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Rojas de Oliveira H, Chud TCS, Oliveira GA, Hermisdorff IC, Narayana SG, Rochus CM, Butty AM, Malchiodi F, Stothard P, Miglior F, Baes CF, Schenkel FS. Genome-wide association analyses reveal copy number variant regions associated with reproduction and disease traits in Canadian Holstein cattle. J Dairy Sci 2024; 107:7052-7063. [PMID: 38788846 DOI: 10.3168/jds.2023-24295] [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: 10/10/2023] [Accepted: 04/01/2024] [Indexed: 05/26/2024]
Abstract
This study aimed to evaluate the impact of copy number variants (CNV) on 13 reproduction and 12 disease traits in Holstein cattle. Intensity signal files containing log R ratio and B allele frequency information from 13,730 Holstein animals genotyped with a 95K SNP panel, and 8,467 Holstein animals genotyped with a 50K SNP panel were used to identify the CNVs. Subsequently, the identified CNVs were validated using whole-genome sequence data from 126 animals, resulting in 870 high-confidence copy number variant regions (CNVR) on 12,131 animals. Out of these, 54 CNVR had frequencies higher than or equal to 1% in the population and were used in the genome-wide association analysis (one CNVR at a time, including the G matrix). Results revealed that 4 CNVR were significantly associated with at least one of the traits analyzed in this study. Specifically, 2 CNVR were associated with 3 reproduction traits (i.e., calf survival, first service to conception, and nonreturn rate), and 2 CNVR were associated with 2 disease traits (i.e., metritis and retained placenta). These CNVR harbored genes implicated in immune response, cellular signaling, and neuronal development, supporting their potential involvement in these traits. Further investigations to unravel the mechanistic and functional implications of these CNVR on the mentioned traits are warranted.
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Affiliation(s)
- Hinayah Rojas de Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1.
| | - Tatiane C S Chud
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Gerson A Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Isis C Hermisdorff
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Saranya G Narayana
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; Lactanet, Guelph, ON, Canada N1K 1E5
| | - Christina M Rochus
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | | | - Francesca Malchiodi
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; Semex, Guelph, ON, Canada N1H 6J2
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada T6G 2H1
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; Lactanet, Guelph, ON, Canada N1K 1E5
| | - Christine F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland 3012
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1.
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Wang K, Luigi-Sierra MG, Castelló A, Figueiredo-Cardoso T, Mercadé A, Martínez A, Delgado JV, Álvarez JF, Noce A, Wang M, Jordana J, Amills M. Identification of nonsense variants in the genomes of 15 Murciano-Granadina bucks and analysis of their segregation in parent-offspring trios. J Dairy Sci 2024:S0022-0302(24)01097-X. [PMID: 39218071 DOI: 10.3168/jds.2024-24952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
Nonsense variants can inactivate gene function by causing the synthesis of truncated proteins or by inducing nonsense mediated decay of messenger RNAs. The occurrence of such variants in the genomes of livestock species is modulated by multiple demographic and selective factors. Even though nonsense variants can have causal effects on embryo lethality, abortions, and disease, their genomic distribution and segregation in domestic goats have not been characterized in depth yet. In this work, we have sequenced the genomes of 15 Murciano-Granadina bucks with an average coverage of 32.92 × ± 1.45 × . Bioinformatic analysis revealed 947 nonsense variants consistently detected with SnpEff and Ensembl-VEP. These variants were especially abundant in the 3'end of the protein-coding regions. Genes related to olfactory perception, ATPase activity coupled to transmembrane movement of substances, defense to virus, hormonal response, and sensory perception of taste were particularly enriched in nonsense variants. Seventeen nonsense variants expected to have harmful effects on fitness were genotyped in parent-offspring trios. We observed that several nonsense variants predicted to be lethal based on mouse knockout data did not have such effect, a finding that could be explained by the existence of multiple mechanisms counteracting lethality. These findings demonstrate that predicting the effects of putative nonsense variants on fitness is extremely challenging. As a matter of fact, such a goal could only be achieved by generating a high quality telomere-to-telomere goat reference genome combined with carefully curated annotation and functional testing of promising candidate variants.
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Affiliation(s)
- Ke Wang
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.; Chinese Academy of Tropical Agricultural Sciences, Zhanjiang Experimental Station, Zhanjiang, Guangdong, 524000, China.; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - María Gracia Luigi-Sierra
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Anna Castelló
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Taina Figueiredo-Cardoso
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Anna Mercadé
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | | | | | - Antonia Noce
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Mingjing Wang
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Marcel Amills
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain..
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Hawkins SJ, Gärtner Y, Offner T, Weiss L, Maiello G, Hassenklöver T, Manzini I. The olfactory network of larval Xenopus laevis regenerates accurately after olfactory nerve transection. Eur J Neurosci 2024; 60:3719-3741. [PMID: 38758670 DOI: 10.1111/ejn.16375] [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: 12/07/2023] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 05/19/2024]
Abstract
Across vertebrate species, the olfactory epithelium (OE) exhibits the uncommon feature of lifelong neuronal turnover. Epithelial stem cells give rise to new neurons that can adequately replace dying olfactory receptor neurons (ORNs) during developmental and adult phases and after lesions. To relay olfactory information from the environment to the brain, the axons of the renewed ORNs must reconnect with the olfactory bulb (OB). In Xenopus laevis larvae, we have previously shown that this process occurs between 3 and 7 weeks after olfactory nerve (ON) transection. In the present study, we show that after 7 weeks of recovery from ON transection, two functionally and spatially distinct glomerular clusters are reformed in the OB, akin to those found in non-transected larvae. We also show that the same odourant response tuning profiles observed in the OB of non-transected larvae are again present after 7 weeks of recovery. Next, we show that characteristic odour-guided behaviour disappears after ON transection but recovers after 7-9 weeks of recovery. Together, our findings demonstrate that the olfactory system of larval X. laevis regenerates with high accuracy after ON transection, leading to the recovery of odour-guided behaviour.
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Affiliation(s)
- Sara J Hawkins
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus Liebig University Gießen, Gießen, Germany
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Yvonne Gärtner
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus Liebig University Gießen, Gießen, Germany
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
- Department of Neurology, Focus Program Translational Neuroscience (FTN) and Immunotherapy (FZI), Rhine-Main Neuroscience Network (rmn2), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Offner
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus Liebig University Gießen, Gießen, Germany
| | - Lukas Weiss
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus Liebig University Gießen, Gießen, Germany
| | - Guido Maiello
- Department of Experimental Psychology, Justus Liebig University Gießen, Gießen, Germany
- School of Psychology, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Thomas Hassenklöver
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus Liebig University Gießen, Gießen, Germany
| | - Ivan Manzini
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus Liebig University Gießen, Gießen, Germany
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Fulton KA, Zimmerman D, Samuel A, Vogt K, Datta SR. Common principles for odour coding across vertebrates and invertebrates. Nat Rev Neurosci 2024; 25:453-472. [PMID: 38806946 DOI: 10.1038/s41583-024-00822-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2024] [Indexed: 05/30/2024]
Abstract
The olfactory system is an ideal and tractable system for exploring how the brain transforms sensory inputs into behaviour. The basic tasks of any olfactory system include odour detection, discrimination and categorization. The challenge for the olfactory system is to transform the high-dimensional space of olfactory stimuli into the much smaller space of perceived objects and valence that endows odours with meaning. Our current understanding of how neural circuits address this challenge has come primarily from observations of the mechanisms of the brain for processing other sensory modalities, such as vision and hearing, in which optimized deep hierarchical circuits are used to extract sensory features that vary along continuous physical dimensions. The olfactory system, by contrast, contends with an ill-defined, high-dimensional stimulus space and discrete stimuli using a circuit architecture that is shallow and parallelized. Here, we present recent observations in vertebrate and invertebrate systems that relate the statistical structure and state-dependent modulation of olfactory codes to mechanisms of perception and odour-guided behaviour.
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Affiliation(s)
- Kara A Fulton
- Department of Neuroscience, Harvard Medical School, Boston, MA, USA
| | - David Zimmerman
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Aravi Samuel
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Katrin Vogt
- Department of Physics, Harvard University, Cambridge, MA, USA.
- Department of Biology, University of Konstanz, Konstanz, Germany.
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany.
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5
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Espinoza-Carhuancho F, Mauricio F, Mauricio-Vilchez C, Galarza-Valencia D, Medina J, Pacheco-Mendoza J, Mayta-Tovalino F. A scientometric analysis of research trends, visualization, and emerging patterns in canine olfactory detection for cancer. Vet World 2024; 17:1430-1434. [PMID: 39185062 PMCID: PMC11344121 DOI: 10.14202/vetworld.2024.1430-1434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/30/2024] [Indexed: 08/27/2024] Open
Abstract
Background and Aim Dogs can detect specific cancer odors with their exceptional sense of smell. This study aimed to conduct a scientometric analysis of canine olfactory detection in oncology, identifying trends, visualizations, and patterns. Materials and Methods A retrospective observational study was conducted using a quantitative-scientometric approach. Scopus was comprehensively searched using terms related to canine olfactory detection in oncology. Documents indexed in Scival software (Elsevier) and published between 2013 and 2022 were included. Results Claire M. Guest, Rob Harris, and Giuseppe Lippi authored significant academic work. Journals such as Journal of Breath Research and PLoS One rank highly in publications and citations due to significant citation ratios, according to CiteScore's quartile-based impact analysis. According to Lotka's and Bradford's laws, a small group of authors and the Journal of Breath Research, respectively, dominate production in their fields. Conclusion This analysis forms a solid base for future research on canine olfactory detection in oncology. The collaborative essence of this multidisciplinary field is emphasized by the key contributors and identified patterns, with journals in the Q1 and Q2 quartiles of CiteScore holding significant importance.
