Relevant bibliographies by topics / Direct sequencing

Academic literature on the topic 'Direct sequencing'

Author: Grafiati
Published: 4 June 2021
Last updated: 11 March 2023

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Contents

Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Direct sequencing.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Journal articles on the topic "Direct sequencing"

1

Ozsolak, Fatih, Adam R. Platt, Dan R. Jones, Jeffrey G. Reifenberger, Lauryn E. Sass, Peter McInerney, John F. Thompson, Jayson Bowers, Mirna Jarosz, and Patrice M. Milos. "Direct RNA sequencing." Nature 461, no. 7265 (September 23, 2009): 814–18. http://dx.doi.org/10.1038/nature08390.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Linder, Jodell E., Tatyana E. Plachco, Romina Libster, and E. Kathryn Miller. "Sequencing human rhinoviruses: Direct sequencing versus plasmid cloning." Journal of Virological Methods 211 (January 2015): 64–69. http://dx.doi.org/10.1016/j.jviromet.2014.09.020.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Chalapati, Sachin, Conor A. Crosbie, Dixita Limbachiya, and Nimesh Pinnamaneni. "Direct oligonucleotide sequencing with nanopores." Open Research Europe 1 (August 24, 2021): 47. http://dx.doi.org/10.12688/openreseurope.13578.2.

Full text
Abstract:
Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5’ phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5’ end of the oligos and to leave a 3’ adenosine overhang after binding to their target. The 3’ adenosine overhang of the adapter and the terminal phosphate makes the 5’ end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.
APA, Harvard, Vancouver, ISO, and other styles
4

Chalapati, Sachin, Conor A. Crosbie, Dixita Limbachiya, and Nimesh Pinnamaneni. "Direct oligonucleotide sequencing with nanopores." Open Research Europe 1 (May 12, 2021): 47. http://dx.doi.org/10.12688/openreseurope.13578.1.

Full text
Abstract:
Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5’ phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5’ end of the oligos and to leave a 3’ adenosine overhang after binding to their target. The 3’ adenosine overhang of the adapter and the terminal phosphate makes the 5’ end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.
APA, Harvard, Vancouver, ISO, and other styles
5

Rudi, Heidi, Knut‐Erik Gylder, Odd Arne Rognli, and Knut Rudi. "Direct Haplotype‐Specific DNA Sequencing." Preparative Biochemistry and Biotechnology 36, no. 3 (September 2006): 253–57. http://dx.doi.org/10.1080/10826060600716687.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Zhang, Jinyue, Shuanghong Yan, Le Chang, Weiming Guo, Yuqin Wang, Yu Wang, Panke Zhang, Hong-Yuan Chen, and Shuo Huang. "Direct microRNA Sequencing Using Nanopore-Induced Phase-Shift Sequencing." iScience 23, no. 3 (March 2020): 100916. http://dx.doi.org/10.1016/j.isci.2020.100916.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Kilger, Christian, Matthias Krings, Hendrik Poinar, and Svante Pääbo. "“Colony Sequencing”: Direct Sequencing of Plasmid DNA from Bacterial Colonies." BioTechniques 22, no. 3 (March 1997): 412–18. http://dx.doi.org/10.2144/97223bm08.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Petry, H., K. Pekrun, K. Wäse, I. Schedel, W. Lüke, and G. Hunsmann. "Direct sequencing versus cloned amplicon sequencing in HIV-1 diagnosis." Experientia 52, no. 4 (April 1996): 303–4. http://dx.doi.org/10.1007/bf01919520.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Obata, Hiroko, Tatsuya Tanaka, Tsuneko Fujii, Chikako Sasho, Yukihiro Yamaguchi, and Keiichiro Suzuki. "Dye Terminator Re-cycle-sequencing Method: Phage Plaque Direct Sequencing." Analytical Biochemistry 297, no. 1 (October 2001): 102–5. http://dx.doi.org/10.1006/abio.2001.5328.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Zhang, Jinyue. "Direct MicroRNA Sequencing using Nanopore Induced Phase-Shift Sequencing (NIPSS)." Biophysical Journal 118, no. 3 (February 2020): 475a—476a. http://dx.doi.org/10.1016/j.bpj.2019.11.2638.

Full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

Dissertations / Theses on the topic "Direct sequencing"

1

Fillion, Bergeron Marianne. "Plasmid isolation and purification by electrofiltration and comparison of different direct colony sequencing methods and PCR-based sequencing methods." Thesis, University of Ottawa (Canada), 2002. http://hdl.handle.net/10393/6050.

Full text
Abstract:
We have designed an electrophoresis system that can purify plasmid DNA from a culture without centrifugation. This system is based on electrofiltration where bacterial cell lysates are loaded in one chamber and the purified plasmid DNA is recovered in an adjacent chamber. These two chambers are separated by a membrane made of regenerated cellulose, which allows plasmid DNA to migrate to the recovery chamber while retaining most contaminants in the loading chamber. Unfortunately, even with the optimization of the parameters involved in the electrofiltration, the only DNA that can pass through the middle membrane still has some contaminants, which prevent sequencing of the plasmid. Our results have shown that a pure plasmid cannot cross a membrane with pores small enough to prevent the migration of most of the contaminants. Only a plasmid complexed with some contaminants can cross a small pore membrane. In parallel, we have compared six direct sequencing methods that do not require any plasmid purification prior to the sequencing reaction. We compared the reliability, quality of sequences, time required, and cost of these six methods. We found that the best method was that of Zhang et al. (1999). This method is fast, reliable, produces good quality sequences and is inexpensive. The performance of this method is due to the amount of ABI's ready reaction mix used, the pre-sequencing heating step to lyse the cell, the large volume of the PCR sequencing reaction and the addition of BSA.
APA, Harvard, Vancouver, ISO, and other styles
2

梁秀敏 and Sau-man Leung. "Direct detection of rifampin-resistant mycobacterium tuberculosis in clinical specimens by DNA sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B31970102.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Leung, Sau-man. "Direct detection of rifampin-resistant mycobacterium tuberculosis in clinical specimens by DNA sequencing." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk/hkuto/record.jsp?B2329498X.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Otten, Nathalie. "DNA of bovine papillomavirus type 1 and 2 in equine sarcoids : PCR detection and direct sequencing /." [S.l.] : [s.n.], 1992. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Rocha, Ana Laís Bignotto da. "Sequenciamento direto dos genes SIX3, SHH, TGIF1, ZIC2 e array-CGH no estudo de pacientes com holoprosencefalia." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/61/61132/tde-12112013-150520/.

