1
|
Zhang KS, Rodriguez R, Tang SKY. SMORES: a simple microfluidic operating room for the examination and surgery of Stentor coeruleus. Sci Rep 2024; 14:8684. [PMID: 38622246 PMCID: PMC11018760 DOI: 10.1038/s41598-024-59286-y] [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: 01/06/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
Ciliates are powerful unicellular model organisms that have been used to elucidate fundamental biological processes. However, the high motility of ciliates presents a major challenge in studies using live-cell microscopy and microsurgery. While various immobilization methods have been developed, they are physiologically disruptive to the cell and incompatible with microscopy and/or microsurgery. Here, we describe a Simple Microfluidic Operating Room for the Examination and Surgery of Stentor coeruleus (SMORES). SMORES uses Quake valve-based microfluidics to trap, compress, and perform surgery on Stentor as our model ciliate. Compared with previous methods, immobilization by physical compression in SMORES is more effective and uniform. The mean velocity of compressed cells is 24 times less than that of uncompressed cells. The compression is minimally disruptive to the cell and is easily applied or removed using a 3D-printed pressure rig. We demonstrate cell immobilization for up to 2 h without sacrificing cell viability. SMORES is compatible with confocal microscopy and is capable of media exchange for pharmacokinetic studies. Finally, the modular design of SMORES allows laser ablation or mechanical dissection of a cell into many cell fragments at once. These capabilities are expected to enable biological studies previously impossible in ciliates and other motile species.
Collapse
Affiliation(s)
- Kevin S Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ramon Rodriguez
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
2
|
Zhang KS, Rodriguez R, Tang SK. SMORES: A Simple Microfluidic Operating Room for the Examination and Surgery of Stentor coeruleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.578956. [PMID: 38370688 PMCID: PMC10871274 DOI: 10.1101/2024.02.05.578956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Ciliates are powerful unicellular model organisms that have been used to elucidate fundamental biological processes. However, the high motility of ciliates presents a major challenge in studies using live-cell microscopy and microsurgery. While various immobilization methods have been developed, they are physiologically disruptive to the cell and incompatible with microscopy and/or microsurgery. Here, we describe a Simple Microfluidic Operating Room for the Examination and Surgery of Stentor coeruleus (SMORES). SMORES uses Quake valve-based microfluidics to trap, compress, and perform surgery on Stentor as our model ciliate. Compared with previous methods, immobilization by physical compression in SMORES is more effective and uniform. The mean velocity of compressed cells is 24 times less than that of uncompressed cells. The compression is minimally disruptive to the cell and is easily applied or removed using a 3D-printed pressure rig. We demonstrate cell immobilization for up to 2 hours without sacrificing cell viability. SMORES is compatible with confocal microscopy and is capable of media exchange for pharmacokinetic studies. Finally, the modular design of SMORES allows laser ablation or mechanical dissection of a cell into many cell fragments at once. These capabilities are expected to enable biological studies previously impossible in ciliates and other motile species.
Collapse
Affiliation(s)
- Kevin S. Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ramon Rodriguez
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Sindy K.Y. Tang
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| |
Collapse
|
3
|
Fokin SI, Lebedeva NA, Potekhin A, Gammuto L, Petroni G, Serra V. Holospora-like bacteria "Candidatus Gortzia yakutica" and Preeria caryophila: Ultrastructure, promiscuity, and biogeography of the symbionts. Eur J Protistol 2023; 90:125998. [PMID: 37356197 DOI: 10.1016/j.ejop.2023.125998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/06/2023] [Indexed: 06/27/2023]
Abstract
Two already known representatives of Holospora-like bacteria, "Candidatus Gortzia yakutica" from Paramecium putrinum and Preeria caryophila, originally retrieved from the Paramecium aurelia complex, were found in new hosts: Paramecium nephridiatum and Paramecium polycaryum, respectively. In the present study, these bacteria were investigated using morphological and molecular methods. For "Ca. G. yakutica", the first details of the electron microscopic structure in the main and new hosts were provided. Regarding Pr. caryophila, the ultrastructural description of this species was implemented by several features previously unknown, such as the so called "membrane cluster" dividing periplasm from cytoplasm and fine composition of infectious forms before and during its releasing from the infected macronucleus. The new combinations of these Holospora-like bacteria with ciliate hosts were discussed from biogeographical and ecological points of view. Host specificity of symbionts as a general paradigm was critically reviewed as well.
