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Journal articles on the topic 'DNA and RNA sampling'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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1

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,

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2

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 dir

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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,

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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

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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 se

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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

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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 0.2

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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 resulte

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9

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 sp

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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 varia

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Khaleefah, Omar Talib, Ahmed M. El-Baz, and Amany Elsaid Badr. "Assessment of access cavity disinfection for bacterial DNA and RNA before root canal sampling using molecular analysis." Ain Shams Dental Journal 37, no. 1 (2025): 195–202. https://doi.org/10.21608/asdj.2024.302807.1362.

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12

Ding, Xinghua, Wensheng Lan, and Ji-Dong Gu. "A Review on Sampling Techniques and Analytical Methods for Microbiota of Cultural Properties and Historical Architecture." Applied Sciences 10, no. 22 (2020): 8099. http://dx.doi.org/10.3390/app10228099.

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World cultural heritage suffers from deterioration caused by both natural and anthropogenic processes, among which microorganisms are significantly involved. Among the key issues of this topic, sampling techniques and analytical methods for revealing the microbiome are fundamental to obtaining useful results for understanding the key players and processes involved, and also for effective protection and management of the cultural heritage for humanity. A non-invasive and non-destructive sampling method is required for sampling of cultural properties prior to further analysis of the microbiome.

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13

Danforth, David N., Andrew C. Warner, Darawalee Wangsa, et al. "An Improved Breast Epithelial Sampling Method for Molecular Profiling and Biomarker Analysis in Women at Risk for Breast Cancer." Breast Cancer: Basic and Clinical Research 9 (January 2015): BCBCR.S23577. http://dx.doi.org/10.4137/bcbcr.s23577.

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Background There is a strong need to define the molecular changes in normal at-risk breast epithelium to identify biomarkers and new targets for breast cancer prevention and to develop a molecular signature for risk assessment. Improved methods of breast epithelial sampling are needed to promote whole-genome molecular profiling, increase ductal epithelial cell yield, and reduce sample cell heterogeneity. Methods We developed an improved method of breast ductal sampling with ductal lavage through a 22-gauge catheter and collection of ductal samples with a microaspirator. Women at normal risk or

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14

Liu, Qingyang. "Application of Environmental DNA in the Air for Monitoring Biodiversity." Sustainability 17, no. 12 (2025): 5530. https://doi.org/10.3390/su17125530.

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There is a profound interdependence between biodiversity and the UN Sustainable Development Goals (SDGs). Biodiversity underpins the functioning of global ecosystems and human welfare, and the achievement of numerous SDGs is directly or indirectly linked to protecting and sustainably managing biodiversity. In recent years, environmental DNA (eDNA) technology has exerted a great impact in the field of biodiversity monitoring. Airborne eDNA plays a significant role due to its non-invasive nature and the ability to monitor multiple taxonomic groups simultaneously. This review summarizes the techn

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15

Dang, Zhenyu, Jixuan Yang, Lin Wang, et al. "Sampling Variation of RAD-Seq Data from Diploid and Tetraploid Potato (Solanum tuberosum L.)." Plants 10, no. 2 (2021): 319. http://dx.doi.org/10.3390/plants10020319.

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The new sequencing technology enables identification of genome-wide sequence-based variants at a population level and a competitively low cost. The sequence variant-based molecular markers have motivated enormous interest in population and quantitative genetic analyses. Generation of the sequence data involves a sophisticated experimental process embedded with rich non-biological variation. Statistically, the sequencing process indeed involves sampling DNA fragments from an individual sequence. Adequate knowledge of sampling variation of the sequence data generation is one of the key statistic

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16

Zhang, Qian, Ziting Chen, Fangzhu Wang, et al. "Efficient DNA interrogation of SpCas9 governed by its electrostatic interaction with DNA beyond the PAM and protospacer." Nucleic Acids Research 49, no. 21 (2021): 12433–44. http://dx.doi.org/10.1093/nar/gkab1139.

