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1. A pragmatic approach for integrating molecular tools into biodiversity conservation

Author

Laura D. Bertola, Anna Brüniche‐Olsen, Francine Kershaw, Isa‐Rita M. Russo, Anna J. MacDonald, Paul Sunnucks, Michael W. Bruford, Carlos Daniel Cadena, Kyle M. Ewart, Mark deBruyn, Mark D. B. Eldridge, Richard Frankham, Juan M. Guayasamin, Catherine E. Grueber, Thierry B. Hoareau, Sean Hoban, Paul A. Hohenlohe, Margaret E. Hunter, Antoinette Kotze, Josiah Kuja, Robert C. Lacy, Linda Laikre, Nathan Lo, Mariah H. Meek, Joachim Mergeay, Cinnamon Mittan‐Moreau, Linda E. Neaves, David O'Brien, Joel W. Ochieng, Rob Ogden, Pablo Orozco‐terWengel, Mónica Páez‐Vacas, Jennifer Pierson, Katherine Ralls, Robyn E. Shaw, Etotépé A. Sogbohossou, Adam Stow, Tammy Steeves, Cristiano Vernesi, Mrinalini Watsa, and Gernot Segelbacher

Subjects
conservation, management, molecular tools, Ecology, QH540-549.5, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Abstract Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation.

Published
2024
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3. DNA methylation episignature and comparative epigenomic profiling of HNRNPU-related neurodevelopmental disorder

Author

Rooney, Kathleen, van der Laan, Liselot, Trajkova, Slavica, Haghshenas, Sadegheh, Relator, Raissa, Lauffer, Peter, Vos, Niels, Levy, Michael A., Brunetti-Pierri, Nicola, Terrone, Gaetano, Mignot, Cyril, Keren, Boris, de Villemeur, Thierry B., Volker-Touw, Catharina M.L., Verbeek, Nienke, van der Smagt, Jasper J., Oegema, Renske, Brusco, Alfredo, Ferrero, Giovanni B., Misra-Isrie, Mala, Hochstenbach, Ron, Alders, Mariëlle, Mannens, Marcel M.A.M., Sadikovic, Bekim, van Haelst, Mieke M., and Henneman, Peter

Published
2023
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16. A pragmatic approach for integrating molecular tools into biodiversity conservation

Author

Bertola, Laura D., primary, Brüniche‐Olsen, Anna, additional, Kershaw, Francine, additional, Russo, Isa‐Rita M., additional, MacDonald, Anna J., additional, Sunnucks, Paul, additional, Bruford, Michael W., additional, Cadena, Carlos Daniel, additional, Ewart, Kyle M., additional, de Bruyn, Mark, additional, Eldridge, Mark D. B., additional, Frankham, Richard, additional, Guayasamin, Juan M., additional, Grueber, Catherine E., additional, Hoareau, Thierry B., additional, Hoban, Sean, additional, Hohenlohe, Paul A., additional, Hunter, Margaret E., additional, Kotze, Antoinette, additional, Kuja, Josiah, additional, Lacy, Robert C., additional, Laikre, Linda, additional, Lo, Nathan, additional, Meek, Mariah H., additional, Mergeay, Joachim, additional, Mittan‐Moreau, Cinnamon, additional, Neaves, Linda E., additional, O'Brien, David, additional, Ochieng, Joel W., additional, Ogden, Rob, additional, Orozco‐terWengel, Pablo, additional, Páez‐Vacas, Mónica, additional, Pierson, Jennifer, additional, Ralls, Katherine, additional, Shaw, Robyn E., additional, Sogbohossou, Etotépé A., additional, Stow, Adam, additional, Steeves, Tammy, additional, Vernesi, Cristiano, additional, Watsa, Mrinalini, additional, and Segelbacher, Gernot, additional

Published
2023
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20. A pragmatic approach for integrating molecular tools into biodiversity conservation.

Author

Bertola, Laura D., Brüniche‐Olsen, Anna, Kershaw, Francine, Russo, Isa‐Rita M., MacDonald, Anna J., Sunnucks, Paul, Bruford, Michael W., Cadena, Carlos Daniel, Ewart, Kyle M., de Bruyn, Mark, Eldridge, Mark D. B., Frankham, Richard, Guayasamin, Juan M., Grueber, Catherine E., Hoareau, Thierry B., Hoban, Sean, Hohenlohe, Paul A., Hunter, Margaret E., Kotze, Antoinette, and Kuja, Josiah

Subjects
BIODIVERSITY conservation, BIODIVERSITY monitoring, MICROSATELLITE repeats, SENSITIVITY analysis, DECISION making
Abstract

Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation. [ABSTRACT FROM AUTHOR]

Published
2024
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23. DNA methylation episignature and comparative epigenomic profiling of HNRNPU-related neurodevelopmental disorder

