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6. Standard methods for Apis mellifera venom research

Author

de Graaf, Dirk C., primary, Brochetto Braga, Márcia Regina, additional, de Abreu, Rusleyd Maria Magalhães, additional, Blank, Simon, additional, Bridts, Chris H., additional, De Clerck, Luc S., additional, Devreese, Bart, additional, Ebo, Didier G., additional, Ferris, Timothy J., additional, Hagendorens, Margo M., additional, Justo Jacomini, Débora Laís, additional, Kanchev, Iliya, additional, Kokot, Zenon J., additional, Matysiak, Jan, additional, Mertens, Christel, additional, Sabato, Vito, additional, Van Gasse, Athina L., additional, and Van Vaerenbergh, Matthias, additional

Published
2020
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7. Standard methods for Apis mellifera venom research.

Author

de Graaf, Dirk C., Brochetto Braga, Márcia Regina, de Abreu, Rusleyd Maria Magalhães, Blank, Simon, Bridts, Chris H., De Clerck, Luc S., Devreese, Bart, Ebo, Didier G., Ferris, Timothy J., Hagendorens, Margo M., Justo Jacomini, Débora Laís, Kanchev, Iliya, Kokot, Zenon J., Matysiak, Jan, Mertens, Christel, Sabato, Vito, Van Gasse, Athina L., and Van Vaerenbergh, Matthias

Abstract

Copyright of Journal of Apicultural Research is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2021
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8. Standard methods for Apis melliferavenom research

Author

de Graaf, Dirk C., Brochetto Braga, Márcia Regina, de Abreu, Rusleyd Maria Magalhães, Blank, Simon, Bridts, Chris H., De Clerck, Luc S., Devreese, Bart, Ebo, Didier G., Ferris, Timothy J., Hagendorens, Margo M., Justo Jacomini, Débora Laís, Kanchev, Iliya, Kokot, Zenon J., Matysiak, Jan, Mertens, Christel, Sabato, Vito, Van Gasse, Athina L., and Van Vaerenbergh, Matthias

Abstract

Honey bees have a sting which allows them to inject venomous substances into the body of an opponent or attacker. As the sting originates from a modified ovipositor, it only occurs in the female insect, and this is a defining feature of the bee species that belong to a subclade of the Hymenoptera called Aculeata. There is considerable interest in bee venom research, primarily because of an important subset of the human population who will develop a sometimes life threatening allergic response after a bee sting. However, the use of honey bee venom goes much further, with alleged healing properties in ancient therapies and recent research. The present paper aims to standardize selected methods for honey bee venom research. It covers different methods of venom collection, characterization and storage. Much attention was also addressed to the determination of the biological activity of the venom and its use in the context of biomedical research, more specifically venom allergy. Finally, the procedure for the assignment of new venom allergens has been presented. Métodos estándar para la investigación del veneno de Apis melliferaLas abejas melíferas tienen un aguijón que les permite inyectar sustancias venenosas en el cuerpo de un oponente o atacante. El aguijón es un ovipositor modificado que solo se manifiesta en el insecto hembra, siendo este una característica que define a las especies de abejas que pertenecen al subclado de himenópteros llamada Aculeata. Hay un interés considerable en la investigación del veneno de abeja, principalmente debido a que un porcentaje importante de la población humana desarrollará una respuesta alérgica - a veces mortal - a la picadura de abeja. Sin embargo, el uso del veneno de la abeja melífera abarca mucho más, con presuntas propiedades curativas en terapias antiguas e investigaciones recientes. El presente trabajo tiene como objetivo estandarizar métodos seleccionados para la investigación del veneno de las abejas melíferas. Cubre diferentes métodos de recolección, caracterización y almacenamiento de veneno. También se prestó mucha atención a la determinación de la actividad biológica del veneno y su uso en el contexto de la investigación biomédica, más específicamente la alergia al veneno. Finalmente, se ha presentado el procedimiento para la asignación de nuevos alérgenos de veneno.