Collapse
Affiliation(s)
| | - Natalia A Lebedeva
- Centre of Core Facilities "Culture Collections of Microorganisms", Saint Petersburg State University, Russia
| | - Alexey Potekhin
- Laboratory of Cellular and Molecular Protistology, Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russia; Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | | | - Giulio Petroni
- Department of Biology, University of Pisa, Italy; CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy; CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, Italy
| | | |
Collapse
|
4
|
Tian M, Cai X, Liu Y, Liucong M, Howard-Till R. A practical reference for studying meiosis in the model ciliate Tetrahymena thermophila. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:595-608. [PMID: 37078080 PMCID: PMC10077211 DOI: 10.1007/s42995-022-00149-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 09/28/2022] [Indexed: 05/03/2023]
Abstract
Meiosis is a critical cell division program that produces haploid gametes for sexual reproduction. Abnormalities in meiosis are often causes of infertility and birth defects (e.g., Down syndrome). Most organisms use a highly specialized zipper-like protein complex, the synaptonemal complex (SC), to guide and stabilize pairing of homologous chromosomes in meiosis. Although the SC is critical for meiosis in many eukaryotes, there are organisms that perform meiosis without a functional SC. However, such SC-less meiosis is poorly characterized. To understand the features of SC-less meiosis and its adaptive significance, the ciliated protozoan Tetrahymena was selected as a model. Meiosis research in Tetrahymena has revealed intriguing aspects of the regulatory programs utilized in its SC-less meiosis, yet additional efforts are needed for obtaining an in-depth comprehension of mechanisms that are associated with the absence of SC. Here, aiming at promoting a wider application of Tetrahymena for meiosis research, we introduce basic concepts and core techniques for studying meiosis in Tetrahymena and then suggest future directions for expanding the current Tetrahymena meiosis research toolbox. These methodologies could be adopted for dissecting meiosis in poorly characterized ciliates that might reveal novel features. Such data will hopefully provide insights into the function of the SC and the evolution of meiosis from a unique perspective. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00149-8.
Collapse
Affiliation(s)
- Miao Tian
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
- Institute of Human Genetics, CNRS, University of Montpellier, 34090 Montpellier, France
| | - Xia Cai
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yujie Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Mingmei Liucong
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Rachel Howard-Till
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA USA
| |
Collapse
|
5
|
Melekhin M, Yakovleva Y, Lebedeva N, Nekrasova I, Nikitashina L, Castelli M, Mayén-Estrada R, Romanovich AE, Petroni G, Potekhin A. Cryptic Diversity in Paramecium multimicronucleatum Revealed with a Polyphasic Approach. Microorganisms 2022; 10:microorganisms10050974. [PMID: 35630417 PMCID: PMC9143557 DOI: 10.3390/microorganisms10050974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/01/2022] [Accepted: 05/03/2022] [Indexed: 02/06/2023] Open
Abstract
Paramecium (Ciliophora) systematics is well studied, and about twenty morphological species have been described. The morphological species may include several genetic species. However, molecular phylogenetic analyses revealed that the species diversity within Paramecium could be even higher and has raised a problem of cryptic species whose statuses remain uncertain. In the present study, we provide the morphological and molecular characterization of two novel Paramecium species. While Paramecium lynni n. sp., although morphologically similar to P. multimicronucleatum, is phylogenetically well separated from all other Paramecium species, Paramecium fokini n. sp. appears to be a cryptic sister species to P. multimicronucleatum. The latter two species can be distinguished only by molecular methods. The number and structure of micronuclei, traditionally utilized to discriminate species in Paramecium, vary not only between but also within each of the three studied species and, thus, cannot be considered a reliable feature for species identification. The geographic distribution of the P. multimicronucleatum and P. fokini n. sp. strains do not show defined patterns, still leaving space for a role of the geographic factor in initial speciation in Paramecium. Future findings of new Paramecium species can be predicted from the molecular data, while morphological characteristics appear to be unstable and overlapping at least in some species.