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Abstract Streptococcus pyogenes Cas9 (SpCas9), a programmable RNA-guided DNA endonuclease, has been widely repurposed for biological and medical applications. Critical interactions between SpCas9 and DNA confer the high specificity of the enzyme in genome engineering. Here, we unveil that an essential SpCas9–DNA interaction located beyond the protospacer adjacent motif (PAM) is realized through electrostatic forces between four positively charged lysines among SpCas9 residues 1151–1156 and the negatively charged DNA backbone. Modulating this interaction by substituting lysines with amino acids

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17

Ray, Dhiman, and Ioan Andricioaei. "Hoogsteen Base Pairing in DNA vs RNA: Thermodynamics and Kinetics from Enhanced Sampling Simulation and Markov State Modeling." Biophysical Journal 118, no. 3 (2020): 299a—300a. http://dx.doi.org/10.1016/j.bpj.2019.11.1697.

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18

Li, Meihui, Hong Zhao, Fengxi Zhao, et al. "Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)." Annals of Botany 124, no. 2 (2019): 233–43. http://dx.doi.org/10.1093/aob/mcz062.

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Abstract Background and Aims Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models. Methods We examined the phylogenetic implications of the CBC process by using a comprehensive

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19

Turgeon, Nathalie, Marie-Josée Toulouse, Bruno Martel, Sylvain Moineau, and Caroline Duchaine. "Comparison of Five Bacteriophages as Models for Viral Aerosol Studies." Applied and Environmental Microbiology 80, no. 14 (2014): 4242–50. http://dx.doi.org/10.1128/aem.00767-14.

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ABSTRACTBacteriophages are perceived to be good models for the study of airborne viruses because they are safe to use, some of them display structural features similar to those of human and animal viruses, and they are relatively easy to produce in large quantities. Yet, only a few studies have investigated them as models. It has previously been demonstrated that aerosolization, environmental conditions, and sampling conditions affect viral infectivity, but viral infectivity is virus dependent. Thus, several virus models are likely needed to study their general behavior in aerosols. The aim of

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20

Pitz, Kathleen, Collin Closek, Anni Djurhuus, et al. "Rewards and Challenges of eDNA Sequencing with Multiple Genetic Markers for Marine Observation Programs." Proceedings of TDWG 1 (August 24, 2017): e20548. https://doi.org/10.3897/tdwgproceedings.1.20548.

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Metabarcoding of environmental DNA (eDNA) samples holds new promise to increase our ability to measure changes in biodiversity and community composition over time. It can allow the characterization of large groups of organisms where traditional sampling may be impractical or not cost-effective. However, it is still unclear how best to compare and combine this information with morphological counts in order to inform policies and biodiversity metrics that are based on traditional sampling results. Under the Marine Biodiversity Observation Network (MBON) initiative, multiple taxonomic marker gene

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Zhang, Yu Long, and Tao Dong. "A Membrane-Based Sample Preparation Kit for Waterborne Pathogens: Design and Manufacture." Applied Mechanics and Materials 281 (January 2013): 75–79. http://dx.doi.org/10.4028/www.scientific.net/amm.281.75.

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Membrane-based microfluidic devices have been demonstrated in recent literature to show a significant potential in developing low-cost but high-efficient analytical devices. Usually, the step of sampling and sample preparation is the most importance processes in the whole analytical experiments. This study designed and manufactured a low-cost kit for water sampling and sample preparation of waterborne pathogens, especially protozoan parasites. Subsequently, Saccharomyces cerevisiae was employed as the model microbe to verify the function of kit. The concepts of green design and agile manufactu

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22

Tardif, D., H. Glémet, P. Brodeur, and M. Mingelbier. "RNA/DNA ratio and total length of yellow perch (Perca flavescens) in managed and natural wetlands of a large fluvial lake." Canadian Journal of Fisheries and Aquatic Sciences 62, no. 10 (2005): 2211–18. http://dx.doi.org/10.1139/f05-137.

