1
|
Elagoz AM, Van Dijck M, Lassnig M, Seuntjens E. Embryonic development of a centralised brain in coleoid cephalopods. Neural Dev 2024; 19:8. [PMID: 38907272 PMCID: PMC11191162 DOI: 10.1186/s13064-024-00186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
The last common ancestor of cephalopods and vertebrates lived about 580 million years ago, yet coleoid cephalopods, comprising squid, cuttlefish and octopus, have evolved an extraordinary behavioural repertoire that includes learned behaviour and tool utilization. These animals also developed innovative advanced defence mechanisms such as camouflage and ink release. They have evolved unique life cycles and possess the largest invertebrate nervous systems. Thus, studying coleoid cephalopods provides a unique opportunity to gain insights into the evolution and development of large centralised nervous systems. As non-model species, molecular and genetic tools are still limited. However, significant insights have already been gained to deconvolve embryonic brain development. Even though coleoid cephalopods possess a typical molluscan circumesophageal bauplan for their central nervous system, aspects of its development are reminiscent of processes observed in vertebrates as well, such as long-distance neuronal migration. This review provides an overview of embryonic coleoid cephalopod research focusing on the cellular and molecular aspects of neurogenesis, migration and patterning. Additionally, we summarize recent work on neural cell type diversity in embryonic and hatchling cephalopod brains. We conclude by highlighting gaps in our knowledge and routes for future research.
Collapse
Affiliation(s)
- Ali M Elagoz
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium.
| | - Marie Van Dijck
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Mark Lassnig
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium.
- Leuven Brain Institute, KU Leuven, Leuven, Belgium.
- Leuven Institute for Single Cell Omics, KU Leuven, Leuven, Belgium.
| |
Collapse
|
2
|
Homa J, Konończuk K, Frankowski R, Zgoła-Grześkowiak A, Ławniczak Ł, Chrzanowski Ł, Stachowiak W, Niemczak M. Cations impact the biodegradation of iodosulfuron-methyl herbicidal ionic liquids by fungi. ENVIRONMENTAL TECHNOLOGY 2024:1-14. [PMID: 38849972 DOI: 10.1080/09593330.2024.2357696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/12/2024] [Indexed: 06/09/2024]
Abstract
In the framework of this study, six fungal isolates which demonstrated a high capability for biodegrading iodosulphuron-methyl sodium as well as herbicidal ionic liquids based on this herbicide were isolated from different soil samples. The isolates were identified based on the ITS region, whereas biodegradation residues were determined based on LC-MS/MS. Depending on the isolate, the half-lives values of the biodegraded herbicide or herbicidal ionic liquid ranged significantly from just 1.25 days to more than 40 days. The research findings unveiled that the structure of cations is a central limiting factor affecting fungal growth and herbicide transformation in case of ionic liquids. The length of the alkyl chain has been identified as the primary driver of herbicide toxicity, emphasizing the importance of structural factors in herbicide design. In cases when dodecyl(2-hydroxyethyl)dimethyl cation was used, its biodegradation ranged from 0 to approx. 20% and the biodegradability of the iodosulfuron-methyl was notably limited for the majority of the studied isolates. This knowledge provides guidance for development and selection of herbicides with reduced environmental impact. This study highlights the ecological importance of soil fungi, their potential role in herbicide biodegradation, the influence of cations on fungal growth and herbicide transformation, and the structural factors governing herbicide toxicity. Further research in these areas may lead to more efficient and environmentally friendly approaches to herbicide management.