Collapse
Affiliation(s)
- Maksim Melekhin
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, 199034 Saint Petersburg, Russia
| | - Yulia Yakovleva
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Natalia Lebedeva
- Centre for Culture Collection of Microorganisms, Saint Petersburg State University, 198504 Saint Petersburg, Russia
| | - Irina Nekrasova
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Liubov Nikitashina
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Michele Castelli
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, 27100 Pavia, Italy
| | - Rosaura Mayén-Estrada
- Laboratorio de Protozoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Ext. s/núm. Ciudad Universitaria, Av. Universidad 3000, Coyoacán, Ciudad de Mexico 04510, Mexico
| | - Anna E Romanovich
- Center for Molecular and Cell Technologies, Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Giulio Petroni
- Department of Biology, University of Pisa, 56126 Pisa, Italy
| | - Alexey Potekhin
- Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, 199034 Saint Petersburg, Russia
| |
Collapse
|
6
|
Castelli M, Lanzoni O, Giovannini M, Lebedeva N, Gammuto L, Sassera D, Melekhin M, Potekhin A, Fokin S, Petroni G. 'Candidatus Gromoviella agglomerans', a novel intracellular Holosporaceae parasite of the ciliate Paramecium showing marked genome reduction. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:34-49. [PMID: 34766443 DOI: 10.1111/1758-2229.13021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Holosporales are an alphaproteobacterial lineage encompassing bacteria obligatorily associated with multiple diverse eukaryotes. For most representatives, little is known on the interactions with their hosts. In this study, we characterized a novel Holosporales symbiont of the ciliate Paramecium polycaryum. This bacterium inhabits the host cytoplasm, frequently forming quite large aggregates. Possibly due to such aggregates, host cells sometimes displayed lethal division defects. The symbiont was also able to experimentally stably infect another Paramecium polycaryum strain. The bacterium is phylogenetically related with symbionts of other ciliates and diplonemids, forming a putatively fast-evolving clade within the family Holosporaceae. Similarly to many close relatives, it presents a very small genome (<600 kbp), and, accordingly, a limited predicted metabolism, implying a heavy dependence on Paramecium, thanks also to some specialized membrane transporters. Characterized features, including the presence of specific secretion systems, are overall suggestive of a mild parasitic effect on the host. From an evolutionary perspective, a potential ancestral trend towards pronounced genome reduction and possibly linked to parasitism could be inferred, at least among fast-evolving Holosporaceae, with some lineage-specific traits. Interestingly, similar convergent features could be observed in other host-associated lineages, in particular Rickettsiales among Alphaproteobacteria.
Collapse
Affiliation(s)
- Michele Castelli
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Olivia Lanzoni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | | | - Natalia Lebedeva
- Centre of Core Facilities "Culture Collections of Microorganisms", Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Davide Sassera
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Maksim Melekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Sergei Fokin
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
- Department of Invertebrate Zoology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| |
Collapse
|
7
|
The Cilioprotist Cytoskeleton , a Model for Understanding How Cell Architecture and Pattern Are Specified: Recent Discoveries from Ciliates and Comparable Model Systems. Methods Mol Biol 2021; 2364:251-295. [PMID: 34542858 DOI: 10.1007/978-1-0716-1661-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The cytoskeletons of eukaryotic, cilioprotist microorganisms are complex, highly patterned, and diverse, reflecting the varied and elaborate swimming, feeding, reproductive, and sensory behaviors of the multitude of cilioprotist species that inhabit the aquatic environment. In the past 10-20 years, many new discoveries and technologies have helped to advance our understanding of how cytoskeletal organelles are assembled in many different eukaryotic model systems, in relation to the construction and modification of overall cellular architecture and function. Microtubule organizing centers, particularly basal bodies and centrioles, have continued to reveal their central roles in architectural engineering of the eukaryotic cell, including in the cilioprotists. This review calls attention to (1) published resources that illuminate what is known of the cilioprotist cytoskeleton; (2) recent studies on cilioprotists and other model organisms that raise specific questions regarding whether basal body- and centriole-associated nucleic acids, both DNA and RNA, should continue to be considered when seeking to employ cilioprotists as model systems for cytoskeletal research; and (3) new, mainly imaging, technologies that have already proven useful for, but also promise to enhance, future cytoskeletal research on cilioprotists.
