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   Microviridae (isometric ssDNA phages) 

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   Missing 
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Latest Articles on ssDNA from uBioRSS
Evolution on the inside track: How viruses in gut bacteria change over time - EurekAlert! - Breaking News
Rapid evolution of the human gut virome. - PubMed: species


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1.  A Novelty Stable DNA Nanoscale Material and Its Application on Specific Enrichment of DNA.LinkIT
Wang X, Yu J, Lan W, Yang S, Wang S, Mi Y, Ye Q, Li Y, Liu Y
ACS applied materials & interfaces, 2020
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0

2.  Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ.LinkIT
Wu T, Lyu R, You Q, He C
Nature methods, 2020
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0

3.  Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa.LinkIT
Li Y, Liu X, Tang K, Wang W, Guo Y, Wang X
Microbial biotechnology Microb Biotechnol Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa. 10.1111/1751-7915.13570 Pf prophages are ssDNA filamentous prophages that are prevalent among various Pseudomonas aeruginosa strains. The genomes of Pf prophages contain not only core genes encoding functions involved in phage replication, structure and assembly but also accessory genes. By studying the accessory genes in the Pf4 prophage in P. aeruginosa PAO1, we provided experimental evidence to demonstrate that PA0729 and the upstream ORF Rorf0727 near the right attachment site of Pf4 form a type II toxin/antitoxin (TA) pair. Importantly, we found that the deletion of the toxin gene PA0729 greatly increased Pf4 phage production. We thus suggest the toxin PA0729 be named PfiT for Pf4 inhibition toxin and Rorf0727 be named PfiA for PfiT antitoxin. The PfiT toxin directly binds to PfiA and functions as a corepressor of PfiA for the TA operon. The PfiAT complex exhibited autoregulation by binding to a palindrome (5'-AATTCN5 GTTAA-3') overlapping the -35 region of the TA operon. The deletion of pfiT disrupted TA autoregulation and activated pfiA expression. Additionally, the deletion of pfiT also activated the expression of the replication initiation factor gene PA0727. Moreover, the Pf4 phage released from the pfiT deletion mutant overcame the immunity provided by the phage repressor Pf4r. Therefore, this study reveals that the TA systems in Pf prophages can regulate phage production and phage immunity, providing new insights into the function of TAs in mobile genetic elements. © 2020 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology. Li Yangmei Y Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China. University of Chinese Academy of Sciences, Beijing, China. Liu Xiaoxiao X Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China. Tang Kaihao K Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China. Wang Weiquan W Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China. University of Chinese Academy of Sciences, Beijing, China. Guo Yunxue Y https://orcid.org/0000-0002-2006-1746 Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China. Wang Xiaoxue X https://orcid.org/0000-0002-7257-1916 Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China. Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China. University of Chinese Academy of Sciences, Beijing, China. eng 31625001 National Science Foundation of China 91951203 National Science Foundation of China 31970037 National Science Foundation of China 2018YFC1406500 National Key R&D Program of China 2017A030313125 National Science Foundation of Guangdong Province XDA13020301 the Strategic Priority Research Program of the Chinese Academy of Sciences Journal Article 2020 04 04 United States Microb Biotechnol 101316335 1751-7915 IM 2020 01 15 2020 02 19 2020 02 19 2020 4 5 6 0 2020 4 5 6 0 2020 4 5 6 0 aheadofprint 32246813 10.1111/1751-7915.13570 References, 2020</i></font><br><font color=#008000>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0<br></font></span><br>4.  <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0 class=title>Probing Conformational Polymorphism of DNA Assemblies with Nanopores.