Relevant bibliographies by topics / DNA and RNA sampling

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'DNA and RNA sampling'

Author: Grafiati
Published: 5 June 2025
Last updated: 16 July 2025

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Journal articles on the topic "DNA and RNA sampling"

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Maass, Kendra K., Paulina S. Schad, Agnes M. E. Finster, et al. "From Sampling to Sequencing: A Liquid Biopsy Pre-Analytic Workflow to Maximize Multi-Layer Genomic Information from a Single Tube." Cancers 13, no. 12 (2021): 3002. http://dx.doi.org/10.3390/cancers13123002.

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Liquid biopsies hold great promise for the management of cancer. Reliable liquid biopsy data depend on stable and reproducible pre-analytical protocols that comply with quality measures, irrespective of the sampling and processing site. We established a workflow for plasma preservation, followed by processing, cell-free nucleic acid isolation, quantification, and enrichment of potentially tumor-derived cell-free DNA and RNA. Employing the same input material for a direct comparison of different kits and protocols allowed us to formulate unbiased recommendations for sample collection, storage, and processing. The presented workflow integrates the stabilization in Norgen, PAX, or Streck tubes and subsequent parallel isolation of cell-free DNA and RNA with NucleoSnap and NucleoSpin. Qubit, Bioanalyzer, and TapeStation quantification and quality control steps were optimized for minimal sample use and high sensitivity and reproducibility. We show the efficiency of the proposed workflow by successful droplet digital PCR amplification of both cell-free DNA and RNA and by detection of tumor-specific alterations in low-coverage whole-genome sequencing and DNA methylation profiling of plasma-derived cell-free DNA. For the first time, we demonstrated successful parallel extraction of cell-free DNA and RNA from plasma samples. This workflow paves the road towards multi-layer genomic analysis from one single liquid biopsy sample.
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Shim, Hyunjin. "NAD: Noise-augmented direct sequencing of target nucleic acids by augmenting with noise and selective sampling." F1000Research 14 (April 10, 2025): 423. https://doi.org/10.12688/f1000research.163516.1.

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Background Next-generation sequencing necessitates a minimum quantity and concentration of DNA/RNA samples, typically achieved through amplification using the PCR technique. However, this amplification step introduces several drawbacks to biological insights, including PCR bias and the loss of epigenetic information. The advent of long-read sequencing technologies facilitates direct sequencing, with the primary constraint being the limited amount of DNA/RNA present in biological samples. Methods Here, we present a novel method called Noise-Augmented Direct (NAD) sequencing that enables the direct sequencing of target DNA even when it falls below the minimum quantity and concentration required for long-read sequencing by augmenting with noise DNA and adaptive sampling. Adaptive sampling is an emerging technology of nanopore sequencing, allowing the enhanced sequencing of target DNA by selectively depleting noise DNA. In this study, we use the DNA standard of the Lambda phage genome as the noise DNA to augment samples containing low amounts of bacterial genomes (1 ng to 300 ng). Results The results with cost-effective flow cells indicate that NAD sequencing successfully detects the target DNA with an input quantity as low as 1 ng, and the bacterial genome of Salmonella enterica can be assembled to 30% completion at an accuracy of 98% with an input quantity of 3 ng. With high throughput flow cells, the bacterial genome of Pseudomonas aeruginosa was assembled to near completion (99.9%) at an accuracy of 99.97% with an input quantity of 300 ng. Conclusions This proof-of-concept study demonstrates the potential of NAD sequencing in enhancing the robustness of long-read sequencing for small input DNA/RNA samples with noise augmentation and adaptive sampling.
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Liu, Jun, and Ning Gao. "Impact of sample characteristics on RNA-based next-generation sequencing (NGS) for fusion gene detection in non-small cell lung cancer (NSCLC)." Journal of Clinical Oncology 43, no. 16_suppl (2025): 3132. https://doi.org/10.1200/jco.2025.43.16_suppl.3132.

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3132 Background: RNA-based next-generation sequencing (NGS) has been widely employed for detecting fusion genes in NSCLC, due to its superior sensitivity and simplified design compared to DNA-based NGS. However, the impact of sample quality on fusion variant detection using RNA-based NGS remains unclear. Methods: The study analyzed 5,386 and 5,538 NSCLC samples using DNA- or RNA-based NGS to detect common fusion genes (ALK, RET, ROS1, NTRK, NRG1, MET exon 14 skipping, and FGFR). NGS libraries were constructed using capture-based or amplicon-based methods for DNA and RNA samples, respectively, focusing on pathogenic mutations. Results: RNA-based NGS detected 2.44% more fusions than DNA-based NGS [9.50% (526/5538) vs. 7.06% (380/5386)], with notable advantages for NTRK (0.13% vs. 0.02%), NRG1 (0.25% vs. 0.06%), MET exon 14 skipping (2.15% vs. 1.36%), and FGFR fusions (0.40% vs. 0.02%). Tumor cell content analysis showed no significant impact on fusion detection rates within the 20%-90% range for either method. However, higher tumor cell content (≥80%) significantly increased RNA-based NGS detection rates compared to DNA-based NGS, nearly doubling the total detection rate (17.3% vs. 8.88%), primarily due to increased ALK fusion detection (8.97% vs. 5.02%). The type of sampling (surgical, biopsy, or others) did not significantly affect overall fusion detection rates for either method (p > 0.05). However, gene-specific analyses showed significantly higher detection rates for ROS1, MET, and RET using RNA-based NGS in biopsy samples compared to DNA-based methods (ROS1: 11.83% vs. 1.18%, MET exon 14 skipping: 2.87% vs. 1.62%, RET: 1.24% vs. 0.79%). Conversely, RNA-based detection of ALK and NRG1 fusions was higher in surgical samples (ALK: 4.00% vs. 3.25%, NRG1: 0.34% vs. 0.08%) compared to DNA-based methods. Regarding sample types, pleural/peritoneal effusions showed higher detection rates than FFPE samples, though not statistically significant. RNA-based NGS consistently showed superior detection rates for ALK and MET exon 14 skipping in all sample types compared to DNA-based methods, with the most substantial increase for MET exon 14 skipping in pleural/peritoneal effusions (2.14% vs. 0.98%). Conversely, RNA-based NGS for NRG1 and ROS1 fusions showed a greater relative increase in detection rate in 10% neutral formalin-fixed tissue/FFPE sections/unstained slides compared to pleural/peritoneal effusions. Conclusions: Sample characteristics did not significantly impact the overall detection rate of RNA-based fusion assays. However, detection rates for specific fusions like ALK, NRG1, and MET exon 14 skipping varied with sample type, sampling method, and tumor cell content. Optimizing testing strategies and sample handling is crucial to improving diagnostic accuracy in NSCLC.
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Chu, T. Y., K. S. Hwang, M. H. Yu, H. S. Lee, H. C. Lai, and J. Y. Liu. "A research-based tumor tissue bank of gynecologic oncology: characteristics of nucleic acids extracted from normal and tumor tissues from different sites." International Journal of Gynecologic Cancer 12, no. 2 (2002): 171–76. http://dx.doi.org/10.1136/ijgc-00009577-200203000-00006.