Full text
Abstract:
Objetivos: Analisar por meio da técnica de sequenciamento direto a presença de alterações moleculares nos genes SHH, SIX3, ZIC2 e TGIF1 em indivíduos com diagnóstico clínico de HPE. Analisar por meio da técnica de CGH-array a presença de alterações moleculares em indivíduos com diagnóstico clínico de HPE previamente submetidos à análise por sequenciamento direto. Local: Laboratório de Genética e Citogenética Humana HRAC/USP, Bauru-SP. Casuística e metodologia: Foram selecionados 50 indivíduos, de ambos os sexos com idades entre 03 meses a 50 anos com diagnóstico clínico para HPE. Todos foram analisados por meio da técnica de sequenciamento direto para os genes SHH e TGIF1 completamente e para os genes ZIC2 e SIX3 parcialmente. Dentre os indivíduos que não apresentaram alterações na técnica de sequenciamento oito indivíduos com fenótipo mais grave foram selecionados para a análise por CGH-array. Resultados e discussão: Foram analisados 50 indivíduos por meio da técnica de sequenciamento direto dos gene SHH e TGIF1, foram encontradas duas variantes patogênicas na análise do gene SHH, no caso 1 a variante p.24G>P foi identificada, e no caso 2 foi identificada a variante c.1031del C. No gene TGIF1 foram encontrados cinco polimorfismos já descritos na literatura. Foi identificada uma nova variante silenciosa no éxon 1 do gene ZIC2 p.Q46Q (c. 431 G>A) e um polimorfismo já descrito na literatura em dois indivíduos no gene SIX3. A análise por CGH-array revelou a presença de uma microdeleção no caso 37, de 1,5Mb no cromossomo 17p12 entre as posições genômicas 14,052,279-15,102,307. A mesma deleção foi encontrada na mãe, sendo que esta região nunca foi associada a HPE. Conclusão: A técnica de sequenciamento direto é uma ferramenta muito importante no diagnóstico molecular da HPE, a padronização do sequenciamento direto para os genes ZIC2 e SIX3 poderá auxiliar em diagnósticos mais precisos em estudos futuros dentro do HRAC/USP. O emprego de novas técnicas como CGH-array pode indicar novas relações entre regiões cromossômicas e os múltiplos fatores envolvidos na formação da HPE.
Objective: Analyze through direct sequencing technique the presence of molecular changes on the genes SHH, SIX3, ZIC2 and TGIF1 on individuals with clinical diagnosis of HPE. Analyze through array-CGH technique the presence of molecular changes on individuals with clinical diagnosis of HPE previously submitted to the direct sequencing analyzes. Local: Genetics and Human Cytogenetics Laboratory, HRAC/USP, Bauru-SP. Methods: Were selected 50 individuals from both genders with ages between 03 months and 50 years clinically diagnosed with HPE. Everyone was analyzed through the direct sequencing technique for the genes SHH and TGIF1 completely and for the genes ZIC2 and SIX3 partially. From those individuals which did not have shown changes on the direct sequencing technique, eight individuals with more severe phenotype were selected to the analysis through array-CGH. Results an Discussion: Were analyzed 50 individuals through the technique of direct sequencing of the genes SHH and TGIF1, were found two pathogenic variants in the analysis of SHH gene, in the case 1, the variant p.G24P was identified, and in the case 2 was identified the variant c.1031delC. On the TGIF1 gene were found five polymorphisms already described on the literature. Was identified a new silent variant on the exon 1 of the ZIC2 gene p. Q46Q(c.431G>A) and a polymorphism already described in the literature in two individuals on the gene SIX3. The analysis through array-CGH revealed the presence of one microdeletion in the case 37, of 1,5 Mb on the region 17p12 between the genomic positions 14,052,279-15,102,307. The same deletion was detected in the mother, though this region was never associated to the HPE. Conclusion: The direct sequencing technique is a very important tool for the molecular diagnosis of the HPE, and the direct sequencing standardization for the genes ZIC2 and SIX3 might help in more precise diagnostics on HRAC/USP future studies. The employ of new techniques such as array-CGH may indicate new relations between chromosomal regions and the multiple hit involved in the development of HPE.
APA, Harvard, Vancouver, ISO, and other styles
6

Vander, Wiede Jamie. "Direct, hands-on or inquiry instruction a study of instructional sequencing and motivation in the science classroom." Master's thesis, University of Central Florida, 2011. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/5073.

Full text
Abstract:
Currently, a debate exists between the strengths and weaknesses of direct and inquiry instruction. Inquiry instruction is related to positive effect on learner motivation whereas supporters of direct instruction point to its ability to adequately support learners' working memories (Hmelo-Silver, Duncan, & Chinn, 2007; Kirschner, Sweller, & Clark, 2006; Kuhn, 2007; Sweller, 1988). This study examined the possibility of combining the best features of both inquiry and direct instruction by sequencing them together. A two-part lesson on electrical circuits was presented in three separate sequences of instruction to middle school students to determine if differences in student motivation and academic achievement emerge depending on whether a guided inquiry lab followed or preceded direct instruction. Results indicated equal levels of perceived competence by students across all instructional sequences and greater interest/enjoyment and perceived autonomy support when the instructional sequence began with a guided inquiry lesson. No significant differences in achievement were reported among the sequences.
ID: 030423060; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Thesis (M.A.)--University of Central Florida, 2011.; Includes bibliographical references (p. 42-48).
M.A.
Masters
Teaching, Learning and Leadership
Education
Applied Learning and Instrucation
APA, Harvard, Vancouver, ISO, and other styles
7

Koziol, Adam. "Application of Direct-sequencing Peptide Proteomics to the Characterization of Antagonistic (Endogenous and Exogenous) Proteins in Cereal Grains." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/23853.

Full text
Abstract:
The cereal seed plays a crucial role in society – both in the “food as medicine” paradigm, but also in food security. It is the starch and proteins present in the seed that lend it importance in these dissimilar anthropomorphic activities. This thesis investigation first characterized the post-translational processing of the potential diabetogen, wheat globulin-3. Globulin-3-like peptides were observed primarily in the embryo. These peptides varied significantly in their molecular masses and isoelectric points, as determined by two dimensional electrophoresis and immunoblotting. Five major polypeptide spots were sequenced by mass spectrometry, allowing for the development of a model of the post-translational events contributing to the globulin-3 processing profile. Three separate investigations of starch granules from different cereal species were performed. In the first series of experiments, pathogen-susceptible maize kernels were injected with either conidia of the fungal pathogen Fusarium graminearum or sterile water controls. Proteins in the desiccated fungal remnants on the surface of the kernels as well as in the endosperm and embryo tissues of the control and infected kernels were isolated and these proteomes were sequenced using tandem mass spectrometry. Approximately 250 maize proteins were identified. These proteins were classified into functional categories. There was an increased representation of defense proteins in the both the embryo and endosperm tissues of infected maize samples. The proteome of the fungal remnants was composed of 18 proteins. Several of these proteins were categorized as being involved in the metabolism of plant-sourced molecules, or in stress response. The second series of experiments detail the investigation of commercially prepared rice and maize starches using tandem mass spectrometry. The majority of identified proteins, in both rice and maize samples, were involved in either carbohydrate metabolism or storage. Markers for seed maturity and for starch mobilization were also documented. Finally, the third series of experiments investigated the non-host proteomes present in commercially-prepared starches. Non-host proteins from a variety of species, including Homarus americanus were found in the starch samples. This documentation of H. americanus proteins in these starch samples may have food safety implications with regards to shellfish allergies.
APA, Harvard, Vancouver, ISO, and other styles
8

Nguyen, Thuy. "Ultra-deep sequencing applications in virology research." Electronic Thesis or Diss., Sorbonne université, 2018. http://www.theses.fr/2018SORUS282.