</a><a href=http://ubio.org/tools/linkit.php?map%5B%5D=all&link_type=2&url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0><img src=linkit.png border=0 title='LinkIT' alt='LinkIT'></a> <br><span class=j>Sheng Y, Zhou K, Liu Q, Liu L, Wu HC<br><font color=gray><i>Analytical chemistry, 2020</i></font><br><font color=#008000>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0<br></font></span><br>5.  <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0 class=title>Hair follicle stem cell replication stress drives IFI16/STING-dependent inflammation in hidradenitis suppurativa.</a><a href=http://ubio.org/tools/linkit.php?map%5B%5D=all&link_type=2&url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0><img src=linkit.png border=0 title='LinkIT' alt='LinkIT'></a> <br><span class=j>Orvain C, Lin YL, Jean-Louis F, Hocini H, Hersant B, Bennasser Y, Ortonne N, Hotz C, Wolkenstein P, Boniotto M, Tisserand P, Lefebvre C, Lelievre JD, Benkirane M, Pasero P, Levy Y, Hue S<br><font color=gray><i>The Journal of clinical investigation, 2020</i></font><br><font color=#008000>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0<br></font></span><br>6.  <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0 class=title>CtIP promotes the motor activity of DNA2 to accelerate long-range DNA end resection.</a><a href=http://ubio.org/tools/linkit.php?map%5B%5D=all&link_type=2&url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0><img src=linkit.png border=0 title='LinkIT' alt='LinkIT'></a> <br><span class=j>Ceppi I, Howard SM, Kasaciunaite K, Pinto C, Anand R, Seidel R, Cejka P<br><font color=gray><i>Proceedings of the National Academy of Sciences of the United States of America, 2020</i></font><br><font color=#008000>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0<br></font></span><br>7.  <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0 class=title>Probing CRISPR-Cas12a Nuclease Activity Using Double-Stranded DNA-Templated Fluorescent Substrates.</a><a href=http://ubio.org/tools/linkit.php?map%5B%5D=all&link_type=2&url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0><img src=linkit.png border=0 title='LinkIT' alt='LinkIT'></a> <br><span class=j>Smith CW, Nandu N, Kachwala MJ, Chen YS, Uyar TB, Yigit MV<br><font color=gray><i>Biochemistry, 2020</i></font><br><font color=#008000>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0<br></font></span><br>8.  <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0 class=title>RS-1 enhances CRISPR-mediated targeted knock-in in bovine embryost.</a><a href=http://ubio.org/tools/linkit.php?map%5B%5D=all&link_type=2&url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0><img src=linkit.png border=0 title='LinkIT' alt='LinkIT'></a> <br><span class=j>Lamas-Toranzo I, Martínez-Moro A, O Callaghan E, Millán-Blanca G, Sánchez JM, Lonergan P, Bermejo-Álvarez P<br><font color=gray><i>Molecular reproduction and development Mol. Reprod. Dev. RS-1 enhances CRISPR-mediated targeted knock-in in bovine embryost. 10.1002/mrd.23341 Targeted knock-in (KI) can be achieved in embryos by clustered regularly interspaced short palindromic repeats (CRISPR)-assisted homology directed repair (HDR). However, HDR efficiency is constrained by the competition of nonhomologous end joining. The objective of this study was to explore whether CRISPR-assisted targeted KI rates can be improved in bovine embryos by exposure to the HDR enhancer RS-1. In vitro produced zygotes were injected with CRISPR components (300?ng/µl Cas9 messenger RNA and 100?ng/µl single guide RNA against a noncoding region) and a single-stranded DNA (ssDNA) repair template (100?ng/µl). ssDNA template contained a 6?bp XbaI site insert, allowing targeted KI detection by restriction analysis, flanked by 50?bp homology arms. Following microinjection, zygotes were exposed to 0, 3.75, or 7.5?µM RS-1 for 24?hr. No differences were noted between groups in terms of development or genome edition rates. However, targeted KI rates were doubled in the group exposed to 7.5?µM RS-1 compared to the others (52.8% vs. 25% and 23.1%, for 7.5, 0, and 3.75?µM, respectively). In conclusion, transient exposure to 7.5?