Published
2021
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10. Finding the Missing Honey Bee Genes: Lessons Learned From a Genome Upgrade

Author

Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, HGSC production teams, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin FA, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Van Vaerenbergh, Matthias, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A

Subjects
Apis mellifera, GC content, Gene annotation, Gene prediction, Genome assembly, Genome improvement, Genome sequencing, Repetitive DNA, Transcriptome, fungi
Abstract

Background The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Published
2014

11. Honeybee (Apis mellifera) and bumblebee (Bombus terrestris) venom: analysis and immunological importance of the proteome

Author

Van Vaerenbergh, Matthias, de Graaf, Dirk, and Devreese, Bart

Subjects
proteomics, Biology and Life Sciences, allergens, venom allergy, complex mixtures, genome
Abstract

This PhD thesis consists of two main parts. The first part focused on further unraveling the venom composition of the honeybee (A. mellifera) and bumblebee (B. terrestris) by integrating genome, transcriptome and proteome information. Second, this work aimed to advance knowledge about the immunological implications of the venom proteome by investigating the allergenic properties of immunologically uncharacterized venom compounds and by analyzing the immunological relevance of allergen protein heterogeneity. In chapter 1, liquid chromatography-mass spectrometry was used to identify novel honeybee venom compounds, an approach which overcomes the issues of gel-based proteomics. In addition, we investigated if the antigen 5-like sequence, previously found by mining the honeybee genome, is expressed by the honeybee venom glands. Finally, we tried to confirm the presence of novel identified compounds and the antigen 5-like compound in the venom by analyzing their IgG4-reactivity using sera of immune beekeepers. In chapter 2 we explored the hidden honeybee venom proteome by integrating a combinatorial peptide ligand library venom pre-treatment with FTMS, while in chapter 3 the venom proteome of the European buff-tailed bumblebee, B. terrestris, was unraveled using an identical approach. Also genome information was used to obtain further insights in the venom composition of both species. In chapter 4 we investigated the nature of Api m 10 protein heterogeneity and explored its effect on IgE-reactivity using sera of honeybee venom allergic patients. In chapter 5, we evaluated the allergenic potential of the honeybee venom C1q-like and PVF1 proteins by analyzing IgE-reactivity and basophil activation.

