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165 results on '"Rye M"'

3. Applying genetic technologies to combat infectious diseases in aquaculture

Author

Robinson, NA, Robledo, D, Sveen, L, Daniels, RR, Krasnov, A, Coates, A, Jin, YH, Barrett, LT, Lillehammer, M, Kettunen, AH, Phillips, BL, Dempster, T, Doeschl-Wilson, A, Samsing, F, Difford, G, Salisbury, S, Gjerde, B, Haugen, J-E, Burgerhout, E, Dagnachew, BS, Kurian, D, Fast, MD, Rye, M, Salazar, M, Bron, JE, Monaghan, SJ, Jacq, C, Birkett, M, Browman, HI, Skiftesvik, AB, Fields, DM, Selander, E, Bui, S, Sonesson, A, Skugor, S, Ostbye, T-KK, Houston, RD, Robinson, NA, Robledo, D, Sveen, L, Daniels, RR, Krasnov, A, Coates, A, Jin, YH, Barrett, LT, Lillehammer, M, Kettunen, AH, Phillips, BL, Dempster, T, Doeschl-Wilson, A, Samsing, F, Difford, G, Salisbury, S, Gjerde, B, Haugen, J-E, Burgerhout, E, Dagnachew, BS, Kurian, D, Fast, MD, Rye, M, Salazar, M, Bron, JE, Monaghan, SJ, Jacq, C, Birkett, M, Browman, HI, Skiftesvik, AB, Fields, DM, Selander, E, Bui, S, Sonesson, A, Skugor, S, Ostbye, T-KK, and Houston, RD