Author

Kathleen Rooney, Liselot van der Laan, Slavica Trajkova, Sadegheh Haghshenas, Raissa Relator, Peter Lauffer, Niels Vos, Michael A. Levy, Nicola Brunetti-Pierri, Gaetano Terrone, Cyril Mignot, Boris Keren, Thierry B. de Villemeur, Catharina M.L. Volker-Touw, Nienke Verbeek, Jasper J. van der Smagt, Renske Oegema, Alfredo Brusco, Giovanni B. Ferrero, Mala Misra-Isrie, Ron Hochstenbach, Mariëlle Alders, Marcel M.A.M. Mannens, Bekim Sadikovic, Mieke M. van Haelst, Peter Henneman, Human genetics, Amsterdam Reproduction & Development (AR&D), Amsterdam Neuroscience - Complex Trait Genetics, Rooney, Kathleen, van der Laan, Liselot, Trajkova, Slavica, Haghshenas, Sadegheh, Relator, Raissa, Lauffer, Peter, Vos, Niel, Levy, Michael A, Brunetti-Pierri, Nicola, Terrone, Gaetano, Mignot, Cyril, Keren, Bori, Billette de Villemeur, Thierry, Volker-Touw, Catharina M L, Verbeek, Nienke, van der Smagt, Jasper J, Oegema, Renske, Brusco, Alfredo, Ferrero, Giovanni Battista, Misra-Isrie, Mala, Hochstenbach, Ron, Alders, Mariëlle, Mannens, Marcel M A M, Sadikovic, Bekim, van Haelst, Mieke M, and Henneman, Peter

Subjects
DNA methylation, Epilepsy, HNRNPU, Neurodevelopmental Disorder, CNV, Intellectual disability, Epigenetic, Epigenetics, Episignature, Genetics (clinical)
Abstract

Purpose: HNRNPU haploinsufficiency is associated with Developmental and Epileptic Encephalopathy 54. This neurodevelopmental disorder is characterized by developmental delay, intellectual disability, speech impairment, and early onset epilepsy. We performed genome-wide DNA methylation (DNAm) analysis in a cohort of individuals to develop a diagnostic biomarker and gain functional insights into the molecular pathophysiology of HNRNPU-related disorder. Methods: DNAm profiles of individuals carrying pathogenic HNRNPU variants, identified through an international multi-center collaboration, were assessed using Infinium Methylation EPIC arrays. Statistical and functional correlation analyses were performed comparing the HNRNPU cohort to 56 previously reported DNAm episignatures. Results: A robust and reproducible DNAm episignature and global DNAm profile were identified. Correlation analysis identified partial overlap and similarity of the global HNRNPU DNAm profile to several other rare disorders. Conclusion: This study demonstrates new evidence of a specific and sensitive DNAm episignature associated with pathogenic heterozygous HNRNPU-variants, establishing its utility as a clinical biomarker for the expansion of the EpiSignTM diagnostic test.

Published
2023

42. Reconstructing early routes of invasion of the bronze bug Thaumastocoris peregrinus (Hemiptera: Thaumastocoridae): cities as bridgeheads for global pest invasions

Author

Bernard Slippers, Jeffrey R. Garnas, Michael J. Wingfield, Eston K. Mutitu, Brett Phillip Hurley, and Thierry B. Hoareau

Subjects
0106 biological sciences, Genetic diversity, Ecology, Thaumastocoris peregrinus, Range (biology), 010604 marine biology & hydrobiology, Outbreak, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Eucalyptus, Hemiptera, Peregrinus, PEST analysis, Ecology, Evolution, Behavior and Systematics
Abstract

Insect pest invasions pose a major threat to agriculture, forestry and many natural ecosystems. Thaumastocoris peregrinus is an invasive sap-sucking pest of significant economic importance to Eucalyptus forestry that has recently invaded several countries worldwide. In this study we identify the origin and retrace the invasion history of T. peregrinus. We analysed samples from six locations in Africa, South America and Australia using microsatellites markers and a combination of clustering methods and scenario testing using Approximate Bayesian Clustering. We detected clear genetic substructure differentiating African and South American samples, with representatives of both present in Australia. The Australian population from New South Wales showed substantially higher genetic diversity than the Queensland source, which could indicate that this region could be part of the core range and evolutionary origin of the species. Africa and South America were colonised by independent introductions that occurred more or less concurrently. The study illustrates the impact of the bridgehead effect on global invasions following an outbreak or ‘invasion’ within a city in the native range of the insect.

Published
2020

43. Inertial Microfluidic Purification of CAR-T-Cell Products

Author

Elsemary, MT, Maritz, MF, Smith, LE, Warkiani, M, Bandara, V, Napoli, S, Barry, SC, Coombs, JT, and Thierry, B

Subjects
Receptors, Chimeric Antigen, Microfluidics, Cell- and Tissue-Based Therapy, Humans, Lymphocyte Count, Immunotherapy, Adoptive
Abstract

Chimeric antigen receptor T (CAR-T) cell therapy is rapidly becoming a frontline cancer therapy. However, the manufacturing process is time-, labor- and cost-intensive, and it suffers from significant bottlenecks. Many CAR-T products fail to reach the viability release criteria set by regulators for commercial cell therapy products. This results in non-recoupable costs for the manufacturer and is detrimental to patients who may not receive their scheduled treatment or receive out-of-specification suboptimal formulation. It is demonstrated here that inertial microfluidics can, within minutes, efficiently deplete nonviable cells from low-viability CAR-T cell products. The percentage of viable cells increases from 40% (SD ± 0.12) to 71% (SD ± 0.09) for untransduced T cells and from 51% (SD ± 0.12) to 71% (SD ± 0.09) for CAR-T cells, which meets the clinical trials' release parameters. In addition, the processing of CAR-T cells formulated in CryStor yields a 91% reduction in the amount of the cryoprotectant dimethyl sulfoxide. Inertial microfluidic processing has no detrimental effects on the proliferation and cytotoxicity of CAR-T cells. Interestingly, ≈50% of T-regulatory and T-suppressor cells are depleted, suggesting the potential for inertial microfluidic processing to tune the phenotypical composition of T-cell products.

Published
2021

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