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Hanke M, Dornbusch D, Tomm E, Grundmeier G, Fahmy K, Keller A. Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants. Nanoscale 2023; 15:16590-16600. [PMID: 37747200 DOI: 10.1039/d3nr02045b] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The structural stability of DNA origami nanostructures in various chemical environments is an important factor in numerous applications, ranging from biomedicine and biophysics to analytical chemistry and materials synthesis. In this work, the stability of six different 2D and 3D DNA origami nanostructures is assessed in the presence of three different chaotropic salts, i.e., guanidinium sulfate (Gdm2SO4), guanidinium chloride (GdmCl), and tetrapropylammonium chloride (TPACl), which are widely employed denaturants. Using atomic force microscopy (AFM) to quantify nanostructural integrity, Gdm2SO4 is found to be the weakest and TPACl the strongest DNA origami denaturant, respectively. Despite different mechanisms of actions of the selected salts, DNA origami stability in each environment is observed to depend on DNA origami superstructure. This is especially pronounced for 3D DNA origami nanostructures, where mechanically more flexible designs show higher stability in both GdmCl and TPACl than more rigid ones. This is particularly remarkable as this general dependence has previously been observed under Mg2+-free conditions and may provide the possibility to optimize DNA origami design toward maximum stability in diverse chemical environments. Finally, it is demonstrated that melting temperature measurements may overestimate the stability of certain DNA origami nanostructures in certain chemical environments, so that such investigations should always be complemented by microscopic assessments of nanostructure integrity.
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Affiliation(s)
- Marcel Hanke
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Daniel Dornbusch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Emilia Tomm
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
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2
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Elkomos BE, Fahmy K, Kamel KA. Laparoscopic adhesiolysis versus open adhesiolysis in acute adhesive small bowel obstruction. J Minim Access Surg 2023; 19:511-517. [PMID: 37357493 PMCID: PMC10695316 DOI: 10.4103/jmas.jmas_43_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/11/2023] [Accepted: 04/07/2023] [Indexed: 06/27/2023] Open
Abstract
Introduction Exploratory laparotomy is still the standard therapy for patients who need surgical intervention for adhesive small bowel obstruction (SBO). However, the use of laparoscopy in the management of adhesive SBO is still controversial. We aimed to detect the short-term outcomes between open and laparoscopic adhesiolysis for SBO. Patients and Methods This is a retrospective study of patients with adhesive SBO who underwent either laparoscopic or open surgery from June 2019 to July 2022 at Ain Shams University Hospitals. Intraoperative and early post-operative outcomes were compared in the two groups. Results A total of 89 patients with adhesive SBO were included in our study. Fifty-one cases underwent open adhesiolysis and 38 cases underwent laparoscopic adhesiolysis. Laparoscopic adhesiolysis is associated with a remarkable decrease in the operative time (71 min vs. 107 min, P = 0.001) and blood loss (50 ml vs. 120 ml, P = 0.001) in comparison to open adhesiolysis. In addition to that, those who underwent adhesiolysis by laparoscopy had a short hospital stay (2.4 days vs. 3.8 days, P = 0.001), early recovery (time to pass flatus 1.3 days vs. 2.8 days) and less post-operative complications (surgical site infection [SSI] 2.6% vs. 19.6%, P = 0.001). Moreover, open adhesiolysis is associated with a higher rate of early post-operative mortality. In addition to that, the incidence of iatrogenic injury was higher in the open group. Conclusion Laparoscopic adhesiolysis is a safe and feasible approach for the management of SBO and has better short-term outcomes, especially if done by skilled surgeons in advanced laparoscopic techniques.
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Affiliation(s)
| | - Karim Fahmy
- Department of General Surgery, Ain Shams University Hospital, Cairo, Egypt
| | - Kareem Ahmed Kamel
- Department of General Surgery, Ain Shams University Hospital, Cairo, Egypt
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3
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Ruiz-Fresneda MA, Schaefer S, Hübner R, Fahmy K, Merroun ML. Exploring Antibacterial Activity and Bacterial-Mediated Allotropic Transition of Differentially Coated Selenium Nanoparticles. ACS Appl Mater Interfaces 2023. [PMID: 37294110 DOI: 10.1021/acsami.3c05100] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The use of metal nanoparticles (NPs) as antimicrobial agents has become a promising alternative to the problem of antibiotic-resistant bacteria and other applications. Silver nanoparticles (AgNPs) are well-known as one of the most universal biocide compounds. However, selenium nanoparticles (SeNPs) recently gained more attention as effective antimicrobial agents. This study aims to investigate the antibacterial activity of SeNPs with different surface coatings (BSA-coated, chitosan-coated, and undefined coating) on the Gram-negative Stenotrophomonas bentonitica and the Gram-positive Lysinibacillus sphaericus in comparison to AgNPs. The tested NPs had similar properties, including shape (spheres), structure (amorphous), and size (50-90 nm), but differed in their surface charge. Chitosan SeNPs exhibited a positive surface charge, while the remaining NPs assayed had a negative surface charge. We have found that cell growth and viability of both bacteria were negatively affected in the presence of the NPs, as indicated by microcalorimetry and flow cytometry. Specifically, undefined coating SeNPs displayed the highest percentage values of dead cells for both bacteria (85-91%). An increase in reactive oxygen species (ROS) production was also detected. Chitosan-coated and undefined SeNPs caused the highest amount of ROS (299.7 and 289% over untreated controls) for S. bentonitica and L. sphaericus, respectively. Based on DNA degradation levels, undefined-SeNPs were found to be the most hazardous, causing nearly 80% DNA degradation. Finally, electron microscopy revealed the ability of the cells to transform the different SeNP types (amorphous) to crystalline SeNPs (trigonal/monoclinical Se), which could have environmentally positive implications for bioremediation purposes and provide a novel green method for the formation of crystalline SeNPs. The results obtained herein demonstrate the promising potential of SeNPs for their use in medicine as antimicrobial agents, and we propose S. bentonitica and L. sphaericus as candidates for new bioremediation strategies and NP synthesis with potential applications in many fields.