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Affiliation(s)
- Fran Espinoza-Carhuancho
- Bibliometrics, Evidence Evaluation and Systematic Review Group, Human Medicine Career, Universidad Cientifica del Sur, Lima, Peru
| | - Franco Mauricio
- Research, Innovation and Entrepreneurship Unit, Universidad Nacional Federico Villarreal, Lima, Peru
| | - Cesar Mauricio-Vilchez
- Department of Academic, Faculty of Medical Technology, Universidad Nacional Federico Villarreal, Lima, Peru
| | - Diego Galarza-Valencia
- Research, Innovation and Entrepreneurship Unit, Universidad Nacional Federico Villarreal, Lima, Peru
| | - Julia Medina
- Research, Innovation and Entrepreneurship Unit, Universidad Nacional Federico Villarreal, Lima, Peru
| | - Josmel Pacheco-Mendoza
- Bibliometrics, Evidence Evaluation and Systematic Review Group, Human Medicine Career, Universidad Cientifica del Sur, Lima, Peru
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Choi YR, Na HJ, Lee JA, Kim Y, Kim YS, Kim MJ. Discovery of (-)-epigallocatechin gallate, a novel olfactory receptor 2AT4 agonist that regulates proliferation and apoptosis in leukemia cells. Heliyon 2024; 10:e30298. [PMID: 38778941 PMCID: PMC11108860 DOI: 10.1016/j.heliyon.2024.e30298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Olfactory receptors (ORs), the largest family of G protein-coupled receptors (GPCRs), are ectopically expressed in cancer cells and are involved in cellular physiological processes, but their function as anticancer targets is still potential. OR2AT4 is expressed in leukemia cells, influencing the proliferation and apoptosis, yet the limited number of known OR2AT4 agonists makes it challenging to fully generalize the receptor's function. In this study, we aimed to identify new ligands for OR2AT4 and to investigate their functions and mechanisms in K562 leukemia cells. After producing the recombinant OR2AT4 protein, immobilizing it on a surface plasmon resonance chip, and conducting screening to confirm binding activity using 258 chemicals, five novel OR2AT4 ligands were discovered. As a result of examining changes in intracellular calcium by five ligands in OR2AT4-expressing cells and K562 cells, (-)-epigallocatechin gallate (EGCG) was identified as an OR2AT4 agonist in both cells. EGCG reduced the viability of K562 cells and induced apoptosis in K562 cells. EGCG increased the expression of cleaved caspase 3/8 and had no effect on the expression of Bax and Bcl-2, indicating that it induced apoptosis through the extrinsic pathway. Additionally, the initiation of the extrinsic apoptosis pathway in EGCG-induced K562 cells was due to the activation of OR2AT4, using an OR2AT4 antagonist. This study highlights the potential of EGCG as an anti-cancer agent against leukemia and OR2AT4 as a target, making it a new anti-cancer drug.
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Affiliation(s)
- Yae Rim Choi
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hyun-Jin Na
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea
| | - Jin-Ah Lee
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea
| | - Yiseul Kim
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea
| | - Young-Suk Kim
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Min Jung Kim
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea
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7
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Chen HW, Ma CP, Chin E, Chen YT, Wang TC, Kuo YP, Su CH, Huang PJ, Tan BCM. Imbalance in Unc80 RNA Editing Disrupts Dynamic Neuronal Activity and Olfactory Perception. Int J Mol Sci 2024; 25:5985. [PMID: 38892173 PMCID: PMC11172567 DOI: 10.3390/ijms25115985] [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: 03/29/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
A-to-I RNA editing, catalyzed by the ADAR protein family, significantly contributes to the diversity and adaptability of mammalian RNA signatures, aligning with developmental and physiological needs. Yet, the functions of many editing sites are still to be defined. The Unc80 gene stands out in this context due to its brain-specific expression and the evolutionary conservation of its codon-altering editing event. The precise biological functions of Unc80 and its editing, however, are still largely undefined. In this study, we first demonstrated that Unc80 editing occurs in an ADAR2-dependent manner and is exclusive to the brain. By employing the CRISPR/Cas9 system to generate Unc80 knock-in mouse models that replicate the natural editing variations, our findings revealed that mice with the "gain-of-editing" variant (Unc80G/G) exhibit heightened basal neuronal activity in critical olfactory regions, compared to the "loss-of-editing" (Unc80S/S) counterparts. Moreover, an increase in glutamate levels was observed in the olfactory bulbs of Unc80G/G mice, indicating altered neurotransmitter dynamics. Behavioral analysis of odor detection revealed distinctive responses to novel odors-both Unc80 deficient (Unc80+/-) and Unc80S/S mice demonstrated prolonged exploration times and heightened dishabituation responses. Further elucidating the olfactory connection of Unc80 editing, transcriptomic analysis of the olfactory bulb identified significant alterations in gene expression that corroborate the behavioral and physiological findings. Collectively, our research advances the understanding of Unc80's neurophysiological functions and the impact of its editing on the olfactory sensory system, shedding light on the intricate molecular underpinnings of olfactory perception and neuronal activity.
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Affiliation(s)
- Hui-Wen Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Chung-Pei Ma
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
| | - En Chin
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Yi-Tung Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan;
| | - Teh-Cheng Wang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Yu-Ping Kuo
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan;
| | - Chia-Hao Su
- Center for General Education, Chang Gung University, Taoyuan 333, Taiwan;
- Department of Radiation Oncology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Genomic Medicine Core Laboratory, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-W.C.); (C.-P.M.); (E.C.); (Y.-T.C.); (P.-J.H.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Division of Colon and Rectal Surgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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Cardoso JCR, Mc Shane JC, Li Z, Peng M, Power DM. Revisiting the evolution of Family B1 GPCRs and ligands: Insights from mollusca. Mol Cell Endocrinol 2024; 586:112192. [PMID: 38408601 DOI: 10.1016/j.mce.2024.112192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
Family B1 G protein-coupled receptors (GPCRs) are one of the most well studied neuropeptide receptor families since they play a central role in many biological processes including endocrine, gastrointestinal, cardiovascular and reproduction in animals. The genes for these receptors emerged from a common ancestral gene in bilaterian genomes and evolved via gene/genome duplications and deletions in vertebrate and invertebrate genomes. Their existence and function have mostly been characterized in vertebrates and few studies exist in invertebrate species. Recently, an increased interest in molluscs, means a series of genomes have become available, and since they are less modified than insect and nematode genomes, they are ideal to explore the origin and evolution of neuropeptide gene families. This review provides an overview of Family B1 GPCRs and their peptide ligands and incorporates new data obtained from Mollusca genomes and taking a comparative approach challenges existing models on their origin and evolution.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Jennifer C Mc Shane
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Zhi Li
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Maoxiao Peng
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
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9
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Shi Y, Cui C, Chen S, Chen S, Wang Y, Xu Q, Yang L, Ye J, Hong Z, Hu H. Worm-Based Diagnosis Combining Microfluidics toward Early Cancer Screening. MICROMACHINES 2024; 15:484. [PMID: 38675295 PMCID: PMC11052135 DOI: 10.3390/mi15040484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]
Abstract
Early cancer diagnosis increases therapy efficiency and saves huge medical costs. Traditional blood-based cancer markers and endoscopy procedures demonstrate limited capability in the diagnosis. Reliable, non-invasive, and cost-effective methods are in high demand across the world. Worm-based diagnosis, utilizing the chemosensory neuronal system of C. elegans, emerges as a non-invasive approach for early cancer diagnosis with high sensitivity. It facilitates effectiveness in large-scale cancer screening for the foreseeable future. Here, we review the progress of a unique route of early cancer diagnosis based on the chemosensory neuronal system of C. elegans. We first introduce the basic procedures of the chemotaxis assay of C. elegans: synchronization, behavior assay, immobilization, and counting. Then, we review the progress of each procedure and the various cancer types for which this method has achieved early diagnosis. For each procedure, we list examples of microfluidics technologies that have improved the automation, throughput, and efficiency of each step or module. Finally, we envision that microfluidics technologies combined with the chemotaxis assay of C. elegans can lead to an automated, cost-effective, non-invasive early cancer screening technology, with the development of more mature microfluidic modules as well as systematic integration of functional modules.
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Affiliation(s)
- Yutao Shi
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining 314400, China (S.C.); (Q.X.)
| | - Chen Cui
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining 314400, China (S.C.); (Q.X.)
| | - Shengzhi Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining 314400, China (S.C.); (Q.X.)
| | - Siyu Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining 314400, China (S.C.); (Q.X.)
| | - Yiheng Wang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining 314400, China (S.C.); (Q.X.)
| | - Qingyang Xu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining 314400, China (S.C.); (Q.X.)
| | - Lan Yang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining 314400, China (S.C.); (Q.X.)
| | - Jiayi Ye
- Zhejiang University-University of Illinois Urbana-Champaign Institute (ZJU-UIUC Institute), International Campus, Zhejiang University, Haining 314400, China
| | - Zhi Hong
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining 314400, China (S.C.); (Q.X.)
| | - Huan Hu
- Zhejiang University-University of Illinois Urbana-Champaign Institute (ZJU-UIUC Institute), International Campus, Zhejiang University, Haining 314400, China
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10
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Chidambara Thanu V, Jabeen A, Ranganathan S. iBio-GATS-A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors. Int J Mol Sci 2024; 25:3055. [PMID: 38474300 DOI: 10.3390/ijms25053055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Insects utilize seven transmembrane (7TM) odorant receptor (iOR) proteins, with an inverted topology compared to G-protein coupled receptors (GPCRs), to detect chemical cues in the environment. For pest biocontrol, chemical attractants are used to trap insect pests. However, with the influx of invasive insect pests, novel odorants are urgently needed, specifically designed to match 3D iOR structures. Experimental structural determination of these membrane receptors remains challenging and only four experimental iOR structures from two evolutionarily distant organisms have been solved. Template-based modelling (TBM) is a complementary approach, to generate model structures, selecting templates based on sequence identity. As the iOR family is highly divergent, a different template selection approach than sequence identity is needed. Bio-GATS template selection for GPCRs, based on hydrophobicity correspondence, has been morphed into iBio-GATS, for template selection from available experimental iOR structures. This easy-to-use semi-automated workflow has been extended to generate high-quality models from any iOR sequence from the selected template, using Python and shell scripting. This workflow was successfully validated on Apocrypta bakeri Orco and Machilis hrabei OR5 structures. iBio-GATS models generated for the fruit fly iOR, OR59b and Orco, yielded functional ligand binding results concordant with experimental mutagenesis findings, compared to AlphaFold2 models.
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Affiliation(s)
| | - Amara Jabeen
- Applied Biosciences, Macquarie University, Sydney 2109, Australia
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11
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Abrams KL, Ward DA, Sabiniewicz A, Hummel T. Olfaction evaluation in dogs with sudden acquired retinal degeneration syndrome. Vet Ophthalmol 2024; 27:127-138. [PMID: 37399129 DOI: 10.1111/vop.13121] [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: 12/15/2022] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 07/05/2023]
Abstract
PURPOSE To evaluate olfaction in dogs with sudden acquired retinal degeneration syndrome (SARDS) compared with sighted dogs and blind dogs without SARDS as control groups. ANIMALS STUDIED Forty client-owned dogs. PROCEDURE Olfactory threshold testing was performed on three groups: SARDS, sighted, and blind/non-SARDS using eugenol as the test odorant. The olfactory threshold was determined when subjects indicated the detection of a specific eugenol concentration with behavioral responses. Olfactory threshold, age, body weight, and environmental room factors were evaluated. RESULTS Sixteen dogs with SARDS, 12 sighted dogs, and 12 blind/non-SARDS dogs demonstrated mean olfactory threshold pen numbers of 2.8 (SD = 1.4), 13.8 (SD = 1.4), and 13.4 (SD = 1.1), respectively, which correspond to actual mean concentrations of 0.017 g/mL, 1.7 × 10-13 g/mL and 4.26 × 10-13 g/mL, respectively. Dogs with SARDS had significantly poorer olfactory threshold scores compared with the two control groups (p < .001), with no difference between the control groups (p = .5). Age, weight, and room environment did not differ between the three groups. CONCLUSIONS Dogs with SARDS have severely decreased olfaction capabilities compared with sighted dogs and blind/non-SARDS dogs. This finding supports the suspicion that SARDS is a systemic disease causing blindness, endocrinopathy, and hyposmia. Since the molecular pathways are similar in photoreceptors, olfactory receptors, and steroidogenesis with all using G-protein coupled receptors in the cell membrane, the cause of SARDS may exist at the G-protein associated interactions with intracellular cyclic nucleotides. Further investigations into G-protein coupled receptors pathway and canine olfactory receptor genes in SARDS patients may be valuable in revealing the cause of SARDS.