Full text
Abstract:
Les deux virus d’ARN VIH et VHC attirent beaucoup d’attention de la santé publique parce qu’ils partagent des mêmes facteurs de risque de transmission par le sang et par des contacts sexuels. En plus, les maladies associées aux infections par le VIH et par le VHC sont des causes principales de mortalité et de morbidité globalement. Néanmoins, grâce à l’introduction des thérapies d’antirétroviraux pour le traitement de l’infection par le VIH et les antiviraux à action directe (AADs) pour le traitement de l’infection par le VHC, les patients infectés par ces virus constatent une amélioration significative de leur qualité de vie. Cependant, le taux de réplication élevé et l'absence de mécanisme de correction d'erreur de ces virus génèrent une population virale diversifiée appelée des quasi-espèces. Sous la pression sélective de traitement, les quasi-espèces virales sélectionnent des variants de résistance au médicament correspondant et rendent la thérapie inefficace, en particulier dans les cas où une surveillance appropriée du traitement n'est pas assurée. Afin de réserver un large choix de traitement antirétroviral tout au long de la vie chez les patients infectés par le VIH et, parallèlement, de réduire le coût de traitement des infections par le VIH et le VHC, il est fondamental de mener des recherches ciblées sur la détection, la surveillance et la transmission des mutations de résistance aux antiviraux. Dans cette thèse, nous avons utilisé les technologies de séquençage haut-débit (UDS) ou de séquençage de nouvelle génération (NGS) pour chercher des variants de résistance minoritaires (MiRVs) qui sont classiquement considérés comme représentant moins de 15%-25% de la population virale et ne sont pas trouvés par la technique de séquençage Sanger. La présence des MiRVs à baseline est responsable possiblement de l'échec de traitement et leur présence à l'échec peut limiter les options des traitements ultérieurs. Dans cette thèse, nous avons évalué la prévalence et l’impact clinique des MiRVs sur le gène de l’intégrase chez les patients infectés par le VIH qui ont été en échec d’un régime thérapeutique contenant un inhibiteur de l’intégrase. Nous avons également évalué l’impact des MiRVs chez les patients infectés par le VHC de génotype 3 et de génotype 4 et ayant échoué aux AADs. De plus, nous avons utilisé la technique UDS pour identifier et caractériser les chaines de transmission du VHC parmi une population clé d'hommes ayant des rapports sexuels avec des hommes, co-infectés par le VIH ou ayant un risque élevé d'acquisition du VIH. Nous avons également observé plusieurs cas d’infections mixtes de génotype du VHC dans cette population, probablement à cause du risque élevé de multiples expositions au VHC. Les questions sur l’avantage de l'UDS dans la recherche en virologie et l'applicabilité de cette technique en clinique ont été posées et vérifiées au travers de multiples types de projets dans cette thèse. L’UDS n’a pas été établi de manière concluante comme étant plus intéressant et bénéfique que la technique de séquençage de Sanger pour prévenir l’échec au traitement chez les patients infectés par le VIH ou le VHC et pour identifier les chaînes de transmission à grande échelle si le coût et le temps de l’expérience pour l’analyse des données sont pris en compte. Cependant, le développement dynamique des nouvelles technologies de l’UDS et les efforts sans cesse afin d’optimiser des procédures d'analyse montrent un rôle prometteur de l’UDS. Et l'applicabilité de l'UDS en pratique clinique devra encore être élucidée dans différents types de projets de recherche
The two RNA viruses HIV and HCV are getting a lot of public health concerns because both of them have overlapping risk factors for transmission through direct blood and sexual contacts. Furthermore, HIV and HCV infections are the leading cause of mortality and morbidity globally due to related diseases. However, with the introduction of antiretroviral therapy (ART) for the treatment of HIV infection and direct-acting antivirals (DAAs) for the treatment of HCV infection, patients infected by these viruses are witnessing significant improvement in their quality of life. However, the high replication rate and the lack of error correction mechanism of these viruses result in a diverse viral population referred to as quasispecies. Under drug- selective pressure, the viral quasispecies select resistance variants against corresponding drug and render the therapy ineffective especially in cases an appropriate treatment monitoring is not ensured.To reserve a wide range of possibilities for a life-long ART in HIV-infected patients and in parallel to reduce cost for treatment of both HIV and HCV infection, research focusing on detection, surveillance and transmission of resistance mutations is fundamental to prevent treatment failure on antivirals. In this PhD, we employed the ultra-deep sequencing (UDS) or next-generation sequencing (NGS) technologies to look for minority resistant variants (MiRVs) which are conventionally considered to represent less than 15%-25% of viral population and undetectable by Sanger sequencing. The presence of MiRVs at baseline is possibly responsible for the treatment failure and their presence at failure may limit options for subsequent therapies. In this PhD, we evaluated the prevalence and clinical impact of MiRVs on integrase gene in HIV-infected patients failing an integrase inhibitor containing regimen. We also evaluated the impact of MiRVs in HCV genotype 3 and genotype 4-infected patients failing DAAs. Furthermore, we used the UDS technique to identify and characterize the HCV transmission networks among a key population of men having sex with men either co-infected with HIV or at high risk of HIV acquisition. We also discovered several cases of mixed HCV genotype infections in this population probably for their high risk of multiple HCV exposures. The advantages of UDS in virology research and the applicability of this technique in clinic have been questioned and verified throughout multiple types of projects in this PhD. UDS has not been conclusively established to be more interesting and beneficial than Sanger sequencing in prevention of treatment failure in patients infected by HIV or HCV and in identifying the viral transmission networks at large scale if taking into account the experiment cost and time for data analysis. However, the dynamic development of UDS technologies and the continuing attempts in optimizing analysis procedures display a promising role of UDS. And the applicability of UDS in clinical practice still needs to be elucidated in different kinds of research projects
APA, Harvard, Vancouver, ISO, and other styles
9

Engström, Erik. "Direct poly(A) RNA nanopore sequencing on the freshwater duck mussel Anodonta anatina following exposure to copper : A pilot study." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-17508.

Full text
Abstract:
Aquatic ecotoxicology is the study of toxic chemicals and its effects on aquatic biological systems with the aim of minimising threats to human health and ensure self-sustained ecosystems. Freshwater bivalves are excellent sentinels for use in ecotoxilogical research due to their filter feeding properties, stationary lifestyle and inability to regulate body temperature. This project aimed to assess the feasibility and use of nanopore sequencing, a real-time single-molecule sequencing technology in comparative expression analysis by sequencing transcriptomic RNA from the freshwater mussel Anodonta anatina following exposure to copper. RNAs were extracted from 80 mg hepatopancreas tissue, followed by poly(A) RNA selection. Furthermore, the poly(A) RNA was used to construct a nanopore sequencing library. Sequencing a total amount of 560 ng poly(A) RNA over the course of two separate runs generated 239,448 reads, in which 75% of the reads were obtained during the first run (control) and 25% of the reads were obtained during the second run (case). The median read lengths ranged between 534-650 nucleotides, with a base call accuracy <90%. Due to the big differences in sequence data output between the two sequencing runs, the data was ineligible for comparative analysis. The findings conclude that nanopore sequencing is capable of generating longer read lengths when compared to other sequencing platforms. However, the technology is error-prone in terms of accurate base call identifications and relies on other platforms for error corrections. Future advances include de novo transcriptome assembly for efficient use of Anodonta anatina as a bioindicator in aquatic ecotoxicology.
APA, Harvard, Vancouver, ISO, and other styles
10

Busson, Laurent. "Evolution of direct diagnostic techniques in Virology; analytical performances and clinical input." Doctoral thesis, Universite Libre de Bruxelles, 2020. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/313391.