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Affiliation(s)
- Miguel A Ruiz-Fresneda
- Department of Microbiology, University of Granada, Campus Fuentenueva, 18071 Granada, Spain
| | - Sebastian Schaefer
- Department of Microbiology, University of Granada, Campus Fuentenueva, 18071 Granada, Spain
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - René Hübner
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Mohamed L Merroun
- Department of Microbiology, University of Granada, Campus Fuentenueva, 18071 Granada, Spain
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4
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Phan CM, Ross M, Fahmy K, McEwen B, Hofmann I, Chan VWY, Clark-Baba C, Jones L. Evaluating Viscosity and Tear Breakup Time of Contemporary Commercial Ocular Lubricants on an In Vitro Eye Model. Transl Vis Sci Technol 2023; 12:29. [PMID: 37382574 PMCID: PMC10318592 DOI: 10.1167/tvst.12.6.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/31/2023] [Indexed: 06/30/2023] Open
Abstract
Purpose To evaluate the link between the viscosity of ophthalmic formulation and tear film stability using a novel in vitro eye model. Methods The viscosities and noninvasive tear breakup time (NIKBUT) of 13 commercial ocular lubricants were measured to evaluate the correlation between viscosity and NIKBUT. The complex viscosity of each lubricant was measured three times for each angular frequency (ranging from 0.1 to 100 rad/s) using the Discovery HR-2 hybrid rheometer. The NIKBUT measurements were performed eight times for each lubricant using an advanced eye model mounted on the OCULUS Keratograph 5M. A contact lens (CL; ACUVUE OASYS [etafilcon A]) or a collagen shield (CS) was used as the simulated corneal surface. Phosphate-buffered saline was used as a simulated fluid. Results The results showed a positive correlation between viscosity and NIKBUT at high shear rates (at 10 rad/s, r = 0.67) but not at low shear. This correlation was even better for viscosities between 0 and 100 mPa*s (r = 0.85). Most of the lubricants tested in this study also had shear-thinning properties. OPTASE INTENSE, I-DROP PUR GEL, I DROP MGD, OASIS TEARS PLUS, and I-DROP PUR had higher viscosity in comparison to other lubricants (P < 0.05). All of the formulations had a higher NIKBUT than the control (2.7 ± 1.2 seconds for CS and 5.4 ± 0.9 seconds for CL) without any lubricant (P < 0.05). I-DROP PUR GEL, OASIS TEARS PLUS, I-DROP MGD, REFRESH OPTIVE ADVANCED, and OPTASE INTENSE had the highest NIKBUT using this eye model. Conclusions The results show that the viscosity is correlated with NIKBUT, but further work is necessary to determine the underlying mechanisms. Translational Relevance The viscosity of ocular lubricants can affect NIKBUT and tear film stability, so it is an important property to consider when formulating ocular lubricants.
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Affiliation(s)
- Chau-Minh Phan
- Centre for Ocular Research & Education (CORE), School of Optometry and Vision Science, University of Waterloo, Waterloo, ON, Canada
- Centre for Eye and Vision Research (CEVR), Hong Kong
| | - Mitchell Ross
- Department of Chemical Engineering, McMaster University, Hamilton, ON, Canada
| | | | | | | | - Vivian W. Y. Chan
- Centre for Ocular Research & Education (CORE), School of Optometry and Vision Science, University of Waterloo, Waterloo, ON, Canada
| | - Connor Clark-Baba
- Centre for Ocular Research & Education (CORE), School of Optometry and Vision Science, University of Waterloo, Waterloo, ON, Canada
| | - Lyndon Jones
- Centre for Ocular Research & Education (CORE), School of Optometry and Vision Science, University of Waterloo, Waterloo, ON, Canada
- Centre for Eye and Vision Research (CEVR), Hong Kong
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5
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Matulis D, Wadsö L, Fahmy K. Special Issue "Advances in Monitoring Metabolic Activities of Microorganisms by Calorimetry". Microorganisms 2023; 11:1204. [PMID: 37317176 DOI: 10.3390/microorganisms11051204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/20/2023] [Indexed: 06/16/2023] Open
Abstract
In recent decades, the calorimetric monitoring of microbial metabolism, i [...].
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Affiliation(s)
- Daumantas Matulis
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, 10257 Vilnius, Lithuania
| | - Lars Wadsö
- Division of Building Materials, Lund University, Box 118, 221 00 Lund, Sweden
| | - Karim Fahmy
- Department of Biophysics, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
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6
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Oertel J, Sachs S, Flemming K, Obeid MH, Fahmy K. Distinct Effects of Chemical Toxicity and Radioactivity on Metabolic Heat of Cultured Cells Revealed by “Isotope-Editing”. Microorganisms 2023; 11:microorganisms11030584. [PMID: 36985158 PMCID: PMC10056173 DOI: 10.3390/microorganisms11030584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/30/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Studying the toxicity of chemical compounds using isothermal microcalorimetry (IMC), which monitors the metabolic heat from living microorganisms, is a rapidly expanding field. The unprecedented sensitivity of IMC is particularly attractive for studies at low levels of stressors, where lethality-based data are inadequate. We have revealed via IMC the effect of low dose rates from radioactive β−-decay on bacterial metabolism. The low dose rate regime (<400 µGyh−1) is typical of radioactively contaminated environmental sites, where chemical toxicity and radioactivity-mediated effects coexist without a predominance or specific characteristic of either of them. We found that IMC allows distinguishing the two sources of metabolic interference on the basis of “isotope-editing” and advanced thermogram analyses. The stable and radioactive europium isotopes 153Eu and 152Eu, respectively, were employed in monitoring Lactococcus lactis cultures via IMC. β−-emission (electrons) was found to increase initial culture growth by increased nutrient uptake efficiency, which compensates for a reduced maximal cell division rate. Direct adsorption of the radionuclide to the biomass, revealed by mass spectrometry, is critical for both the initial stress response and the “dilution” of radioactivity-mediated damage at later culture stages, which are dominated by the chemical toxicity of Eu.