Collapse
|
8
|
Neuroscience Research using Small Animals on a Chip: From Nematodes to Zebrafish Larvae. BIOCHIP JOURNAL 2021. [DOI: 10.1007/s13206-021-00012-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
9
|
Castelli M, Lanzoni O, Nardi T, Lometto S, Modeo L, Potekhin A, Sassera D, Petroni G. 'Candidatus Sarmatiella mevalonica' endosymbiont of the ciliate Paramecium provides insights on evolutionary plasticity among Rickettsiales. Environ Microbiol 2021; 23:1684-1701. [PMID: 33470507 DOI: 10.1111/1462-2920.15396] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Members of the bacterial order Rickettsiales are obligatorily associated with a wide range of eukaryotic hosts. Their evolutionary trajectories, in particular concerning the origin of shared or differential traits among distant sub-lineages, are still poorly understood. Here, we characterized a novel Rickettsiales bacterium associated with the ciliate Paramecium tredecaurelia and phylogenetically related to the Rickettsia genus. Its genome encodes significant lineage-specific features, chiefly the mevalonate pathway gene repertoire, involved in isoprenoid precursor biosynthesis. Not only this pathway has never been described in Rickettsiales, it also is very rare among bacteria, though typical in eukaryotes, thus likely representing a horizontally acquired trait. The presence of these genes could enable an efficient exploitation of host-derived intermediates for isoprenoid synthesis. Moreover, we hypothesize the reversed reactions could have replaced canonical pathways for producing acetyl-CoA, essential for phospholipid biosynthesis. Additionally, we detected phylogenetically unrelated mevalonate pathway genes in metagenome-derived Rickettsiales sequences, likely indicating evolutionary convergent effects of independent horizontal gene transfer events. Accordingly, convergence, involving both gene acquisitions and losses, is highlighted as a relevant evolutionary phenomenon in Rickettsiales, possibly favoured by plasticity and comparable lifestyles, representing a potentially hidden origin of other more nuanced similarities among sub-lineages.
Collapse
Affiliation(s)
- Michele Castelli
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Olivia Lanzoni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy.,Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Tiago Nardi
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Stefano Lometto
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Letizia Modeo
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, Italy
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Davide Sassera
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| |
Collapse
|
10
|
Zabihihesari A, Hilliker AJ, Rezai P. Fly-on-a-Chip: Microfluidics for Drosophila melanogaster Studies. Integr Biol (Camb) 2020; 11:425-443. [DOI: 10.1093/intbio/zyz037] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/21/2019] [Accepted: 10/26/2019] [Indexed: 12/16/2022]
Abstract
Abstract
The fruit fly or Drosophila melanogaster has been used as a promising model organism in genetics, developmental and behavioral studies as well as in the fields of neuroscience, pharmacology, and toxicology. Not only all the developmental stages of Drosophila, including embryonic, larval, and adulthood stages, have been used in experimental in vivo biology, but also the organs, tissues, and cells extracted from this model have found applications in in vitro assays. However, the manual manipulation, cellular investigation and behavioral phenotyping techniques utilized in conventional Drosophila-based in vivo and in vitro assays are mostly time-consuming, labor-intensive, and low in throughput. Moreover, stimulation of the organism with external biological, chemical, or physical signals requires precision in signal delivery, while quantification of neural and behavioral phenotypes necessitates optical and physical accessibility to Drosophila. Recently, microfluidic and lab-on-a-chip devices have emerged as powerful tools to overcome these challenges. This review paper demonstrates the role of microfluidic technology in Drosophila studies with a focus on both in vivo and in vitro investigations. The reviewed microfluidic devices are categorized based on their applications to various stages of Drosophila development. We have emphasized technologies that were utilized for tissue- and behavior-based investigations. Furthermore, the challenges and future directions in Drosophila-on-a-chip research, and its integration with other advanced technologies, will be discussed.
