53,224 results match your criteria single-stranded rna


Strawberry, a new natural host of Brassica yellows virus in China.

Plant Dis 2021 Sep 21. Epub 2021 Sep 21.

China Agricultural University College of Horticulture, 534806, Department of Fruit Science, Beijing, China;

Brassica yellows virus (BrYV; genus Polerovirus, family Solemoviridae) has an icosahedral spherical virion with a positive-sense single-stranded RNA genome and it is distinguished from turnip yellows virus (TuYV) based on differences in ORF0 and ORF5 (Xiang et al., 2011). To investigate the occurrence and distribution of viruses infecting strawberry (Fragaria ananassa) in the main production areas in China, a survey of nine greenhouses (667 m2 each) was conducted in the cities of Yantai and Beijing, China in August 2020. Read More

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September 2021

A Novel Miniature CRISPR-Cas13 System for SARS-CoV-2 Diagnostics.

ACS Synth Biol 2021 Sep 21. Epub 2021 Sep 21.

Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.

Rapid, point-of-care (POC) diagnostics are essential to mitigate the impacts of current (and future) epidemics; however, current methods for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) require complicated laboratory tests that are generally conducted off-site and require substantial time. CRISPR-Cas systems have been harnessed to develop sensitive and specific platforms for nucleic acid detection. These detection platforms take advantage of CRISPR enzymes' RNA-guided specificity for RNA and DNA targets and collateral trans activities on single-stranded RNA and DNA reporters. Read More

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September 2021

A 2021 taxonomy update for the family Smacoviridae.

Arch Virol 2021 Sep 21. Epub 2021 Sep 21.

The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA.

The family Smacoviridae (order Cremevirales, class Arfiviricetes, phylum Cressdnaviricota) is comprised of viruses with small circular single-stranded DNA genomes of ~2.3-3 kb in length that have primarily been identified in fecal sample of various animals. Smacovirus genomes carry two genes in ambisense orientation encoding a capsid protein and a rolling-circle replication initiation protein, respectively. Read More

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September 2021

Unwinding of a DNA replication fork by a hexameric viral helicase.

Nat Commun 2021 Sep 20;12(1):5535. Epub 2021 Sep 20.

Department of Biological Sciences, Birkbeck College, Institute of Structural and Molecular Biology, Malet Street, London, WC1E 7HX, UK.

Hexameric helicases are motor proteins that unwind double-stranded DNA (dsDNA) during DNA replication but how they are optimised for strand separation is unclear. Here we present the cryo-EM structure of the full-length E1 helicase from papillomavirus, revealing all arms of a bound DNA replication fork and their interactions with the helicase. The replication fork junction is located at the entrance to the helicase collar ring, that sits above the AAA + motor assembly. Read More

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September 2021

Nucleotide proofreading functions by nematode RAD51 paralogs facilitate optimal RAD51 filament function.

Nat Commun 2021 Sep 20;12(1):5545. Epub 2021 Sep 20.

International Clinical Research Center, St. Anne's University Hospital in Brno, 62500, Brno, Czech Republic.

The RAD51 recombinase assembles as helical nucleoprotein filaments on single-stranded DNA (ssDNA) and mediates invasion and strand exchange with homologous duplex DNA (dsDNA) during homologous recombination (HR), as well as protection and restart of stalled replication forks. Strand invasion by RAD51-ssDNA complexes depends on ATP binding. However, RAD51 can bind ssDNA in non-productive ADP-bound or nucleotide-free states, and ATP-RAD51-ssDNA complexes hydrolyse ATP over time. Read More

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September 2021

Colicin-Mediated Transport of DNA through the Iron Transporter FepA.

mBio 2021 Sep 21:e0178721. Epub 2021 Sep 21.

Department of Biochemistry, University of Oxfordgrid.4991.5, Oxford, United Kingdom.

