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Добірка наукової літератури з теми "SsRNA"

Автор: Grafiati

Опубліковано: 11 березня 2023

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Статті в журналах з теми "SsRNA"

Lin, Jinzhong, Anders Fuglsang, Anders Lynge Kjeldsen, Kaiyan Sun, Yuvaraj Bhoobalan-Chitty, and Xu Peng. "DNA targeting by subtype I-D CRISPR–Cas shows type I and type III features." Nucleic Acids Research 48, no. 18 (September 22, 2020): 10470–78. http://dx.doi.org/10.1093/nar/gkaa749.

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Abstract Prokaryotic CRISPR–Cas immune systems are classified into six types based on their effector complexes which cleave dsDNA specifically (types I, II and V), ssRNA exclusively (type VI) or both ssRNA via a ruler mechanism and ssDNA unspecifically (type III). To date, no specific cleavage of ssDNA target has been reported for CRISPR–Cas. Here, we demonstrate dual dsDNA and ssDNA cleavage activities of a subtype I-D system which carries a type III Cas10-like large subunit, Cas10d. In addition to a specific dsDNA cleavage activity dependent on the HD domain of Cas10d, the helicase Cas3′ and a compatible protospacer adjacent motif (PAM), the subtype I-D effector complex can cleave ssDNA that is complementary in sequence to the crRNA. Significantly, the ssDNA cleavage sites occur at 6-nt intervals and the cleavage is catalysed by the backbone subunit Csc2 (Cas7), similar to the periodic cleavage of ssRNA by the backbone subunit of type III effectors. The typical type I cleavage of dsDNA combined with the exceptional 6-nt spaced cleavage of ssDNA and the presence of a type III like large subunit provide strong evidence for the subtype I-D system being an evolutionary intermediate between type I and type III CRISPR–Cas systems.

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Roner, Michael R., and Bradley G. Steele. "Features of the mammalian orthoreovirus 3 Dearing l1 single-stranded RNA that direct packaging and serotype restriction." Journal of General Virology 88, no. 12 (December 1, 2007): 3401–12. http://dx.doi.org/10.1099/vir.0.83209-0.

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A series of recombinant mammalian orthoreoviruses (mammalian orthoreovirus 3 Dearing, MRV-3De) were generated that express an MRV-3De λ3–CAT fusion protein. Individual viruses contain L1CAT double-stranded (ds) RNAs that range in length from a minimum of 1020 bp to 4616 bp. The engineered dsRNAs were generated from in vitro-transcribed single-stranded (ss) RNAs and incorporated into infectious virus particles by using reverse genetics. In addition to defining the sequences required for these ssRNAs to be ‘identified’ as l1 ssRNAs, the individual nucleotides in these regions that ‘mark’ each ssRNA as originating from mammalian orthoreovirus 1 Lang (MRV-1La), mammalian orthoreovirus 2 D5/Jones (MRV-2Jo) or MRV-3De have been identified. A C at position 81 in the MRV-1La 5′ 129 nt sequence was able to be replaced with a U, as normally present in MRV-3De; this toggled the activity of the MRV-1La ssRNA to that of an MRV-3De 5′ l1. RNA secondary-structure predictions for the 5′ 129 nt of both the biologically active MRV-3De l1 ssRNA and the U81-MRV-3De-restored MRV-1La 5′ ssRNA predicted a common structure.

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Li, Jiacheng, Tong Luo, Yao He, Hui Liu, ZhiWei Deng, Jiaqi Bu, Xi Long, Shian Zhong, and Yanjing Yang. "Discovery of the Rnase activity of CRISPR–Cas12a and its distinguishing cleavage efficiency on various substrates." Chemical Communications 58, no. 15 (2022): 2540–43. http://dx.doi.org/10.1039/d1cc06295f.

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LbCas12a bound to ssDNA (a) or ssRNA (b) target exhibits different activities to different substrates. a. The order of cleavage speed: hairpin DNA > short ssDNA > hairpin RNA > linear RNA; b. The order of cleavage speed: hairpin DNA > hairpin RNA > short ssDNA. TS means targeted strand. Substrates are all single strands with different secondary structures (hairpin and linear).

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Kolundžija, Sandra, Dong-Qiang Cheng, and Federico M. Lauro. "RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics." Viruses 14, no. 4 (March 28, 2022): 702. http://dx.doi.org/10.3390/v14040702.

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Massive amounts of data from nucleic acid sequencing have changed our perspective about diversity and dynamics of marine viral communities. Here, we summarize recent metatranscriptomic and metaviromic studies targeting predominantly RNA viral communities. The analysis of RNA viromes reaffirms the abundance of lytic (+) ssRNA viruses of the order Picornavirales, but also reveals other (+) ssRNA viruses, including RNA bacteriophages, as important constituents of extracellular RNA viral communities. Sequencing of dsRNA suggests unknown diversity of dsRNA viruses. Environmental metatranscriptomes capture the dynamics of ssDNA, dsDNA, ssRNA, and dsRNA viruses simultaneously, unravelling the full complexity of viral dynamics in the marine environment. RNA viruses are prevalent in large size fractions of environmental metatranscriptomes, actively infect marine unicellular eukaryotes larger than 3 µm, and can outnumber bacteriophages during phytoplankton blooms. DNA and RNA viruses change abundance on hourly timescales, implying viral control on a daily temporal basis. Metatranscriptomes of cultured protists host a diverse community of ssRNA and dsRNA viruses, often with multipartite genomes and possibly persistent intracellular lifestyles. We posit that RNA viral communities might be more diverse and complex than formerly anticipated and that the influence they exert on community composition and global carbon flows in aquatic ecosystems may be underestimated.