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RNA/DNA ratios and total lengths were compared to determine growth patterns of age-0 yellow perch (Perca flavescens) in managed and natural habitats of a large fluvial lake (Lake Saint-Pierre, St. Lawrence River, Quebec, Canada) over seasonal and yearly temporal scales. In 2002, the RNA/DNA ratio responded to degree-days accumulated over periods of 78 days before sampling, while in 2003, no relationship with temperature was established. The growth patterns obtained each year probably reflect indices responding to different limiting variables. In 2002, temperature would have been limiting, whe

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23

Sakairi, Yuichi, Sakae Itoga, Kenichi Sato, et al. "Molecular profiling of patients with non-small cell lung cancer (NSCLC) using bronchoscopic ultra-micro sampling." Journal of Clinical Oncology 30, no. 15_suppl (2012): 7046. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.7046.

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7046 Background: Genetic information is essential for molecular targeted therapy for personalized medicine, although tissue sampling for genetic analysis remains challenging. In this study, we investigated the utility of bronchoscopic ultra-micro samples compared with conventional histological materials for multiple gene analyses for NSCLC. Methods: Patients with NSCLC proven by on-site cytological examinations during bronchoscopic survey were eligible. Following conventional needle aspiration biopsy by flexible bronchofiberscope (from primary lesion) or convex probe endobronchial ultrasound (

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24

Muse, S. V. "Evolutionary analyses of DNA sequences subject to constraints of secondary structure." Genetics 139, no. 3 (1995): 1429–39. http://dx.doi.org/10.1093/genetics/139.3.1429.

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Abstract Evolutionary models appropriate for analyzing nucleotide sequences that are subject to constraints on secondary structure are developed. The models consider the evolution of pairs of nucleotides, and they incorporate the effects of base-pairing constraints on nucleotide substitution rates by introducing a new parameter to extensions of standard models of sequence evolution. To illustrate some potential uses of the models, a likelihood-ratio test is constructed for the null hypothesis that two (prespecified) regions of DNA evolve independently of each other. The sampling properties of

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Arnaout, Youssef, Evelyne Picard-Meyer, Emmanuelle Robardet, et al. "Assessment of virus and Leptospira carriage in bats in France." PLOS ONE 18, no. 10 (2023): e0292840. http://dx.doi.org/10.1371/journal.pone.0292840.

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With over 1,400 species worldwide, bats represent the second largest order of mammals after rodents, and are known to host major zoonotic pathogens. Here, we estimate the presence of pathogens in autochthonous bat populations. First, we set out to check our samples for PCR amplification efficiency by assessing the occurrence of inhibited PCR reactions from different types of bat samples with amplifying the housekeeping gene β-actin. Second, we investigated the presence of five targeted pathogens in a French bat population using PCR. We targeted viral RNA of Canine distemper virus, Alphacoronav

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Nurjanah, Uli, P. Maria Hendrati, Anton Budi Dharmawan, and Nur Signa A. Gumilas. "Deteksi Gen Laten Membrane Protein-1 Epstein-Barr Virus Pada Karsinoma Nasofaring." Biosfera 33, no. 2 (2017): 76. http://dx.doi.org/10.20884/1.mib.2016.33.2.466.

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Penelitian ini bertujuan untuk mengidentifikasi gen LMP-1 EBV sebagai biomarka diagnosis KNF. Desain penelitian ini adalah studi cross-sectional dengan teknik consecutive sampling. Sampel adalah darah total pasien KNF WHO-3 yang dikumpulkan dari pasien yang belum menjalani terapi dari tahun 2014 pada Departemen Telinga Hidung Tenggorok - Kepala Leher, Rumah Sakit Prof. dr. Margono Soekarjo, Purwokerto. Total subyek penelitian adalah 22 orang untuk NPC WHO-3 pasien dengan informed consent. Sampel diisolasi dengan protokol kit Purelink® DNA / RNA (Invitrogen) untuk mendapatkan larutan DNA 100μL