Collapse
Affiliation(s)
- Jan Homa
- Institute of Chemical Technology and Engineering, Poznań University of Technology, Poznań, Poland
| | - Kosma Konończuk
- Institute of Chemical Technology and Engineering, Poznań University of Technology, Poznań, Poland
| | - Robert Frankowski
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Poznań, Poland
| | | | - Łukasz Ławniczak
- Institute of Chemical Technology and Engineering, Poznań University of Technology, Poznań, Poland
| | - Łukasz Chrzanowski
- Institute of Chemical Technology and Engineering, Poznań University of Technology, Poznań, Poland
| | - Witold Stachowiak
- Institute of Chemical Technology and Engineering, Poznań University of Technology, Poznań, Poland
| | - Michał Niemczak
- Institute of Chemical Technology and Engineering, Poznań University of Technology, Poznań, Poland
| |
Collapse
|
3
|
Chen L, Li C, Li B, Zhou X, Bai Y, Zou X, Zhou Z, He Q, Chen B, Wang M, Xue Y, Jiang Z, Feng J, Zhou T, Liu Z, Xu P. Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success. FUNDAMENTAL RESEARCH 2024; 4:589-602. [PMID: 38933191 PMCID: PMC11197550 DOI: 10.1016/j.fmre.2023.06.011] [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: 10/25/2022] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 06/28/2024] Open
Abstract
Hybridization and polyploidization have made great contributions to speciation, heterosis, and agricultural production within plants, but there is still limited understanding and utilization in animals. Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success. However, the mechanisms have not yet been comprehensively assessed in animals. Here, we produced a high-fidelity reference genome sequence for common carp, a typical allotetraploid fish species cultured worldwide. This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses. Most genes were expressed with subgenome biases, with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development. While subgenome A evolved more rapidly, subgenome B contributed to a greater level of expression during development and under stressful conditions. Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome. Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis. The plasticity of subgenomes and their shifting of dominant expression during early development, and in response to stressful conditions, provide novel insights into the molecular basis of the successful speciation, evolution, and heterosis of the allotetraploid common carp.
Collapse
Affiliation(s)
- Lin Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Chengyu Li
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Bijun Li
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaofan Zhou
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaoqing Zou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Zhixiong Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Qian He
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Baohua Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Mei Wang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yaguo Xue
- College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Zhou Jiang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jianxin Feng
- Henan Academy of Fishery Science, Zhengzhou 450044, China
| | - Tao Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse 13244, USA
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| |
Collapse
|
4
|
Khoreva A, Butov KR, Nikolaeva EI, Martyanov A, Kulakovskaya E, Pershin D, Alexenko M, Kurnikova M, Abasov R, Raykina E, Abramov D, Arnaudova K, Rodina Y, Trubina N, Skvortsova Y, Balashov D, Sveshnikova A, Maschan A, Novichkova G, Panteleev M, Shcherbina A. Novel hemizygous CORO1A variant leads to combined immunodeficiency with defective platelet calcium signaling and cell mobility. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100172. [PMID: 37915722 PMCID: PMC10616384 DOI: 10.1016/j.jacig.2023.100172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/31/2023] [Accepted: 06/16/2023] [Indexed: 11/03/2023]
Abstract
Background To date, fewer than 20 patients have been identified as having germline biallelic mutations in the coronin-1A gene (CORO1A) and its protein with clinical features of combined immunodeficiency characterized by T-cell lymphopenia ranging from the severe phenotype to the mild phenotype, recurrent infections, and lymphoproliferative disorders. However, the effects of CORO1A protein disruption on actin-dependent functions in primary cells have not been fully delineated. Objective We sought to characterize the underlying defects of actin-dependent cellular functions in a female patient with combined immunodeficiency caused by a novel missense variant in the CORO1A gene in combination with a de novo heterozygous microdeletion of chromosome 16p11.2 and also to provide evidence of the pathogenicity of this gene mutation. Methods To identify the genetic defect, next-generation sequencing followed by Sanger confirmation and array comparative genomic hybridization were performed. Western blot and quantitative PCR tests were used to assess the effects on the protein. Flow cytometry and live microscopy were performed to investigate cellular motility and immune cell counts and function. Results We demonstrated that the CORO1A hemizygous variant c.19C>T, p. A7C induces significant decreases in cellular levels of the CORO1A protein while leaving mRNA concentrations unaffected. The observed mutation resulted in impaired natural killer cell cytotoxicity and platelet calcium signaling. In addition, primary granulocytes and mesenchymal cells showed significant defects in motility. Conclusion Collectively, we added new data about the CORO1A gene as a key player in actin cytoskeleton dynamics and cell signaling. Our findings expand the clinical spectrum regarding CORO1A protein deficiency and confirm the importance of a personalized therapeutic approach for each patient.
