173 research outputs found
Developing staining protocols for visualization of tissue-engineering scaffolds using micro computed tomography in native wet state
- Publication venue
- Publication date
- 02/08/2017
- Field of study
Ab-initio study of model guanine assemblies: The role of pi-pi coupling and band transport
- Author
- A. Aviram
- A. D. Becke
- Anna Garbesi
- Arrigo Calzolari
- B. Giese
- C. Joachim
- C. Lee
- D. Porath
- E. Braun
- E. Meggers
- Elisa Molinari
- F. D. Lewis
- G. B. Schuster
- G. Gottarelli
- G. Gottarelli
- H. J. Monkhorst
- H. Sugiyama
- H.-W. Fink
- J. Hutter
- J. Jortner
- J. Ć poner
- J. Ć poner
- K. Nakatani
- L. Kleinman
- M. Bixon
- M. Bockstedte
- M. W. Grinstaff
- N. Troullier
- P. F. Barbara
- P. Gomes Da Costa
- P. Hobza
- P. J. de Pablo
- R. A. Marcus
- R. Car
- R. Rinaldi
- R. Taylor
- Rosa Di Felice
- S. K. Pugh
- Y. Okahata
- Y.-J. Ye
- Y.-J. Ye
- Publication venue
- 'American Physical Society (APS)'
- Publication date
- 30/10/2001
- Field of study
Several assemblies of guanine molecules are investigated by means of
first-principle calculations. Such structures include stacked and
hydrogen-bonded dimers, as well as vertical columns and planar ribbons,
respectively, obtained by periodically replicating the dimers. Our results are
in good agreement with experimental data for isolated molecules, isolated
dimers, and periodic ribbons. For stacked dimers and columns, the stability is
affected by the relative charge distribution of the pi orbitals in adjacent
guanine molecules. pi-pi coupling in some stacked columns induces dispersive
energy bands, while no dispersion is identified in the planar ribbons along the
connections of hydrogen bonds. The implications for different materials
comprised of guanine aggregates are discussed. The bandstructure of dispersive
configurations may justify a contribution of band transport (Bloch type) in the
conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations
band transport should be negligible.Comment: 21 pages, 6 figures, 3 tables, to be published in Phys. Rev.
Insights on the mechanism of formation of protein microspheres in a biphasic system
- Author
- Aharon Gedanken
- Anandan S.
- Artur Cavaco-Paulo
- Ashcroft G. S.
- Avivi S.
- Bala I.
- Bala I.
- Branco M. C.
- Bunjes H.
- Byler D. M.
- Childers W. S.
- Chittur K. K.
- Dong A.
- Feng S.-S.
- Fu K.
- Giuliano Freddi
- Greenspan P.
- Grinstaff M. W.
- Grinstaff M. W.
- GĂŒlseren I.
- Haris P. I.
- Helena Ferreira
- Hess B.
- Kong H.
- Little C.
- Lotz B.
- Lowry O. H.
- Mason T. J.
- Nuno G. Azoia
- Oostenbrink C.
- Peters T. J.
- Rae J.
- Raquel Silva
- Suslick K. S.
- Suslick K. S.
- Suslick K. S.
- Suslick K. S.
- Takeda K.
- Ulyana Shimanovich
- Vasconcelos A.
- Vauthey S.
- Wong M.
- Yamaguchi K.
- Yampolskaya G. P.
