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Schultz DT, Heath-Heckman EA, Winchell CJ, Kuo DH, Yu YS, Oberauer F, Kocot KM, Cho SJ, Simakov O, Weisblat DA. Acceleration of genome rearrangement in clitellate annelids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593736. [PMID: 38798472 PMCID: PMC11118384 DOI: 10.1101/2024.05.12.593736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Comparisons of multiple metazoan genomes have revealed the existence of ancestral linkage groups (ALGs), genomic scaffolds sharing sets of orthologous genes that have been inherited from ancestral animals for hundreds of millions of years (Simakov et al. 2022; Schultz et al. 2023) These ALGs have persisted across major animal taxa including Cnidaria, Deuterostomia, Ecdysozoa and Spiralia. Notwithstanding this general trend of chromosome-scale conservation, ALGs have been obliterated by extensive genome rearrangements in certain groups, most notably including Clitellata (oligochaetes and leeches), a group of easily overlooked invertebrates that is of tremendous ecological, agricultural and economic importance (Charles 2019; Barrett 2016). To further investigate these rearrangements, we have undertaken a comparison of 12 clitellate genomes (including four newly sequenced species) and 11 outgroup representatives. We show that these rearrangements began at the base of the Clitellata (rather than progressing gradually throughout polychaete annelids), that the inter-chromosomal rearrangements continue in several clitellate lineages and that these events have substantially shaped the evolution of the otherwise highly conserved Hox cluster.
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Affiliation(s)
- Darrin T. Schultz
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Elizabeth A.C. Heath-Heckman
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Christopher J. Winchell
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
| | - Dian-Han Kuo
- Department of Life Science & Museum of Zoology, National Taiwan University, No. 1 Section 4 Roosevelt Rd., Taipei 10617, Taiwan
| | - Yun-sang Yu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Fabian Oberauer
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Kevin M. Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - David A. Weisblat
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
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Meiser S, Sleeboom JM, Arkhypchuk I, Sandbote K, Kretzberg J. Cell anatomy and network input explain differences within but not between leech touch cells at two different locations. Front Cell Neurosci 2023; 17:1186997. [PMID: 37565030 PMCID: PMC10411907 DOI: 10.3389/fncel.2023.1186997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
Mechanosensory cells in the leech share several common features with mechanoreceptors in the human glabrous skin. Previous studies showed that the six T (touch) cells in each body segment of the leech are highly variable in their responses to somatic current injection and change their excitability over time. Here, we investigate three potential reasons for this variability in excitability by comparing the responses of T cells at two soma locations (T2 and T3): (1) Differential effects of time-dependent changes in excitability, (2) divergent synaptic input from the network, and (3) different anatomical structures. These hypotheses were explored with a combination of electrophysiological double recordings, 3D reconstruction of neurobiotin-filled cells, and compartmental model simulations. Current injection triggered significantly more spikes with shorter latency and larger amplitudes in cells at soma location T2 than at T3. During longer recordings, cells at both locations increased their excitability over time in the same way. T2 and T3 cells received the same amount of synaptic input from the unstimulated network, and the polysynaptic connections between both T cells were mutually symmetric. However, we found a striking anatomical difference: While in our data set all T2 cells innervated two roots connecting the ganglion with the skin, 50% of the T3 cells had only one root process. The sub-sample of T3 cells with one root process was significantly less excitable than the T3 cells with two root processes and the T2 cells. To test if the additional root process causes higher excitability, we simulated the responses of 3D reconstructed cells of both anatomies with detailed multi-compartment models. The anatomical subtypes do not differ in excitability when identical biophysical parameters and a homogeneous channel distribution are assumed. Hence, all three hypotheses may contribute to the highly variable T cell responses, but none of them is the only factor accounting for the observed systematic difference in excitability between cells at T2 vs. T3 soma location. Therefore, future patch clamp and modeling studies are needed to analyze how biophysical properties and spatial distribution of ion channels on the cell surface contribute to the variability and systematic differences of electrophysiological phenotypes.