Colicins are protein antibiotics deployed by Escherichia coli to eliminate competing strains. Colicins frequently exploit outer membrane (OM) nutrient transporters to penetrate the selectively permeable bacterial cell envelope. Here, by applying live-cell fluorescence imaging, we were able to monitor the entry of the pore-forming toxin colicin B (ColB) into E. Read More

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September 2021

Label-free and reagentless electrochemical genosensor based on graphene acid for meat adulteration detection.

Biosens Bioelectron 2021 Sep 12;195:113628. Epub 2021 Sep 12.

Catalan Institute of Nanoscience and Nanotechnology, Autonomous University of Barcelona, 08193, Bellaterra, Barcelona, Spain. Electronic address:

With the increased demand for beef in emerging markets, the development of quality-control diagnostics that are fast, cheap and easy to handle is essential. Especially where beef must be free from pork residues, due to religious, cultural or allergic reasons, the availability of such diagnostic tools is crucial. In this work, we report a label-free impedimetric genosensor for the sensitive detection of pork residues in meat, by leveraging the biosensing capabilities of graphene acid - a densely and selectively functionalized graphene derivative. Read More

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September 2021

Palindromic-assisted self-annealing transcription amplification for reliable genotyping of epidermal growth factor receptor exon mutations.

Biosens Bioelectron 2021 Sep 13;194:113633. Epub 2021 Sep 13.

Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China. Electronic address:

Reliable discrimination of specific epidermal growth factor receptor (EGFR) gene mutations plays a critical role in guiding lung cancer therapeutics. Until now, convenient and accurate recognition of the specific deletion of EGFR exons has remained particularly challenging. Herein, we propose a palindromic-assisted self-annealing transcription amplification (PASTA) strategy for the reliable detection of circulating EGFR exon mutations. Read More

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September 2021

Highly Sensitive CRISPR/Cas12a-Based Fluorescence Detection of Porcine Reproductive and Respiratory Syndrome Virus.

ACS Synth Biol 2021 Sep 20. Epub 2021 Sep 20.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture & Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, PR China.

Porcine reproductive and respiratory syndrome (PRRS) is an economically important disease of swine that is caused by PRRS virus (PRRSV). In this study, we established a fluorescence assay for highly sensitive detection of PRRSV through integration of the reverse transcription-recombinase polymerase amplification (RT-RPA)-coupled Cas12a system with an optical property of single stranded DNA-fluorescently quenched (ssDNA-FQ) reporter. This technique can achieve isothermal and visual detection of PRRSV in 25 min. Read More

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September 2021

Phase separation of a plant virus movement protein and cellular factors support virus-host interactions.

PLoS Pathog 2021 Sep 20;17(9):e1009622. Epub 2021 Sep 20.

Department of Cell and Molecular Biology and Biochemistry, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Kansas City, Missouri, United States of America.

Both cellular and viral proteins can undergo phase separation and form membraneless compartments that concentrate biomolecules. The p26 movement protein from single-stranded, positive-sense Pea enation mosaic virus 2 (PEMV2) separates into a dense phase in nucleoli where p26 and related orthologues must interact with fibrillarin (Fib2) as a pre-requisite for systemic virus movement. Using in vitro assays, viral ribonucleoprotein complexes containing p26, Fib2, and PEMV2 genomic RNAs formed droplets that may provide the basis for self-assembly in planta. Read More

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September 2021

Random Base Editing for Genome Evolution in .

ACS Synth Biol 2021 Sep 20. Epub 2021 Sep 20.

Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.

Because of the limited understanding of cellular metabolism and regulatory networks, the rational engineering of complex industrial traits remains a grand challenge for the construction of microbial cell factories. Thus the development of simple, efficient, and programmable genome evolution techniques is still in high demanded for industrial biotechnology. In the present study, we established a random base editing (rBE) system for genome evolution in . Read More

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September 2021

Improving CRISPR Gene Editing Efficiency by Proximal dCas9 Targeting.

Bio Protoc 2017 Aug 5;7(15):e2432. Epub 2017 Aug 5.