Full text
Abstract:
Le diagnostic virologique est un sujet d’actualité particulièrement du fait des récentes épidémiesou pandémies telles que la pandémie d’influenza A(H1N1) en 2009 ou la diffusion du virus Zika dansles Amériques et la région du Pacifique entre 2014 et 2017, associée à des cas de microcéphalie et dessyndromes de Guillain Barré. Encore plus récemment, en août 2018, le ministre de la santé de laRépublique Démocratique du Congo annonçait la 10e épidémie de virus Ebola dans le pays et endécembre 2019, le coronavirus SARS-CoV-2 est à l’origine d’une pandémie au départ de la Chine. Avecle nombre croissant de migrants et de voyageurs favorisant la dissémination des maladies virales, leslaboratoires diagnostiques doivent être parés à la fois pour l’identification des virus communs maisaussi de ceux importés.Les techniques les plus anciennes de diagnostic virologique tendent à devenir obsolètes suite audéveloppement rapide des techniques moléculaires depuis les années 90. Cependant, nous utilisonstoujours un mélange de techniques moléculaires et non moléculaires au sein de notre laboratoire.Les objectifs de ce travail sont de passer en revue les différentes techniques communémentutilisées pour la détection directe des virus avec leurs avantages et leurs inconvénients et de fournirune réflexion sur la place de chaque technique, en 2020, dans un laboratoire diagnostique.Nous aborderons tout d’abord les cultures cellulaires et nous insisterons sur leur polyvalence quipermet parfois de mettre en évidence des micro-organismes que l’on ne suspectait pas. Nousillustrerons ce point par un article relatant la mise en évidence de Chlamydia trachomatis du serovar Lresponsables de la lymphogranulomatose vénérienne dans des prélèvements envoyés pour suspiciond’infection herpétique.Le travail se focalisera ensuite plus particulièrement sur le diagnostic des infections viralesrespiratoires. Nous verrons les principes des tests de détection antigéniques et discuterons de leurslimites en se basant sur un article qui traite du diagnostic des virus influenza A et B par 3 différentstests immunochromatographiques. Cet article montre que la sensibilité des tests varie en fonction dela charge virale dans le prélèvement ainsi que du sous-type de virus.Nous poursuivrons avec les tests d’amplification d’acides nucléiques (tests moléculaires) enexpliquant la technique de PCR (Polymerase Chain Reaction) et une technique d’amplificationisothermique (Nicking Enzyme Amplification Reaction - NEAR). Nous illustrerons par un article portantsur l’évaluation du test Alere i influenza A&B (technique NEAR) en comparaison du test Sofia influenzaA+B (immunochromatographie). Cet article montre un gain de sensibilité de l’Alere i par rapport auSofia pour le diagnostic de l’influenza A mais pas pour l’influenza B. Il constitue également un travailpréliminaire sur l’appréciation de l’utilité d’une technique PCR rapide dans la prise en charge despatients. La conclusion est qu’il pourrait y avoir un apport de ce type de technique pour la diminutiondes hospitalisations, de la prescription des examens complémentaires et des antibiotiques. Celapermettrait également une prescription plus adéquate de l’oseltamivir pour le traitement de la grippe.Le point important est que l’impact du résultat est d’autant plus grand qu’il est délivré précocementdans la prise en charge des patients, idéalement lorsqu’ils sont encore aux urgences.Suite au travail sur l’Alere i, nous avons entrepris d’évaluer un test PCR multiplex (FilmArrayRespiratory Panel) pour le diagnostic des virus afin de voir si la détection d’un plus grand nombre depathogènes pourrait avoir un impact plus grand sur la prise en charge des patients. Cette évaluation adonné lieu à deux articles. Le premier détaille les avantages et inconvénients des différents outils dediagnostic pour la détection des virus respiratoires et sert d’état des lieux sur les tests utilisésactuellement dans les laboratoires de virologie. Le deuxième article porte plus particulièrement surl’apport du FilmArray dans la prise en charge des patients. La conclusion est que ce n’est pas le résultatdu test qui a un impact sur cette prise en charge mais plutôt d’autres facteurs notamment l’âge ou desmarqueurs inflammatoires biologiques.Nous terminerons ce travail par un aperçu des techniques de séquençage qui seront sans aucundoute de plus en plus utilisées pour le diagnostic en virologie.
Doctorat en Sciences médicales (Médecine)
info:eu-repo/semantics/nonPublished
APA, Harvard, Vancouver, ISO, and other styles
More sources

Books on the topic "Direct sequencing"

1

1937-, Jost J. P., ed. A laboratory guide to genomic sequencing: The direct sequencing of native uncloned DNA. Basel: Birkhäuser, 1987.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
2

Jost and Saluz. Laboratory Guide to Genomic Sequencing: The Direct Sequencing of Native Uncloned DNA. Birkhauser Verlag, 2013.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
3

Jost and Saluz. A Laboratory Guide to Genomic Sequencing: The Direct Sequencing of Native Uncloned DNA. Birkhäuser, 2011.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
4

Jost, J. P., and H. P. Saluz. A Laboratory Guide to Genomic Sequencing: The Direct Sequencing of Native Uncloned DNA (Biomethods). Birkhauser, 1988.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
5

Caillaud, Catherine, and Frédéric Sedel. Neuronal Ceroid Lipofuscinoses. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199972135.003.0059.

Full text
Abstract:
Neuronal ceroid lipofuscinoses (NCLs) are inherited neurodegenerative disorders beginning mainly in childhood, rarely in adults. They are characterized by the accumulation of autofluorescent lipopigments in brain, especially in neurons. Their clinical heterogeneity is now explained by the huge number of genes (from CLN1 to CLN14) involved in their pathogenesis. Their diagnosis is possible using enzymatic tests and/or direct sequencing of the corresponding genes. Different therapeutic approaches are in development for these diseases such as enzyme replacement therapy or gene transfer.
APA, Harvard, Vancouver, ISO, and other styles
6

Ellingboe, James. The PCR Technique : DNA Sequencing. Eaton Publishing Company/Biotechniques Books, 1992.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
7

Graves, Tracey. Neurogenetic disease. Edited by Patrick Davey and David Sprigings. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780199568741.003.0223.

Full text
Abstract:
There are many genetic diseases which affect the nervous system. Although some of these are extremely rare, several are quite common and, as a group, they comprise a significant proportion of neurological disease. Almost all clinical neurological syndromes can have a genetic cause. Not all of these have been genetically elucidated, but some have been extensively characterized in terms of clinical phenotype, molecular genetics, and cellular pathophysiology. Given the improvement in laboratory techniques and subsequent reduction in the cost of direct DNA sequencing, there is likely to be a rapid expansion over the next decade in the identification of causative genes and hence the availability of genetic tests. Thus, all clinicians should have a basic understanding about genetic disease; inheritance patterns; availability of genetic tests; genetic counselling; and ethics. Particular subspeciality areas where neurogenetic disease is common include neuromuscular disease and movement disorders.
APA, Harvard, Vancouver, ISO, and other styles
8

Harms, Matthew B., and Timothy M. Miller. Amyotrophic Lateral Sclerosis. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0027.

Full text
Abstract:
Recent advances in sequencing technologies have dramatically expanded the number of genes associated with amyotrophic lateral sclerosis, including rare but highly penetrant causative mutations as well as common risk alleles. This chapter discusses these gene discoveries and how they have implicated a diverse array of biological pathways essential for motor neuron health and have begun to inform our understanding of ALS pathogenesis as a heterogeneous and multistep process. Insights from these discoveries are leading to a new generation of targeted therapies directed at specific genes and are poised to inform how patients with amyotrophic lateral sclerosis are evaluated and treated in the clinic.
APA, Harvard, Vancouver, ISO, and other styles
9

Vaheri, Antti, James N. Mills, Christina F. Spiropoulou, and Brian Hjelle. Hantaviruses. Oxford University Press, 2011. http://dx.doi.org/10.1093/med/9780198570028.003.0035.