- Publication venue
- 'American Chemical Society (ACS)'
- Publication date
- 01/01/2012
- Field of study
Microspheres of bovine serum albumin (BSA) and silk fibroin are produced by applying ultrasound in a biphasic system consisting of an aqueous protein solution and an organic solvent. The protein microspheres are dispersed in an aqueous media where the protein remains at the interface covering the organic solvent. This only occurs when high shear forces are applied that induce changes to force the protein to the interface. Fourier transform infrared results indicate a large increase in the content of the ÎČ-sheet during the formation of silk fibroin microspheres. Molecular dynamics simulations show a clear adaption on the 3D structure of BSA when stabilized at the interface, without major changes in secondary structure. Further studies demonstrate that high water content, oil solvents, and larger peptides with separated and clear hydrophobic and hydrophilic areas lead to more stable and smaller spheres. This is the first time that these results are presented. We also present herein the rationale to produce tailored protein microspheres with a controlled size, controlled charge, and increased stability.This work was supported by Lidwine Project-Multifunctional medical textiles for wound (e.g., Decubitus) prevention and improved wound healing NMP2-CT-2006-026741. H.F. thanks POPH/FSE for cofinancing and FCT for Fellowship SFRH/BPD/38939/2007. We acknowledge Silvia Cappellozza from "Sezione Specializzata per la Bachicoltura" for the supply of silk cocoons
Releasing dye encapsulated in proteinaceous microspheres on conductive fabrics by electric current
- Author
- Publication venue
- 'American Chemical Society (ACS)'
- Publication date
- 01/01/2012
- Field of study
The current paper reports on the relase properties of conductive fabrics coated with proteinaceous microspheres containing a dye. The release of the dye was achieved by passing an electric current through the fabric. The conductivity of the polyester fibers resulted from nanosilver (Ag NPs) coated on the surface of these fibers. Both types of coatings (nanosilver coating and the coating of the proteinaceous microspheres) were performed using high-intensity ultrasonic waves. Two different types of dyes, hydrophilic RBBR (Remazol Brilliant Blue R) and hydrophobic ORO (Oil Red O), were encapsulated inside the microspheres (attached to the surface of polyester) and then released by applying an electric current. The Proteinaceous Microsphere (PM)-coated conductive fabrics could be used in medicine for drug release. The encapsulated dye can be replaced with a drug that could be released from the surface of fabrics by applying a low voltage
Triple Contrast CT Method Enables Simultaneous Evaluation of Articular Cartilage Composition and Segmentation
- Author
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 28/10/2022
- Field of study
Early degenerative changes of articular cartilage are detected using contrast-enhanced computed tomography (CT) with a cationic contrast agent (CA). However, cationic CA diffusion into degenerated cartilage decreases with proteoglycan depletion and increases with elevated water content, thus hampering tissue evaluation at early diffusion time points. Furthermore, the contrast at synovial fluid-cartilage interface diminishes as a function of diffusion time hindering accurate cartilage segmentation. For the first time, we employ quantitative dual-energy CT (QDECT) imaging utilizing a mixture of three CAs (cationic CA4+ and non-ionic gadoteridol which are sensitive to proteoglycan and water contents, respectively, and bismuth nanoparticles which highlight the cartilage surface) to simultaneously segment the articulating surfaces and determine of the cartilage condition. Intact healthy, proteoglycan-depleted, and mechanically injured bovine cartilage samples (n = 27) were halved and imaged with synchrotron microCT 2-h post immersion in triple CA or in dual CA (CA4+ and gadoteridol). CA4+ and gadoteridol partitions were determined using QDECT, and pairwise evaluation of these partitions was conducted for samples immersed in dual and triple CAs. In conclusion, the triple CA method is sensitive to proteoglycan depletion while maintaining sufficient contrast at the articular surface to enable detection of cartilage lesions caused by mechanical impact
Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent
- Author
- Arnott S.
- Barnett R. N.
- Bixon M.
- Breslin D. T.
- Cadet J.
- Cadet J.
- Candeias L. P.
- Chandrasekaran R.
- Colson A.-O.
- Dekker C.
- Dewar M. J. S.
- Dewar M. J. S.
- Gasper S. M.
- Gervasio F. L.
- Giese B.
- Giese B.
- Grinstaff M. W.
- Hall D. B.
- Ito K.
- Jackson J. D.
- Kim N. S.
- Kim N. S.
- Kino K.
- Klamt A.
- Klamt A.
- Klamt A.
- Kovacic P.
- Kurnikov I. V.
- Lewis F. D.
- Lu X.-J.
- Lu X.-J.
- Luo W.
- Matsugo S.
- Meggers M.
- Melvin T.
- Nakatani K.
- Nakatani K.
- NĂșñez M. E.
- Oikawa S.
- Orlov V. M.
- Prat F.
- Premilat S.
- Pullman A.
- Ravanat J.-L.
- Reynisson J.
- Saito I.
- Saito I.
- Saito I.
- Saito I.
- Schuster G. B.
- Seidel C. A. M.