Genome Engineering, MilliporeSigma, Saint Louis, MO, USA.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems function as an adaptive immune system in bacteria and archaea for defense against invading viruses and plasmids (Barrangou and Marraffini, 2014). The effector nucleases from some class 2 CRISPR-Cas systems have been repurposed for heterologous targeting in eukaryotic cells ( Jinek , 2012 ; Cong , 2013 ; Mali , 2013 ; Zetsche , 2015 ). However, the genomic environments of eukaryotes are distinctively different from that of prokaryotes in which CRISPR-Cas systems have evolved. Read More

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Construction of a Highly Diverse mRNA Library for Selection of Monobodies.

Bio Protoc 2021 Aug 20;11(16):e4125. Epub 2021 Aug 20.

Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.

Recently, we developed transcription/translation coupled with the association of puromycin linker (TRAP) display as a quick selection method to obtain antibody-like proteins. For the selection, it is important to prepare mRNA libraries among which the diversity is high. Here, we describe a method for the preparation of monobody mRNA libraries with greater than 10 theoretical diversity. Read More

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Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae).

R Soc Open Sci 2021 Sep 15;8(9):210474. Epub 2021 Sep 15.

Evolutionary and Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.

After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, , in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. Read More

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September 2021

Physical and Functional Interaction of Mitochondrial Single-Stranded DNA-Binding Protein and the Catalytic Subunit of DNA Polymerase Gamma.

Front Genet 2021 1;12:721864. Epub 2021 Sep 1.

Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.

The maintenance of the mitochondrial genome depends on a suite of nucleus-encoded proteins, among which the catalytic subunit of the mitochondrial replicative DNA polymerase, Pol γα, plays a pivotal role. Mutations in the Pol γα-encoding gene, , are a major cause of human mitochondrial disorders. Here we present a study of direct and functional interactions of Pol γα with the mitochondrial single-stranded DNA-binding protein (mtSSB). Read More

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September 2021

Rapid and sensitive detection of Salmonella in milk based on hybridization chain reaction and graphene oxide fluorescence platform.

J Dairy Sci 2021 Sep 15. Epub 2021 Sep 15.

State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China. Electronic address:

Salmonella is a foodborne pathogen that has contributed to numerous food safety accidents worldwide, making it necessary to detect contamination at an early stage. A pair of specific primers based on the invA gene of Salmonella was designed for PCR. Target double-stranded DNA (dsDNA) from PCR was purified and denatured at high temperature to obtain target single-stranded DNA (ssDNA). Read More

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September 2021

Targeting purinergic receptors to suppress the cytokine storm induced by SARS-CoV-2 infection in pulmonary tissue.

Int Immunopharmacol 2021 Sep 13;100:108150. Epub 2021 Sep 13.

Graduate Program in Medical Sciences, Federal University of Fronteira Sul, Chapecó, SC, Brazil. Electronic address:

The etiological agent of coronavirus disease (COVID-19) is the new member of the Coronaviridae family, a severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2), responsible for the pandemic that is plaguing the world. The single-stranded RNA virus is capable of infecting the respiratory tract, by binding the spike (S) protein on its viral surface to receptors for the angiotensin II-converting enzyme (ACE2), highly expressed in the pulmonary tissue, enabling the interaction of the virus with alveolar epithelial cells promoting endocytosis and replication of viral material. The infection triggers the activation of the immune system, increased purinergic signaling, and the release of cytokines as a defense mechanism, but the response can become exaggerated and prompt the so-called "cytokine storm", developing cases such as severe acute respiratory syndrome (SARS). Read More

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September 2021

SARS-CoV-2 viral RNA levels are not 'viral load'.

Trends Microbiol 2021 Sep 4. Epub 2021 Sep 4.

MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France; Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France.

Ct values are commonly used as proxies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 'viral load'. Since coronaviruses are positive single-stranded RNA [(+)ssRNA] viruses, current reverse transcription (RT)-qPCR target amplification does not distinguish replicative from transcriptional RNA. Although analyses of Ct values remain informative, equating them with viral load may lead to flawed conclusions as it is presently unknown whether (and to what extent) variation in Ct reflects variation in viral load or in gene expression. Read More

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September 2021

Aptamer functionalized DNA hydrogels: Design, applications and kinetics.