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This article describes a gynecology and pathology-oriented tumor tissue bank that is approaching the research requirements of modern molecular oncology and compared characteristics of nucleic acids extracted from preserved tissues. Through August 2000, 8869 specimens, including fresh neoplastic tissues and normal counterparts, body fluids (ascites, tumor content, and blood), and cervical scrapings, were procured from 1853 patients. DNA and RNA were extracted from a random sampling of normal (n= 50) and tumor (n= 53) tissues from the uterine cervix (n= 47), endometrium (n= 24), and ovary (n= 32). As expected, tumor tissues conferred a higher yield of DNA (1.56 ± 1.24 versus 0.94 ± 0.72 μg/mg tissue,P= 0.001) and RNA (5.04 ± 6.21 versus 2.12 ± 1.76 μg/ml,P< 0.001) than normal tissues. However, the RNA message abundance, as measured by RNA yield/DNA yield, was not different between tumor and normal tissues. With a similar content of DNA in the endometrium, uterine cervix, and ovary, RNA yield was higher in the endometrium than the others (P= 0.013). In tumors from these three sites, similar yields of DNA and RNA were noted. Overall the yield of DNA remained unchanged from specimens preserved for as long as 7 years, although at this length of storage, RNA yield became lower and variable. This study provides the basic characteristics of nucleic acids derived from normal and tumor tissues and ensures future research utility of these frozen specimens.
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Kapadia, Jay Bhakti, Nawwaf Kharma, Alen Nellikulam Davis, Nicolas Kamel, and Jonathan Perreault. "Toehold-mediated strand displacement to measure released product from self-cleaving ribozymes." RNA 28, no. 2 (2021): 263–73. http://dx.doi.org/10.1261/rna.078823.121.

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This paper presents a probe comprising a fluorophore and a quencher, enabling measurement of released product from self-cleaving hammerhead ribozyme, without labeled RNA molecules, regular sampling or use of polyacrylamide gels. The probe is made of two DNA strands; one strand is labeled with a fluorophore at its 5′-end, while the other strand is labeled with a quencher at its 3′-end. These two DNA strands are perfectly complementary, but with a 3′-overhang of the fluorophore strand. These unpaired nucleotides act as a toehold, which is utilized by a detached cleaved fragment (coming from a self-cleaving hammerhead ribozyme) as the starting point for a strand displacement reaction. This reaction causes the separation of the fluorophore strand from the quencher strand, culminating in fluorescence, detectable in a plate reader. Notably, the emitted fluorescence is proportional to the amount of detached cleaved-off RNAs, displacing the DNA quencher strand. This method can replace or complement radio-hazardous unstable 32P as a method of measurement of the product release from ribozyme cleavage reactions; it also eliminates the need for polyacrylamide gels, for the same purpose. Critically, this method allows to distinguish between the total amount of cleaved ribozymes and the amount of detached fragments, resulting from that cleavage reaction.
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Martell, Danya J., Chandra P. Joshi, Ahmed Gaballa, et al. "Metalloregulator CueR biases RNA polymerase’s kinetic sampling of dead-end or open complex to repress or activate transcription." Proceedings of the National Academy of Sciences 112, no. 44 (2015): 13467–72. http://dx.doi.org/10.1073/pnas.1515231112.

