also alter the gut microbiota, further influencing the barrier and immune system. Aims The present study examines how chronic stress affects the crypt stem cell niche and function in the small intestine. Methods Restraint stress was applied to 6-8 weeks-old mice in a plastic container for 1 hour daily for 7 days. The dark/light transition box test evaluated stress-induced behavior change. The Ussing chamber technique was used to assess the paracellular permeability of the small intestine. RNA was extracted from the mucosa and submucosa layers of the small intestine, after removing the muscle layer, and RNA sequencing analysis was performed. Immunofluorescence analysis was also performed on the small intestinal tissues to detect the expression of various markers. To assess the in vivo effect of cortisol, dexamethasone (a synthetic steroid activating the same receptors as cortisol), or metyrapone (an 11β-hydroxylation blocker to inhibit cortisol production), was applied. To assess the possible involvement of microbiota, antibiotics were applied before and during the restraint stress. Results We found that restraint stress-induced anxiety-like behavior, increased small intestinal epithelial permeability and reduced villus and crypt length in mice. RNA sequencing analysis revealed that restraint stress downregulated the markers of Paneth cells and stem cells in the small intestinal mucosa. Immunofluorescence analysis confirmed that restraint stress reduced the expression of stem cell marker Olfm-4 and proliferation markers Ki-67 and p-H3 in the small intestinal crypts. 16s rRNA analysis showed increased Streptococcus and decreased Bifidobacterium in stressed mice fecal samples. Ablation of gut microbiota by antibiotics attenuated the stress-induced downregulation of stem cell markers but did not affect the Paneth cell markers. Dexamethasone, a synthetic glucocorticoid, mimicked the effects of restraint stress on crypt stem cells and Paneth cells, while metyrapone, a steroid synthesis inhibitor, attenuated both. Conclusions Chronic stress induces anxiety, gut microbiota alteration, and barrier dysfunction. The change in epithelial villi and crypts in the small intestine is in a microbiota-dependent manner. These findings show how chronic stress impacts intestinal epithelial renewal and differentiation, which may affect intestinal health and disease. Funding Agencies JSPS KAKENHI
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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.
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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/s0308229600029937.
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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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 (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 (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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Furmanik, Malgorzata, Martijn Chatrou, Rick van Gorp, et al. "Reactive Oxygen-Forming Nox5 Links Vascular Smooth Muscle Cell Phenotypic Switching and Extracellular Vesicle-Mediated Vascular Calcification." Circulation Research 127, no. 7 (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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Khalid, Maria, Alvina Gul, Rabia Amir, et al. "QTL mapping for seedling morphology under drought stress in wheat cross synthetic (W7984)/Opata." Plant Genetic Resources: Characterization and Utilization 16, no. 4 (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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Molfetta, Matteo Gianluca, Maria Francesca Bruno, Luigi Pratola, et al. "A Sterescopic System to Measure Water Waves in Laboratories." Remote Sensing 12, no. 14 (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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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 (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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Farman, M. L., and S. A. Leong. "Genetic and physical mapping of telomeres in the rice blast fungus, Magnaporthe grisea." Genetics 140, no. 2 (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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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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Iwagaki, Hiromi, Akio Hizuta, Kenta Kobashi, Hiroshi Isozaki, Norihisa Takakura, and Noriaki Tanaka. "Clinical Value of Neopterin In Infectious Complications." Pteridines 10, no. 1 (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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Shafea Saad, Farina Hanif, Shabana Usman Simjee, Shaheen Faizi, Lubna Khan, and Ambreen Ashfaque. "Modulation of Apoptotic and Akt/PI3K/mTOR pathways to target Glioblastoma Cells using synthetic compound PGEA-AN." Journal of the Pakistan Medical Association 74, no. 2 (2024): S39—S46. http://dx.doi.org/10.47391/jpma-duhs-s09.
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Objective: To investigate the anticancer potential of a novel synthetic derivative of a naturally occurringditerpenoid against glioblastoma.Method: The in vitro study was conducted at the Ojha Campus of Dow University of Health Sciences, Karachi, fromFebruary to December 2021, and comprised U87 cells. The 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide assay was used to determine the growth inhibitory effect of 16(R and S) – phenylamino-cleroda3, 13(14) Zdiene-15, 16 olide and standard drug temozolomide against glioblastoma cells, and half-maximal inhibitoryconcentration was calculated. Microscopy and immunocytochemistry were used to investigate apoptoticmorphology and active caspase-3 and B-cell lymphoma 2 (Bcl-2) expression. Quantitative real time polymerasechain reaction was used to investigate the expression of proliferation markers. Data was analysed using SPSS 21.Results: Both the synthetic derivative and the standard drug significantly inhibited growth of U87 cells (p<0.001)with half-maximal inhibitory concentration of 19uM and 185uM, respectively. Apoptotic morphology andupregulation of active caspase-3 protein expression was observed in cells treated with half-maximal inhibitoryconcentration doses of both the synthetic derivative (p<0.05) and the standard drug (p<0.001), and Bcl-2 was downregulatedin both the synthetic derivative (p<0.01) and the standard drug (p=0.05). However, no significantdifference was observed in the expression of proliferation markers (p>0.05).Conclusion: The synthetic diterpene derivative PGEA-AN showed growth inhibitory actiity against glioblastoma.Key Words: Temozolomide, Caspase, Glioblastoma, Diterpenes.