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Samanta, Ayan
Publications (10 of 20) Show all publications
Cantoni, F., Hilborn, J., Johansson, S., Pohlit, H., Porras, A. M., Samanta, A. & Tenje, M. (2018). 2D and 3D patterning of biological hydrogels for organ-on-chip applications. In: : . Paper presented at 44th International Conference on Micro and Nano Engineering (MNE 2018), Copenhagen, Denmark, September 24-27 2018..
Open this publication in new window or tab >>2D and 3D patterning of biological hydrogels for organ-on-chip applications
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2018 (English)Conference paper, Oral presentation with published abstract (Other academic)
Keywords
Organs-on-chip, Hydrogels, UV lithography, Microfluidics, TEER
National Category
Engineering and Technology Other Medical Engineering
Research subject
Engineering Science with specialization in Microsystems Technology
Identifiers
urn:nbn:se:uu:diva-369364 (URN)
Conference
44th International Conference on Micro and Nano Engineering (MNE 2018), Copenhagen, Denmark, September 24-27 2018.
Funder
Knut and Alice Wallenberg Foundation, WAF 2016-0112EU, European Research Council
Available from: 2018-12-13 Created: 2018-12-13 Last updated: 2018-12-13Bibliographically approved
Griffith, M., Samanta, A. & Jangamreddy, J. R. (2018). COLLAGEN AND COLLAGEN LIKE PEPTIDE BASED HYDROGELS, CORNEAL IMPLANTS, FILLER GLUE AND USES THEREOF. in WO 2018/069873 Al.
Open this publication in new window or tab >>COLLAGEN AND COLLAGEN LIKE PEPTIDE BASED HYDROGELS, CORNEAL IMPLANTS, FILLER GLUE AND USES THEREOF
2018 (English)Patent (Other (popular science, discussion, etc.))
Abstract [en]

The present invention provides for collagen and collagen like peptide based hydrogels, corneal implants, filler glue 00 and uses thereof. The invention represents an advancement in the field of hydrogels, corneal implants, filler glue based on collagen o and collagen like peptides. The invention discloses collagen and novel collagen like peptides crosslinked with DMTMM and their use in preparation of hydrogel, corneal implant and filler glue which are highly efficacious and robust as compared to existing corneal implants. Further, the invention relates to method of treating corneal defects and diseases.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-374377 (URN)
Patent
IN WO 2018/069873 Al
Available from: 2019-01-21 Created: 2019-01-21 Last updated: 2019-01-21
Samarawickrama, C., Samanta, A., Liszka, A., Fagerholm, P., Buznyk, O., Griffith, M. & Allan, B. (2018). Collagen-Based Fillers as Alternatives to Cyanoacrylate Glue for the Sealing of Large Corneal Perforations. Cornea, 37(5), 609-616
Open this publication in new window or tab >>Collagen-Based Fillers as Alternatives to Cyanoacrylate Glue for the Sealing of Large Corneal Perforations
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2018 (English)In: Cornea, ISSN 0277-3740, E-ISSN 1536-4798, Vol. 37, no 5, p. 609-616Article in journal (Refereed) Published
Abstract [en]

Purpose: To describe the use of collagen-based alternatives to cyanoacrylate glue for the sealing of acute corneal perforations. Methods: A collagen analog comprising a collagen-like peptide conjugated to polyethylene glycol (CLP-PEG) and its chemical crosslinker were tested for biocompatibility. These CLP-PEG hydrogels, which are designed to act as a framework for corneal tissue regeneration, were then tested as potential fillers in ex vivo human corneas with surgically created full-thickness perforations. Bursting pressures were measured in each of 3 methods (n = 10 for each condition) of applying a seal: 1) cyanoacrylate glue with a polyethylene patch applied ab externo (gold standard); 2) a 100-mu m thick collagen hydrogel patch applied ab interno, and 3) the same collagen hydrogel patch applied ab interno supplemented with CLP-PEG hydrogel molded in situ to fill the remaining corneal stromal defect. Results: Cyanoacrylate gluing achieved a mean bursting pressure of 325.9 mm Hg, significantly higher than the ab interno patch alone (46.3 mm Hg) and the ab interno patch with the CLP-PEG filler (86.6 mm Hg). All experimental perforations were sealed effectively using 100 mu m hydrogel sheets as an ab interno patch, whereas conventional ab externo patching with cyanoacrylate glue failed to provide a seal in 30% (3/10) cases. Conclusions: An ab interno patch system using CLP-PEG hydrogels designed to promote corneal tissue regeneration may be a viable alternative to conventional cyanoacrylate glue patching for the treatment of corneal perforation. Further experimentation and material refinement is required in advance of clinical trials.