Abstract

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Published
2023

8. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Author

Grapotte M., Saraswat M., Bessiere C., Menichelli C., Ramilowski J. A., Severin J., Hayashizaki Y., Itoh M., Tagami M., Murata M., Kojima-Ishiyama M., Noma S., Noguchi S., Kasukawa T., Hasegawa A., Suzuki H., Nishiyori-Sueki H., Frith M. C., Abugessaisa I., Aitken S., Aken B. L., Alam I., Alam T., Alasiri R., Alhendi A. M. N., Alinejad-Rokny H., Alvarez M. J., Andersson R., Arakawa T., Araki M., Arbel T., Archer J., Archibald A. L., Arner E., Arner P., Asai K., Ashoor H., Astrom G., Babina M., Baillie J. K., Bajic V. B., Bajpai A., Baker S., Baldarelli R. M., Balic A., Bansal M., Batagov A. O., Batzoglou S., Beckhouse A. G., Beltrami A. P., Beltrami C. A., Bertin N., Bhattacharya S., Bickel P. J., Blake J. A., Blanchette M., Bodega B., Bonetti A., Bono H., Bornholdt J., Bttcher M., Bougouffa S., Boyd M., Breda J., Brombacher F., Brown J. B., Bult C. J., Burroughs A. M., Burt D. W., Busch A., Caglio G., Califano A., Cameron C. J., Cannistraci C. V., Carbone A., Carlisle A. J., Carninci P., Carter K. W., Cesselli D., Chang J. -C., Chen J. C., Chen Y., Chierici M., Christodoulou J., Ciani Y., Clark E. L., Coskun M., Dalby M., Dalla E., Daub C. O., Davis C. A., de Hoon M. J. L., de Rie D., Denisenko E., Deplancke B., Detmar M., Deviatiiarov R., Di Bernardo D., Diehl A. D., Dieterich L. C., Dimont E., Djebali S., Dohi T., Dostie J., Drablos F., Edge A. S. B., Edinger M., Ehrlund A., Ekwall K., Elofsson A., Endoh M., Enomoto H., Enomoto S., Faghihi M., Fagiolini M., Farach-Carson M. C., Faulkner G. J., Favorov A., Fernandes A. M., Ferrai C., Forrest A. R. R., Forrester L. M., Forsberg M., Fort A., Francescatto M., Freeman T. C., Frith M., Fukuda S., Funayama M., Furlanello C., Furuno M., Furusawa C., Gao H., Gazova I., Gebhard C., Geier F., Geijtenbeek T. B. H., Ghosh S., Ghosheh Y., Gingeras T. R., Gojobori T., Goldberg T., Goldowitz D., Gough J., Greco D., Gruber A. J., Guhl S., Guigo R., Guler R., Gusev O., Gustincich S., Ha T. J., Haberle V., Hale P., Hallstrom B. M., Hamada M., Handoko L., Hara M., Harbers M., Harrow J., Harshbarger J., Hase T., Hashimoto K., Hatano T., Hattori N., Hayashi R., Herlyn M., Hettne K., Heutink P., Hide W., Hitchens K. J., Sui S. H., 't Hoen P. A. C., Hon C. C., Hori F., Horie M., Horimoto K., Horton P., Hou R., Huang E., Huang Y., Hugues R., Hume D., Ienasescu H., Iida K., Ikawa T., Ikemura T., Ikeo K., Inoue N., Ishizu Y., Ito Y., Ivshina A. V., Jankovic B. R., Jenjaroenpun P., Johnson R., Jorgensen M., Jorjani H., Joshi A., Jurman G., Kaczkowski B., Kai C., Kaida K., Kajiyama K., Kaliyaperumal R., Kaminuma E., Kanaya T., Kaneda H., Kapranov P., Kasianov A. S., Katayama T., Kato S., Kawaguchi S., Kawai J., Kawaji H., Kawamoto H., Kawamura Y. I., Kawasaki S., Kawashima T., Kempfle J. S., Kenna T. J., Kere J., Khachigian L., Kiryu H., Kishima M., Kitajima H., Kitamura T., Kitano H., Klaric E., Klepper K., Klinken S. P., Kloppmann E., Knox A. J., Kodama Y., Kogo Y., Kojima M., Kojima S., Komatsu N., Komiyama H., Kono T., Koseki H., Koyasu S., Kratz A., Kukalev A., Kulakovskiy I., Kundaje A., Kunikata H., Kuo R., Kuo T., Kuraku S., Kuznetsov V. A., Kwon T. J., Larouche M., Lassmann T., Law A., Le-Cao K. -A., Lecellier C. -H., Lee W., Lenhard B., Lennartsson A., Li K., Li R., Lilje B., Lipovich L., Lizio M., Lopez G., Magi S., Mak G. K., Makeev V., Manabe R., Mandai M., Mar J., Maruyama K., Maruyama T., Mason E., Mathelier A., Matsuda H., Medvedeva Y. A., Meehan T. F., Mejhert N., Meynert A., Mikami N., Minoda A., Miura H., Miyagi Y., Miyawaki A., Mizuno Y., Morikawa H., Morimoto M., Morioka M., Morishita S., Moro K., Motakis E., Motohashi H., Mukarram A. K., Mummery C. L., Mungall C. J., Murakawa Y., Muramatsu M., Nagasaka K., Nagase T., Nakachi Y., Nakahara F., Nakai K., Nakamura K., Nakamura Y., Nakazawa T., Nason G. P., Nepal C., Nguyen Q. H., Nielsen L. K., Nishida K., Nishiguchi K. M., Nishiyori H., Nitta K., Notredame C., Ogishima S., Ohkura N., Ohno H., Ohshima M., Ohtsu T., Okada Y., Okada-Hatakeyama M., Okazaki Y., Oksvold P., Orlando V., Ow G. S., Ozturk M., Pachkov M., Paparountas T., Parihar S. P., Park S. -J., Pascarella G., Passier R., Persson H., Philippens I. H., Piazza S., Plessy C., Pombo A., Ponten F., Poulain S., Poulsen T. M., Pradhan S., Prezioso C., Pridans C., Qin X. -Y., Quackenbush J., Rackham O., Ramilowski J., Ravasi T., Rehli M., Rennie S., Rito T., Rizzu P., Robert C., Roos M., Rost B., Roudnicky F., Roy R., Rye M. B., Sachenkova O., Saetrom P., Sai H., Saiki S., Saito M., Saito A., Sakaguchi S., Sakai M., Sakaue S., Sakaue-Sawano A., Sandelin A., Sano H., Sasamoto Y., Sato H., Saxena A., Saya H., Schafferhans A., Schmeier S., Schmidl C., Schmocker D., Schneider C., Schueler M., Schultes E. A., Schulze-Tanzil G., Semple C. A., Seno S., Seo W., Sese J., Sheng G., Shi J., Shimoni Y., Shin J. W., SimonSanchez J., Sivertsson A., Sjostedt E., Soderhall C., Laurent G. S., Stoiber M. H., Sugiyama D., Summers K. M., Suzuki A. M., Suzuki K., Suzuki M., Suzuki N., Suzuki T., Swanson D. J., Swoboda R. K., Taguchi A., Takahashi H., Takahashi M., Takamochi K., Takeda S., Takenaka Y., Tam K. T., Tanaka H., Tanaka R., Tanaka Y., Tang D., Taniuchi I., Tanzer A., Tarui H., Taylor M. S., Terada A., Terao Y., Testa A. C., Thomas M., Thongjuea S., Tomii K., Triglia E. T., Toyoda H., Tsang H. G., Tsujikawa M., Uhlen M., Valen E., van de Wetering M., van Nimwegen E., Velmeshev D., Verardo R., Vitezic M., Vitting-Seerup K., von Feilitzen K., Voolstra C. R., Vorontsov I. E., Wahlestedt C., Wasserman W. W., Watanabe K., Watanabe S., Wells C. A., Winteringham L. N., Wolvetang E., Yabukami H., Yagi K., Yamada T., Yamaguchi Y., Yamamoto M., Yamamoto Y., Yamanaka Y., Yano K., Yasuzawa K., Yatsuka Y., Yo M., Yokokura S., Yoneda M., Yoshida E., Yoshida Y., Yoshihara M., Young R., Young R. S., Yu N. Y., Yumoto N., Zabierowski S. E., Zhang P. G., Zucchelli S., Zwahlen M., Chatelain C., Brehelin L., Grapotte, M., Saraswat, M., Bessiere, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I., Aitken, S., Aken, B. L., Alam, I., Alam, T., Alasiri, R., Alhendi, A. M. N., Alinejad-Rokny, H., Alvarez, M. J., Andersson, R., Arakawa, T., Araki, M., Arbel, T., Archer, J., Archibald, A. L., Arner, E., Arner, P., Asai, K., Ashoor, H., Astrom, G., Babina, M., Baillie, J. K., Bajic, V. B., Bajpai, A., Baker, S., Baldarelli, R. M., Balic, A., Bansal, M., Batagov, A. O., Batzoglou, S., Beckhouse, A. G., Beltrami, A. P., Beltrami, C. A., Bertin, N., Bhattacharya, S., Bickel, P. J., Blake, J. A., Blanchette, M., Bodega, B., Bonetti, A., Bono, H., Bornholdt, J., Bttcher, M., Bougouffa, S., Boyd, M., Breda, J., Brombacher, F., Brown, J. B., Bult, C. J., Burroughs, A. M., Burt, D. W., Busch, A., Caglio, G., Califano, A., Cameron, C. J., Cannistraci, C. V., Carbone, A., Carlisle, A. J., Carninci, P., Carter, K. W., Cesselli, D., Chang, J. -C., Chen, J. C., Chen, Y., Chierici, M., Christodoulou, J., Ciani, Y., Clark, E. L., Coskun, M., Dalby, M., Dalla, E., Daub, C. O., Davis, C. A., de Hoon, M. J. L., de Rie, D., Denisenko, E., Deplancke, B., Detmar, M., Deviatiiarov, R., Di Bernardo, D., Diehl, A. D., Dieterich, L. C., Dimont, E., Djebali, S., Dohi, T., Dostie, J., Drablos, F., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Elofsson, A., Endoh, M., Enomoto, H., Enomoto, S., Faghihi, M., Fagiolini, M., Farach-Carson, M. C., Faulkner, G. J., Favorov, A., Fernandes, A. M., Ferrai, C., Forrest, A. R. R., Forrester, L. M., Forsberg, M., Fort, A., Francescatto, M., Freeman, T. C., Frith, M., Fukuda, S., Funayama, M., Furlanello, C., Furuno, M., Furusawa, C., Gao, H., Gazova, I., Gebhard, C., Geier, F., Geijtenbeek, T. B. H., Ghosh, S., Ghosheh, Y., Gingeras, T. R., Gojobori, T., Goldberg, T., Goldowitz, D., Gough, J., Greco, D., Gruber, A. J., Guhl, S., Guigo, R., Guler, R., Gusev, O., Gustincich, S., Ha, T. J., Haberle, V., Hale, P., Hallstrom, B. M., Hamada, M., Handoko, L., Hara, M., Harbers, M., Harrow, J., Harshbarger, J., Hase, T., Hashimoto, K., Hatano, T., Hattori, N., Hayashi, R., Herlyn, M., Hettne, K., Heutink, P., Hide, W., Hitchens, K. J., Sui, S. H., 't Hoen, P. A. C., Hon, C. C., Hori, F., Horie, M., Horimoto, K., Horton, P., Hou, R., Huang, E., Huang, Y., Hugues, R., Hume, D., Ienasescu, H., Iida, K., Ikawa, T., Ikemura, T., Ikeo, K., Inoue, N., Ishizu, Y., Ito, Y., Ivshina, A. V., Jankovic, B. R., Jenjaroenpun, P., Johnson, R., Jorgensen, M., Jorjani, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kajiyama, K., Kaliyaperumal, R., Kaminuma, E., Kanaya, T., Kaneda, H., Kapranov, P., Kasianov, A. S., Katayama, T., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y. I., Kawasaki, S., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L., Kiryu, H., Kishima, M., Kitajima, H., Kitamura, T., Kitano, H., Klaric, E., Klepper, K., Klinken, S. P., Kloppmann, E., Knox, A. J., Kodama, Y., Kogo, Y., Kojima, M., Kojima, S., Komatsu, N., Komiyama, H., Kono, T., Koseki, H., Koyasu, S., Kratz, A., Kukalev, A., Kulakovskiy, I., Kundaje, A., Kunikata, H., Kuo, R., Kuo, T., Kuraku, S., Kuznetsov, V. A., Kwon, T. J., Larouche, M., Lassmann, T., Law, A., Le-Cao, K. -A., Lecellier, C. -H., Lee, W., Lenhard, B., Lennartsson, A., Li, K., Li, R., Lilje, B., Lipovich, L., Lizio, M., Lopez, G., Magi, S., Mak, G. K., Makeev, V., Manabe, R., Mandai, M., Mar, J., Maruyama, K., Maruyama, T., Mason, E., Mathelier, A., Matsuda, H., Medvedeva, Y. A., Meehan, T. F., Mejhert, N., Meynert, A., Mikami, N., Minoda, A., Miura, H., Miyagi, Y., Miyawaki, A., Mizuno, Y., Morikawa, H., Morimoto, M., Morioka, M., Morishita, S., Moro, K., Motakis, E., Motohashi, H., Mukarram, A. K., Mummery, C. L., Mungall, C. J., Murakawa, Y., Muramatsu, M., Nagasaka, K., Nagase, T., Nakachi, Y., Nakahara, F., Nakai, K., Nakamura, K., Nakamura, Y., Nakazawa, T., Nason, G. P., Nepal, C., Nguyen, Q. H., Nielsen, L. K., Nishida, K., Nishiguchi, K. M., Nishiyori, H., Nitta, K., Notredame, C., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Ohtsu, T., Okada, Y., Okada-Hatakeyama, M., Okazaki, Y., Oksvold, P., Orlando, V., Ow, G. S., Ozturk, M., Pachkov, M., Paparountas, T., Parihar, S. P., Park, S. -J., Pascarella, G., Passier, R., Persson, H., Philippens, I. H., Piazza, S., Plessy, C., Pombo, A., Ponten, F., Poulain, S., Poulsen, T. M., Pradhan, S., Prezioso, C., Pridans, C., Qin, X. -Y., Quackenbush, J., Rackham, O., Ramilowski, J., Ravasi, T., Rehli, M., Rennie, S., Rito, T., Rizzu, P., Robert, C., Roos, M., Rost, B., Roudnicky, F., Roy, R., Rye, M. B., Sachenkova, O., Saetrom, P., Sai, H., Saiki, S., Saito, M., Saito, A., Sakaguchi, S., Sakai, M., Sakaue, S., Sakaue-Sawano, A., Sandelin, A., Sano, H., Sasamoto, Y., Sato, H., Saxena, A., Saya, H., Schafferhans, A., Schmeier, S., Schmidl, C., Schmocker, D., Schneider, C., Schueler, M., Schultes, E. A., Schulze-Tanzil, G., Semple, C. A., Seno, S., Seo, W., Sese, J., Sheng, G., Shi, J., Shimoni, Y., Shin, J. W., Simonsanchez, J., Sivertsson, A., Sjostedt, E., Soderhall, C., Laurent, G. S., Stoiber, M. H., Sugiyama, D., Summers, K. M., Suzuki, A. M., Suzuki, K., Suzuki, M., Suzuki, N., Suzuki, T., Swanson, D. J., Swoboda, R. K., Taguchi, A., Takahashi, H., Takahashi, M., Takamochi, K., Takeda, S., Takenaka, Y., Tam, K. T., Tanaka, H., Tanaka, R., Tanaka, Y., Tang, D., Taniuchi, I., Tanzer, A., Tarui, H., Taylor, M. S., Terada, A., Terao, Y., Testa, A. C., Thomas, M., Thongjuea, S., Tomii, K., Triglia, E. T., Toyoda, H., Tsang, H. G., Tsujikawa, M., Uhlen, M., Valen, E., van de Wetering, M., van Nimwegen, E., Velmeshev, D., Verardo, R., Vitezic, M., Vitting-Seerup, K., von Feilitzen, K., Voolstra, C. R., Vorontsov, I. E., Wahlestedt, C., Wasserman, W. W., Watanabe, K., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yabukami, H., Yagi, K., Yamada, T., Yamaguchi, Y., Yamamoto, M., Yamamoto, Y., Yamanaka, Y., Yano, K., Yasuzawa, K., Yatsuka, Y., Yo, M., Yokokura, S., Yoneda, M., Yoshida, E., Yoshida, Y., Yoshihara, M., Young, R., Young, R. S., Yu, N. Y., Yumoto, N., Zabierowski, S. E., Zhang, P. G., Zucchelli, S., Zwahlen, M., Chatelain, C., Brehelin, L., Institute of Biotechnology, Biosciences, Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), National Institute of Advanced Industrial Science and Technology (AIST), SANOFI Recherche, University of British Columbia (UBC), Experimental Immunology, Infectious diseases, AII - Infectious diseases, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)

