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High-throughput cellular RNA device engineering

Brent Townshend, Andrew B Kennedy, Joy S Xiang, Christina D Smolke
2015 Nature Methods  
We apply our method to building biosensors for diverse ligands and determine consensus sequences that enable ligand-responsive tertiary interactions.  ...  Our methodology utilizes cell sorting, high-throughput sequencing, and statistical data analyses to enable parallel measurements of the activities of hundreds of thousands of sequences from RNA device  ...  Consensus Analyses Analyses of NGS data for consensus sequences were performed using custom MATLAB software.  ... 
doi:10.1038/nmeth.3486 pmid:26258292 pmcid:PMC4589471 fatcat:bewqta5kd5bepalg5hpyo26oau

Highly Available Primary-Backup Mechanism for Internet Services with Optimistic Consensus

Koji Hasebe, Naofumi Nishita, Kazuhiko Kato
2014 2014 IEEE International Conference on Cloud Engineering  
To this end, each service in our method creates replicas in different data centers and coordinates them with an optimistic consensus algorithm instead of a majority-based consensus algorithm such as Paxos  ...  We present an optimistic primary-backup (so-called passive replication) mechanism for highly available Internet services on intercloud platforms.  ...  To realize consistency in replication, the well-known primary-backup replication method (i.e., passive replication) is often used [3] .  ... 
doi:10.1109/ic2e.2014.71 dblp:conf/ic2e/HasebeNK14 fatcat:cl6luxrfenf4bnpfqxj3rxgnym

Leader Confirmation Replication for Millisecond Consensus in Geo-distributed Systems [article]

Dongjie Zhu, Haiwen Du, Yundong Sun, Zhaoshuo Tian
2021 arXiv   pre-print
Secondly, we designed a Generation Re-replication strategy, which can ensure the security and consistency of future-logs when the number of nodes changes.  ...  First, we demonstrate the efficacy of the approach by designing the Future-Log Replication model, which the followers are responsible for non-transactional log replication.  ...  In this paper, we propose Leader Confirm Replication (LCR), a method for optimizing leader-based consensus performance in geo-distributed consensus.  ... 
arXiv:2101.05462v2 fatcat:ud5znmzs3ffdhlst6kgl7vtdh4

A flexible content repository to enable a peer-to-peer-based wiki

Udo Bartlang, Jörg P. Müller
2009 Concurrency and Computation  
However, if replication strategies are applied in distributed systems, the consistency of data needs to be ensured. Therefore, these techniques usually employ a point of central coordination.  ...  This paper presents the method of using a flexible content repository system to implement a P2P-based wiki engine to achieve a more decentralized vision of a dynamic environment for the future Web 3.0.  ...  In contrast, we present a consensus-based group communication stack for P2P service groups to implement replicated index data structures.  ... 
doi:10.1002/cpe.1465 fatcat:3xqus7ajtrfelfviscqurcgoz4

Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs

Ivan Kosik, William L. Ince, Lauren E. Gentles, Andrew J. Oler, Martina Kosikova, Matthew Angel, Javier G. Magadán, Hang Xie, Christopher B. Brooke, Jonathan W. Yewdell, Paul G. Thomas
2018 PLoS Pathogens  
Here, we utilize the primerID method of error-correcting viral population sequencing to reveal an unexpected role for hemagglutinin (HA) glycosylation in compensating for fitness defects resulting from  ...  Understanding viral mechanisms that enable antigenic evolution is critical for designing durable vaccines and therapeutics.  ...  replicate p-values using Fisher's method.  ... 
doi:10.1371/journal.ppat.1006796 pmid:29346435 pmcid:PMC5773227 fatcat:zltkyl7d5nd47a6cblvzgx73eq

Template switching in DNA replication can create and maintain RNA hairpins

Heli A. M. Mönttinen, Ari Löytynoja
2022 Proceedings of the National Academy of Sciences of the United States of America  
Here, we show that the reconstructed ancestral histories of RNA genes contain mutation patterns consistent with the DNA replication–related template switching.  ...  Interestingly, template switching also provides an elegant explanation for the asymmetric base pair frequencies within RNA stems.  ...  This study was enabled by Academy of Finland Grant 322681.  ... 
doi:10.1073/pnas.2107005119 pmid:35046021 pmcid:PMC8794818 fatcat:ol7apxufrrel3afpbrml3bhiia

Expanding Epigenomics to Archived FFPE Tissues: An Evaluation of DNA Repair Methodologies

E. M. Siegel, A. E. Berglund, B. M. Riggs, S. A. Eschrich, R. M. Putney, A. O. Ajidahun, D. Coppola, D. Shibata
2014 Cancer Epidemiology, Biomarkers and Prevention  
Results: The Illumina Restore kit outperformed the REPLI-g ligation method with respect to reproducibility of replicates (R 2 > 0.970), highly correlated b-values between FF-FFPE (R 2 > 0.888), and fewest  ...  Until recently, these methods were only valid for DNA from flash frozen (FF) tissues.  ...  Kathryn Winters and Jen Moughan) in the use of RTOG 98-11 tissue and data.  ... 
doi:10.1158/1055-9965.epi-14-0464 pmid:25472669 pmcid:PMC4256717 fatcat:gvkg5k2slraarnaoyerw7pzkmq

Conflict-Free Replicated Data Types [chapter]

Marc Shapiro, Nuno Preguiça, Carlos Baquero, Marek Zawirski
2011 Lecture Notes in Computer Science  
Replicating data under Eventual Consistency (EC) allows any replica to accept updates without remote synchronisation.  ...  Under a formal Strong Eventual Consistency (SEC) model, we study sufficient conditions for convergence.  ...  State-based Convergent Replicated Data Type (CvRDT) We now propose a sufficient condition for strong convergence in state-based objects.  ... 
doi:10.1007/978-3-642-24550-3_29 fatcat:4v2kxf663jej3aj4usl7ndaamy