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Affiliation(s)
- Kenneth L Abrams
- Veterinary Ophthalmology Services, North Kingstown, Rhode Island, USA
| | - Daniel A Ward
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, Tennessee, USA
| | - Agnieszka Sabiniewicz
- Department of Otorhinolaryngology, Smell and Taste Clinic, Technische Universität Dresden, Dresden, Germany
- Institute of Psychology, University of Wrocław, Wrocław, Poland
| | - Thomas Hummel
- Department of Otorhinolaryngology, Smell and Taste Clinic, Technische Universität Dresden, Dresden, Germany
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12
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Osakabe N, Shimizu T, Fujii Y, Fushimi T, Calabrese V. Sensory Nutrition and Bitterness and Astringency of Polyphenols. Biomolecules 2024; 14:234. [PMID: 38397471 PMCID: PMC10887135 DOI: 10.3390/biom14020234] [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: 01/11/2024] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Recent studies have demonstrated that the interaction of dietary constituents with taste and olfactory receptors and nociceptors expressed in the oral cavity, nasal cavity and gastrointestinal tract regulate homeostasis through activation of the neuroendocrine system. Polyphenols, of which 8000 have been identified to date, represent the greatest diversity of secondary metabolites in plants, most of which are bitter and some of them astringent. Epidemiological studies have shown that polyphenol intake contributes to maintaining and improving cardiovascular, cognitive and sensory health. However, because polyphenols have very low bioavailability, the mechanisms of their beneficial effects are unknown. In this review, we focused on the taste of polyphenols from the perspective of sensory nutrition, summarized the results of previous studies on their relationship with bioregulation and discussed their future potential.
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Affiliation(s)
- Naomi Osakabe
- Functional Control Systems, Graduate School of Engineering and Science, Shibaura Institute of Technology, Tokyo 135-8548, Japan
- Systems Engineering and Science, Graduate School of Engineering and Science, Shibaura Institute of Technology, Tokyo 135-8548, Japan;
- Department of Bio-Science and Engineering, Faculty of System Science and Engineering, Shibaura Institute of Technology, Tokyo 135-8548, Japan; (T.S.); (Y.F.)
| | - Takafumi Shimizu
- Department of Bio-Science and Engineering, Faculty of System Science and Engineering, Shibaura Institute of Technology, Tokyo 135-8548, Japan; (T.S.); (Y.F.)
| | - Yasuyuki Fujii
- Department of Bio-Science and Engineering, Faculty of System Science and Engineering, Shibaura Institute of Technology, Tokyo 135-8548, Japan; (T.S.); (Y.F.)
| | - Taiki Fushimi
- Systems Engineering and Science, Graduate School of Engineering and Science, Shibaura Institute of Technology, Tokyo 135-8548, Japan;
| | - Vittorio Calabrese
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95125 Catania, Italy;
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13
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Liu X, Chen W, Huang B, Wang X, Peng Y, Zhang X, Chai W, Khan MZ, Wang C. Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits. Front Vet Sci 2024; 10:1334434. [PMID: 38274664 PMCID: PMC10808162 DOI: 10.3389/fvets.2023.1334434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
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14
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Li L, Quan J, Liu H, Yu H, Chen H, Xia C, Zhao S, Gao C. Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing. BMC Genomics 2024; 25:17. [PMID: 38166615 PMCID: PMC10759622 DOI: 10.1186/s12864-023-09928-8] [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: 08/31/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. RESULTS We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. CONCLUSIONS In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.
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Affiliation(s)
- Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
- College of Animal Science & Technology, Ningxia University, Yinchuan, 750021, P.R. China
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China.
| | - Hongyi Liu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Haibo Yu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Changyou Xia
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China.
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15
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Dias BG. Legacies of salient environmental experiences-insights from chemosensation. Chem Senses 2024; 49:bjae002. [PMID: 38219073 PMCID: PMC10825851 DOI: 10.1093/chemse/bjae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Indexed: 01/15/2024] Open
Abstract
Evidence for parental environments profoundly influencing the physiology, biology, and neurobiology of future generations has been accumulating in the literature. Recent efforts to understand this phenomenon and its underlying mechanisms have sought to use species like rodents and insects to model multi-generational legacies of parental experiences like stress and nutritional exposures. From these studies, we have come to appreciate that parental exposure to salient environmental experiences impacts the cadence of brain development, hormonal responses to stress, and the expression of genes that govern cellular responses to stress in offspring. Recent studies using chemosensory exposure have emerged as a powerful tool to shed new light on how future generations come to be influenced by environments to which parents are exposed. With a specific focus on studies that have leveraged such use of salient chemosensory experiences, this review synthesizes our current understanding of the concept, causes, and consequences of the inheritance of chemosensory legacies by future generations and how this field of inquiry informs the larger picture of how parental experiences can influence offspring biology.
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Affiliation(s)
- Brian G Dias
- Developmental Neuroscience and Neurogenetics Program, The Saban Research Institute, Los Angeles, CA, United States
- Division of Endocrinology, Diabetes and Metabolism, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Department of Pediatrics, Keck School of Medicine of USC, Los Angeles, CA, United States
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16
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Kim WK, Choi K, Hyeon C, Jang SJ. General Chemical Reaction Network Theory for Olfactory Sensing Based on G-Protein-Coupled Receptors: Elucidation of Odorant Mixture Effects and Agonist-Synergist Threshold. J Phys Chem Lett 2023; 14:8412-8420. [PMID: 37712530 DOI: 10.1021/acs.jpclett.3c02310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
This work presents a general chemical reaction network theory for olfactory sensing processes that employ G-protein-coupled receptors as olfactory receptors (ORs). The theory can be applied to general mixtures of odorants and an arbitrary number of ORs. Reactions of ORs with G-proteins, in both the presence and absence of odorants, are explicitly considered. A unique feature of the theory is the definition of an odor activity vector consisting of strengths of odorant-induced signals from ORs relative to those due to background G-protein activity in the absence of odorants. It is demonstrated that each component of the odor activity defined this way reduces to a Michaelis-Menten form capable of accounting for cooperation or competition effects between different odorants. The main features of the theory are illustrated for a two-odorant mixture. Known and potential mixture effects, such as suppression, shadowing, inhibition, and synergy, are quantitatively described. Effects of relative values of rate constants, basal activity, and G-protein concentration are also demonstrated.
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Affiliation(s)
- Won Kyu Kim
- Korea Institute for Advanced Study, Hoegiro 85, Dongdaemun-gu, Seoul 02455, Korea
| | - Kiri Choi
- Korea Institute for Advanced Study, Hoegiro 85, Dongdaemun-gu, Seoul 02455, Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Hoegiro 85, Dongdaemun-gu, Seoul 02455, Korea
| | - Seogjoo J Jang
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, United States
- PhD Programs in Chemistry and Physics, Graduate Center, City University of New York, New York, New York 10016, United States
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17
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Kawabata Y, Takai S, Sanematsu K, Iwata S, Kawabata F, Kanematsu T, Jimi E, Shigemura N. The G protein-coupled receptor GPRC5C is a saccharide sensor with a novel 'off' response. FEBS Lett 2023; 597:2006-2016. [PMID: 37418589 DOI: 10.1002/1873-3468.14695] [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: 05/08/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
GPRC5C is an orphan G protein-coupled receptor (GPCR) that belongs to the class C GPCR family. Although GPRC5C is expressed in various organs, its function and ligand are still undetermined. We found that GPRC5C is expressed in mouse taste cells, enterocytes, and pancreatic α-cells. In functional imaging assays, HEK293 cells heterologously expressing GPRC5C and the chimeric G protein α subunit Gα16-gust44 showed robust intracellular Ca2+ increases in response to monosaccharides, disaccharides, and a sugar alcohol, but not an artificial sweetener or sweet-tasting amino acid. Notably, Ca2+ increases occurred after washout, not during stimulation. Our findings suggest that GPRC5C has receptor properties which lead to novel 'off' responses to saccharide detachment and may work as an internal or external chemosensor specifically tuned to natural sugars.
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Affiliation(s)
- Yuko Kawabata
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, Fukuoka, Japan
| | - Shingo Takai
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, Fukuoka, Japan
- Dent-Craniofacial Development and Regeneration Center, Kyushu University, Fukuoka, Japan
| | - Keisuke Sanematsu
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, Fukuoka, Japan
- Oral Health/Brain Health/Total Health Research Center, Kyushu University, Fukuoka, Japan
- Research and Development Center for Five-Sense Devices Taste and Odor Sensing, Kyushu University, Fukuoka, Japan
| | - Shusuke Iwata
- Department of Oral Physiology, Asahi University School of Dentistry, Mizuho, Japan
| | - Fuminori Kawabata
- Physiology of Domestic Animals, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Takashi Kanematsu
- Division of Oral Biological Sciences, Department of Cell Biology, Aging Science, and Pharmacology, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Eijiro Jimi
- Oral Health/Brain Health/Total Health Research Center, Kyushu University, Fukuoka, Japan
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Dental Science, Kyushu University, Fukuoka, Japan
| | - Noriatsu Shigemura
- Section of Oral Neuroscience, Graduate School of Dental Science, Kyushu University, Fukuoka, Japan
- Research and Development Center for Five-Sense Devices Taste and Odor Sensing, Kyushu University, Fukuoka, Japan
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18
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Perfilyeva A, Bespalova K, Bespalov S, Begmanova M, Kuzovleva Y, Vishnyakova O, Nazarenko I, Abylkassymova G, Perfilyeva Y, Plakhov K, Djansugurova L, Bekmanov B. Homozygosity mapping in the Kazakh national dog breed Tazy. Sci Rep 2023; 13:10735. [PMID: 37400480 DOI: 10.1038/s41598-023-37990-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023] Open
Abstract
The Tazy is a breed of sighthound common in Kazakhstan. The identification of runs of homozygosity (ROH) is an informative approach to assessing the history and possible patterns of directional selection pressure. To our knowledge, the present study is the first to provide an overview of the ROH pattern in the Tazy dogs from a genome-wide perspective. The ROH of the Tazy was found to be mainly composed of shorter segments (1-2 Mb), accounting for approximately 67% of the total ROH. The estimated ROH-based inbreeding coefficients (FROH) ranged from 0.028 to 0.058 with a mean of 0.057. Five genomic regions under positive selection were identified on chromosomes 18, 22, and 25. The regions on chromosomes 18 and 22 may be breed specific, while the region on chromosome 22 overlaps with regions of hunting traits in other hunting dog breeds. Among the 12 candidate genes located in these regions, the gene CAB39L may be a candidate that affects running speed and endurance of the Tazy dog. Eight genes could belong to an evolutionarily conserved complex as they were clustered in a large protein network with strong linkages. The results may enable effective interventions when incorporated into conservation planning and selection of the Tazy breed.
