myTXTL – Featured Publications

Please browse some recent publications utilizing targeted sequencing with myTXTL.

Liang, J. et al.. (2022) Directed Evolution of Replication-Competent Double-Stranded DNA Bacteriophage toward New Host Specificity  ACS Synthetic Biology 2022 bacteriophage. featured myTXTL

Wandera, K. et al (2022). Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases Molecular Cell 2022 CRISPR technology myTXTL

Wandera, K. et al (2022) Rapidly Characterizing CRISPR-Cas13 Nucleases Using Cell-Free Transcription-Translation Systems Post-Transcriptional Gene Regulation CRISPR technology myTXTL

Lin, P. et al. (2022) Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses Nucleic Acids Research 2022 CRISPR technology, SARS-CoV-2, myTXTL T7 expression Kit myTXTL

Haslinger, K. et al. (2021) Rapid in vitro prototyping of O-methyltransferases for pathway applications in Escherichia coli [featured] Cell Chemical Biology 2021 assay development, featured, protein production myTXTL

Taxiarchi, C. et al. (2021) A genetically encoded anti-CRISPR protein constrains gene drive spread and prevents population suppression Nature Communications 2021 CRISPR technology myTXTL

Khakimzhan, A. et al. (2021) Complex dependence of CRISPR-Cas9 binding strength on guide RNA spacer lengths Physical Biology 2021 CRISPR technology myTXTL

Collins, S. et al. (2021) Sequence-independent RNA sensing and DNA targeting by a split domain CRISPRCas12a gRNA switch Nucleic Acids Research 2021 CRISPR technology myTXTL

Blume, C. et al. A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection Nature Genetics 2021 SARS-CoV-2, protein production myTXTL

Kato, S. et al., (2021) Phase separation and exclusive protein localizations in compartmentalized cell-free expression reactions, arXiv 2021, artificial cell myTXTL

ASV Conference 2022

Booth #1

Madison, Wisconsin

myBaits® Featured Publications for Viral Research
Please browse some recent publications utilizing targeted sequencing with myBaits® kits and/or myReads® services.

Alfano, N., Dayaram, A., Axtner, J., Tsangaras, K., Kampmann, M., Mohamed, A., Wong, S. T., Gilbert, M. T. P., Wilting, A., & Greenwood, A. D. (2021). Non‐invasive surveys of mammalian viruses using environmental DNA. Methods in Ecology and Evolution, 12(10), 1941–1952.

Alfsnes, K., Eldholm, V., Gaunt, M. W., de Lamballerie, X., Gould, E. A., & Pettersson, J. H.-O. (2021). Tracing and tracking the emergence, epidemiology and dispersal of dengue virus to Africa during the 20th century. One Health, 13, 100337.

Binder, F., Reiche, S., Roman-Sosa, G., Saathoff, M., Ryll, R., Trimpert, J., Kunec, D., Höper, D., & Ulrich, R. G. (2020). Isolation and characterization of new Puumala orthohantavirus strains from Germany. Virus Genes, 56(4), 448–460.

Bokelmann, M., Vogel, U., Debeljak, F., Düx, A., Riesle-Sbarbaro, S., Lander, A., Wahlbrink, A., Kromarek, N., Neil, S., Couacy-Hymann, E., Prescott, J., & Kurth, A. (2021). Tolerance and Persistence of Ebola Virus in Primary Cells from Mops condylurus, a Potential Ebola Virus Reservoir. Viruses, 13(11), 2186.

Burrel, S., Boutolleau, D., Ryu, D., Agut, H., Merkel, K., Leendertz, F. H., & Calvignac-Spencer, S. (2017). Ancient Recombination Events between Human Herpes Simplex Viruses. Molecular Biology and Evolution, 34(7), 1713–1721.

Calvelage, S., Tammiranta, N., Nokireki, T., Gadd, T., Eggerbauer, E., Zaeck, L. M., Potratz, M., Wylezich, C., Höper, D., Müller, T., Finke, S., & Freuling, C. M. (2021). Genetic and Antigenetic Characterization of the Novel Kotalahti Bat Lyssavirus (KBLV). Viruses, 13(1), 69.

Carrai, M., Van Brussel, K., Shi, M., Li, C.-X., Chang, W.-S., Munday, J. S., Voss, K., McLuckie, A., Taylor, D., Laws, A., Holmes, E. C., Barrs, V. R., & Beatty, J. A. (2020). Identification of a Novel Papillomavirus Associated with Squamous Cell Carcinoma in a Domestic Cat. Viruses, 12(1), 124.