Biosens Bioelectron 2021 Sep 3;194:113597. Epub 2021 Sep 3.

Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China. Electronic address:

DNA hydrogels have received considerable attention in various promising applications due to their excellent biocompatibility, controlled biodegradability, adjustable mechanical properties, stability against proteases, self-healing ability, and stimuli responsiveness. To obtain the specific molecular recognition capability, aptamers and many other functional motifs are utilized. Aptamers are short single-stranded DNA or RNA selected through SELEX to bind with specific target with high affinity and specificity. Read More

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September 2021

DNAzyme based three-way junction assay for antibody-free detection of locus-specific N-methyladenosine modifications.

Biosens Bioelectron 2021 Sep 11;194:113625. Epub 2021 Sep 11.

Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China. Electronic address:

N-methyladenosine (m6A) is the most abundant post-transcriptional modification in RNA and has important implications in physiological processes and tumor development. However, sensitive and specific quantification of locus-specific m6A modification levels remains a challenging task. In the present work, a novel m6A-sensitive DNAzyme was utilized to directly detect m6A by coupling with a three-way junction-mediated isothermal exponential CRISPR amplification reaction for the first time. Read More

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September 2021

A CRISPR/Cas12a-assisted in vitro diagnostic tool for identification and quantification of single CpG methylation sites.

Biosens Bioelectron 2021 Sep 11;194:113624. Epub 2021 Sep 11.

BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Centre, Max Planck Institute for Complex Fluid Dynamics, University of Twente, P.O. box 217 7500 AE Enschede, the Netherlands.

The excellent specificity and selectivity of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/associated nuclease (Cas) is determined by CRISPR RNA's (crRNA's) interchangeable spacer sequence, as well as the position and number of mismatches between target sequence and the crRNA sequence. Some diseases are characterized by epigenetic alterations rather than nucleotide changes, and are therefore unsuitable for CRISPR-assisted sensing methods. Here we demonstrate an in vitro diagnostic tool to discriminate single CpG site methylation in DNA by the use of methylation-sensitive restriction enzymes (MSREs) followed by Cas12a-assisted sensing. Read More

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September 2021

Multiple hPOT1-TPP1 cooperatively unfold contiguous telomeric G-quadruplexes proceeding from 3' toward 5', a feature due to a 3'-end binding preference and to structuring of telomeric DNA.

Nucleic Acids Res 2021 Sep 17. Epub 2021 Sep 17.

Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France.

Telomeres are DNA repeated sequences that associate with shelterin proteins and protect the ends of eukaryotic chromosomes. Human telomeres are composed of 5'TTAGGG repeats and ends with a 3' single-stranded tail, called G-overhang, that can be specifically bound by the shelterin protein hPOT1 (human Protection of Telomeres 1). In vitro studies have shown that the telomeric G-strand can fold into stable contiguous G-quadruplexes (G4). Read More

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September 2021

Influence of viral transport media and freeze-thaw cycling on the sensitivity of qRT-PCR detection of SARS-CoV-2 nucleic acids.

Nanoscale 2021 Sep 17. Epub 2021 Sep 17.

School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland.

: The events of the last year have highlighted the complexity of implementing large-scale molecular diagnostic testing for novel pathogens. The purpose of this study was to determine the chemical influences of sample collection media and storage on the stability and detection of viral nucleic acids by qRT-PCR. We studied the mechanism(s) through which viral transport media (VTM) and number of freeze-thaw cycles influenced the analytical sensitivity of qRT-PCR detection of SARS-CoV-2. Read More

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September 2021

Ultrasensitive colorimetric strategy for Hg detection based on T-Hg-T configuration and target recycling amplification.

Anal Bioanal Chem 2021 Sep 16. Epub 2021 Sep 16.

School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, People's Republic of China.

