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Barman M, Tenhaken R, Dötterl S. Negative and sex-specific effects of drought on flower production, resources and pollinator visitation, but not on floral scent in monoecious Cucurbita pepo. THE NEW PHYTOLOGIST 2024; 244:1013-1023. [PMID: 39117354 DOI: 10.1111/nph.20016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/10/2024] [Indexed: 08/10/2024]
Abstract
The globally changing climatic condition is increasing the incidences of drought in several parts of the world. This is predicted and already shown to not only impact plant growth and flower development, but also plant-pollinator interactions and the pollination success of entomophilous plants. However, there is a large gap in our understanding of how drought affects the different flowers and pollen transfer among flowers in sexually polymorphic species. Here, we evaluated in monoecious Styrian oil pumpkin, and separately for female and male flowers, the responses of drought stress on flower production, petal size, nectar, floral scent and visitation by bumblebee pollinators. Drought stress adversely affected all floral traits studied, except floral scent. Although both flower sexes were adversely affected by drought stress, the effects were more severe on female flowers, with most of the female flowers even aborted before opening. The drought had negative effects on floral visitation by the pollinators, which generally preferred female flowers. Overall, our study highlights that the two flower sexes of a monoecious plant species are differently affected by drought stress and calls for further investigations to better understand the cues used by the pollinators to discriminate against male flowers and against flowers of drought-stressed plants.
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Affiliation(s)
- Monica Barman
- Department of Environment and Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, Salzburg, 5020, Austria
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany
| | - Raimund Tenhaken
- Department of Environment and Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, Salzburg, 5020, Austria
| | - Stefan Dötterl
- Department of Environment and Biodiversity, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, Salzburg, 5020, Austria
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102
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Romeijn L, Bernatavicius A, Vu D. MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences. Mol Ecol Resour 2024; 24:e14006. [PMID: 39152642 DOI: 10.1111/1755-0998.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/12/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
Efficient and accurate classification of DNA barcode data is crucial for large-scale fungal biodiversity studies. However, existing methods are either computationally expensive or lack accuracy. Previous research has demonstrated the potential of deep learning in this domain, successfully training neural networks for biological sequence classification. We introduce the MycoAI Python package, featuring various deep learning models such as BERT and CNN tailored for fungal Internal Transcribed Spacer (ITS) sequences. We explore different neural architecture designs and encoding methods to identify optimal models. By employing a multi-head output architecture and multi-level hierarchical label smoothing, MycoAI effectively generalizes across the taxonomic hierarchy. Using over 5 million labelled sequences from the UNITE database, we develop two models: MycoAI-BERT and MycoAI-CNN. While we emphasize the necessity of verifying classification results by AI models due to insufficient reference data, MycoAI still exhibits substantial potential. When benchmarked against existing classifiers such as DNABarcoder and RDP on two independent test sets with labels present in the training dataset, MycoAI models demonstrate high accuracy at the genus and higher taxonomic levels, with MycoAI-CNN being the fastest and most accurate. In terms of efficiency, MycoAI models can classify over 300,000 sequences within 5 min. We publicly release the MycoAI models, enabling mycologists to classify their ITS barcode data efficiently. Additionally, MycoAI serves as a platform for developing further deep learning-based classification methods. The source code for MycoAI is available under the MIT Licence at https://github.com/MycoAI/MycoAI.
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Affiliation(s)
- Luuk Romeijn
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, Netherlands
| | - Andrius Bernatavicius
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, Netherlands
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Duong Vu
- Westerdijk Fungal Biodiveristy Institute, Utrecht, Netherlands
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103
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Morel VJ, Rössler J, Bernasconi M. Targeted immunotherapy and nanomedicine for rhabdomyosarcoma: The way of the future. Med Res Rev 2024; 44:2730-2773. [PMID: 38885148 DOI: 10.1002/med.22059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 04/17/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024]
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. Histology separates two main subtypes: embryonal RMS (eRMS; 60%-70%) and alveolar RMS (aRMS; 20%-30%). The aggressive aRMS carry one of two characteristic chromosomal translocations that result in the expression of a PAX3::FOXO1 or PAX7::FOXO1 fusion transcription factor; therefore, aRMS are now classified as fusion-positive (FP) RMS. Embryonal RMS have a better prognosis and are clinically indistinguishable from fusion-negative (FN) RMS. Next to histology and molecular characteristics, RMS risk groupings are now available defining low risk tumors with excellent outcomes and advanced stage disease with poor prognosis, with an overall survival of about only 20% despite intensified multimodal treatment. Therefore, development of novel effective targeted strategies to increase survival and to decrease long-term side effects is urgently needed. Recently, immunotherapies and nanomedicine have been emerging for potent and effective tumor treatments with minimal side effects, raising hopes for effective and safe cures for RMS patients. This review aims to describe the most relevant preclinical and clinical studies in immunotherapy and targeted nanomedicine performed so far in RMS and to provide an insight in future developments.
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Affiliation(s)
- Victoria Judith Morel
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Jochen Rössler
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michele Bernasconi
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
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104
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Nimbeshaho F, Nihorimbere G, Arias AA, Liénard C, Steels S, Nibasumba A, Nihorimbere V, Legrève A, Ongena M. Unravelling the secondary metabolome and biocontrol potential of the recently described species Bacillus nakamurai. Microbiol Res 2024; 288:127841. [PMID: 39153465 DOI: 10.1016/j.micres.2024.127841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/02/2024] [Accepted: 07/14/2024] [Indexed: 08/19/2024]
Abstract
In the prospect of novel potential biocontrol agents, a new strain BDI-IS1 belonging to the recently described Bacillus nakamurai was selected for its strong in vitro antimicrobial activities against a range of bacterial and fungal phytopathogens. Genome mining coupled with metabolomics revealed that BDI-IS1 produces multiple non-ribosomal secondary metabolites including surfactin, iturin A, bacillaene, bacillibactin and bacilysin, together with some some ribosomally-synthesized and post-translationally modified peptides (RiPPs) such as plantazolicin, and potentially amylocyclicin, bacinapeptin and LCI. Reverse genetics further showed the specific involvement of some of these compounds in the antagonistic activity of the strain. Comparative genomics between the five already sequenced B. nakamurai strains showed that non-ribosomal products constitute the core metabolome of the species while RiPPs are more strain-specific. Although the secondary metabolome lacks some key bioactive metabolites found in B. velezensis, greenhouse experiments show that B. nakamurai BDI-IS1 is able to protect tomato and maize plants against early blight and northern leaf blight caused by Alternaria solani and Exserohilum turcicum, respectively, at levels similar to or better than B. velezensis QST713. The reduction of these foliar diseases, following root or leaf application of the bacterial suspension demonstrates that BDI-IS1 can act by direct antibiosis and by inducing plant defence mechanisms. These findings indicate that B. nakamurai BDI-IS1 can be considered as a good candidate for biocontrol of plant diseases prevailing in tropical regions, and encourage further research into its spectrum of activity, its requirements and the conditions needed to ensure its efficacy.
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Affiliation(s)
- François Nimbeshaho
- Microbial Processes and Interactions (MiPI), Teaching and Research Centre (TERRA), Gembloux Agro-BioTech, University of Liège, Avenue de la Faculté 2B, Gembloux 5030, Belgium; Laboratoire de Nutrition-Phytochimie, d'Ecologie et d'Environnement Appliquée, Centre Universitaire de Recherche et de Pédagogie Appliquées aux Sciences, Institut de Pédagogie Appliquée, Université du Burundi, Avenue de l'Unesco 2, P.O Box 1550, Bujumbura, Burundi.
| | - Gaspard Nihorimbere
- Earth and Life Institute-Applied Microbiology, Université Catholique de Louvain, Croix du Sud 2, Louvain-la-Neuve 1348, Belgium; Research department, Institut des Sciences Agronomiques du Burundi (ISABU), Boulevard du Japon, Rohero 1, P.O Box 795, Bujumbura, Burundi.
| | - Anthony Argüelles Arias
- Microbial Processes and Interactions (MiPI), Teaching and Research Centre (TERRA), Gembloux Agro-BioTech, University of Liège, Avenue de la Faculté 2B, Gembloux 5030, Belgium.
| | - Charlotte Liénard
- Earth and Life Institute-Applied Microbiology, Université Catholique de Louvain, Croix du Sud 2, Louvain-la-Neuve 1348, Belgium.
| | - Sébastien Steels
- Microbial Processes and Interactions (MiPI), Teaching and Research Centre (TERRA), Gembloux Agro-BioTech, University of Liège, Avenue de la Faculté 2B, Gembloux 5030, Belgium.
| | - Anaclet Nibasumba
- Institut Supérieur de Formation Agricole, Université du Burundi, P.O Box 241, Gitega, Burundi.
| | - Venant Nihorimbere
- Laboratoire de Microbiologie, Faculté d'Agronomie et de BioIngéniérie (FABI), Université du Burundi, Avenue de l'Unesco 2, P.O Box 2940, Bujumbura, Burundi.
| | - Anne Legrève
- Earth and Life Institute-Applied Microbiology, Université Catholique de Louvain, Croix du Sud 2, Louvain-la-Neuve 1348, Belgium.
| | - Marc Ongena
- Microbial Processes and Interactions (MiPI), Teaching and Research Centre (TERRA), Gembloux Agro-BioTech, University of Liège, Avenue de la Faculté 2B, Gembloux 5030, Belgium.
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105
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de Amaral M, Von Dentz MC, Cubas GK, de Oliveira DR, Simões LAR, Model JFA, Oliveira GT, Kucharski LC. Coping with dry spells: Investigating oxidative balance and metabolic responses in the subtropical tree frog Boana pulchella (Hylidae) during dehydration and rehydration exposure. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111728. [PMID: 39147093 DOI: 10.1016/j.cbpa.2024.111728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 08/11/2024] [Accepted: 08/11/2024] [Indexed: 08/17/2024]
Abstract
In the face of climate change, understanding the metabolic responses of vulnerable animals to abiotic stressors like anurans is crucial. Water restriction and subsequent dehydration is a condition that can threaten populations and lead to species decline. This study examines metabolic variations in the subtropical frog Boana pulchella exposed to dehydration resulting in a 40% loss of body water followed by 24 h of rehydration. During dehydration, the scaled mass index decreases, and concentrations of metabolic substrates alter in the brain and liver. The activity of antioxidant enzymes increases in the muscle and heart, emphasizing the importance of catalase in the rehydration period. Glycogenesis increases in the muscle and liver, indicating a strategy to preserve tissue water through glycogen storage. These findings suggest that B. pulchella employs specific metabolic mechanisms to survive exposure to water restriction, highlighting tissue-specific variations in metabolic pathways and antioxidant defenses. These findings contribute to a deeper understanding of anuran adaptation to water stress and emphasize the importance of further research in other species to complement existing knowledge and provide physiological tools to conservation.
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Affiliation(s)
- Marjoriane de Amaral
- Laboratory of Metabolism and Comparative Endocrinology, Department of Physiology, Federal University of Rio Grande do Sul, 2600 Ramiro Barcelos Street, 90035003 Porto Alegre, Rio Grande do Sul, Brazil.
| | - Maiza Cristina Von Dentz
- Laboratory of Metabolism and Comparative Endocrinology, Department of Physiology, Federal University of Rio Grande do Sul, 2600 Ramiro Barcelos Street, 90035003 Porto Alegre, Rio Grande do Sul, Brazil
| | - Gustavo Kasper Cubas
- Laboratory of Metabolism and Comparative Endocrinology, Department of Physiology, Federal University of Rio Grande do Sul, 2600 Ramiro Barcelos Street, 90035003 Porto Alegre, Rio Grande do Sul, Brazil
| | - Diogo Reis de Oliveira
- Conservation Physiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, 6681 Ipiranga Avenue, 90619900, Rio Grande do Sul, Brazil
| | - Leonardo Airton Ressel Simões
- Laboratory of Metabolism and Comparative Endocrinology, Department of Physiology, Federal University of Rio Grande do Sul, 2600 Ramiro Barcelos Street, 90035003 Porto Alegre, Rio Grande do Sul, Brazil
| | - Jorge Felipe Argenta Model
- Laboratory of Metabolism and Comparative Endocrinology, Department of Physiology, Federal University of Rio Grande do Sul, 2600 Ramiro Barcelos Street, 90035003 Porto Alegre, Rio Grande do Sul, Brazil
| | - Guendalina Turcato Oliveira
- Conservation Physiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, 6681 Ipiranga Avenue, 90619900, Rio Grande do Sul, Brazil
| | - Luiz Carlos Kucharski
- Laboratory of Metabolism and Comparative Endocrinology, Department of Physiology, Federal University of Rio Grande do Sul, 2600 Ramiro Barcelos Street, 90035003 Porto Alegre, Rio Grande do Sul, Brazil
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106
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Amaral-Silva L, Santin J. Neural Processing without O 2 and Glucose Delivery: Lessons from the Pond to the Clinic. Physiology (Bethesda) 2024; 39:0. [PMID: 38624246 DOI: 10.1152/physiol.00030.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024] Open
Abstract
Neuronal activity requires a large amount of ATP, leading to a rapid collapse of brain function when aerobic respiration fails. Here, we summarize how rhythmic motor circuits in the brain stem of adult frogs, which normally have high metabolic demands, transform to produce proper output during severe hypoxia associated with emergence from hibernation. We suggest that general principles underlying plasticity in brain bioenergetics may be uncovered by studying nonmammalian models that face extreme environments, yielding new insights to combat neurological disorders involving dysfunctional energy metabolism.