Caruso, L. B., Guo, R., Keith, K., Madzo, J., Maestri, D., Boyle, S., Wasserman, J., Kossenkov, A., Gewurz, B. E., & Tempera, I. (2022). The nuclear lamina binds the EBV genome during latency and regulates viral gene expression. PLOS Pathogens, 18(4), e1010400.

Colson, P., Dhiver, C., Tamalet, C., Delerce, J., Glazunova, O. O., Gaudin, M., Levasseur, A., & Raoult, D. (2020). Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection. Scientific Reports, 10(1), 1–9.

Dashdorj, N. J., Dashdorj, N. D., Mishra, M., Danzig, L., Briese, T., Lipkin, W. I., & Mishra, N. (2022). Molecular and Serologic Investigation of the 2021 COVID-19 Case Surge Among Vaccine Recipients in Mongolia. JAMA Network Open, 5(2), e2148415.

Dayaram, A., Seeber, P., Courtiol, A., Soilemetzidou, S., Tsangaras, K., Franz, M., McEwen, G., Azab, W., Kaczensky, P., Melzheimer, J., East, M., Ganbaatar, O., Walzer, C., Osterrieder, N., & Greenwood, A. D. (2021). Seasonal host and ecological drivers may promote restricted water as a viral vector. Science of The Total Environment, 145446.

Di Giallonardo, F., Duchene, S., Puglia, I., Curini, V., Profeta, F., Cammà, C., Marcacci, M., Calistri, P., Holmes, E. C., & Lorusso, A. (2020). Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy. Viruses, 12(12), 1438.

Doremalen, N. van, Purushotham, J. N., Schulz, J. E., Holbrook, M. G., Bushmaker, T., Carmody, A., Port, J. R., Yinda, C. K., Okumura, A., Saturday, G., Amanat, F., Krammer, F., Hanley, P. W., Smith, B. J., Lovaglio, J., Anzick, S. L., Barbian, K., Martens, C., Gilbert, S. C., … Munster, V. J. (2021). Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces viral shedding after SARS-CoV-2 D614G challenge in preclinical models. Science Translational Medicine.

Duggan, A. T., Klunk, J., Porter, A. F., Dhody, A. N., Hicks, R., Smith, G. L., Humphreys, M., McCollum, A. M., Davidson, W. B., Wilkins, K., Li, Y., Burke, A., Polasky, H., Flanders, L., Poinar, D., Raphenya, A. R., Lau, T. T. Y., Alcock, B., McArthur, A. G., … Poinar, H. N. (2020). The origins and genomic diversity of American Civil War Era smallpox vaccine strains. Genome Biology, 21(1), 175.

Duggan, A. T., Perdomo, M. F., Piombino-Mascali, D., Marciniak, S., Poinar, D., Emery, M. V., Buchmann, J. P., Duchêne, S., Jankauskas, R., Humphreys, M., Golding, G. B., Southon, J., Devault, A., Rouillard, J.-M., Sahl, J. W., Dutour, O., Hedman, K., Sajantila, A., Smith, G. L., … Poinar, H. N. (2016). 17th Century Variola Virus Reveals the Recent History of Smallpox. Current Biology, 26(24), 3407–3412.

Fischer, R. J., van Doremalen, N., Adney, D. R., Yinda, C. K., Port, J. R., Holbrook, M. G., Schulz, J. E., Williamson, B. N., Thomas, T., Barbian, K., Anzick, S. L., Ricklefs, S., Smith, B. J., Long, D., Martens, C., Saturday, G., de Wit, E., Gilbert, S. C., Lambe, T., & Munster, V. J. (2021). ChAdOx1 nCoV-19 (AZD1222) protects Syrian hamsters against SARS-CoV-2 B.1.351 and B.1.1.7. Nature Communications, 12(1), 5868.

Forth, J. H., Forth, L. F., King, J., Groza, O., Hübner, A., Olesen, A. S., Höper, D., Dixon, L. K., Netherton, C. L., Rasmussen, T. B., Blome, S., Pohlmann, A., & Beer, M. (2019). A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. Viruses, 11(9), 846.

Forth, J. H., Tignon, M., Cay, A. B., Forth, L. F., Höper, D., Blome, S., & Beer, M. (2019). Comparative Analysis of Whole-Genome Sequence of African Swine Fever Virus Belgium 2018/1. Emerging Infectious Diseases, 25(6).