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Vidhyasagar, Venkatasubramanian, Yujiong He, Manhong Guo, Tanu Talwar, Ravi Shankar Singh, Manisha Yadav, George Katselis, Franco J. Vizeacoumar, Kiven E. Lukong, and Yuliang Wu. "Biochemical characterization of INTS3 and C9ORF80, two subunits of hNABP1/2 heterotrimeric complex in nucleic acid binding." Biochemical Journal 475, no. 1 (January 2, 2018): 45–60. http://dx.doi.org/10.1042/bcj20170351.

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Human nucleic acid-binding protein 1 and 2 (hNABP1 and hNABP2, also known as hSSB2 and hSSB1 respectively) form two separate and independent complexes with two identical proteins, integrator complex subunit 3 (INTS3) and C9ORF80. We and other groups have demonstrated that hNABP1 and 2 are single-stranded (ss) DNA- and RNA-binding proteins, and function in DNA repair; however, the function of INTS3 and C9OFR80 remains elusive. In the present study, we purified recombinant proteins INTS3 and C9ORF80 to near homogeneity. Both proteins exist as a monomer in solution; however, C9ORF80 exhibits anomalous behavior on SDS–PAGE and gel filtration because of 48% random coil present in the protein. Using electrophoretic mobility shift assay (EMSA), INTS3 displays higher affinity toward ssRNA than ssDNA, and C9ORF80 binds ssDNA but not ssRNA. Neither of them binds dsDNA, dsRNA, or RNA : DNA hybrid. INTS3 requires minimum of 30 nucleotides, whereas C9OFR80 requires 20 nucleotides for its binding, which increased with the increasing length of ssDNA. Interestingly, our GST pulldown results suggest that the N-terminus of INTS3 is involved in protein–protein interaction, while EMSA implies that the C-terminus is required for nucleic acid binding. Furthermore, we purified the INTS3–hNABP1/2–C9ORF80 heterotrimeric complex. It exhibits weaker binding compared with the individual hNABP1/2; interestingly, the hNABP1 complex prefers ssDNA, whereas hNABP2 complex prefers ssRNA. Using reconstituted heterotrimeric complex from individual proteins, EMSA demonstrates that INTS3, but not C9ORF80, affects the nucleic acid-binding ability of hNABP1 and hNABP2, indicating that INTS3 might regulate hNABP1/2's biological function, while the role of C9ORF80 remains unknown.

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Karlowicz, Anna, and Michal R. Szymanski. "Exog Displays 5′-Exonuclease Activity on Both ssDNA and ssRNA." Biophysical Journal 116, no. 3 (February 2019): 76a. http://dx.doi.org/10.1016/j.bpj.2018.11.452.

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Tourís-Otero, Fernando, José Martínez-Costas, Vikram N. Vakharia та Javier Benavente. "Characterization of the nucleic acid-binding activity of the avian reovirus non-structural protein σNS". Journal of General Virology 86, № 4 (1 квітня 2005): 1159–69. http://dx.doi.org/10.1099/vir.0.80491-0.

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The avian reovirus non-structural protein σNS has previously been shown to bind single-stranded (ss) RNA in vitro in a sequence-independent manner. The results of the present study further reveal that σNS binds poly(A), poly(U) and ssDNA, but not poly(C), poly(G) or duplex nucleic acids, suggesting that σNS has some nucleotide-sequence specificity for ssRNA binding. The current findings also show that σNS is present in large ribonucleoprotein complexes in the cytoplasm of avian reovirus-infected cells, indicating that it exists in intimate association with ssRNAs in vivo. Removal of RNA from the complexes generates a σNS protein form that sediments between 4·5 and 7 S, suggesting that RNA-free σNS associates into small oligomers. Expression and purification of recombinant σNS in insect cells allowed us to generate specific antibodies and to perform a variety of assays. The results of these assays revealed that: (i) RNA-free σNS exists as homodimers and homotrimers; (ii) the minimum RNA size for σNS binding is between 10 and 20 nt; (iii) σNS does not have a preference for viral mRNA sequences; and (iv) its RNA-binding activity is conformation-dependent. Baculovirus expression of point and deletion σNS mutants in insect cells showed that the five conserved basic amino acids that are important for RNA binding and ribonucleoprotein-complex formation are dispersed throughout the entire σNS sequence, suggesting that this protein binds ssRNA through conformational domains. Finally, the properties of the avian reovirus protein σNS are compared with those of its mammalian reovirus counterpart.

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Rūmnieks, Jānis, Ilva Liekniņa, Gints Kalniņš, Mihails Šišovs, Ināra Akopjana, Jānis Bogans, and Kaspars Tārs. "Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes." Science Advances 6, no. 36 (September 2020): eabc0023. http://dx.doi.org/10.1126/sciadv.abc0023.

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The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins (CPs) in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome-derived ssRNA phage CPs to produce virus-like particles and determined the three-dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage–based vaccine design.

