15 results on '"Akıl C"'
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2. A generalization of the Wiener rational basis functions on infinite intervals
- Author
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Narayan, Akil C. and Hesthaven, Jan S.
- Subjects
Mathematics - Numerical Analysis ,65D15,41A20,42A10 - Abstract
We formulate and derive a generalization of an orthogonal rational-function basis for spectral expansions over the infinite or semi-infinite interval. The original functions, first presented by Wiener are a mapping and weighting of the Fourier basis to the infinite interval. By identifying the Fourier series as a biorthogonal composition of Jacobi polynomials/functions, we are able to define generalized Fourier series' which, appropriately mapped to the whole real line and weighted, form a generalization of Wiener's basis functions. It is known that the original Wiener rational functions inherit sparse Galerkin matrices for differentiation, and can utilize the fast Fourier transform (FFT) for computation of the modal coefficients. We show that the generalized basis sets also have a sparse differentiation matrix and we discuss connection problems, which are necessary theoretical developments for application of the FFT., Comment: 35 pages, 9 figures
- Published
- 2009
3. A generalization of the Wiener rational basis functions on infinite intervals, Part II — Numerical investigation
- Author
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Narayan, Akil C. and Hesthaven, Jan S.
- Published
- 2013
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4. A GENERALIZATION OF THE WIENER RATIONAL BASIS FUNCTIONS ON INFINITE INTERVALS: PART I—DERIVATION AND PROPERTIES
- Author
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NARAYAN, AKIL C. and HESTHAVEN, JAN S.
- Published
- 2011
5. Nature-based solutions for regulating moisture content in an expansive clay soil
- Author
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Akil Crichlow, Ronald Roopnarine, Gaius Eudoxie, and Federick Pinongcos
- Subjects
Clay soils ,Coconut matting ,Nature-based solutions ,Slope instability ,Vetiver grass ,Environmental sciences ,GE1-350 - Abstract
Land degradation in the form of mass movement is a major challenge in the humid tropics, where intense rainfall and tropical cyclones are common. Rainfall increases soil moisture content, which often acts as a triggering factor for mass movement events, particularly in clay soils with expansive minerals, where moisture changes impact structural integrity. Growing evidence suggests that Nature-based Solutions (NbS) can regulate soil moisture levels, which can assist in maintaining cohesion and hence reduce slope instability. This paper examines soil moisture changes due to Coconut Matting (CM), Coconut Matting-Natural Vegetation Hybrid (CMNV), Natural Vegetation (NV), and Vetiver grass (VET) and discusses moisture content regulation as it relates to slope stability, with a particular focus on expansive clays. Soil moisture trends were measured for 90 days at four depths (20 cm, 40 cm, 60 cm, and 100 cm) using soil moisture loggers, while precipitation levels were monitored using a rain gauge. GLM ANOVA analysis showed a significant depth*treatment interaction (P < 0.05) on soil moisture. The Vetiver grass treatment had the lowest soil moisture levels, with a (27.62 %) reduction compared to the control (bare plot). The CMNV treatment had the second-greatest-% soil moisture reduction (7.68 %). Contrastingly, CM and NV resulted in limited moisture reduction (1.99 %) and (0.73 %) respectively. The role of Vetiver grass was therefore highlighted in mitigating water saturation towards preventing potential slope instability.