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Nicoletti, Arturo, Paola Pregel, Laura Starvaggi Cucuzza, Francesca Tiziana Cannizzo, Alessandra Sereno, and Frine Eleonora Scaglione. "Coping with Tissue Sampling in Suboptimal Conditions: Comparison of Different Tissue Preservation Methods for Histological and Molecular Analysis." Animals 11, no. 3 (2021): 649. http://dx.doi.org/10.3390/ani11030649.

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A high quality of samples is crucial for the success of the analysis and diagnostic purposes, and therefore the right method of conservation is vitally important for an optimal preservation of tissues. Indeed, the time to deliver the sample to the laboratory could be remarkably long, especially under suboptimal conditions, and the use of specific fixatives or cold storage may not be possible. Moreover, the portability and cost of storage equipment, their toxicity, and their ease of use play a central role when choosing the correct preservation method. The aim of this study was the identificati

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Kuchboev, Abdurakhim E., Oybek O. Amirov, Makhamadi B. Abramatov, Bakhtiyor H. Ruziev, Mehmonjon Kh. Egamberdiyev, and Rokhatoy R. Karimova. "Species identification based on the fecal DNA samples of the Caprinae." Acta Biologica Sibirica 10 (December 7, 2024): 1433–43. https://doi.org/10.5281/zenodo.14279887.

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Fecal analysis is a useful tool for studying the species identity of rare mammals. The possibility of using non-invasive biological materials in molecular genetic studies of rare bovids is shown, using the example of the markhor and Siberian ibex of Uzbekistan. Field work including noninvasive genetic sampling collection was carried out in the study area in spring and autumn 2022-2023 in the Hissar, Surkhan State Reserves and Ugam-Chatkal State National Natural Park and Termez zoo in Uzbekistan. We used species-specific 16S rRNA mitochondrial gene fragments for polymerase chain reaction amplif

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Kero, Katja, Niina Hieta, Teemu Kallonen, et al. "Optimal sampling and analysis methods for clinical diagnostics of vaginal microbiome." European Journal of Clinical Microbiology & Infectious Diseases 42, no. 2 (2023): 201–8. http://dx.doi.org/10.1007/s10096-022-04545-x.

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AbstractNext-generation sequencing-based microbiological analysis is a complex way to profile vaginal microbiome samples since each step affects the results gained. Methodologies for sample collection lack golden standards. We compared Puritan DNA/RNA swab (PS) and Copan FLOQ swab (CS) and provided consistent and reliable microbiome profiles analyzed by 16S rRNA gene sequencing. We collected two consecutive vaginal samples utilizing PS with room temperature storing and CS with instant freezing from 26 women. Variable region 4 of bacterial 16S rRNA gene was amplified with single PCR by custom-d

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Terrazos Miani, Miguel A., Loïc Borcard, Sonja Gempeler, et al. "NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples." Pathogens 13, no. 1 (2024): 61. http://dx.doi.org/10.3390/pathogens13010061.

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Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput sequencing of PCR amplicons derived from cDNA molecules. Here, we present a new approach called NASCarD (Nanopore Adaptive Sampling with Carrier DNA), which allows a low amount of nucleic acids to be sequenced while selectively enriching for sequences of interest, hence limiting the production of non-target sequences. Using COVID-19 positive samples available d

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Murwani, Antik, and Muhammad Taufiq Qurrohman. "Gambaran Nilai Ct Value qRT-Pcr Sars Cov-2 Dengan Metode Ekstraksi Manual Dan Otomatis." JOURNAL OF MUHAMMADIYAH MEDICAL LABORATORY TECHNOLOGIST 6, no. 2 (2023): 205–12. http://dx.doi.org/10.30651/jmlt.v6i2.18597.