Structural and functional conservation of cis -acting RNA elements in coronavirus 5'-terminal genome regions

Ramakanth Madhugiri, Nadja Karl, Daniel Petersen, Kevin Lamkiewicz, Markus Fricke, Ulrike Wend, Robina Scheuer, Manja Marz, John Ziebuhr
2018 Virology  
The data provide conclusive evidence for the critical role of SL1 and SL2 in HCoV-229E replication and, in some cases, revealed parallels with previously characterized betacoronavirus SL1 and SL2 elements  ...  The data obtained in this study reveal a remarkable degree of structural and functional conservation of 5'-terminal RNA structural elements across coronavirus genus boundaries.  ...  Supplementary material Supplementary data associated with this article can be found in the online version at  ... 
doi:10.1016/j.virol.2017.11.025 pmid:29223446 pmcid:PMC7112051 fatcat:xs3ow7cju5ge3lwgz4uihcsq54

A single DnaA box is sufficient for initiation from the P1 plasmid origin

A L Abeles, L D Reaves, S J Austin
1990 Journal of Bacteriology  
Three more boxes lie 200 base pairs to the right of these, in the leader region for the P1 repA gene. We show that either set alone is active for origin function.  ...  One of the two origin boxes is relatively inactive. Constructs with just one of the five boxes are active for specific origin function as long as the box conforms exactly to the published consensus.  ...  A minimal P1 plasmid replication origin has been defined and consists of a maximum of some 254 base pairs (bp) (13) (Fig. 1) .  ... 
doi:10.1128/jb.172.8.4386-4391.1990 pmid:2165477 pmcid:PMC213265 fatcat:4tphfvndgnfmtksc7iv473tqmy

Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1

A. F.Y. Poon, L. C. Swenson, W. W.Y. Dong, W. Deng, S. L. Kosakovsky Pond, Z. L. Brumme, J. I. Mullins, D. D. Richman, P. R. Harrigan, S. D.W. Frost
2009 Molecular biology and evolution  
We used a phylogenetic comparative method on these data to identify putative epistatic interactions between residues.  ...  Experimental error associated with MPP was quantified by performing replicates at two different stages of the protocol, which were pooled prior to analysis to reduce this source of variation.  ...  in exchange for MBE reduced viral replicative capacity can induce further compensatory mutations that restore viral fitness (Crawford et al. 2007; Troyer et al. 2009 ).  ... 
doi:10.1093/molbev/msp289 pmid:19955476 pmcid:PMC2877536 fatcat:e5zoevhtq5gkllpwtaitbrepee

Evolution of naturally occurring 5' non-translated region variants of hepatitis C virus genotype 1b in selectable replicons

H. C. van Leeuwen
2004 Journal of General Virology  
Interestingly, during selection of colonies supporting autonomous replication, mutations emerged that restored the base pairing in the stem-loop.  ...  The extreme 59 end of the virus' genome, containing signals essential for replication, is followed by an internal ribosomal entry site (IRES) essential for protein translation as well as replication.  ...  L. and the Netherlands Organization for Scientific Research grant 901-02-099 from the Council for Medical and Health Research and Gisela Thier Foundation of the Leiden University Medical Center.  ... 
doi:10.1099/vir.0.79924-0 pmid:15218170 fatcat:rrbqpxlzvrh4hpeoyrinlxczba

A base-paired structure in the avian sarcoma virus 5' leader is required for efficient encapsidation of RNA

J B Knight, Z H Si, C M Stoltzfus
1994 Journal of Virology  
A construct in which these mutations were combined to restore potential base pairing between the two elements displayed a partially restored packaging phenotype.  ...  These results strongly suggest that the structure, referred to as the 03 stem, is required for efficient encapsidation of avian sarcoma virus RNA.  ...  Combining these mutations restores the potential for base pairing in mutant 164bp230.  ... 
doi:10.1128/jvi.68.7.4493-4502.1994 fatcat:dslbklpspnecrlrpby7f2bhlqa

Systematic content analysis: A combined method to analyse the literature on the daylighting (de-culverting) of urban streams

Luna Khirfan, Megan Peck, Niloofar Mohtat
2020 MethodsX  
Therefore, this study reassesses the literature on stream daylighting with a particular focus on its role, as a nature-based solution, for climate change mitigation and adaptation and for socio-environmental  ...  Yet, the growing body of literature on stream daylighting spreads over an array of seemingly disconnected disciplines and lacks consistency in the terminology and the definitions of the practice.  ...  We would like to acknowledge the effort s of Nathan Woodcock, for his assistance in data management and for the creation of the Tableau dashboard's interface.  ... 
doi:10.1016/j.mex.2020.100984 pmid:32728527 pmcid:PMC7381689 fatcat:7nntbsot3fcafieofmyzpc2k7y

SL1 revisited: functional analysis of the structure and conformation of HIV-1 genome RNA

Sayuri Sakuragi, Masaru Yokoyama, Tatsuo Shioda, Hironori Sato, Jun-ichi Sakuragi
2016 Retrovirology  
We also report on our further investigation of the roles of the palindromic sequences on viral replication.  ...  In particular, a six-base palindromic sequence is always present at the hairpin loop of SL1 and the formation of kissing-loop structure at this position between the two strands of genomic RNA is suggested  ...  replication, which are consistent with the current consensus.  ... 
doi:10.1186/s12977-016-0310-9 pmid:27835956 pmcid:PMC5106843 fatcat:k5u54unet5esjfoygkfrgyv4dm
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