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  1. AU="Gary Newnam"
  2. AU="Zornitsa Mitkova"
  3. AU="Nicholas Tadros"
  4. AU="Ntelkis, Nikolaos"
  5. AU=Pitrou Isabelle
  6. AU="Ouwehand, Willem"
  7. AU=Glover Natasha M.
  8. AU=Guo Zhinian
  9. AU="Alison M. Lee"
  10. AU="Walcher, Felix"
  11. AU=Marupudi Neena I.
  12. AU="Earp, Karly M"
  13. AU="Zeng, Hui Hui"
  14. AU="Marco Pallecchi"
  15. AU=Marcus Adam I
  16. AU="Martin, Phillip"
  17. AU=Ouyang Yi-Bing
  18. AU="Tam, Patrick Chung Kay"
  19. AU="Patrick R. H. Steinmetz"
  20. AU="Odierna, Francesco"
  21. AU="Monteiro, Valter" AU="Monteiro, Valter"
  22. AU=Konkel Alex
  23. AU="Alnakib, Yasir"
  24. AU=Tallerico Rossana
  25. AU=Scherer Kai
  26. AU="Cao, Guiyun"
  27. AU="Zarrouki, Youssef"
  28. AU="Abayomi, Akin"
  29. AU=Kpatcha Tchazou
  30. AU=Glaeser Robert M
  31. AU="Mioara Cristea"
  32. AU="Turiegano, Enrique"
  33. AU="Russcher, H"
  34. AU="Lim, Kean-Jin"
  35. AU="Spurek, Monika"
  36. AU="Giulia A. Zamboni"

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  1. Artikel ; Online: Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii

    Waleed M.M. El-Sayed / Alli L. Gombolay / Penghao Xu / Taehwan Yang / Youngkyu Jeon / Sathya Balachander / Gary Newnam / Sijia Tao / Nicole E. Bowen / Tomáš Brůna / Mark Borodovsky / Raymond F. Schinazi / Baek Kim / Yongsheng Chen / Francesca Storici

    iScience, Vol 24, Iss 1, Pp 102005- (2021)

    2021  

    Abstract: Summary: Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has been studied only in limited genomes. Using the ribose-seq protocol and the Ribose-Map ... ...

    Abstract Summary: Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has been studied only in limited genomes. Using the ribose-seq protocol and the Ribose-Map bioinformatics toolkit, we reveal the distribution of rNMPs incorporated into the whole genome of a photosynthetic unicellular green alga, Chlamydomonas reinhardtii. We discovered a disproportionate incorporation of adenosine in the mitochondrial and chloroplast DNA, in contrast to the nuclear DNA, relative to the corresponding nucleotide content of these C. reinhardtii organelle genomes. Our results demonstrate that the rNMP content in the DNA of the algal organelles reflects an elevated ATP level present in the algal cells. We reveal specific biases and patterns in rNMP distributions in the algal mitochondrial, chloroplast, and nuclear DNA. Moreover, we identified the C. reinhardtii orthologous genes for all three subunits of the RNase H2 enzyme using GeneMark-EP + gene finder.
    Schlagwörter Molecular Biology ; Genomics ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2021-01-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: SalivaSTAT

    Nikhil S. Sahajpal / Ashis K. Mondal / Sudha Ananth / Allan Njau / Pankaj Ahluwalia / Gary Newnam / Adriana Lozoya-Colinas / Nicholas V. Hud / Vamsi Kota / Ted M. Ross / Michelle D. Reid / Sadanand Fulzele / Alka Chaubey / Madhuri Hegde / Amyn M. Rojiani / Ravindra Kolhe

    Diagnostics, Vol 11, Iss 904, p

    Direct-PCR and Pooling of Saliva Samples Collected in Healthcare and Community Setting for SARS-CoV-2 Mass Surveillance

    2021  Band 904

    Abstract: Objectives: Limitations of widespread current COVID-19 diagnostic testing exist in both the pre-analytical and analytical stages. To alleviate these limitations, we developed a universal saliva processing protocol (SalivaSTAT) that would enable an ... ...

    Abstract Objectives: Limitations of widespread current COVID-19 diagnostic testing exist in both the pre-analytical and analytical stages. To alleviate these limitations, we developed a universal saliva processing protocol (SalivaSTAT) that would enable an extraction-free RT-PCR test using commercially available RT-PCR kits. Methods: We optimized saliva collection devices, heat-shock treatment, and homogenization. Saliva samples (879) previously tested using the FDA-EUA method were reevaluated with the optimized SalivaSTAT protocol using two widely available commercial RT-PCR kits. A five-sample pooling strategy was evaluated as per FDA guidelines. Results: Saliva collection (done without any media) showed performance comparable to that of the FDA-EUA method. The SalivaSTAT protocol was optimized by incubating saliva samples at 95 °C for 30-min and homogenization, followed by RT-PCR assay. The clinical sample evaluation of 630 saliva samples using the SalivaSTAT protocol with PerkinElmer (600-samples) and CDC (30-samples) RT-PCR assay achieved positive (PPA) and negative percent agreements (NPAs) of 95.0% and 100%, respectively. The LoD was established as ~60–180 copies/mL by absolute quantification. Furthermore, a five-sample-pooling evaluation using 250 saliva samples achieved a PPA and NPA of 92% and 100%, respectively. Conclusion: We have optimized an extraction-free RT-PCR assay for saliva samples that demonstrates comparable performance to FDA-EUA assay (Extraction and RT-PCR).
    Schlagwörter saliva ; extraction-free ; RT-PCR ; pooling ; Medicine (General) ; R5-920
    Thema/Rubrik (Code) 630
    Sprache Englisch
    Erscheinungsdatum 2021-05-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine

    Sathya Balachander / Alli L. Gombolay / Taehwan Yang / Penghao Xu / Gary Newnam / Havva Keskin / Waleed M. M. El-Sayed / Anton V. Bryksin / Sijia Tao / Nicole E. Bowen / Raymond F. Schinazi / Baek Kim / Kyung Duk Koh / Fredrik O. Vannberg / Francesca Storici

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Band 14

    Abstract: Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and ... ...

    Abstract Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and nuclear DNA show preference for cytosine and guanosine preceded by deoxyadenosine.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2020-05-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine

    Sathya Balachander / Alli L. Gombolay / Taehwan Yang / Penghao Xu / Gary Newnam / Havva Keskin / Waleed M. M. El-Sayed / Anton V. Bryksin / Sijia Tao / Nicole E. Bowen / Raymond F. Schinazi / Baek Kim / Kyung Duk Koh / Fredrik O. Vannberg / Francesca Storici

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Band 14

    Abstract: Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and ... ...

    Abstract Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and nuclear DNA show preference for cytosine and guanosine preceded by deoxyadenosine.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2020-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

    Volltext online

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