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Affiliation(s)
- Anastassiya Perfilyeva
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Kira Bespalova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan.
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, 050040, Almaty, Kazakhstan.
| | - Sergey Bespalov
- Department of Theriology, Institute of Zoology, 050060, Almaty, Kazakhstan
| | - Mamura Begmanova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Yelena Kuzovleva
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Olga Vishnyakova
- Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", 050008, Almaty, Kazakhstan
| | - Inna Nazarenko
- Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", 020000, Astana, Kazakhstan
| | - Gulnar Abylkassymova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Yuliya Perfilyeva
- Laboratory of Molecular Immunology and Immunobiotechnology, M.A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, 050012, Almaty, Kazakhstan
| | - Konstantin Plakhov
- Laboratory of Biocenology and Hunting Management, Institute of Zoology, 050060, Almaty, Kazakhstan
| | - Leyla Djansugurova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Bakhytzhan Bekmanov
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, 050040, Almaty, Kazakhstan
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19
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Shen S, Zhao C, Wu C, Sun S, Li Z, Yan W, Shao Z. Allosteric modulation of G protein-coupled receptor signaling. Front Endocrinol (Lausanne) 2023; 14:1137604. [PMID: 36875468 PMCID: PMC9978769 DOI: 10.3389/fendo.2023.1137604] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of transmembrane proteins, regulate a wide array of physiological processes in response to extracellular signals. Although these receptors have proven to be the most successful class of drug targets, their complicated signal transduction pathways (including different effector G proteins and β-arrestins) and mediation by orthosteric ligands often cause difficulties for drug development, such as on- or off-target effects. Interestingly, identification of ligands that engage allosteric binding sites, which are different from classic orthosteric sites, can promote pathway-specific effects in cooperation with orthosteric ligands. Such pharmacological properties of allosteric modulators offer new strategies to design safer GPCR-targeted therapeutics for various diseases. Here, we explore recent structural studies of GPCRs bound to allosteric modulators. Our inspection of all GPCR families reveals recognition mechanisms of allosteric regulation. More importantly, this review highlights the diversity of allosteric sites and presents how allosteric modulators control specific GPCR pathways to provide opportunities for the development of new valuable agents.
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Affiliation(s)
| | | | | | | | | | - Wei Yan
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhenhua Shao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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20
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Mohanty SK, Maryam S, Gautam V, Mittal A, Gupta K, Arora R, Bhadra W, Mishra T, Sengupta D, Ahuja G. Transcriptional advantage influence odorant receptor gene choice. Brief Funct Genomics 2022; 22:281-290. [DOI: 10.1093/bfgp/elac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/13/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Abstract
Odorant receptors (ORs) obey mutual exclusivity and monoallelic mode of expression. Efforts are ongoing to decipher the molecular mechanism that drives the ‘one-neuron-one-receptor’ rule of olfaction. Recently, single-cell profiling of olfactory sensory neurons (OSNs) revealed the expression of multiple ORs in the immature neurons, suggesting that the OR gene choice mechanism is much more complex than previously described by the silence-all-and-activate-one model. These results also led to the genesis of two possible mechanistic models i.e. winner-takes-all and stochastic selection. We developed Reverse Cell Tracking (RCT), a novel computational framework that facilitates OR-guided cellular backtracking by leveraging Uniform Manifold Approximation and Projection embeddings from RNA Velocity Workflow. RCT-based trajectory backtracking, coupled with statistical analysis, revealed the OR gene choice bias for the transcriptionally advanced (highest expressed) OR during neuronal differentiation. Interestingly, the observed selection bias was uniform for all ORs across different spatial zones or their relative expression within the olfactory organ. We validated these findings on independent datasets and further confirmed that the OR gene selection may be regulated by Upf3b. Lastly, our RNA dynamics-based tracking of the differentiation cascade revealed a transition cell state that harbors mixed molecular identities of immature and mature OSNs, and their relative abundance is regulated by Upf3b.
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Affiliation(s)
- Sanjay Kumar Mohanty
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Sidrah Maryam
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Vishakha Gautam
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Aayushi Mittal
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Krishan Gupta
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computer Science and Engineering, , Okhla, Phase III, New Delhi 110020, India
| | - Radhika Arora
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Wrik Bhadra
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Tripti Mishra
- Pathfinder Research and Training Foundation , Uttar Pradesh 201308, India
| | - Debarka Sengupta
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computer Science and Engineering, , Okhla, Phase III, New Delhi 110020, India
| | - Gaurav Ahuja
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
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21
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The Role of G Protein-Coupled Receptor Kinase 6 Regulation in Inflammation and Pain. Int J Mol Sci 2022; 23:ijms232415880. [PMID: 36555521 PMCID: PMC9784940 DOI: 10.3390/ijms232415880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
The G protein-coupled receptor kinase 6 is associated with inflammation and pathological pain. Impairment of GRK6 expression was described in chronic inflammatory diseases such as rheumatoid arthritis and this was shown to be accompanied by an imbalance of downstream signaling pathways. Here, we discuss novel aspects of GRK6 interaction and its impact upon hyperalgesia and inflammatory processes. In this review, we compile important findings concerning GRK6 regulation for a better pathophysiological understanding of the intracellular interaction in the context of inflammation and show clinical implications-for example, the identification of possible therapy goals in the treatment of chronic inflammatory hyperalgesia.
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22
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Bentz EJ, Ophir AG. Chromosome-scale genome assembly of the African giant pouched rat (Cricetomys ansorgei) and evolutionary analysis reveals evidence of olfactory specialization. Genomics 2022; 114:110521. [PMID: 36351561 DOI: 10.1016/j.ygeno.2022.110521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/07/2022]
Abstract
The Southern giant pouched rat, Cricetomys ansorgei, is a large rodent best known for its ability to detect landmines using its impressive sense of smell. Their powerful chemosensory abilities enable subtle discrimination of chemical social signals, and female pouched rats demonstrate a unique reproductive physiology hypothesized to be mediated by pheromonal mechanisms. Thus, C. ansorgei represents a novel mammalian model for chemosensory physiology, social behavior, and pheromonal control of reproductive physiology. We present the first chromosome-scale genomic sequence of the pouched rat encoding 22,671 protein coding genes, including 1571 olfactory receptors, and provide a glance into the evolutionary history of this species. Functional enrichment analysis reveals genetic expansions specific to the pouched rat are enriched for functions related to olfactory specialization. Overall, this assembly is of reference-quality, and will serve as a useful and informative genomic sequence on which we can confidently base future molecular research involving the pouched rat.
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Affiliation(s)
- Ehren J Bentz
- Department of Psychology, Cornell University, Ithaca, NY, USA.
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23
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Xu J, Moore BN, Pluznick JL. Short-Chain Fatty Acid Receptors and Blood Pressure Regulation: Council on Hypertension Mid-Career Award for Research Excellence 2021. Hypertension 2022; 79:2127-2137. [PMID: 35912645 PMCID: PMC9458621 DOI: 10.1161/hypertensionaha.122.18558] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The gut microbiome influences host physiology and pathophysiology through several pathways, one of which is microbial production of chemical metabolites which interact with host signaling pathways. Short-chain fatty acids (SCFAs) are a class of gut microbial metabolites known to activate multiple signaling pathways in the host. Growing evidence indicates that the gut microbiome is linked to blood pressure, that SCFAs modulate blood pressure regulation, and that delivery of exogenous SCFAs lowers blood pressure. Given that hypertension is a key risk factor for cardiovascular disease, the examination of novel contributors to blood pressure regulation has the potential to lead to novel approaches or treatments. Thus, this review will discuss SCFAs with a focus on their host G protein-coupled receptors including GPR41 (G protein-coupled receptor 41), GPR43, and GPR109A, as well as OLFR78 (olfactory receptor 78) and OLFR558. This includes a discussion of the ligand profiles, G protein coupling, and tissue distribution of each receptor. We will also review phenotypes relevant to blood pressure regulation which have been reported to date for Gpr41, Gpr43, Gpr109a, and Olfr78 knockout mice. In addition, we will consider how SCFA signaling influences physiology at baseline, and, how SCFA signaling may contribute to blood pressure regulation in settings of hypertension. In sum, this review will integrate current knowledge regarding how SCFAs and their receptors regulate blood pressure.
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Affiliation(s)
- Jiaojiao Xu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Brittni N. Moore
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jennifer L. Pluznick
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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24
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Bruce K, Ma J, Lawler C, Xie W, Stevenson PG, Farrell HE. Recent Advancements in Understanding Primary Cytomegalovirus Infection in a Mouse Model. Viruses 2022; 14:v14091934. [PMID: 36146741 PMCID: PMC9505653 DOI: 10.3390/v14091934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Animal models that mimic human infections provide insights in virus–host interplay; knowledge that in vitro approaches cannot readily predict, nor easily reproduce. Human cytomegalovirus (HCMV) infections are acquired asymptomatically, and primary infections are difficult to capture. The gap in our knowledge of the early events of HCMV colonization and spread limits rational design of HCMV antivirals and vaccines. Studies of natural infection with mouse cytomegalovirus (MCMV) have demonstrated the olfactory epithelium as the site of natural colonization. Systemic spread from the olfactory epithelium is facilitated by infected dendritic cells (DC); tracking dissemination uncovered previously unappreciated DC trafficking pathways. The olfactory epithelium also provides a unique niche that supports efficient MCMV superinfection and virus recombination. In this review, we summarize recent advances to our understanding of MCMV infection and spread and the tissue-specific mechanisms utilized by MCMV to modulate DC trafficking. As these mechanisms are likely conserved with HCMV, they may inform new approaches for preventing HCMV infections in humans.
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25
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Namgong C, Kim JH, Lee MH, Midkiff D. Non-invasive cancer detection in canine urine through Caenorhabditis elegans chemotaxis. Front Vet Sci 2022; 9:932474. [PMID: 36016810 PMCID: PMC9396970 DOI: 10.3389/fvets.2022.932474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer is the leading cause of death in companion animals, and successful early treatment has been a challenge in the veterinary field. We have developed the Non-Invasive Cancer Screening (N.C.S.) Study to perform cancer detection through the analysis of canine urine samples. The test makes use of the strong olfactory system of the nematode Caenorhabditis elegans, which was previously shown to positively respond to urine samples from human cancer patients. We performed a proof-of-concept study to optimize the detection capability in urine samples obtained from dogs with naturally occurring cancers. In this study, we established a scale for identifying the cancer risk based on the magnitude of the chemotaxis index of C. elegans toward a canine urine sample. Through validation, the N.C.S. Study achieved a sensitivity of 85%, showing that it is highly sensitive to indicate the presence of cancer across multiple types of common canine cancers. The test also showed a 90% specificity to cancer samples, indicating a low rate of over-identifying cancer risk. From these results, we have demonstrated the ability to perform low-cost, non-invasive cancer detection in companion animals—a method that can increase the ability to perform cancer diagnosis and treatment.