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Affiliation(s)
- Lara Amaral-Silva
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States
- Division of Biology, University of Missouri, Columbia, Missouri, United States
| | - Joseph Santin
- Division of Biology, University of Missouri, Columbia, Missouri, United States
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107
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Savoca PW, Glynn LM, Fox MM, Richards MC, Callaghan BL. Interoception in pregnancy: Implications for peripartum depression. Neurosci Biobehav Rev 2024; 166:105874. [PMID: 39243875 DOI: 10.1016/j.neubiorev.2024.105874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/12/2024] [Accepted: 09/02/2024] [Indexed: 09/09/2024]
Affiliation(s)
- Paul W Savoca
- Department of Psychology, University of California, Los Angeles, USA.
| | | | - Molly M Fox
- Department of Anthropology, University of California, Los Angeles, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, USA
| | - Misty C Richards
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, USA; David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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108
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Ruiz Miñano M, Uller T, Pettersen AK, Nord A, Fitzpatrick LJ, While GM. Sexual color ornamentation, microhabitat choice, and thermal physiology in the common wall lizard (Podarcis muralis). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:1041-1052. [PMID: 39101273 DOI: 10.1002/jez.2859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 08/06/2024]
Abstract
Common wall lizards (Podarcis muralis) in Italy show a striking variation in body coloration across the landscape, with highly exaggerated black and green colors in hot and dry climates and brown and white colors in cool and wet climates. Males are more intensely colored than females, and previous work has suggested that the maintenance of variation in coloration across the landscape reflects climatic effects on the strength of male-male competition, and through this sexual selection. However climatic effects on the intensity of male-male competition would need to be exceptionally strong to fully explain the geographic patterns of color variation. Thus, additional processes may contribute to the maintenance of color variation. Here we test the hypothesis that selection for green and black ornamentation in the context of male-male competition is opposed by selection against ornamentation because the genes involved in the regulation of coloration have pleiotropic effects on thermal physiology, such that ornamentation is selected against in cool climates. Field observations revealed no association between body coloration and microhabitat use or field active body temperatures. Consistent with these field data, lizards at the extreme ends of the phenotypic distribution for body coloration did not show any differences in critical minimum temperature, preferred body temperature, temperature-dependent metabolic rate, or evaporative water loss when tested in the laboratory. Combined, these results provide no evidence that genes that underlie sexual ornamentation are selected against in cool climate because of pleiotropic effects on thermal biology.
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Affiliation(s)
- Maravillas Ruiz Miñano
- Discipline of Biological Sciences, University of Tasmania, Hobart, Australia
- Department of Biology, Lund University, Lund, Sweden
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
| | - Amanda K Pettersen
- Department of Biology, Lund University, Lund, Sweden
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Andreas Nord
- Department of Biology, Lund University, Lund, Sweden
| | - Luisa J Fitzpatrick
- Discipline of Biological Sciences, University of Tasmania, Hobart, Australia
| | - Geoffrey M While
- Discipline of Biological Sciences, University of Tasmania, Hobart, Australia
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109
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Haubrock PJ, Kurtul I, Macêdo RL, Mammola S, Franco ACS, Soto I. Competency in invasion science: addressing stagnation challenges by promoting innovation and creative thinking. ENVIRONMENTAL MANAGEMENT 2024; 74:916-927. [PMID: 39235460 PMCID: PMC11438655 DOI: 10.1007/s00267-024-02035-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/16/2024] [Indexed: 09/06/2024]
Abstract
In today's ever-evolving scientific landscape, invasion science faces a plethora of challenges, such as terminological inconsistency and the rapidly growing literature corpus with few or incomplete syntheses of knowledge, which may be perceived as a stagnation in scientific progress. We explore the concept of 'competency', which is extensively debated across disciplines such as psychology, philosophy, and linguistics. Traditionally, it is associated with attributes that enable superior performance and continuous ingenuity. We propose that the concept of competency can be applied to invasion science as the ability to creatively and critically engage with global challenges. For example, competency may help develop innovative strategies for understanding and managing the multifaceted, unprecedented challenges posed by the spread and impacts of non-native species, as well as identifying novel avenues of inquiry for management. Despite notable advancements and the exponential increase in scholarly publications, invasion science still encounters obstacles such as insufficient interdisciplinary collaboration paralleled by a lack of groundbreaking or actionable scientific advancements. To enhance competency in invasion science, a paradigm shift is needed. This shift entails fostering interdisciplinary collaboration, nurturing creative and critical thinking, and establishing a stable and supportive environment for early career researchers, thereby promoting the emergence of competency and innovation. Embracing perspectives from practitioners and decision makers, alongside diverse disciplines beyond traditional ecological frameworks, can further add novel insights and innovative methodologies into invasion science. Invasion science must also address the ethical implications of its practices and engage the public in awareness and education programs. Such initiatives can encourage a more holistic understanding of invasions, attracting and cultivating competent minds capable of thinking beyond conventional paradigms and contributing to the advancement of the field in a rapidly changing world.
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Affiliation(s)
- Phillip J Haubrock
- Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum, Frankfurt, Gelnhausen, Germany.
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic.
- CAMB, Center for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Al-Abdullah, Kuwait.
| | - Irmak Kurtul
- Marine and Inland Waters Sciences and Technology Department, Faculty of Fisheries, Ege University, İzmir, Türkiye
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, Dorset, UK
| | - Rafael L Macêdo
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195, Berlin, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587, Berlin, Germany
- Graduate Program in Ecology and Natural Resources, Department of Ecology and Evolutionary Biology, Federal University of São Carlos, UFSCar, São Carlos, Brazil
| | - Stefano Mammola
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council (CNR), Corso Tonolli, 50, Verbania, 28922, Italy
- Finnish Museum of Natural History (LUOMUS), University of Helsinki, Pohjoinen Rautatiekatu 13, Helsinki, 00100, Finland
- NBFC, National Biodiversity Future Center, Palermo, 90133, Italy
| | - Ana Clara S Franco
- Institute of Aquatic Ecology, University of Girona, 17003, Girona, Catalonia, Spain
| | - Ismael Soto
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
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110
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Salis R, Sunde J, Gubonin N, Franzén M, Forsman A. Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity. Mol Ecol Resour 2024; 24:e14018. [PMID: 39285627 DOI: 10.1111/1755-0998.14018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 06/25/2024] [Accepted: 08/06/2024] [Indexed: 10/03/2024]
Abstract
For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.
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Affiliation(s)
- Romana Salis
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
| | - Johanna Sunde
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
| | - Nikolaj Gubonin
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
| | - Markus Franzén
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Department of Biology and Environmental Sciences, Linnaeus University, Kalmar, Sweden
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111
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Li X, Gao X, Tang N, Wang L, Xing W. Functional traits of exotic submerged macrophytes mediate diversity-invasibility relationship in freshwater communities under eutrophication. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175060. [PMID: 39067607 DOI: 10.1016/j.scitotenv.2024.175060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/28/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Plant diversity may respond differently in terms of whether it can drive plant invasions in freshwater ecosystem. Linkages and interactions between diversity and invasibility have not been clearly resolved, and it is unclear how nutrient enrichment (e.g., eutrophication) will affect this relationship. As a key predictor of plant growth, the ability of functional traits to mediate trade-offs in the diversity-invasibility relationship is unknown. Here, we conducted a series of experiments to determine the role of exotic plant functional traits in the diversity-invasibility relationship of submerged macrophyte communities under eutrophication. We selected common native and exotic submerged macrophytes in the subtropics to construct different diverse submerged macrophyte communities to simulate invasion. Meanwhile, to test the adaptability and importance of functional traits, we experimentally verified the differences in functional traits between exotic and native species. Our results showed a positive correlation between native plant diversity and community invasibility. Moreover, the invader's performance was predominantly determined by functional traits of exotic species, such as plant biomass and tissue nutrients, which were significantly altered by species diversity. Furthermore, our results suggested that functional traits contribute significantly more to the invasiveness of exotic submerged macrophytes than the other factors to which they are subjected. Plant functional traits can mediate the diversity-invasibility relationship because of the higher intrinsic dominance of exotic submerged macrophyte species. In summary, our study revealed diversity-invasibility relationship in submerged macrophyte communities and highlighted functional traits as key drivers of invasion of high-risk exotic submerged macrophyte species. Although previous studies have elucidated the importance of functional trait studies for plant invasions, our study provides the only current evidence demonstrating the important role of invaders' functional traits in mediating the diversity-invasibility relationship. This novel perspective offers valuable insights into the management and control of invasive aquatic plants.
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Affiliation(s)
- Xiaowei Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Xueyuan Gao
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Na Tang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Lei Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Wei Xing
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Wuhan 430074, China.
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112
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Poncelet G, Parolini L, Shimeld SM. A microfluidic chip for immobilization and imaging of Ciona intestinalis larvae. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:443-452. [PMID: 38847208 DOI: 10.1002/jez.b.23267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 04/17/2024] [Accepted: 05/21/2024] [Indexed: 10/05/2024]
Abstract
Sea squirts (Tunicata) are chordates and develop a swimming larva with a small and defined number of individually identifiable cells. This offers the prospect of connecting specific stimuli to behavioral output and characterizing the neural activity that links these together. Here, we describe the development of a microfluidic chip that allows live larvae of the sea squirt Ciona intestinalis to be immobilized and recorded. By generating transgenic larvae expressing GCaAMP6m in defined cells, we show that calcium ion levels can be recorded from immobilized larvae, while microfluidic control allows larvae to be exposed to specific waterborne stimuli. We trial this on sea water carrying increased levels of carbon dioxide, providing evidence that larvae can sense this gas.
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Affiliation(s)
| | - Lucia Parolini
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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113
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Sun P, Fan K, Jiang Y, Chu H, Chen Y, Wu Y. Accumulated temperature dictates the regional structural variation of prokaryotic periphyton at soil-water interface in paddy fields. WATER RESEARCH 2024; 265:122259. [PMID: 39154398 DOI: 10.1016/j.watres.2024.122259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/30/2024] [Accepted: 08/12/2024] [Indexed: 08/20/2024]
Abstract
As a pervasive microbial aggregate found at the water-soil interface in paddy fields, periphyton plays crucial roles in modulating nutrient biogeochemical cycling. Consequently, it effectively mitigates non-point source pollution due to its diverse composition. Despite its significance, the mechanisms governing periphyton diversity across different rice planting regions remain poorly understood. To bridge this gap, we investigated periphyton grown in 200 paddy fields spanning 25° of latitude. Initially, we analyzed local diversity and latitudinal variations in prokaryotic communities within paddy field periphyton, identifying 7 abundant taxa, 42 moderate taxa, and 39 rare taxa as the fundamental prokaryotic framework. Subsequently, to elucidate the mechanisms governing periphyton diversity across large scales, we constructed interaction models illustrating triangular relationships among local richness, assembly, and regional variation of prokaryotic subcommunities. Our findings suggest that accumulated temperature-driven environmental filtering partially influences the assembly process of prokaryotes, thereby impacting local species richness and ultimately governing regional structural variations in periphyton. Furthermore, we determined that a latitude of 39° represents the critical threshold maximizing local species richness of periphyton in paddy fields. This study advances our understanding of the factors shaping periphyton geo-imprints and provides valuable insights into predicting their responses to environmental changes, potentially influencing rice production outcomes.
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Affiliation(s)
- Pengfei Sun
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Kunkun Fan
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Yuji Jiang
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Haiyan Chu
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Yin Chen
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK.
| | - Yonghong Wu
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China.
