All Publications

  • Immunomodulatory receptors are differentially expressed in B and T cell subsets relevant to autoimmune disease. Clinical immunology (Orlando, Fla.) Murphy, K. A., Bhamidiphati, K., Rubin, S. J., Kipp, L., Robinson, W. H., Lanz, T. V. 2019: 108276


    Inhibitory cell-surface receptors on lymphocytes, often called immune checkpoints, are powerful targets for cancer therapy. Despite their direct involvement in autoimmune pathology, they are currently not exploited therapeutically for autoimmune diseases. Understanding the receptors' expression patterns in health and disease is essential for targeted drug design. Here, we designed three 23-colour flow cytometry panels for peripheral-blood T cells, including 15 lineage-defining markers and 21 immunomodulatory cell-surface receptors, and a 22-marker panel for B cells. Blood samples from healthy individuals, multiple sclerosis (MS), and lupus (SLE) patients were included in the study. Several receptors show differential expression on regulatory T cells (Treg) compared to T helper (Th) 1 and Th17 cells, and functional relevance of this difference could be shown for BTLA and CD5. Unbiased multiparametric analysis revealed a subset of activated CD8+ T cells and a subset of unswitched memory B cells that are diminished in MS and SLE, respectively.

    View details for DOI 10.1016/j.clim.2019.108276

    View details for PubMedID 31669582

  • Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD GENES & DEVELOPMENT Fu, J., Murphy, K. A., Zhou, M., Li, Y. H., Lam, V. H., Tabuloc, C. A., Chiu, J. C., Liu, Y. 2016; 30 (15): 1761–75


    Codon usage bias is a universal feature of all genomes, but its in vivo biological functions in animal systems are not clear. To investigate the in vivo role of codon usage in animals, we took advantage of the sensitivity and robustness of the Drosophila circadian system. By codon-optimizing parts of Drosophila period (dper), a core clock gene that encodes a critical component of the circadian oscillator, we showed that dper codon usage is important for circadian clock function. Codon optimization of dper resulted in conformational changes of the dPER protein, altered dPER phosphorylation profile and stability, and impaired dPER function in the circadian negative feedback loop, which manifests into changes in molecular rhythmicity and abnormal circadian behavioral output. This study provides an in vivo example that demonstrates the role of codon usage in determining protein structure and function in an animal system. These results suggest a universal mechanism in eukaryotes that uses a codon usage "code" within genetic codons to regulate cotranslational protein folding.

    View details for PubMedID 27542830

  • Accelerating research on Spotted Wing Drosophila management using genomic technologies JOURNAL OF PEST SCIENCE Murphy, K. A., West, J. D., Kwok, R. S., Chiu, J. C. 2016; 89 (3): 631–41
  • Ingestion of genetically modified yeast symbiont reduces fitness of an insect pest via RNA interference SCIENTIFIC REPORTS Murphy, K. A., Tabuloc, C. A., Cervantes, K. R., Chiu, J. C. 2016; 6: 22587


    RNA interference has had major advances as a developing tool for pest management. In laboratory experiments, double-stranded RNA (dsRNA) is often administered to the insect by genetic modification of the crop, or synthesized in vitro and topically applied to the crop. Here, we engineered genetically modified yeast that express dsRNA targeting y-Tubulin in Drosophila suzukii. Our design takes advantage of the symbiotic interactions between Drosophila, yeast, and fruit crops. Yeast is naturally found growing on the surface of fruit crops, constitutes a major component of the Drosophila microbiome, and is highly attractive to Drosophila. Thus, this naturally attractive yeast biopesticide can deliver dsRNA to an insect pest without the need for genetic crop modification. We demonstrate that this biopesticide decreases larval survivorship, and reduces locomotor activity and reproductive fitness in adults, which are indicative of general health decline. To our knowledge, this is the first study to show that yeast can be used to deliver dsRNA to an insect pest.