Subjects
0301 basic medicine, General Physics and Astronomy, Genome, Mice, 0302 clinical medicine, Transcription (biology), Promoter Regions, Genetic, Transcription Initiation, Genetic, 0303 health sciences, Multidisciplinary, 1184 Genetics, developmental biology, physiology, High-Throughput Nucleotide Sequencing, Neurodegenerative Diseases, 222 Other engineering and technologies, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], humanities, Enhancer Elements, Genetic, Microsatellite Repeat, Transcription Initiation Site, Sequence motif, Transcription Initiation, Human, Enhancer Elements, Neural Networks, Science, 610 Medicine & health, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Promoter Regions, 03 medical and health sciences, Computer, Deep Learning, Tandem repeat, Genetic, Clinical Research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Machine learning, Genetics, Animals, Humans, Polymorphism, Enhancer, Transcriptomics, Gene, A549 Cell, 030304 developmental biology, Polymorphism, Genetic, Neurodegenerative Disease, Base Sequence, Animal, Genome, Human, Human Genome, Computational Biology, Promoter, General Chemistry, 113 Computer and information sciences, Cap analysis gene expression, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Cardiovascular and Metabolic Diseases, A549 Cells, Minion, Generic health relevance, 3111 Biomedicine, Neural Networks, Computer, 610 Medizin und Gesundheit, 030217 neurology & neurosurgery, FANTOM consortium, Microsatellite Repeats
Abstract