- Published
- 2024
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6. Integrating wastewater reuse into water management schemes of Caribbean SIDS: A Trinidad and Tobago case study
- Author
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Ronald Roopnarine, Kervelle Baird, Mikella Hosein, Renee Jackson, Shehnaaz Salim, Anisha Cephas, Oral Daley, Samantha Gangapersad, Sara-Jade Govia, Adrian Cashman, Akil Crichlow, and Federick Pinongcos
- Subjects
caribbean ,public awareness ,wastewater ,wastewater reuse ,River, lake, and water-supply engineering (General) ,TC401-506 - Abstract
Integrating Wastewater Reuse (WWRU) into national Water Management Schemes (WMS) is crucial as Small Island Developing States (SIDS) attempt to cope with water resource constraints in a changing climate. In 2022, the Global Environment Facility Caribbean Regional Fund (GEF CReW+) on Wastewater Management, the Ministry of Public Utilities (MPU), Trinidad and Tobago and the Trinidad and Tobago Bureau of Standards (TTBS) spearheaded the development of a national voluntary standard for treated wastewater reuse focused on agricultural and landscaping uses. During the process, the MPU conducted a Knowledge, Attitudes and Practices (KAP) and Willingness to Pay (WTP) assessment to inform the standard and subsequent implementation. Results indicated `good' knowledge on wastewater and WWRU (59.3%), however attitudes and practices were considered `poor'. Inferential Statistics performed on numerically coded survey response data revealed no statistically significant relation with the demographic factors assessed; 84.1% of respondents were willing to use treated wastewater with health concerns identified as the main barrier; 27.3% of respondents were willing to pay the same price as conventional water, while 31.2% were willing to pay 25 -50% less. This assessment can inform the implementation and pricing process and provide valuable insights to increase the uptake of WWRU in the region. HIGHLIGHTS Explains the regional dynamics associated with WWRU.; Examines knowledge, attitudes, practices and Willingness to Pay (WTP) in the context of WWRU in Trinidad and Tobago.; Outlines the key barrier in terms of public perception related to WWRU.;
- Published
- 2023
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7. The impact of COVID-19 and natural disasters on water consumption across sectors: case studies of Barbados and Trinidad and Tobago
- Author
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Ronald Roopnarine, Adrian Cashman, Gaius Eudoxie, Sara-Jade Govia, Crisanne Davis-Rostant, Renee Jackson, and Akil Crichlow
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caribbean sids ,compound disasters ,consumer behaviour ,covid-19 ,water consumption ,River, lake, and water-supply engineering (General) ,TC401-506 ,Water supply for domestic and industrial purposes ,TD201-500 - Abstract
The Small Island Developing States of the Caribbean (SIDS) are among the most vulnerable to natural hazards, particularly hydroclimatic and, in some cases, geological. In 2020, the COVID-19 pandemic added another layer of complexity to the already disruptive risk profiles of these countries. Understanding how these hazards, both individually and cumulatively, impact sectors, particularly essential sectors such as the water sector, is crucial. This paper examines the impact of the COVID-19 pandemic on water consumption along with concurrent natural hazards in two Caribbean countries: Barbados, and Trinidad and Tobago. The assessment indicated a marked influence on consumption levels in various sectors consistent with imposed public health restrictions. In the case of Barbados, monthly consumption decreased during the pandemic across all categories when compared to the pre-Covid period, except for residential consumption, which increased by approximately 9%. For Trinidad and Tobago, a decrease in average monthly water consumption across all categories, ranging from 3% to 13% was noted. Although available data did not permit conclusive analysis, we have discerned some general trends, identified gaps, and provided recommendations. Our findings can provide useful guidance for water utilities in the region to better understand consumer behaviour and address demand and supply issues. HIGHLIGHTS The paper highlights the impact of the COVID-19 pandemic in relation to water consumption.; The paper examines the impact across sectors.; The paper examines the impact of the COVID-19 regulations/restrictions in a unique region with heightened vulnerability to natural hazards.; The paper presents two case studies (tourist-based vs. industrialised).; The paper provides interesting findings and useful recommendations.;
- Published
- 2023
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8. Impact of Scala Tympani Geometry on Insertion Forces during Implantation
- Author
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Filip Hrncirik, Iwan V. Roberts, Chloe Swords, Peter J. Christopher, Akil Chhabu, Andrew H. Gee, and Manohar L. Bance
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cochlear implant ,3D printing ,scala tympani ,insertion forces ,micro-CT ,Biotechnology ,TP248.13-248.65 - Abstract
(1) Background: During a cochlear implant insertion, the mechanical trauma can cause residual hearing loss in up to half of implantations. The forces on the cochlea during the insertion can lead to this mechanical trauma but can be highly variable between subjects which is thought to be due to differing anatomy, namely of the scala tympani. This study presents a systematic investigation of the influence of different geometrical parameters of the scala tympani on the cochlear implant insertion force. The influence of these parameters on the insertion forces were determined by testing the forces within 3D-printed, optically transparent models of the scala tympani with geometric alterations. (2) Methods: Three-dimensional segmentations of the cochlea were characterised using a custom MATLAB script which parametrised the scala tympani model, procedurally altered the key shape parameters (e.g., the volume, vertical trajectory, curvature, and cross-sectional area), and generated 3D printable models that were printed using a digital light processing 3D printer. The printed models were then attached to a custom insertion setup that measured the insertion forces on the cochlear implant and the scala tympani model during a controlled robotic insertion. (3) Results: It was determined that the insertion force is largely unaffected by the overall size, curvature, vertical trajectory, and cross-sectional area once the forces were normalised to an angular insertion depth. A Capstan-based model of the CI insertion forces was developed and matched well to the data acquired. (4) Conclusion: By using accurate 3D-printed models of the scala tympani with geometrical alterations, it was possible to demonstrate the insensitivity of the insertion forces to the size and shape of the scala tympani, after controlling for the angular insertion depth. This supports the Capstan model of the cochlear implant insertion force which predicts an exponential growth of the frictional force with an angular insertion depth. This concludes that the angular insertion depth, rather than the length of the CI inserted, should be the major consideration when evaluating the insertion force and associated mechanical trauma caused by cochlear implant insertion.