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Metalloregulators respond to metal ions to regulate transcription of metal homeostasis genes. MerR-family metalloregulators act on σ70-dependent suboptimal promoters and operate via a unique DNA distortion mechanism in which both the apo and holo forms of the regulators bind tightly to their operator sequence, distorting DNA structure and leading to transcription repression or activation, respectively. It remains unclear how these metalloregulator−DNA interactions are coupled dynamically to RNA polymerase (RNAP) interactions with DNA for transcription regulation. Using single-molecule FRET, we study how the copper efflux regulator (CueR)—a Cu+-responsive MerR-family metalloregulator—modulates RNAP interactions with CueR’s cognate suboptimal promoter PcopA, and how RNAP affects CueR−PcopAinteractions. We find that RNAP can form two noninterconverting complexes at PcopAin the absence of nucleotides: a dead-end complex and an open complex, constituting a branched interaction pathway that is distinct from the linear pathway prevalent for transcription initiation at optimal promoters. Capitalizing on this branched pathway, CueR operates via a “biased sampling” instead of “dynamic equilibrium shifting” mechanism in regulating transcription initiation; it modulates RNAP’s binding–unbinding kinetics, without allowing interconversions between the dead-end and open complexes. Instead, the apo-repressor form reinforces the dominance of the dead-end complex to repress transcription, and the holo-activator form shifts the interactions toward the open complex to activate transcription. RNAP, in turn, locks CueR binding at PcopAinto its specific binding mode, likely helping amplify the differences between apo- and holo-CueR in imposing DNA structural changes. Therefore, RNAP and CueR work synergistically in regulating transcription.
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Lin, Lynlee L., Tarl W. Prow, Anthony P. Raphael, et al. "Microbiopsy engineered for minimally invasive and suture-free sub-millimetre skin sampling." F1000Research 2 (May 2, 2013): 120. http://dx.doi.org/10.12688/f1000research.2-120.v1.

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We describe the development of a sub-millimetre skin punch biopsy device for painless and suture-free skin sampling for molecular diagnosis and research. Conventional skin punch biopsies range from 2-4 mm in diameter. Local anaesthesia is required and sutures are usually used to close the wound. Our microbiopsy is 0.50 mm wide and 0.20 mm thick. The microbiopsy device is fabricated from three stacked medical grade stainless steel plates tapered to a point and contains a chamber within the centre plate to collect the skin sample. We observed that the application of this device resulted in a 0.21 ± 0.04 mm wide puncture site in volunteer skin using reflectance confocal microscopy. Histological sections from microbiopsied skin revealed 0.22 ± 0.12 mm wide and 0.26 ± 0.09 mm deep puncture sites. Longitudinal observation in microbiopsied volunteers showed that the wound closed within 1 day and was not visible after 7 days. Reflectance confocal microscope images from these same sites showed the formation of a tiny crust that resolved by 3 weeks and was completely undetectable by the naked eye. The design parameters of the device were optimised for molecular analysis using sampled DNA mass as the primary end point in volunteer studies. Finally, total RNA was characterized. The optimised device extracted 5.9 ± 3.4 ng DNA and 9.0 ± 10.1 ng RNA. We foresee that minimally invasive molecular sampling will play an increasingly significant role in diagnostic dermatology and skin research.
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Lin, Lynlee L., Tarl W. Prow, Anthony P. Raphael, et al. "Microbiopsy engineered for minimally invasive and suture-free sub-millimetre skin sampling." F1000Research 2 (July 31, 2013): 120. http://dx.doi.org/10.12688/f1000research.2-120.v2.

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We describe the development of a sub-millimetre skin punch biopsy device for minimally invasive and suture-free skin sampling for molecular diagnosis and research. Conventional skin punch biopsies range from 2-4 mm in diameter. Local anaesthesia is required and sutures are usually used to close the wound. Our microbiopsy is 0.50 mm wide and 0.20 mm thick. The microbiopsy device is fabricated from three stacked medical grade stainless steel plates tapered to a point and contains a chamber within the centre plate to collect the skin sample. We observed that the application of this device resulted in a 0.21 ± 0.04 mm wide puncture site in volunteer skin using reflectance confocal microscopy. Histological sections from microbiopsied skin revealed 0.22 ± 0.12 mm wide and 0.26 ± 0.09 mm deep puncture sites. Longitudinal observation in microbiopsied volunteers showed that the wound closed within 1 day and was not visible after 7 days. Reflectance confocal microscope images from these same sites showed the formation of a tiny crust that resolved by 3 weeks and was completely undetectable by the naked eye. The design parameters of the device were optimised for molecular analysis using sampled DNA mass as the primary end point in volunteer studies. Finally, total RNA was characterized. The optimised device extracted 5.9 ± 3.4 ng DNA and 9.0 ± 10.1 ng RNA. We foresee that minimally invasive molecular sampling will play an increasingly significant role in diagnostic dermatology and skin research.
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Porter, Ashleigh F., Mang Shi, John-Sebastian Eden, Yong-Zhen Zhang, and Edward C. Holmes. "Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics." Viruses 11, no. 12 (2019): 1092. http://dx.doi.org/10.3390/v11121092.

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DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. By incorporating the sequence of a “blank” experimental control we also highlight the importance of reagent contamination in metagenomic studies. In sum, this work expands our knowledge of the diversity and evolution of DNA viruses and illustrates the utility of meta-transcriptomic data in identifying organisms with DNA genomes.
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Vasudevan, Harish, Abrar Choudhury, Stephanie Hilz, et al. "PATH-36. INTRATUMOR HETEROGENEITY AND BIOINFORMATIC DIFFERENCES INFLUENCE MENINGIOMA MOLECULAR CLASSIFICATION." Neuro-Oncology 23, Supplement_6 (2021): vi123. http://dx.doi.org/10.1093/neuonc/noab196.488.