Published
2013

12. The genomes of two key bumblebee species with primitive eusocial organization

Author

Sadd, Ben M., Barribeau, Seth M., Bloch, Guy, de Graaf, Dirk C., Dearden, Peter, Elsik, Christine G., Gadau, Jürgen, Grimmelikhuijzen, Cornelis J. P., Hasselmann, Martin, Lozier, Jeffrey D., Robertson, Hugh M., Smagghe, Guy, Stolle, Eckart, Van Vaerenbergh, Matthias, Waterhouse, Robert M., Bornberg-Bauer, Erich, Klasberg, Steffen, Bennett, Anna K., Câmara, Francisco, Guigó, Roderic, Hoff, Katharina, Mariotti, Marco, Munoz-Torres, Monica, Murphy, Terence, Santesmasses, Didac, Amdam, Gro V., Beckers, Matthew, Beye, Martin, Biewer, Matthias, Bitondi, Márcia M. G., Blaxter, Mark L., Bourke, Andrew F. G., Brown, Mark J. F., Buechel, Severine D., Cameron, Rossanah, Cappelle, Kaat, Carolan, James C., Christiaens, Olivier, Ciborowski, Kate L., Clarke, David F., Colgan, Thomas J., Collins, David H., Cridge, Andrew G., Dalmay, Tamas, Dreier, Stephanie, du Plessis, Louis, Duncan, Elizabeth, Erler, Silvio, Evans, Jay, Falcon, Tiago, Flores, Kevin, Freitas, Flávia C. P., Fuchikawa, Taro, Gempe, Tanja, Hartfelder, Klaus, Hauser, Frank, Helbing, Sophie, Humann, Fernanda C., Irvine, Frano, Jermiin, Lars S., Johnson, Claire E., Johnson, Reed M., Jones, Andrew K., Kadowaki, Tatsuhiko, Kidner, Jonathan H., Koch, Vasco, Köhler, Arian, Kraus, F. Bernhard, Lattorff, H. Michael G., Leask, Megan, Lockett, Gabrielle A., Mallon, Eamonn B., Antonio, David S. Marco, Marxer, Monika, Meeus, Ivan, Moritz, Robin F. A., Nair, Ajay, Näpflin, Kathrin, Nissen, Inga, Niu, Jinzhi, Nunes, Francis M. F., Oakeshott, John G., Osborne, Amy, Otte, Marianne, Pinheiro, Daniel G., Rossié, Nina, Rueppell, Olav, Santos, Carolina G., Schmid-Hempel, Regula, Schmitt, Björn D., Schulte, Christina, Simões, Zilá L. P., Soares, Michelle P. M., Swevers, Luc, Winnebeck, Eva C., Wolschin, Florian, Yu, Na, Zdobnov, Evgeny M., Aqrawi, Peshtewani K., Blankenburg, Kerstin P., Coyle, Marcus, Francisco, Liezl, Hernandez, Alvaro G., Holder, Michael, Hudson, Matthew E., Jackson, LaRonda, Jayaseelan, Joy, Joshi, Vandita, Kovar, Christie, Lee, Sandra L., Mata, Robert, Mathew, Tittu, Newsham, Irene F., Ngo, Robin, Okwuonu, Geoffrey, Pham, Christopher, Pu, Ling-Ling, Saada, Nehad, Santibanez, Jireh, Simmons, DeNard, Thornton, Rebecca, Venkat, Aarti, Walden, Kimberly Ko, Wu, Yuan-Qing, Debyser, Griet, Devreese, Bart, Asher, Claire, Blommaert, Julie, Chipman, Ariel D., Chittka, Lars, Fouks, Bertrand, Liu, Jisheng, O'Neill, Meaghan P., Sumner, Seirian, Puiu, Daniela, Qu, Jiaxin, Salzberg, Steven L., Scherer, Steven E., Muzny, Donna M., Richards, Stephen, Robinson, Gene