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Bermúdez-Cruz, Rosa Ma, Jaime García-Mena, and Cecilia Montañez. "Polynucleotide phosphorylase binds to ssRNA with same affinity as to ssDNA." Biochimie 84, no. 4 (April 2002): 321–28. http://dx.doi.org/10.1016/s0300-9084(02)01385-8.

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Deng, Yong-Jie, Lei Feng, Huan Zhou, Xiang Xiao, Feng-Ping Wang, and Xi-Peng Liu. "NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA." DNA Repair 65 (May 2018): 54–63. http://dx.doi.org/10.1016/j.dnarep.2018.03.005.

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Дисертації з теми "SsRNA"

Powalowska, Paulina Klaudyna. "Development of ssRNA for therapeutic gene knock-down." Thesis, University of Nottingham, 2017. http://eprints.nottingham.ac.uk/40508/.

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Work presented in this thesis shows how chemical modifications of ssRNAs can increase their nuclease resistance, resulting in potent gene inhibition. The first part of thesis describes how a range of chemical modifications were introduced into the ssRNAs to test their effect on oligonucleotide stability and ability to inhibit gene expression. The ssRNAs were tested in a cancer cell line that stably expresses firefly luciferase. This work demonstrates that DNA nucleotides can be incorporated into ssRNA sequences without loss of potency in the RNAi mechanism. By using additional chemical modifications (2’-OMe and 2’-F) further improvement of ssRNA stability and a significant inhibition of firefly luciferase activity, reaching 91%, was achieved. Moreover, we show that the level of inhibition can be improved when the DNA dinucleotide linked by the (E)-vinylphosphonate is used as a protection of the 5’-end of the ASO (95% KD). The use of ssRNAs rather than dsRNAs is beneficial, since the possibility of off-target effects caused by the remaining sense strand is eliminated and the cost of production of such a medicine is reduced. The second part of this thesis focuses on development of an experimental system that will allow detection of the inhibition of a disease relevant target. Several approaches were used in order to detect KD of the target by the unmodified dsRNAs. First a western blotting technique was employed for detection. Although different ASOs and concentrations were used no KD was observed. More attempts were taken in order to generate target KD, but unfortunately they were unsuccessful so far.

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McCauley, Sephen Jude. "The annotation and evolutionary analysis of overlapping CDS in ssRNA viral genomes." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670151.

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Ha, Cuong Viet. "Detection and identification of potyviruses and geminiviruses in Vietnam." Thesis, Queensland University of Technology, 2007. https://eprints.qut.edu.au/16540/1/Cuong_Viet_Ha_Thesis.pdf.

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Prior to the commencement of this project, few plant viruses had been identified from Vietnam despite virus-like symptoms being commonly observed on many crops and weeds. In limited surveys in the late 1990's, preliminary evidence was obtained indicating that potyviruses and geminiviruses were causing significant diseases. As a result, this study was aimed at developing generic PCR-based methods for the rapid detection of viruses belonging to viruses in the families Potyviridae and Geminiviridae in plant samples collected from Vietnam, and to characterise the viruses at the molecular level. Novel degenerate PCR primers were developed for the identification of begomoviruses. Using these primers, 17 begomoviruses species infecting seven crop and nine weed species in Vietnam were identified and characterised. Sequence analyses showed that ten of the viruses (six monopartite and four bipartite) were new species. Of the seven previously characterized begomoviruses, five were identified in Vietnam for the first time. Additionally, eight DNA-ß and three nanovirus-like DNA-1 molecules were also found associated with the monopartite viruses. Five of the DNA-β molecules were putatively novel. Two novel bipartite begomoviruses, named Corchorus yellow vein virus (CoYVV) and Corchorus golden mosaic virus (CoGMV), were isolated from jute plants. Analysis of these viruses showed that they were more similar to New World begomoviruses than to viruses from the Old World. This was based on the absence of an AV2 open reading frame, the presence of an N-terminal PWRLMAGT motif in the coat protein and phylogenetic analysis of the DNA A and DNA B nucleotide and deduced amino acid sequences. This is the first known occurrence of Old World viruses bearing features of New World viruses, and their presence in Vietnam suggests the presence of a "New World" virus in the Old World prior to Gondwana separation. Other interesting features relating to begomoviruses identified in Vietnam were; (i) the detection of several recombination events, particularly between the newly identified Tomato yellow leaf curl Vietnam virus (TYLCVNV), and the previously characterised, Tomato leaf curl Vietnam virus (ToLCVV), (ii) the identification of new natural hosts of Sida leaf curl virus (SiLCV), Papaya leaf curl China virus (PaLCuCNV) and Alternanthera yellow vein virus (AlYVV), (iii) the first report of variation in the geminivirus stem-loop nonanucleotide sequence (CoGMV sequence was TATTATTAC rather than TAATATTAC) and (iv) the first report of different stem sequences in the stem-loop structure of two genomic components from a bipartite begomovirus, Kudzu mosaic virus (KuMV). The sequence and phylogenetic analyses of the begomoviruses and begomovirus-associated DNAs identified in this study suggested that South East Asia, and Vietnam in particular, may be a centre of begomovirus diversity. Two pairs of degenerate primers, designed in the CI gene (CIFor/CIRev) and HC-Pro gene (HPFo/HPRev), were developed for the detection of viruses in the genus Potyvirus. Using these primers, three novel potyviruses from Vietnam were detected, namely Telosma mosaic virus (TelMV) infecting telosma (Telosma cordata), Peace lily mosaic virus (PeLMV) infecting peace lily (Spathiphyllum patinii) and Wild tomato mosaic virus (WTMV) infecting wild tomato (Solanum torvum). The fragments amplified by the two sets of primers enabled additional PCR and complete genomic sequencing of these three viruses and a Banana bract mosaic virus (BBrMV) isolate from the Philippines. All four viruses shared genomic features typical of potyviruses. Sequence comparisons and phylogenetic analyses indicated that WTMV was most closely related to Chilli veinal mottle virus (ChiVMV) and Pepper veinal mottle virus (PVMV) while PeLMV, TelMV were related to different extents with members of the BCMV subgroup. The incidence of potyviruses infecting plants in Vietnam was investigated using the potyvirus-specific primers. Fifty two virus isolates from 13 distinct potyvirus species infecting a broad range of crops were identified in Vietnam by PCR and sequence analysis of the 3' region of the genome. The viruses were Bean common mosaic virus (BCMV), Potato virus Y (PVY), Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), Chilli veinal mottle virus (ChiVMV), Zucchini yellow mosaic virus (ZYMV), Leek yellow stripe virus (LYMV), Shallot yellow stripe virus (SYSV), Onion yellow dwarf virus (OYDV), Turnip mosaic virus (TuMV), Dasheen mosaic virus (DsMV), Sweet potato feathery mottle virus (SPFMV) and a novel potyvirus infecting chilli, which was tentatively named Chilli ringspot virus (ChiRSV). With the exception of BCMV and PVY, this is first report of these viruses in Vietnam. Further, rabbit bell (Crotalaria anagyroides) and typhonia (Typhonium trilobatum) were identified as new natural hosts of the Peanut stunt virus (PStV) strain of BCMV and of DsMV, respectively. Sequence and phylogenetic analyses, based on the nucleotide sequence of the entire CP-coding region of all 52 virus isolates, revealed considerable variability in BCMV, SCMV, PVY, ZYMV and DsMV. The phylogenetic analyses also suggested the possible presence of ancestral groups of BCMV, SCMV and ZYMV in Vietnam.