Collapse
Affiliation(s)
- Anna Khoreva
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Kirill R. Butov
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
| | - Elena I. Nikolaeva
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
| | - Alexey Martyanov
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
| | - Elena Kulakovskaya
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitry Pershin
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Maxim Alexenko
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Maria Kurnikova
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ruslan Abasov
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Elena Raykina
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitry Abramov
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | | | - Yulia Rodina
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Natalia Trubina
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Yulia Skvortsova
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitry Balashov
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anastasia Sveshnikova
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
| | - Alexey Maschan
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Galina Novichkova
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Mikhail Panteleev
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Shcherbina
- Dmitry Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| |
Collapse
|
5
|
Taghizadeh MS, Niazi A, Afsharifar A. Virus-like particles (VLPs): A promising platform for combating against Newcastle disease virus. Vaccine X 2024; 16:100440. [PMID: 38283623 PMCID: PMC10811427 DOI: 10.1016/j.jvacx.2024.100440] [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: 10/12/2023] [Revised: 12/11/2023] [Accepted: 01/13/2024] [Indexed: 01/30/2024] Open
Abstract
The global poultry industry plays a pivotal role in providing eggs and meat for human consumption. However, outbreaks of viral disease, especially Newcastle virus disease (NDV), within poultry farms have detrimental effects on various zootechnical parameters, such as body weight gain, feed intake, feed conversion ratio, as well as the quality of egg and meat production. Cases of vaccine failure have been reported in regions where highly pathogenic strains of NDV are prevalent. To tackle this challenge, virus-like particles (VLPs) have emerged as a potential solution. VLPs closely resemble natural viruses, offering biocompatibility and immune-stimulating properties that make them highly promising for therapeutic applications against NDV. Hence, this review emphasizes the significance of NDV and the need for effective treatments. The manuscript will contain several key aspects, starting with an exploration of the structure and properties of NDV. Subsequently, the paper will delve into the characteristics and benefits of VLPs compared to conventional drug delivery systems. A comprehensive analysis of VLPs as potential vaccine candidates targeting NDV will be presented, along with a discussion on strategies for loading cargo into these NDV-targeting VLPs. The review will also examine various expression systems utilized in the production of NDV-targeting VLPs. Additionally, the manuscript will address future prospects and challenges in the field, concluding with recommendations for further research.
Collapse
Affiliation(s)
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Alireza Afsharifar
- Plant Virus Research Center, School of Agriculture, Shiraz University, Shiraz, Iran
| |
Collapse
|
6
|
Druce E, Grego M, Bolhuis H, Johnes PJ, Sánchez-Baracaldo P. Draft Genome Sequences of Synechococcus sp. strains CCAP1479/9, CCAP1479/10, CCAP1479/13, CCY0621, and CCY9618: Five Freshwater Syn/Pro Clade Picocyanobacteria. J Genomics 2023; 11:26-36. [PMID: 37152813 PMCID: PMC10161378 DOI: 10.7150/jgen.81013] [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: 11/18/2022] [Accepted: 03/13/2023] [Indexed: 05/09/2023] Open
Abstract
Picocyanobacteria are essential primary producers in freshwaters yet little is known about their genomic diversity and ecological niches. We report here five draft genomes of freshwater picocyanobacteria: Synechococcus sp. CCAP1479/9, Synechococcus sp. CCAP1479/10, and Synechococcus sp. CCAP1479/13 isolated from Lake Windermere in the Lake District, UK; and Synechococcus sp. CCY0621 and Synechococcus sp. CCY9618 isolated from lakes in The Netherlands. Phylogenetic analysis reveals all five strains belonging to sub-cluster 5.2 of the Synechococcus and Prochlorococcus clade of Cyanobacteria. These five strains are divergent from Synechococcus elongatus, an often-used model for freshwater Synechococcus. Functional annotation revealed significant differences in the number of genes involved in the transport and metabolism of several macro-molecules between freshwater picocyanobacteria from sub-cluster 5.2 and Synechococcus elongatus, including amino acids, lipids, and carbohydrates. Comparative genomic analysis identified further differences in the presence of photosynthesis-associated proteins while gene neighbourhood comparisons revealed alternative structures of the nitrate assimilation operon nirA.