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114
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White OW, Walkington S, Carter H, Hughes L, Clark M, Mock T, Tarling GA, Clark MD. Exome capture of Antarctic krill (Euphausia superba) for cost effective genotyping and population genetics with historical collections. Mol Ecol Resour 2024; 24:e14022. [PMID: 39268695 DOI: 10.1111/1755-0998.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/12/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024]
Abstract
Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean ecosystem, with ecological and commercial significance. However, its vulnerability to climate change requires an urgent investigation of its adaptive potential to future environmental conditions. Historical museum collections of krill from the early 20th century represent an ideal opportunity to investigate how krill have changed over time due to predation, fishing and climate change. However, there is currently no cost-effective method for implementing population scale collection genomics for krill given its genome size (48 Gbp). Here, we assessed the utility of two inexpensive methods for population genetics using historical krill samples, specifically low-coverage shotgun sequencing (i.e. 'genome-skimming') and exome capture. Two full-length transcriptomes were generated and used to identify 166 putative gene targets for exome capture bait design. A total of 20 historical krill samples were sequenced using shotgun and exome capture. Mitochondrial and nuclear ribosomal sequences were assembled from both low-coverage shotgun and off-target of exome capture data demonstrating that endogenous DNA sequences could be assembled from historical collections. Although, mitochondrial and ribosomal sequences are variable across individuals from different populations, phylogenetic analysis does not identify any population structure. We find exome capture provides approximately 4500-fold enrichment of sequencing targeted genes, suggesting this approach can generate the sequencing depth required to call identify a significant number of variants. Unlocking historical collections for genomic analyses using exome capture, will provide valuable insights into past and present biodiversity, resilience and adaptability of krill populations to climate change.
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Affiliation(s)
- Oliver W White
- The Natural History Museum, London, UK
- NERC Environmental Omics Facility (NEOF), NEOF Visitor Facility, School of Biosciences, University of Sheffield, Sheffield, UK
- NERC Environmental Omics Facility, Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | | | | | | | | | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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115
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Liu Z, Zhao M, Tennakoon K, Liu C. Climate factors determine large-scale spatial patterns of stomatal index in Chinese herbaceous and woody dicotyledonous plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175112. [PMID: 39084391 DOI: 10.1016/j.scitotenv.2024.175112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/03/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
The stomatal index (SI, %) and its response to climate factors (temperature and precipitation) can help our understanding of terrestrial carbon and water cycling and plant adaptation in the ecosystem, however, consensus has not yet been reached in this regard. In this study, we compiled an extensive dataset from the Chinese flora to investigate the response of SI to environmental change, including 891 herbaceous and woody species from 188 published papers. The results showed that mean values of the adaxial SI and abaxial SI for all species were 14.06 and 19.22, respectively, and the ratio of adaxial to abaxial SI was 0.84. For the adaxial SI, abaxial SI, and the ratio of adaxial to abaxial SI, the range of these values varied between 0.05-43.67, 0.01-48.17, and 0.03-4.31, respectively. Compared with woody plants, herbaceous plants showed higher values in both adaxial and abaxial SI. In terms of the impact of climate factors, the abaxial SI of herbaceous plants changed slower than the adaxial SI, while woody plants showed the opposite trend. Threshold effects of increased temperature and precipitation on SI were observed, indicating that SI responded differently to changes in climate factors at different levels. Climate factors play a crucial role in driving the adaxial SI than abaxial SI. Our findings highlight the significant challenges posed by divergent responses of SI in forecasting future water and carbon cycles associated with climatic and environmental change.
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Affiliation(s)
- Zhaogang Liu
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Co-Innovation Center for Sustainable Forestry in Southern China, Laboratory of Biodiversity and Conservation, College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Zhao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Kushan Tennakoon
- Institute of Innovation, Science and Sustainability, Federation University Australia Berwick Campus, No.100 Clyde Road, Berwick, VIC 3806, Australia
| | - Congcong Liu
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
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116
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Suarez-Trujillo A, Vorland CJ, Nicholls GT, Chusyd DE, Parker C, Golzarri-Arroyo L, Swann S, Funnell BJ, Stewart KR, Allison DB. Fetal sex effects on maternal health can now be tested via randomization: A first-in-class illustration in cows on glucoregulatory outcomes. Theriogenology 2024; 229:41-46. [PMID: 39151322 PMCID: PMC11391945 DOI: 10.1016/j.theriogenology.2024.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/09/2024] [Accepted: 08/10/2024] [Indexed: 08/19/2024]
Abstract
BACKGROUND The maternal-offspring relationship, such as whether fetal sex influences maternal health, is essential to explore to advance prenatal and maternal health. While associations exist between fetal sex and maternal health outcomes, it is unclear whether these reflect a causal relationship. OBJECTIVE To demonstrate that fetal sex can be randomly assigned to test the causal effect of fetal sex on maternal outcomes. METHODS Holstein dairy cows were stratified and randomized using sealed opaque envelopes to be artificially inseminated with either X- or Y-sorted bull semen until 40 cows became pregnant. Monthly body weight measurements were recorded, and an intravenous glucose tolerance test was performed 30 days before the expected calving day. The primary outcome was insulin area under the curve (AUC), and secondary outcomes were clearance rate, half-life, and AUC for glucose, insulin, and non-esterified fatty acid concentrations. An intention-to-treat (ITT) approach using multiple imputation was employed for primary analysis, and an as-treated (AT) approach was used for secondary analysis. RESULTS We demonstrated that we could successfully randomize the assignment of fetal sex to dams and test for causal effects of fetal sex on glucoregulatory outcomes using dairy cows as a model. Insulin AUC was not statistically different between groups (ITT p = 0.857, AT p = 0.874), and other outcomes were also not statistically different (p > 0.05). CONCLUSION We demonstrated that causal effects of fetal sex on maternal outcomes can be causally tested in dairy cows. Our study did not provide statistical evidence to support an effect of fetal sex on maternal glucose-related outcomes.
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Affiliation(s)
| | - Colby J Vorland
- Indiana University School of Public Health-Bloomington, Bloomington, IN, 47405, USA
| | - Griffin T Nicholls
- Department of Animal Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Daniella E Chusyd
- Indiana University School of Public Health-Bloomington, Bloomington, IN, 47405, USA
| | - Chelsie Parker
- Indiana University School of Public Health-Bloomington, Bloomington, IN, 47405, USA
| | | | - Sophia Swann
- Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA
| | - Bethany J Funnell
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Kara R Stewart
- Department of Animal Science, Purdue University, West Lafayette, IN, 47907, USA
| | - David B Allison
- Indiana University School of Public Health-Bloomington, Bloomington, IN, 47405, USA.
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117
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Colasurdo M, Ahmed AK, Gandhi D. MR-guided Focused Ultrasound Thalamotomy for Chronic Pain. Magn Reson Imaging Clin N Am 2024; 32:661-672. [PMID: 39322355 DOI: 10.1016/j.mric.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
MR-guided focused ultrasound (FUS) represents a promising alternative for patients with chronic neuropathic who have failed medical management and other treatment options. Early single-center experience with chronic neuropathic pain and trigeminal neuralgia has demonstrated favorable long-term outcomes. Excellent safety profile with low risk of motor and sensory complications and so far anecdotal permanent neurologic deficits make FUS a powerful tool to treat patients who are otherwise hopeless. Neuromodulation may be the most influential factor driving outcomes and studies devised to detect neuroplasticity will be critical to guide such therapies.
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Affiliation(s)
- Marco Colasurdo
- Department of Interventional Radiology, Oregon Health and Science University, Portland, OR 97239, USA
| | | | - Dheeraj Gandhi
- Department of Neurosurgery, University of Maryland School of Medicine; Division of Neurointerventional Surgery, Department of Diagnostic Radiology, University of Maryland School of Medicine, University of Maryland, 22 South Green Street, Baltimore, MD 21201, USA; Department of Radiology, University of Maryland School of Medicine, 22 South Green Street, Baltimore, MD 21201, USA; Department of Neurology, University of Maryland School of Medicine, 22 South Green Street, Baltimore, MD 21201, USA; Department of Neurosurgery, University of Maryland School of Medicine, 22 South Green Street, Baltimore, MD 21201, USA.
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118
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Zhang H, Liu Q, Lu J, Wu L, Cheng Z, Qiao G, Huang X. Genomic and transcriptomic analyses of a social hemipteran provide new insights into insect sociality. Mol Ecol Resour 2024; 24:e14019. [PMID: 39262229 DOI: 10.1111/1755-0998.14019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 08/17/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
The origin of sociality represents one of the most important evolutionary transitions. Insect sociality evolved in some hemipteran aphids, which can produce soldiers and normal nymphs with distinct morphology and behaviour through parthenogenesis. The lack of genomic data resources has hindered the investigations into molecular mechanisms underlying their social evolution. Herein, we generated the first chromosomal-level genome of a social hemipteran (Pseudoregma bambucicola) with highly specialized soldiers and performed comparative genomic and transcriptomic analyses to elucidate the molecular signatures and regulatory mechanisms of caste differentiation. P. bambucicola has a larger known aphid genome of 582.2 Mb with an N50 length of 11.24 Mb, and about 99.6% of the assembly was anchored to six chromosomes with a scaffold N50 of 98.27 Mb. A total of 14,027 protein-coding genes were predicted and 37.33% of the assembly were identified as repeat sequences. The social evolution is accompanied by a variety of changes in genome organization, including expansion of gene families related to transcription factors, transposable elements, as well as species-specific expansions of certain sugar transporters and UGPases involved in carbohydrate metabolism. We also characterized large candidate gene sets linked to caste differentiation and found evidence of expression regulation and positive selection acting on energy metabolism and muscle structure, explaining the soldier-specific traits including morphological and behavioural specialization, developmental arrest and infertility. Overall, this study offers new insights into the molecular basis of social aphids and the evolution of insect sociality and also provides valuable data resources for further comparative and functional studies.
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Affiliation(s)
- Hui Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianjun Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liying Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhentao Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Insect Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
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119
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Huber ED, Hintz LL, Wilmoth B, McKenna JR, Hintz WD. Coping with stress: Salt type, concentration, and exposure history limit life history tradeoffs in response to road salt salinization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174998. [PMID: 39053528 DOI: 10.1016/j.scitotenv.2024.174998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/22/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Substantial increases in the salinity of freshwater ecosystems has occurred around the globe from causes such as climate change, industrial operations, and the application of road deicing salts. We know very little about how plastic responses in life history traits or rapid evolution of new traits among freshwater organisms could promote stability in ecological communities affected by salinization. We performed a cohort life history analysis from birth to death with 180 individuals of a ubiquitous freshwater zooplankter to understand how life history traits are affected by exposure to two common salt types causing salinization-sodium chloride (NaCl) and calcium chloride (CaCl2)-across two environmentally relevant concentrations. We also tested if a multi-generational exposure history to high salinity altered life-history responses. We tracked and measured lifespan, time to maturation, brood size, brood interval, and body size. We found smaller brood sizes but slightly longer lifespans occurred at a low concentration of NaCl (230 mg Cl-/L). The longer lifespans led to more, albeit smaller broods, which generated a similar lifetime reproductive output compared to the no-salt control populations. At higher concentrations of NaCl and CaCl2, we found lifetime reproductive output was reduced by 23 % to 83 % relative to control populations because no tradeoff among life history traits occurred. In CaCl2, we observed shorter life spans, longer time intervals between smaller broods, and smaller body sizes leading to reduced lifetime reproductive output. We also found that a multi-generational exposure to the salt types did not convey any advantages for lifetime reproductive output. In some cases, the exposure history worsened the life history trait responses suggesting maladaptation. Our findings suggest that life history tradeoffs for freshwater species can occur in response to salinization, but these tradeoffs will largely depend on salt type and concentration, which will have implications for biodiversity and ecological stability.
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Affiliation(s)
- Eric D Huber
- Department of Environmental Sciences and Lake Erie Center, The University of Toledo, 6200 Bay Shore Rd., Oregon, OH, USA
| | - Leslie L Hintz
- Department of Environmental Sciences and Lake Erie Center, The University of Toledo, 6200 Bay Shore Rd., Oregon, OH, USA
| | - Bayley Wilmoth
- Department of Environmental Sciences and Lake Erie Center, The University of Toledo, 6200 Bay Shore Rd., Oregon, OH, USA
| | - Jorden R McKenna
- Department of Environmental Sciences and Lake Erie Center, The University of Toledo, 6200 Bay Shore Rd., Oregon, OH, USA
| | - William D Hintz
- Department of Environmental Sciences and Lake Erie Center, The University of Toledo, 6200 Bay Shore Rd., Oregon, OH, USA.