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Affiliation(s)
- Chan Namgong
- Animal Cancer Dx, Raleigh, NC, United States
- *Correspondence: Chan Namgong
| | - Jong Hyuk Kim
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
- IntelligentComparative Oncology Lab, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Myon Hee Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC, United States
| | - Daniel Midkiff
- Animal Cancer Dx, Raleigh, NC, United States
- Daniel Midkiff
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26
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Copy Number Variation (CNV): A New Genomic Insight in Horses. Animals (Basel) 2022; 12:ani12111435. [PMID: 35681904 PMCID: PMC9179425 DOI: 10.3390/ani12111435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary This study aimed to contribute to our knowledge of CNVs, a type of genomic marker in equines, by producing, for the first time, a fine-scale characterization of the CNV regions (CNVRs) in the Pura Raza Española horse breed. We found not only the existence of a unique pattern of genomic regions enriched in CNVs in the PRE in comparison with the data available from other breeds but also the incidence of CNVs across the entire genome. Since these regions could affect the structure and dose of the genes involved, we also performed a gene ontology analysis which revealed that most of the genes overlapping in CNVRs were related to the olfactory pathways and immune response. Abstract Copy number variations (CNVs) are a new-fangled source of genetic variation that can explain changes in the phenotypes in complex traits and diseases. In recent years, their study has increased in many livestock populations. However, the study and characterization of CNVs in equines is still very limited. Our study aimed to investigate the distribution pattern of CNVs, characterize CNV regions (CNVRs), and identify the biological pathways affected by CNVRs in the Pura Raza Española (PRE) breed. To achieve this, we analyzed high-density SNP genotyping data (670,804 markers) from a large cohort of 654 PRE horses. In total, we identified 19,902 CNV segments and 1007 CNV regions in the whole population. The length of the CNVs ranged from 1.024 kb to 4.55 Mb, while the percentage of the genome covered by CNVs was 4.4%. Interestingly, duplications were more abundant than deletions and mixed CNVRs. In addition, the distribution of CNVs across the chromosomes was not uniform, with ECA12 being the chromosome with the largest percentage of its genome covered (19.2%), while the highest numbers of CNVs were found in ECA20, ECA12, and ECA1. Our results showed that 71.4% of CNVRs contained genes involved in olfactory transduction, olfactory receptor activity, and immune response. Finally, 39.1% of the CNVs detected in our study were unique when compared with CNVRs identified in previous studies. To the best of our knowledge, this is the first attempt to reveal and characterize the CNV landscape in PRE horses, and it contributes to our knowledge of CNVs in equines, thus facilitating the understanding of genetic and phenotypic variations in the species. However, further research is still needed to confirm if the CNVs observed in the PRE are also linked to variations in the specific phenotypical differences in the breed.
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27
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Sims C, Birkett MA, Withall DM. Enantiomeric Discrimination in Insects: The Role of OBPs and ORs. INSECTS 2022; 13:368. [PMID: 35447810 PMCID: PMC9030700 DOI: 10.3390/insects13040368] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/27/2023]
Abstract
Olfaction is a complex recognition process that is critical for chemical communication in insects. Though some insect species are capable of discrimination between compounds that are structurally similar, little is understood about how this high level of discrimination arises. Some insects rely on discriminating between enantiomers of a compound, demonstrating an ability for highly selective recognition. The role of two major peripheral olfactory proteins in insect olfaction, i.e., odorant-binding proteins (OBPs) and odorant receptors (ORs) has been extensively studied. OBPs and ORs have variable discrimination capabilities, with some found to display highly specialized binding capability, whilst others exhibit promiscuous binding activity. A deeper understanding of how odorant-protein interactions induce a response in an insect relies on further analysis such as structural studies. In this review, we explore the potential role of OBPs and ORs in highly specific recognition, specifically enantiomeric discrimination. We summarize the state of research into OBP and OR function and focus on reported examples in the literature of clear enantiomeric discrimination by these proteins.
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Affiliation(s)
- Cassie Sims
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; (C.S.); (M.A.B.)
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Michael A. Birkett
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; (C.S.); (M.A.B.)
| | - David M. Withall
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; (C.S.); (M.A.B.)
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28
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Xu Z, Guo L, Qian X, Yu C, Li S, Zhu C, Ma X, Li H, Zhu G, Zhou H, Dai W, Li Q, Gao X. Two entry tunnels in mouse TAAR9 suggest the possibility of multi-entry tunnels in olfactory receptors. Sci Rep 2022; 12:2691. [PMID: 35177711 PMCID: PMC8854740 DOI: 10.1038/s41598-022-06591-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022] Open
Abstract
Orthosteric binding sites of olfactory receptors have been well understood for ligand-receptor interactions. However, a lack of explanation for subtle differences in ligand profile of olfactory receptors even with similar orthosteric binding sites promotes more exploration into the entry tunnels of the receptors. An important question regarding entry tunnels is the number of entry tunnels, which was previously believed to be one. Here, we used TAAR9 that recognizes important biogenic amines such as cadaverine, spermine, and spermidine as a model for entry tunnel study. We identified two entry tunnels in TAAR9 and described the residues that form the tunnels. In addition, we found two vestibular binding pockets, each located in one tunnel. We further confirmed the function of two tunnels through site-directed mutagenesis. Our study challenged the existing views regarding the number of entry tunnels in the subfamily of olfactory receptors and demonstrated the possible mechanism how the entry tunnels function in odorant recognition.
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Affiliation(s)
- ZhengRong Xu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - LingNa Guo
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Institute of Life Sciences, Southeast University, Nanjing, 210096, China
| | - XiaoYun Qian
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - ChenJie Yu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - ShengJu Li
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - ChengWen Zhu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - XiaoFeng Ma
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Hui Li
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - GuangJie Zhu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Han Zhou
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - WenXuan Dai
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Qian Li
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, 201210, China.
| | - Xia Gao
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China. .,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.
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29
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Williams DL, Sikora VM, Hammer MA, Amin S, Brinjikji T, Brumley EK, Burrows CJ, Carrillo PM, Cromer K, Edwards SJ, Emri O, Fergle D, Jenkins MJ, Kaushik K, Maydan DD, Woodard W, Clowney EJ. May the Odds Be Ever in Your Favor: Non-deterministic Mechanisms Diversifying Cell Surface Molecule Expression. Front Cell Dev Biol 2022; 9:720798. [PMID: 35087825 PMCID: PMC8787164 DOI: 10.3389/fcell.2021.720798] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
How does the information in the genome program the functions of the wide variety of cells in the body? While the development of biological organisms appears to follow an explicit set of genomic instructions to generate the same outcome each time, many biological mechanisms harness molecular noise to produce variable outcomes. Non-deterministic variation is frequently observed in the diversification of cell surface molecules that give cells their functional properties, and is observed across eukaryotic clades, from single-celled protozoans to mammals. This is particularly evident in immune systems, where random recombination produces millions of antibodies from only a few genes; in nervous systems, where stochastic mechanisms vary the sensory receptors and synaptic matching molecules produced by different neurons; and in microbial antigenic variation. These systems employ overlapping molecular strategies including allelic exclusion, gene silencing by constitutive heterochromatin, targeted double-strand breaks, and competition for limiting enhancers. Here, we describe and compare five stochastic molecular mechanisms that produce variety in pathogen coat proteins and in the cell surface receptors of animal immune and neuronal cells, with an emphasis on the utility of non-deterministic variation.
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Affiliation(s)
- Donnell L. Williams
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Veronica Maria Sikora
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Max A. Hammer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Sayali Amin
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Taema Brinjikji
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Emily K. Brumley
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Connor J. Burrows
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Paola Michelle Carrillo
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Kirin Cromer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Summer J. Edwards
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Olivia Emri
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Fergle
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - M. Jamal Jenkins
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Krishangi Kaushik
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniella D. Maydan
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Wrenn Woodard
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - E. Josephine Clowney
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
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30
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Olfactory Receptor OR7A17 Expression Correlates with All- Trans Retinoic Acid (ATRA)-Induced Suppression of Proliferation in Human Keratinocyte Cells. Int J Mol Sci 2021; 22:ijms222212304. [PMID: 34830183 PMCID: PMC8623719 DOI: 10.3390/ijms222212304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Olfactory receptors (ORs), which belong to the G-protein-coupled receptor family, have been widely studied as ectopically expressed receptors in various human tissues, including the skin. However, the physiological functions of only a few OR types have been elucidated in skin cells. All-trans retinoic acid (ATRA) is a well-known medication for various skin diseases. However, many studies have shown that ATRA can have adverse effects, resulting from the suppression of cell proliferation. Here, we investigated the involvement of OR7A17 in the ATRA-induced suppression of human keratinocyte (HaCaT) proliferation. We demonstrated that OR7A17 is expressed in HaCaT keratinocytes, and its expression was downregulated by ATRA. The ATRA-induced downregulation of OR7A17 was attenuated via RAR α or RAR γ antagonist treatment, indicating that the effects of ATRA on OR7A17 expression were mediated through nuclear retinoic acid receptor signaling. Moreover, we found that the overexpression of OR7A17 induced the proliferation of HaCaT cells while counteracting the antiproliferative effect of ATRA. Mechanistically, OR7A17 overexpression reversed the ATRA-induced attenuation of Ca2+ entry. Our findings indicated that ATRA suppresses cell proliferation through the downregulation of OR7A17 via RAR α- and γ-mediated retinoid signaling. Taken together, OR7A17 is a potential therapeutic target for ameliorating the anti-proliferative effects of ATRA.
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31
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Pheromones that correlate with reproductive success in competitive conditions. Sci Rep 2021; 11:21970. [PMID: 34754031 PMCID: PMC8578420 DOI: 10.1038/s41598-021-01507-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/09/2021] [Indexed: 11/08/2022] Open
Abstract
The major urinary proteins (MUPs) of house mice (Mus musculus) bind and stabilize the release of pheromones and other volatile organic compounds (VOCs) from urinary scent marks, which mediate chemical communication. Social status influences MUP and VOC excretion, and the urinary scent of dominant males is attractive to females. Urinary pheromones influence the sexual behavior and physiology of conspecifics, and yet it is not known whether they also affect reproductive success. We monitored the excretion of urinary protein and VOCs of wild-derived house mice living in large seminatural enclosures to compare the sexes and to test how these compounds correlate with reproductive success. Among males, urinary protein concentration and VOC expression correlated with reproductive success and social status. Territorial dominance also correlated with reproductive success in both sexes; but among females, no urinary compounds were found to correlate with social status or reproductive success. We found several differences in the urinary protein and volatile pheromones of mice in standard cages versus seminatural enclosures, which raises caveats for conventional laboratory studies. These findings provide novel evidence for chemical signals that correlate with male reproductive success of house mice living in competitive conditions.