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Ha, Cuong Viet. "Detection and identification of potyviruses and geminiviruses in Vietnam." Queensland University of Technology, 2007. http://eprints.qut.edu.au/16540/.

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ANTUNES, T. F. S. "Associação do papaya meleira virus e de um segundo vírus de ssRNA à meleira do mamoeiro." Universidade Federal do Espírito Santo, 2017. http://repositorio.ufes.br/handle/10/7135.

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Made available in DSpace on 2018-08-01T21:35:19Z (GMT). No. of bitstreams: 1 tese_10610_Tese_Tathiana Ferreira Sá Antunes.pdf: 3860933 bytes, checksum: 5017916178f4c05d9627a10384150d23 (MD5) Previous issue date: 2017-01-23
Associação do papaya meleira virus e de um segundo vírus de ssRNA à meleira do mamoeiro.

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Boine, Barbara. "A study of the interaction between the plant pathogenic fungus Botrytis cinerea and the filamentous ssRNA mycoviruses Botrytis virus X and Botrytis virus F." Thesis, University of Auckland, 2012. http://hdl.handle.net/2292/16777.

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The ecological significance of mycoviruses is becoming increasingly recognised, not just for their potential as biocontrol agents but also as driving forces in the evolution and diversification of fungi. Therefore, it is important to understand how mycoviruses and fungi interact on the molecular and biochemical level. To this end the interaction between Botrytis cinerea and the mycoviruses Botrytis virus F and Botrytis virus X was studied. Relative and absolute real time PCR protocols were developed for monitoring the titres of BVX and BVF during transfection studies to monitor changes in virus titre in relation to phenotypic and metabolic changes in the fungal host. Phenotypic changes included severe phenotypical alterations, which were associated with extreme up regulation of carbohydrate, amino acid and lipid metabolism, and induction of stress responses (vacuolisation/cell lysis, increased pigmentation). To study the location and distribution of BVX in infected Botrytis the BVX coat protein was recombinantly expressed in E. coli, BVX specific polyclonal antibodies produced, and protocols developed for the serological detection and visualisation of BVX. Immuno-fluorescence microscopy was used to studying the distribution of BVX within growing Botrytis cultures indicated that the virus is present in aggregates located attached to the cell membrane, the septum, in spores, and in hyphal tips. A combination of light and electron microscopy showed that BVX is often closely associated with cell walls, suggesting that the virus may be moving across the cell wall by altering cell wall composition. If this is shown to be the case then it provides an alternative method to transmission via hyphal anastomosis, which is currently considered to be the only method of horizontal transfer.

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Croci, R. "RNA DEPENDENT RNA POLYMERASE: A VALUABLE TARGET TO BLOCK VIRAL REPLICATION IN SINGLE-STRANDED (+)SENSE RNA VIRUSES." Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/243352.