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Affiliation(s)
- Jana Oertel
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Susanne Sachs
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Katrin Flemming
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Muhammad Hassan Obeid
- Protection and Safety Department, Atomic Energy Commission of Syria, Damascus P.O. Box 6091, Syria
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
- Correspondence:
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7
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Yang Y, Huang J, Dornbusch D, Grundmeier G, Fahmy K, Keller A, Cheung DL. Effect of Surface Hydrophobicity on the Adsorption of a Pilus-Derived Adhesin-like Peptide. Langmuir 2022; 38:9257-9265. [PMID: 35876027 PMCID: PMC9352356 DOI: 10.1021/acs.langmuir.2c01016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Bacterial colonization of abiotic surfaces such as those of medical implants, membrane filters, and everyday household items is a process of tremendous importance for public health. Bacteria use adhesive cell surface structures called adhesins to establish contact with abiotic surfaces. Among them, protein filaments called type IV pili are particularly important and found in many Gram-negative pathogens such as Pseudomonas aeruginosa. Understanding the interaction of such adhesin proteins with different abiotic surfaces at the molecular level thus represents a fundamental prerequisite for impeding bacterial colonization and preventing the spread of infectious diseases. In this work, we investigate the interaction of a synthetic adhesin-like peptide, PAK128-144ox, derived from the type IV pilus of P. aeruginosa with hydrophilic and hydrophobic self-assembled monolayers (SAMs). Using a combination of molecular dynamics (MD) simulations, quartz crystal microbalance with dissipation monitoring (QCM-D), and spectroscopic investigations, we find that PAK128-144ox has a higher affinity for hydrophobic than for hydrophilic surfaces. Additionally, PAK128-144ox adsorption on the hydrophobic SAM is furthermore accompanied by a strong increase in α-helix content. Our results show a clear influence of surface hydrophobicity and further indicate that PAK128-144ox adsorption on the hydrophobic surface is enthalpically favored, while on the hydrophilic surface, entropic contributions are more significant. However, our spectroscopic investigations also suggest aggregation of the peptide under the employed experimental conditions, which is not considered in the MD simulations and should be addressed in more detail in future studies.
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Affiliation(s)
- Yu Yang
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Jingyuan Huang
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Daniel Dornbusch
- Institute
of Resource Ecology, Biophysics Department, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Center
for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Guido Grundmeier
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Karim Fahmy
- Institute
of Resource Ecology, Biophysics Department, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Center
for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Adrian Keller
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - David L. Cheung
- School
of Chemistry, National University of Ireland
Galway, Galway H91 TK33, Ireland
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Fahmy K. Simple Growth–Metabolism Relations Are Revealed by Conserved Patterns of Heat Flow from Cultured Microorganisms. Microorganisms 2022; 10:microorganisms10071397. [PMID: 35889118 PMCID: PMC9318308 DOI: 10.3390/microorganisms10071397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022] Open
Abstract
Quantitative analyses of cell replication address the connection between metabolism and growth. Various growth models approximate time-dependent cell numbers in culture media, but physiological implications of the parametrizations are vague. In contrast, isothermal microcalorimetry (IMC) measures with unprecedented sensitivity the heat (enthalpy) release via chemical turnover in metabolizing cells. Hence, the metabolic activity can be studied independently of modeling the time-dependence of cell numbers. Unexpectedly, IMC traces of various origins exhibit conserved patterns when expressed in the enthalpy domain rather than the time domain, as exemplified by cultures of Lactococcus lactis (prokaryote), Trypanosoma congolese (protozoan) and non-growing Brassica napus (plant) cells. The data comply extraordinarily well with a dynamic Langmuir adsorption reaction model of nutrient uptake and catalytic turnover generalized here to the non-constancy of catalytic capacity. Formal relations to Michaelis–Menten kinetics and common analytical growth models are briefly discussed. The proposed formalism reproduces the “life span” of cultured microorganisms from exponential growth to metabolic decline by a succession of distinct metabolic phases following remarkably simple nutrient–metabolism relations. The analysis enables the development of advanced enzyme network models of unbalanced growth and has fundamental consequences for the derivation of toxicity measures and the transferability of metabolic activity data between laboratories.