    View details for DOI 10.1038/srep22587

    View details for Web of Science ID 000371175400001

    View details for PubMedID 26931800

    View details for PubMedCentralID PMC4773866

  • Using comparative genomics to develop a molecular diagnostic for the identification of an emerging pest Drosophila suzukii BULLETIN OF ENTOMOLOGICAL RESEARCH Murphy, K. A., Unruh, T. R., Zhou, L. M., Zalom, F. G., Shearer, P. W., Beers, E. H., Walton, V. M., Miller, B., Chiu, J. C. 2015; 105 (3): 364–72


    Drosophila suzukii (Spotted Wing Drosophila) has recently become a serious invasive pest of fruit crops in the USA, Canada, and Europe, leading to substantial economic losses. D. suzukii is a direct pest, ovipositing directly into ripe or ripening fruits; in contrast, other Drosophilids utilize decaying or blemished fruits and are nuisance pests at worst. Immature stages of D. suzukii are difficult to differentiate from other Drosophilids, posing problems for research and for meeting quarantine restrictions designed to prevent the spread of this pest in fruit exports. Here we used a combined phylogenetic and bioinformatic approach to discover genetic markers suitable for a species diagnostic protocol of this agricultural pest. We describe a molecular diagnostic for rapid identification of single D. suzukii larva using multiplex polymerase chain reaction. Our molecular diagnostic was validated using nine different species of Drosophila for specificity and 19 populations of D. suzukii from different geographical regions to ensure utility within species.

    View details for DOI 10.1017/S0007485315000218

    View details for Web of Science ID 000354104000011

    View details for PubMedID 25804294

  • Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes SCIENCE Neafsey, D. E., Waterhouse, R. M., Abai, M. R., Aganezov, S. S., Alekseyev, M. A., Allen, J. E., Amon, J., Arca, B., Arensburger, P., Artemov, G., Assour, L. A., Basseri, H., Berlin, A., Birren, B. W., Blandin, S. A., Brockman, A. I., Burkot, T. R., Burt, A., Chan, C. S., Chauve, C., Chiu, J. C., Christensen, M., Costantini, C., Davidson, V. M., Deligianni, E., Dottorini, T., Dritsou, V., Gabriel, S. B., Guelbeogo, W. M., Hall, A. B., Han, M. V., Hlaing, T., Hughes, D. T., Jenkins, A. M., Jiang, X., Jungreis, I., Kakani, E. G., Kamali, M., Kemppainen, P., Kennedy, R. C., Kirmitzoglou, I. K., Koekemoer, L. L., Laban, N., Langridge, N., Lawniczak, M. N., Lirakis, M., Lobo, N. F., Lowy, E., MacCallum, R. M., Mao, C., Maslen, G., Mbogo, C., McCarthy, J., Michel, K., Mitchell, S. N., Moore, W., Murphy, K. A., Naumenko, A. N., Nolan, T., Novoa, E. M., O'Loughlin, S., Oringanje, C., Oshaghi, M. A., Pakpour, N., Papathanos, P. A., Peery, A. N., Povelones, M., Prakash, A., Price, D. P., Rajaraman, A., Reimer, L. J., Rinker, D. C., Rokas, A., Russell, T. L., Sagnon, N., Sharakhova, M. V., Shea, T., Simao, F. A., Simard, F., Slotman, M. A., Somboon, P., Stegniy, V., Struchiner, C. J., Thomas, G. C., Tojo, M., Topalis, P., Tubio, J. C., Unger, M. F., Vontas, J., Walton, C., Wilding, C. S., Willis, J. H., Wu, Y., Yan, G., Zdobnov, E. M., Zhou, X., Catteruccia, F., Christophides, G. K., Collins, F. H., Cornman, R. S., Crisanti, A., Donnelly, M. J., Emrich, S. J., Fontaine, M. C., Gelbart, W., Hahn, M. W., Hansen, I. A., Howell, P. I., Kafatos, F. C., Kellis, M., Lawson, D., Louis, C., Luckhart, S., Muskavitch, M. T., Ribeiro, J. M., Riehle, M. A., Sharakhov, I. V., Tu, Z., Zwiebel, L. J., Besansky, N. J. 2015; 347 (6217): 1258522


    Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

    View details for DOI 10.1126/science.1258522

    View details for Web of Science ID 000347102300042

    View details for PubMedID 25554792

    View details for PubMedCentralID PMC4380271