µM RS-1 enhances targeted KI rates resulting in approximately half of the embryos containing the intended mutation, hence allowing direct KI generation in embryos. © 2020 Wiley Periodicals, Inc. Lamas-Toranzo I I Animal Reproduction Department, INIA, Madrid, Spain. Martínez-Moro A A Animal Reproduction Department, INIA, Madrid, Spain. Procreatec, Madrid, Spain. O Callaghan E E School of Agriculture and Food Science, University College Dublin, Dublin, Ireland. Millán-Blanca G G Animal Reproduction Department, INIA, Madrid, Spain. Sánchez J M JM School of Agriculture and Food Science, University College Dublin, Dublin, Ireland. Lonergan P P School of Agriculture and Food Science, University College Dublin, Dublin, Ireland. Bermejo-Álvarez P P http://orcid.org/0000-0001-9907-2626 Animal Reproduction Department, INIA, Madrid, Spain. eng FPI contract BES-2015-072774 Ministerio de Economía y Competitividad AGL2014-58739-R Ministerio de Economía y Competitividad AGL2017-84908-R Ministerio de Economía y Competitividad IND2017/BIO7748 Consejería de Educación e Investigación Comunidad de Madrid 13/IA/1983 SFI_ Science Foundation Ireland Ireland StG-757886-ELONGAN H2020 European Research Council Journal Article 2020 03 30 United States Mol Reprod Dev 8903333 1040-452X IM DNA repair RS-1 bovine embryo gene editing 2020 01 12 2020 03 08 2020 03 11 2020 4 1 6 0 2020 4 1 6 0 2020 4 1 6 0 aheadofprint 32227559 10.1002/mrd.23341 REFERENCES, 2020</i></font><br><font color=#008000>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0<br></font></span><br>9.  <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0 class=title>Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with <b>ssDNA</b> bound to both N- and C-terminal domains.</a><a href=http://ubio.org/tools/linkit.php?map%5B%5D=all&link_type=2&url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0><img src=linkit.png border=0 title='LinkIT' alt='LinkIT'></a> <br><span class=j>Cao N, Tan K, Zuo X, Annamalai T, Tse-Dinh YC<br><font color=gray><i>Nucleic acids research, 2020</i></font><br><font color=#008000>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0<br></font></span><br>10.  <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0 class=title>Characterization and application of a family B DNA polymerase from the hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans.</a><a href=http://ubio.org/tools/linkit.php?map%5B%5D=all&link_type=2&url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0><img src=linkit.png border=0 title='LinkIT' alt='LinkIT'></a> <br><span class=j>Zhang L, Jiang D, Shi H, Wu M, Gan Q, Yang Z, Oger P<br><font color=gray><i>International journal of biological macromolecules, 2020</i></font><br><font color=#008000>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=0<br></font></span><br><br><br><table cellspacing=0 cellpadding=0 align=center><tr valign=bottom><td align=center><img src=p.png border=0></td><td align=center><img src=o_red.png border=0></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=2><img src=o_yellow.png border=0></a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=3><img src=o_yellow.png border=0></a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=4><img src=o_yellow.png border=0></a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=5><img src=o_yellow.png border=0></a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=6><img src=o_yellow.png border=0></a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=7><img src=o_yellow.png border=0></a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=8><img src=o_yellow.png border=0></a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=9><img src=o_yellow.png border=0></a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=10><img src=o_yellow.png border=0></a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=2><img src=rtal.png border=0></a></td></tr><td align=center></td><td align=center>1</td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=2>2</a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=3>3</a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=4>4</a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=5>5</a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=6>6</a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=7>7</a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=8>8</a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=9>9</a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=10>10</a></td><td align=center><a href=http://ubio.org/portal/index.php?search=ssDNA&category=l&client=pubmed&startPage=2>»</a></td></tr></table></table></tr></table></td><script src="http://www.google-analytics.com/urchin.js" type="text/javascript"> </script> <script type="text/javascript"> _uacct = "UA-634822-1"; urchinTracker(); </script> </BODY> </HTML>