Collapse
Affiliation(s)
| | | | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| |
Collapse
|
11
|
Zinskie JA, Roig M, Janetopoulos C, Myers KA, Bruist MF. Live-cell imaging of small nucleolar RNA tagged with the broccoli aptamer in yeast. FEMS Yeast Res 2019; 18:5078348. [PMID: 30137288 DOI: 10.1093/femsyr/foy093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/20/2018] [Indexed: 11/14/2022] Open
Abstract
The development of the RNA 'vegetable' aptamers, Spinach and Broccoli, has simplified RNA imaging, especially in live cells. These RNA aptamers interact with a fluorophore (DFHBI or DFHBI-1T) to produce a green fluorescence signal. Although used in mammalian and Escherichia coli cells, the use of these aptamers in yeast has been limited. Here we describe how the Saccharomyces cerevisiae snoRNA, snR30, was tagged with the Spinach or the Broccoli aptamers and observed in live cells. The ability to observe aptamer fluorescence in polyacrylamide gels stained with a fluorophore or with a microplate reader can ease preliminary screening of the aptamers in different RNA scaffolds. In snR30 a tandem repeat of the Broccoli aptamer produced the best signal in vitro. Multiple factors in cell preparation were vital for obtaining a good fluorescence signal. These factors included the clearance of the native unmodified snR30, the amount and length of dye incubation and the rinsing of cells. In cells, the aptamers did not interfere with the structure or essential function of snR30, as the tagged RNA localized to the nucleolus and directed processing of ribosomal RNA in yeast. High-resolution images of the tagged snoRNA were obtained with live cells immobilized by a microcompressor.
Collapse
Affiliation(s)
- Jessica A Zinskie
- University of the Sciences, Department of Chemistry & Biochemistry, 600 S. 43rd St., Philadelphia, PA 19104.,Rowan University, School of Osteopathic Medicine, Department of Cell Biology and Neuroscience, 2 Medical Center Dr., Stratford, NJ 08084
| | - Meghan Roig
- University of the Sciences, Department of Chemistry & Biochemistry, 600 S. 43rd St., Philadelphia, PA 19104.,Florida International University, Department of Biochemistry and Biochemistry, 11200 SW 8th St., Miami, FL 33199
| | | | - Kenneth A Myers
- University of the Sciences, Department of Biological Sciences, Philadelphia, PA 19104
| | - Michael F Bruist
- University of the Sciences, Department of Chemistry & Biochemistry, 600 S. 43rd St., Philadelphia, PA 19104
| |
Collapse
|
12
|
Howard-Till R, Loidl J. Condensins promote chromosome individualization and segregation during mitosis, meiosis, and amitosis in Tetrahymena thermophila. Mol Biol Cell 2017; 29:466-478. [PMID: 29237819 PMCID: PMC6014175 DOI: 10.1091/mbc.e17-07-0451] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 11/27/2017] [Accepted: 12/07/2017] [Indexed: 11/11/2022] Open
Abstract
Condensin is a protein complex with diverse functions in chromatin packaging and chromosome condensation and segregation. We studied condensin in the evolutionarily distant protist model Tetrahymena, which features noncanonical nuclear organization and divisions. In Tetrahymena, the germline and soma are partitioned into two different nuclei within a single cell. Consistent with their functional specializations in sexual reproduction and gene expression, condensins of the germline nucleus and the polyploid somatic nucleus are composed of different subunits. Mitosis and meiosis of the germline nucleus and amitotic division of the somatic nucleus are all dependent on condensins. In condensin-depleted cells, a chromosome condensation defect was most striking at meiotic metaphase, when Tetrahymena chromosomes are normally most densely packaged. Live imaging of meiotic divisions in condensin-depleted cells showed repeated nuclear stretching and contraction as the chromosomes failed to separate. Condensin depletion also fundamentally altered chromosome arrangement in the polyploid somatic nucleus: multiple copies of homologous chromosomes tended to cluster, consistent with a previous model of condensin suppressing default somatic pairing. We propose that failure to form discrete chromosome territories is the common cause of the defects observed in the absence of condensins.