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Corona Virus Infection Disease (COVID)-19 is a disease caused by a new coronavirus C derivative. The SARS-CoV-2 genome has six main open reading frames (ORFs): ORF 1a and 1b, envelope protein/E genes, membrane protein/M genes, spike protein/S gene, and nucleocapsid protein/N genes.Â Realtime RT-PCR is a DNA amplification technique in which amplification products can be analyzed at each cycle using fluorogenic probes.Â The RT-PCR method is used for amplification, isolation, or identification of sequences from RNA cells or tissues. The extraction of nucleic acids in the form of DNA and RNA is th

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Peplies, Jörg, Christine Lachmund, Frank Oliver Glöckner, and Werner Manz. "A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities." Applied and Environmental Microbiology 72, no. 7 (2006): 4829–38. http://dx.doi.org/10.1128/aem.02949-05.

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ABSTRACT A DNA microarray platform for the characterization of bacterial communities in freshwater sediments based on a heterogeneous set of 70 16S rRNA-targeted oligonucleotide probes and directly labeled environmental RNA was developed and evaluated. Application of a simple protocol for the efficient background blocking of aminosilane-coated slides resulted in an improved signal-to-noise ratio and a detection limit of 10 ng for particular 16S rRNA targets. An initial specificity test of the system using RNA from pure cultures of different phylogenetic lineages showed a fraction of false-posi

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Grønseth, Rune, Christine Drengenes, Harald G. Wiker, et al. "Protected sampling is preferable in bronchoscopic studies of the airway microbiome." ERJ Open Research 3, no. 3 (2017): 00019–2017. http://dx.doi.org/10.1183/23120541.00019-2017.

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The aim was to evaluate susceptibility of oropharyngeal contamination with various bronchoscopic sampling techniques.67 patients with obstructive lung disease and 58 control subjects underwent bronchoscopy with small-volume lavage (SVL) through the working channel, protected bronchoalveolar lavage (PBAL) and bilateral protected specimen brush (PSB) sampling. Subjects also provided an oral wash (OW) sample, and negative control samples were gathered for each bronchoscopy procedure. DNA encoding bacterial 16S ribosomal RNA was sequenced and bioinformatically processed to cluster into operational

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Savira, Maya, Resty Yuwandari, Yossi Maryanti, Rahmat Azhari Kemal, and Donel S. "Studi Awal Analisis Molekuler Human Papillomavirus dari Apusan Glans dan Batang Penis." Jurnal Kesehatan Andalas 9, no. 4 (2021): 433. http://dx.doi.org/10.25077/jka.v9i4.1493.

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Pria juga dapat mengalami keganasan akibat infeksi Human Papillomavirus (HPV) serta bertindak sebagai reservoir virus. Metode skrining HPV pada wanita telah terstandardisasi, namun belum ada standar metode skrining pada pria di Indonesia. Beberapa studi pada populasi pria di luar negeri menunjukkan potensi sampling pada daerah genitalia eksterna untuk skrining HPV. Tujuan: mengoptimasi metode skrining HPV secara molekuler pada pria. Metode: Responden adalah partner seksual wanita pansien kanker serviks di RSUD Arifin Achmad Provinsi Riau. Apusan dari glans dan batang penis diambil menggunakan

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Debattista, Jessica, Laura Grech, Christian Scerri, and Godfrey Grech. "Copy Number Variations as Determinants of Colorectal Tumor Progression in Liquid Biopsies." International Journal of Molecular Sciences 24, no. 2 (2023): 1738. http://dx.doi.org/10.3390/ijms24021738.