Full text
Abstract:
Hantaviruses (genus Hantavirus, family Bunyaviridae) are rodent- and insectivore-borne zoonotic viruses. Several hantaviruses are human pathogens, some with 10-35% mortality, and cause two diseases: hemorrhagic fever with renal syndrome (HFRS) in Eurasia, and hantavirus cardiopulmonary syndrome (HCPS) in the Americas. Hantaviruses are enveloped and have a three-segmented, single-stranded, negative-sense RNA genome. The L gene encodes an RNA-dependent RNA polymerase, the M gene encodes two glycoproteins (Gn and Gc), and the S gene encodes a nucleocapsid protein. In addition, the S genes of some hantaviruses have an NSs open reading frame that can act as an interferon antagonist. Similarities between phylogenies have suggested ancient codivergence of the viruses and their hosts to many authors, but increasing evidence for frequent, recent host switching and local adaptation has led to questioning of this model. Infected rodents establish persistent infections with little or no effect on the host. Humans are infected from aerosols of rodent excreta, direct contact of broken skin or mucous membranes with infectious virus, or rodent bite. One hantavirus, Andes virus, is unique in that it is known to be transmitted from person-to-person. HFRS and HCPS, although primarily affecting kidneys and lungs, respectively, share a number of clinical features, such as capillary leakage, TNF-, and thrombocytopenia; notably, hemorrhages and alterations in renal function also occur in HCPS and cardiac and pulmonary involvement are not rare in HFRS. Of the four structural proteins, both in humoral and cellular immunity, the nucleocapsid protein appears to be the principal immunogen. Cytotoxic T-lymphocyte responses are seen in both HFRS and HCPS and may be important for both protective immunity and pathogenesis. Diagnosis is mainly based on detection of IgM antibodies although viral RNA (vRNA) may be readily, although not invariably, detected in blood, urine and saliva. For sero/genotyping neutralization tests/RNA sequencing are required. Formalin-inactivated vaccines have been widely used in China and Korea but not outside Asia. Hantaviruses are prime examples of emerging and re-emerging infections and, given the limited number of rodents and insectivores thus far studied, it is likely that many new hantaviruses will be detected in the near future.
APA, Harvard, Vancouver, ISO, and other styles

Book chapters on the topic "Direct sequencing"

1

Schieltz, David M., and John R. Yates. "Direct Identification of Proteins in Ultracomplex Mixtures." In Protein Sequencing Protocols, 235–45. Totowa, NJ: Humana Press, 2003. http://dx.doi.org/10.1385/1-59259-342-9:235.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Ray, Kunal, Arijit Mukhopadhyay, and Mainak Sengupta. "Gene Discovery by Direct Genome Sequencing." In Gene Discovery for Disease Models, 215–33. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9780470933947.ch11.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Mazars, Georges-Raoul, and Charles Theillet. "Direct Sequencing by Thermal Asymmetric PCR." In PCR Protocols, 355–59. Totowa, NJ: Humana Press, 2003. http://dx.doi.org/10.1007/978-1-4612-0055-0_52.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Smith, Linda K. "HLA Typing by Direct DNA Sequencing." In Methods in Molecular Biology™, 67–86. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-842-9_5.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Hong, Tao. "Direct Nucleotide Sequencing for Amplification Product Identification." In Advanced Techniques in Diagnostic Microbiology, 389–402. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-33900-9_19.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Džunková, Mária. "Flow Cytometry and Direct Sequencing of Viruses." In The Human Virome, 3–14. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8682-8_1.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Hong, Tao. "Direct Nucleotide Sequencing for Amplification Product Identification." In Advanced Techniques in Diagnostic Microbiology, 383–95. Boston, MA: Springer US, 2012. http://dx.doi.org/10.1007/978-1-4614-3970-7_22.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Krautwurst, Sebastian, Ronald Dijkman, Volker Thiel, Andi Krumbholz, and Manja Marz. "Direct RNA Sequencing for Complete Viral Genomes." In Virus Bioinformatics, 35–50. Boca Raton: Chapman and Hall/CRC, 2021. http://dx.doi.org/10.1201/9781003097679-3.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Hansen, C., M. Jørgensen, M. Bévort, R. Hummel, M. Løfgreen, N. Pallisgaard, and H. Leffers. "Direct Automated Sequencing of DDRT-PCR Fragments." In Fingerprinting Methods Based on Arbitrarily Primed PCR, 345–51. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60441-6_35.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Gyllensten, Ulf. "Direct Sequencing of In Vitro Amplified DNA." In PCR Technology, 45–60. London: Palgrave Macmillan UK, 1989. http://dx.doi.org/10.1007/978-1-349-20235-5_5.

Full text
APA, Harvard, Vancouver, ISO, and other styles

Conference papers on the topic "Direct sequencing"

1

Heath, Samuel A., Franco P. Preparata, and Joel Young. "Sequencing by hybridization using direct and reverse cooperating spectra." In the sixth annual international conference. New York, New York, USA: ACM Press, 2002. http://dx.doi.org/10.1145/565196.565220.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Yanagi, Itaru, Rena Akahori, Tomio Iwasaki, Yusuke Goto, Kazuma Matsui, Yoshikazu Nara, Naomi Manri, Mayu Aoki, Takahide Yokoi, and Ken-ichi Takeda. "Fabrication and analysis of SiN nanopores for direct DNA sequencing." In 2015 IEEE International Electron Devices Meeting (IEDM). IEEE, 2015. http://dx.doi.org/10.1109/iedm.2015.7409692.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Cox, M., S. Carney, L. Hoyles, S. Roy, R. Williams, J. Breuer, V. Chalker, and M. Moffatt. "Legionella Pneumophila Typing by Direct Sequencing of Clinical and Environmental Samples." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2121.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Schmitt, Michael W., Jesse J. Salk, Edward J. Fox, Justin R. Pritchard, J. Graeme Hodgson, Victor M. Rivera, Pamela S. Becker, Jerald P. Radich, and Lawrence A. Loeb. "Abstract 2395: Direct assessment of sequence heterogeneity in human cancers by Duplex Sequencing." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-2395.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Kolodziejski, Noah J., Rajan Gurjar, Karthik Vishwanath, and David Wolf. "Tip-Enhanced Raman Spectroscopy: Focusing in on a Direct Sequencing Method for Oxidized DNA." In Biomedical Optics. Washington, D.C.: OSA, 2014. http://dx.doi.org/10.1364/biomed.2014.bt3a.29.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Yanagi, Itaru, Takeshi Oura, Takanobu Haga, Masahiko Ando, Jiro Yamamoto, Toshiyuki Mine, Takeshi Ishida, et al. "A novel side-gated ultrathin-channel nanopore FET (SGNAFET) sensor for direct DNA sequencing." In 2013 IEEE International Electron Devices Meeting (IEDM). IEEE, 2013. http://dx.doi.org/10.1109/iedm.2013.6724629.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Sianipar, Nesti Fronika, Reflinur, Muhammad Dzulkifly Ashan, Khoirunnisa Assidqi, Dwityantari Widyaningrum, and Ragapadmi Purnamaningsih. "Direct verification of bogor superior mutant (Typhonium flagelliforme) using RAPD marker techniques and sequencing analysis." In THE 8TH INTERNATIONAL CONFERENCE AND WORKSHOP ON BASIC AND APPLIED SCIENCE (ICOWOBAS) 2021. AIP Publishing, 2023. http://dx.doi.org/10.1063/5.0104057.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Karunyakorn, Jirachote, Naruemon Pratanwanich, Monnat Pongpanich, and Pornchai Kaewsapsak. "A Computational Workflow for Estimation of Short RNA Polyadenylation using Direct RNA Nanopore Sequencing with Polyuridylation." In 2022 19th International Joint Conference on Computer Science and Software Engineering (JCSSE). IEEE, 2022. http://dx.doi.org/10.1109/jcsse54890.2022.9836262.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Flusberg, Benjamin, Dale Webster, Kevin Travers, Eric Olivares, Jonas Korlach, and Stephen Turner. "Abstract 1154: Direct detection of DNA methylation and mutagenic damage through single-molecule, real-time (SMRTTM) DNA sequencing." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-1154.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Shekhar, Sudip, Rajesh Inti, James Jaussi, Tzu-Chien Hsueh, and Bryan Casper. "A 1.2–5Gb/s 1.4–2pJ/b serial link in 22nm CMOS with a direct data-sequencing blind oversampling CDR." In 2015 Symposium on VLSI Circuits. IEEE, 2015. http://dx.doi.org/10.1109/vlsic.2015.7231319.