Hartley, P. D., Tillett, R. L., AuCoin, D. P., Sevinsky, J. R., Xu, Y., Gorzalski, A., Pandori, M., Buttery, E., Hansen, H., Picker, M. A., Rossetto, C. C., & Verma, S. C. (2021). Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. Journal of Genetics and Genomics, 48(1), 40–51.

Hirschbühl, K., Schaller, T., Märkl, B., Claus, R., Sipos, E., Rentschler, L., Maccagno, A., Grosser, B., Kling, E., Neidig, M., Kröncke, T., Spring, O., Braun, G., Bösmüller, H., Seidl, M., Esposito, I., Pablik, J., Hilsenbeck, J., Boor, P., … Wylezich, C. (2022). High viral loads: What drives fatal cases of COVID-19 in vaccinees? – an autopsy study. Modern Pathology, 1–9.

Kaymaz, Y., Oduor, C. I., Aydemir, O., Luftig, M. A., Otieno, J. A., Ong’echa, J. M., Bailey, J. A., & Moormann, A. M. (2020). Epstein-Barr Virus Genomes Reveal Population Structure and Type 1 Association with Endemic Burkitt Lymphoma. Journal of Virology, 94(17), e02007-19.

Keita, A. K., Koundouno, F. R., Faye, M., Düx, A., Hinzmann, J., Diallo, H., Ayouba, A., Le Marcis, F., Soropogui, B., Ifono, K., Diagne, M. M., Sow, M. S., Bore, J. A., Calvignac-Spencer, S., Vidal, N., Camara, J., Keita, M. B., Renevey, A., Diallo, A., … Magassouba, N. F. (2021). Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks. Nature, 1–5.

Lam, W. K. J., Ji, L., Tse, O. Y. O., Cheng, S. H., Jiang, P., Lee, P. H. P., Lin, S. V., Hui, E. P., Ma, B. B. Y., Chan, A. T. C., Chan, K. C. A., Chiu, R. W. K., & Lo, Y. M. D. (2020). Sequencing Analysis of Plasma Epstein-Barr Virus DNA Reveals Nasopharyngeal Carcinoma-Associated Single Nucleotide Variant Profiles. Clinical Chemistry.

Mehta, S. K., Szpara, M. L., Rooney, B. V., Diak, D. M., Shipley, M. M., Renner, D. W., Krieger, S. S., Nelman-Gonzalez, M. A., Zwart, S. R., Smith, S. M., & Crucian, B. E. (2022). Dermatitis during Spaceflight Associated with HSV-1 Reactivation. Viruses, 14(4), 789.

Mielonen, O. I., Pratas, D., Hedman, K., Sajantila, A., & Perdomo, M. F. (2022). Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation. Viruses, 14(1), 133.

Mileto, P., da Conceição, F., Stevens, V., Cummins, D., Certoma, A., Neave, M. J., Bendita da Costa Jong, J., & Williams, D. T. (2021). Complete Genome Sequence of African Swine Fever Virus Isolated from a Domestic Pig in Timor-Leste, 2019. Microbiology Resource Announcements, 10(26), e00263-21.

Mishra, M., Zahra, A., Chauhan, L. V., Thakkar, R., Ng, J., Joshi, S., Spitzer, E. D., Marcos, L. A., Lipkin, W. I., & Mishra, N. (2022). A Short Series of Case Reports of COVID-19 in Immunocompromised Patients. Viruses, 14(5), 934.

Mollerup, S., Asplund, M., Friis-Nielsen, J., Kjartansdóttir, K. R., Fridholm, H., Hansen, T. A., Herrera, J. A. R., Barnes, C. J., Jensen, R. H., Richter, S. R., Nielsen, I. B., Pietroni, C., Alquezar-Planas, D. E., Rey-Iglesia, A., Olsen, P. V. S., Rajpert-De Meyts, E., Groth-Pedersen, L., von Buchwald, C., Jensen, D. H., … Hansen, A. J. (2019). High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach. The Journal of Infectious Diseases, 220(8), 1312–1324.

Morgan, S. M., Tanizawa, H., Caruso, L. B., Hulse, M., Kossenkov, A., Madzo, J., Keith, K., Tan, Y., Boyle, S., Lieberman, P. M., & Tempera, I. (2022). The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity. Nature Communications, 13(1), 187.