Collapse
Affiliation(s)
- Elliot Druce
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, BS8 1SS, United Kingdom
| | - Michele Grego
- CNRS and Sorbonne Université, FR 2424, Roscoff Culture Collection, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Hoorn, the Netherlands
| | - Penny J. Johnes
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, BS8 1SS, United Kingdom
| | - Patricia Sánchez-Baracaldo
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, BS8 1SS, United Kingdom
| |
Collapse
|
7
|
Zumkeller S, Knoop V. Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases. BMC Ecol Evol 2023; 23:5. [PMID: 36915058 PMCID: PMC10012718 DOI: 10.1186/s12862-023-02108-y] [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: 09/20/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Group II introns are common in the two endosymbiotic organelle genomes of the plant lineage. Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) mitogenomes is highly variable and specific for the seven major clades: liverworts, mosses, hornworts, lycophytes, ferns, gymnosperms and flowering plants. Each plant group features "signature selections" of ca. 20-30 paralogues from a superset of altogether 105 group II introns meantime identified in embryophyte mtDNAs, suggesting massive intron gains and losses along the backbone of plant phylogeny. We report on systematically categorizing plant mitochondrial group II introns into "families", comprising evidently related paralogues at different insertion sites, which may even be more similar than their respective orthologues in phylogenetically distant taxa. Including streptophyte (charophyte) algae extends our sampling to 161 and we sort 104 streptophyte mitochondrial group II introns into 25 core families of related paralogues evidently arising from retrotransposition events. Adding to discoveries of only recently created intron paralogues, hypermobile introns and twintrons, our survey led to further discoveries including previously overlooked "fossil" introns in spacer regions or e.g., in the rps8 pseudogene of lycophytes. Initially excluding intron-borne maturase sequences for family categorization, we added an independent analysis of maturase phylogenies and find a surprising incongruence between intron mobility and the presence of intron-borne maturases. Intriguingly, however, we find that several examples of nuclear splicing factors meantime characterized simultaneously facilitate splicing of independent paralogues now placed into the same intron families. Altogether this suggests that plant group II intron mobility, in contrast to their bacterial counterparts, is not intimately linked to intron-encoded maturases.
Collapse
Affiliation(s)
- Simon Zumkeller
- IZMB, Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Volker Knoop
- IZMB, Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany.
| |
Collapse
|
8
|
Zainal Abidin NA, Timofeeva M, Szydzik C, Akbaridoust F, Lav C, Marusic I, Mitchell A, Hamilton JR, Ooi AS, Nesbitt WS. A microfluidic method to investigate platelet mechanotransduction under extensional strain. Res Pract Thromb Haemost 2023; 7:100037. [PMID: 36846647 PMCID: PMC9944983 DOI: 10.1016/j.rpth.2023.100037] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
Background Blood platelets have evolved a complex mechanotransduction machinery to rapidly respond to hemodynamic conditions. A variety of microfluidic flow-based approaches have been developed to explore platelet mechanotransduction; however, these experimental models primarily focus on the effects of increased wall shear stress on platelet adhesion events and do not consider the critical effects of extensional strain on platelet activation in free flow. Objectives We report the development and application of a hyperbolic microfluidic assay that allows for investigation of platelet mechanotransduction under quasi-homogenous extensional strain rates in the absence of surface adhesions. Methods Using a combined computational fluid dynamic and experimental microfluidic approach, we explore 5 extensional strain regimes (geometries) and their effect on platelet calcium signal transduction. Results We demonstrate that in the absence of canonical adhesion, receptor engagement platelets are highly sensitive to both initial increase and subsequent decrease in extensional strain rates within the range of 747 to 3319/s. Furthermore, we demonstrate that platelets rapidly respond to the rate of change in extensional strain and define a threshold of ≥7.33 × 106/s/m, with an optimal range of 9.21 × 107 to 1.32 × 108/s/m. In addition, we demonstrate a key role of both the actin-based cytoskeleton and annular microtubules in the modulation of extensional strain-mediated platelet mechanotransduction. Conclusion This method opens a window onto a novel platelet signal transduction mechanism and may have potential diagnostic utility in the identification of patients who are prone to thromboembolic complications associated with high-grade arterial stenosis or are on mechanical circulatory support systems, for which the extensional strain rate is a predominant hemodynamic driver.
Collapse
Affiliation(s)
- Nurul A. Zainal Abidin
- The Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Mariia Timofeeva
- Department of Mechanical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Crispin Szydzik
- The Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- School of Engineering, RMIT University, Melbourne, Victoria, Australia
| | - Farzan Akbaridoust
- Department of Mechanical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chitrarth Lav
- Department of Mechanical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, Victoria, Australia
- Scuderia AlphaTauri F1, Bicester, UK
| | - Ivan Marusic
- Department of Mechanical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Arnan Mitchell
- School of Engineering, RMIT University, Melbourne, Victoria, Australia
| | - Justin R. Hamilton
- The Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Andrew S.H. Ooi
- Department of Mechanical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Warwick S. Nesbitt
- The Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Correspondence Warwick S. Nesbitt, The Australian Centre for Blood Diseases, Monash University, 99 Commercial Road, Melbourne, Victoria 3004, Australia.