Full text
APA, Harvard, Vancouver, ISO, and other styles

Reports on the topic "Direct sequencing"

1

Rhodes, C. K. Human genome sequencing with direct x-ray holographic imaging. Office of Scientific and Technical Information (OSTI), June 1993. http://dx.doi.org/10.2172/6288788.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Rhodes, C. K. Human genome sequencing with direct x-ray holographic imaging. Final report. Office of Scientific and Technical Information (OSTI), June 1993. http://dx.doi.org/10.2172/10168190.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Gelb, Jr., Jack, Yoram Weisman, Brian Ladman, and Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, December 2003. http://dx.doi.org/10.32747/2003.7586470.bard.

Full text
Abstract:
Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.
APA, Harvard, Vancouver, ISO, and other styles
4

Mehmood, Hamid, Surya Karthik Mukkavilli, Ingmar Weber, Atsushi Koshio, Chinaporn Meechaiya, Thanapon Piman, Kenneth Mubea, Cecilia Tortajada, Kimberly Mahadeo, and Danielle Liao. Strategic Foresight to Applications of Artificial Intelligence to Achieve Water-related Sustainable Development Goals. United Nations University Institute for Water, Environment and Health, April 2020. http://dx.doi.org/10.53328/lotc2968.

Full text
Abstract:
The report recommends that: 1) Policymakers should conduct holistic assessments of social, economic, and cultural factors before AI adoption in the water sector, as prospective applications of AI are case- specific. It is also important to conduct baseline studies to measure the implementation capacity, return on investment, and impact of intervention. 2) To ensure positive development outcomes, policies regarding the use of AI for water-related challenges should be coupled with capacity and infrastructure development policies. Capacity development policies need to address the AI and Information and Communications Technology (ICT) needs for the AI-related skill development of all water-related stakeholders. Infrastructure development policies should address the underlying requirements of computation, energy, data generation, and storage. The sequencing of these policies is critical. 3) To mitigate the predicted job displacement that will accompany AI-led innovation in the water sector, policies should direct investments towards enabling a skilled workforce by developing water sector-related education at all levels. This skilled workforce should be strategically placed to offset dependency on the private sector. 4) Water-related challenges are cross-cutting running from grassroots to the global level and require an understanding of the water ecosystem. It is important for countries connected by major rivers and watersheds to collaborate in developing policies that advance the use of AI to address common water-related challenges. 5) A council or agency with representation from all stakeholders should be constituted at the national level, to allow for the successful adoption of AI by water agencies. This council or agency should be tasked with the development of policies, guidelines, and codes of conduct for the adoption of AI in the water-sector. These key policy recommendations can be used as primary guidelines for the development of strategies and plans to use AI to help achieve water-related SDGs.
APA, Harvard, Vancouver, ISO, and other styles
5

Fahima, Tzion, and Jorge Dubcovsky. Map-based cloning of the novel stripe rust resistance gene YrG303 and its use to engineer 1B chromosome with multiple beneficial traits. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598147.bard.

Full text
Abstract:
Research problem: Bread wheat (Triticumaestivum) provides approximately 20% of the calories and proteins consumed by humankind. As the world population continues to increase, it is necessary to improve wheat yields, increase grain quality, and minimize the losses produced by biotic and abiotic stresses. Stripe rust, caused by Pucciniastriiformisf. sp. tritici(Pst), is one of the most destructive diseases of wheat. The new pathogen races are more virulent and aggressive than previous ones and have produced large economic losses. A rich source for stripe-rust resistance genes (Yr) was found in wild emmer wheat populations from Israel. Original Project goals: Our long term goal is to identify, map, clone, characterize and deploy in breeding, novel wild emmer Yr genes, and combine them with multiple beneficial traits. The current study was aiming to map and clone YrG303 and Yr15, located on chromosome 1BS and combine them with drought resistance and grain quality genes. Positional cloning of YrG303/Yr15: Fine mapping of these genes revealed that YrG303 is actually allelic to Yr15. Fine genetic mapping using large segregating populations resulted in reduction of the genetic interval spanning Yr15 to less than 0.1 cM. Physical mapping of the YrG303/Yr15 locus was based on the complete chromosome 1BS physical map of wheat constructed by our group. Screening of 1BS BAC library with Yr15 markers revealed a long BAC scaffold covering the target region. The screening of T. dicoccoidesaccession-specific BAC library with Yr15 markers resulted in direct landing on the target site. Sequencing of T. dicoccoidesBAC clones that cover the YrG303/Yr15 locus revealed a single candidate gene (CG) with conserved domains that may indicate a role in disease resistance response. Validation of the CG was carried out using EMS mutagenesis (loss-of- function approach). Sequencing of the CG in susceptible yr15/yrG303 plants revealed three independent mutants that harbour non-functional yr15/yrG303 alleles within the CG conserved domains, and therefore validated its function as a Pstresistance gene. Evaluation of marker-assisted-selection (MAS) for Yr15. Introgressions of Yr15 into cultivated wheat are widely used now. Recently, we have shown that DNA markers linked to Yr15 can be used as efficient tools for introgression of Yr15 into cultivated wheat via MAS. The developed markers were consistent and polymorphic in all 34 tested introgressions and are the most recommended markers for the introgression of Yr15. These markers will facilitate simultaneous selection for multiple Yr genes and help to avoid escapees during the selection process. Engineering of improved chromosome 1BS that harbors multiple beneficial traits. We have implemented the knowledge and genetic resources accumulated in this project for the engineering of 1B "super-chromosome" that harbors multiple beneficial traits. We completed the generation of a chromosome including the rye 1RS distal segment associated with improved drought tolerance with the Yr gene, Yr15, and the strong gluten allele 7Bx-over-expressor (7Bxᴼᴱ). We have completed the introgression of this improved chromosome into our recently released variety Patwin-515HP and our rain fed variety Kern, as well as to our top breeding lines UC1767 and UC1745. Elucidating the mechanism of resistance exhibited by Yr36 (WKS1). The WHEAT KINASE START1 (WKS1) resistance gene (Yr36) confers partial resistance to Pst. We have shown that wheat plants transformed with WKS1 transcript are resistant to Pst. WKS1 is targeted to the chloroplast where it phosphorylates the thylakoid-associatedascorbateperoxidase (tAPX) and reduces its ability to detoxify peroxides. Based on these results, we propose that the phosphorylation of tAPX by WKS1 reduces the ability of the cells to detoxify ROS and contributes to cell death. Distribution and diversity of WKS in wild emmer populations. We have shown that WKS1 is present only in the southern distribution range of wild emmer in the Fertile Crescent. Sequence analysis revealed a high level of WKS1 conservation among wild emmer populations, in contrast to the high level of diversity observed in NB-LRR genes. This phenomenon shed some light on the evolution of genes that confer partial resistance to Pst. Three new WKS1 haplotypes displayed a resistance response, suggesting that they can be useful to improve wheat resistance to Pst. In summary, we have improved our understanding of cereals’ resistance mechanisms to rusts and we have used that knowledge to develop improved wheat varieties.
APA, Harvard, Vancouver, ISO, and other styles
6

Tang, Jiqin, Gong Zhang, Jinxiao Xing, Ying Yu, and Tao Han. Network Meta-analysis of Heat-clearing and Detoxifying Oral Liquid of Chinese Medicines in Treatment of Children’s Hand-foot-mouth Disease：a protocol for systematic review. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, January 2022. http://dx.doi.org/10.37766/inplasy2022.1.0032.