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism., Nature Communications, 12 (1), ISSN:2041-1723

Published
2020

13. Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test

Author

Lillehammer, M, Bangera, R, Salazar, M, Vela, S, Erazo, EC, Suarez, A, Cock, J, Rye, M, Robinson, NA, Lillehammer, M, Bangera, R, Salazar, M, Vela, S, Erazo, EC, Suarez, A, Cock, J, Rye, M, and Robinson, NA

Abstract

White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine the power and accuracy of genomic selection to improve WSSV resistance in Litopenaeus vannamei. Shrimp were experimentally challenged with WSSV and resistance was evaluated as dead or alive (DOA) 23 days after infestation. All shrimp in the challenge test were genotyped for 18,643 single nucleotide polymorphisms. Breeding candidates (G0) were ranked on genomic breeding values for WSSV resistance. Two G1 populations were produced, one from G0 breeders with high and the other with low estimated breeding values. A third population was produced from “random” mating of parent stock. The average survival was 25% in the low, 38% in the random and 51% in the high-genomic breeding value groups. Genomic heritability for DOA (0.41 in G1) was high for this type of trait. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection.

Published
2020

16. Camber and aerodynamic performance of compliant membrane wings

Author

Kenneth S. Breuer and Rye M. Waldman

Subjects
020301 aerospace & aeronautics, Engineering, Wing, business.industry, Angle of attack, Mechanical Engineering, 02 engineering and technology, Aerodynamics, Structural engineering, Aeroelasticity, 01 natural sciences, 010305 fluids & plasmas, Membrane, 0203 mechanical engineering, Camber (aerodynamics), 0103 physical sciences, Fluid dynamics, Potential flow, business
Abstract

We present a self-consistent theory to predict the behavior of compliant membrane wings subject to aerodynamic loads. The theory incorporates the Young–Laplace equation to treat nonlinear deformation of the membrane at low angles of attack and uses a potential flow model to estimate the aerodynamic load associated with the thin wing. The model is able to account for finite span wings as well as to predict the occurrence of lift hysteresis, in which a lightly pretensioned membrane adopts camber at zero angle of attack. The theory is compared with results from numerical simulations that couple the structural deformation of the membrane with the fluid flow and also with experimental measurements of free tip and supported tip membrane wings tested over a range of aeroelastic conditions. Predictions of camber, lift and vibrational frequency are in good general agreement with both numerical and experimental observations.