- Senthilkumar K.
- Spassky A.
- Starikov E. B.
- Steenken S.
- Sugiyama H.
- Tanielian C.
- Vialas C.
- Voityuk A. A.
- Wetmore S. D.
- Wiley J. R.
- Yokojima S.
- Yoshioka Y.
- Yoshioka Y.
- Zhang Q.
- Zhu Q.
- Publication venue
- American Chemical Society
- Publication date
- 01/01/2009
- Field of study
We examined the ionization potential (IP) corresponding to the free energy of a hole on duplex DNA by semiempirical molecular orbital theory with a continuum solvent model. As for the contiguous guanines (a guanine run), we found that the IP in the gas phase significantly decreases with the increasing number of nucleotide pairs of the guanine run, whereas the IP in water (OP, oxidation potential) only slightly does. The latter result is consistent with the experimental result for DNA oligomers in water. This decrease in the IP is mainly due to the attractive electrostatic interaction between the hole and a nucleotide pair in the duplex DNA. This interaction is reduced in water, which results in the small decrease in the IP in water. This mechanism explains the discrepancy between the experimental result and the previous computational results obtained by neglecting the solvent. As for the chemically modified guanine, the previous work showed that the removal of some solvent (water) molecules due to the attachment of a neutral functional group to a guanine in a duplex DNA stabilizes the hole on the guanine. One might naively have expected the opposite case, since a polar solvent usually stabilizes ions. This mechanism also explains this unexpected stabilization of a hole as follows. When some water molecules are removed, the attractive electrostatic interaction stabilizing the hole increases, and thus, the hole is stabilized. In order to design the hole energetics by a chemical modification of DNA, this mechanism has to be taken into account and can be used. 1
Charge Transport in DNA-Based Devices
- Author
- A Aviram
- A Bezryadin
- A Bezryadin
- A Calzolari
- A Nitzan
- A Rakitin
- AA Voityuk
- AA Voityuk
- AA Voityuk
- ADA Becke
- ADA Becke
- ADA Becke
- AJ Storm
- AY Kasumov
- B Giese
- B Giese
- BG Johnson
- C Adessi
- C GĂłmez-Navarro
- C Joachim
- C-Z Li
- CJ Murphy
- CM Niemeyer
- CM Niemeyer
- CP Collier
- CP Collier
- CT Lee
- D Porath
- D Porath
- DB Hall
- DD Eley
- E Artacho
- E Braun
- E Meggers
- EM Conwell
- FD Lewis
- FR Gervasio
- G Cuniberti
- G Cuniberti
- GB Schuster
- GN Parkinson
- H Watanabe
- HW Fink
- HY Lee
- J Chen
- J Jortner
- J Jortner
- J Richter
- J Ć poner
- J Ć poner
- JL DâAmato
- JM Lehn
- JM Tour
- JM Warman
- JP Perdew
- K Keren
- K Phillips
- K Tanaka
- K Tanaka
- K-H Yoo
- L Cai
- M Bixon
- M Bixon
- M Bixon
- M Brandbyge
- M BĂŒttiker
- M Elstner
- M Hjort
- M Thorwart
- M Zwolak
- MA OâNeill
- MA Reed
- MW Grinstaff
- NJ Turro
- P Aich
- P Alberti
- P Carloni
- PF Barbara
- PT Henderson
- R Di Felice
- R Gutierrez
- R Marcus
- R Rinaldi
- R Rinaldi
- R Rinaldi
- RA Friesner
- RM Metzger
- RN Barnett
- SD Wettig
- SG Lemay
- SO Kelley
- T Frauenheim
- T La Bean
- T Shigematsu
- W Liang
- WB Davis
- XQ Li
- XQ Li
- Y Benenson
- Y Benenson
- Y Okahata
- Y Ye
- Y Zhang
- Y Zhang
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2004
- Field of study
Charge migration along DNA molecules has attracted scientific interest for
over half a century. Reports on possible high rates of charge transfer between
donor and acceptor through the DNA, obtained in the last decade from solution
chemistry experiments on large numbers of molecules, triggered a series of
direct electrical transport measurements through DNA single molecules, bundles
and networks. These measurements are reviewed and presented here. From these
experiments we conclude that electrical transport is feasible in short DNA
molecules, in bundles and networks, but blocked in long single molecules that
are attached to surfaces. The experimental background is complemented by an
account of the theoretical/computational schemes that are applied to study the
electronic and transport properties of DNA-based nanowires. Examples of
selected applications are given, to show the capabilities and limits of current
theoretical approaches to accurately describe the wires, interpret the
transport measurements, and predict suitable strategies to enhance the
conductivity of DNA nanostructures.Comment: A single pdf file of 52 pages, containing the text and 23 figures.