E., Gibbs, Richard A., Schmid-Hempel, Paul, Worley, Kim C., Sadd, Ben M., Barribeau, Seth M., Bloch, Guy, de Graaf, Dirk C., Dearden, Peter, Elsik, Christine G., Gadau, Jürgen, Grimmelikhuijzen, Cornelis J. P., Hasselmann, Martin, Lozier, Jeffrey D., Robertson, Hugh M., Smagghe, Guy, Stolle, Eckart, Van Vaerenbergh, Matthias, Waterhouse, Robert M., Bornberg-Bauer, Erich, Klasberg, Steffen, Bennett, Anna K., Câmara, Francisco, Guigó, Roderic, Hoff, Katharina, Mariotti, Marco, Munoz-Torres, Monica, Murphy, Terence, Santesmasses, Didac, Amdam, Gro V., Beckers, Matthew, Beye, Martin, Biewer, Matthias, Bitondi, Márcia M. G., Blaxter, Mark L., Bourke, Andrew F. G., Brown, Mark J. F., Buechel, Severine D., Cameron, Rossanah, Cappelle, Kaat, Carolan, James C., Christiaens, Olivier, Ciborowski, Kate L., Clarke, David F., Colgan, Thomas J., Collins, David H., Cridge, Andrew G., Dalmay, Tamas, Dreier, Stephanie, du Plessis, Louis, Duncan, Elizabeth, Erler, Silvio, Evans, Jay, Falcon, Tiago, Flores, Kevin, Freitas, Flávia C. P., Fuchikawa, Taro, Gempe, Tanja, Hartfelder, Klaus, Hauser, Frank, Helbing, Sophie, Humann, Fernanda C., Irvine, Frano, Jermiin, Lars S., Johnson, Claire E., Johnson, Reed M., Jones, Andrew K., Kadowaki, Tatsuhiko, Kidner, Jonathan H., Koch, Vasco, Köhler, Arian, Kraus, F. Bernhard, Lattorff, H. Michael G., Leask, Megan, Lockett, Gabrielle A., Mallon, Eamonn B., Antonio, David S. Marco, Marxer, Monika, Meeus, Ivan, Moritz, Robin F. A., Nair, Ajay, Näpflin, Kathrin, Nissen, Inga, Niu, Jinzhi, Nunes, Francis M. F., Oakeshott, John G., Osborne, Amy, Otte, Marianne, Pinheiro, Daniel G., Rossié, Nina, Rueppell, Olav, Santos, Carolina G., Schmid-Hempel, Regula, Schmitt, Björn D., Schulte, Christina, Simões, Zilá L. P., Soares, Michelle P. M., Swevers, Luc, Winnebeck, Eva C., Wolschin, Florian, Yu, Na, Zdobnov, Evgeny M., Aqrawi, Peshtewani K., Blankenburg, Kerstin P., Coyle, Marcus, Francisco, Liezl, Hernandez, Alvaro G., Holder, Michael, Hudson, Matthew E., Jackson, LaRonda, Jayaseelan, Joy, Joshi, Vandita, Kovar, Christie, Lee, Sandra L., Mata, Robert, Mathew, Tittu, Newsham, Irene F., Ngo, Robin, Okwuonu, Geoffrey, Pham, Christopher, Pu, Ling-Ling, Saada, Nehad, Santibanez, Jireh, Simmons, DeNard, Thornton, Rebecca, Venkat, Aarti, Walden, Kimberly Ko, Wu, Yuan-Qing, Debyser, Griet, Devreese, Bart, Asher, Claire, Blommaert, Julie, Chipman, Ariel D., Chittka, Lars, Fouks, Bertrand, Liu, Jisheng, O'Neill, Meaghan P., Sumner, Seirian, Puiu, Daniela, Qu, Jiaxin, Salzberg, Steven L., Scherer, Steven E., Muzny, Donna M., Richards, Stephen, Robinson, Gene E., Gibbs, Richard A., Schmid-Hempel, Paul, and Worley, Kim C.