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Affiliation(s)
- Sonja Meiser
- Department of Neuroscience, Computational Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
| | - Jana Marie Sleeboom
- Department of Neuroscience, Computational Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
- Institute of Physiology II, Faculty of Medicine, University Clinic Bonn (UKB), University of Bonn, Bonn, Germany
| | - Ihor Arkhypchuk
- Department of Neuroscience, Computational Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
| | - Kevin Sandbote
- Department of Neuroscience, Computational Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
| | - Jutta Kretzberg
- Department of Neuroscience, Computational Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
- Department of Neuroscience, Cluster of Excellence Hearing4all, Faculty VI, University of Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, University of Oldenburg, Oldenburg, Germany
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Ma X, Yan X, Ke R, Shan H, Rehman SU, Feng T, Zheng Y, Chuang C, Zhou W, Liu Q, Zheng J. Comparative Transcriptome Sequencing Analysis of Hirudo nipponia in Different Growth Periods. Front Physiol 2022; 13:873831. [PMID: 35812329 PMCID: PMC9259933 DOI: 10.3389/fphys.2022.873831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Hirudo nipponia is the only blood-sucking leech included in Chinese Pharmacopoeia having distinct features of anticoagulation, exorcizing blood stasis, and promoting menstruation. Despite such significant characteristics, very little is known about its molecular genetics and related physiological mechanisms. In this study, the transcriptomes of H. nipponia at three developmental stages (larvae, young, and adults), revealed a total of 1,348 differentially expressed genes (DEGs), 223 differentially expressed lncRNAs, and 88 novel mRNAs. A significant diverse gene expression patterns were observed at different developmental stages which were analyzed by differential gene expression trends, and the overall gene expression trends consist of three overall down-regulated trends, and two overall up-regulated trends. Furthermore, the GO and KEGG enrichment functional annotation analysis revealed that these DEGs were mainly associated with protein hydrolysis, signal transduction, energy metabolism, and lipid metabolism while growth, development, metabolism, and reproduction-related DEGs were also found. Additionally, real-time quantitative PCR results confirmed deep sequencing results based on the relative expression levels of nine randomly selected genes. This is the first transcriptome-based comprehensive study of H. irudo nipponia at different developmental stages which provided considerable deep understanding related to gene expression patterns and their relevant developmental pathways, neurodevelopmental and reproductive characteristics of the leech.
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Affiliation(s)
- Xiaocong Ma
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Xiuying Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Ren Ke
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Huiquan Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Yalin Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Chen Chuang
- Guangxi Medical University Cancer Hospital, Nanning, China
| | - Weiguan Zhou
- Thai Natural Hirudin Co, Ltd., Bangkok, Thailand
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
- *Correspondence: Qingyou Liu, ; Jinghui Zheng,
| | - Jinghui Zheng
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
- *Correspondence: Qingyou Liu, ; Jinghui Zheng,
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Scherer JS, Riedesel OE, Arkhypchuk I, Meiser S, Kretzberg J. Initial Variability and Time-Dependent Changes of Neuronal Response Features Are Cell-Type-Specific. Front Cell Neurosci 2022; 16:858221. [PMID: 35573827 PMCID: PMC9092978 DOI: 10.3389/fncel.2022.858221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Different cell types are commonly defined by their distinct response features. But several studies proved substantial variability between cells of the same type, suggesting rather the appraisal of response feature distributions than a limitation to "typical" responses. Moreover, there is growing evidence that time-dependent changes of response features contribute to robust and functional network output in many neuronal systems. The individually characterized Touch (T), Pressure (P), and Retzius (Rz) cells in the medicinal leech allow for a rigid analysis of response features, elucidating differences between and variability within cell types, as well as their changes over time. The initial responses of T and P cells to somatic current injection cover a wide range of spike counts, and their first spike is generated with a high temporal precision after a short latency. In contrast, all Rz cells elicit very similar low spike counts with variable, long latencies. During prolonged electrical stimulation the resting membrane potential of all three cell types hyperpolarizes. At the same time, Rz cells reduce their spiking activity as expected for a departure from the spike threshold. In contrast, both mechanoreceptor types increase their spike counts during repeated stimulation, consistent with previous findings in T cells. A control experiment reveals that neither a massive current stimulation nor the hyperpolarization of the membrane potential is necessary for the mechanoreceptors' increase in excitability over time. These findings challenge the previously proposed involvement of slow K+-channels in the time-dependent activity changes. We also find no indication for a run-down of HCN channels over time, and a rigid statistical analysis contradicts several potential experimental confounders as the basis of the observed variability. We conclude that the time-dependent change in excitability of T and P cells could indicate a cell-type-specific shift between different spiking regimes, which also could explain the high variability in the initial responses. The underlying mechanism needs to be further investigated in more naturalistic experimental situations to disentangle the effects of varying membrane properties versus network interactions. They will show if variability in individual response features serves as flexible adaptation to behavioral contexts rather than just "randomness".