Collapse
Affiliation(s)
- Rachel Howard-Till
- Department of Chromosome Biology, University of Vienna, 1190 Vienna, Austria
| | - Josef Loidl
- Department of Chromosome Biology, University of Vienna, 1190 Vienna, Austria
| |
Collapse
|
13
|
Sardo L, Lin A, Khakhina S, Beckman L, Ricon L, Elbezanti W, Jaison T, Vishwasrao H, Shroff H, Janetopoulos C, Klase ZA. Real-time visualization of chromatin modification in isolated nuclei. J Cell Sci 2017; 130:2926-2940. [PMID: 28743737 PMCID: PMC5612227 DOI: 10.1242/jcs.205823] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/13/2017] [Indexed: 12/31/2022] Open
Abstract
Chromatin modification is traditionally assessed in biochemical assays that provide average measurements of static events given that the analysis requires components from many cells. Microscopy can visualize single cells, but the cell body and organelles can hamper staining and visualization of the nucleus. Normally, chromatin is visualized by immunostaining a fixed sample or by expressing exogenous fluorescently tagged proteins in a live cell. Alternative microscopy tools to observe changes of endogenous chromatin in real-time are needed. Here, we isolated transcriptionally competent nuclei from cells and used antibody staining without fixation to visualize changes in endogenous chromatin. This method allows the real-time addition of drugs and fluorescent probes to one or more nuclei while under microscopy observation. A high-resolution map of 11 endogenous nuclear markers of the histone code, transcription machinery and architecture was obtained in transcriptionally active nuclei by performing confocal and structured illumination microscopy. We detected changes in chromatin modification and localization at the single-nucleus level after inhibition of histone deacetylation. Applications in the study of RNA transcription, viral protein function and nuclear architecture are presented. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Luca Sardo
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Angel Lin
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Svetlana Khakhina
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Lucas Beckman
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Luis Ricon
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Weam Elbezanti
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Tara Jaison
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Harshad Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 28092, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 28092, USA
| | - Christopher Janetopoulos
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Zachary A Klase
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| |
Collapse
|
14
|
Chaudhury AR, Insolera R, Hwang RD, Fridell YW, Collins C, Chronis N. On chip cryo-anesthesia of Drosophila larvae for high resolution in vivo imaging applications. LAB ON A CHIP 2017; 17:2303-2322. [PMID: 28613308 PMCID: PMC5559736 DOI: 10.1039/c7lc00345e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We present a microfluidic chip for immobilizing Drosophila melanogaster larvae for high resolution in vivo imaging. The chip creates a low-temperature micro-environment that anaesthetizes and immobilizes the larva in under 3 minutes. We characterized the temperature distribution within the chip and analyzed the resulting larval body movement using high resolution fluorescence imaging. Our results indicate that the proposed method minimizes submicron movements of internal organs and tissue without affecting the larva physiology. It can be used to continuously immobilize larvae for short periods of time (minutes) or for longer periods (several hours) if used intermittently. The same chip can be used to accommodate and immobilize arvae across all developmental stages (1st instar to late 3rd instar), and loading larvae onto the chip does not require any specialized skills. To demonstrate the usability of the chip, we observed mitochondrial trafficking in neurons from the cell bodies to the axon terminals along with mitochondrial fusion and neuro-synaptic growth through time in intact larvae. Besides studying sub-cellular processes and cellular development, we envision the use of on chip cryo-anesthesia in a wide variety of biological in vivo imaging applications, including observing organ development of the salivary glands, fat bodies and body-wall muscles.
Collapse
Affiliation(s)
- Amrita Ray Chaudhury
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | | | | | | | | | | |
Collapse
|
15
|
Mayne R, Whiting J, Adamatzky A. Toxicity and Applications of Internalised Magnetite Nanoparticles Within Live Paramecium caudatum Cells. BIONANOSCIENCE 2017; 8:90-94. [PMID: 29600158 PMCID: PMC5866280 DOI: 10.1007/s12668-017-0425-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nanotechnology revolution has allowed us to speculate on the possibility of hybridising nanoscale materials with live substrates, yet significant doubt still remains pertaining to the effects of nanomaterials on biological matter. In this investigation, we cultivate the ciliated protistic pond-dwelling microorganism Paramecium caudatum in the presence of excessive quantities of magnetite nanoparticles in order to deduce potential beneficial applications for this technique, as well as observe any deleterious effects on the organisms’ health. Our findings indicate that this variety of nanoparticle is well-tolerated by P. caudatum cells, who were observed to consume them in quantities exceeding 5–12% of their body volume: cultivation in the presence of magnetite nanoparticles does not alter P. caudatum cell volume, swimming speed, growth rate or peak colony density and cultures may persist in nanoparticle-contaminated media for many weeks. We demonstrate that P. caudatum cells ingest starch-coated magnetite nanoparticles which facilitates their being magnetically immobilised whilst maintaining apparently normal ciliary dynamics, thus demonstrating that nanoparticle biohybridisation is a viable alternative to conventional forms of ciliate quieting. Ingested magnetite nanoparticle deposits appear to aggregate, suggesting that (a) the process of being internalised concentrates and may therefore detoxify (i.e. render less reactive) nanomaterial suspensions in aquatic environments, and (b) P. caudatum is a candidate organism for programmable nanomaterial manipulation and delivery.
