Tag Archive for: myReads

PAG 2023 Website

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

Number PO0067

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. 

View Poster

Number PE0068

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. 

View Poster

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

[ab_icon icon=”file-pdf-o”] myTXTL Product Sheet

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!

myTagsmyTags Custom FISH Probes

myReadsmyReads NGS Services

myBaits myBaits Expert Wheat Exome Panel

myBaitsmyBaits Custom Panels

Protein Engineering Biocatalysis Congress 2022

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.”

Evolution Conference – in person conference June 24-28, 2022

Booths are centrally located in Exhibit Hall C.

myBaits® Featured Publications 
Please browse some recent publications utilizing targeted sequencing with myBaits® kits and/or myReads® services for evolutionary biology and ecology research in plants, animals, and more.

Bataillon, T., Gauthier, P., Villesen, P., Santoni, S., Thompson, J. D., & Ehlers, B. K. (2022). From genotype to phenotype: Genetic redundancy and the maintenance of an adaptive polymorphism in the context of high gene flow. Evolution Letters, evl3.277.

Derkarabetian, S., Starrett, J., & Hedin, M. (2022). Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data. Frontiers in Zoology, 19(1), 8.

Hart, P. B., Arnold, R. J., Alda, F., Kenaley, C. P., Pietsch, T. W., Hutchinson, D., & Chakrabarty, P. (2022). Evolutionary Relationships Of Anglerfishes (Lophiiformes) Reconstructed Using Ultraconserved Elements. Molecular Phylogenetics and Evolution, 107459.

Kearns, A. M., Campana, M. G., Slikas, B., Berry, L., Saitoh, T., Cibois, A., & Fleischer, R. C. (2022). Conservation genomics and systematics of a near-extinct island radiation. Molecular Ecology, 31(7), 1995-2012.

Manuzzi, A., Jiménez-Mena, B., Henriques, R., Holmes, B. J., Pepperell, J., Edson, J., Bennett, M. B., Huveneers, C., Ovenden, J. R., & Nielsen, E. E. (2022). Retrospective genomics highlights changes in genetic composition of tiger sharks (Galeocerdo cuvier) and potential loss of a south-eastern Australia population. Scientific Reports, 12(1), 6582.

Montes, J., Peláez, P., Moreno‐Letelier, A., & Gernandt, D. S. (2022). Coalescent‐based species delimitation in North American pinyon pines using low‐copy nuclear genes and plastomes. American Journal of Botany, ajb2.1847.

Parker, L. D., Campana, M. G., Quinta, J. D., Cypher, B., Rivera, I., Fleischer, R. C., Ralls, K., Wilbert, T. R., Boarman, R., Boarman, W. I., & Maldonado, J. E. (2022). An efficient method for simultaneous species, individual, and sex identification via in‐solution single nucleotide polymorphism capture from low‐quality scat samples. Molecular Ecology Resources, 22(4), 1345–1361.

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

Singhal, S., Colli, G. R., Grundler, M. R., Costa, G. C., Prates, I., & Rabosky, D. L. (2022). No link between population isolation and speciation rate in squamate reptiles. Proceedings of the National Academy of Sciences, 119(4).

Stiller, J., Short, G., Hamilton, H., Saarman, N., Longo, S., Wainwright, P., Rouse, G. W., & Simison, W. B. (2022). Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates. BMC Biology, 20(1), 75.

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.

Weise, E. M., Scribner, K. T., Adams, J. V., Boeberitz, O., Jubar, A. K., Bravener, G., Johnson, N. S., & Robinson, J. D. (2022). Pedigree analysis and estimates of effective breeding size characterize sea lamprey reproductive biology Evolutionary Applications, eva.13364.

PAG 2022 Website

Daicel Arbor Biosciences – Booth #310

We are sorry that PAG was canceled. Our scientists really want to meet you virtually to learn about your scientific achievements and to discuss your new projects. You can use the ZOOM Meeting link here from 9:00 a.m. to 5:00 p.m., EST, on January 10, to talk to our scientists. Please click here for link. 

Welcome to the PAG 2022 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: Palm 1-2

Date: Monday, January 10, 12:50 p.m.

Speakers:

Jacob Enk, PhD (Daicel Arbor Biosciences) – 12:55 p.m. PT – Introduction to Renseq from Daicel Arbor Biosciences
Sanu Arora, PhD (John Innes Centre) – 1:15 p.m. PT – Understanding the Genetic Basis of Disease Resistance in Peas
Ingo Hein, PhD (James Hutton Institute) – 1:35 p.m. PT
Tim Hewitt, PhD (CSIRO) – 1:55 p.m. PT – Target Acquired: Using Renseq on Knockout Mutants to Rapidly Clone R Genes in Wheat

The resistance gene enrichment sequencing (RenSeq) workflow supports the comprehensive study of highly complex disease resistance gene (R-gene) families within crop plant genomes. Over the last few years, RenSeq and related NGS approaches have been utilized in or contributed to hundreds of studies across a wide range of plant species. In this workshop, we will highlight the major principles, benefits, and recent advances of RenSeq, and hear from several leading researchers who are actively utilizing it and related NGS techniques in their crop research programs, facilitated by myBaits® Custom hybridization capture kits. 