- Published
- 2022
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9. Prebiotic Nucleoside Phosphorylation in a Simulated Deep-Sea Supercritical Carbon Dioxide-Water Two-Phase Environment.
- Author
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Tagawa S, Hatami R, Morino K, Terazawa S, Akıl C, Johnson-Finn K, Shibuya T, and Fujishima K
- Abstract
Prebiotic synthesis of complex organic molecules in water-rich environments has been a long-standing challenge. In the modern deep sea, emission of liquid CO
2 has been observed in multiple locations, which indicates the existence of benthic CO2 pools. Recently, a liquid/supercritical CO2 (ScCO2 ) hypothesis has been proposed that a two-phase ScCO2 -water environment could lead to efficient dehydration and condensation of organics. To confirm this hypothesis, we conducted a nucleoside phosphorylation reaction in a hydrothermal reactor creating ScCO2 -water two-phase environment. After 120 h of uridine, cytosine, guanosine, and adenosine phosphorylation at 68.9°C, various nucleoside monophosphates (NMPs), nucleotide diphosphates, and carbamoyl nucleosides were produced. The addition of urea enhanced the overall production of phosphorylated species with 5'-NMPs, the major products that reached over 10% yield. As predicted, phosphorylation did not proceed in the fully aqueous environment without ScCO2 . Further, a glass window reactor was introduced for direct observation of the two-phase environment, where the escape of water into the ScCO2 phase was observed. These results are similar to those of a wet-dry cycle experiment simulating the terrestrial hot spring environment, indicating that the presence of ScCO2 can create a comparatively dry condition in the deep sea. In addition, the high acidity present in the aqueous phase further supports nucleotide synthesis by enabling the release of orthophosphate from the hydroxyapatite mineral solving the phosphate problem. Thus, the present study highlights the potential of the unique ScCO2 -water two-phase environment to drive prebiotic nucleotide synthesis and likely induce condensation reactions of various organic and inorganic compounds in the deep-sea CO2 pool on Earth and potentially other ocean worlds.- Published
- 2024
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10. The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea.
- Author
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Tran LT, Akıl C, Senju Y, and Robinson RC
- Subjects
- Archaea metabolism, Protein Transport, Monomeric GTP-Binding Proteins chemistry
- Abstract
Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes., (© 2024. The Author(s).)
- Published
- 2024
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11. Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis.