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120
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Gianasi FM, de Andrade Maia V, Oliveira AM, Pompeu PV, de Souza CR, Farrapo CL, da Silva-Sene AM, de Oliveira F, Meireles TM, de Carvalho Rodrigues AL, Madeira DM, Araújo FC, Silva LCA, Ferreira LAS, Santos LR, Reis MG, Pereira RT, Souza TA, de Oliveira Alves Braga M, de Lima E Silva VFP, van Meerveld I, Dos Santos RM. Water level regime variation is a crucial driver for taxonomic, functional, and phylogenetic diversity in seasonally flooded tropical forests. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175195. [PMID: 39094665 DOI: 10.1016/j.scitotenv.2024.175195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/24/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Floodplains contribute significantly to terrestrial ecosystem service provision but are also among the most vulnerable and degraded ecosystems worldwide. Heterogeneity in floodplain properties arises from variations in river-specific flood regimes, watershed characteristics, and valley morphology, influencing seasonally flooded forests' taxonomic, functional, and phylogenetic diversity. This study addresses persisting knowledge gaps in floodplain ecology, focusing on the seasonally dry tropics. We explore the relationships between flood regime, environmental conditions, vegetation composition, functional and phylogenetic diversity, and the impact of environmental variables on above-ground biomass (AGB) and ecological strategies. The study spans six rivers in southeastern Brazil's main river basins: Rio Grande and São Francisco. We identified five eco-units in each floodplain based on flooding regimes and surveyed six plots per eco-unit. We measured trees with DBH > 5 cm and collected functional traits, along with detailed soil, climate, and water level data. We calculated plot-level floristic composition, taxonomic, functional, and phylogenetic diversity, wood density, and AGB. Functional and phylogenetic dissimilarity were analyzed, and the effects of climate, soil, and hydrological variables were quantified using generalized linear mixed models. We show how flood frequency and duration affect floristic composition across the floodplains. Taxonomic and phylogenetic diversity responded to climate, soil, and hydrological variables, while functional diversity responded primarily to hydrological variables, emphasizing the role of environmental filtering. Hydrological seasonality, soil fertility, and flood regime emerged as key factors shaping community structure and ecological strategies in the studied seasonally flooded tropical forests. Plot-level AGB responded to phosphorus but not to climate or hydrological variables. The study also highlights functional and phylogenetic dissimilarities among eco-units and basins, indicating potential climate change impacts.
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Affiliation(s)
- Fernanda Moreira Gianasi
- Department of Biology, Graduate Program in Applied Botany, Federal University of Lavras, Lavras, MG 37200-000, Brazil; Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil.
| | - Vinícius de Andrade Maia
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | | | | | - Cléber Rodrigo de Souza
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Camila Laís Farrapo
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - André Maciel da Silva-Sene
- Department of Biology, Graduate Program in Applied Botany, Federal University of Lavras, Lavras, MG 37200-000, Brazil; Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Fernanda de Oliveira
- Department of Biology, Graduate Program in Applied Botany, Federal University of Lavras, Lavras, MG 37200-000, Brazil; Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Thiago Magalhães Meireles
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Ana Lívia de Carvalho Rodrigues
- Department of Biology, Graduate Program in Applied Botany, Federal University of Lavras, Lavras, MG 37200-000, Brazil; Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Denise Moura Madeira
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Felipe Carvalho Araújo
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Lidiany Carolina Arantes Silva
- Department of Biology, Graduate Program in Applied Botany, Federal University of Lavras, Lavras, MG 37200-000, Brazil; Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Leony Aparecido Silva Ferreira
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Lucélia Rodrigues Santos
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Miguel Gama Reis
- Department of Biology, Graduate Program in Applied Botany, Federal University of Lavras, Lavras, MG 37200-000, Brazil; Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Rafaella Tavares Pereira
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Tatiane Almeida Souza
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Michael de Oliveira Alves Braga
- Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | | | | | - Rubens Manoel Dos Santos
- Department of Biology, Graduate Program in Applied Botany, Federal University of Lavras, Lavras, MG 37200-000, Brazil; Phytogeography and Evolutionary Ecology Laboratory, Department of Forest Sciences, Federal University of Lavras, Lavras, MG 37200-000, Brazil
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Guo X, Luo G, Hou F, Zhou C, Liu X, Lei Z, Niu D, Ran T, Tan Z. A review of bacteriophage and their application in domestic animals in a post-antibiotic era. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174931. [PMID: 39043300 DOI: 10.1016/j.scitotenv.2024.174931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/25/2024]
Abstract
Bacteriophages (phages for short) are the most abundant biological entities on Earth and are natural enemies of bacteria. Genomics and molecular biology have identified subtle and complex relationships among phages, bacteria and their animal hosts. This review covers composition, diversity and factors affecting gut phage, their lifecycle in the body, and interactions with bacteria and hosts. In addition, research regarding phage in poultry, aquaculture and livestock are summarized, and application of phages in antibiotic substitution, phage therapy and food safety are reviewed.
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Affiliation(s)
- Xinyu Guo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Guowang Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Chuanshe Zhou
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xiu Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhaomin Lei
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Dongyan Niu
- Faculty of Veterinary Medicine, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Tao Ran
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhiliang Tan
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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de Oliveira Rosa SA, Titon Junior B, de Figueiredo AC, Lima AS, Gomes FR, Titon SCM. Baseline and stress-induced changes in plasma bacterial killing ability against gram-negative bacteria are partially mediated by the complement system in Rhinella diptycha toads. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111701. [PMID: 39029618 DOI: 10.1016/j.cbpa.2024.111701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/26/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
The plasma bacterial killing ability (BKA) is modulated by the stress response in vertebrates, including amphibians. The complement system is an effector mechanism comprised of a set of proteins present in the plasma that once activated can promote bacterial lysis. Herein, we investigated whether changes in plasma BKA as a result of the acute stress response and an immune challenge are mediated by the complement system in Rhinella diptycha toads. Additionally, we investigated whether the observed changes in plasma BKA are associated with changes in plasma corticosterone levels (CORT). We subjected adult male toads to a restraint or an immune challenge (with three concentrations of Aeromonas hydrophila heat inactivated), and then evaluated the plasma BKA against A. hydrophila, in vitro. We determined the complement system activity on plasma BKA, by treating the plasma (baseline, 1 h and 24 h post-restraint, and after the immune challenge) with ethylenediaminetetraacetic acid, heat, or protease. Our results showed increased CORT 1 h and 24 h after restraint and decreased plasma BKA 24 h post-restraint. The inhibitors of the complement system decreased the plasma BKA compared with untreated plasma at all times (baseline, 1 h, and 24 h after restraint), demonstrating that the plasma BKA activity is partially mediated by the complement system. The immune challenge increased CORT, with the highest values being observed in the highest bacterial concentration, compared with control. The plasma BKA was not affected by the immune challenge but was demonstrated to be partially mediated by the complement system. Our results demonstrated that restraint and the immune challenge activated the hypothalamus-pituitary-interrenal axis, by increasing plasma CORT levels in R. diptycha. Also, our results demonstrated the complement system is participative in the plasma BKA for baseline and post-stress situations in these toads.
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Affiliation(s)
| | - Braz Titon Junior
- Department of Physiology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
| | | | - Alan Siqueira Lima
- Department of Physiology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
| | - Fernando Ribeiro Gomes
- Department of Physiology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
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Hoffman AJ, Finger JW, Kavazis AN, Wada H. Early life thermal conditioning alters heat-shock protein expression in response to an adult thermal stressor. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:1030-1040. [PMID: 39005228 DOI: 10.1002/jez.2858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024]
Abstract
Developmental environmental stressors can have instructive effects on an organism's phenotype. This developmental plasticity can prepare organisms for potentially stressful future environments, circumventing detrimental effects on fitness. However, the physiological mechanisms underlying such adaptive plasticity are understudied, especially in vertebrates. We hypothesized that captive male zebra finches (Taeniopygia castanotis) exposed to a mild heat conditioning during development would acquire a persisting thermotolerance, and exhibit increased heat-shock protein (HSP) levels associated with a decrease in oxidative damage when exposed to a high-intensity stressor in adulthood. To test this, we exposed male finches to a prolonged mild heat conditioning (38°C) or control (22°C) treatment as juveniles. Then in a 2 × 2 factorial manner, these finches were exposed to a high heat stressor (42°C) or control (22°C) treatment as adults. Following the adult treatment, we collected testes and liver tissue and measured HSP70, HSP90, and HSP60 protein levels. In the testes, finches exhibited lower levels of HSP90 and HSP60 when exposed to the high heat stressor in adulthood if they were exposed to the mild heat conditioning as juveniles. In the liver, finches exposed to the high heat stressor in adulthood had reduced HSP90 and HSP60 levels, regardless of whether they were conditioned as juveniles. In some cases, elevated testes HSP60 levels were associated with increased liver oxidative damage and diminishment of a condition-dependent trait, indicating potential stress-induced tradeoffs. Our results indicate that a mild conditioning during development can have persisting effects on HSP expression and acquired thermotolerance.
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Affiliation(s)
| | - John W Finger
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
- Biomedical Sciences Department, Missouri State University, Springfield, Missouri, USA
| | | | - Haruka Wada
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
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Vučić T, Drobnjaković M, Ajduković M, Bugarčić M, Wielstra B, Ivanović A, Cvijanović M. A staging table of Balkan crested newt embryonic development to serve as a baseline in evolutionary developmental studies. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:465-482. [PMID: 38953174 DOI: 10.1002/jez.b.23269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/08/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024]
Abstract
There is an increased interest in the evolution and development of newts from the genus Triturus because: (1) morphological differentiation among the nine constituent species largely corresponds to different ecological preferences, (2) hybridization between different species pairs has various evolutionary outcomes in terms of life history traits and morphology, and (3) the genus expresses a balanced lethal system that causes arrested growth and death of half of the embryos. These features provide natural experimental settings for molecular, morphological, and life-history studies. Therefore, we produce a staging table for the Balkan crested newt (T. ivanbureschi). We provide detailed descriptions of 34 embryonic stages based on easily observable and interpretable external morphological characters, to ensure reproducibility. Compared with previous staging tables for Triturus, we include a vastly increased sample size and provide high-resolution photographs in lateral, ventral, and dorsal view, complemented by videos of specific developmental periods, and accompanied by detailed explanations on how to delineate the specific stages. Our staging table will serve as a baseline in comparative studies on Triturus newts: an emerging model system in evolutionary and developmental studies.
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Affiliation(s)
- Tijana Vučić
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Marija Drobnjaković
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Maja Ajduković
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marko Bugarčić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ben Wielstra
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ana Ivanović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Milena Cvijanović
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
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Dobrushina O, Tamim Y, Wald IY, Maimon A, Amedi A. Interoceptive training with real-time haptic versus visual heartbeat feedback. Psychophysiology 2024; 61:e14648. [PMID: 39152653 DOI: 10.1111/psyp.14648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/12/2024] [Accepted: 06/25/2024] [Indexed: 08/19/2024]
Abstract
The perception of signals from within the body, known as interoception, is increasingly recognized as a prerequisite for physical and mental health. This study is dedicated to the development of effective technological approaches for enhancing interoceptive abilities. We provide evidence of the effectiveness and practical feasibility of a novel real-time haptic heartbeat supplementation technology combining principles of biofeedback and sensory augmentation. In a randomized controlled study, we applied the developed naturalistic haptic feedback on a group of 30 adults, while another group of 30 adults received more traditional real-time visual heartbeat feedback. A single session of haptic, but not visual heartbeat feedback resulted in increased interoceptive accuracy and confidence, as measured by the heart rate discrimination task, and in a shift of attention toward the body. Participants rated the developed technology as more helpful and pleasant than the visual feedback, thus indicating high user satisfaction. The study highlights the importance of matching sensory characteristics of the feedback provided to the natural bodily prototype. Our work suggests that real-time haptic feedback might be a superior approach for strengthening the mind-body connection in interventions for physical and mental health.
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Affiliation(s)
- Olga Dobrushina
- The Baruch Ivcher Institute for Brain, Cognition & Technology, The Baruch Ivcher School of Psychology, Reichman University, Herzliya, Israel
| | - Yossi Tamim
- The Baruch Ivcher Institute for Brain, Cognition & Technology, The Baruch Ivcher School of Psychology, Reichman University, Herzliya, Israel
| | - Iddo Yehoshua Wald
- The Baruch Ivcher Institute for Brain, Cognition & Technology, The Baruch Ivcher School of Psychology, Reichman University, Herzliya, Israel
| | - Amber Maimon
- The Baruch Ivcher Institute for Brain, Cognition & Technology, The Baruch Ivcher School of Psychology, Reichman University, Herzliya, Israel
| | - Amir Amedi
- The Baruch Ivcher Institute for Brain, Cognition & Technology, The Baruch Ivcher School of Psychology, Reichman University, Herzliya, Israel
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126
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Bayraktar M. Analysing the genetic diversity of three sheep breeds in Turkey and nearby countries using 50 K SNPs data. Anim Biotechnol 2024; 35:2329106. [PMID: 38497403 DOI: 10.1080/10495398.2024.2329106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
This study analysed the genetic diversity and population structure of eight sheep breeds in Turkey and nearby countries. Moderate genetic diversity was observed, with the Sakiz (SKZ) exhibiting the highest diversity based on heterozygosity and allelic richness (AR) values. Genetic distances revealed differentiation between the populations, with the most significant divergence between the Cyprus Fat Tail (CFT) and SKZ breeds. PCA demonstrated SKZ and Chios (CHI) clustering together, indicating genetic similarity. Karakas (KRS), Norduz (NDZ), Afshari (AFS), Moghani (MOG) and others showed overlap, reflecting genetic relationships. Ancestry analysis found that KRS was predominantly inherited from the second ancestral population, while SKZ and NDZ were primarily derived from the first and second ancestral lineages. This illustrated the populations' diverse origins. Most genetic variation (96.84%) was within, not between, populations. The phi-statistic (PhiPT) indicated moderate differentiation overall. Phylogenetic analysis further demonstrated the genetic distinctiveness of the SKZ breed. ROH and FROH analyses showed that SKZ exhibited the highest homozygosity and inbreeding, while KRS displayed the lowest. This study elucidates these breeds' genetic diversity, structure and relationships. Key findings include moderate diversity, evidence of differentiation between breeds, diverse ancestral origins and distinct ROH patterns. This provides insights into the population's genetic characteristics and conservation requirements.