Published
2017

17. Optimising silica-based solid phase DNA extraction methods for low concentration forensic samples

Author

Chapman, Brendan, Pagan, F., Cornwell, S., Rye, M., Dilley, Katherine, Chapman, Brendan, Pagan, F., Cornwell, S., Rye, M., and Dilley, Katherine

Abstract

Trace DNA analysis from minute biological samples has become commonplace in modern forensic laboratories due to increased sensitivities in genotyping systems and improved extraction chemistries. However, analysis still remains a challenge as no single protocol exists that will isolate DNA in both sufficient quantity and quality for downstream applications. Extraction is the most crucial step for maximising recovery of DNA, and thorough optimisation of procedures is needed to ensure informative genetic profiles can be generated. This review will investigate the efficiency of different methods available for isolating trace quantities of DNA from forensic samples, discussing their advantages and limitations. It will explore improvements to the extraction methodology, including optimisation of the elution volume and methods of post-extraction purification. Lastly, centrifugal filters will be debated for their concentrating properties and ability to improve the recovery of trace DNA.

Published
2019

18. High-Speed Imaging to Quantify Transient Ice Accretion Process over an Airfoil

Author

Hui Hu and Rye M. Waldman

Subjects
Airfoil, Meteorology, 020209 energy, Aerospace Engineering, 02 engineering and technology, Aerodynamics, Mechanics, 01 natural sciences, Atmospheric icing, 010305 fluids & plasmas, NACA airfoil, Icing conditions, Sea ice growth processes, 0103 physical sciences, 0202 electrical engineering, electronic engineering, information engineering, Environmental science, Deposition (phase transition), Icing
Abstract

Ice accretion on aircraft wings poses a performance and safety threat as aircraft encounter supercooled droplets suspended in the cloud layer. The details of the ice accretion depend on the atmospheric conditions and the flight parameters. The icing process on the wing consists of a complex interaction of water deposition, surface water transport, and freezing. The aerodynamics affect the water deposition, the heat and mass transport, and ice accumulation; meanwhile, the accumulating ice affects the aerodynamics. Until now, most experimental measurements of aircraft icing have focused on the final ice shapes formed after exposure for a set duration to icing conditions. This approach fails to capture the transient processes that form the final ice formations. Here, we present experiments conducted in the Iowa State Icing Research Tunnel on a NACA 0012 airfoil to study the transient ice accretion process under varying icing conditions. High-speed video of the icing process was acquired under controlled envi...

Published
2016

20. An Experimental Study on Icing Physics for Wind Turbine Icing Mitigation

Author

Hui Hu, Hao Guo, Kai Zhang, and Rye M. Waldman

Subjects
020209 energy, 0103 physical sciences, 0202 electrical engineering, electronic engineering, information engineering, 02 engineering and technology, 01 natural sciences, Turbine, 010305 fluids & plasmas, Icing, Marine engineering
Published
2017

22. Aerodynamic Characterization of a Wing Membrane with Variable Compliance

Author

Kenneth S. Breuer, Oscar M. Curet, Rye M. Waldman, and Alex Carrere

Subjects
Lift-to-drag ratio, animal structures, Wing, Materials science, Angle of attack, business.industry, Aerospace Engineering, Stall (fluid mechanics), Aerodynamics, Structural engineering, Camber (aerodynamics), Wing twist, business, Wind tunnel
Abstract

Membrane wings with variable compliance have a great potential to improve the maneuverability and performance of micro air vehicles. Moreover, changes in membrane wing compliance might be used by flying animals, such as bats, to control aerodynamic performance. In this work, the mechanical properties and aerodynamic performance of a low-aspect-ratio membrane wing with variable compliance was characterized. The membrane was made of dielectric material coated with compliant electrodes and supported by a rigid frame. The compliance of the wing was controlled by applying a voltage across a membrane. The wing model was tested in a wind tunnel. It was found that, when a fixed voltage is applied across the wing membrane, the camber increases, accompanied by a small increase in lift. However, lift is significantly increased when the wing is forced with an oscillating field at specific frequencies. In addition, stall is delayed, and for a range of angle of attacks, there is an increase in lift-to-drag ratio. Fluid...

Published
2014

24. An Experimental Investigation on Unsteady Heat Transfer and Transient Icing Process upon Impingement of Water Droplets

Author

Haixing Li, Hui Hu, and Rye M. Waldman

Subjects
Materials science, Reynolds number, Thermodynamics, 02 engineering and technology, Substrate (electronics), 021001 nanoscience & nanotechnology, 01 natural sciences, 010305 fluids & plasmas, symbols.namesake, Scientific method, 0103 physical sciences, Heat transfer, symbols, Weber number, Transient (oscillation), Composite material, 0210 nano-technology, Supercooling, Icing
Abstract

This study presents an experimental investigation of a single droplet with different impingement velocity impinge on the hydrophilic and superhydrophobic substrates under normal and icing temperature by using high-speed image and infrared image techniques. The aim is to better understand the unsteady heat transfer and transient icing process of the aircraft icing caused by the supercooled large droplets, which has been recently identified as a severe hazard in aviation. The Reynolds number and Weber number of the impingement droplet ranged from 3708 to 6109 and from 117 to 319, respectively, while the temperature of the impingement substrate ranged from -5˚C to 5˚C. Droplet impingement, spreading, receding, and rebound phenomenon was recorded by a high-speed imaging system, while the surface temperature variation upon the impingement droplet on the substrate was recorded by an infrared imaging system. The time needed for the impingement droplet to be static on the superhydrophobic surface was much shorter than that on hydrophilic surface, while the time needed for cooling the impingement droplet on the superhydrophobic surface was much longer. The temperature variation on the surface of the impingement droplet was gradually on superhydrophobic substrate, while that on the hydrophilic substrate under icing temperature had obvious fluctuation. For the hydrophilic substrate, the temperature had little influence to the maximum spreading diameter of the impingement droplet, while the final receding diameter of the impingement increased with the decreasing of the substrate temperature, moreover, the water temperature decreasing speed increased while the icing process was faster. Lower droplet impingement velocity would lead to a slower cooing process of water and a slower icing process, while the temperature fluctuation at the surface center of the impingement droplet decreased for a shorter water receding time.

