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Robang A, Roy A, Dodd-o JB, He D, Le JV, McShan AC, Hu Y, Kumar VA, Paravastu AK. Structural Consequences of Introducing Bioactive Domains to Designer β-Sheet Peptide Self-Assemblies. Biomacromolecules 2024; 25:1429-1438. [PMID: 38408372 PMCID: PMC10934295 DOI: 10.1021/acs.biomac.3c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
We applied solid- and solution-state nuclear magnetic resonance spectroscopy to examine the structure of multidomain peptides composed of self-assembling β-sheet domains linked to bioactive domains. Bioactive domains can be selected to stimulate specific biological responses (e.g., via receptor binding), while the β-sheets provide the desirable nanoscale properties. Although previous work has established the efficacy of multidomain peptides, molecular-level characterization is lacking. The bioactive domains are intended to remain solvent-accessible without being incorporated into the β-sheet structure. We tested for three possible anticipated molecular-level consequences of introducing bioactive domains to β-sheet-forming peptides: (1) the bioactive domain has no effect on the self-assembling peptide structure; (2) the bioactive domain is incorporated into the β-sheet nanofiber; and (3) the bioactive domain interferes with self-assembly such that nanofibers are not formed. The peptides involved in this study incorporated self-assembling domains based on the (SL)6 motif and bioactive domains including a VEGF-A mimic (QK), an IGF-mimic (IGF-1c), and a de novo SARS-CoV-2 binding peptide (SBP3). We observed all three of the anticipated outcomes from our examination of peptides, illustrating the unintended structural effects that could adversely affect the desired biofunctionality and biomaterial properties of the resulting peptide hydrogel. This work is the first attempt to evaluate the structural effects of incorporating bioactive domains into a set of peptides unified by a similar self-assembling peptide domain. These structural insights reveal unmet challenges in the design of highly tunable bioactive self-assembling peptide hydrogels.
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Affiliation(s)
- Alicia
S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Abhishek Roy
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Joseph B. Dodd-o
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Dongjing He
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Justin V. Le
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andrew C. McShan
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Yuhang Hu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vivek A. Kumar
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Chemicals and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department
of Biology, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Barden P, Sosiak CE, Grajales J, Hawkins J, Rizzo L, Clark A, Gatley S, Gatley I, Federici J. Non-destructive comparative evaluation of fossil amber using terahertz time-domain spectroscopy. PLoS One 2022; 17:e0262983. [PMID: 35353830 PMCID: PMC8967008 DOI: 10.1371/journal.pone.0262983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/11/2022] [Indexed: 11/19/2022] Open
Abstract
Fossilized plant resins, or ambers, offer a unique paleontological window into the history of life. A natural polymer, amber can preserve aspects of ancient environments, including whole organisms, for tens or even hundreds of millions of years. While most amber research involves imaging with visual light, other spectra are increasingly used to characterize both organismal inclusions as well as amber matrix. Terahertz (THz) radiation, which occupies the electromagnetic band between microwave and infrared light wavelengths, is non-ionizing and frequently used in polymer spectroscopy. Here, we evaluate the utility of amber terahertz spectroscopy in a comparative setting for the first time by analyzing the terahertz optical properties of samples from 10 fossil deposits ranging in age from the Miocene to the Early Cretaceous. We recover no clear relationships between amber age or botanical source and terahertz permittivity; however, we do find apparent deposit-specific permittivity among transparent amber samples. By comparing the suitability of multiple permittivity models across sample data we find that models with a distribution of dielectric relaxation times best describe the spectral permittivity of amber. We also demonstrate a process for imaging amber inclusions using terahertz transmission and find that terahertz spectroscopy can be used to identify some synthetic amber forgeries.
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Affiliation(s)
- Phillip Barden
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- * E-mail:
| | - Christine E. Sosiak
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Jonpierre Grajales
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - John Hawkins
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Louis Rizzo
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Alexander Clark
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Samuel Gatley
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Ian Gatley
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - John Federici
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey, United States of America
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Abstract
Tardigrades are a diverse group of charismatic microscopic invertebrates that are best known for their ability to survive extreme conditions. Despite their long evolutionary history and global distribution in both aquatic and terrestrial environments, the tardigrade fossil record is exceedingly sparse. Molecular clocks estimate that tardigrades diverged from other panarthropod lineages before the Cambrian, but only two definitive crown-group representatives have been described to date, both from Cretaceous fossil deposits in North America. Here, we report a third fossil tardigrade from Miocene age Dominican amber. Paradoryphoribius chronocaribbeus gen. et sp. nov. is the first unambiguous fossil representative of the diverse superfamily Isohypsibioidea, as well as the first tardigrade fossil described from the Cenozoic. We propose that the patchy tardigrade fossil record can be explained by the preferential preservation of these microinvertebrates as amber inclusions, coupled with the scarcity of fossiliferous amber deposits before the Cretaceous.