Abstract

BACKGROUND: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. RESULTS: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. CONCLUSIONS: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.

Published
2015
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14. The genomes of two key bumblebee species with primitive eusocial organization

Author

Sadd, Ben M, primary, Barribeau, Seth M, additional, Bloch, Guy, additional, de Graaf, Dirk C, additional, Dearden, Peter, additional, Elsik, Christine G, additional, Gadau, Jürgen, additional, Grimmelikhuijzen, Cornelis JP, additional, Hasselmann, Martin, additional, Lozier, Jeffrey D, additional, Robertson, Hugh M, additional, Smagghe, Guy, additional, Stolle, Eckart, additional, Van Vaerenbergh, Matthias, additional, Waterhouse, Robert M, additional, Bornberg-Bauer, Erich, additional, Klasberg, Steffen, additional, Bennett, Anna K, additional, Câmara, Francisco, additional, Guigó, Roderic, additional, Hoff, Katharina, additional, Mariotti, Marco, additional, Munoz-Torres, Monica, additional, Murphy, Terence, additional, Santesmasses, Didac, additional, Amdam, Gro V, additional, Beckers, Matthew, additional, Beye, Martin, additional, Biewer, Matthias, additional, Bitondi, Márcia MG, additional, Blaxter, Mark L, additional, Bourke, Andrew FG, additional, Brown, Mark JF, additional, Buechel, Severine D, additional, Cameron, Rossanah, additional, Cappelle, Kaat, additional, Carolan, James C, additional, Christiaens, Olivier, additional, Ciborowski, Kate L, additional, Clarke, David F, additional, Colgan, Thomas J, additional, Collins, David H, additional, Cridge, Andrew G, additional, Dalmay, Tamas, additional, Dreier, Stephanie, additional, du Plessis, Louis, additional, Duncan, Elizabeth, additional, Erler, Silvio, additional, Evans, Jay, additional, Falcon, Tiago, additional, Flores, Kevin, additional, Freitas, Flávia CP, additional, Fuchikawa, Taro, additional, Gempe, Tanja, additional, Hartfelder, Klaus, additional, Hauser, Frank, additional, Helbing, Sophie, additional, Humann, Fernanda C, additional, Irvine, Frano, additional, Jermiin, Lars S, additional, Johnson, Claire E, additional, Johnson, Reed M, additional, Jones, Andrew K, additional, Kadowaki, Tatsuhiko, additional, Kidner, Jonathan H, additional, Koch, Vasco, additional, Köhler, Arian, additional, Kraus, F Bernhard, additional, Lattorff, H Michael G, additional, Leask, Megan, additional, Lockett, Gabrielle A, additional, Mallon, Eamonn B, additional, Antonio, David S Marco, additional, Marxer, Monika, additional, Meeus, Ivan, additional, Moritz, Robin FA, additional, Nair, Ajay, additional, Näpflin, Kathrin, additional, Nissen, Inga, additional, Niu, Jinzhi, additional, Nunes, Francis MF, additional, Oakeshott, John G, additional, Osborne, Amy, additional, Otte, Marianne, additional, Pinheiro, Daniel G, additional, Rossié, Nina, additional, Rueppell, Olav, additional, Santos, Carolina G, additional, Schmid-Hempel, Regula, additional, Schmitt, Björn D, additional, Schulte, Christina, additional, Simões, Zilá LP, additional, Soares, Michelle PM, additional, Swevers, Luc, additional, Winnebeck, Eva C, additional, Wolschin, Florian, additional, Yu, Na, additional, Zdobnov, Evgeny M, additional, Aqrawi, Peshtewani K, additional, Blankenburg, Kerstin P, additional, Coyle, Marcus, additional, Francisco, Liezl, additional, Hernandez, Alvaro G, additional, Holder, Michael, additional, Hudson, Matthew E, additional, Jackson, LaRonda, additional, Jayaseelan, Joy, additional, Joshi, Vandita, additional, Kovar, Christie, additional, Lee, Sandra L, additional, Mata, Robert, additional, Mathew, Tittu, additional, Newsham, Irene F, additional, Ngo, Robin, additional, Okwuonu, Geoffrey, additional, Pham, Christopher, additional, Pu, Ling-Ling, additional, Saada, Nehad, additional, Santibanez, Jireh, additional, Simmons, DeNard, additional, Thornton, Rebecca, additional, Venkat, Aarti, additional, Walden, Kimberly KO, additional, Wu, Yuan-Qing, additional, Debyser, Griet, additional, Devreese, Bart, additional, Asher, Claire, additional, Blommaert, Julie, additional, Chipman, Ariel D, additional, Chittka, Lars, additional, Fouks, Bertrand, additional, Liu, Jisheng, additional, O’Neill, Meaghan P, additional, Sumner, Seirian, additional, Puiu, Daniela, additional, Qu, Jiaxin, additional, Salzberg, Steven L, additional, Scherer, Steven E, additional, Muzny, Donna M, additional, Richards, Stephen, additional, Robinson, Gene E, additional, Gibbs, Richard A, additional, Schmid-Hempel, Paul, additional, and Worley, Kim C, additional

Published
2015
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17. In vitro diagnosis of Hymenoptera venom allergy and further development of component resolved diagnostics.

Author

Ebo, Didier G, Van Vaerenbergh, Matthias, de Graaf, Dirk C, Bridts, Chris H, De Clerck, Luc S, and Sabato, Vito

Subjects
HYMENOPTERA, VENOM, ALLERGIES, IMMUNOTHERAPY, IMMUNOGLOBULINS, IMMUNOGLOBULIN E, SKIN tests, PROTEOMICS
Abstract

For most people Hymenoptera stings result in transient and bothersome local inflammatory responses characterized by pain, itching, redness and swelling. In contrast, for those presenting an IgE-mediated allergic reaction, a re-sting may cause life-threatening reactions. In such patients, correct diagnosis is an absolute prerequisite for effective management, i.e. venom-specific immunotherapy. Generally, identification of the offending insect involves a detailed history along with quantification of venom-specific IgE antibodies and venom skin tests. Unfortunately, due to uncertainties associated with both tests, correct diagnosis is not always straightforward. This review summarizes the potentials and limitations of the various in vitro tests that are currently being used in the diagnosis of Hymenoptera venom allergy. Particular attention is paid to the potential of novel cellular tests such as basophil activation tests and component-resolved diagnosis with recombinant venom allergens in the diagnostic approach of patients with difficult diagnosis, i.e. cases in whom traditional venom specific IgE and skin tests yield equivocal or negative results. Finally, this review also covers the recent discoveries in the field of proteome research of Hymenoptera venoms and the selection of cell types for recombinant allergens production. [ABSTRACT FROM AUTHOR]

Published
2014
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