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Affiliation(s)
- Mervan Bayraktar
- Department of Animal Science, Faculty of Agriculture, Çukurova University, Adana, Turkey
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Yan H, Chen J, Qing E, Li X, Wang W, Ling Z, Chen Z, Jiang S, Yan Y, Deng S, Hu J, Li L, Wang J, Hu S. Developmental variations of the reproductive organs of ganders from different goose breeds and the underlying mechanisms. Poult Sci 2024; 103:104233. [PMID: 39214052 PMCID: PMC11402047 DOI: 10.1016/j.psj.2024.104233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
A deep understanding of the dynamics and mechanisms of male reproductive tract development is necessary for adoption of either genetic techniques or environmental management practices for improving fertility and hatchability in poultry. However, compared with other poultry such as chickens and ducks, less is known about the age- and breed-related changes in the reproductive tract development of domestic goose ganders exhibiting relatively poor reproductive performance as well as the regulatory mechanisms. In the present study, by taking 2 Chinese domestic goose breeds (Sichuan White goose, SW and Gang goose, GE; Anser cygnoides) and one European goose breed (Landes goose, LD; Anser anser) as the experimental objects, we comprehensive analyzed the morphological, histological, and genome-wide transcriptomic variations in their testicular and external genital development during the period from hatching to sexual maturity. Results from histomorphological analysis demonstrated that the reproductive tract of all goose breeds developed in both age- and breed-dependent manners, and the left and right testis developed asymmetrically throughout posthatch development. The tenth week posthatch was a critical developmental stage for all goose ganders, because both the testicular and external genital histomorphological parameters significantly changed before and after this period. During the first 10 wk posthatch, the weight, organ index, or size of male reproductive organs developed more rapidly in SW than in LD, and so were the testicular parenchymal-to-interstitial ratio and the external genital lymphatic lumen diameter. However, the testicular seminiferous epithelium thickness, seminiferous tubule diameter, and Leydig cell number, as well as the external genital keratinized epithelium thickness were significantly higher in LD than in SW at 10 wk of age. Through comparative transcriptomics analysis and RT-qPCR validation, several pathways related to germ and somatic cell function, organ remodeling, and energy metabolism were thought to be responsible for the developmental variations in the early testicular development between Chinese and European domestic ganders, where 10 hub genes involved in the cell cycle, RNA polymerase II-dependent transcription, and mitotic cell division pathways might play essential roles. These data shed new light on the interbreed differences in the male goose reproductive tract development and the molecular mechanisms regulating male goose testicular functions and fertility.
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Affiliation(s)
- Haoyu Yan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiasen Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Enhua Qing
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaopeng Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Wanxia Wang
- Department of Animal Production, General Station of Animal Husbandry of Sichuan Province, Chengdu 610041, China
| | - Zihan Ling
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhengyang Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuhan Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yue Yan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shilin Deng
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiwei Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Liang Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiwen Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shenqiang Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics Ministry of Agriculture and Rural Affair, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
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128
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He R, Shi H, Hu M, Zhou Q, Dang H, Zhang Q. Differential phenotypic plasticity of subalpine trees predicts trait integration under climate warming. THE NEW PHYTOLOGIST 2024; 244:1074-1085. [PMID: 39155709 DOI: 10.1111/nph.20067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
Understanding limiting factors of phenotypic plasticity is essential given its critical role in shaping biological adaptation and evolution in changing environments. It has been proposed that the pattern of phenotypic correlation could constrain trait plasticity. However, the interplay between phenotypic plasticity and integration has remained contentious. We experimentally simulated climate warming in juveniles of three subalpine tree species by exposing them to three-year in situ open-top chambers (OTCs), and then measured functional plasticity of 72 eco-physiological traits to evaluate whether phenotypic integration constituted an intrinsic constraint to plasticity. We also tested the relationship between the differences in plasticity and maintenance in trait integration. Phenotypic plasticity was positively associated with integration in deciduous tree species under warming. The difference in the plasticity of two paired traits could predict their integration in different environments, where traits displaying more similar plasticity were more likely to be correlated. Our study showed no indication that phenotypic integration constrained plasticity. More importantly, we demonstrated that differential plasticity between traits might result in a notable reorganization of the trait associations, and that warming commonly induced a tighter phenotype. Our study provides new insights into the interplay between phenotypic plasticity and integration in subalpine trees under climate warming.
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Affiliation(s)
- Rui He
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| | - Hang Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| | - Man Hu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| | - Quan Zhou
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Haishan Dang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
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Mendoza-Maya E, Giles-Pérez GI, Vargas-Hernández JJ, Sáenz-Romero C, Martínez-Trujillo M, de Los Angeles Beltrán-Nambo M, Hernández-Díaz JC, Prieto-Ruíz JÁ, Jaramillo-Correa JP, Wehenkel C. Evolutionary drivers of reproductive fitness in two endangered forest trees. THE NEW PHYTOLOGIST 2024; 244:1086-1100. [PMID: 39187985 DOI: 10.1111/nph.20073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024]
Abstract
Population genetics theory predicts a relationship between fitness, genetic diversity (H0) and effective population size (Ne), which is often tested through heterozygosity-fitness correlations (HFCs). We tested whether population and individual fertility and heterozygosity are correlated in two endangered Mexican spruces (Picea martinezii and Picea mexicana) by combining genomic, demographic and reproductive data (seed development and germination traits). For both species, there was a positive correlation between population size and seed development traits, but not germination rate. Individual genome-wide heterozygosity and seed traits were only correlated in P. martinezii (general-effects HFC), and none of the candidate single nucleotide polymorphisms (SNPs) associated with individual fertility showed heterozygote advantage in any species (no local-effects HFC). We observed a single and recent (c. 30 thousand years ago (ka)) population decline for P. martinezii; the collapse of P. mexicana occurred in two phases separated by a long period of stability (c. 800 ka). Recruitment always contributed more to total population census than adult trees in P. mexicana, while this was only the case in the largest populations of P. martinezii. Equating fitness to either H0 or Ne, as traditionally proposed in conservation biology, might not always be adequate, as species-specific evolutionary factors can decouple the expected correlation between these parameters.
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Affiliation(s)
- Eduardo Mendoza-Maya
- Programa Institucional de Doctorado en Ciencias Agropecuarias y Forestales, Universidad Juárez del Estado de Durango, 34000, Durango, Mexico
| | - Gustavo Ibrahim Giles-Pérez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - J Jesús Vargas-Hernández
- Postgrado en Ciencias Forestales, Colegio de Postgraduados, Montecillo, Texcoco, 56264, Estado de México, Mexico
| | - Cuauhtémoc Sáenz-Romero
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, 58330, Michoacán, Mexico
| | - Miguel Martínez-Trujillo
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, 58030, Michoacán, Mexico
| | | | - José Ciro Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, 34120, Durango, Mexico
| | - José Ángel Prieto-Ruíz
- Facultad de Ciencias Forestales y Ambientales, Universidad Juárez del Estado de Durango, 34120, Durango, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, 34120, Durango, Mexico
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Porras-Rivera G, Górski K, Colin N. Behavioral biomarkers in fishes: A non-lethal approach to assess the effects of chemical pollution on freshwater ecosystems. ENVIRONMENTAL RESEARCH 2024; 260:119607. [PMID: 39002628 DOI: 10.1016/j.envres.2024.119607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/11/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
The expansion of the human population and the escalating use of chemical products pose a considerable threat to aquatic biodiversity. Consequently, there is an imperative need for the implementation of non-lethal, cost-effective, and easily deployable biomonitoring tools. In this context, fish and their behavior as biomarkers have gained prominence in monitoring of freshwater ecosystems. The aim of this study was to assess the state of art in the use of behavioral biomarkers in ecotoxicology, emphasizing their role as informative tools for global environmental monitoring. Through a systematic literature search, ninety-two articles focusing on the evaluation of behavioral changes in freshwater fish in response to pollution were identified. The most prevalent keywords were "behavior" (7%) and "zebrafish" (6%). Experiments were conducted in countries with expansive territories, such as the United States (18%) and Brazil (17%). Exotic species were primarily employed (58%), with Danio rerio (26%) being the most frequently studied species. Among pollutants, pesticides (32%) and medicines (25%) were the most frequently studied, while locomotion (38%) and social behaviors (18%) were the most frequently evaluated behaviors. Across these studies, authors consistently reported significant changes in the behavior of fish exposed to contaminants, including decreased swimming speed and compromised feeding efficiency. The review findings affirm that evaluating behavioral biomarkers in freshwater fish offers an informative, non-lethal, cost-effective, and easily implementable approach to understanding pollution impacts on freshwater ecosystems. Although few studies on behavioral biomarkers were available to date, the number has rapidly increased in recent years. Furthermore, a variety of novel approaches and study models are being included. Research into behavioral biomarkers is crucial for understanding and managing environmental risks in freshwater ecosystems. Nevertheless, further studies are needed to enhance our understanding of behavioral toxicity indicators, considering factors such as life stage, sex, and breeding season in the tested species.
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Affiliation(s)
- Geraldine Porras-Rivera
- Doctorado en Ciencias Mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Konrad Górski
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile; Facultad de Ciencias, Universidad Católica de La Santísima Concepción, Concepción, 4030000, Chile
| | - Nicole Colin
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile; Programa Austral Patagonia, Universidad Austral de Chile, Valdivia, 5090000, Chile.
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131
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Costa P, Pereira C, Romalde JL, Almeida A. A game of resistance: War between bacteria and phages and how phage cocktails can be the solution. Virology 2024; 599:110209. [PMID: 39186863 DOI: 10.1016/j.virol.2024.110209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
While phages hold promise as an antibiotic alternative, they encounter significant challenges in combating bacterial infections, primarily due to the emergence of phage-resistant bacteria. Bacterial defence mechanisms like superinfection exclusion, CRISPR, and restriction-modification systems can hinder phage effectiveness. Innovative strategies, such as combining different phages into cocktails, have been explored to address these challenges. This review delves into these defence mechanisms and their impact at each stage of the infection cycle, their challenges, and the strategies phages have developed to counteract them. Additionally, we examine the role of phage cocktails in the evolving landscape of antibacterial treatments and discuss recent studies that highlight the effectiveness of diverse phage cocktails in targeting essential bacterial receptors and combating resistant strains.
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Affiliation(s)
- Pedro Costa
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Carla Pereira
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CRETUS & CIBUS - Faculty of Biology, University of Santiago de Compostela, CP 15782 Santiago de Compostela, Spain.
| | - Adelaide Almeida
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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Liu K, Liu Y, Yan Q, Guo X, Wang W, Zhang Z, Hu A, Xiao X, Ji M, Liu P. Temperature-driven shifts in bacterioplankton biodiversity: Implications for cold-preferred species in warming Tibetan proglacial lakes. WATER RESEARCH 2024; 265:122263. [PMID: 39180953 DOI: 10.1016/j.watres.2024.122263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/02/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Recent climate warming and associated glacier retreat have dramatically changed the environmental conditions and microbial inhabitants of proglacial lakes. However, our understanding of the effects of climate warming and glacial influence on microbial biodiversity in these lakes remain relatively limited. Here, we studied bacterioplankton communities in 22 proglacial lakes on the Tibetan Plateau, spanning a range of nearly 7 °C in mean annual temperature (MAT), and examined the effects of climate and glaciers on their biodiversity by a space-to-time substitution. MAT emerged as the primary environmental driver of bacterioplankton biodiversity compared to glacial influence, increasing species richness and decreasing β-diversity. We identified 576 low-MAT (cold-preferred) species and 2,088 high-MAT (warm-preferred) species, and found that low-MAT species are less environmentally adapted, with their numbers declining as temperature increased. These results advance our understanding of temperature-driven bacterioplankton dynamics by disentangling the contrasting responses and adaptations of cold-preferred and warm-preferred species. Our findings highlight the vulnerability of cold-specialist taxa and the potential biodiversity losses associated with climate warming in the rapidly changing proglacial lakes.