Collapse
Affiliation(s)
- Richard Mayne
- Unconventional Computing Laboratory, University of the West of England, Bristol, UK
| | - James Whiting
- Unconventional Computing Laboratory, University of the West of England, Bristol, UK
| | - Andrew Adamatzky
- Unconventional Computing Laboratory, University of the West of England, Bristol, UK
| |
Collapse
|
16
|
Aufderheide KJ. Refinements of and commentary on the silver staining techniques of Fernández-Galiano. Biotech Histochem 2016; 91:352-6. [DOI: 10.1080/10520295.2016.1175665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
17
|
Chin LK, Lee CH, Chen BC. Imaging live cells at high spatiotemporal resolution for lab-on-a-chip applications. LAB ON A CHIP 2016; 16:2014-24. [PMID: 27121367 DOI: 10.1039/c5lc01556a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Conventional optical imaging techniques are limited by the diffraction limit and difficult-to-image biomolecular and sub-cellular processes in living specimens. Novel optical imaging techniques are constantly evolving with the desire to innovate an imaging tool that is capable of seeing sub-cellular processes in a biological system, especially in three dimensions (3D) over time, i.e. 4D imaging. For fluorescence imaging on live cells, the trade-offs among imaging depth, spatial resolution, temporal resolution and photo-damage are constrained based on the limited photons of the emitters. The fundamental solution to solve this dilemma is to enlarge the photon bank such as the development of photostable and bright fluorophores, leading to the innovation in optical imaging techniques such as super-resolution microscopy and light sheet microscopy. With the synergy of microfluidic technology that is capable of manipulating biological cells and controlling their microenvironments to mimic in vivo physiological environments, studies of sub-cellular processes in various biological systems can be simplified and investigated systematically. In this review, we provide an overview of current state-of-the-art super-resolution and 3D live cell imaging techniques and their lab-on-a-chip applications, and finally discuss future research trends in new and breakthrough research areas of live specimen 4D imaging in controlled 3D microenvironments.
Collapse
Affiliation(s)
- Lip Ket Chin
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798, Singapore
| | - Chau-Hwang Lee
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan. and Institute of Biophotonics, National Yang-Ming University, Taipei 11221, Taiwan and Department of Physics, National Taiwan University, Taipei 10671, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan.
| |
Collapse
|
18
|
Levario TJ, Lim B, Shvartsman SY, Lu H. Microfluidics for High-Throughput Quantitative Studies of Early Development. Annu Rev Biomed Eng 2016; 18:285-309. [PMID: 26928208 DOI: 10.1146/annurev-bioeng-100515-013926] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Developmental biology has traditionally relied on qualitative analyses; recently, however, as in other fields of biology, researchers have become increasingly interested in acquiring quantitative knowledge about embryogenesis. Advances in fluorescence microscopy are enabling high-content imaging in live specimens. At the same time, microfluidics and automation technologies are increasing experimental throughput for studies of multicellular models of development. Furthermore, computer vision methods for processing and analyzing bioimage data are now leading the way toward quantitative biology. Here, we review advances in the areas of fluorescence microscopy, microfluidics, and data analysis that are instrumental to performing high-content, high-throughput studies in biology and specifically in development. We discuss a case study of how these techniques have allowed quantitative analysis and modeling of pattern formation in the Drosophila embryo.