Keywords
perforation, repair, collagen, collagen-like peptide, regeneration
National Category
Biomaterials Science
Identifiers
urn:nbn:se:uu:diva-364066 (URN)10.1097/ICO.0000000000001459 (DOI)000443068700017 ()29176452 (PubMedID)
Funder
VINNOVA
Available from: 2018-11-26 Created: 2018-11-26 Last updated: 2018-11-26Bibliographically approved
Manz, C., Kobitski, A. Y., Samanta, A., Keller, B. G., Jäschke, A. & Nienhaus, G. U. (2018). Energy Landscape Analysis of the Full-Length SAM-I Riboswitch using Single-Molecule FRET Spectroscopy. In: Biophysical Journal: . Paper presented at Biophysical Society. , 114
Open this publication in new window or tab >>Energy Landscape Analysis of the Full-Length SAM-I Riboswitch using Single-Molecule FRET Spectroscopy
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2018 (English)In: Biophysical Journal, 2018, Vol. 114Conference paper, Published paper (Refereed)
Abstract [en]

Binding of the ligand S-adenosyl-L-methionine (SAM) produces major structural changes in the SAM-I riboswitch (RS) and thereby regulates gene expression via transcription termination. As yet, the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I RS have not been deeply investigated. We have studied its conformational energy landscape as a function of Mg2+ and SAM ligand concentrations using single-molecule Förster resonance energy transfer (smFRET) microscopy. smFRET histograms of differently FRET-labeled constructs were so complicated that they could only be resolved with the help of kinetic experiments on immobilized riboswitches and hidden Markov modeling (HMM) analysis. At least four conformational states were identified, both in the presence and the absence of SAM. We determined their Mg2+-dependent fractional populations and conformational dynamics, including state lifetimes, interconversion rate coefficients and equilibration timescales. Riboswitches with terminator and antiterminator folds were found to coexist under all conditions; SAM binding induced only a gradual increase in the population of terminator states. Conformational transitions were much faster with bound SAM, which may be crucial for off-switching during the brief decision window before expression of the downstream gene.

Series
Biophysical journal
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-374202 (URN)10.1016/j.bpj.2017.11.3692 (DOI)
Conference
Biophysical Society
Available from: 2019-01-18 Created: 2019-01-18 Last updated: 2019-09-25Bibliographically approved
Eimont, R., Vailionytė, A., Cėpla, V., Druceikaitė, K., Inokaitis, H., Dabkevičiūtė, L., . . . Jekabsone, A. (2018). Extracellular matrix mimetics by crosslinked peptide hydrogels: application to neural 3D cell cultures. In: International conference Vita Scientia Conference book: . Paper presented at International conference: Vita Scientia. Vilnius, January 3, 2018 (pp. 59-59).
Open this publication in new window or tab >>Extracellular matrix mimetics by crosslinked peptide hydrogels: application to neural 3D cell cultures
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2018 (English)In: International conference Vita Scientia Conference book, 2018, p. 59-59Conference paper, Poster (with or without abstract) (Other academic)
Abstract [en]