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Affiliation(s)
- Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China.
| | - Qi Yan
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Xuezi Guo
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqiang Wang
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiong Xiao
- College of Geographic Science, Hunan Normal University, Changsha, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Pengfei Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
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Yu D, DU S, Wei X, Zhu J, Ding Y, Hu F, Liu M, Zhang F. Whole-genome-based phylogenetic analyses provide new insights into the evolution of springtails (Hexapoda: Collembola). Mol Phylogenet Evol 2024; 200:108169. [PMID: 39121953 DOI: 10.1016/j.ympev.2024.108169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Springtails (Collembola) stand as one of the most abundant, widespread, and ancient terrestrial arthropods on earth. However, their evolutionary history and deep phylogenetic relationships remain elusive. In this study, we employed phylogenomic approaches to elucidate the basal relationships among Collembola. We sampled whole-genome data representing all major collembolan lineages in proportion to their known diversity. To account for potential phylogenomic biases, we implemented various data extraction, locus sampling, and signal filtering strategies to generate matrices. Subsequently, we applied a diverse array of tree-searching and rate-modelling methods to reconstruct the phylogeny. Our analyses, utilizing different matrices and methods, converged on the same unrooted relationships among collembolan ingroups, supporting the current ordinal classification and challenging the monophyly of Arthropleona and Symphypleona s.l. However, discrepancies across analyses existed in the root of Collembola. Among various root positions, those based on more informative matrices and biologically realistic models, favoring a basal topology of Entomobryomorpha + (Symphypleona s.s. + (Neelipleona + Poduromorpha)), were supported by subsequent methodological assessment, topology tests, and rooting analyses. This optimal topology suggests multiple independent reduction of the pronotum in non-poduromorph orders and aligns with the plesiomorphic status of neuroendocrine organs and epicuticular structure of Entomobryomorpha. Fossil-calibrated dating analyses based on the optimal topology indicated late-Paleozoic to mid-Mesozoic origins of the crown Collembola and four orders. In addition, our results questioned the monophyly of Isotomidae and Neanuridae, underscoring the need for further attention to the systematics of these families. Overall, this study provides novel insights into the phylogenetic backbone of Collembola, which will inform future studies on the systematics, ecology, and evolution of this significant arthropod lineage.
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Affiliation(s)
- Daoyuan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shiyu DU
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiping Wei
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jie Zhu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yinhuan Ding
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Nanjing 212400, China.
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Manqiang Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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134
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Gigl F, Abdullahi M, Barnard M, Hollert H, Orsini L. Interactions between phenanthrene exposure and historical chemical stress: Implications for fitness and ecological resilience of the sentinel species Daphnia magna. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174963. [PMID: 39069192 DOI: 10.1016/j.scitotenv.2024.174963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/16/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) arise from incomplete combustion of oil, coal, and gasoline, with lipophilic properties facilitating their widespread distribution and persistence. Due to their biochemical attributes, PAHs can accumulate in animal tissues, potentially causing mutagenic and carcinogenic effects. Since the industrial revolution, PAH concentrations in the environment have risen, with lakes showing levels from 0.159 to 33,090 μg/kg sediment. Despite acute toxicity studies showing adverse effects on freshwater organisms, the long-term impacts and synergistic interactions with other pollutants remain largely unexplored. This study investigates the impact of phenanthrene (PHE), a prominent PAH found in aquatic environments, on Daphnia magna, a species of significant ecological importance in freshwater ecosystems globally, being both a sentinel species for chemical pollution and a keystone organism in freshwater aquatic ecosystems. Leveraging the dormancy of D. magna, which spans decades or even centuries, we exposed strains with diverse histories of chemical contaminant exposure to environmentally relevant concentrations of PHE. Initially, acute exposure experiments were conducted in accordance with OECD guidelines across 16 Daphnia strains, revealing substantial variation in acute toxic responses, with strains naïve to chemical pollutants showing the lowest toxicity. Utilizing the median effect concentration EC10 derived from acute exposures, we assessed the impacts of chronic PHE exposure on life history traits and ecological endpoints of the 16 strains. To elucidate how historical exposure to other environmental stressors may modulate the toxicity of PHE, temporal populations of D. magna resurrected from a lake with a well-documented century-spanning history of environmental impact were utilized. Our findings demonstrate that PHE exposure induces developmental failure, delays sexual maturation, and reduces adult size in Daphnia. Populations of Daphnia historically exposed to chemical stress exhibited significantly greater fitness impacts compared to naïve populations. This study provides crucial insights into the augmented effects of PAHs interacting with other environmental stressors.
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Affiliation(s)
- Florian Gigl
- Department of Evolutionary Ecology and Environmental Toxicology, Faculty of Biological Sciences, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany; Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Muhammad Abdullahi
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Marianne Barnard
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Henner Hollert
- Department of Evolutionary Ecology and Environmental Toxicology, Faculty of Biological Sciences, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany; Department Environmental Media Related Ecotoxicology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Luisa Orsini
- Department of Evolutionary Ecology and Environmental Toxicology, Faculty of Biological Sciences, Goethe University, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany; Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK; Centre for Environmental Research and Justice (CERJ), University of Birmingham, Birmingham B15 2TT, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
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135
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de Klerk J, Tildesley M, Robbins A, Gorsich E. Parameterisation of a bluetongue virus mathematical model using a systematic literature review. Prev Vet Med 2024; 232:106328. [PMID: 39191049 DOI: 10.1016/j.prevetmed.2024.106328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 08/12/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
Bluetongue virus (BT) is a vector-borne virus that causes a disease, called bluetongue, which results in significant economic loss and morbidity in sheep, cattle, goats and wild ungulates across all continents of the world except Antarctica. Despite the geographical breadth of its impact, most BT epidemiological models are informed by parameters derived from the 2006-2009 BTV-8 European outbreak. The aim of this study was to develop a highly adaptable model for BT which could be used elsewhere in the world, as well as to identify the parameters which most influence outbreak dynamics, so that policy makers can be properly informed with the most current information to aid in disease planning. To provide a framework for future outbreak modelling and an updated parameterisation that reflects natural variation in infections, a newly developed and parameterised two-host, two-vector species ordinary differential equation model was formulated and analysed. The model was designed to be adaptable to be implemented in any region of the world and able to model both epidemic and endemic scenarios. It was parameterised using a systematic literature review of host-to-vector and vector-to-host transmission rates, host latent periods, host infectious periods, and vaccine protection factors. The model was demonstrated using the updated parameters, with South Africa as a setting based on the Western Cape's known cattle and sheep populations, local environmental parameters, and Culicoides spp. presence data. The sensitivity analysis identified that the duration of the infectious period for sheep and cows had the greatest impact on the outbreak length and number of animals infected at the peak of the outbreak. Transmission rates from cows and sheep to C. imicola midges greatly influenced the day on which the peak of the outbreak occurred, along with the duration of incubation period, and infectious period for cows. Finally, the protection factor of the vaccine had the greatest influence on the total number of animals infected. This knowledge could aid in the development of control measures. Due to gradual climate and anthropological change resulting in alterations in vector habitat suitability, BT outbreaks are likely to continue to increase in range and frequency. Therefore, this research provides an updated BT modelling framework for future outbreaks around the world to explore transmission, outbreak dynamics and control measures.
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Affiliation(s)
- Joanna de Klerk
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK.
| | - Michael Tildesley
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
| | - Adam Robbins
- Selworthy Vets, Stumpy Post Surgery, Kingsbridge, Devon TQ7 4BL, UK
| | - Erin Gorsich
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
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136
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Travers SL, Hutter CR, Austin CC, Donnellan SC, Buehler MD, Ellison CE, Ruane S. VenomCap: An exon-capture probe set for the targeted sequencing of snake venom genes. Mol Ecol Resour 2024; 24:e14020. [PMID: 39297212 DOI: 10.1111/1755-0998.14020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 08/14/2024] [Accepted: 09/02/2024] [Indexed: 10/03/2024]
Abstract
Snake venoms are complex mixtures of toxic proteins that hold significant medical, pharmacological and evolutionary interest. To better understand the genetic diversity underlying snake venoms, we developed VenomCap, a novel exon-capture probe set targeting toxin-coding genes from a wide range of elapid snakes, with a particular focus on the ecologically diverse and medically important subfamily Hydrophiinae. We tested the capture success of VenomCap across 24 species, representing all major elapid lineages. We included snake phylogenomic probes in the VenomCap capture set, allowing us to compare capture performance between venom and phylogenomic loci and to infer elapid phylogenetic relationships. We demonstrated VenomCap's ability to recover exons from ~1500 target markers, representing a total of 24 known venom gene families, which includes the dominant gene families found in elapid venoms. We find that VenomCap's capture results are robust across all elapids sampled, and especially among hydrophiines, with respect to measures of target capture success (target loci matched, sensitivity, specificity and missing data). As a cost-effective and efficient alternative to full genome sequencing, VenomCap can dramatically accelerate the sequencing and analysis of venom gene families. Overall, our tool offers a model for genomic studies on snake venom gene diversity and evolution that can be expanded for comprehensive comparisons across the other families of venomous snakes.
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Affiliation(s)
- Scott L Travers
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Carl R Hutter
- Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Christopher C Austin
- Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Stephen C Donnellan
- South Australian Museum, Adelaide, Australia
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | - Matthew D Buehler
- Department of Biological Sciences and Auburn Museum of Natural History, Auburn University, Auburn, Alabama, USA
| | | | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, Chicago, Illinois, USA
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137
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Leugger F, Schmidlin M, Lüthi M, Kontarakis Z, Pellissier L. Scanning amplicons with CRISPR-Dx detects endangered amphibians in environmental DNA. Mol Ecol Resour 2024; 24:e14009. [PMID: 39152661 DOI: 10.1111/1755-0998.14009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 06/25/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.
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Affiliation(s)
- Flurin Leugger
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Michel Schmidlin
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Martina Lüthi
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Zacharias Kontarakis
- Genome Engineering and Measurement Lab, Functional Genomic Center Zurich, ETH Zürich, Zürich, Switzerland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
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138
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Guan Y, Jiang L, Wang Y, Liu G, Wu J, Luo H, Chen S, Chen F, Niinemets Ü, Chen F, Jiang Y. CmMYC2-CmMYBML1 module orchestrates the resistance to herbivory by synchronously regulating the trichome development and constitutive terpene biosynthesis in Chrysanthemum. THE NEW PHYTOLOGIST 2024; 244:914-933. [PMID: 39223898 DOI: 10.1111/nph.20081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Accepted: 08/03/2024] [Indexed: 09/04/2024]
Abstract
Trichomes are specialized epidermal outgrowths covering the aerial parts of most terrestrial plants. There is a large species variability in occurrence of different types of trichomes such that the molecular regulatory mechanism underlying the formation and the biological function of trichomes in most plant species remain unexplored. Here, we used Chrysanthemum morifolium as a model plant to explore the regulatory network in trichome formation and terpenoid synthesis and unravel the physical and chemical roles of trichomes in constitutive defense against herbivore feeding. By analyzing the trichome-related genes from transcriptome database of the trichomes-removed leaves and intact leaves, we identified CmMYC2 to positively regulate both development of T-shaped and glandular trichomes as well as the content of terpenoids stored in glandular trichomes. Furthermore, we found that the role of CmMYC2 in trichome formation and terpene synthesis was mediated by interaction with CmMYBML1. Our results reveal a sophisticated molecular mechanism wherein the CmMYC2-CmMYBML1 feedback inhibition loop regulates the formation of trichomes (non-glandular and glandular) and terpene biosynthesis, collectively contributing to the enhanced resistance to Spodoptera litura larvae feeding. Our findings provide new insights into the novel regulatory network by which the plant synchronously regulates trichome density for the physical and chemical defense against herbivory.
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Affiliation(s)
- Yaqin Guan
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Jiang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - You Wang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guanhua Liu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiayi Wu
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong Luo
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sumei Chen
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu, 51006, Estonia
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Yifan Jiang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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139
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Luna Á, Moreno E, Pinzolas JA, Oliver S, Meyer S, Brodermann O, Merino C, Karaardıç H, da Silva LP, Chatton C, Laesser J, Meier CM, Gutiérrez JS, Masero JA, Pérez J, Kullberg C, Pérez-Gómez Á, Mateos-González F, Tigges U, Toledo B, Rausell-Moreno A. Anthropogenic debris as nest material in three swift species: New insights into the interactions of atmospheric pollution with wildlife. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175171. [PMID: 39094648 DOI: 10.1016/j.scitotenv.2024.175171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Plastic pollution has become a global concern, affecting many species around the world. While well-documented for marine ecosystems, the impact of plastic pollution on terrestrial ecosystems is comparatively limited. In fact, only recently have some studies begun to explore the occurrence, pathways, and impacts of plastic in the atmosphere and on terrestrial species. Here, we assess the presence of synthetic material in nests of three swift species breeding in the Western Palearctic: the common swift (Apus apus), the pallid swift (Apus pallidus), and the alpine swift (Tachymarptis melba). Using data from 487 nests spanning 25 colonies and seven European countries, we show that 36.5 % of the examined nests contained anthropogenic materials, mainly plastic debris. Notably, Pallid swifts' nests, with 85 % of the total nests examined with plastic, rank among birds with the highest plastic content in nests. We also demonstrate that the probability of finding plastic in the nest increased substantially with the human footprint of the landscape. Last, we recorded four cases of swifts entangled in their own nest, a low proportion compared to other species studied previously. Our study provides compelling evidence that plastic pollution may also be considered a concern for other terrestrial species, particularly for birds with highly aerial lifestyles, such as other swifts. The correlation with the human footprint suggests that areas with higher human activity contribute more significantly. Moreover, the entanglement cases, although low, indicate a threat to bird health and welfare. To our knowledge, our study is the first to report a direct interaction between floating plastic debris in the atmosphere and any species. Understanding this interaction is key, not only due to the lack of research on the topic, but also because it highlights that plastic pollution is a multifaceted environmental issue affecting various ecosystem categories, and the broader implications of atmospheric plastic circulation on wildlife and ecosystems health.