A novelty aptasensor for ultrasensitive detection of Hg is developed, exploiting the combination of plasmonic properties of gold nanoparticles (AuNPs) and exonuclease III (Exo III)-assisted target recycling for signal amplification. In the presence of Hg, a DNA duplex can be formed due to the strong coordination of Hg and T bases of single-stranded DNA (ssDNA) probe. Exo III digests the DNA duplex from the 3' to 5' direction, resulting in the releasing of Hg. Read More

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September 2021

A mechanism for Rad53 to couple leading- and lagging-strand DNA synthesis under replication stress in budding yeast.

Proc Natl Acad Sci U S A 2021 Sep;118(38)

Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032;

In response to DNA replication stress, DNA replication checkpoint kinase Mec1 phosphorylates Mrc1, which in turn activates Rad53 to prevent the generation of deleterious single-stranded DNA, a process that remains poorly understood. We previously reported that lagging-strand DNA synthesis proceeds farther than leading strand in mutant cells defective in replication checkpoint under replication stress, resulting in the exposure of long stretches of the leading-strand templates. Here, we show that asymmetric DNA synthesis is also observed in and cells defective in replication checkpoint but, surprisingly, not in cells in which both DNA replication and checkpoint functions of Mrc1 are missing. Read More

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September 2021

TLR7 is expressed by support cells, but not sensory neurons, in ganglia.

J Neuroinflammation 2021 Sep 16;18(1):209. Epub 2021 Sep 16.

Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, UHN67, Portland, OR, 97239, USA.

Background: Toll-like receptor 7 (TLR7) is an innate immune receptor that detects viral single-stranded RNA and triggers the production of proinflammatory cytokines and type 1 interferons in immune cells. TLR7 agonists also modulate sensory nerve function by increasing neuronal excitability, although studies are conflicting whether sensory neurons specifically express TLR7. This uncertainty has confounded the development of a mechanistic understanding of TLR7 function in nervous tissues. Read More

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September 2021

A simple fluorescent assay for the detection of peptide nucleic acid-directed double strand duplex invasion.

Biopolymers 2021 Sep 16:e23475. Epub 2021 Sep 16.

Department of Chemistry, The University of Western Ontario, London, Ontario, Canada.

Peptide nucleic acid (PNA) is a mimic of nucleic acids that is able to bind complementary oligonucleotides with high affinity and excellent selectivity. As such, the use of PNA has been proposed in numerous applications in biochemistry, medicine, and biotechnology. Sequences of pseudo-complementary PNAs containing diaminopurine (D)-2-thiouracil ( U) base pairs bind to complementary regions within double-stranded DNA targets. Read More

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September 2021

Symbiotic Interactions Between Mosquitoes and Mosquito Viruses.

Front Cell Infect Microbiol 2021 30;11:694020. Epub 2021 Aug 30.

ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.

Mosquitoes not only transmit human and veterinary pathogens called arboviruses (arthropod-borne viruses) but also harbor mosquito-associated insect-specific viruses (mosquito viruses) that cannot infect vertebrates. In the past, studies investigating mosquito viruses mainly focused on highly pathogenic interactions that were easier to detect than those without visible symptoms. However, the recent advances in viral metagenomics have highlighted the abundance and diversity of viruses which do not generate mass mortality in host populations. Read More

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Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the .

Virus Evol 2021 31;7(2):veab050. Epub 2021 May 31.

Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.

The comprise a genetically diverse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the , in a range of aquatic hosts including fish, amphibians, and reptiles. We sought to identify additional members of the in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data and from this reveal more of the long-term patterns and processes of coronavirus evolution. Read More

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A Cooperative DNA Catalyst.

J Am Chem Soc 2021 Sep 15. Epub 2021 Sep 15.

Computer Science, California Institute of Technology, Pasadena, California 91125, United States.

DNA catalysts are fundamental building blocks for diverse molecular information-processing circuits. Allosteric control of DNA catalysts has been developed to activate desired catalytic pathways at desired times. Here we introduce a new type of DNA catalyst that we call a cooperative catalyst: a pair of reversible reactions are employed to drive a catalytic cycle in which two signal species, which can be interpreted as an activator and an input, both exhibit catalytic behavior for output production. Read More

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September 2021