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Abstract Molecular alterations such as CDKN2A inactivation and TERT promoter mutation are new criteria for grade 3 meningiomas in the 5th edition of the WHO Classification of Tumors of the Central Nervous System. However, consensus approaches to identify copy number variants (CNVs) and short somatic variants in meningiomas are lacking. Here, we performed integrated DNA methylation profiling, RNA-sequencing, and targeted DNA mutational profiling on 10 stereotactically-collected, regionally-distinct samples from 4 meningiomas. Targeted DNA sequencing revealed numerous private short somatic variants from multiple sites within individual meningiomas, including a TERT promoter mutation in only 1 of 2 samples from the same tumor. DNA methylation profiling revealed differences in biologic groups and immune cell enrichment between regionally-distinct samples within individual meningiomas. CNV status was evaluated using DNA methylation profiling and RNA sequencing on 14 stereotactically-collected, regionally-distinct samples from 2 meningiomas. Phylogenetic architectures from DNA methylation profiling and targeted DNA sequencing were highly concordant and shared 99.12% of CNVs while RNA sequencing identified only 39% of the CNVs called from DNA based approaches. Finally, CNV analysis based on single-cell RNA sequencing revealed partially overlapping CNVs across meningioma cells within an individual tumor, suggesting subclonal populations may influence CNV-based meningioma molecular classification and underlie limitations in defining CNVs from bulk RNA-sequencing. In sum, these data highlight the relative strengths and weaknesses of various approaches for molecular analysis of meningiomas complicated by intratumor heterogeneity due to non-tumor cells and subclonal populations of meningioma cells. Future efforts to incorporate molecular analysis into the diagnostic paradigm for meningiomas may require orthogonal validation across multiple platforms or image-guided meningioma sampling to select the most aggressive regions for molecular profiling.
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Dissertations / Theses on the topic "DNA and RNA sampling"

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Michalik, Juraj. "Non-redundant sampling in RNA Bioinformatics." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLX009/document.

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Un échantillonnage statistique est central à de nombreuses méthodes algorithmiques pour la bioinformatique structurale des ARNs, où ils sont couramment utilisés pour identifier des modèles structuraux importants, fournir des résumés des espaces de repliement ou approcher des quantités d'intérêt dans l'équilibre thermodynamique. Dans tous ces exemples, la redondance dans l'ensemble échantillonné est non-informative et inefficace, limitant la portée des applications des méthodes existantes. Dans cette thèse, nous introduisons le concept de l'échantillonnage non-redondante et nous explorons ses applications et conséquences en bioinformatique des ARN.Nous commençons par introduire formellement le concept d'échantillonnage non-redondante et nous démontrons que tout algorithme échantillonnant dans la distribution de Boltzmann peut être modifié en une version non-redondante. Son implémentation repose sur une structure de données spécifique et la modification d'une remontée stochastique pour fournir l'ensemble des structures uniques, avec la même complexité.Nous montrons alors une exemple pratique en implémentant le principe d'échantillonnage non-redondant au sein d'un algorithme combinatoire qui échantillonne des structures localement optimales. Nous exploitons cet outil pour étudier la cinétique des ARN, modélisant des espaces de repliement générés à partir des structures localement optimales. Ces structures agissent comme des pièges cinétiques, rendant leur prise en compte essentielle pour analyser la dynamique des ARN. Des résultats empirique montrent que des espaces de repliement générés à partir des échantillons non-redondants sont plus proches de la réalité que ceux obtenus par un échantillonnage classique.Nous considérons ensuite le problème du calcul efficace d'estimateurs statistiques à partir d'échantillons non redondants. L'absence de la redondance signifie que l'estimateur naïf, obtenu en moyennant des quantités observés dans l'échantillon, est erroné. Par contre, nous établissons un estimateur non-trivial non-biaisé spécifique aux échantillons non-redondants suivant la distribution de Boltzmann. Nous montrons que l'estimateur des échantillons non-redondants est plus efficace que l'estimateur naïf, notamment dans les cas où la majorité des l'espace de recherche est échantillonné.Finalement, nous introduisons l'algorithme d'échantillonnage, avec sa contre-partie non-redondante, pour des structures secondaires présentant des pseudonoeuds de type simple. Des pseudonoeuds sont typiquement omis pour des raisons d'efficacité, bien que beaucoup d'entre eux possèdent une grande importance biologique. Nos commençons par proposer une schéma de programmation dynamique qui permet d'énumérer tous les pseudonoeuds composés de deux hélices pouvant contenir des bases non-appariés qui s'entrecroisent. Ce schéma généralise la proposition de Reeders et Giegerich, choisi pour sa base complexité temporelle et spatiale. Par la suite, nous expliquons comment adapter cette décomposition à un algorithme d'échantillonnage statistique pour des pseudonoeuds simples. Finalement, nous présentons des résultats préliminaires et nous discutons sur l'extension de principe non-redondant dnas ce contexte.Le travail présenté dans cette thèse ouvre non seulement la porte à l'analyse cinétique des séquences d'ARN plus longues, mais aussi l'analyse structurale plus détaillée des séquences d'ARN en général. L'échantillonnage non-redondant peut être employé pour analyser des espaces de recherche pour des problèmes combinatoires susceptibles à l'échantillonnage statistique, y inclus virtuellement tous problèmes solvables par la programmation dynamique. Les principes d'échantillonnage non-redondant sont robustes et typiquement faciles à implémenter, comme démontré par l'inclusion d'échantillonnage non-redondant dans les versions récentes de Vienna package populaire<br>Sampling methods are central to many algorithmic methods in structural RNA bioinformatics, where they are routinely used to identify important structural models, provide summarized pictures of the folding landscapes, or approximate quantities of interest at the thermodynamic equilibrium.In all of these examples, redundancy within sampled sets is uninformative and computationally wasteful, limiting the scope of application of existing methods.In this thesis, we introduce the concept of non-redundant sampling, and explore its applications and consequences in RNA bioinformatics.We begin by formally introducing the concept of non-redundant sampling and demonstrate that any algorithm sampling in Boltzmann distribution can be modified into non-redundant variant. Its implementation relies on a specific data structure and a modification of the stochastic backtrack to return the set of unique structures, with the same complexity.We then show a practical example by implementing the non-redundant principle into a combinatorial algorithm that samples locally optimal structures. We use this tool to study the RNA kinetics by modeling the folding landscapes generated from sets of locally optimal structures. These structures act as kinetic traps, influencing the outcome of the RNA kinetics, thus making their presence crucial. Empirical results show that the landscapes generated from the non-redundant samples are closer to the reality than those obtained by classic approaches.We follow by addressing the problem of the efficient computation of the statistical estimates from non-redundant sampling sets. The absence of redundancy means that the naive estimator, obtained by averaging quantities observed in a sample, is erroneous. However we establish a non-trivial unbiased estimator specific to a set of unique Boltzmann distributed secondary structures. We show that the non-redundant sampling estimator performs better than the naive counterpart in most cases, specifically where most of the search space is covered by the sampling.Finally, we introduce a sampling algorithm, along with its non-redundant counterpart, for secondary structures featuring simple-type pseudoknots. Pseudoknots are typically omitted due to complexity reasons, yet many of them have biological relevance. We begin by proposing a dynamic programming scheme that allows to enumerate all recursive pseudoknots consisting of two crossing helices, possibly containing unpaired bases. This scheme generalizes the one proposed by Reeders and Giegerich, chosen for its low time and space complexities. We then explain how to adapt this decomposition into a statistical sampling algorithm for simple pseudoknots. We then present preliminary results, and discuss about extensions of the non-redundant principle in this context.The work presented in this thesis not only opens the door towards kinetics analysis for longer RNA sequences, but also more detailed structural analysis of RNAs in general. Non-redundant sampling can be applied to analyze search spaces for combinatorial problems amenable to statistical sampling, including virtually any problem solved by dynamic programming. Non-redundant sampling principles are robust and typically easy to implement, as demonstrated by the inclusion of non-redundant sampling in recent versions of the popular Vienna package
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Gil, Ley Alejandro. "Enhanced sampling and force field corrections for RNA oligomers." Doctoral thesis, SISSA, 2016. http://hdl.handle.net/20.500.11767/4628.