| |
Collapse
|
9
|
Napoli FR, Daly CM, Neal S, McCulloch KJ, Zaloga AR, Liu A, Koenig KM. Cephalopod retinal development shows vertebrate-like mechanisms of neurogenesis. Curr Biol 2022; 32:5045-5056.e3. [PMID: 36356573 PMCID: PMC9729453 DOI: 10.1016/j.cub.2022.10.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/10/2022]
Abstract
Coleoid cephalopods, including squid, cuttlefish, and octopus, have large and complex nervous systems and high-acuity, camera-type eyes. These traits are comparable only to features that are independently evolved in the vertebrate lineage. The size of animal nervous systems and the diversity of their constituent cell types is a result of the tight regulation of cellular proliferation and differentiation in development. Changes in the process of development during evolution that result in a diversity of neural cell types and variable nervous system size are not well understood. Here, we have pioneered live-imaging techniques and performed functional interrogation to show that the squid Doryteuthis pealeii utilizes mechanisms during retinal neurogenesis that are hallmarks of vertebrate processes. We find that retinal progenitor cells in the squid undergo nuclear migration until they exit the cell cycle. We identify retinal organization corresponding to progenitor, post-mitotic, and differentiated cells. Finally, we find that Notch signaling may regulate both retinal cell cycle and cell fate. Given the convergent evolution of elaborate visual systems in cephalopods and vertebrates, these results reveal common mechanisms that underlie the growth of highly proliferative neurogenic primordia. This work highlights mechanisms that may alter ontogenetic allometry and contribute to the evolution of complexity and growth in animal nervous systems.
Collapse
Affiliation(s)
- Francesca R Napoli
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Christina M Daly
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Stephanie Neal
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Kyle J McCulloch
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Alexandra R Zaloga
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Alicia Liu
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA
| | - Kristen M Koenig
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
10
|
Styfhals R, Zolotarov G, Hulselmans G, Spanier KI, Poovathingal S, Elagoz AM, De Winter S, Deryckere A, Rajewsky N, Ponte G, Fiorito G, Aerts S, Seuntjens E. Cell type diversity in a developing octopus brain. Nat Commun 2022; 13:7392. [PMID: 36450803 PMCID: PMC9712504 DOI: 10.1038/s41467-022-35198-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
Octopuses are mollusks that have evolved intricate neural systems comparable with vertebrates in terms of cell number, complexity and size. The brain cell types that control their sophisticated behavioral repertoire are still unknown. Here, we profile the cell diversity of the paralarval Octopus vulgaris brain to build a cell type atlas that comprises mostly neural cells, but also multiple glial subtypes, endothelial cells and fibroblasts. We spatially map cell types to the vertical, subesophageal and optic lobes. Investigation of cell type conservation reveals a shared gene signature between glial cells of mouse, fly and octopus. Genes related to learning and memory are enriched in vertical lobe cells, which show molecular similarities with Kenyon cells in Drosophila. We construct a cell type taxonomy revealing transcriptionally related cell types, which tend to appear in the same brain region. Together, our data sheds light on cell type diversity and evolution in the octopus brain.
Collapse
Affiliation(s)
- Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Grygoriy Zolotarov
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115, Berlin, Germany
| | - Gert Hulselmans
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | - Katina I Spanier
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | | | - Ali M Elagoz
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | - Astrid Deryckere
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Department of Biological Sciences, Columbia University, New York, US
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Stein Aerts
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium.
| |
Collapse
|
11
|
Despot-Slade E, Širca S, Mravinac B, Castagnone-Sereno P, Plohl M, Meštrović N. Satellitome analyses in nematodes illuminate complex species history and show conserved features in satellite DNAs. BMC Biol 2022; 20:259. [PMCID: PMC9673304 DOI: 10.1186/s12915-022-01460-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Satellite DNAs (satDNAs) are tandemly repeated non-coding DNA sequences that belong to the most abundant and the fastest evolving parts of the eukaryotic genome. A satellitome represents the collection of different satDNAs in a genome. Due to extreme diversity and methodological difficulties to characterize and compare satDNA collection in complex genomes, knowledge on their putative functional constraints and capacity to participate in genome evolution remains rather elusive. SatDNA transcripts have been detected in many species, however comparative studies of satDNA transcriptome between species are extremely rare.