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Affiliation(s)
- Marc A. Mapalo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Ninon Robin
- Directorate Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Brendon E. Boudinot
- Institut für Spezielle Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Jena, Germany
- University of California, Davis, Department of Entomology, One Shields Avenue, Davis 94596, CA, USA
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, USA
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Abstract
Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm-lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits-extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.
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Affiliation(s)
- Solomon T C Chak
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ
- Department of Biological Sciences, SUNY College at Old Westbury, Old Westbury, NY
| | - Juan Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC
- Smithsonian Institution, Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
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Yu CC(J, Barry NC, Wassie AT, Sinha A, Bhattacharya A, Asano S, Zhang C, Chen F, Hobert O, Goodman MB, Haspel G, Boyden ES. Expansion microscopy of C. elegans. eLife 2020; 9:e46249. [PMID: 32356725 PMCID: PMC7195193 DOI: 10.7554/elife.46249] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/30/2020] [Indexed: 12/20/2022] Open
Abstract
We recently developed expansion microscopy (ExM), which achieves nanoscale-precise imaging of specimens at ~70 nm resolution (with ~4.5x linear expansion) by isotropic swelling of chemically processed, hydrogel-embedded tissue. ExM of C. elegans is challenged by its cuticle, which is stiff and impermeable to antibodies. Here we present a strategy, expansion of C. elegans (ExCel), to expand fixed, intact C. elegans. ExCel enables simultaneous readout of fluorescent proteins, RNA, DNA location, and anatomical structures at resolutions of ~65-75 nm (3.3-3.8x linear expansion). We also developed epitope-preserving ExCel, which enables imaging of endogenous proteins stained by antibodies, and iterative ExCel, which enables imaging of fluorescent proteins after 20x linear expansion. We demonstrate the utility of the ExCel toolbox for mapping synaptic proteins, for identifying previously unreported proteins at cell junctions, and for gene expression analysis in multiple individual neurons of the same animal.
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Affiliation(s)
- Chih-Chieh (Jay) Yu
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Nicholas C Barry
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Asmamaw T Wassie
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Anubhav Sinha
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
- Division of Health Sciences and Technology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Abhishek Bhattacharya
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia UniversityNew YorkUnited States
| | - Shoh Asano
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Chi Zhang
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Fei Chen
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia UniversityNew YorkUnited States
| | - Miriam B Goodman
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Gal Haspel
- Federated Department of Biological Sciences, New Jersey Institute of Technology and Rutgers University-NewarkNewarkUnited States
- The Brain Research Institute, New Jersey Institute of TechnologyNewarkUnited States
| | - Edward S Boyden
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
- Koch Institute, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Brain and Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
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Cohen KE, Flammang BE, Crawford CH, Hernandez LP. Knowing when to stick: touch receptors found in the remora adhesive disc. R Soc Open Sci 2020; 7:190990. [PMID: 32218935 PMCID: PMC7029896 DOI: 10.1098/rsos.190990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 12/05/2019] [Indexed: 06/10/2023]
Abstract
Remoras are fishes that piggyback onto larger marine fauna via an adhesive disc to increase locomotor efficiency, likelihood of finding mates and access to prey. Attaching rapidly to a large, fast-moving host is no easy task, and while research to date has focused on how the disc supports adhesion, no attention has been paid to how or if remoras are able to sense attachment. We identified push-rod-like mechanoreceptor complexes embedded in the soft lip of the remora adhesive disc that are known in other organisms to respond to touch and shear forces. This is, to our knowledge, the first time such mechanoreceptor complexes are described in fishes as they were only known previously in monotremes. The presence of push-rod-like mechanoreceptor complexes suggests not only that fishes may be able to sense their environment in ways not heretofore described but that specialized tactile mechanoreceptor complexes may be a more basal vertebrate feature than previously thought.
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Affiliation(s)
- Karly E. Cohen
- Biology Department, University of Washington, Life Sciences Building, Seattle, WA 98195, USA
- Department of Biological Sciences, The George Washington University, Science and Engineering Hall, Suite 6000, Washington, DC 20052, USA
| | - Brooke E. Flammang
- Department of Biological Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
| | - Callie H. Crawford
- Department of Biological Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
| | - L. Patricia Hernandez
- Biology Department, University of Washington, Life Sciences Building, Seattle, WA 98195, USA
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