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The (+)strand RNA viruses include a very large group of viruses that cause epidemic diseases in humans, including dengue fever and gastroenteritis. The human (+)RNA viruses include Flaviviruses (FV) and Norovirus (NV). Both encode for proteins essential for viral replication, such as the RNA dependent RNA polymerase (RdRp). Since human cells lack RdRp, it appears as one of the most promising targets for antivirals development. I worked on the identification of new non-nucleotide inhibitors against FV and NV, using RdRp as the main target. In this context, suramin and NF023 have been identified in my lab as NV RdRp inhibitors that, however both are hampered in their application by pharmacokinetics problems. To overcome such problems, I analyzed the potential inhibitory role of Naf2, a fragment derived from these two molecules. Although Naf2 showed a low inhibitory activity, the crystal structures of NV RdRp/Naf2 complex revealed a new binding site. To further map this new site, I tested a Naf2 related molecule, PPNDS. The crystal structures of the RdRp/PPNDS complex revealed interesting features about the new binding site. I also focused on structurally related molecules synthesized following structure-driven information. NV RdRp crystal structures in complex with one of these compounds (Cpd6) were analyzed, providing new knowledge on the interactions between a small fragment and NV RdRps, establishing a platform for structure-guided drug optimization. In parallel to the NV work, I screened in silico a library of compounds against FV RdRp. One of the best compounds identified (HeE1-2Tyr) was able to inhibit the RdRp activity and several FVs in cell-based assays. Although the crystallographic analyses don't reveal clear enough electron density for the inhibitor, indirect evidence suggests that HeE1-2Tyr interferes with the RdRp priming loop that appears disordered.

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Panzarino, Nicholas J. "The ssDNA Theory of BRCAness and Genotoxic Agents." eScholarship@UMMS, 2021. https://escholarship.umassmed.edu/gsbs_diss/1131.

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Cancers that are deficient in BRCA1 or BRCA2 are thought to be hypersensitive to genotoxic agents because they cannot prevent or repair DNA double strand breaks, but observations in patients suggest this dogma may no longer agree with experiment. Here, we propose that single stranded DNA underlies the hypersensitivity of BRCA deficient cancers, and that defects in double strand break repair and prevention do not. Specifically, in BRCA deficient cells, ssDNA gaps developed because replication was not effectively restrained in response to stress. In addition, we observed gaps could be suppressed by either restored fork restraint or by gap filling, both of which conferred therapy resistance in tissue culture and BRCA patient tumors. In contrast, restored double strand break repair and prevention did not confer therapy resistance when gaps were present. Critically, double strand breaks were not detected after therapy when apoptosis was inhibited, supporting a framework in which double strand breaks are not directly induced by genotoxic agents, but instead are created by cell death nucleases and are not fundamental to genotoxic agents. Together, these data indicate that ssDNA replication gaps underlie the BRCA cancer phenotype, "BRCAness," and we propose are fundamental to the mechanism-of-action of genotoxic chemotherapy.

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Ramsey, Jon. "Biophysical Characterization of the Sequsingle-Stranded DNA-Binding Properties of Mouse Pur : a Repressor of Smooth Muscle -Actin Gene Expression." ScholarWorks @ UVM, 2008. http://scholarworks.uvm.edu/graddis/189.

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ABSTRACT Regulation of gene transcription by structural interconversions of genomic DNA is an emerging biochemical and genetic paradigm that adds to the already diverse repertoire of eukaryotic gene regulatory mechanisms. The appearance of paranemic structures coincident with changes in gene activity, as well as participation of transcription factors that recognize and bind single-stranded DNA at numerous gene promoters in vivo illustrates the authenticity of this concept and its importance in cellular homeostasis. Despite its acceptance, this concept has been minimally described at the biochemical and biophysical levels, as the means by which sequence-specific single-stranded DNAbinding proteins exert transcriptional influence in double-stranded genomes remains largely undefined. Pur is a sequence-specific single-stranded DNA/RNA-binding protein that acts as a repressor of smooth muscle -actin (SM A) gene transcription, and mRNA translation. SM A is an important cytoskeletal protein that contributes contractile, antimigratory, and nonproliferative functions in smooth muscle. In concert with Pur protein family member Pur , and Y-box protein MSY1, Pur enacts repression of SM A gene expression by interacting with a cryptic cis-regulatory element in the 5’ region of the SM A promoter that has been shown to transiently adopt single-stranded conformations in vivo, and to confer transcriptional activation when trans-activator occupied while in a doublestranded conformation. Downregulation of SM A gene expression has been identified to be a contributing factor to cardiovascular disease progression; therefore a thorough understanding of SM A repression mechanisms is critical for clinical management of these conditions. Although highly homologous at the primary sequence level, Pur and Pur display significant conserved regions of sequence divergence that suggest these paralogs exert distinct cellular functions in various vertebrate classes. A goal of the studies presented herein was to delineate exhibited functional differences with respect to SM A repression in pertinent mouse cell lines. Loss-of-function and chromatin immunoprecipitation studies verified that Pur differs from Pur in that Pur is the dominant Pur protein repressor of SM A expression in embryonic fibroblasts and vascular smooth muscle cells, although by different, cell type-specific mechanisms. Biophysical assessment of Pur single-stranded DNA binding properties showed that despite the ability of Pur to self-dimerize in the absence of nucleic acid, Pur binds to the cryptic SM A enhancer by a sequential and cooperative mechanism, with remarkable affinity and a terminal stoichiometry of 2 to 1. Footprinting and in vitro binding site characterization confirms two Pur binding sites exist within this element and display slight degeneracy from a proposed Pur protein-binding consensus motif. These findings delineate binding mechanisms adopted by Pur and provide a means to identify putative Pur binding sites throughout the genome.