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The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics. Improvement of force fields is however hindered by the diiculties of decoupling those errors from the statistical errors caused by insuicient sampling. We here tackle both problems by introducing a novel enhancing sampling method and using experimental data to improve RNA force fields. In this novel method, concurrent well-tempered metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strength of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers associated to individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. Additionally, a modified metadynamics algorithm is used to calculate correcting potentials designed to enforce distributions of backbone torsion angles taken from experimental structures. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations reveal the importance of the α and ζ backbone angles for the modulation of the RNA conformational ensemble. The correction protocol presented here suggests a systematic procedure for force-field refinement.
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Buttner, M. "RNA polymerase - DNA interactions in Streptomyces." Thesis, University of Bristol, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.354445.

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Nandakumar, Jayakrishnan. "Discrimination of RNA versus DNA by an RNA ligase and distinct modes of substrate recognition by DNA ligases /." Access full-text from WCMC:, 2007. http://proquest.umi.com/pqdweb?did=1428838891&sid=13&Fmt=2&clientId=8424&RQT=309&VName=PQD.

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Gilea, Manuela Aurora. "DNA and RNA synthesis in ionic liquids." Thesis, Queen's University Belfast, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485198.

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The solid-phase synthesis of oligonucleotide derivatives such as phosphorothioates and phosphoroselenoates was investigated. Some ionic liquids containing the trlbexyl(tetradecyl)phosphonium cation and various anions proved to be very effective in dissolving the chalcogens (sulfur and , selenium) and to prepare oligonucleoside chalcogenophosphates. The suitability ofionic liquid-based chalcogen-transfer mixtures for the synthesis of oligonucleoside chalcogenophosphates on solid-phase was evaluated and subsequently the structure-activity relationship studied in detail. The compatibility of ionic liquid-based chalcogen-transfer mixtures with diverse types of solid supports e.g. controlled-pore glass, poly(vinylacetate) and. different synthetic methods. e.g. phosphoramidite and H-phosphonate method makes them useful as replacement of the more expensive and relatively unstable commerciaily avai1able chalcogen-transfer reagents. The distillation of ionic liquids was also studied.
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Antson, Dan-Oscar. "Genotyping RNA and DNA using padlock probes." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-5057-1/.

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Zhu, Jian. "The stabilities of RNA and DNA structural elements." Diss., Georgia Institute of Technology, 1998. http://hdl.handle.net/1853/25194.

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Hill, G. R. "NMR studies of DNA and RNA binding proteins." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604060.

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HMG-D is a 112-residue, non-histone chromosomal protein from <i>Drosophila melanogaster </i>and is a member of the class of non-sequence specific HMGB proteins. The present project was based on the observation that other HMGB complexes that had been solved by NMR had a phenylalanine residue at a key interfacial location (corresponding to position 12 in HMG-D), whereas those like HMG-D that gave few intermolecular NOE cross peaks generally had a tyrosine at this location. This tyrosine was known to be involved in hydrogen-bonding to the DNA in a related complex that had been solved crystallographically. The Y12F mutant of full-length HMG-D was expressed and purified in isotope-labelled form suitable for NMR spectroscopy, and a set of multidimensional triple resonance experiments used to derive assignments for the backbond resonances of the protein both free and in complex with the dA<sub>2 </sub>bulge DNA. Sidechain assignments for the protein were obtained by a combination of “CCH”-transfer-based experiments and NOE spectra, while nearly complete assignments for the DNA in the complex were obtained from a combination of homonuclear 2D NOESY and TOCSY experiments together with filtered NOESY experiments where just cross peaks between protons both of which were not coupled to heteronuclei were selected. Filtered NOESY-based experiments were used to observe intermolecular NOE cross peaks in isolation, and, in contrast to the case of the wild-type complex, these experiments yielded around 50 intermolecular interactions. Together with an extensive set of assigned intramolecular NOE constraints, these formed the basis for a calculation of the structure of the complex starting from random conformations of both protein and DNA chains, which resulted in an NMR structure for the complex that had good precision over the structured region (residues 3-70 of the protein and stem 1 of the DNA).
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O'Hanlon, Karen Ann. "Studies on the enzyme DNA-dependent RNA polymerase." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.266340.