Review about direct measurements of DNA conductivity and related theoretical
studies. For higher-resolution figures contact the authors or retrieve the
original publications cited in the caption
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)
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- A. C. Ma
- A. K. Au
- Abdel-Aziz A. K.
- Abdelfatah S.
- Abdellatif M.
- Abdoli A.
- Abel S.
- Abeliovich H.
- Abildgaard M. H.
- Abudu Y. P.
- Acevedo-Arozena A.
- Adamopoulos I. E.
- Adeli K.
- Adolph T. E.
- Adornetto A.
- Aflaki E.
- Agam G.
- Agarwal A.
- Aggarwal B. B.
- Agnello M.
- Agostinis P.
- Agrewala J. N.
- Agrotis A.
- Aguilar P. V.
- Ahmad S. T.
- Ahmed Z. M.
- Ahumada-Castro U.
- Aits S.
- Aizawa S.
- Akkoc Y.
- Akoumianaki T.
- Akpinar H. A.
- Al-Abd A. M.
- Al-Akra L.
- Al-Gharaibeh A.
- Alaoui-Jamali M. A.
- Alberti S.
- Alcocer-Gomez E.
- Alessandri C.
- Ali M.
- Alim Al-Bari M. A.
- Aliwaini S.
- Alizadeh J.
- Almacellas E.
- Almasan A.
- Alonso A.
- Alonso G. D.
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- Publication venue
- 'Informa UK Limited'
- Publication date
- 01/01/2021
- Field of study
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.
- Author
- Abdel-Aziz AK
- Abdelfatah S
- Abdellatif M
- Abdoli A
- Abel S
- Abeliovich H
- Abildgaard MH
- Abudu YP
- Acevedo-Arozena A
- Adamopoulos IE
- Adeli K
- Adolph TE
- Adornetto A
- Aflaki E
- Agam G
- Agarwal A
- Aggarwal BB
- Agnello M
- Agostinis P
- Agrewala JN
- Agrotis A
- Aguilar PV
- Ahmad ST
- Ahmed ZM
- Ahumada-Castro U
- Aits S
- Aizawa S
- Akkoc Y
- Akoumianaki T
- Akpinar HA
- Al-Abd AM
- Al-Akra L
- Al-Gharaibeh A
- Alaoui-Jamali MA
- Alberti S
- Alcocer-GĂłmez E
- Alessandri C
- Ali M
- Alim Al-Bari MA
- Aliwaini S
- Alizadeh J
- Almacellas E
- Almasan A
- Alonso A
- Alonso GD
- Altan-Bonnet N
- Altieri DC
- Alves da Costa C
- Alves S
- Alzaharna MM
- Amadio M
- Amantini C
- Amaral C
- Ambrosio S
- Amer AO
- Ammanathan V
- An Z
- Andersen SU
- Andrabi SA
- Andrade-Silva M
- Andres AM
- Angelini S
- Ann D
- Anozie UC
- Ansari MY
- Antas P
- Antebi A
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- Apostolova N
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- Araya J
- AraĂșjo WL
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- Armstrong-James D
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- Artero R
- Arévalo M-A
- Asaro DML
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- Ashur-Fabian O
- Atanasov AG
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- Zimmermann CM
- Ziviani E
- Zoladek T
- Zong W-X
- Zorov DB
- Zorzano A
- Zou W
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- Zuryn S
- Zwerschke W
- Ălvarez ĂMC
- Ăvalos Y
- Ănal G
- ĂstĂŒn S
- ÄoliÄ M
- ÄokiÄ J
- Ćœerovnik E
- Publication venue
- 'Informa UK Limited'
- Publication date
- 01/01/2021
- Field of study
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field
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