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Affiliation(s)
- Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, 01328 Dresden, Germany;
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
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9
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Hasan Q, Elfakki E, Fahmy K, Mere O, Ghoniem A, Langar H, Musa N, Attia R, Othman MM, Samhouri D, Chaudhri I, Abubakar A, Hajjeh R, Hutin YJ. Inequities in the deployment of COVID-19 vaccine in the WHO Eastern Mediterranean Region, 2020-2021. BMJ Glob Health 2022; 7:bmjgh-2021-008139. [PMID: 35764354 PMCID: PMC9315235 DOI: 10.1136/bmjgh-2021-008139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/30/2022] [Indexed: 11/04/2022] Open
Abstract
The WHO Eastern Mediterranean Region (EMR) is characterised by a large range in routine immunisation coverage. We reviewed progress in access, deployment efforts, and use of COVID-19 vaccines in the EMR to identify bottlenecks and propose recommendations. We compiled and analysed data reported to WHO regarding the number of vaccines provided emergency use authorisation (EUA) in each country, the number of vaccine doses allocated and delivered by COVAX, the number of vaccine doses received bilaterally, the date of initiation of vaccination, vaccine usage rate and overall vaccination coverage. In June-July and October-November 2021, we conducted two rounds of a regional survey to assess vaccine acceptance and calculated the weighted proportion of individuals who would get vaccinated once a vaccine is available and recommended. We stratified the analysis according to four groups based on their participation status in COVAX, from the highest to lowest income, that is, (1) fully self-financing high-income countries (group 1), (2) fully self-financing upper middle-income countries (group 2), (3) Advance Market Commitment (AMC) countries not eligible to receive Gavi support (group 3) and (4) AMC countries eligible for Gavi support (group 4). As of 31 December 2021, the median number of vaccines provided with EUA was 6 for group 1, 11 for group 2, 8 for group 3 and 9 for group 4. On the same date, COVAX had delivered 179 793 310 doses to EMR countries. Vaccination started on 10 December 2020 in group 1, on 13 December 2020 in group 2, on 30 December 2020 in group 3 and on 20 January 2021 in group 4. The regional acceptance survey (first round) pointed to higher vaccine acceptance in group 1 (96%), than in others, including group 2 (73.9%), group 3 (78.8%) and group 4 (79.3%), with identical patterns in the second round (98%, 78%, 84% and 76%), respectively. Usage of vaccine allocated by COVAX to participating countries was 89% in group 1, 75% in group 2, 78% in group 3 and 42% in group 4. The full dose and partial dose coverage decreased with the income groups of countries, from 70% and 6% in group 1, to 43% and 8% in group 2, to 33% and 11% in group 3, and 20% and 8% in group 4. All 22 EMR countries introduced COVID-19 vaccines by 21 April 2021, but with major inequities in coverage. Additional efforts are needed to address the determinants of unequal vaccine coverage at all stages of the result chain to improve vaccine equity.
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Affiliation(s)
- Q Hasan
- DCD/IVP, WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - E Elfakki
- DCD/IVP, WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - K Fahmy
- DCD/IVP, WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Osama Mere
- DCD/IVP, WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - A Ghoniem
- DCD/IVP, WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - H Langar
- WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - N Musa
- DCD/IVP, WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Rania Attia
- DCD, WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - M M Othman
- DCD/IVP, WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Dahlia Samhouri
- WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Irtaza Chaudhri
- WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | | | - Rana Hajjeh
- WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
| | - Y J Hutin
- DCD, WHO Regional Office for the Eastern Mediterranean, Cairo, Egypt
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10
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Hanke M, Dornbusch D, Hadlich C, Rossberg A, Hansen N, Grundmeier G, Tsushima S, Keller A, Fahmy K. Anion-specific structure and stability of guanidinium-bound DNA origami. Comput Struct Biotechnol J 2022; 20:2611-2623. [PMID: 35685373 PMCID: PMC9163702 DOI: 10.1016/j.csbj.2022.05.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
While the folding of DNA into rationally designed DNA origami nanostructures has been studied extensively with the aim of increasing structural diversity and introducing functionality, the fundamental physical and chemical properties of these nanostructures remain largely elusive. Here, we investigate the correlation between atomistic, molecular, nanoscopic, and thermodynamic properties of DNA origami triangles. Using guanidinium (Gdm) as a DNA-stabilizing but potentially also denaturing cation, we explore the dependence of DNA origami stability on the identity of the accompanying anions. The statistical analyses of atomic force microscopy (AFM) images and circular dichroism (CD) spectra reveals that sulfate and chloride exert stabilizing and destabilizing effects, respectively, already below the global melting temperature of the DNA origami triangles. We identify structural transitions during thermal denaturation and show that heat capacity changes ΔCp determine the temperature sensitivity of structural damage. The different hydration shells of the anions and their potential to form Gdm+ ion pairs in concentrated salt solutions modulate ΔCp by altered wetting properties of hydrophobic DNA surface regions as shown by molecular dynamics simulations. The underlying structural changes on the molecular scale become amplified by the large number of structurally coupled DNA segments and thereby find nanoscopic correlations in AFM images.
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11
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Hanke M, Hansen N, Chen R, Grundmeier G, Fahmy K, Keller A. Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate. Int J Mol Sci 2022; 23:ijms23052817. [PMID: 35269959 PMCID: PMC8911265 DOI: 10.3390/ijms23052817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/16/2022] Open
Abstract
DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out.
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Affiliation(s)
- Marcel Hanke
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Niklas Hansen
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Ruiping Chen
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, 01328 Dresden, Germany;
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
- Correspondence: ; Tel.: +49-5251-605722
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12
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El Moghny AA, Fahmy K, Mohamed AK. Evaluation of Round Block Oncoplastic breast surgery in early Juxta-areolar breast cancer in comparison to conventional breast conservation surgery. QJM 2021; 114. [DOI: 10.1093/qjmed/hcab097.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Abstract
Background
Breast cancer is the most common cancer in women all over the world representing 18% of all women reported cases of cancer. It represents the leading cause of women mortality as representing 23% of all women cancer deaths. The decision in any breast cancer patient is taken by MDT that includes breast surgery consultant, pathology consultant, plastic surgery consultant, radiology consultant and medical oncology consultant. Breast conserving surgeries are now the standard technique for management of breast cancer patient. Oncoplastic techniques are replacing SWLE for their better cosmetic outcomes and better exposure of the tumor.