- Author
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Akıl C, Tran LT, Orhant-Prioux M, Baskaran Y, Senju Y, Takeda S, Chotchuang P, Muengsaen D, Schulte A, Manser E, Blanchoin L, and Robinson RC
- Subjects
- Actin Cytoskeleton metabolism, Archaea metabolism, Gelsolin chemistry, Gelsolin metabolism, Actins metabolism, Calcium metabolism
- Abstract
Charting the emergence of eukaryotic traits is important for understanding the characteristics of organisms that contributed to eukaryogenesis. Asgard archaea and eukaryotes are the only organisms known to possess regulated actin cytoskeletons. Here, we determined that gelsolins (2DGels) from Lokiarchaeota (Loki) and Heimdallarchaeota (Heim) are capable of regulating eukaryotic actin dynamics in vitro and when expressed in eukaryotic cells. The actin filament severing and capping, and actin monomer sequestering, functionalities of 2DGels are strictly calcium controlled. We determined the X-ray structures of Heim and Loki 2DGels bound actin monomers. Each structure possesses common and distinct calcium-binding sites. Loki2DGel has an unusual WH2-like motif (LVDV) between its two gelsolin domains, in which the aspartic acid coordinates a calcium ion at the interface with actin. We conclude that the calcium-regulated actin cytoskeleton predates eukaryogenesis and emerged in the predecessors of the last common ancestor of Loki, Heim and Thorarchaeota., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
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12. Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution.
- Author
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Akıl C, Ali S, Tran LT, Gaillard J, Li W, Hayashida K, Hirose M, Kato T, Oshima A, Fujishima K, Blanchoin L, Narita A, and Robinson RC
- Subjects
- Eukaryota metabolism, Guanosine Triphosphate metabolism, Microtubules metabolism, Eukaryotic Cells metabolism, Tubulin chemistry
- Abstract
Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.
- Published
- 2022
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13. Mythical origins of the actin cytoskeleton.
- Author
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Akıl C, Kitaoku Y, Tran LT, Liebl D, Choe H, Muengsaen D, Suginta W, Schulte A, and Robinson RC
- Subjects
- Actin Cytoskeleton chemistry, Actin Cytoskeleton physiology, Actins chemistry, Actins genetics, Animals, Archaea chemistry, Archaea genetics, Archaea isolation & purification, Archaeal Proteins chemistry, Archaeal Proteins physiology, Eukaryota cytology, Eukaryota genetics, Eukaryota metabolism, Eukaryotic Cells chemistry, Eukaryotic Cells physiology, Humans, Metagenomics, Phylogeny, Sequence Analysis, Protein, Actin Cytoskeleton genetics, Archaea cytology, Archaeal Proteins genetics, Biological Evolution, Eukaryotic Cells cytology
- Abstract
The origin of the eukaryotic cell is one of the greatest mysteries in modern biology. Eukaryotic-wide specific biological processes arose in the lost ancestors of eukaryotes. These distinctive features, such as the actin cytoskeleton, define what it is to be a eukaryote. Recent sequencing, characterization, and isolation of Asgard archaea have opened an intriguing window into the pre-eukaryotic cell. Firstly, sequencing of anaerobic sediments identified a group of uncultured organisms, Asgard archaea, which contain genes with homology to eukaryotic signature genes. Secondly, characterization of the products of these genes at the protein level demonstrated that Asgard archaea have related biological processes to eukaryotes. Finally, the isolation of an Asgard archaeon has produced a model organism in which the morphological consequences of the eukaryotic-like processes can be studied. Here, we consider the consequences for the Asgard actin cytoskeleton and for the evolution of a regulated actin system in the archaea-to-eukaryotic transition., Competing Interests: Conflict of interest statement Nothing declared., (Copyright © 2020 Elsevier Ltd. All rights reserved.)
- Published
- 2021
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14. Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea.