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Labonté, Jessica. "Diversity and evolution of ssDNA viruses in marine environments." Thesis, University of British Columbia, 2013. http://hdl.handle.net/2429/44583.

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Книги з теми "SsRNA"

Kh, Davletov S., I͡U︡lchieva R. T, Ŭzbekiston SSR nashriëtlar, poligrafii͡a︡ va kitob savdosi ishlari bŭĭicha davlat komiteti., and Ŭzbekiston SSR davlat kitob palatasi., eds. Ŭzbekiston SSRda nashr qilingan chet ėl ëzuvchilarining asarlari: Kitoblar kŭrsatkichi. Toshkent: Ŭzbekiston SSR davlat kitob palatasi, 1985.

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Braunstein, Jennifer. Target-unabhängige Effekte von ssDNA-Oligonukleotid-Aptameren auf das Hämostasesystem und vaskuläre Endothelzellen. [S.I: s.n.] 2013., 2013.

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SSRNJ, Savezna konferencija. Šta i kako dalje na Kosovu: Dalja društveno-politička aktivnost SSRNJ u realizaciji političke platforme za akciju SKJ u razvoju socijalističkog samoupravljanja, bratstva i jedinstva i zajedništva na Kosovu. Beograd: Narodna knj, 1985.

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Dragan, Milošević, and Socijalistički savez radnog naroda Jugoslavije. (1985 : Beograd, Yugoslavia), eds. Šta i kako dalje na Kosovu: Dalja društveno-politička aktivnost SSRNJ u realizaciji političke platforme za akciju SKJ u razvoju socijalističkog samoupravljanja bratstva i jedinstva i zajedinštva na Kosovu. Beograd: Narodna knjiga, 1985.

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Частини книг з теми "SsRNA"

Gries, Oliver, and Thomas Ly. "Togaviridae [(+)ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 41–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_1.

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Gries, Oliver, and Thomas Ly. "Arenaviridae [(-)ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 123–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_10.

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Gries, Oliver, and Thomas Ly. "Rhabdoviridae [(-)ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 131–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_11.

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Gries, Oliver, and Thomas Ly. "Filoviridae [(-) ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 137–40. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_12.

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Gries, Oliver, and Thomas Ly. "Paramyxoviridae [(-)ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 141–48. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_13.

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Gries, Oliver, and Thomas Ly. "Pneumoviridae [(-)ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 149–51. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_14.

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Gries, Oliver, and Thomas Ly. "Orthomyxoviridae [(-)ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 152–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_15.

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Gries, Oliver, and Thomas Ly. "Deltaviren [(-)ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 159–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_17.

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Gries, Oliver, and Thomas Ly. "Flaviviridae [(+)ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 56–79. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_2.

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Gries, Oliver, and Thomas Ly. "Picornaviridae [(+)ssRNA]." In Infektologie - Kompendium humanpathogener Infektionskrankheiten und Erreger, 80–90. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-58219-0_3.

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Тези доповідей конференцій з теми "SsRNA"

Han, Xinbing, Xin Li, Medhavi Bole, Asha Anandiah, Sharon Zhou, Benjamin Nelson, Naimish R. Patel, Henry Koziel, and Souvenir D. Tachado. "Human Macrophages Recognize HIV SSRNA Through Endosomal TLR8." In American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado. American Thoracic Society, 2011. http://dx.doi.org/10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a6252.

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Han, Xinbing, Xin Li, Simon Yue, Falah Hashem, Medhavi Bole, Asha Anandaiah, Xiuqin Zhou, et al. "HIV SsRNA Sufficient To Induce TNFa Release Through TLR8-Dependent Histone Modification In Human Macrophages In Vitro." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a4047.

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Rafati, Jacob, Mohsen Asghari, and Sachin Goyal. "Effects of DNA Encapsulation on Buckling Instability of Carbon Nanotube Based on Nonlocal Elasticity Theory." In ASME 2014 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/detc2014-34430.

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Carbon nanotubes (CNTs) are capable to absorb and encapsulate some molecules to create new hybrid nano-structures providing a variety of functionally useful properties. CNTs functionalized by encapsulaitng single-stranded deoxy-ribonucleic acid (ssDNA) promise great potentials for applications in nanotechnology and nano-biotechnology. In this paper, buckling instability of ssDNA@CNT i.e. hybrid nano-structure composed of ssDNA encapsulated inside CNT has been investigated using the nonlocal elasticity theory. The nonlocal elasticity theory is capable to capture the small scale effects due to the discontinuity of nano-structures at atomic scales. The nonlocal elastic rod and shell equations are derived for modeling ssDNA and CNT respectively. Providing numerical examples, it is predicted that, ssDNA@(10,10) CNT is more resistant than the pristine (10,10) CNT against the buckling instability under radial pressure due to the inter-atomic van der Waals interactions between DNA and CNT. Furthermore, nonlocal elasticity theory predicts lower critical buckling pressure than does the local elasticity theory.