Objective
The aim of this work was to assess the round block technique as regard oncological safety, surgical outcomes and patients' satisfaction comparing results with standard wide local excision.
Methods
This is a retrospective study to assess the round block technique as an oncological procedure for management of early breast cancer near to nipple-areola complex as regard oncological safety, surgical outcomes and patients' satisfaction comparing results with standard wide local excision. It was conducted at general surgery department, Ain Shams university hospitals. Approval of the Ethical Committee and written informed consent from all participants were obtained. In our study 40 breast cancer patients are subdivided into group (A) 20 females which underwent round block technique and group (B) 20 femaleswhich underwent standard wide local excision. Patient and tumor criteria including age, co morbidities, tumor size and distance between tumor and nipple-areola complex were considered to be nonsignificant between 2 groups so the only difference is the surgical technique.
Results
The study shows that the round block technique and SWLE have the same results regarding hospital stay, post operative complications and oncological recurrence with the advantage to RBT because of its better cosmetic outcomes. So, the round block technique is superior to SWLE in selected cases.
Conclusion
The round block technique has comparable post operative parameters with better cosmoses as it is scarless operation without nipple and areola shift suggesting that the round block technique is superior to SWLE in selected cases.
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Affiliation(s)
| | - Karim Fahmy
- General Surgery Department - Faculty of Medicine-Ain Shams University
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13
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Maher RA, Osman AGE, Fahmy K, M S, Al Atarash O. Out Come of Wide Local Excision with and without Corticosteroid Therapy in Management of Idiopathic Granulomatous Mastitis. Tumori 2021. [DOI: 10.1177/03008916211012342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Introduction: Idiopathic granulomatous mastitis is a rare benign breast disease. Initial reports from hospitals in Egypt from Departments of Pathology at Cancer Institutes of Cairo, Tanta and Mansoura Universities; indicate that the disease is not as rare as that in the developed countries. It often mimics breast carcinoma both clinically and radiologically. Histological examination is the gold standard for diagnosis. Management of Idiopathic granulomatous mastitis is still debatable. In our study, we aimed to evaluate the addition of corticosteroid therapy to surgical excision in management of idiopathic granulomatous mastitis. Patients and Methods: This is a comparative study was conducted at Ain-Shams University Hospital’s breast clinic on patients with idiopathic granulomatous mastitis from to August 2015 till September 2018. Thirty patients were divided into 2 groups. Group (A) includes patients who underwent surgical management only. Group (B) includes patients who received corticosteroid therapy according to the severity of the cases then surgical Excision was done for the residual lesion. Follow up of all cases up to 1-2 years was done to document the recurrence rate and compare the cosmetic outcome of both groups. Informed consent was obtained from all patients included in the study. Results: The mean age of the affected women was 38.80 and 33.13 in group (A) and group (B), respectively and it wasn’t statistically different (p value = 0.099). The most common presenting symptom was a palpable mass in the breast (66.7% and 93.3%) in group (A) and group (B) respectively. Recurrence rate was higher in group (A) (40%) with no recurrence documented in group (B) however 2 cases were omitted from the study due to steroid noncompliance and complications. Cosmetic outcome was excellent in 76.9% of group (B) and good in 53.3% of group (A). Conclusion: Systemic steroid therapy with surgical resection is the recommended as first-line treatment strategy for IGM as it shows less recurrence rate and surgical scarring. Increased awareness of IGM will increase their understanding and improve their management.
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Affiliation(s)
- R Amira Maher
- Department of General Surgery, Breast surgery unit, Ain Shams University, Egypt
| | | | - K Fahmy
- Department of General Surgery, Breast surgery unit, Ain Shams University, Egypt
| | - Shinamwi M
- Department of General Surgery, Breast surgery unit, Ain Shams University, Egypt
| | - Osama Al Atarash
- Department of General Surgery, Breast surgery unit, Ain Shams University, Egypt
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14
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Berndt N, Bippes CC, Michalk I, Bachmann D, Bachmann J, Puentes-Cala E, Bartsch T, Loureiro LR, Kegler A, Bergmann R, Gross JK, Gross T, Kurien BT, Scofield RH, Farris AD, James JA, Schmitz M, Fahmy K, Feldmann A, Arndt C, Bachmann MP. Two Be or Not Two Be: The Nuclear Autoantigen La/SS-B Is Able to Form Dimers and Oligomers in a Redox Dependent Manner. Int J Mol Sci 2021; 22:3377. [PMID: 33806091 PMCID: PMC8036718 DOI: 10.3390/ijms22073377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
According to the literature, the autoantigen La is involved in Cap-independent translation. It was proposed that one prerequisite for this function is the formation of a protein dimer. However, structural analyses argue against La protein dimers. Noteworthy to mention, these structural analyses were performed under reducing conditions. Here we describe that La protein can undergo redox-dependent structural changes. The oxidized form of La protein can form dimers, oligomers and even polymers stabilized by disulfide bridges. The primary sequence of La protein contains three cysteine residues. Only after mutation of all three cysteine residues to alanine La protein becomes insensitive to oxidation, indicating that all three cysteines are involved in redox-dependent structural changes. Biophysical analyses of the secondary structure of La protein support the redox-dependent conformational changes. Moreover, we identified monoclonal anti-La antibodies (anti-La mAbs) that react with either the reduced or oxidized form of La protein. Differential reactivities to the reduced and oxidized form of La protein were also found in anti-La sera of autoimmune patients.