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Over the years, increasing evidence has shown that copy number variations (CNVs) play an important role in the pathogenesis and prognosis of Colorectal Cancer (CRC). Colorectal adenomas are highly prevalent lesions, but only 5% of these adenomas ever progress to carcinoma. This review summarizes the different CNVs associated with adenoma-carcinoma CRC progression and with CRC staging. Characterization of CNVs in circulating free-RNA and in blood-derived exosomes augers well with the potential of using such assays for patient management and early detection of metastasis. To overcome the limitat

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Wong, Mark V. M., Syed A. Hashsham, Erdogan Gulari, Jean-Marie Rouillard, Tiong Gim Aw, and Joan B. Rose. "Detection and characterization of human pathogenic viruses circulating in community wastewater using multi target microarrays and polymerase chain reaction." Journal of Water and Health 11, no. 4 (2013): 659–70. http://dx.doi.org/10.2166/wh.2013.322.

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Sewage pollution remains the most significant source of human waterborne pathogens. This study describes the detection and characterization of human enteric viruses in community wastewaters using cell culture coupled with multiple target microarrays (with a total of 780 unique probes targeting 27 different groups of both DNA and RNA viruses) and polymerase chain reaction (PCR) assays. Over a 13-month sampling period, RNA viruses (astroviruses and enteroviruses) were more frequently detected compared to DNA viruses (adenoviruses, particularly type 41 and BK polyomavirus). Overall, many more vir

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Gaetano, Anastasia Serena, Sabrina Semeraro, Samuele Greco, et al. "Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant." Microorganisms 12, no. 5 (2024): 965. http://dx.doi.org/10.3390/microorganisms12050965.

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Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatmen

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Fessas, Petros, Sonya Hessey, Corentin Richard, et al. "Abstract 2926: The effect of cancer research autopsy parameters on DNA and RNA sequencing quality." Cancer Research 84, no. 6_Supplement (2024): 2926. http://dx.doi.org/10.1158/1538-7445.am2024-2926.

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Abstract Background: Cancer research autopsy genomic studies offer insight into the metastatic cancer landscape but come with complexities that relate to the sampling and processing of post-mortem tissue. Clarifying the effect of autopsy variables on pre- and post-sequencing quality control (QC) is an unmet need that may inform tissue collection strategies. Methods: The effect of age, sex, post-mortem interval (PMI), and sample type (primary, metastatic, or normal) on pre-sequencing QC (nucleic acid concentration and integrity) was examined in 2678 samples (88.6% metastatic, 8.0% primary, 3.4%

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Athayde, Luiza Maria Ferreira Lopes, Camila Teles Franco da Silveira Albuquerque, Ana Luísa Soares Macedo, Artur Fontenelle Lima Montenegro, Alex Amaral Medeiros, and Alessandro Taunay-Rodrigues. "Detection of Leishmania RNA Virus 1 in Leishmania parasites in Serra do Baturité – Ceará (Brazil)." Revista de Gestão e Secretariado 15, no. 7 (2024): e3897. http://dx.doi.org/10.7769/gesec.v15i7.3897.

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Fundamentals: The human protozoan parasite Leishmania can cause species-related distinct forms of Leishmaniasis: cutaneous, mucocutaneous, or fatal generalized visceral infection. Recent studies have reported that the presence of “Leishmania RNA virus 1” infecting Leishmania is an important factor involved with the severity of mucocutaneous in experimental animal models. By using molecular analysis in the present study, we aimed to evaluate the occurrence of LRV1 in Leishmania species from potential sand fly vectors. Methods: Sandfly sampling was carried out from May 2022 to December 2022 in d

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González, Dolores. "El uso de secuencias génicas para estudios taxonómicos." Botanical Sciences, no. 60 (May 2, 2017): 137. http://dx.doi.org/10.17129/botsci.1526.

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During the last years, the use of molecular characters for taxonomic research has increased notably. Characters most commonly used come from restriction enzymes and sequencing of genes or particular DNA regions. Sequences present potential advantages over other molecular characters. This paper describes sampling procedures to detect DNA variation through sequencing. Among procedures for DNA sequencing, enzymatic methods are of generalized application, and the tendency is toward the use of non-radioactive markers and automated sequencing. A brief introduction to the different stages of cladisti

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Kim, Li Ah, Jin Han, Tae Il Kim, et al. "Circulating RNA Markers Associated with Adenoma–Carcinoma Sequence in Colorectal Cancer." International Journal of Molecular Sciences 26, no. 4 (2025): 1518. https://doi.org/10.3390/ijms26041518.