- Author
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Akıl C, Tran LT, Orhant-Prioux M, Baskaran Y, Manser E, Blanchoin L, and Robinson RC
- Subjects
- Actin Depolymerizing Factors chemistry, Actin Depolymerizing Factors genetics, Actins chemistry, Actins genetics, Amino Acid Sequence, Archaea chemistry, Archaea genetics, Archaeal Proteins chemistry, Archaeal Proteins genetics, Cytoskeleton chemistry, Cytoskeleton genetics, Cytoskeleton metabolism, Evolution, Molecular, Gelsolin chemistry, Gelsolin genetics, Genome, Archaeal, Polymerization, Protein Conformation, alpha-Helical, Sequence Alignment, Actin Depolymerizing Factors metabolism, Actins metabolism, Archaea metabolism, Archaeal Proteins metabolism, Gelsolin metabolism
- Abstract
Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The eukaryotic actin polymerization/depolymerization cycle is critical for providing force and structure in many processes, including membrane remodeling. In general, Asgard genomes encode two classes of actin-regulating proteins from sequence analysis, profilins and gelsolins. Asgard profilins were demonstrated to regulate actin filament nucleation. Here, we identify actin filament severing, capping, annealing and bundling, and monomer sequestration activities by gelsolin proteins from Thorarchaeota (Thor), which complete a eukaryotic-like actin depolymerization cycle, and indicate complex actin cytoskeleton regulation in Asgard organisms. Thor gelsolins have homologs in other Asgard archaea and comprise one or two copies of the prototypical gelsolin domain. This appears to be a record of an initial preeukaryotic gene duplication event, since eukaryotic gelsolins are generally comprise three to six domains. X-ray structures of these proteins in complex with mammalian actin revealed similar interactions to the first domain of human gelsolin or cofilin with actin. Asgard two-domain, but not one-domain, gelsolins contain calcium-binding sites, which is manifested in calcium-controlled activities. Expression of two-domain gelsolins in mammalian cells enhanced actin filament disassembly on ionomycin-triggered calcium release. This functional demonstration, at the cellular level, provides evidence for a calcium-controlled Asgard actin cytoskeleton, indicating that the calcium-regulated actin cytoskeleton predates eukaryotes. In eukaryotes, dynamic bundled actin filaments are responsible for shaping filopodia and microvilli. By correlation, we hypothesize that the formation of the protrusions observed from Lokiarchaeota cell bodies may involve the gelsolin-regulated actin structures., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)
- Published
- 2020
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15. Genomes of Asgard archaea encode profilins that regulate actin.
- Author
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Akıl C and Robinson RC
- Subjects
- Actin Cytoskeleton metabolism, Actins chemistry, Amino Acid Motifs, Animals, Archaea cytology, Cell Movement, Endocytosis, Eukaryotic Cells cytology, Eukaryotic Cells metabolism, Humans, Models, Molecular, Peptides chemistry, Peptides metabolism, Phospholipids metabolism, Phospholipids pharmacology, Phylogeny, Polymerization, Profilins chemistry, Protein Binding drug effects, Rabbits, Actins metabolism, Archaea genetics, Archaea metabolism, Evolution, Molecular, Genome, Archaeal genetics, Profilins genetics, Profilins metabolism
- Abstract
The origin of the eukaryotic cell is unresolved
1,2 . Metagenomics sequencing has recently identified several potential eukaryotic gene homologues in Asgard archaea3,4 , consistent with the hypothesis that the eukaryotic cell evolved from within the Archaea domain. However, many of these eukaryotic-like sequences are highly divergent and the organisms have yet to be imaged or cultivated, which brings into question the extent to which these archaeal proteins represent functional equivalents of their eukaryotic counterparts. Here we show that Asgard archaea encode functional profilins and thereby establish that this archaeal superphylum has a regulated actin cytoskeleton, one of the hallmarks of the eukaryotic cell5 . Loki profilin-1, Loki profilin-2 and Odin profilin adopt the typical profilin fold and are able to interact with rabbit actin-an interaction that involves proteins from species that diverged more than 1.2 billion years ago6 . Biochemical experiments reveal that mammalian actin polymerizes in the presence of Asgard profilins; however, Loki, Odin and Heimdall profilins impede pointed-end elongation. These archaeal profilins also retard the spontaneous nucleation of actin filaments, an effect that is reduced in the presence of phospholipids. Asgard profilins do not interact with polyproline motifs and the profilin-polyproline interaction therefore probably evolved later in the Eukarya lineage. These results suggest that Asgard archaea possess a primordial, polar, profilin-regulated actin system, which may be localized to membranes owing to the sensitivity of Asgard profilins to phospholipids. Because Asgard archaea are also predicted to encode potential eukaryotic-like genes involved in membrane-trafficking and endocytosis3,4 , imaging is now necessary to elucidate whether these organisms are capable of generating eukaryotic-like membrane dynamics that are regulated by actin, such as are observed in eukaryotic cell movement, podosomes and endocytosis.- Published
- 2018
- Full Text
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