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Affiliation(s)
- Nicole Berndt
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Claudia C. Bippes
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
| | - Irene Michalk
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
| | - Dominik Bachmann
- University Cancer Center (UCC), Tumor Immunology, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (D.B.); (J.B.)
| | - Jennifer Bachmann
- University Cancer Center (UCC), Tumor Immunology, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (D.B.); (J.B.)
| | - Edinson Puentes-Cala
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
- Corporación para la Investigación de la Corrosión (CIC), Piedecuesta 681011, Colombia
| | - Tabea Bartsch
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Liliana R. Loureiro
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Alexandra Kegler
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Ralf Bergmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
- Department of Biophysics and Radiobiology, Semmelweis University, 1094 Budapest, Hungary
| | - Joanne K. Gross
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Tim Gross
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Biji T. Kurien
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - R. Hal Scofield
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - A. Darise Farris
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Judith A. James
- The Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.K.G.); (T.G.); (B.T.K.); (R.H.S.); (A.D.F.); (J.A.J.)
| | - Marc Schmitz
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany;
| | - Anja Feldmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Claudia Arndt
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
| | - Michael P. Bachmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; (N.B.); (E.P.-C.); (T.B.); (L.R.L.); (A.K.); (R.B.); (A.F.); (C.A.)
- Institute of Immunology, Medical Faculty Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (C.C.B.); (I.M.); (M.S.)
- University Cancer Center (UCC), Tumor Immunology, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, 01307 Dresden, Germany; (D.B.); (J.B.)
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15
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Abstract
Membrane-scaffolding proteins (MSPs) derived from apolipoprotein A-1 have become a versatile tool in generating nano-sized discoidal membrane mimetics (nanodiscs) for membrane protein research. Recent efforts have aimed at exploiting their controlled lipid protein ratio and size distribution to arrange membrane proteins in regular supramolecular structures for diffraction studies. Thereby, direct membrane protein crystallization, which has remained the limiting factor in structure determination of membrane proteins, would be circumvented. We describe here the formation of multimers of membrane-scaffolding protein MSP1D1-bounded nanodiscs using the thiol reactivity of engineered cysteines. The mutated positions N42 and K163 in MSP1D1 were chosen to support chemical modification as evidenced by fluorescent labeling with pyrene. Minimal interference with the nanodisc formation and structure was demonstrated by circular dichroism spectroscopy, differential light scattering and size exclusion chromatography. The direct disulphide bond formation of nanodiscs formed by the MSP1D1_N42C variant led to dimers and trimers with low yield. In contrast, transmission electron microscopy revealed that the attachment of oligonucleotides to the engineered cysteines of MSP1D1 allowed the growth of submicron-sized tracts of stacked nanodiscs through the hybridization of nanodisc populations carrying complementary strands and a flexible spacer.
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Affiliation(s)
- Madhumalar Subramanian
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Charlotte Kielar
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
| | - Satoru Tsushima
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
| | - Karim Fahmy
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Jana Oertel
- Biophysics Department, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany; (M.S.); (C.K.); (S.T.)
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16
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Fahmy K, Erra A, Soliman M, Khreis M. RARE CAUSE OF PLEURAL EFFUSION. Chest 2020. [DOI: 10.1016/j.chest.2020.08.1292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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17
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Gade VR, Traikov S, Oertel J, Fahmy K, Kurzchalia TV. C. elegans possess a general program to enter cryptobiosis that allows dauer larvae to survive different kinds of abiotic stress. Sci Rep 2020; 10:13466. [PMID: 32778668 PMCID: PMC7417548 DOI: 10.1038/s41598-020-70311-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 07/21/2020] [Indexed: 01/27/2023] Open
Abstract
All organisms encounter abiotic stress but only certain organisms are able to cope with extreme conditions and enter into cryptobiosis (hidden life). Previously, we have shown that C. elegans dauer larvae can survive severe desiccation (anhydrobiosis), a specific form of cryptobiosis. Entry into anhydrobiosis is preceded by activation of a set of biochemical pathways by exposure to mild desiccation. This process called preconditioning induces elevation of trehalose, intrinsically disordered proteins, polyamines and some other pathways that allow the preservation of cellular functionality in the absence of water. Here, we demonstrate that another stress factor, high osmolarity, activates similar biochemical pathways. The larvae that acquired resistance to high osmotic pressure can also withstand desiccation. In addition, high osmolarity significantly increases the biosynthesis of glycerol making larva tolerant to freezing. Thus, to survive abiotic stress, C. elegans activates a combination of genetic and biochemical pathways that serve as a general survival program.