More Info​

Poster Presentations from Daicel Arbor Biosciences & Collaborators

Number PE0340

Authors: Junli Zhang, German Burguener, Juan Debernardi, Frederic Choulet, Etienne Paux, Jacob Enk, Jorge Dubcovsky

As genome resources for wheat expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here we present a regulatory region NGS hybridization capture panel developed for hexaploid and tetraploid wheat. We used the upstream ~2 kbp of each annotated gene in the most up-to-date Chinese Spring wheat genome assembly as the primary target source, supplemented with homologous sequences from a draft assembly of tetraploid Kronos wheat as well as regions of observed open chromatin state identified with ATACseq. To improve specificity compared to similar legacy designs, candidate repetitive sequences were aggressively filtered using a combination of cross-alignment clustering, TREP19 affinity filtration, and kmer frequency capping. Once converted to candidate probes, these were once again filtered for specificity using a standard design pipeline, resulting in a final target space of ~175 Mbp relative to the IWGSC RefSeq v1.0 genome. Test captures using the probe set on both hexaploid and tetraploid wheat exhibit excellent coverage of the target with significantly improved specificity compared to captures performed using legacy probe designs. Captures of 24 lines from the Kronos TILLING population (EMS-induced mutations) detected an average of ~3300 mutations per line (~5 million predicted mutations in the complete TILLING population of 1500 lines). This probe set is available through Daicel Arbor Biosciences as either a stand-alone capture kit or a full service option from library prep through secondary bioinformatics analysis.​

[ab_icon icon=”file-pdf-o”] Poster – PAG XXIX – Genomic Regulatory Element Sequencing in Wheat

Number PO0409

Authors: Brian Brunelle, Alison Devault, Jacob Enk and Tina Lan, Daicel Arbor Biosciences, Ann Arbor, MI 

The detection of pathogenic variants and pathobiome profiling in plant and animal samples using next-generation sequencing (NGS) is often impeded by the dominant host/background DNA and/or RNA, necessitating extremely deep total NGS in order to accurately resolve genomes/genes of interest or to fully characterize community members. Targeted NGS methods can dramatically reduce the overall costs of sequencing and data analysis per sample. Of the available targeted NGS methods, hybridization capture is the best technique for comprehensive, low-bias, and cost-effective genome or community sequencing of viruses and bacteria from complex samples. Here we review the principles of hybridization capture for microbial sequencing applications, and highlight several peer-reviewed studies relevant to the plant and animal research community, powered by efficient myBaits® target capture kits. ​​

[ab_icon icon=”file-pdf-o”] Poster – PAG XXIX – Simplified Pathogen and Commensal Sequencing

Sponsored Workshops

Location: Pacific C

Date: Sunday, January 9, 8:00 a.m.

Duration: 2 hours, 10 minutes

The Feline & Canine Workshop includes presentations of recent genetic studies involving cats, dogs, and their wild relatives. Topics include the basis of morphology, behavior, and inherited disease, conservation, evolution, paleogenomics, genetic testing, and genomic resource development. This session is generously sponsored by Daicel Arbor Biosciences, ThermoFisher, Embark, Hills, Nippon Genetics, and Retsch.

More Info​​

Location: Town and Country C

Date: Sunday, January 9, 10:30 a.m.

Duration: 2 hours, 10 minutes

Though the first DNA sequences from an extinct organism were first extracted 30 years ago, the revolution in sequencing technology has recently allowed for the retrieval and characterization of ancient organisms dating back more than 50,000 years. This new capability has been used to address questions related to admixture, phylogenetic inference, and evolution writ large. This session will attract leading experts in the use of ancient DNA to discuss their recent findings related to both the optimization of methodology, and specific case studies pertaining to humans, plants, and animals.

More Info

Location: Pacific D

Date: Sunday, January 9, 4:00 p.m.

Duration: 2 hours, 10 minutes

Plant and animal domestication genomics, with a focus on evolutionary history, the impacts of domestication on genome-wide variation, and the genomic basis of domestication traits.

More Info

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

  • 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

[ab_icon icon=”file-pdf-o”] myTXTL Product Sheet

  • myCurio

[ab_icon icon=”file-pdf-o”] Curio

Claim your special PAG gift!

Since we cannot personally hand you our great booth gift, you can claim it using promotion code DAB PAG 2022 at Daicel Arbor PAG gift.

myTagsmyTags Custom FISH Probes

myReadsmyReads NGS Services

myBaits myBaits Expert Wheat Exome Panel

myBaitsmyBaits Custom Panels

SARS-CoV-2 research tools for academic, industry, public health, and surveillance applications. More info here.

DOE JGI User Meeting

Postponed until Fall 2020

Oakland, CA

Wednesday, March 25, 2020 11:00 AM – 12:00 PM EDT

 

Summary

Even as sequencing costs decline, high-depth sequencing of the 7-17 Gbp wheat genome remains cost-prohibitive.  With the myBaits Expert Wheat Exome Panel, Daicel Arbor Biosciences provides the wheat research and breeding community a simple tool that reduces focused sequencing of the wheat high-confidence exome by more than an order of magnitude compared to whole genome sequencing. Based on the IWGSC RefSeq v1.0 reference genome, with a total target space of >200Mb, this is the most up-to-date panel currently available on the market for complete wheat exome sequencing.

In this webinar, Dr. Jacob Enk (R&D Manager for NGS at Daicel Arbor Biosciences) will present the latest performance developments of the Wheat Exome Panel, including its utility for hexaploid, tetraploid, and diploid cultivars of wheat, as well as upcoming complementary tools for targeted sequencing of exome-wide promoters and new exons as they are continually updated in RefSeq.

The myBaits Expert Wheat Exome Panel is available for immediate shipment from Daicel Arbor Biosciences, and can also be purchased as part of full-service NGS packages for library preparation, enrichment, sequencing and bioinformatics analysis. IWGSC members receive special discounted rates on all Wheat Exome kits and services.

Present by:

Dr. Jacob Enk
NGS R&D Manager
Daicel Arbor Biosciences

[ab_button text=”Register Here” link=”https://register.gotowebinar.com/register/1301270217479890445″]