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Pritchard, Hannah Louise. "Recognition agents for DNA and RNA quadruplex structures." Thesis, University of Birmingham, 2015. http://etheses.bham.ac.uk//id/eprint/5727/.

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The design and synthesis of a new class of G-quadruplex DNA recognition agents are discussed in this thesis along with their binding abilities to both duplex and G-quadruplex forming DNA. A selection of G-quadruplex binders reported in the literature to date have been reviewed and their interactions with the quadruplex DNA structure analysed. The biisoquinoline ligand used to incorporate into the metal complexes synthesised in this thesis was chosen because of its large aromatic surface area which is ideal for end stacking onto G-quartets. Both the palladium and platinum biisoquinoline complexes bind to quadruplex forming DNA, monitored by UV-vis and circular dichroism. The platinum complex has the most promising DNA binding results showing a selectivity for quadruplex DNA over duplex DNA when examined by gel electrophoresis. Biisoquinoline complex interactions with RNA G-quadruplexes have been investigated to make comparisons of that with DNA. The palladium complex binds less well to parallel quadruplex conformers suggesting its mode of interaction differs from that of the platinum complex. A toxicity assay against two cancer cell lines showed the platinum and palladium complexes to have IC\(_{50}\) values in the nM range. Modifications to the biisoquinoline structure were also attempted in order increase the specificity of the complex to G-quadruplexes by incorporating components that could interact with the quadruplex loops.
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Books on the topic "DNA and RNA sampling"

1

Smith, Harold C., ed. RNA and DNA Editing. John Wiley & Sons, Inc., 2008. http://dx.doi.org/10.1002/9780470262269.

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Erdmann, Volker A., Stefan Jurga, and Jan Barciszewski, eds. RNA and DNA Diagnostics. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-17305-4.

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Sinkovics, Joseph G. RNA/DNA and Cancer. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-22279-0.

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Aphasizhev, Ruslan, ed. RNA and DNA Editing. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-018-8.

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A, Melton Douglas, and Cold Spring Harbor Laboratory, eds. Antisense RNA and DNA. Cold Spring Harbor Laboratory, 1988.

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Valero, Julián, ed. DNA and RNA Origami. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3028-0.

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H, Murray James A., ed. Antisense RNA and DNA. Wiley-Liss, 1992.

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Harwood, Adrian J. Basic DNA and RNA Protocols. Humana Press, 1996. http://dx.doi.org/10.1385/089603402x.

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Anders, Hans-Joachim, and Adriana Migliorini, eds. Innate DNA and RNA Recognition. Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0882-0.

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J, Harwood Adrian, ed. Basic DNA and RNA protocols. Humana Press, 1996.

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Book chapters on the topic "DNA and RNA sampling"

1

Goddard, William A. "DNA-RNA." In Computational Materials, Chemistry, and Biochemistry: From Bold Initiatives to the Last Mile. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-18778-1_69.

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Arnemann, J. "DNA-/RNA-Konzentrationsbestimmung." In Springer Reference Medizin. Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-48986-4_3464.

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Arnemann, J. "DNA-/RNA-Konzentrationsbestimmung." In Lexikon der Medizinischen Laboratoriumsdiagnostik. Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-662-49054-9_3464-1.

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Piro, Benoît, Vincent Noël, and Steeve Reisberg. "DNA and PNA Probes for DNA Detection in Electroanalytical Systems." In RNA Technologies. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-17305-4_3.

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Landweber, Laura. "RNA based computing: Some examples from RNA catalysis and RNA editing." In DNA Based Computers II. American Mathematical Society, 1998. http://dx.doi.org/10.1090/dimacs/044/15.

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Hoehn, Sean J., Naishka E. Caldero-Rodríguez, and Carlos E. Crespo-Hernández. "CHAPTER 9. Photochemistry of RNA, RNA Monomers, and Plausible Prebiotic Precursors." In DNA Photodamage. Royal Society of Chemistry, 2021. http://dx.doi.org/10.1039/9781839165580-00197.

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Kular, Lara, and Maja Jagodic. "DNA Methylation in Multiple Sclerosis." In RNA Technologies. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-14792-1_8.

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Lu, Shuhan, Ying Zhang, and Hao Yin. "Chimeric DNA–RNA Guide RNA Designs." In Methods in Molecular Biology. Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0687-2_6.

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Ulmer, Jeffrey B. "DNA Vaccines Against RNA Viruses." In DNA Vaccines. Springer US, 2003. http://dx.doi.org/10.1007/978-1-4615-0105-3_7.

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Noel, Vincent, Benoit Piro, and Steeve Reisberg. "DNA for Non-nucleic Acid Sensing." In RNA Technologies. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-17305-4_4.

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Conference papers on the topic "DNA and RNA sampling"

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De Paula, Renato, Cruz St Peter, Ian Alex Richardson, et al. "DNA Sequencing of Oilfield Samples: Impact of Protocol Choices on the Microbiological Conclusions." In CORROSION 2018. NACE International, 2018. https://doi.org/10.5006/c2018-11662.