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Affiliation(s)
- Vamshidhar R Gade
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Sofia Traikov
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Jana Oertel
- Institute of Resource Ecology at the Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology at the Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Teymuras V Kurzchalia
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
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18
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Amira Maher R, Osman AGE, Fahmy K, Ebied NM, Eissa R. Anterior Intercostal Artery Perforator Flap as a Simple Technique for Partial Breast Reconstruction: Our Institutional Initial Experience. Tumori 2020. [DOI: 10.1177/0300891620931670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: The oncoplastic surgery has brought new dimensions to breast conserving surgery and added the aesthetic principles of breast surgery to breast cancer management. Recently there's a lot of volume replacement techniques without significant donor site morbidity .The anterior intercostal artery perforator (AICAP) flap is a suitable option in partial breast reconstruction for lower pole tumors in small and medium sized breasts. Objectives: The aim of this study is to report our clinical experience with anterior intercostal perforator flap in partial breast reconstruction Methodology: 25 cases were performed between April 2018 to June 2019 at in Ain shams university hospitals for selected patients with lower breast pole tumors with small and medium sized breast and other option like reduction mMDTmoplasty wasn't favorable for them. Results: A total of 25 patient were selected by the multidisplinary team at Ain shams university hospital for partial breast reconstruction with anterior intercostal artery perforator flap . The mean age of the cases was 45.68 with mean body mass index of 32.32. The mean operative time for the flap was 64 minutes while the hospital stay was ranging from 1-2 days .Follow-up for local recurrence was from 6 to 14 months. There was 1 case with wound complication (4%). The cosmetic outcome was assessed by the MDT and a giving score from 1-5 was used with 1 is the least favorable cosmetic outcome and 5 is the best result 76% of the cases scored 5, 14% scored 4, 8% scored 3. According to patient satisfaction a score from 1 to 5 was used with the score 1 is least satisfied and score 5 represents the most satisfaction level, there was 80% of the patient gave the score 5, 12% of the cases gave the score 4 and 8% of the cases gave the score 3 Conclusions: Based on our experience, partial breast reconstruction using AICAP flap is a reliable option for lower breast tumors in small-to-moderate breast size with perfect cosmetic outcome and negligible rate of complication.
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Affiliation(s)
- R Amira Maher
- Department of General Surgery, Breast Surgery Unit, Ain Shams University, Egypt
| | | | - K Fahmy
- Department of General Surgery, Breast Surgery Unit, Ain Shams University, Egypt
| | - Nouf M. Ebied
- Department of General Surgery, Breast Surgery Unit, Ain Shams University, Egypt
| | - Reda Eissa
- Department of General Surgery, Breast Surgery Unit, Ain Shams University, Egypt
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19
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Penkov S, Raghuraman BK, Erkut C, Oertel J, Galli R, Ackerman EJM, Vorkel D, Verbavatz JM, Koch E, Fahmy K, Shevchenko A, Kurzchalia TV. A metabolic switch regulates the transition between growth and diapause in C. elegans. BMC Biol 2020; 18:31. [PMID: 32188449 PMCID: PMC7081555 DOI: 10.1186/s12915-020-0760-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Metabolic activity alternates between high and low states during different stages of an organism's life cycle. During the transition from growth to quiescence, a major metabolic shift often occurs from oxidative phosphorylation to glycolysis and gluconeogenesis. We use the entry of Caenorhabditis elegans into the dauer larval stage, a developmentally arrested stage formed in response to harsh environmental conditions, as a model to study the global metabolic changes and underlying molecular mechanisms associated with growth to quiescence transition. RESULTS Here, we show that the metabolic switch involves the concerted activity of several regulatory pathways. Whereas the steroid hormone receptor DAF-12 controls dauer morphogenesis, the insulin pathway maintains low energy expenditure through DAF-16/FoxO, which also requires AAK-2/AMPKα. DAF-12 and AAK-2 separately promote a shift in the molar ratios between competing enzymes at two key branch points within the central carbon metabolic pathway diverting carbon atoms from the TCA cycle and directing them to gluconeogenesis. When both AAK-2 and DAF-12 are suppressed, the TCA cycle is active and the developmental arrest is bypassed. CONCLUSIONS The metabolic status of each developmental stage is defined by stoichiometric ratios within the constellation of metabolic enzymes driving metabolic flux and controls the transition between growth and quiescence.
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Affiliation(s)
- Sider Penkov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany. .,Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany. .,Institute for Clinical Chemistry and Laboratory Medicine, University Clinic and Medical Faculty, TU Dresden, Dresden, Germany.
| | | | - Cihan Erkut
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Present address: German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jana Oertel
- Institute of Resource Ecology at the Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Roberta Galli
- Faculty of Medicine Carl Gustav Carus, Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, TU Dresden, Dresden, Germany
| | | | - Daniela Vorkel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jean-Marc Verbavatz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Institut Jacques Monod, Université de Paris/CNRS, Paris, France
| | - Edmund Koch
- Faculty of Medicine Carl Gustav Carus, Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, TU Dresden, Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology at the Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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20
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Hoyer E, Knöppel J, Liebmann M, Steppert M, Raiwa M, Herczynski O, Hanspach E, Zehner S, Göttfert M, Tsushima S, Fahmy K, Oertel J. Calcium binding to a disordered domain of a type III-secreted protein from a coral pathogen promotes secondary structure formation and catalytic activity. Sci Rep 2019; 9:7115. [PMID: 31068617 PMCID: PMC6506597 DOI: 10.1038/s41598-019-42898-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/10/2019] [Indexed: 01/05/2023] Open
Abstract
Strains of the Gram-negative bacterium Vibrio coralliilyticus cause the bleaching of corals due to decomposition of symbiotic microalgae. The V. coralliilyticus strain ATCC BAA-450 (Vc450) encodes a type III secretion system (T3SS). The gene cluster also encodes a protein (locus tag VIC_001052) with sequence homology to the T3SS-secreted nodulation proteins NopE1 and NopE2 of Bradyrhizobium japonicum (USDA110). VIC_001052 has been shown to undergo auto-cleavage in the presence of Ca2+ similar to the NopE proteins. We have studied the hitherto unknown secondary structure, Ca2+-binding affinity and stoichiometry of the “metal ion-inducible autocleavage” (MIIA) domain of VIC_001052 which does not possess a classical Ca2+-binding motif. CD and fluorescence spectroscopy revealed that the MIIA domain is largely intrinsically disordered. Binding of Ca2+ and other di- and trivalent cations induced secondary structure and hydrophobic packing after partial neutralization of the highly negatively charged MIIA domain. Mass spectrometry and isothermal titration calorimetry showed two Ca2+-binding sites which promote structure formation with a total binding enthalpy of −110 kJ mol−1 at a low micromolar Kd. Putative binding motifs were identified by sequence similarity to EF-hand domains and their structure analyzed by molecular dynamics simulations. The stoichiometric Ca2+-dependent induction of structure correlated with catalytic activity and may provide a “host-sensing” mechanism that is shared among pathogens that use a T3SS for efficient secretion of disordered proteins.