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Affiliation(s)
- Jens-Steffen Scherer
- Computational Neuroscience, Department of Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
| | - Oda E. Riedesel
- Computational Neuroscience, Department of Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
| | - Ihor Arkhypchuk
- Computational Neuroscience, Department of Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
| | - Sonja Meiser
- Computational Neuroscience, Department of Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
| | - Jutta Kretzberg
- Computational Neuroscience, Department of Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
- Cluster of Excellence Hearing4all, Department of Neuroscience, Faculty VI, University of Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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Glossiphoniid leeches as a touchstone for studies of development in clitellate annelids. Curr Top Dev Biol 2022; 147:433-468. [PMID: 35337458 DOI: 10.1016/bs.ctdb.2021.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
My goals in this chapter are to share my enthusiasm for studying the biology of leeches, to place this work in context by presenting my rationale for studying non-traditional biological models in general, and to sample just three of the questions that intrigue me in leech biology, namely segmentation, genome evolution and neuronal fate specification. I first became excited about the idea of using leeches as a subject of investigation as an undergraduate in 1970 and have been engaged in this work since I arrived at Berkeley as a postdoc in 1976, intending to study leech neurobiology. Both my research interests and the rationale for the work have expanded greatly since then. What follows is a fragmentary personal and historical account-the interested reader may find more comprehensive treatments elsewhere (Kuo et al., 2020; Shankland & Savage, 1997; Shain, 2009; Weisblat & Huang, 2001; Weisblat & Kuo, 2009, 2014; Weisblat & Winchell, 2020).
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Paulsen RT, Burrell BD. Activity-Dependent Modulation of Tonic GABA Currents by Endocannabinoids in Hirudo verbana. Front Synaptic Neurosci 2022; 14:760330. [PMID: 35368247 PMCID: PMC8964407 DOI: 10.3389/fnsyn.2022.760330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/21/2022] [Indexed: 01/21/2023] Open
Abstract
Endocannabinoids are lipid neuromodulators that are synthesized on demand and primarily signal in a retrograde manner to elicit depression of excitatory and inhibitory synapses. Despite the considerable interest in their potential analgesic effects, there is evidence that endocannabinoids can have both pro-nociceptive and anti-nociceptive effects. The mechanisms contributing to the opposing effects of endocannabinoids in nociception need to be better understood before cannabinoid-based therapies can be effectively utilized to treat pain. Using the medicinal leech, Hirudo verbana, this work investigates whether endocannabinoids modulate tonic inhibition onto non-nociceptive afferents. In voltage clamp recordings, we analyzed changes in the tonic inhibition in pressure-sensitive (P) cells following pre-treatment with endocannabinoids, 2-arachidonoylglycerol (2-AG) or anandamide (AEA). We also tested whether high frequency stimulation (HFS) of nociceptive (N) cells could also modulate tonic inhibition. Both endocannabinoid application and N cell HFS depressed tonic inhibition in the P cell. Depression of tonic inhibition by N cell HFS was blocked by SB 366791 (a TRPV1 inhibitor). SB 366791 also prevented 2-AG-and AEA-induced depression of tonic inhibition. HFS-induced depression was not blocked by tetrahydrolipstatin (THL), which prevents 2-AG synthesis, nor AM 251 (a CB1 receptor inverse agonist). These results illustrate a novel activity-dependent modulation of tonic GABA currents that is mediated by endocannabinoid signaling and is likely to play an important role in sensitization of non-nociceptive afferent pathways.
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