Self-supporting, shapeable hydrogels that consist of self-assembling synthetic peptides mimic the structural blocks of the extracellular matrix (ECM). Although they have been developed for regenerative medicine purposes, with a potential of grafting into patients without transplantation from organ donors, this class of materials are attractive as scaffolds for advanced cell culture/ in vitro tissue applications. In the present study, we have combined a series of peptides with functional motives (collagen, fibronectin, and laminin-like) for promoting granule layer-like organization of primary cerebellar cells and for controlling the cell attachment, neuritogenesis, cluster size and organization. We show that the micro/nanofabricated hydrogel scaffolds are applicable as multiwell plate inserts helping to analyse cell migration, differentiation, proliferation, adhesion, ultimately forming organotypic cell culture and artificial tissue structures.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-374371 (URN)
Conference
International conference: Vita Scientia. Vilnius, January 3, 2018
Available from: 2019-01-21 Created: 2019-01-21 Last updated: 2019-01-21Bibliographically approved
Pupkaite, J., Griffith, M., Hilborn, J., Suuronen, E. & Samanta, A. (2018). Non-toxic chemically crosslinked collagen hydrogels for cell delivery. Journal of Molecular and Cellular Cardiology, 124(Nov), 104
Open this publication in new window or tab >>Non-toxic chemically crosslinked collagen hydrogels for cell delivery
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2018 (English)In: Journal of Molecular and Cellular Cardiology, Vol. 124, no Nov, p. 104-Article in journal (Refereed) Published
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-374199 (URN)10.1016/j.yjmcc.2018.07.066 (DOI)
Available from: 2019-01-18 Created: 2019-01-18 Last updated: 2019-09-25Bibliographically approved
Zakaria, N., Haagdorens, M., Liszka, A., Ulcinas, A., Cepla, V., Valiokas, R., . . . Griffith, M. (2018). Recombinant human collagen type I hydrogels as superior cell carriers for corneal epithelial stem cells. Paper presented at Annual Meeting of the Association-for-Research-in-Vision-and-Ophthalmology (ARVO), APR 29-MAY 03, 2018, Honolulu, HI. Investigative Ophthalmology and Visual Science, 59(9)
Open this publication in new window or tab >>Recombinant human collagen type I hydrogels as superior cell carriers for corneal epithelial stem cells
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2018 (English)In: Investigative Ophthalmology and Visual Science, ISSN 0146-0404, E-ISSN 1552-5783, Vol. 59, no 9Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
ASSOC RESEARCH VISION OPHTHALMOLOGY INC, 2018
National Category
Ophthalmology
Identifiers
urn:nbn:se:uu:diva-367150 (URN)000442912506270 ()
Conference
Annual Meeting of the Association-for-Research-in-Vision-and-Ophthalmology (ARVO), APR 29-MAY 03, 2018, Honolulu, HI
Available from: 2018-11-28 Created: 2018-11-28 Last updated: 2018-11-28Bibliographically approved
Manz, C., Kobitski, A., Samanta, A., Jäschke, A. & Nienhaus, G. (2018). The multi-state energy landscape of the SAM-I riboswitch:: A single-molecule Förster resonance energy transfer spectroscopy study. Journal of Chemical Physics, 148(12), Article ID 123324.
Open this publication in new window or tab >>The multi-state energy landscape of the SAM-I riboswitch:: A single-molecule Förster resonance energy transfer spectroscopy study
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2018 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 148, no 12, article id 123324Article in journal (Refereed) Published
Abstract [en]