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Affiliation(s)
- Álvaro Luna
- Department of Biosciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Madrid, Spain.
| | - Elena Moreno
- Ecourbe, Association for the Protection of Urban Environment, Seville, Spain
| | | | | | | | | | - Carlos Merino
- Departamento de Zoología, Universidad de Sevilla, Spain
| | - Hakan Karaardıç
- Alanya Alaaddin Keykubat University, Education Faculty, Department of Math and Science Education, Alanya, Antalya, Türkiye
| | - Luis P da Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Caroline Chatton
- Musée d'histoire naturelle Fribourg MHNF, Chemin du Musée 6, CH-1700 Fribourg, Switzerland.
| | - Jacques Laesser
- Swiss Ornithological Institute, Seerose 1, CH-6204 Sempach, Switzerland.
| | - Christoph M Meier
- Swiss Ornithological Institute, Seerose 1, CH-6204 Sempach, Switzerland.
| | - Jorge S Gutiérrez
- Department of Anatomy, Cell Biology and Zoology, Faculty of Sciences, University of Extremadura, 06006 Badajoz, Spain; Ecology in the Anthropocene, Associated Unit CSIC-UEX, Faculty of Sciences, University of Extremadura, 06006 Badajoz, Spain.
| | - José A Masero
- Department of Anatomy, Cell Biology and Zoology, Faculty of Sciences, University of Extremadura, 06006 Badajoz, Spain; Ecology in the Anthropocene, Associated Unit CSIC-UEX, Faculty of Sciences, University of Extremadura, 06006 Badajoz, Spain
| | | | - Cecilia Kullberg
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Álvaro Pérez-Gómez
- Universidad de Cádiz, Departamento de Biología (Área de Botánica), Campus Río San Pedro, 11510 Puerto Real, Spain.
| | | | | | - Bernardo Toledo
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), 41092 Sevilla, Spain
| | - Armand Rausell-Moreno
- Department of Biogeography and Global Change, National Museum of Natural Sciences (MNCN-CSIC), Madrid, Spain.
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140
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Liu X, Yu Y, Yu H, Sarkar B, Zhang Y, Yang Y, Qin S. Nonbiodegradable microplastic types determine the diversity and structure of soil microbial communities: A meta-analysis. ENVIRONMENTAL RESEARCH 2024; 260:119663. [PMID: 39043354 DOI: 10.1016/j.envres.2024.119663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/07/2024] [Accepted: 07/20/2024] [Indexed: 07/25/2024]
Abstract
As an emerging contaminant, microplastics (MPs) have received considerable attention for their potential threat to the soil environment. However, the response of soil bacterial and fungal communities to MPs exposure remains unclear. In this study, we conducted a global meta-analysis of 95 publications and 2317 observations to assess the effects of nonbiodegradable MP properties and exposure conditions on soil microbial biomass, alpha and beta diversity, and community structure. Our results indicate that MPs increased (p < 0.05) soil active microbial biomass by 42%, with the effect varying with MPs type, exposure concentration, exposure time and soil pH. MPs concentration was identified as the most important factor controlling the response of soil microbial biomass to MPs. MPs addition decreased (p < 0.05) the soil bacterial Shannon and Chao1 indices by 2% and 3%, respectively, but had limited effects (p > 0.05) on soil fungal Shannon and Chao1 indices. The type of MPs and exposure time determined the effects of MPs on bacterial Shannon and Chao1 indices, while the type of MPs and soil pH controlled the response ratios of fungal Shannon and Chao1 indices to MPs. Specifically, soil organic carbon (SOC) was the major factor regulating the response ratio of bacterial alpha diversity index to MPs. The presence of MPs did not affect soil bacterial community structure and beta diversity. Our results highlight that MPs reduced bacterial diversity and richness but increased the soil active microbial biomass, suggesting that MPs could disrupt biogeochemical cycles by promoting the growth of specific microorganisms.
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Affiliation(s)
- Xinhui Liu
- Hebei Provincial Key Laboratory of Soil Ecology, Hebei Provincial Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, Hebei, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongxiang Yu
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
| | - Haiyang Yu
- College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Binoy Sarkar
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Yanyan Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuyi Yang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Shuping Qin
- Hebei Provincial Key Laboratory of Soil Ecology, Hebei Provincial Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, Hebei, China.
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141
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Oostdijk M, Elsler LG, Van Deelen J, Auping WL, Kwakkel J, Schadeberg A, Vastenhoud BMJ, Nedelciu CE, Berzaghi F, Prellezo R, Wisz MS. Modeling fisheries and carbon sequestration ecosystem services under deep uncertainty in the ocean twilight zone. AMBIO 2024; 53:1632-1648. [PMID: 39207669 PMCID: PMC11436683 DOI: 10.1007/s13280-024-02044-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/17/2024] [Accepted: 05/21/2024] [Indexed: 09/04/2024]
Abstract
Mesopelagic fishes are a vital component of the biological carbon pump and are, to date, largely unexploited. In recent years, there has been an increased interest in harvesting the mesopelagic zone to produce fish feed for aquaculture. However, great uncertainties exist in how the mesopelagic zone interacts with the climate and food webs, presenting a dilemma for policy. Here, we investigate the consequences of potential policies relating to mesopelagic harvest quotas with a dynamic social-ecological modeling approach, combining system dynamics and global sensitivity analyses informed by participatory modeling. Our analyses reveal that, in simulations of mesopelagic fishing scenarios, uncertainties about mesopelagic fish population dynamics have the most pronounced influence on potential outcomes. The analysis also shows that prioritizing the development of the fishing industry over environmental protection would lead to a significantly higher social cost of climate change to society. Given the large uncertainties and the potential large impacts on oceanic carbon sequestration, a precautionary approach to developing mesopelagic fisheries is warranted.
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Affiliation(s)
- Maartje Oostdijk
- Faculty of Agricultural Sciences, Agricultural University of Iceland, Keldnaholt, Árleynir 22, 112, Reykjavík, Iceland.
| | - Laura G Elsler
- Harvard. T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Julie Van Deelen
- Policy Analysis Section, Department of Multi-Actor Systems, Faculty of Technology, Policy and Management, Delft University of Technology, Jaffalaan 5, 2628 BX, Delft, The Netherlands
| | - Willem L Auping
- Policy Analysis Section, Department of Multi-Actor Systems, Faculty of Technology, Policy and Management, Delft University of Technology, Jaffalaan 5, 2628 BX, Delft, The Netherlands.
| | - Jan Kwakkel
- Policy Analysis Section, Department of Multi-Actor Systems, Faculty of Technology, Policy and Management, Delft University of Technology, Jaffalaan 5, 2628 BX, Delft, The Netherlands
| | - Amanda Schadeberg
- Environmental Economics and Natural Resources Group, Wageningen University, Hollandseweg 1, 6706 KN, Wageningen, The Netherlands
- Environmental Policy Group, Wageningen University, Hollandseweg 1, 6706 KN, Wageningen, The Netherlands
| | - Berthe M J Vastenhoud
- National Institute of Aquatic Resources, Technical University of Denmark, Kemitorvet 201, 2800, Kgs. Lyngby, Denmark
| | - Claudiu Eduard Nedelciu
- Department of Geography, System Dynamics Group, University of Bergen, Fosswinckelsgate 6, 5007, Bergen, Norway
| | - Fabio Berzaghi
- Ocean Sustainability, Governance and Management, World Maritime University, Fiskehamnsgatan 1, 211 18, Malmö, Sweden
| | - Raul Prellezo
- AZTI. Marine Research Unit. Txatxarramendi Ugartea Z/G, 48395, Txatxarramendi, Sukarrieta, Spain
| | - Mary S Wisz
- Science Institute, University of Iceland, Saemundargata 2, 101, Reykjavik, Iceland
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142
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Caccavo JA, Arantes LS, Celemín E, Mbedi S, Sparmann S, Mazzoni CJ. Whole-genome resequencing improves the utility of otoliths as a critical source of DNA for fish stock research and monitoring. Mol Ecol Resour 2024; 24:e14013. [PMID: 39233613 DOI: 10.1111/1755-0998.14013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/23/2024] [Accepted: 08/15/2024] [Indexed: 09/06/2024]
Abstract
Fish ear bones, known as otoliths, are often collected in fisheries to assist in management, and are a common sample type in museum and national archives. Beyond their utility for ageing, morphological and trace element analysis, otoliths are a repository of valuable genomic information. Previous work has shown that DNA can be extracted from the trace quantities of tissue remaining on the surface of otoliths, despite the fact that they are often stored dry at room temperature. However, much of this work has used reduced representation sequencing methods in clean lab conditions, to achieve adequate yields of DNA, libraries and ultimately single-nucleotide polymorphisms (SNPs). Here, we pioneer the use of small-scale (spike-in) sequencing to screen contemporary otolith samples prepared in regular molecular biology (in contrast to clean) laboratories for contamination and quality levels, submitting for whole-genome resequencing only samples above a defined endogenous DNA threshold. Despite the typically low quality and quantity of DNA extracted from otoliths, we are able to produce whole-genome libraries and ultimately sets of filtered, unlinked and even putatively adaptive SNPs of ample numbers for downstream uses in population, climate and conservation genomics. By comparing with a set of tissue samples from the same species, we are able to highlight the quality and efficacy of otolith samples from DNA extraction and library preparation, to bioinformatic preprocessing and SNP calling. We provide detailed schematics, protocols and scripts of our approach, such that it can be adopted widely by the community, improving the use of otoliths as a source of valuable genomic data.
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Affiliation(s)
- Jilda Alicia Caccavo
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung, IZW, Berlin, Germany
| | - Larissa S Arantes
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung, IZW, Berlin, Germany
| | - Enrique Celemín
- Institute of Biochemistry and Biology, Evolutionary Biology & Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Susan Mbedi
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Museum für Naturkunde, Berlin, Germany
| | - Sarah Sparmann
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), Berlin, Germany
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung, IZW, Berlin, Germany
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143
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Camenzind T, Aguilar-Trigueros CA, Heuck MK, Maerowitz-McMahan S, Rillig MC, Cornwell WK, Powell JR. Progressing beyond colonization strategies to understand arbuscular mycorrhizal fungal life history. THE NEW PHYTOLOGIST 2024; 244:752-759. [PMID: 39229862 DOI: 10.1111/nph.20090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 08/07/2024] [Indexed: 09/05/2024]
Abstract
Knowledge of differential life-history strategies in arbuscular mycorrhizal (AM) fungi is relevant for understanding the ecology of this group and its potential role in sustainable agriculture and carbon sequestration. At present, AM fungal life-history theories often focus on differential investment into intra- vs extraradical structures among AM fungal taxa, and its implications for plant benefits. With this Viewpoint we aim to expand these theories by integrating a mycocentric economics- and resource-based life-history framework. As in plants, AM fungal carbon and nutrient demands are stoichiometrically coupled, though uptake of these elements is spatially decoupled. Consequently, investment in morphological structures for carbon vs nutrient uptake is not in competition. We argue that understanding the ecology and evolution of AM fungal life-history trade-offs requires increased focus on variation among structures foraging for the same element, that is within intra- or extraradical structures (in our view a 'horizontal' axis), not just between them ('vertical' axis). Here, we elaborate on this argument and propose a range of plausible life-history trade-offs that could lead to the evolution of strategies in AM fungi, providing testable hypotheses and creating opportunities to explain AM fungal co-existence, and the context-dependent effects of AM fungi on plant growth and soil carbon dynamics.
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Affiliation(s)
- Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Carlos A Aguilar-Trigueros
- Department of Biological and Environmental Sciences, University of Jyväskylä, 40014, Jyväskylä, Finland
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Meike K Heuck
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Solomon Maerowitz-McMahan
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Will K Cornwell
- Ecology and Evolution Research Centre, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
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144
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Cuartero J, Querejeta JI, Prieto I, Frey B, Alguacil MM. Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175006. [PMID: 39069184 DOI: 10.1016/j.scitotenv.2024.175006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.