Collapse
Affiliation(s)
- Thomas J Levario
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332;
| | - Bomyi Lim
- Department of Chemical and Biological Engineering and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544;
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544;
| | - Hang Lu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332;
| |
Collapse
|
19
|
Stanley CE, Grossmann G, i Solvas XC, deMello AJ. Soil-on-a-Chip: microfluidic platforms for environmental organismal studies. LAB ON A CHIP 2016; 16:228-41. [PMID: 26645910 DOI: 10.1039/c5lc01285f] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Soil is the habitat of countless organisms and encompasses an enormous variety of dynamic environmental conditions. While it is evident that a thorough understanding of how organisms interact with the soil environment may have substantial ecological and economical impact, current laboratory-based methods depend on reductionist approaches that are incapable of simulating natural diversity. The application of Lab-on-a-Chip or microfluidic technologies to organismal studies is an emerging field, where the unique benefits afforded by system miniaturisation offer new opportunities for the experimentalist. Indeed, precise spatiotemporal control over the microenvironments of soil organisms in combination with high-resolution imaging has the potential to provide an unprecedented view of biological events at the single-organism or single-cell level, which in turn opens up new avenues for environmental and organismal studies. Herein we review some of the most recent and interesting developments in microfluidic technologies for the study of soil organisms and their interactions with the environment. We discuss how so-called "Soil-on-a-Chip" technology has already contributed significantly to the study of bacteria, nematodes, fungi and plants, as well as inter-organismal interactions, by advancing experimental access and environmental control. Most crucially, we highlight where distinct advantages over traditional approaches exist and where novel biological insights will ensue.
Collapse
Affiliation(s)
- Claire E Stanley
- Institute of Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland.
| | - Guido Grossmann
- Cell Networks-Cluster of Excellence and Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120 Heidelberg, Germany
| | | | - Andrew J deMello
- Institute of Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland.
| |
Collapse
|
20
|
Zinskie JA, Shribak M, Bruist MF, Aufderheide KJ, Janetopoulos C. A mechanical microcompressor for high resolution imaging of motile specimens. Exp Cell Res 2015; 337:249-56. [PMID: 26192819 DOI: 10.1016/j.yexcr.2015.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/11/2015] [Indexed: 11/17/2022]
Abstract
In order to obtain fine details in 3 dimensions (3D) over time, it is critical for motile biological specimens to be appropriately immobilized. Of the many immobilization options available, the mechanical microcompressor offers many benefits. Our device, previously described, achieves gentle flattening of a cell, allowing us to image finely detailed structures of numerous organelles and physiological processes in living cells. We have imaged protozoa and other small metazoans using differential interference contrast (DIC) microscopy, orientation-independent (OI) DIC, and real-time birefringence imaging using a video-enhanced polychromatic polscope. We also describe an enhancement of our previous design by engineering a new device where the coverslip mount is fashioned onto the top of the base; so the entire apparatus is accessible on top of the stage. The new location allows for easier manipulation of the mount when compressing or releasing a specimen on an inverted microscope. Using this improved design, we imaged immobilized bacteria, yeast, paramecia, and nematode worms and obtained an unprecedented view of cell and specimen details. A variety of microscopic techniques were used to obtain high resolution images of static and dynamic cellular and physiological events.
Collapse
Affiliation(s)
- Jessica A Zinskie
- University of the Sciences Chemistry and Biochemistry, 600 S 43rd Street, Philadelphia, PA 19104, United States
| | - Michael Shribak
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, United States
| | - Michael F Bruist
- University of the Sciences Chemistry and Biochemistry, 600 S 43rd Street, Philadelphia, PA 19104, United States
| | - Karl J Aufderheide
- Texas A&M University, Department of Biology, College Station, TX 77843, United States
| | - Chris Janetopoulos
- University of the Sciences, Department of Biological Sciences, 600 S 43rd Street, Philadelphia, PA 19104, United States.
| |
Collapse
|
21
|
Bell WE, Hallworth R, Wyatt TA, Sisson JH. Use of a novel cell adhesion method and digital measurement to show stimulus-dependent variation in somatic and oral ciliary beat frequency in Paramecium. J Eukaryot Microbiol 2015; 62:144-8. [PMID: 25066640 PMCID: PMC4450440 DOI: 10.1111/jeu.12153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 11/30/2022]
Abstract
When Paramecium encounters positive stimuli, the membrane hyperpolarizes and ciliary beat frequency increases. We adapted an established immobilization protocol using a biological adhesive and a novel digital analysis system to quantify beat frequency in immobilized Paramecium. Cells showed low mortality and demonstrated beat frequencies consistent with previous studies. Chemoattractant molecules, reduction in external potassium, and posterior stimulation all increased somatic beat frequency. In all cases, the oral groove cilia maintained a higher beat frequency than mid-body cilia, but only oral cilia from cells stimulated with chemoattactants showed an increase from basal levels.
Collapse
Affiliation(s)
- Wade E Bell
- Department of Biology, Virginia Military Institute, Lexington, Virginia, 24450
| | | | | | | |
Collapse
|