Published
2016

25. Accurate measurement of streamwise vortices using dual-plane PIV

Author

Rye M. Waldman and Kenneth S. Breuer

Subjects
Fluid Flow and Transfer Processes, Computer science, business.industry, Acoustics, Computational Mechanics, General Physics and Astronomy, Reynolds number, Aerodynamics, Wake, Vortex, Aerodynamic force, symbols.namesake, Optics, Mechanics of Materials, Temporal resolution, symbols, Flapping, Measurement uncertainty, business
Abstract

Low Reynolds number aerodynamic experiments with flapping animals (such as bats and small birds) are of particular interest due to their application to micro air vehicles which operate in a similar parameter space. Previous PIV wake measurements described the structures left by bats and birds and provided insight into the time history of their aerodynamic force generation; however, these studies have faced difficulty drawing quantitative conclusions based on said measurements. The highly three-dimensional and unsteady nature of the flows associated with flapping flight are major challenges for accurate measurements. The challenge of animal flight measurements is finding small flow features in a large field of view at high speed with limited laser energy and camera resolution. Cross-stream measurement is further complicated by the predominately out-of-plane flow that requires thick laser sheets and short inter-frame times, which increase noise and measurement uncertainty. Choosing appropriate experimental parameters requires compromise between the spatial and temporal resolution and the dynamic range of the measurement. To explore these challenges, we do a case study on the wake of a fixed wing. The fixed model simplifies the experiment and allows direct measurements of the aerodynamic forces via load cell. We present a detailed analysis of the wake measurements, discuss the criteria for making accurate measurements, and present a solution for making quantitative aerodynamic load measurements behind free-flyers.

Published
2012

29. The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Author

Liang, C, Alam, I, Albanese, D, Altschuler, G, Andersson, R, Arakawa, T, Archer, J, Arner, E, Arner, P, Babina, M, Baillie, K, Bajic, V, Baker, S, Balic, A, Balwierz, P, Beckhouse, A, Bertin, N, Blake, Ja, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Burroughs, M, Califano, A, Cannistraci, C, Carbajo, D, Carninci, P, Chen, Yang, Chierici, M, Ciani, Y, Clevers, H, Dalla, Emiliano, Daub, C, Davis, C, De Hoon, M, De Lima Morais, D, Dermar, M, Diehl, A, Dimont, E, Dohl, T, Drabros, F, Edge, A, Edinger, M, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, L, Fang, H, Farach Carson, Mc, Faulkner, G, Favorov, A, Fisher, M, Forrest, A, Francescatto, M, Freeman, T, Frith, M, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, J, Geijtenbeek, Tb, Gibson, A, Gingeras, T, Goldowithz, D, Gough, J, Guhl, S, Guler, R, Gustincich, Stefano, Ha, T, Haberle, V, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Hayashizaki, Y, Herlyn, M, Heutink, P, Hide, W, Hitchens, K, Ho Sui, S, Hofmann, O, Hoof, I, Hori, F, Hume, D, Huminiecki, L, Iida, K, Ikawa, T, Ishizu, Y, Itoh, M, Jankovic, B, Jia, H, Jorgensen, M, Joshi, A, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kaiho, A, Kajiyama, K, Kanamori Katayama, M, Kasianov, A, Kasukawa, T, Katayama, S, Kato Ishikawa, S, Kawaguchi, S, Kawai, J, Kawaji, H, Kawamoto, H, Kawamura, Y, Kawashima, T, Kempfle, J, Kenna, T, Kere, J, Khachigian, L, Kitamura, T, Klinken, P, Knox, A, Kojima, M, Kojima, S, Kondo, N, Koseki, H, Koyasu, S, Krampitz, S, Kubosaki, A, Kulakovskiy, I, Kwon, At, Laros, J, Lassmann, T, Lenhard, B, Lennartsson, A, Li, K, Lilji, B, Lipovich, L, Lizio, M, Mackay Sim, A, Makeev, V, Manabe, R, Mar, J, Marchand, B, Mathelier, A, Medvedeva, Y, Meehan, Tf, Mejhert, N, Meynert, A, Mizuno, Y, Morikawa, H, Morimoto, M, Moro, K, Motakis, E, Motohashi, H, Mummery, C, Mungall, Cj, Murata, M, Nagao Sato, S, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nakazato, K, Ninomiya Fukuda, N, Nishiyori Sueki, H, Noma, S, Nozaki, T, Ogishima, S, Ohkura, N, Ohmiya, H, Ohno, H, Ohshima, M, Okada Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, D, Pain, A, Passier, R, Persson, H, Piazza, Silvano, Plessy, C, Pradhan Bhatt, S, Prendergast, J, Rackham, O, Ramilowski, J, Rashid, M, Ravasi, T, Rehli, M, Rizzu, P, Roncador, M, Roy, S, Rye, M, Saijyo, E, Sajantila, A, Saka, A, Sakaguchi, S, Sakai, M, Sandelin, A, Sato, H, Satoh, H, Suzana, S, Alka, S, Schaefer, U, Schmeier, S, Schmidl, C, Schneider, C, Schultes, Ea, Schulze Tanzil, G, Schwegmann, A, Semple, C, Sengstag, T, Severin, J, Sheng, G, Shimoji, H, Shimoni, Y, Shin, J, Simon, C, Sugiyama, D, Sugiyama, T, Summers, K, Suzuki, H, Suzuki, M, Suzuki, N, Swoboda, R, Hoen P, T, Tagami, M, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tatum, Z, Taylor, M, Thompson, M, Toyoda, H, Toyoda, T, Valen, E, Van De Wetering, M, Van Den Berg, L, Van Nimwegen, E, Verardo, R, Vijayan, D, Vitezic, M, Vorontzov, I, Wasserman, W, Watanabe, S, Wells, C, Winteringham, L, Wolvetang, E, Wood, Ej, Yamaguchi, Y, Yamamoto, M, Yoneda, M, Yonekura, Y, Yoshida, Shin'Ichirou, Young, R, Zabierowski, Se, Zhang, P, Zhao, X, Zucchelli, Silvia, Forrest, Ar, Wagner, Gp, Hubrecht Institute for Developmental Biology and Stem Cell Research, AII - Amsterdam institute for Infection and Immunity, Infectious diseases, and Experimental Immunology