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Abstract In the last decade, molecular microbiology techniques have significantly expanded the understanding of the resident microflora in hydrocarbon reservoirs and production systems. These methods have been steadily accepted by the industry and are widely viewed as accurate, comprehensive and highly valuable tools that augment or may eventually replace conventional methods. The resulting information has helped operators and service companies to develop better monitoring programs, assess risks and tailor mitigation strategies to control undesired microbial activities in wells, flowlines and separation facilities. Nonetheless, many molecular procedures cannot be performed onsite and samples are typically sent offsite for specialized analyses. The lack of standard procedures hinders comparison of findings between laboratories. Operators currently use dissimilar sampling and preservation protocols, different methods for DNA extraction, separate sequencing platforms and varied approaches for the analyses of the resulting molecular data. In this study, we retrieved multiple samples from several wells in an onshore oilfield and submitted them for 16S rDNA taxonomic analysis in two different laboratories. The results showed significant differences between laboratories in the total abundance of organisms, their taxonomic composition and the presence/absence of certain diagnostic bacteria. Close examination of the protocols revealed that the sample preservation techniques and specific 16S rDNA gene primer sets likely had a significant impact on the resulting information. Collectively, this experience suggests that while molecular techniques are extremely powerful tools to analyze oilfield microbiology, the lack of consensus on an industry wide protocol may lead to discrepancies that could negatively impact the exploitation of these promising methods.
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Triananda, Gregory, Dylan Febrian, Bakti Amirul Jabar, Fredy Purnomo, and Simeon Yuda Prasetyo. "Use of Deep Learning to Identify COVID-19 through DNA/RNA Sequencing." In 2024 4th International Conference on Electronic and Electrical Engineering and Intelligent System (ICE3IS). IEEE, 2024. https://doi.org/10.1109/ice3is62977.2024.10775533.

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Anika, Niranjana S, Prerna Kriti, Sumathra M, and A. H. Manjunath Reddy. "Fluorescent Nucleic Acid Biosensors: A Comparative Study of DNA and RNA-Based Sensing Platforms." In 2024 8th International Conference on Computational System and Information Technology for Sustainable Solutions (CSITSS). IEEE, 2024. https://doi.org/10.1109/csitss64042.2024.10816759.

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Whulanza, Yudan, Andriko Indriantomo, Cosmas Nurdiyantoko, and Ridho Irwansyah. "Characterisation of Microfluidic Systems for Automated Extraction Device of DNA Sampling." In Seminar Nasional Tahunan Teknik Mesin XXII 2024. Badan Kerja Sama Teknik Mesin Indonesia, 2025. https://doi.org/10.71452/590886.

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Engels, Joachim W., Thomas J. Lehmann, Jörg Parsch, and Thorsten Strube. "Fluorine substituted DNA and RNA." In XIIth Symposium on Chemistry of Nucleic Acid Components. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2002. http://dx.doi.org/10.1135/css200205245.

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Joby, George, K. Vrinda, Govindan Chandana, Surendran Arundhathy, and Biju Avany. "DNA RNA binding protein prediction." In MULTIMEDIA UNIVERSITY ENGINEERING CONFERENCE 2023 (MECON2023). AIP Publishing, 2024. http://dx.doi.org/10.1063/5.0230564.

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Oktaviani, Deti Astrit, Mohamad Zulman Hakim, and Dirvi Surya Abbas. "Pengaruh Leverage, Profitabilitas, Ukuran Perusahaan, Dan Likuiditas Terhadap Tax Avoidance." In SEMINAR NASIONAL DAN CALL FOR PAPER 2020 FAKULTAS EKONOMI DAN BISNIS UNIVERSITAS MUHAMMADIYAH JEMBER. UM Jember Press, 2021. http://dx.doi.org/10.32528/psneb.v0i0.5195.

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Tujuan dari penelitian ini untuk mengetahui pengaruh leverage (DER), Profitabilitas (ROA), Ukuran perusahaan (SIZE), dan Likuiditas (CR) terhadap Tax Avoidance. Dengan variable dependen tax avoidance yang di proksikann kepada CETR (Cash Effective Tax Rate). Populasi dalam penelitian ini meliputi seluruh perusahaan Food and Beverage yang terdaftar di Bursa Efek Indonesia (BEI) pada tahun 2017 – 2019 yang berjumlah 24 perusahaan dengan menggunakan purposive sampling diperoleh 17 perusahaan yang memenuhi kriteria, dengan jumlah data observasi sebanyak 51 data. Penelitian ini menggunakan analisis regresi data panel dengan bantuan program Eviews 9 . Hasil penelitian ini menunjukkan bahwa secara secara simultan variabel DAR, ROA,SIZE , dan CR berpengaruh terhadap CETR. Sedangkan secara parsial variabel SIZE, dan CR tidak berpengaruh terhadap CETR, sedangkan DAR dan ROA berpengaruh terhadap CETR.Leverage, Profitabilitas, Ukuran Perusahaan, Likuiditas
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Galitsyna, Aleksandra, Anastasia Zharikova, Maria Logacheva, Sergey Razin, Andrey Mironov, and Alexey Gavrilov. "Large-scale analysis of RNA-DNA interactions." In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2018. http://dx.doi.org/10.1109/bibm.2018.8621137.

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Fang, Xiaohong, Sheldon Schuster, Xiaojing Liu, et al. "Molecular beacon biosensors for DNA/RNA analysis." In BiOS 2000 The International Symposium on Biomedical Optics, edited by Patrick A. Limbach, John C. Owicki, Ramesh Raghavachari, and Weihong Tan. SPIE, 2000. http://dx.doi.org/10.1117/12.380499.