Full text
Abstract:
Review question / Objective: The type of study was clinical randomized controlled trial (RCT). The object of study is the patients with HFMD. There is no limit to gender and race. In the case of clear diagnosis standard, curative effect judgment standard and consistent baseline treatment, the experimental group was treated with pure oral liquid of traditional Chinese medicine(A: Fuganlin oral liquid, B: huangzhihua oral liquid, C: Lanqin oral liquid, D: antiviral oral liquid, E: Huangqin oral liquid, F: Pudilan oral liquid, G: Shuanghuanglian oral liquid.)and the control group was treated with ribavirin or any oral liquid of traditional Chinese medicine. The data were extracted by two researchers independently, cross checked and reviewed according to the pre-determined tables. The data extraction content is (1) Basic information (including the first author, published journal and year, research topic). (2) Relevant information (including number of cases, total number of cases, gender, age, intervention measures, course of treatment of the experimental group and the control group in the literature). (3) Design type and quality evaluation information of the included literature. (4) Outcome measures (effective rate, healing time of oral ulcer, regression time of hand and foot rash, regression time of fever, adverse reactions.). The seven traditional Chinese medicine oral liquids are comparable in clinical practice, but their actual clinical efficacy is lack of evidence-based basis. Therefore, the purpose of this study is to use the network meta-analysis method to integrate the clinical relevant evidence of direct and indirect comparative relationship, to make quantitative comprehensive statistical analysis and sequencing of different oral liquid of traditional Chinese medicine with the same evidence body for the treatment of the disease, and then to explore the advantages and disadvantages of the efficacy and safety of different oral liquid of traditional Chinese medicine to get the best treatment plan, so as to provide reference value and evidence-based medicine evidence for clinical optimization of drug selection. Condition being studied: Hand foot mouth disease (HFMD) is a common infectious disease in pediatrics caused by a variety of enteroviruses. Its clinical manifestations are mainly characterized by persistent fever, hand foot rash, oral herpes, ulcers, etc. Because it is often found in preschool children, its immune system development is not perfect, so it is very vulnerable to infection by pathogens and epidemic diseases, resulting in rapid progress of the disease. A few patients will also have neurogenic pulmonary edema Meningitis, myocarditis and other serious complications even lead to death, so effectively improve the cure rate, shorten the course of disease, prevent the deterioration of the disease as the focus of the study. In recent years, traditional Chinese medicine has played an important role in the research of antiviral treatment. Many clinical practices have confirmed that oral liquid of traditional Chinese medicine can effectively play the role of antiviral and improve the body's immunity.
APA, Harvard, Vancouver, ISO, and other styles
7

Dubcovsky, Jorge, Tzion Fahima, Ann Blechl, and Phillip San Miguel. Validation of a candidate gene for increased grain protein content in wheat. United States Department of Agriculture, January 2007. http://dx.doi.org/10.32747/2007.7695857.bard.

Full text
Abstract:
High Grain Protein Content (GPC) of wheat is important for improved nutritional value and industrial quality. However, selection for this trait is limited by our poor understanding of the genes involved in the accumulation of protein in the grain. A gene with a large effect on GPC was detected on the short arm of chromosome 6B in a Triticum turgidum ssp. dicoccoides accession from Israel (DIC, hereafter). During the previous BARD project we constructed a half-million clones Bacterial Artificial Chromosome (BAC) library of tetraploid wheat including the high GPC allele from DIC and mapped the GPC-B1 locus within a 0.3-cM interval. Our long-term goal is to provide a better understanding of the genes controlling grain protein content in wheat. The specific objectives of the current project were to: (1) complete the positional cloning of the GPC-B1 candidate gene; (2) characterize the allelic variation and (3) expression profile of the candidate gene; and (4) validate this gene by using a transgenic RNAi approach to reduce the GPC transcript levels. To achieve these goals we constructed a 245-kb physical map of the GPC-B1 region. Tetraploid and hexaploid wheat lines carrying this 245-kb DIC segment showed delayed senescence and increased GPC and grain micronutrients. The complete sequencing of this region revealed five genes. A high-resolution genetic map, based on approximately 9,000 gametes and new molecular markers enabled us to delimit the GPC-B1 locus to a 7.4-kb region. Complete linkage of the 7.4-kb region with earlier senescence and increase in GPC, Zn, and Fe concentrations in the grain suggested that GPC-B1 is a single gene with multiple pleiotropic effects. The annotation of this 7.4-kb region identified a single gene, encoding a NAC transcription factor, designated as NAM-B1. Allelic variation studies demonstrated that the ancestral wild wheat allele encodes a functional NAC transcription factor whereas modern wheat varieties carry a non-functional NAM-B1 allele. Quantitative PCR showed that transcript levels for the multiple NAMhomologues were low in flag leaves prior to anthesis, after which their levels increased significantly towards grain maturity. Reduction in RNA levels of the multiple NAMhomologues by RNA interference delayed senescence by over three weeks and reduced wheat grain protein, Zn, and Fe content by over 30%. In the transgenic RNAi plants, residual N, Zn and Fe in the dry leaves was significantly higher than in the control plants, confirming a more efficient nutrient remobilization in the presence of higher levels of GPC. The multiple pleiotropic effects of NAM genes suggest a central role for these genes as transcriptional regulators of multiple processes during leaf senescence, including nutrient remobilization to the developing grain. The cloning of GPC-B1 provides a direct link between the regulation of senescence and nutrient remobilization and an entry point to characterize the genes regulating these two processes. This may contribute to their more efficient manipulation in crops and translate into food with enhanced nutritional value. The characterization of the GPC-B1 gene will have a significant impact on wheat production in many regions of the world and will open the door for the identification of additional genes involved in the accumulation of protein in the grain.
APA, Harvard, Vancouver, ISO, and other styles
8

Bercovier, Herve, and Ronald P. Hedrick. Diagnostic, eco-epidemiology and control of KHV, a new viral pathogen of koi and common carp. United States Department of Agriculture, December 2007. http://dx.doi.org/10.32747/2007.7695593.bard.