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Affiliation(s)
- J Cuartero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland.
| | - J I Querejeta
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - I Prieto
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain; Area de Ecología, Facultad de Ciencias Biológicas y Ambientales, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - B Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - M M Alguacil
- Departamento de Conservación de Suelos y Agua, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas, Murcia, Spain
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145
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Downs CJ, Sobolewski ME. The Promise of a Pointillist Perspective for Comparative Immunology. Physiology (Bethesda) 2024; 39:0. [PMID: 38808754 DOI: 10.1152/physiol.00012.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 05/30/2024] Open
Abstract
Most studies in comparative immunology involve investigations into the detailed mechanisms of the immune system of a nonmodel organism. Although this approach has been insightful, it has promoted a deep understanding of only a handful of species, thus inhibiting the recognition of broad taxonomic patterns. Here, we call for investigating the immune defenses of numerous species within a pointillist framework, that is, the meticulous, targeted collection of data from dozens of species and investigation of broad patterns of organismal, ecological, and evolutionary forces shaping those patterns. Without understanding basic immunological patterns across species, we are limited in our ability to extrapolate and/or translate our findings to other organisms, including humans. We illustrate this point by focusing predominantly on the biological scaling literature with some integrations of the pace of life literature, as these perspectives have been the most developed within this framework. We also highlight how the more traditional approach in comparative immunology works synergistically with a pointillist approach, with each approach feeding back into the other. We conclude that the pointillist approach promises to illuminate comprehensive theories about the immune system and enhance predictions in a wide variety of domains, including host-parasite dynamics and disease ecology.
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Affiliation(s)
- Cynthia J Downs
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States
| | - Marissa E Sobolewski
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States
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146
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Telles-de-Deus J, Guimarães LDO, Rocha EC, Helfstein VC, Reginato SL, Mucci LF, Bergo ES, de Camargo-Neves VLF, Kirchgatter K. COI DNA barcoding to differentiate Haemagogus janthinomys and Haemagogus capricornii (Diptera: Culicidae) mosquitoes. Acta Trop 2024; 259:107377. [PMID: 39245155 DOI: 10.1016/j.actatropica.2024.107377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/10/2024]
Abstract
The genus Haemagogus (Diptera: Culicidae) includes species that are important vectors of pathogens such as the yellow fever virus. The accurate identification of these species is essential for the control of zoonoses. Females of Hg. capricornii and Hg. janthinomys are morphologically indistinguishable, which makes the use of alternative identification techniques desirable. This study aimed to obtain sequences of the mitochondrial cytochrome c oxidase I (COI) gene, in the region widely used for DNA barcoding, of Haemagogus specimens from the state of São Paulo, Brazil, to evaluate the effectiveness of these sequences in the molecular identification of the species. A total of 37 female and 2 male mosquitoes were collected in various locations in the state of São Paulo, using methods such as hand-nets, Shannon traps, CDC light traps with CO2 bait and Nasci aspirators. The sequences of a 710 bp fragment of the COI gene were amplified by PCR and sequenced. A phylogenetic tree reconstruction was conducted using the Bayesian approach implemented in MrBayes v3.2.2, providing support values for taxa where genetic clusters may indicate the presence of new or cryptic species. We obtained 39 COI sequences representing three species: Haemagogus capricornii, Haemagogus leucocelaenus, and Haemagogus janthinomys. Bayesian analysis of the sequences produced clades that corroborate the morphological identification of the species. The separation of Hg. capricornii and Hg. janthinomys received 100 % statistical support and the Hg. capricornii was very well supported (91 %). The two sequences from male specimens, morphologically identified as Hg. capricornii, were grouped in the same clade, a sister clade of Hg. janthinomys. It is important to highlight that the Hg. janthinomys were positioned in several subclades, showing a polymorphism of this species within the state, a situation not observed for Hg. capricornii. For the first time, sequences of the mtCOI gene from Hg. capricornii were obtained and related to morphologically identified specimens. COI sequences proved effective in the molecular identification of Haemagogus species. This study contributes to the expansion of the GenBank database, providing the first sequences of Hg. capricornii and new sequences for Hg. janthinomys and Hg. leucocelaenus.
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Affiliation(s)
| | | | - Esmenia Coelho Rocha
- Postgraduate Program in Tropical Medicine, School of Medicine, University of São Paulo, São Paulo 05403-000, SP, Brazil
| | - Vanessa Christe Helfstein
- Pasteur Institute, São Paulo 01027-000, SP, Brazil; Postgraduate Program in Tropical Medicine, School of Medicine, University of São Paulo, São Paulo 05403-000, SP, Brazil
| | | | | | | | | | - Karin Kirchgatter
- Pasteur Institute, São Paulo 01027-000, SP, Brazil; Postgraduate Program in Tropical Medicine, School of Medicine, University of São Paulo, São Paulo 05403-000, SP, Brazil.
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147
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Koller D, Kocot KM, Degnan BM, Wollesen T. Developmental gene expression in the eyes of the pygmy squid Xipholeptos notoides. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:483-498. [PMID: 39161250 DOI: 10.1002/jez.b.23270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 06/11/2024] [Accepted: 07/24/2024] [Indexed: 08/21/2024]
Abstract
The eyes of squids, octopuses, and cuttlefish are a textbook example for evolutionary convergence, due to their striking similarity to those of vertebrates. For this reason, studies on cephalopod photoreception and vision are of importance for a broader audience. Previous studies showed that genes such as pax6, or certain opsin-encoding genes, are evolutionarily highly conserved and play similar roles during ontogenesis in remotely related bilaterians. In this study, genes that encode photosensitive proteins and Reflectins are identified and characterized. The expression patterns of rhodopsin, xenopsin, retinochrome, and two reflectin genes have been visualized in developing embryos of the pygmy squid Xipholeptos notoides by in situ hybridization experiments. Rhodopsin is not only expressed in the retina of X. notoides but also in the olfactory organ and the dorsal parolfactory vesicles, the latter a cephalopod apomorphy. Both reflectin genes are expressed in the eyes and in the olfactory organ. These findings corroborate previous studies that found opsin genes in the transcriptomes of the eyes and several extraocular tissues of various cephalopods. Expression of rhodopsin, xenopsin, retinochrome, and the two reflectin genes in the olfactory organ is a finding that has not been described so far. In other organisms, it has been shown that Retinochrome and Rhodopsin proteins are obligatorily associated with each other as both molecules rely on each other for Retinal isomerisation. In addition, we demonstrate that retinochrome is expressed in the retina of X. notoides and in the olfactory organ. This study shows numerous new expression patterns for Opsin-encoding genes in organs that have not been associated with photoreception before, suggesting that either Opsins may not only be involved in photoreception or organs such as the olfactory organ are involved in photoreception.
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Affiliation(s)
- David Koller
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Kevin M Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| | - Bernard M Degnan
- Centre for Marine Science and School of the Environment, University of Queensland, Brisbane, Queensland, Australia
| | - Tim Wollesen
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
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148
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Song T, Huang Y, Fang L, Li Y, Li J, Chang J. Non-native species in marine protected areas: Global distribution patterns. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 22:100453. [PMID: 39175512 PMCID: PMC11338962 DOI: 10.1016/j.ese.2024.100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 08/24/2024]
Abstract
Marine protected areas (MPAs) across various countries have contributed to safeguarding coastal and marine environments. Despite these efforts, marine non-native species (NNS) continue to threaten biodiversity and ecosystems, even within MPAs. Currently, there is a lack of comprehensive studies on the inventories, distribution patterns, and effect factors of NNS within MPAs. Here we show a database containing over 15,000 occurrence records of 2714 marine NNS across 16,401 national or regional MPAs worldwide. To identify the primary mechanisms driving the occurrence of NNS, we utilize model selection with proxies representing colonization pressure, environmental variables, and MPA characteristics. Among the environmental predictors analyzed, sea surface temperature emerged as the sole factor strongly associated with NNS richness. Higher sea surface temperatures are linked to increased NNS richness, aligning with global marine biodiversity trends. Furthermore, human activities help species overcome geographical barriers and migration constraints. Consequently, this influences the distribution patterns of marine introduced species and associated environmental factors. As global climate change continues to alter sea temperatures, it is crucial to protect marine regions that are increasingly vulnerable to intense human activities and biological invasions.
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Affiliation(s)
- Tianjian Song
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yuxin Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Lei Fang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yonghua Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Junsheng Li
- Command Center for Comprehensive Survey of Natural Resources, China Geological Survey Bureau, Beijing, 100055, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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149
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Hsieh EM, Dolezal AG. Nutrition, pesticide exposure, and virus infection interact to produce context-dependent effects in honey bees (Apis mellifera). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175125. [PMID: 39084359 DOI: 10.1016/j.scitotenv.2024.175125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
Declines in pollinator health are frequently hypothesized to be the combined result of multiple interacting biotic and abiotic stressors; namely, nutritional limitations, pesticide exposure, and infection with pathogens and parasites. Despite this hypothesis, most studies examining stressor interactions have been constrained to two concurrent factors, limiting our understanding of multi-stressor dynamics. Using honey bees as a model, we addressed this gap by studying how variable diet, field-realistic levels of multiple pesticides, and virus infection interact to affect survival, infection intensity, and immune and detoxification gene expression. Although we found evidence that agrochemical exposure (a field-derived mixture of chlorpyrifos and two fungicides) can exacerbate infection and increase virus-induced mortality, this result was nutritionally-dependent, only occurring when bees were provided artificial pollen. Provisioning with naturally-collected polyfloral pollen inverted the effect, reducing virus-induced mortality and suggesting a hormetic response. To test if the response was pesticide specific, we repeated our experiment with a pyrethroid (lambda-cyhalothrin) and a neonicotinoid (thiamethoxam), finding variable results. Finally, to understand the underpinnings of these effects, we measured viral load and expression of important immune and detoxification genes. Together, our results show that multi-stressor interactions are complex and highly context-dependent, but have great potential to affect bee health and physiology.
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Affiliation(s)
- Edward M Hsieh
- Department of Entomology, University of Illinois Urbana-Champaign, 505 S. Goodwin, Urbana, IL 61801-3795, USA.
| | - Adam G Dolezal
- Department of Entomology, University of Illinois Urbana-Champaign, 505 S. Goodwin, Urbana, IL 61801-3795, USA
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150
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Shichijo T, Ikeda T, Higashide D, Omori A, Suzuki T, Suzuki M. Quantification of wildlife visits to pig farms via camera traps in Japan. Prev Vet Med 2024; 232:106318. [PMID: 39241525 DOI: 10.1016/j.prevetmed.2024.106318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 07/31/2024] [Accepted: 08/20/2024] [Indexed: 09/09/2024]
Abstract
Infectious diseases in livestock not only cause significant economic losses but also affect food security. Although wildlife may be involved in these infectious diseases by serving as reservoirs, research has primarily focused on livestock and related species. Moreover, while these species represent a potential threat in wildlife-borne infectious diseases, comprehensive surveys of the presence of various species are limited. In this study, we aimed to quantitatively investigate the occurrence of various mammals and birds at three pig farms in Japan. We conducted camera trap surveys from October 15, 2020, to March 24, 2022, and determined the relative abundance index inside and outside the sanitary control zone. Wild boar (Sus scrofa), sika deer (Cervus nippon), and Japanese serow (Capricornis crispus) were photographed only outside the sanitary control zone. In contrast, small and medium-sized mammals, such as feral cats (Felis catus), raccoons (Procyon lotor), and rodent species (Muridae), and birds, such as the rufous oriental turtle dove (Streptopelia orientalis) and crows of the genus Corvus, were photographed both inside and outside the sanitary control zone. This comprehensive quantitative evidence suggests that various mammals and birds may be in indirect contact with livestock, highlighting the need to improve biosecurity at livestock farms. Moreover, while fences are effective against large mammals, they are inefficient against small to medium-sized mammals and birds. Therefore, the results of this study provide important insights into enhancing biosecurity on livestock farms by strengthening physical fencing, disinfecting clothing and equipment, and complying with standards of hygiene management.
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Affiliation(s)
- Tomoya Shichijo
- Research Center for Wildlife Management, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Joint Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
| | - Takashi Ikeda
- Research Center for Wildlife Management, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Gifu Wildlife Management Promotion Center, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan.
| | - Daishi Higashide
- Research Center for Wildlife Management, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Gifu Wildlife Management Promotion Center, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.
| | - Akitaka Omori
- Research Center for Wildlife Management, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Yamaguchi Museum, 8-2 Kasuga, Yamaguchi, Yamaguchi 753-0073, Japan.
| | - Takaaki Suzuki
- Research Center for Wildlife Management, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan; Gifu Wildlife Management Promotion Center, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
| | - Masatsugu Suzuki
- Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
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