RNA (ribonucleic acid) molecules are highly flexible biopolymers fluctuating at physiological temperatures among many different conformations that are represented by minima in a hierarchical conformational free energy landscape. Here we have employed single-molecule FRET (smFRET) to explore the energy landscape of the B. subtilis yitJ SAM-I riboswitch (RS). In this small RNA molecule, specific binding of an S-adenosyl-L-methionine (SAM) ligand in the aptamer domain regulates gene expression by inducing structural changes in another domain, the expression platform, causing transcription termination by the RNA polymerase. We have measured smFRET histograms over wide ranges of Mg2+ concentration for three RS variants that were specifically labeled with fluorescent dyes on different sites. In the analysis, different conformations are associated with discrete Gaussian model distributions, which are typically fairly broad on the FRET efficiency scale and thus can be extremely challenging to unravel due to their mutual overlap. Our earlier work on two SAM-I RS variants revealed four major conformations. By introducing a global fitting procedure which models both the Mg2+ concentration dependencies of the fractional populations and the average FRET efficiencies of the individual FRET distributions according to Mg2+ binding isotherms, we were able to consistently describe the histogram data of both variants at all studied Mg2+ concentrations. With the third FRET-labeled variant, however, we found significant deviations when applying the four-state model to the data. This can arise because the different FRET labeling of the new variant allows two states to be distinguished that were previously not separable due to overlap. Indeed, the resulting five-state model presented here consistently describes the smFRET histograms of all three variants as well as their variations with Mg2+ concentration. We also performed a triangulation of the donor position for two of the constructs to explore how the expression platform is oriented with respect to the aptamer.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-374197 (URN)10.1063/1.5003783 (DOI)
Available from: 2019-01-18 Created: 2019-01-18 Last updated: 2020-02-28Bibliographically approved
Samanta, A., Merrett, K., Gerasimov, M. & Griffith, M. (2017). Ocular applications of bioresorbable polymers: from basic research to clinical trials. In: Bioresorbable Polymers for Biomedical Applications: From Fundamentals to Translational Medicine (pp. 497-523). Woodhead Publishing Limited
Open this publication in new window or tab >>Ocular applications of bioresorbable polymers: from basic research to clinical trials
2017 (English)In: Bioresorbable Polymers for Biomedical Applications: From Fundamentals to Translational Medicine, Woodhead Publishing Limited, 2017, p. 497-523Chapter in book (Refereed)
Abstract [en]

Bioresorbable and biodegradable polymers have been heavily used for the treatment of various ocular diseases as well as in basic ophthalmology research. These polymers, owing to their biocompatibility and prolonged biodegradability, are suitable substances as ocular drug delivery vehicles and temporary devices or implants to support ocular tissue regeneration. Such polymers can be either synthetic or of natural origin, although only a handful of synthetic bioresorbable polymers are known to date. In this chapter, we describe the use of various such polymers in ophthalmic research with an emphasis on the clinical translation of discoveries. We also provide a brief overview on the current status of ocular application of bioresorbable polymers and future directions of research required to introduce better treatments for corneal blindness.

Place, publisher, year, edition, pages
Woodhead Publishing Limited, 2017
Keywords
Bioresorbable polymers, Chitosan, Clinical trial, Collagen crosslinking, Corneal blindness, Hydrogels, Implant, Ocular drug delivery, Poly-lactic acids
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-374201 (URN)10.1016/B978-0-08-100262-9.00021-5 (DOI)
Available from: 2019-01-18 Created: 2019-01-18 Last updated: 2019-09-13Bibliographically approved
Manz, C., Kobitski, A., Samanta, A., Keller, B. & Jäschke, A. (2017). Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nature Chemical Biology, 13, 1172-1178
Open this publication in new window or tab >>Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch
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2017 (English)In: Nature Chemical Biology, ISSN 1552-4450, E-ISSN 1552-4469, Vol. 13, p. 1172-1178Article in journal (Refereed) Published
Abstract [en]

S-adenosyl-L-methionine (SAM) ligand binding induces major structural changes in SAM-I riboswitches, through which gene expression is regulated via transcription termination. Little is known about the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I riboswitch. Therefore, we have explored its conformational energy landscape as a function of Mg2+ and SAM ligand concentrations using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling analysis. We resolved four conformational states both in the presence and the absence of SAM and determined their Mg2+-dependent fractional populations and conformational dynamics, including state lifetimes, interconversion rate coefficients and equilibration timescales. Riboswitches with terminator and antiterminator folds coexist, and SAM binding only gradually shifts the populations toward terminator states. We observed a pronounced acceleration of conformational transitions upon SAM binding, which may be crucial for off-switching during the brief decision window before expression of the downstream gene.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-374186 (URN)10.1038/nchembio.2476 (DOI)
Available from: 2019-01-18 Created: 2019-01-18 Last updated: 2019-07-18Bibliographically approved
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