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Si, Wei, Jingjie Sha, Lei Liu, Yin Zhang, and Yunfei Chen. "The Molecular Dynamics Study for Detection of ssDNA by Monolayer Graphene Nanopore." In ASME 2013 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/imece2013-62384.

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Molecular dynamics simulations are performed to provide valuable information about the translocation of four single-stranded DNAs with ten identical bases through graphene nanopore with diameter of 2 nm. The monolayer graphene nanopore is highly sensitive to ssDNA translocation events and the 10-base resolution detection can be realized by electrophoreticly threading ssDNA through graphene nanopore. Due to the similar sizes of the four nucleotides, the blockage current is unlikely to provide a distinguishable signal. However, by simply monitoring and analyzing the translocation time of poly(dA)10, poly(dC)10, poly(dG)10 and poly(dT)10 though graphene pore, each ssDNA can be identified and characterized.

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Babakuliyev, Alisir, Niladri Maiti, Annie Aglin Antony, Mohammad Javed Ansari, Santosh S. Chobe, and Chandra Kumar Dixit. "Detection of Cancer Cells Using G-Rich DNA Based Target Binding-Switching Calorimetric Biosensor." In International Conference on Recent Advancements in Biomedical Engineering. Switzerland: Trans Tech Publications Ltd, 2022. http://dx.doi.org/10.4028/p-3o604e.

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This paper reports the G-rich ssDNA for the colorimetric detection of cancer cells. The ssDNA-1 sequence has explored for the potential application of “Turn-On” colorimetric sensor for selective and sensitive detection of cancer cells. While complementary G-rich DNA strand form G-quadruplex with hemin molecule, which is more effective to catalyze the peroxidase mimicking activity towards TMB chromogenic substrate. The ssDNA-1 exhibits good selectivity for cancer cells. The colorimetric intensity of TMB was enhanced upon interaction of leukemic lymphoblasts cancer cells. The effect of pH has turned the selective sensing performances of the biosensor for detecting cancer cells with a lower detection limit of 0.54 nM, 0.18 nM, and 0.2 nM respectively.

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Delport, F., J. i. Hotta, A. Deres, J. Pollet, B. Sels, J. Hofkens, and J. Lammertyn. "Counting ssDNA on a single nanoparticle." In 2008 IEEE Sensors. IEEE, 2008. http://dx.doi.org/10.1109/icsens.2008.4716499.

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Moore, Erin J., and Thirimachos Bourlai. "Biclustering for ssDNA aptamer motif prototypes." In 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI). IEEE, 2016. http://dx.doi.org/10.1109/bhi.2016.7455892.

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Meng, Debiao, Hong-Zhong Huang, Zhonglai Wang, Xiaoling Zhang, and Yu Liu. "Reliability-Based Multidisciplinary Design Optimization Using Subset Simulation Analysis and its Application in the Hydraulic Transmission Mechanism Design." In ASME 2014 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/detc2014-34732.

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The traditional Monte Carlo Simulation (MCS) approach can provide high reliability analysis accuracy, however, with low computational efficiency. Especially, it is computationally expensive to evaluate a very small failure probability. In this paper, a Subset Simulation-based Reliability Analysis (SSRA) approach is combined with the Multidisciplinary Design Optimization (MDO) to improve the computational efficiency in the Reliability based Multidisciplinary Design Optimization (RBMDO) problems. Furthermore, the Sequential Optimization and Reliability Assessment (SORA) approach is utilized to decouple the RBMDO into MDO and reliability analysis. The formula of MDO with SSRA within the framework of SORA (MDO-SSRA-SORA) is proposed to solve the design optimization problem of hydraulic transmission mechanism.

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Li, Kun, Wei Si, Jingjie Sha, and Yunfei Chen. "Molecular Dynamics Study of DNA Translocation Through Graphene Nanopores With Controllable Speed." In ASME 2015 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/imece2015-50858.

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All-atom steered molecular dynamics (SMD) simulations provide the means to study the single-stranded DNA (ssDNA) translocation through graphene nanopores at a controllable speed. The ssDNA is pulled by an elastic force similar to the manipulation by an AFM tip. At the same time, an electric field is applied across the reservoir along the direction of the pulling force, in order to hold the ssDNA strand taut and drive the ions in the solutions through the nanopore. By monitoring and analyzing the average ionic current blockage of poly(dA)10, poly(dC)10, poly(dG)10 and poly(dT)10, it is found that one can indeed discriminate the different DNA bases from each other by holding each nucleotide in the pore for sufficiently long time. It is obtained the average blocked ionic currents can be listed, in a increasing order, as IG<IA<IT, which is almost in agreement with the order of sizes of the four nucleotides (VG>VA>VT>VC), apart from C. The results indicate that physical occupancy of the nucleotide plays the major role in affecting average blocked ionic current when the DNA translocation speed is effectively slowed down. This work provides a clue for the further investigation to realize the discrimination of the four nucleotides by the method of actively controlling DNA molecule translocation speed through the nanopores.

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Gusev, Yu S., I. V. Volokhina, V. V. Fadeev, and M. I. Chumakov. "Study of the agrobacterial protein VirE2 - ssDNA interaction under various conditions for delivery technology development." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.100.

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The effects of DNA length and conditions on the formation of VirE2-ssDNA complexes were studied by dynamic light scattering and electron microscopy. The disordered regions of the VirE2 protein are predicted.