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Cheema JA, Carraher C, Plank NOV, Travas-Sejdic J, Kralicek A. Insect odorant receptor-based biosensors: Current status and prospects. Biotechnol Adv 2021; 53:107840. [PMID: 34606949 DOI: 10.1016/j.biotechadv.2021.107840] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/02/2021] [Accepted: 09/27/2021] [Indexed: 02/01/2023]
Abstract
Whilst the senses of vision and hearing have been successfully automated and miniaturized in portable formats (e.g. smart phone), this is yet to be achieved with the sense of smell. This is because the sensing challenge is not trivial as it involves navigating a chemosensory space comprising thousands of volatile organic compounds. Distinct aroma recognition is based on detecting unique combinations of volatile organic compounds. In natural olfactory systems this is accomplished by employing odorant receptors (ORs) with varying specificities, together with combinatorial neural coding mechanisms. Attempts to mimic the remarkable sensitivity and accuracy of natural olfactory systems has therefore been challenging. Current portable chemical sensors for odorant detection are neither sensitive nor selective, prompting research exploring artificial olfactory devices that use natural OR proteins for sensing. Much research activity to develop OR based biosensors has concentrated on mammalian ORs, however, insect ORs have not been explored as extensively. Insects possess an extraordinary sense of smell due to a repertoire of odorant receptors evolved to interpret olfactory cues vital to the insects' survival. The potential of insect ORs as sensing elements is only now being unlocked through recent research efforts to understand their structure, ligand binding mechanisms and development of odorant biosensors. Like their mammalian counterparts, there are many challenges with working with insect ORs. These include expression, purification and presentation of the insect OR in a stable display format compatible with an effective transduction methodology while maintaining OR structure and function. Despite these challenges, significant progress has been demonstrated in developing OR-based biosensors which exploit insect ORs in cells, lipid bilayers, liposomes and nanodisc formats. Ultrasensitive and highly selective detection of volatile organic compounds has been validated by coupling these insect OR display formats with transduction methodologies spanning optical (fluorescence) and electrical (field effect transistors, electrochemical impedance spectroscopy) techniques. This review summarizes the current status of insect OR based biosensors and their future outlook.
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Affiliation(s)
- Jamal Ahmed Cheema
- Polymer Biointerface Centre, School of Chemical Sciences, The University of Auckland, Auckland 1023, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand; The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Colm Carraher
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Natalie O V Plank
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand; School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6021, New Zealand
| | - Jadranka Travas-Sejdic
- Polymer Biointerface Centre, School of Chemical Sciences, The University of Auckland, Auckland 1023, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand.
| | - Andrew Kralicek
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand; Scentian Bio Limited, 1c Goring Road, Sandringham, Auckland 1025, New Zealand.
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Sharma A, Saha BK, Kumar R, Varadwaj PK. OlfactionBase: a repository to explore odors, odorants, olfactory receptors and odorant-receptor interactions. Nucleic Acids Res 2021; 50:D678-D686. [PMID: 34469532 PMCID: PMC8728123 DOI: 10.1093/nar/gkab763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/13/2021] [Accepted: 08/28/2021] [Indexed: 12/04/2022] Open
Abstract
Olfaction is a multi-stage process that initiates with the odorants entering the nose and terminates with the brain recognizing the odor associated with the odorant. In a very intricate way, the process incorporates various components functioning together and in synchronization. OlfactionBase is a free, open-access web server that aims to bring together knowledge about many aspects of the olfaction mechanism in one place. OlfactionBase contains detailed information of components like odors, odorants, and odorless compounds with physicochemical and ADMET properties, olfactory receptors (ORs), odorant- and pheromone binding proteins, OR-odorant interactions in Human and Mus musculus. The dynamic, user-friendly interface of the resource facilitates exploration of different entities: finding chemical compounds having desired odor, finding odorants associated with OR, associating chemical features with odor and OR, finding sequence information of ORs and related proteins. Finally, the data in OlfactionBase on odors, odorants, olfactory receptors, human and mouse OR-odorant pairs, and other associated proteins could aid in the inference and improved understanding of odor perception, which might provide new insights into the mechanism underlying olfaction. The OlfactionBase is available at https://bioserver.iiita.ac.in/olfactionbase/.
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Affiliation(s)
- Anju Sharma
- Department of Applied Science, Indian Institute of Information Technology, Allahabad, Uttar Pradesh 211015, India
| | | | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Uttar Pradesh 226028, India
| | - Pritish Kumar Varadwaj
- Department of Applied Science, Indian Institute of Information Technology, Allahabad, Uttar Pradesh 211015, India
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Francia S, Lodovichi C. The role of the odorant receptors in the formation of the sensory map. BMC Biol 2021; 19:174. [PMID: 34452614 PMCID: PMC8394594 DOI: 10.1186/s12915-021-01116-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/02/2021] [Indexed: 11/10/2022] Open
Abstract
In the olfactory system, odorant receptors (ORs) expressed at the cell membrane of olfactory sensory neurons detect odorants and direct sensory axons toward precise target locations in the brain, reflected in the presence of olfactory sensory maps. This dual role of ORs is corroborated by their subcellular expression both in cilia, where they bind odorants, and at axon terminals, a location suitable for axon guidance cues. Here, we provide an overview and discuss previous work on the role of ORs in establishing the topographic organization of the olfactory system and recent findings on the mechanisms of activation and function of axonal ORs.
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Affiliation(s)
- Simona Francia
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy.,Veneto Institute of Molecular Medicine, Padua, Italy
| | - Claudia Lodovichi
- Veneto Institute of Molecular Medicine, Padua, Italy. .,Neuroscience Institute CNR, Via Orus 2, 35129, Padua, Italy. .,Department of Biomedical Sciences, University of Padua, Padua, Italy. .,Padova Neuroscience Center, Padua, Italy.
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Manzini I, Schild D, Di Natale C. Principles of odor coding in vertebrates and artificial chemosensory systems. Physiol Rev 2021; 102:61-154. [PMID: 34254835 DOI: 10.1152/physrev.00036.2020] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The biological olfactory system is the sensory system responsible for the detection of the chemical composition of the environment. Several attempts to mimic biological olfactory systems have led to various artificial olfactory systems using different technical approaches. Here we provide a parallel description of biological olfactory systems and their technical counterparts. We start with a presentation of the input to the systems, the stimuli, and treat the interface between the external world and the environment where receptor neurons or artificial chemosensors reside. We then delineate the functions of receptor neurons and chemosensors as well as their overall I-O relationships. Up to this point, our account of the systems goes along similar lines. The next processing steps differ considerably: while in biology the processing step following the receptor neurons is the "integration" and "processing" of receptor neuron outputs in the olfactory bulb, this step has various realizations in electronic noses. For a long period of time, the signal processing stages beyond the olfactory bulb, i.e., the higher olfactory centers were little studied. Only recently there has been a marked growth of studies tackling the information processing in these centers. In electronic noses, a third stage of processing has virtually never been considered. In this review, we provide an up-to-date overview of the current knowledge of both fields and, for the first time, attempt to tie them together. We hope it will be a breeding ground for better information, communication, and data exchange between very related but so far little connected fields.
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Affiliation(s)
- Ivan Manzini
- Animal Physiology and Molecular Biomedicine, Justus-Liebig-University Gießen, Gießen, Germany
| | - Detlev Schild
- Institute of Neurophysiology and Cellular Biophysics, University Medical Center, University of Göttingen, Göttingen, Germany
| | - Corrado Di Natale
- Department of Electronic Engineering, University of Rome Tor Vergata, Rome, Italy
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Jang J, Kim K, Lee YH, Kim H. Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids. BMC Genomics 2021; 22:531. [PMID: 34253178 PMCID: PMC8276479 DOI: 10.1186/s12864-021-07808-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/10/2021] [Indexed: 01/10/2023] Open
Abstract
Background CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV. Results Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics VST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs. Conclusion For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07808-7.
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Affiliation(s)
- Jisung Jang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Kwondo Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Ho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. .,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. .,eGnome, Inc, Seoul, South Korea.
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Liu N, Li T, Wang Y, Liu S. G-Protein Coupled Receptors (GPCRs) in Insects-A Potential Target for New Insecticide Development. Molecules 2021; 26:2993. [PMID: 34069969 PMCID: PMC8157829 DOI: 10.3390/molecules26102993] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
G-protein coupled receptors (GPCRs) play important roles in cell biology and insects' physiological processes, toxicological response and the development of insecticide resistance. New information on genome sequences, proteomic and transcriptome analysis and expression patterns of GPCRs in organs such as the central nervous system in different organisms has shown the importance of these signaling regulatory GPCRs and their impact on vital cell functions. Our growing understanding of the role played by GPCRs at the cellular, genome, transcriptome and tissue levels is now being utilized to develop new targets that will sidestep many of the problems currently hindering human disease control and insect pest management. This article reviews recent work on the expression and function of GPCRs in insects, focusing on the molecular complexes governing the insect physiology and development of insecticide resistance and examining the genome information for GPCRs in two medically important insects, mosquitoes and house flies, and their orthologs in the model insect species Drosophila melanogaster. The tissue specific distribution and expression of the insect GPCRs is discussed, along with fresh insights into practical aspects of insect physiology and toxicology that could be fundamental for efforts to develop new, more effective, strategies for pest control and resistance management.
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Affiliation(s)
- Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (T.L.); (Y.W.)
| | - Ting Li
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (T.L.); (Y.W.)
| | - Yifan Wang
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (T.L.); (Y.W.)
| | - Shikai Liu
- College of Fisheries, Ocean University of China, Qingdao 266100, China;
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Liu N, Wang Y, Li T, Feng X. G-Protein Coupled Receptors (GPCRs): Signaling Pathways, Characterization, and Functions in Insect Physiology and Toxicology. Int J Mol Sci 2021; 22:ijms22105260. [PMID: 34067660 PMCID: PMC8156084 DOI: 10.3390/ijms22105260] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are known to play central roles in the physiology of many organisms. Members of this seven α-helical transmembrane protein family transduce the extracellular signals and regulate intracellular second messengers through coupling to heterotrimeric G-proteins, adenylate cyclase, cAMPs, and protein kinases. As a result of the critical function of GPCRs in cell physiology and biochemistry, they not only play important roles in cell biology and the medicines used to treat a wide range of human diseases but also in insects’ physiological functions. Recent studies have revealed the expression and function of GPCRs in insecticide resistance, improving our understanding of the molecular complexes governing the development of insecticide resistance. This article focuses on the review of G-protein coupled receptor (GPCR) signaling pathways in insect physiology, including insects’ reproduction, growth and development, stress responses, feeding, behaviors, and other physiological processes. Hormones and polypeptides that are involved in insect GPCR regulatory pathways are reviewed. The review also gives a brief introduction of GPCR pathways in organisms in general. At the end of the review, it provides the recent studies on the function of GPCRs in the development of insecticide resistance, focusing in particular on our current knowledge of the expression and function of GPCRs and their downstream regulation pathways and their roles in insecticide resistance and the regulation of resistance P450 gene expression. The latest insights into the exciting technological advances and new techniques for gene expression and functional characterization of the GPCRs in insects are provided.
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Affiliation(s)
- Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (Y.W.); (T.L.)