Subjects
Cell type, General Physics and Astronomy, rna-seq data, phylogenetic networks, Biology, ENCODE, General Biochemistry, Genetics and Molecular Biology, Divergence, Transcriptome, Models, Settore BIO/13 - Biologia Applicata, Neoplasms, Humans, Genetics, Models, Statistical, Multidisciplinary, Statistical model, General Chemistry, Statistical, Biological Evolution, Body plan, Tree structure, Evolutionary biology, Cancer cell
Abstract

In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination.

Published
2015

30. An Experimental Investigation on the Unsteady Heat Transfer Process Over an Ice Accreting NACA 0012 Airfoil

Author

Hui Hu, Rye M. Waldman, and Yang Liu

Subjects
Convection, Dynamic scraped surface heat exchanger, Icing conditions, Convective heat transfer, Sea ice growth processes, Chemistry, Latent heat, Heat transfer, Thermodynamics, Astrophysics::Earth and Planetary Astrophysics, Mechanics, Glaze ice, Physics::Atmospheric and Oceanic Physics
Abstract

The in-flight ice formation and accretion are highly dependent on weather conditions that essentially affect the heat transfer capability. When the temperature is sufficiently cold, the heat transfer is adequate to remove all of the latent heat from the collected water. The rate of rime ice accretion is controlled by the droplet collection efficiency. Otherwise, when the heat transfer is inadequate to remove all of the latent heat in collected water, the rate of glaze ice accretion is essentially controlled by the local convective heat transfer, which determines the amount of latent heat removal from the collected water. To better understand the physical details during an ice accretion process, time resolved heat transfer information is important and strongly desired. In this study, a methodology based on infrared thermography was developed to achieve nonintrusive measurements of unsteady heat transfer process over an ice accreting NACA 0012 airfoil. Comprehensive 2-D surface temperature distribution measurements under various icing conditions (e.g. air temperature, liquid water content, and wind speed) were performed in an icing wind tunnel. A heat balance model was formulated based on the current measurement model. The dynamic surface temperature distribution variations were characterized based on the measurements. The temperature variation history at different chordwise positions during ice accretion process was fully recorded and illustrated. Based on the temperature variation history along the airfoil surface, the heat transfer evolution in chordwise direction was evaluated. Finally, The effects of the liquid water content on the heat transfer process were elucidated based on the measurement results.

Published
2015

35. Shape, lift, and vibrations of highly compliant membrane wings

Author

Kenny S. Breuer and Rye M. Waldman

Subjects
Physics, Wing, business.industry, Reynolds number, Mechanics, Structural engineering, Wake, Vortex shedding, Aeroelasticity, Vortex, Aerodynamic force, symbols.namesake, symbols, business, Freestream
Abstract

Membrane wings are common in flying animals such as bats, lemurs, flying squirrels, and pterosaurs, as well as in low Reynolds number Micro Air Vehicles. Vortices shed from the sharp leading and trailing edges and wingtips of membrane wings, and the vortex interactions with the membrane play an important role in the wing’s performance. With compliant membrane wings that are initially tension-free at rest, there are two issues to consider: (a) the static relationship between the net aerodynamic forces and the bulk wing deformation, and (b) the interaction between the membrane dynamics and unsteady flow structures. We present a simple model of the finite deformation and natural frequency of an initially tension-free membrane wing, which depends only on an aeroelastic parameter. We extend our theory with a computer model that accounts for nonuniform chordwise load. We conduct experiments on low aspect ratio membrane wings with different support structures and thicknesses, over a broad range of freestream velocities and angles of attack. We measure wing shape and dynamics, aerodynamic force, and the wake, and find good agreement between the experimental results, the computer model, and our theoretical model. Membrane deformation affects the membrane vibration modes, which in turn affects the coupling between the membrane and vortex shedding. Wings with different wingtip support, but similar stiffness show similar static behavior, but exhibit markedly different dynamic behavior.

Published
2013

36. Aerodynamic Characterization of Wing Membrane with Adaptive Compliance

Author

Oscar M. Curet, Kenny S. Breuer, Rye M. Waldman, and Alex Carrere

Subjects
Lift-to-drag ratio, animal structures, Wing, Materials science, business.industry, Camber (aerodynamics), Rigid frame, Stall (fluid mechanics), Structural engineering, Aerodynamics, business, Wind tunnel, Voltage
Abstract

Membrane wings with adaptive compliance have a great potential to improve the maneuverability and performance of micro air vehicles. Moreover, adaptive compliance might be used by flying animals with membrane wings such as bats, to control aerodynamic performance. In this work, we characterized the mechanical properties and aerodynamic performance of a low aspect ratio membrane wing with adaptive compliance. The membrane was made of dielectric material coated with compliant electrodes, and supported by a rigid frame. The compliance of the wing was controlled by applying a voltage across membrane. We tested the wing model in a wind tunnel. We found that when a fixed voltage is applied across the wing membrane the camber increases, accompanied by a small increase in lift. However, lift is significantly increased when the wing is forced with an oscillating field at specific frequencies. In addition, stall is delayed, and for a range of angle of attacks there is an increase in lift to drag ratio. Fluid dynamics measurements are needed to identify the source of lift enhancement and analyze the fluid-membrane interaction.