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Звіти організацій з теми "SsRNA"

Knezovich, J. Student Science Research Associates (SSRA) 1996 Research Journal. Office of Scientific and Technical Information (OSTI), December 1996. http://dx.doi.org/10.2172/515980.

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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.

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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.

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Subedi, Abishkar, Gerrit-Jan van Uffelen, and Charleen Malkowsky. Building seed system resilience in protracted crisis situations : Seed system resilience assessment and facilitation tool (SSRA-FT). Wageningen: Wageningen Centre for Development Innovation, 2020. http://dx.doi.org/10.18174/528796.

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Antignus, Yehezkiel, Ernest Hiebert, Shlomo Cohen, and Susan Webb. Approaches for Studying the Interaction of Geminiviruses with Their Whitefly Vector Bemisia tabaci. United States Department of Agriculture, July 1995. http://dx.doi.org/10.32747/1995.7604928.bard.

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The DNA of tomato yellow leaf curl virus (TYLCB) was detected in its whitefly vector, Bemisia tabaci, by dot spot hybridization as early as 1 h after acquisition access. The retention of the virus nucleic acid in the vector was at least 23 days after a 48 h acquisition access. However, the retention of TYLCV coat protein did not exceed 10 days. No replicative forms of TYLCV could be detected in B. tabaci, indicating a non-propagative relationship with the vector. Whiteflies were not able to accumulate naked virion ssDNA, virus cloned dsDNA, or virions with impaired coat protein. Deletion, frameshift, and single amino acid mutations were inserted into open reading frames (ORFs) V1 and V2 (Coat protein) of TYLCV. The ability of these mutants to replicate, to spread and to induce symptoms was tested both in leaf disks and in intact plants. No replication was found in tissues that were infected with a deletion mutant that lacked the carboxy half of the coat protein gene. Residual amounts of ssDNA and dsDNA were detected i tissues infected with a frameshift mutant in which an early termination at the extreme part of the protein. Two other mutants in which a single amino acid was changed in the overlapping part of V1 and V2 were able to spread systemically but infections remained symptomless and the production of ssDNA and dsDNA were significantly lower. These mutants were acquired and transmitted by Bemisia tabaci. Procedures for the the dissection, fixation and embedding of whiteflies were developed. The anatomy and ultrastructure of the salivary gland and the midgut of Bemisia tabaci and Trialeurodes vaporariorum (a vector and non-vector of geminiviruses respectively) was studied and described. Monoclonal antibodies against bean golden mosaic virus (BGMV) with narrow and broad spectrum were prepared. Transmission studies of tomato mottle geminivirus (TMoV) by B. tabaci were carried out. These studies were essential for a further work aimed to understand the interaction of geminiviruses with the insect and their localization in its tissues. To enable the production of transgenic plants procedures were developed for tomato transformation with both Agrobacterium and microparticle bombardment.

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Gafni, Yedidya, and Vitaly Citovsky. Molecular interactions of TYLCV capsid protein during assembly of viral particles. United States Department of Agriculture, April 2007. http://dx.doi.org/10.32747/2007.7587233.bard.

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Tomato yellow leaf curl geminivirus (TYLCV) is a major pathogen of cultivated tomato, causing up to 100% crop loss in many parts of the world. The present proposal, a continuation of a BARD-funded project, expanded our understanding of the molecular mechanisms by which CP molecules, as well as its pre-coat partner V2, interact with each other (CP), with the viral genome, and with cellular proteins during assembly and movement of the infectious virions. Specifically, two major objectives were proposed: I. To study in detail the molecular interactions between CP molecules and between CP and ssDNA leading to assembly of infectious TYLCV virions. II. To study the roles of host cell factors in TYLCV assembly. Our research toward these goals has produced the following major achievements: • Characterization of the CP nuclear shuttling interactor, karyopherin alpha 1, its pattern of expression and the putative involvement of auxin in regulation of its expression. (#1 in our list of publication, Mizrachy, Dabush et al. 2004). • Identify a single amino acid in the capsid protein’s sequence that is critical for normal virus life-cycle. (#2 in our list of publications, Yaakov, Levy et al. in preparation). • Development of monoclonal antibodies with high specificity to the capsid protein of TYLCV. (#3 in our list of publications, Solmensky, Zrachya et al. in press). • Generation of Tomato plants resistant to TYLCV by expressing transgene coding for siRNA targeted at the TYLCV CP. (#4 in our list of publications, Zrachya, Kumar et al. in press). •These research findings provided significant insights into (i) the molecular interactions of TYLCV capsid protein with the host cell nuclear shuttling receptor, and (ii) the mechanism by which TYLCV V2 is involved in the silencing of PTGS and contributes to the virus pathogenicity effect. Furthermore, the obtained knowledge helped us to develop specific strategies to attenuate TYLCV infection, for example, by blocking viral entry into and/or exit out of the host cell nucleus via siRNA as we showed in our publication recently (# 4 in our list of publications). Finally, in addition to the study of TYLCV nuclear import and export, our research contributed to our understanding of general mechanisms for nucleocytoplasmic shuttling of proteins and nucleic acids in plant cells. Also integration for stable transformation of ssDNA mediated by our model pathogen Agrobacterium tumefaciens led to identification of plant specific proteins involved.

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