Munster, V. J., Flagg, M., Singh, M., Yinda, C. K., Williamson, B. N., Feldmann, F., Pérez-Pérez, L., Schulz, J., Brumbaugh, B., Holbrook, M. G., Adney, D. R., Okumura, A., Hanley, P. W., Smith, B. J., Lovaglio, J., Anzick, S. L., Martens, C., van Doremalen, N., Saturday, G., & de Wit, E. (2021). Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Science Advances, 7(43), eabj3627.

Patrono, L. V., Pléh, K., Samuni, L., Ulrich, M., Röthemeier, C., Sachse, A., Muschter, S., Nitsche, A., Couacy-Hymann, E., Boesch, C., Wittig, R. M., Calvignac-Spencer, S., & Leendertz, F. H. (2020). Monkeypox virus emergence in wild chimpanzees reveals distinct clinical outcomes and viral diversity. Nature Microbiology, 5(7), 955–965.

Patrono, L. V., Röthemeier, C., Kouadio, L., Couacy‐Hymann, E., Wittig, R. M., Calvignac‐Spencer, S., & Leendertz, F. H. (2022). Non‐invasive genomics of respiratory pathogens infecting wild great apes using hybridisation capture. Influenza and Other Respiratory Viruses, irv.12984.

Pfaff, F., Breithaupt, A., Rubbenstroth, D., Nippert, S., Baumbach, C., Gerst, S., Langner, C., Wylezich, C., Ebinger, A., Höper, D., Ulrich, R. G., & Beer, M. (2022). Revisiting Rustrela Virus: New Cases of Encephalitis and a Solution to the Capsid Enigma. Microbiology Spectrum, 10(2), e00103-22.

Port, J. R., Adney, D. R., Schwarz, B., Schulz, J. E., Sturdevant, D. E., Smith, B. J., Avanzato, V. A., Holbrook, M. G., Purushotham, J. N., Stromberg, K. A., Leighton, I., Bosio, C. M., Shaia, C., & Munster, V. J. (2021). High-Fat High-Sugar Diet-Induced Changes in the Lipid Metabolism Are Associated with Mildly Increased COVID-19 Severity and Delayed Recovery in the Syrian Hamster. Viruses, 13(12), 2506.

Port, J. R., Yinda, C. K., Avanzato, V. A., Schulz, J. E., Holbrook, M. G., van Doremalen, N., Shaia, C., Fischer, R. J., & Munster, V. J. (2022). Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo. Nature Microbiology, 1–11.

Port, J. R., Yinda, C. K., Owusu, I. O., Holbrook, M., Fischer, R., Bushmaker, T., Avanzato, V. A., Schulz, J. E., Martens, C., van Doremalen, N., Clancy, C. S., & Munster, V. J. (2021). SARS-CoV-2 disease severity and transmission efficiency is increased for airborne compared to fomite exposure in Syrian hamsters. Nature Communications, 12(1), 4985.

Rathbun, M. M., Shipley, M. M., Bowen, C. D., Selke, S., Wald, A., Johnston, C., & Szpara, M. L. (2022). Comparison of herpes simplex virus 1 genomic diversity between adult sexual transmission partners with genital infection. PLOS Pathogens, 18(5), e1010437.

Ross, Z. P., Klunk, J., Fornaciari, G., Giuffra, V., Duchêne, S., Duggan, A. T., Poinar, D., Douglas, M. W., Eden, J.-S., Holmes, E. C., & Poinar, H. N. (2018). The paradox of HBV evolution as revealed from a 16th century mummy. PLOS Pathogens, 14(1), e1006750.

Santos, P. D., Michel, F., Wylezich, C., Höper, D., Keller, M., Holicki, C. M., Szentiks, C. A., Eiden, M., Muluneh, A., Neubauer‐Juric, A., Thalheim, S., Globig, A., Beer, M., Groschup, M. H., & Ziegler, U. (2022). Co-Infections: Simultaneous Detections of West Nile Virus and Usutu Virus in Birds from Germany. Transboundary and Emerging Diseases, 69(2), 776-792.

Schilling-Loeffler, K., Viera-Segura, O., Corman, V. M., Schneider, J., Gadicherla, A. K., Schotte, U., & Johne, R. (2021). Cell Culture Isolation and Whole Genome Characterization of Hepatitis E Virus Strains from Wild Boars in Germany. Microorganisms, 9(11), 2302.

