Daicel Arbor Biosciences – Booth #310
Welcome to the PAG 2023 web page for Daicel Arbor Biosciences. Thank you for visiting. Please click on one of the sections below for additional information.
Our Industry Workshops
Location: Pacific C
Date: Monday, January 16, 12:50 p.m., PT
Speakers:
12:50 p.m. Introductory Remarks
Sofia Granja Martins, MSc – University of Oxford – UK (Presenting Author) – 1:00 p.m. Adventures in Capturing Mitochondrial Genomes from Ancient DNA Libraries
Junli Zhang, Ph.D. – University of California, Davis – USA (Presenting Author) 1:25 p.m. A Second Generation Capture Panel for Cost-Effective Sequencing of Genome Regulatory Regions in Wheat and Relatives
Alexandre R. Zuntini, Ph.D. – Royal Botanic Gardens, Kew – UK (Presenting Author) – 1:50 p.m. (TBD)
In this workshop, we will hear from researchers from the University of Oxford, the University of California, Davis, and the Royal Botanic Gardens, Kew about their recent work on plant and animal applications of phylogenetics, functional genomics, and evolutionary biology, all enabled by the myBaits® targeted next-generation sequencing (NGS) system from Daicel Arbor Biosciences.
Poster Presentations from Daicel Arbor Biosciences & Collaborators
Authors: Alison Devault, Ph.D. (Daicel Arbor Biosciences)
With the recent launch of multiple novel high-throughput sequencing (HTS) platforms, the landscape of HTS workflow options is richer than ever before. Choosing a targeted sequencing solution that is compatible with sequencing on any current or future HTS platform is important for maximizing the utility of a given assay. The myBaits® hybridization capture system from Daicel Arbor Biosciences is by design universally compatible with virtually any HTS workflow, whether short- or long-read. With highly versatile custom probe design algorithms and platform-agnostic protocol options, myBaits is a robust solution for achieving any DNA or RNA targeted sequencing need for any species or sample type. In this poster, we highlight the technical features of myBaits that permit its unique versatility in the modern HTS landscape, including data examples demonstrating its universal application with both short- and long-read HTS platforms relevant to the plant and animal genomics community.
Authors: Linda Barthel, Jake Enk, Tina Lan, Benjamin Steil (Daicel Arbor Biosciences)
Abstract: In situ hybridization (ISH) probes built from pools of synthetic single-stranded oligonucleotides are more specific and versatile than probes derived from BACs and other biological sources. The myTags® Custom ISH probe system from Daicel Arbor Biosciences utilizes a sophisticated in silico design process to identify and eliminate repetitive and other nonspecific elements that BAC-derived probes typically retain. Here we demonstrate the high specificity of customized myTags probe sets compared to BAC-derived alternatives, and outline design and experimental recommendations key to plant and animal genomics applications where enhanced specificity and versatility is critical. Combined with flexible synthesis and reporter labeling configurations, myTags represents an ideal and cost-effective toolset for a wide variety of genomics applications including chromosome painting and identification, haplotyping, and 3D/4D spatial genomics analysis.
Sponsored Workshops
Location: Town and County A
Date: Sunday, January 15, 2023 – 1:30 p.m. PT
Location: Pacific H-I (2nd floor)
Date: Sunday, January 15, 2023 – 4:00 p.m. PT
Location: Pacific C
Date: Sunday, January 15, 2023 – 8:00 a.m. PT
Product Sheets and Application Notes
Click on the product below to view PDF.
- myTags
[ab_icon icon=”file-pdf-o”] myTags Chromosome Indexing by FISH App Note
[ab_icon icon=”file-pdf-o”] myTags Custom Product Sheet
- myReads
[ab_icon icon=”file-pdf-o”] myReads NGS Services Product Sheet
[ab_icon icon=”file-pdf-o”] myReads NGS Service Packages
[ab_icon icon=”file-pdf-o” myReads NGS Service Packages for Wheat
- myBaits
[ab_icon icon=”file-pdf-o”] myBaits Hybridization Capture Kits Product Sheet
[ab_icon icon=”file-pdf-o”] myBaits Custom DNA Seq Product Sheet
[ab_icon icon=”file-pdf-o”] myBaits Custom RNA Seq Product Sheet
[ab_icon icon=”file-pdf-o”] myBaits Custom Methyl Seq Product Sheet
[ab_icon icon=”file-pdf-o”] myBaits Microbial Targeted Genomics App Note
[ab_icon icon=”file-pdf-o”] myBaits NLR_Gene_Resequencing Expression using cDNA RenSeq App Note
- myTXTL
From Our Partners
Location: Town and Country B
Date: Tuesday, January 17, 2023 – 4:00 p.m. PT
Speaker: Shawn Quinn – Curio Genomics – USA
Workshop: IWGSC – From Structural to Functional Wheat Genomics
Have questions for our technical team? Would you like to meet with us at PAG? Please complete this form
to contact us!
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.
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