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Bielińska-Wa̧ż, D., P. Wa̧ż, W. Nowak, et al. "Similarity and Dissimilarity of DNA∕RNA Sequences." In COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING: Theory and Computation: Old Problems and New Challenges. Lectures Presented at the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007): VOLUME 1. AIP, 2007. http://dx.doi.org/10.1063/1.2836064.

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Reports on the topic "DNA and RNA sampling"

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Fang, Wenwen. RNA-Guided DNA Rearrangements in Breast Cancer. Defense Technical Information Center, 2012. http://dx.doi.org/10.21236/ada574382.

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Dr. Boris Fain. Collective motion sampling in proteins and DNA. Office of Scientific and Technical Information (OSTI), 2000. http://dx.doi.org/10.2172/765120.

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Dugan, L. Elucidation of the Mechanism of Gene Silencing using Small Interferin RNA: DNA Hybrid Molecules. Office of Scientific and Technical Information (OSTI), 2006. http://dx.doi.org/10.2172/900164.

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Laurence, Jeffrey. Antibody to the RNA-Dependent DNA Polymerase of HTLV-III: Characterization and Clinical Associations. Defense Technical Information Center, 1990. http://dx.doi.org/10.21236/ada231466.

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Laurence, Jeffrey. Antibody to the RNA-Dependent DNA Polymerase of HTLV-III: characterization and Clinical Associations. Defense Technical Information Center, 1988. http://dx.doi.org/10.21236/ada227404.

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Laurence, Jeffrey. Antibody to the RNA-Dependent DNA Polymerase of HTLV-III: characterization and Clinical Associations. Defense Technical Information Center, 1988. http://dx.doi.org/10.21236/ada227519.

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Gal-On, Amit, Shou-Wei Ding, Victor P. Gaba, and Harry S. Paris. role of RNA-dependent RNA polymerase 1 in plant virus defense. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7597919.bard.

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Objectives: Our BARD proposal on the impact of RNA-dependent RNA polymerase 1 (RDR1) in plant defense against viruses was divided into four original objectives. 1. To examine whether a high level of dsRNA expression can stimulate RDR1 transcription independent of salicylic acid (SA) concentration. 2. To determine whether the high or low level of RDR1 transcript accumulation observed in virus resistant and susceptible cultivars is associated with viral resistance and susceptibility. 3. To define the biogenesis and function of RDR1-dependent endogenous siRNAs. 4. To understand why Cucumber mosaic virus (CMV) can overcome RDR1-dependent resistance. The objectives were slightly changed due to the unique finding that cucumber has four different RDR1 genes. Background to the topic: RDR1 is a key plant defense against viruses. RDR1 is induced by virus infection and produces viral and plant dsRNAs which are processed by DICERs to siRNAs. siRNAs guide specific viral and plant RNA cleavage or serve as primers for secondary amplification of viral-dsRNA by RDR. The proposal is based on our preliminary results that a. the association of siRNA and RDR1 accumulation with multiple virus resistance, and b. that virus infection induced the RDR1-dependent production of a new class of endogenous siRNAs. However, the precise mechanisms underlying RDR1 induction and siRNA biogenesis due to virus infection remain to be discovered in plants. Major conclusions, solutions and achievements: We found that in the cucurbit family (cucumber, melon, squash, watermelon) there are 3-4 RDR1 genes not documented in other plant families. This important finding required a change in the emphasis of our objectives. We characterized 4 RDR1s in cucumber and 3 in melon. We demonstrated that in cucumber RDR1b is apparently a new broad spectrum virus resistance gene, independent of SA. In melon RDR1b is truncated, and therefore is assumed to be the reason that melon is highly susceptible to many viruses. RDR1c is dramatically induced due to DNA and RNA virus infection, and inhibition of RDR1c expression led to increased virus accumulation which suggested its important on gene silencing/defense mechanism. We show that induction of antiviral RNAi in Arabidopsis is associated with production of a genetically distinct class of virus-activated siRNAs (vasiRNAs) by RNA dependent RNA polymerase-1 targeting hundreds of host genes for RNA silencing by Argonaute-2. Production of vasiRNAs is induced by viruses from two different super groups of RNA virus families, targeted for inhibition by CMV, and correlated with virus resistance independently of viral siRNAs. We propose that antiviral RNAi activate broad-spectrum antiviral activity via widespread silencing of host genes directed by vasiRNAs, in addition to specific antiviral defense Implications both scientific and agricultural: The RDR1b (resistance) gene can now be used as a transcription marker for broad virus resistance. The discovery of vasiRNAs expands the repertoire of siRNAs and suggests that the siRNA-processing activity of Dicer proteins may play a more important role in the regulation of plant and animal gene expression than is currently known. We assume that precise screening of the vasiRNA host targets will lead in the near future for identification of plant genes associate with virus diseases and perhaps other pathogens.
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Hingerty, B. DUPLEX: A molecular mechanics program in torsion angle space for computing structures of DNA and RNA. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/7250412.

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Hingerty, B. DUPLEX: A molecular mechanics program in torsion angle space for computing structures of DNA and RNA. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/10179029.

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Research, Gratis. Vaccines Through History: Smallpox to COVID-19. Gratis Research, 2021. http://dx.doi.org/10.47496/gr.blog.011.

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More recently, as genomes turned out to be promptly decodable, scientists have developed proficient knowledge at developing vaccines that depend on extraction of RNA or DNA from microbes and injecting these into the body.
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