Published
2013

37. Measurement of streamwise vortices in low-speed flight

Author

Kenneth S. Breuer and Rye M. Waldman

Subjects
Engineering, business.industry, Reynolds number, Aerodynamics, Wake, Vortex, Aerodynamic force, symbols.namesake, Temporal resolution, symbols, Flapping, Measurement uncertainty, Aerospace engineering, business
Abstract

Low Reynolds number aerodynamic experiments with flapping animals (such as bats and small birds) are of particular interest due to their application to Micro Air Vehicles (MAVs) which operate in a similar parameter space. Previous PIV wake measurements described the structures left by bats and birds and provided insight to the time history of their aerodynamic force generation; however, these studies have faced difficulty drawing quantitative conclusions based on said measurements. The highly three-dimensional and unsteady nature of the flows associated with flapping flight are major challenges for accurate measurements. The challenge of animal flight measurements is finding small flow features in a large field of view at high speed with limited laser energy and camera resolution. Cross-stream measurement is further complicated by the predominately out-of-plane flow that requires thick laser sheets and short inter-frame times, which increase noise and measurement uncertainty. Choosing appropriate experimental parameters requires compromise between the spatial and temporal resolution and the dynamic range of the measurement. To explore these challenges, we do a case study on the wake of a fixed wing. The fixed model simplifies the experiment and allows direct measurements of the aerodynamic forces via load cell. We present a detailed analysis of the wake measurements, discuss the criteria for making accurate measurements, and present a solution for making quantitative aerodynamic load measurements behind free flyers.

Published
2012

40. Aerodynamic Behavior of Compliant Membranes as Related to Bat Flight

Author

Daniel K. Riskin, Rye M. Waldman, Kenneth S. Breuer, Sharon M. Swartz, and Arnold Song

Subjects
Airfoil, Physics, XFOIL, Wing, business.industry, Inviscid flow, Kutta condition, Potential flow, Aerodynamics, Mechanics, Aerospace engineering, business, Wind tunnel
Abstract

We present computations of membrane airfoil behavior subject to aerodynamic loading and compare them with in vivo measurements of membrane wings of bats during flight. The computational method assumes an inviscid potential flow (with net circulation determined by a Kutta condition), is computed using XFOIL and iteratively coupled with a finite element model describing the membrane behavior. We find that a simple model assuming uniform loading is largely confirmed, particularly for very compliant membranes in which the pressure loading is focused at the center of the airfoil. Stiffer wings transition to the more traditional pressure distribution predicted by thin airfoil theory for rigid wings. Comparisons with sail theories are also made, illustrating the effect of compliance. Additionally, the in vivo measurements of membrane deformation during bat flight are acquired from detailed kinematics recorded from Cynopterus brachyotis, flying in a wind tunnel. We demonstrate that the expansion of the wing area during the downstroke of the flight cycle exhibits area increases of up to 100% during the downstroke. In addition, comparisons with the computational theory show good qualitative agreement.

Published
2008

41. European sea bass - Dicentrarchus labrax

Author

Haffray, Pierrick, Tsigenopoulos, C.s., Bonhomme, Francois, Chatain, Beatrice, Magoulas, Antonio, Rye, M, Triantafyllidis, A, and Triantafyllidis, C

Published
2007

42. Gilthead seabream - Sparus aurata

Author

Sola, Luciana, Moretti, A, Crosetti, D, Karaiskou, N, Magoulas, A, Rossi, Anna Rita, Rye, M, Triantafyllidis, A, and Tsigenopoulos, C. S.

Published
2007

44. The aerodynamic cost of flight in the short-tailed fruit bat (Carollia perspicillata): comparing theory with measurement

Author

Rhea von Busse, Kenneth S. Breuer, Rye M. Waldman, Sharon M. Swartz, and Christian C. Voigt

Subjects
Plane (geometry), Acoustics, Biomedical Engineering, Biophysics, Bioengineering, Aerodynamics, Wake, Models, Biological, Biochemistry, Power (physics), Biomaterials, Particle image velocimetry, Chiroptera, Flight, Animal, Range (statistics), Animals, Environmental science, Research Articles, Simulation, Biotechnology, Interpolation, Wind tunnel
Abstract

Aerodynamic theory has long been used to predict the power required for animal flight, but widely used models contain many simplifications. It has been difficult to ascertain how closely biological reality matches model predictions, largely because of the technical challenges of accurately measuring the power expended when an animal flies. We designed a study to measure flight speed-dependent aerodynamic power directly from the kinetic energy contained in the wake of bats flying in a wind tunnel. We compared these measurements with two theoretical predictions that have been used for several decades in diverse fields of vertebrate biology and to metabolic measurements from a previous study using the same individuals. A high-accuracy displaced laser sheet stereo particle image velocimetry experimental design measured the wake velocities in the Trefftz plane behind four bats flying over a range of speeds (3–7 m s−1). We computed the aerodynamic power contained in the wake using a novel interpolation method and compared these results with the power predicted by Pennycuick's and Rayner's models. The measured aerodynamic power falls between the two theoretical predictions, demonstrating that the models effectively predict the appropriate range of flight power, but the models do not accurately predict minimum power or maximum range speeds. Mechanical efficiency—the ratio of aerodynamic power output to metabolic power input—varied from 5.9% to 9.8% for the same individuals, changing with flight speed.

Published
2014

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