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Colorectal cancer progresses through a well-defined adenoma–carcinoma sequence (ACS), which is pivotal for early detection and intervention. While ACS-based surveillance has been instrumental, its reliance on tissue sampling limits accurate staging. Liquid biopsies, including circulating tumor DNA (ctDNA) and extracellular RNA, have emerged as non-invasive alternatives, yet they primarily detect genetic alterations or passive RNA release rather than active biological processes. Thus, there is a need for biomarkers that reflect real-time immune responses and tumor–microenvironment interactions

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Usha Shri, P. "ALTERATIONS IN THE NUCLEIC ACID AND PROTEIN CONTENT IN SORGHUM BICOLOR PLANTS UNDER ZINC EXCESS." International Journal of Advanced Research 12, no. 03 (2024): 1069–76. http://dx.doi.org/10.21474/ijar01/18494.

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Trace metals like zinc are natural components of the environment but, elevated and potentially toxic levels sometimes occur. The use of zinc fertilizers and pesticides is a common agricultural practice, which over the years lead to elevated levels of zinc in the soil.In the present investigation seven-day old Sorghum bicolor plants were treated with five different concentrations of zinc solution and sampling was done at different stages of plant growth to estimate the nucleic acid and protein content. The results revealed a significant reduction in DNA, RNA and proteins in the plants growing a

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Ståhlberg, Anders, Christer Thomsen, David Ruff, and Pierre Åman. "Quantitative PCR Analysis of DNA, RNAs, and Proteins in the Same Single Cell." Clinical Chemistry 58, no. 12 (2012): 1682–91. http://dx.doi.org/10.1373/clinchem.2012.191445.

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BACKGROUND The single cell represents the basic unit of all organisms. Most investigations have been performed on large cell populations, but understanding cell dynamics and heterogeneity requires single-cell analysis. Current methods for single-cell analysis generally can detect only one class of analytes. METHODS Reverse transcription and the proximity ligation assay were coupled with quantitative PCR and used to quantify any combination of DNA, mRNAs, microRNAs (miRNAs), noncoding RNAs (ncRNAs), and proteins from the same single cell. The method was used on transiently transfected human cel

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Bellinger, Christina, Michael Bernstein, Hans Lee, et al. "Molecular profiling of dedicated lung cancer biopsy tissue sample collected at time of diagnostic bronchoscopy." Journal of Clinical Oncology 40, no. 16_suppl (2022): e20587-e20587. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e20587.

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e20587 Background: The combined use of molecular biomarker testing and targeted precision therapeutics has led to improved survival in lung cancer. Broadening access to national guideline recommended comprehensive molecular testing requires overcoming the challenges of inadequate tissue biopsies, which can lead to the need for additional procedures and ultimately, delays in initiation of care. We show Percepta Genomic Atlas identifies key molecular alterations in transbronchial needle aspirate (TBNA) and transbronchial biopsy (TBB) samples of lung or lymph node collected during the initial dia

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Bellinger, Christina, Michael Bernstein, Hans Lee, et al. "Molecular profiling of dedicated lung cancer biopsy tissue sample collected at time of diagnostic bronchoscopy." Journal of Clinical Oncology 40, no. 16_suppl (2022): e20587-e20587. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e20587.

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e20587 Background: The combined use of molecular biomarker testing and targeted precision therapeutics has led to improved survival in lung cancer. Broadening access to national guideline recommended comprehensive molecular testing requires overcoming the challenges of inadequate tissue biopsies, which can lead to the need for additional procedures and ultimately, delays in initiation of care. We show Percepta Genomic Atlas identifies key molecular alterations in transbronchial needle aspirate (TBNA) and transbronchial biopsy (TBB) samples of lung or lymph node collected during the initial dia

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Feist, Sheena M., and Richard F. Lance. "Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions." NeoBiota 66 (July 13, 2021): 117–59. https://doi.org/10.3897/neobiota.66.60751.