Full text
Abstract:
Original objectives and revisions-The proposed research included these original objectives: field validation of diagnostic tests (PCR), the development and evaluation of new sensitive tools (LC-PCR/TaqManPCR, antibody detection by ELISA) including their use to study the ecology and the epidemiology of KHV (virus distribution in the environment and native cyprinids) and the carrier status of fish exposed experimentally or naturally to KHV (sites of virus replication and potential persistence or latency). In the course of the study we completed the genome sequence of KHV and developed a DNA array to study the expression of KHV genes in different conditions. Background to the topics-Mass mortality of koi or common carp has been observed in Israel, USA, Europe and Asia. These outbreaks have reduced exports of koi from Israel and have created fear about production, import, and movements of koi and have raised concerns about potential impacts on native cyprinid populations in the U.S.A. Major conclusions-A suite of new diagnostic tools was developed that included 3 PCR assays for detection of KHV DNA in cell culture and fish tissues and an ELISA assay capable of detecting anti-KHV antibodies in the serum of koi and common carp. The TKPCR assay developed during the grant has become an internationally accepted gold standard for detection of viral DNA. Additionally, the ELISA developed for detecting serum anti-KHV antibodies is now in wide use as a major nonlethal screening tool for evaluating virus status of koi and common carp populations. Real time PCR assays have been able to detect viral DNA in the internal organs of survivors of natural and wild type vaccine exposures at 1 and 10³ genome equivalents at 7 months after exposure. In addition, vaccinated fish were able to transmit the virus to naive fish. Potential control utilizing hybrids of goldfish and common carp for production demonstrated they were considerably more resistant than pure common carp or koi to both KHV (CyHV-3). There was no evidence that goldfish or other tested endemic cyprinids species were susceptible to KHV. The complete genomic sequencing of 3 strains from Japan, the USA, and Israel revealed a 295 kbp genome containing a 22 kbp terminal direct repeat encoding clear gene homologs to other fish herpesviruses in the family Herpesviridae. The genome encodes156 unique protein-coding genes, eight of which are duplicated in the terminal repeat. Four to seven genes are fragmented and the loss of these genes may be associated with the high virulence of the virus. Viral gene expression was studies by a newly developed chip which has allowed verification of transcription of most all hypothetical genes (ORFs) as well as their kinetics. Implications, both scientific and agricultural- The results from this study have immediate application for the control and management of KHV. The proposal provides elements key to disease management with improved diagnostic tools. Studies on the ecology of the virus also provide insights into management of the virus at the farms that farmers will be able to apply immediately to reduce risks of infections. Lastly, critical issues that surround present procedures used to create “resistant fish” must be be resolved (e.g. carriers, risks, etc.). Currently stamping out may be effective in eradicating the disease. The emerging disease caused by KHV continues to spread. With the economic importance of koi and carp and the vast international movements of koi for the hobby, this disease has the potential for even further spread. The results from our studies form a critical component of a comprehensive program to curtail this emerging pathogen at the local, regional and international levels.
APA, Harvard, Vancouver, ISO, and other styles
9

Mawassi, Munir, and Valerian V. Dolja. Role of the viral AlkB homologs in RNA repair. United States Department of Agriculture, June 2014. http://dx.doi.org/10.32747/2014.7594396.bard.

Full text
Abstract:
AlkB proteins that repair DNA via reversing methylation damage are conserved in a broad range of prokaryotes and eukaryotes including plants. Surprisingly, AlkB-domains were discovered in the genomes of numerous plant positive-strand RNA viruses, majority of which belong to the family Flexiviridae. The major goal of this research was to reveal the AlkB functions in the viral infection cycle using a range of complementary genetic and biochemical approaches. Our hypotheses was that AlkB is required for efficient replication and genetic stability of viral RNA genomes The major objectives of the research were to identify the functions of GVA AlkB domain throughout the virus infection cycle in N. benthamiana and grapevine, to investigate possible RNA silencing suppression activity of the viral AlkBs, and to characterize the RNA demethylation activity of the mutated GVA AlkBs in vitro and in vivo to determine methylation status of the viral RNA. Over the duration of project, we have made a very substantial progress with the first two objectives. Because of the extreme low titer of the virus particles in plants infected with the AlkB mutant viruses, we were unable to analyze RNA demethylation activity and therefore had to abandon third objective. The major achievements with our objectives were demonstration of the AlkB function in virus spread and accumulation in both experimental and natural hosts of GVA, discovery of the functional cooperation and physical interaction between AlkB and p10 AlkB in suppression of plant RNA silencing response, developing a powerful virus vector technology for grapevine using GLRaV-2-derived vectors for functional genomics and pathogen control in grapevine, and in addition we used massive parallel sequencing of siRNAs to conduct comparative analysis of the siRNA populations in grape plants infected with AlkB-containing GLRaV-3 versus GLRaV-2 that does not encode AlkB. This analysis revealed dramatically reduced levels of virus-specific siRNAs in plants infected with GLRaV-3 compared to that in GLRaV-2 infection implicating AlkB in suppression of siRNA formation. We are pleased to report that BARD funding resulted in 5 publications directly supported by BARD, one US patent, and 9 more publications also relevant to project. Moreover, two joint manuscripts that summarize work on GVA AlkB (led by Israeli PI) and on viral siRNAs in grapevine (led by US PI in collaboration with University of Basel) are in preparation.
APA, Harvard, Vancouver, ISO, and other styles
10

Levisohn, Sharon, Maricarmen Garcia, David Yogev, and Stanley Kleven. Targeted Molecular Typing of Pathogenic Avian Mycoplasmas. United States Department of Agriculture, January 2006. http://dx.doi.org/10.32747/2006.7695853.bard.

Full text
Abstract:
Intraspecies identification (DNA "fingerprinting") of pathogenic avian mycoplasmas is a powerful tool for epidemiological studies and monitoring strain identity. However the only widely method available for Mycoplasma gallisepticum (MG) and M. synoviae (MS)wasrandom amplified polymorphic DNA (RAPD). This project aimed to develop alternative and supplementary typing methods that will overcome the major constraints of RAPD, such as the need for isolation of the organism in pure culture and the lack of reproducibility intrinsic in the method. Our strategy focussed on recognition of molecular markers enabling identification of MG and MS vaccine strains and, by extension, pathogenic potential of field isolates. Our first aim was to develop PCR-based systems which will allow amplification of specific targeted genes directly from clinical material. For this purpose we evaluated the degree of intraspecies heterogeneity in genes encoding variable surface antigens uniquely found in MG all of which are putative pathogenicity factors. Phylogenic analysis of targeted sequences of selected genes (pvpA, gapA, mgc2, and lp) was employed to determine the relationship among MG strains.. This method, designated gene targeted sequencing (GTS), was successfully employed to identify strains and to establish epidemiologically-linked strain clusters. Diagnostic PCR tests were designed and validated for each of the target genes, allowing amplification of specific nucleotide sequences from clinical samples. An mgc2-PCR-RFLP test was designed for rapid differential diagnosis of MG vaccine strains in Israel. Addressing other project goals, we used transposon mutagenesis and in vivo and in vitro models for pathogenicity to correlated specific changes in target genes with biological properties that may impact the course of infection. An innovative method for specific detection and typing of MS strains was based on the hemagglutinin-encoding gene vlhA, uniquely found in this species. In parallel, we evaluated the application of amplified fragment length polymorphism (AFLP) in avian mycoplasmas. AFLP is a highly discriminatory method that scans the entire genome using infrequent restriction site PCR. As a first step the method was found to be highly correlated with other DNA typing methods for MG species and strain differentiation. The method is highly reproducible and relatively rapid, although it is necessary to isolate the strain to be tested. Both AFLP and GTS are readily to amenable to computer-assisted analysis of similarity and construction of a data-base resource. The availability of improved and diverse tools will help realize the full potential of molecular typing of avian mycoplasmas as an integral and essential part of mycoplasma control programs.
APA, Harvard, Vancouver, ISO, and other styles
You might also be interested in the extended bibliographies on the topic 'Direct sequencing' for particular source types:
Journal articles Dissertations / Theses
We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!

To the bibliography