- Correspondence: ; Tel.: +1-334-844-5076
| | - Yifan Wang
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (Y.W.); (T.L.)
| | - Ting Li
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (Y.W.); (T.L.)
| | - Xuechun Feng
- Department of Biology Sciences, University of California, San Diego, CA 92093, USA;
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Rethinavel HS, Ravichandran S, Radhakrishnan RK, Kandasamy M. COVID-19 and Parkinson's disease: Defects in neurogenesis as the potential cause of olfactory system impairments and anosmia. J Chem Neuroanat 2021; 115:101965. [PMID: 33989761 PMCID: PMC8111887 DOI: 10.1016/j.jchemneu.2021.101965] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/23/2022]
Abstract
Anosmia, a neuropathogenic condition of loss of smell, has been recognized as a key pathogenic hallmark of the current pandemic SARS-CoV-2 infection responsible for COVID-19. While the anosmia resulting from olfactory bulb (OB) pathology is the prominent clinical characteristic of Parkinson's disease (PD), SARS-CoV-2 infection has been predicted as a potential risk factor for developing Parkinsonism-related symptoms in a significant portion of COVID-19 patients and survivors. SARS-CoV-2 infection appears to alter the dopamine system and induce the loss of dopaminergic neurons that have been known to be the cause of PD. However, the underlying biological basis of anosmia and the potential link between COVID-19 and PD remains obscure. Ample experimental studies in rodents suggest that the occurrence of neural stem cell (NSC) mediated neurogenesis in the olfactory epithelium (OE) and OB is important for olfaction. Though the occurrence of neurogenesis in the human forebrain has been a subject of debate, considerable experimental evidence strongly supports the incidence of neurogenesis in the human OB in adulthood. To note, various viral infections and neuropathogenic conditions including PD with olfactory dysfunctions have been characterized by impaired neurogenesis in OB and OE. Therefore, this article describes and examines the recent reports on SARS-CoV-2 mediated OB dysfunctions and defects in the dopaminergic system responsible for PD. Further, the article emphasizes that COVID-19 and PD associated anosmia could result from the regenerative failure in the replenishment of the dopaminergic neurons in OB and olfactory sensory neurons in OE.
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Affiliation(s)
- Harini Sri Rethinavel
- Laboratory of Stem Cells and Neuroregeneration, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Sowbarnika Ravichandran
- Laboratory of Stem Cells and Neuroregeneration, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India; School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Risna Kanjirassery Radhakrishnan
- Laboratory of Stem Cells and Neuroregeneration, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Mahesh Kandasamy
- Laboratory of Stem Cells and Neuroregeneration, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India; School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India; Faculty Recharge Programme, University Grants Commission (UGC-FRP), New Delhi, 110002, India.
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da Silva MC, Canário AVM, Hubbard PC, Gonçalves DMF. Physiology, endocrinology and chemical communication in aggressive behaviour of fishes. JOURNAL OF FISH BIOLOGY 2021; 98:1217-1233. [PMID: 33410154 PMCID: PMC8247941 DOI: 10.1111/jfb.14667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/26/2020] [Accepted: 01/05/2021] [Indexed: 05/10/2023]
Abstract
Fishes show remarkably diverse aggressive behaviour. Aggression is expressed to secure resources; adjusting aggression levels according to context is key to avoid negative consequences for fitness and survival. Nonetheless, despite its importance, the physiological basis of aggression in fishes is still poorly understood. Several reports suggest hormonal modulation of aggression, particularly by androgens, but contradictory studies have been published. Studies exploring the role of chemical communication in aggressive behaviour are also scant, and the pheromones involved remain to be unequivocally characterized. This is surprising as chemical communication is the most ancient form of information exchange and plays a variety of other roles in fishes. Furthermore, the study of chemical communication and aggression is relevant at the evolutionary, ecological and economic levels. A few pioneering studies support the hypothesis that aggressive behaviour, at least in some teleosts, is modulated by "dominance pheromones" that reflect the social status of the sender, but there is little information on the identity of the compounds involved. This review aims to provide a global view of aggressive behaviour in fishes and its underlying physiological mechanisms including the involvement of chemical communication, and discusses the potential use of dominance pheromones to improve fish welfare. Methodological considerations and future research directions are also outlined.
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Affiliation(s)
- Melina Coelho da Silva
- CCMAR – Centro e Ciências do MarUniversidade do AlgarveFaroPortugal
- ISE – Institute of Science and EnvironmentUniversity of Saint JosephMacauChina
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Goyache F, Fernández I, Tapsoba ASR, Traoré A, Menéndez-Arias NA, Álvarez I. Functional characterization of Copy Number Variations regions in Djallonké sheep. J Anim Breed Genet 2021; 138:600-612. [PMID: 33682236 DOI: 10.1111/jbg.12542] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/04/2021] [Accepted: 02/12/2021] [Indexed: 12/22/2022]
Abstract
A total of 184 Djallonké (West African Dwarf) sheep of Burkina Faso were analysed for Copy Number Variations (CNV) using Ovine 50 K SNP BeadChip genotyping data and two different CNV calling platforms: PennCNV and QuantiSNP. Analyses allowed to identify a total of 63 candidate Copy Number Variations Regions (CNVR) on 11 different ovine chromosomes covering about 82.5 Mb of the sheep genome. Gene-annotation enrichment analysis allowed to identify a total of 751 potential candidate ovine genes located in the candidate CNVR bounds. Functional annotation allowed to identify five statistically significant Functional Clusters (FC; enrichment factor > 1.3) involving 61 candidate genes. All genes forming significantly enriched FC were located on ovine chromosome (OAR) 21. FC1 (22 genes including PAG4 and PAG6) and FC5 (three genes: CTSC, CTSW and CTSF), coding proteases (peptidases and cathepsins, respectively), were involved in reproductive performance and modulation of gestation. Both FC3 and FC4 were involved in inflammatory and immunologic response through coding serum amyloid A and B-box-type zinc finger proteins, respectively. Finally, FC2 consisted of 27 genes (including OR10G6 and OR8B8) involved in olfactory receptor activity, key for animals adapting to new food resources. CNVR identified on at least 15% of individuals were considered CNVR hotspots and further overlapped with previously reported quantitative trait loci (QTL). CNVR hotspots spanning genes putatively involved with lipid metabolism (SKP1, TCF7, JADE2, UBE2B and SAR1B) and differential expression in mammary gland (SEC24A and CDKN2AIPNL) on OAR5 and dairy traits (CCDC198 and SLC35F4) on OAR7 overlapped with QTL associated with lipid metabolism, milk protein yield and milk fat percentage. Information obtained from local sheep populations naturally adapted to harsh environments contributes to increase our understanding of the genomic importance of CNV.
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Affiliation(s)
- Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA, Gijón, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA, Gijón, Spain
| | | | | | | | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA, Gijón, Spain
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The G-Protein-Coupled Receptor SRX-97 Is Required for Concentration-Dependent Sensing of Benzaldehyde in Caenorhabditis elegans. eNeuro 2021; 8:ENEURO.0011-20.2020. [PMID: 33397797 PMCID: PMC7877458 DOI: 10.1523/eneuro.0011-20.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
The G-protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors (GPCRs) in the olfactory system function to sense the surrounding environment and respond to various odorants. The genes coding for olfactory receptors in Caenorhabditis elegans are larger in number in comparison to those in mammals, suggesting complexity in the receptor-odorant relationships. Recent studies have shown that the same odorant in different concentrations could act on multiple receptors in different neurons to induce attractive or repulsive responses. The ASH neurons are known to be responsible for responding to high concentrations of volatile odorants. Here, we characterize a new GPCR, SRX-97. We found that the srx-97 promoter drives expression specifically in the head ASH and tail PHB chemosensory neurons of C. elegans. Moreover, the SRX-97 protein localizes to the ciliary ends of the ASH neurons. Analysis of clustered regularly interspaced short palindromic repeats (CRISPR)-based deletion mutants of the srx-97 locus suggests that this gene is involved in recognition of high concentrations of benzaldehyde. This was further confirmed through rescue and neuronal ablation experiments. Our work brings novel insights into concentration-dependent receptor function in the olfactory system, and provides details of an additional molecule that helps the animal navigate its surroundings.
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Camilieri-Asch V, Caddy HT, Hubbard A, Rigby P, Doyle B, Shaw JA, Mehnert A, Partridge JC, Yopak KE, Collin SP. Multimodal Imaging and Analysis of the Neuroanatomical Organization of the Primary Olfactory Inputs in the Brownbanded Bamboo Shark, Chiloscyllium punctatum. Front Neuroanat 2020; 14:560534. [PMID: 33324175 PMCID: PMC7726474 DOI: 10.3389/fnana.2020.560534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/23/2020] [Indexed: 11/22/2022] Open
Abstract
There is currently a limited understanding of the morphological and functional organization of the olfactory system in cartilaginous fishes, particularly when compared to bony fishes and terrestrial vertebrates. In this fish group, there is a clear paucity of information on the characterization, density, and distribution of olfactory receptor neurons (ORNs) within the sensory olfactory epithelium lining the paired olfactory rosettes, and their functional implications with respect to the hydrodynamics of incurrent water flow into the nares. This imaging study examines the brownbanded bamboo shark Chiloscyllium punctatum (Elasmobranchii) and combines immunohistochemical labeling using antisera raised against five G-protein α-subunits (Gαs/olf, Gαq/11/14, Gαi–1/2/3, Gαi–3, Gαo) with light and electron microscopy, to characterize the morphological ORN types present. Three main ORNs (“long”, “microvillous” and “crypt-like”) are confirmed and up to three additional microvilli-bearing types are also described; “Kappe-like” (potential or homologous “Kappe” as in teleosts), “pear-shaped” and “teardrop-shaped” cells. These morphotypes will need to be confirmed molecularly in the future. Using X-ray diffusible iodine-based contrast-enhanced computed tomography (diceCT), high-resolution scans of the olfactory rosettes, olfactory bulbs (OBs), peduncles, and telencephalon reveal a lateral segregation of primary olfactory inputs within the OBs, with distinct medial and lateral clusters of glomeruli, suggesting a potential somatotopic organization. However, most ORN morphotypes are found to be ubiquitously distributed within the medial and lateral regions of the olfactory rosette, with at least three microvilli-bearing ORNs labeled with anti-Gαo found in significantly higher densities in lateral lamellae [in lateral lamellae] and on the anterior portion of lamellae (facing the olfactory cavity). These microvilli-bearing ORN morphotypes (microvillous, “Kappe-like,” “pear-shaped,” and “teardrop-shaped”) are the most abundant across the olfactory rosette of this species, while ciliated ORNs are less common and crypt cells are rare. Spatial simulations of the fluid dynamics of the incurrent water flow into the nares and within the olfactory cavities indicate that the high densities of microvilli-bearing ORNs located within the lateral region of the rosette are important for sampling incoming odorants during swimming and may determine subsequent tracking behavior.