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Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts invol

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Heinemeier, Katja M., Marc P. Lorentzen, Jacob K. Jensen, et al. "Local trauma in human patellar tendon leads to widespread changes in the tendon gene expression." Journal of Applied Physiology 120, no. 9 (2016): 1000–1010. http://dx.doi.org/10.1152/japplphysiol.00870.2015.

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Low cellular activity and slow tissue turnover in human tendon may prolong resolution of tendinopathy. This may be stimulated by moderate localized traumas such as needle penetrations, but whether this results in a widespread cellular response in tendons is unknown. In an initial hypothesis-generating study, a trauma-induced tendon cell activity (increased total RNA and collagen I mRNA) was observed after repeated patellar tendon biopsies in young men. In a subsequent controlled study, 25 young men were treated with two 0.8-mm-diameter needle penetrations [ n = 13, needle-group (NG)] or one 2.

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Després, V. R., J. F. Nowoisky, M. Klose, R. Conrad, M. O. Andreae, and U. Pöschl. "Characterization of primary biogenic aerosol particles in urban, rural, and high-alpine air by DNA sequence and restriction fragment analysis of ribosomal RNA genes." Biogeosciences 4, no. 6 (2007): 1127–41. http://dx.doi.org/10.5194/bg-4-1127-2007.

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Abstract. This study explores the applicability of DNA analyses for the characterization of primary biogenic aerosol (PBA) particles in the atmosphere. Samples of fine particulate matter (PM2.5) and total suspended particulates (TSP) have been collected on different types of filter materials at urban, rural, and high-alpine locations along an altitude transect in the south of Germany (Munich, Hohenpeissenberg, Mt. Zugspitze). From filter segments loaded with about one milligram of air particulate matter, DNA could be extracted and DNA sequences could be determined for bacteria, fungi, plants a

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Avent, Neil D., A. Webb, TE Madgett, et al. "Non Invasive Prenatal Diagnosis of Aneuploidy: Next Generation Sequencing or Fetal DNA Enrichment?" Balkan Journal of Medical Genetics 15, Supplement (2012): 17–26. http://dx.doi.org/10.2478/v10034-012-0013-z.

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ABSTRACT Current invasive procedures [amniocentesis and chorionic villus sampling (CVS)] pose a risk to mother and fetus and such diagnostic procedures are available only to high risk pregnancies limiting aneuploidy detection rate. This review seeks to highlight the necessity of investing in non invasive prenatal diagnosis (NIPD) and how NIPD would improve patient safety and detection rate as well as allowing detection earlier in pregnancy. Non invasive prenatal diagnosis can take either a proteomics approach or nucleic acid-based approach; this review focuses on the latter. Since the discover

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Fan, Xing, Chuanfeng Wu, Diego Espinoza, et al. "Clonal Tracking of the Source of Red Cell and Platelet Production in Rhesus Macaques." Blood 130, Suppl_1 (2017): 932. http://dx.doi.org/10.1182/blood.v130.suppl_1.932.932.

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Abstract The classical model of hematopoietic hierarchies is being reconsidered, based on data from in vitro assays and single cell expression profiling. Recent experiments suggest that erythroid and megakaryocytic lineages might differentiate directly from multipotent hematopoietic stem/progenitor cells (HSPC) or from a highly biased subpopulations of HSPC, rather than transiting through a common MEP or CMP. We examined the clonal ontogeny of the erythroid lineage using genetic barcoding of rhesus macaque HSPC (Wu Cell Stem Cell, 2014; Koelle Blood, 2017), allowing quantitative and sensitive

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