Shobayo, B., Mishra, M., Sameroff, S., Petrosov, A., Ng, J., Gokden, A., MaCauley, J., Jain, K., Renken, C., Duworko, J. T., Badio, M., Jallah, W., Hensley, L., Briese, T., Lipkin, W. I., & Mishra, N. (2021). SARS-CoV-2 Sequence Analysis during COVID-19 Case Surge, Liberia, 2021. Emerging Infectious Diseases, 27(12), 3185–3188.

Stoek, F., Barry, Y., Ba, A., Schulz, A., Rissmann, M., Wylezich, C., Sadeghi, B., Beyit, A. D., Eisenbarth, A., N’diaye, F. B., Haki, M. L., Doumbia, B. A., Gueya, M. B., Bah, M. Y., Eiden, M., & Groschup, M. H. (2022). Mosquito survey in Mauritania: Detection of Rift Valley fever virus and dengue virus and the determination of feeding patterns. PLOS Neglected Tropical Diseases, 16(4), e0010203.

Tillett, R. L., Sevinsky, J. R., Hartley, P. D., Kerwin, H., Crawford, N., Gorzalski, A., Laverdure, C., Verma, S. C., Rossetto, C. C., Jackson, D., Farrell, M. J., Hooser, S. V., & Pandori, M. (2020). Genomic evidence for reinfection with SARS-CoV-2: A case study. The Lancet Infectious Diseases, 21(1), P52-58.

Toppinen, M., Sajantila, A., Pratas, D., Hedman, K., & Perdomo, M. F. (2021). The Human Bone Marrow Is Host to the DNAs of Several Viruses. Frontiers in Cellular and Infection Microbiology, 11.

Ulrich, L., Halwe, N. J., Taddeo, A., Ebert, N., Schön, J., Devisme, C., Trüeb, B. S., Hoffmann, B., Wider, M., Fan, X., Bekliz, M., Essaidi-Laziosi, M., Schmidt, M. L., Niemeyer, D., Corman, V. M., Kraft, A., Godel, A., Laloli, L., Kelly, J. N., … Benarafa, C. (2022). Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Nature, 602(7896), 307–313.

Williamson, B. N., Feldmann, F., Schwarz, B., Meade-White, K., Porter, D. P., Schulz, J., van Doremalen, N., Leighton, I., Yinda, C. K., Pérez-Pérez, L., Okumura, A., Lovaglio, J., Hanley, P. W., Saturday, G., Bosio, C. M., Anzick, S., Barbian, K., Cihlar, T., Martens, C., … de Wit, E. (2020). Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2. Nature, 585(7824), 273–276.

Wylezich, C., Calvelage, S., Schlottau, K., Ziegler, U., Pohlmann, A., Höper, D., & Beer, M. (2021). Next-generation diagnostics: Virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2. Microbiome, 9(1), 51.

Daicel Arbor Biosciences, a division of Daicel Chiral Technologies, and leader in developing molecular biology research tools, is pleased to introduce Ravindra Ramadhar as its new President.

Previously Mr. Ramadhar was Director, Strategy & Business Development within Thermo Fisher Scientific’s Genetics Science Division. Ramadhar brings a vast technical background to Daicel Arbor Biosciences with his prior experience as a director in the life and genetic sciences sectors, specifically focusing on applied markets in Agribusiness. His leadership will positively impact Daicel Arbor’s vision, strategy and portfolio development.

Mr. Ramadhar earned a Master of Business Administration (M.B.A.) from Whitman School of Management, Syracuse University, and Bachelor of Science from Rutgers University. He also received many hours of executive education from various programs at Harvard University.

With the addition of Mr. Ramadhar to the team, Daicel Arbor’s current President, Joseph M. Barendt, Ph.D., will continue to serve as President of Daicel Chiral Technologies and shift his attention to strategic growth projects within the newly formed Life Sciences Business area of Daicel Group. “I am excited to add someone of Mr. Ramadhar’s depth of experience, enthusiasm and leadership skills to the Daicel Arbor team and look forward to working closely with him over the coming years.”

Ramadhar adds “Daicel Arbor Biosciences’ extensive capabilities in genomics and tools for synthetic biology coupled with its passion for science provide a strong foundation for growth. Daicel Arbor Biosciences’ solutions enable genomics and synthetic biology researchers to answer key biological questions, advancing their research goals.”