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Affiliation(s)
- Victoria Camilieri-Asch
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia.,The Neuroecology Group, UWA Oceans Institute, The University of Western Australia, Perth, WA, Australia
| | - Harrison T Caddy
- Vascular Engineering Laboratory, Centre for Medical Research, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia.,School of Engineering, The University of Western Australia, Perth, WA, Australia
| | - Alysia Hubbard
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Paul Rigby
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Barry Doyle
- Vascular Engineering Laboratory, Centre for Medical Research, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia.,School of Engineering, The University of Western Australia, Perth, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics Technologies, Perth, WA, Australia.,BHF Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jeremy A Shaw
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Andrew Mehnert
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia.,National Imaging Facility, Brisbane, QLD, Australia
| | - Julian C Partridge
- The Neuroecology Group, UWA Oceans Institute, The University of Western Australia, Perth, WA, Australia
| | - Kara E Yopak
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Shaun P Collin
- The Neuroecology Group, UWA Oceans Institute, The University of Western Australia, Perth, WA, Australia.,School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
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44
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Anderson MJ, Sullivan JG, Horiuchi TK, Fuller SB, Daniel TL. A bio-hybrid odor-guided autonomous palm-sized air vehicle. BIOINSPIRATION & BIOMIMETICS 2020; 16:026002. [PMID: 33002883 DOI: 10.1088/1748-3190/abbd81] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
Biohybrid systems integrate living materials with synthetic devices, exploiting their respective advantages to solve challenging engineering problems. One challenge of critical importance to society is detecting and localizing airborne volatile chemicals. Many flying animals depend their ability to detect and locate the source of aerial chemical plumes for finding mates and food sources. A robot with comparable capability could reduce human hazard and drastically improve performance on tasks such as locating disaster survivors, hazardous gas leaks, incipient fires, or explosives. Three advances are needed before they can rival their biological counterparts: (1) a chemical sensor with a much faster response time that nevertheless satisfies the size, weight, and power constraints of flight, (2) a design, sensor suite, and control system that allows it to move toward the source of a plume fully autonomously while navigating obstacles, and (3) the ability to detect the plume with high specificity and sensitivity among the assortment of chemicals that invariably exist in the air. Here we address the first two, introducing a human-safe palm-sized air vehicle equipped with the odor-sensing antenna of an insect, the first odor-sensing biohybrid robot system to fly. Using this sensor along with a suite of additional navigational sensors, as well as passive wind fins, our robot orients upwind and navigates autonomously toward the source of airborne plumes. Our robot is the first flying biohybrid system to successfully perform odor localization in a confined space, and it is able to do so while detecting and avoiding obstacles in its flight path. We show that insect antennae respond more quickly than metal oxide gas sensors, enabling odor localization at an improved speed over previous flying robots. By using the insect antennae, we anticipate a feasible path toward improved chemical specificity and sensitivity by leveraging recent advances in gene editing.
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Affiliation(s)
- Melanie J Anderson
- University of Washington, Department of Mechanical Engineering, Seattle WA-98195, United States of America
| | - Joseph G Sullivan
- University of Washington, Department of Electrical and Computer Engineering, Seattle WA-98195, United States of America
| | - Timothy K Horiuchi
- University of Maryland, Department of Electrical and Computer Engineering, College Park MD-20742, United States of America
| | - Sawyer B Fuller
- University of Washington, Department of Mechanical Engineering, Seattle WA-98195, United States of America
- University of Washington, Paul G. Allen School of Computer Science, Seattle WA-98195, United States of America
| | - Thomas L Daniel
- University of Washington, Department of Mechanical Engineering, Seattle WA-98195, United States of America
- University of Washington, Department of Biology, Seattle WA-98195, United States of America
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45
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Abstract
A detailed description of olfactory system development in ants reveals that - unlike in Drosophila and as in mammals - olfactory receptors may play a role, providing new insights into the developmental evolution of complex chemosensory systems.
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Affiliation(s)
- Qichen Duan
- Department of Biology, Duke University, Durham, NC 27708, USA
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46
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Zak JD, Reddy G, Vergassola M, Murthy VN. Antagonistic odor interactions in olfactory sensory neurons are widespread in freely breathing mice. Nat Commun 2020; 11:3350. [PMID: 32620767 PMCID: PMC7335155 DOI: 10.1038/s41467-020-17124-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/10/2020] [Indexed: 12/24/2022] Open
Abstract
Odor landscapes contain complex blends of molecules that each activate unique, overlapping populations of olfactory sensory neurons (OSNs). Despite the presence of hundreds of OSN subtypes in many animals, the overlapping nature of odor inputs may lead to saturation of neural responses at the early stages of stimulus encoding. Information loss due to saturation could be mitigated by normalizing mechanisms such as antagonism at the level of receptor-ligand interactions, whose existence and prevalence remains uncertain. By imaging OSN axon terminals in olfactory bulb glomeruli as well as OSN cell bodies within the olfactory epithelium in freely breathing mice, we find widespread antagonistic interactions in binary odor mixtures. In complex mixtures of up to 12 odorants, antagonistic interactions are stronger and more prevalent with increasing mixture complexity. Therefore, antagonism is a common feature of odor mixture encoding in OSNs and helps in normalizing activity to reduce saturation and increase information transfer.
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Affiliation(s)
- Joseph D Zak
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.
- Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA.
| | - Gautam Reddy
- NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Massimo Vergassola
- Laboratoire de Physique de l'Ecole Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, Paris, F-75005, France
| | - Venkatesh N Murthy
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.
- Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA.
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47
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Wang Z, Guo J, Guo Y, Yang Y, Teng T, Yu Q, Wang T, Zhou M, Zhu Q, Wang W, Zhang Q, Yang H. Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays. Front Genet 2020; 11:558. [PMID: 32582291 PMCID: PMC7297042 DOI: 10.3389/fgene.2020.00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/07/2020] [Indexed: 01/30/2023] Open
Abstract
Copy number variations (CNVs) are important genomic structural variations and can give rise to significant phenotypic diversity. Herein, we used high-density 600K SNP arrays to detect CNVs in two synthetic lines of sheep (DS and SHH) and in Hu sheep (a local Chinese breed). A total of 919 CNV regions (CNVRs) were detected with a total length of 48.17 Mb, accounting for 1.96% of the sheep genome. These CNVRs consisted of 730 gains, 102 losses, and 87 complex CNVRs. These CNVRs were significantly enriched in the segmental duplication (SD) region. A CNVR-based cluster analysis of the three breeds revealed that the DS and SHH breeds share a close genetic relationship. Functional analysis revealed that some genes in these CNVRs were also significantly enriched in the olfactory transduction pathway (oas04740), including members of the OR gene family such as OR6C76, OR4Q2, and OR4K14. Using association analyses and previous gene annotations, we determined that a subset of identified genes was likely to be associated with body weight, including FOXF2, MAPK12, MAP3K11, STRBP, and C14orf132. Together, these results offer valuable information that will guide future efforts to explore the genetic basis for body weight in sheep.
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Affiliation(s)
- Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Jing Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Teng Teng
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Tao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Meng Zhou
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Qiusi Zhu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Wenwen Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Qin Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
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48
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Acid-Sensing Ion Channels Contribute to Type III Adenylyl Cyclase-Independent Acid Sensing of Mouse Olfactory Sensory Neurons. Mol Neurobiol 2020; 57:3042-3056. [PMID: 32458389 DOI: 10.1007/s12035-020-01943-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/13/2020] [Indexed: 10/24/2022]
Abstract
Acids can disturb the ecosystem of wild animals through altering their olfaction and olfaction-related survival behaviors. It is known that the main olfactory epithelia (MOE) of mammals rely on odorant receptors and type III adenylyl cyclase (AC3) to detect general odorants. However, it is unknown how the olfactory system sense protons or acidic odorants. Here, we show that while the MOE of AC3 knockout (KO) mice failed to respond to an odor mix in electro-olfactogram (EOG) recordings, it retained a small fraction of acid-evoked EOG responses. The acetic acid-induced EOG responses in wild-type (WT) MOE can be dissected into two components: the big component dependent on the AC3-mediated cAMP pathway and the much smaller component not. The small acid-evoked EOG response of the AC3 KOs was blocked by diminazene, an inhibitor of acid-sensing ion channels (ASICs), but not by forskolin/IBMX that desensitize the cAMP pathway. AC3 KO mice lost their sensitivity to detect pungent odorants but maintained sniffing behavior to acetic acid. Immunofluorescence staining demonstrated that ASIC1 proteins were highly expressed in olfactory sensory neurons (OSNs), mostly enriched in the knobs, dendrites, and somata, but not in olfactory cilia. Real-time polymerase chain reaction further detected the mRNA expression of ASIC1a, ASIC2b, and ASIC3 in the MOE. Additionally, mice exhibited reduced preference to attractive objects when placed in an environment with acidic volatiles. Together, we conclude that the mouse olfactory system has a non-conventional, likely ASIC-mediated ionotropic mechanism for acid sensing.
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49
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Marquet N, Cardoso JCR, Louro B, Fernandes SA, Silva SC, Canário AVM. Holothurians have a reduced GPCR and odorant receptor-like repertoire compared to other echinoderms. Sci Rep 2020; 10:3348. [PMID: 32098989 PMCID: PMC7042368 DOI: 10.1038/s41598-020-60167-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/05/2020] [Indexed: 01/13/2023] Open
Abstract
Sea cucumbers lack vision and rely on chemical sensing to reproduce and survive. However, how they recognize and respond to environmental cues remains unknown. Possible candidates are the odorant receptors (ORs), a diverse family of G protein-coupled receptors (GPCRs) involved in olfaction. The present study aimed at characterizing the chemosensory GPCRs in sea cucumbers. At least 246 distinct GPCRs, of which ca. 20% putative ORs, were found in a transcriptome assembly of putative chemosensory (tentacles, oral cavity, calcareous ring, and papillae/tegument) and reproductive (ovary and testis) tissues from Holothuria arguinensis (57 ORs) and in the Apostichopus japonicus genome (79 ORs). The sea cucumber ORs clustered with those of sea urchin and starfish into four main clades of gene expansions sharing a common ancestor and evolving under purifying selection. However, the sea cucumber ORs repertoire was the smallest among the echinoderms and the olfactory receptor signature motif LxxPxYxxxxxLxxxDxxxxxxxxP was better conserved in cluster OR-l1 which also had more members. ORs were expressed in tentacles, oral cavity, calcareous ring, and papillae/tegument, supporting their potential role in chemosensing. This study is the first comprehensive survey of chemosensory GPCRs in sea cucumbers, and provides the molecular basis to understand how they communicate.
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Affiliation(s)
- Nathalie Marquet
- CCMAR - Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - João C R Cardoso
- CCMAR - Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Bruno Louro
- CCMAR - Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Stefan A Fernandes
- CCMAR - Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Sandra C Silva
- CCMAR - Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Adelino V M Canário
- CCMAR - Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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50
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Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S. Common activation mechanism of class A GPCRs. eLife 2019; 8:e50279. [PMID: 31855179 PMCID: PMC6954041 DOI: 10.7554/elife.50279] [Citation(s) in RCA: 320] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.
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Affiliation(s)
- Qingtong Zhou
- iHuman InstituteShanghaiTech UniversityShanghaiChina
| | - Dehua Yang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Meng Wu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yu Guo
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Wanjing Guo
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Li Zhong
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Antao Dai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Zhi-Jie Liu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Raymond C Stevens
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ming-Wei Wang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- School of PharmacyFudan UniversityShanghaiChina
| | - Suwen Zhao
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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