Results
We conducted a genome-wide survey and comparative analyses of satellitomes among different closely related Meloidogyne spp. nematodes. The evolutionary trends of satDNAs suggest that each round of proposed polyploidization in the evolutionary history is concomitant with the addition of a new set of satDNAs in the satellitome of any particular Meloidogyne species. Successive incorporation of new sets of satDNAs in the genome along the process of polyploidization supports multiple hybridization events as the main factor responsible for the formation of these species. Through comparative analyses of 83 distinct satDNAs, we found a CENP-B box-like sequence motif conserved among 11 divergent satDNAs (similarity ranges from 36 to 74%). We also found satDNAs that harbor a splice leader (SL) sequence which, in spite of overall divergence, shows conservation across species in two putative functional regions, the 25-nt SL exon and the Sm binding site. Intra- and interspecific comparative expression analyses of the complete satDNA set in the analyzed Meloidogyne species revealed transcription profiles including a subset of 14 actively transcribed satDNAs. Among those, 9 show active transcription in every species where they are found in the genome and throughout developmental stages.
Conclusions
Our results demonstrate the feasibility and power of comparative analysis of the non-coding repetitive genome for elucidation of the origin of species with a complex history. Although satDNAs generally evolve extremely quickly, the comparative analyses of 83 satDNAs detected in the analyzed Meloidogyne species revealed conserved sequence features in some satDNAs suggesting sequence evolution under selective pressure. SatDNAs that are actively transcribed in related genomes and throughout nematode development support the view that their expression is not stochastic.
Collapse
|
12
|
Stern-Mentch N, Winter G, Belenky M, Moroz L, Hochner B. Neurotransmission and neuromodulation systems in the learning and memory network of Octopus vulgaris. J Morphol 2022; 283:557-584. [PMID: 35107842 PMCID: PMC9303212 DOI: 10.1002/jmor.21459] [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: 11/03/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 11/15/2022]
Abstract
The vertical lobe (VL) in the octopus brain plays an essential role in its sophisticated learning and memory. Early anatomical studies suggested that the VL is organized in a “fan‐out fan‐in” connectivity matrix comprising only three morphologically identified neuron types; input axons from the median superior frontal lobe (MSFL) innervating en passant millions of small amacrine interneurons (AMs), which converge sharply onto large VL output neurons (LNs). Recent physiological studies confirmed the feedforward excitatory connectivity; a glutamatergic synapse at the first MSFL‐to‐AM synaptic layer and a cholinergic AM‐to‐LNs synapse. MSFL‐to‐AMs synapses show a robust hippocampal‐like activity‐dependent long‐term potentiation (LTP) of transmitter release. 5‐HT, octopamine, dopamine and nitric oxide modulate short‐ and long‐term VL synaptic plasticity. Here, we present a comprehensive histolabeling study to better characterize the neural elements in the VL. We generally confirmed glutamatergic MSFLs and cholinergic AMs. Intense labeling for NOS activity in the AMs neurites were in‐line with the NO‐dependent presynaptic LTP mechanism at the MSFL‐to‐AM synapse. New discoveries here reveal more heterogeneity of the VL neurons than previously thought. GABAergic AMs suggest a subpopulation of inhibitory interneurons in the first input layer. Clear γ‐amino butyric acid labeling in the cell bodies of LNs supported an inhibitory VL output, yet the LNs co‐expressed FMRFamide‐like neuropeptides, suggesting an additional neuromodulatory role of the VL output. Furthermore, a group of LNs was glutamatergic. A new cluster of cells organized as a “deep nucleus” showed rich catecholaminergic labeling and may play a role in intrinsic neuromodulation. In‐situ hybridization and immunolabeling allowed characterization and localization of a rich array of neuropeptides and neuromodulators, likely involved in reward/punishment signals. This analysis of the fast transmission system, together with the newly found cellular elements, help integrate behavioral, physiological, pharmacological and connectome findings into a more comprehensive understanding of an efficient learning and memory network.
Collapse
Affiliation(s)
- Naama Stern-Mentch
- Department of Neurobiology, Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Gabriela Winter
- Department of Neuroscience and McKnight Brain Institute, and Whitney Laboratory for Marine Bioscience, University of Florida, Gainesville, Florida, USA.,Ocean Genome Atlas Project, San Francisco, USA
| | - Michael Belenky
- Department of Neurobiology, Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Leonid Moroz
- Department of Neuroscience and McKnight Brain Institute, and Whitney Laboratory for Marine Bioscience, University of Florida, Gainesville, Florida, USA
| | - Binyamin Hochner
- Department of Neurobiology, Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| |
Collapse
|