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Affiliation(s)
- Elisabeth Hoyer
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany.,Ludwig-Maximilians-Universität München, Department of Biology I, Microbiology, Großhaderner Str. 2, D-82152, Planegg-Martinsried, Germany
| | - Julius Knöppel
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Martina Liebmann
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Michael Steppert
- Leibniz University Hannover, Institute of Radioecology and Radiation Protection, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Manuel Raiwa
- Leibniz University Hannover, Institute of Radioecology and Radiation Protection, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Olivia Herczynski
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Erik Hanspach
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Susanne Zehner
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Michael Göttfert
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Satoru Tsushima
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Jana Oertel
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany.
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21
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Thommen A, Werner S, Frank O, Philipp J, Knittelfelder O, Quek Y, Fahmy K, Shevchenko A, Friedrich BM, Jülicher F, Rink JC. Body size-dependent energy storage causes Kleiber's law scaling of the metabolic rate in planarians. eLife 2019; 8:e38187. [PMID: 30608231 PMCID: PMC6320072 DOI: 10.7554/elife.38187] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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: 05/12/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
Kleiber's law, or the 3/4 -power law scaling of the metabolic rate with body mass, is considered one of the few quantitative laws in biology, yet its physiological basis remains unknown. Here, we report Kleiber's law scaling in the planarian Schmidtea mediterranea. Its reversible and life history-independent changes in adult body mass over 3 orders of magnitude reveal that Kleiber's law does not emerge from the size-dependent decrease in cellular metabolic rate, but from a size-dependent increase in mass per cell. Through a combination of experiment and theoretical analysis of the organismal energy balance, we further show that the mass allometry is caused by body size dependent energy storage. Our results reveal the physiological origins of Kleiber's law in planarians and have general implications for understanding a fundamental scaling law in biology.
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Affiliation(s)
- Albert Thommen
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
| | - Steffen Werner
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- FOM Institute AMOLFAmsterdamThe Netherlands
| | - Olga Frank
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Jenny Philipp
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource EcologyDresdenGermany
| | | | - Yihui Quek
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Massachusetts Institute of TechnologyCambridgeUnited States
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource EcologyDresdenGermany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Benjamin M Friedrich
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Center for Advancing Electronics DresdenTechnische Universität DresdenDresdenGermany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
| | - Jochen C Rink
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
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22
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Iric K, Subramanian M, Oertel J, Agarwal NP, Matthies M, Periole X, Sakmar TP, Huber T, Fahmy K, Schmidt TL. DNA-encircled lipid bilayers. Nanoscale 2018; 10:18463-18467. [PMID: 30272763 DOI: 10.1039/c8nr06505e] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lipid bilayers and lipid-associated proteins play crucial roles in biology. As in vivo studies and manipulation are inherently difficult, membrane-mimetic systems are useful for the investigation of lipidic phases, lipid-protein interactions, membrane protein function and membrane structure in vitro. In this work, we describe a route to leverage the programmability of DNA nanotechnology and create DNA-encircled bilayers (DEBs). DEBs are made of multiple copies of an alkylated oligonucleotide hybridized to a single-stranded minicircle, in which up to two alkyl chains per helical turn point to the inside of the toroidal DNA ring. When phospholipids are added, a bilayer is observed to self-assemble within the ring such that the alkyl chains of the oligonucleotides stabilize the hydrophobic rim of the bilayer to prevent formation of vesicles and support thermotropic lipid phase transitions. The DEBs are completely free of protein and can be synthesized from commercially available components using routine equipment. The diameter of DEBs can be varied in a predictable manner. The well-established toolbox from structural DNA nanotechnology, will ultimately enable the rational design of DEBs so that their size, shape or functionalization can be adapted to the specific needs of biophysical investigations of lipidic phases and the properties of membrane proteins embedded into DEB nanoparticle bilayers.
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Affiliation(s)
- Katarina Iric
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany.
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23
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24
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Bauer A, Jäschke A, Schöne S, Barthen R, März J, Schmeide K, Patzschke M, Kersting B, Fahmy K, Oertel J, Brendler V, Stumpf T. Uranium(VI) Complexes with a Calix[4]arene-Based 8-Hydroxyquinoline Ligand: Thermodynamic and Structural Characterization Based on Calorimetry, Spectroscopy, and Liquid-Liquid Extraction. ChemistryOpen 2018; 7:467-474. [PMID: 29930893 PMCID: PMC6010010 DOI: 10.1002/open.201800085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Indexed: 01/13/2023] Open
Abstract
The environmental aspects of ore processing and waste treatment call for an optimization of applied technologies. There, understanding of the structure and complexation mechanism on a molecular scale is indispensable. Here, the complexation of UVI with a calix[4]arene-based 8-hydroxyquinoline ligand was investigated by applying a wide range of complementary methods. In solution, the formation of two complex species was proven with stability constants of log ß1:1=5.94±0.02 and log ß2:1=6.33±0.01, respectively. The formation of the 1:1 complex was found to be enthalpy driven [ΔH1:1=(-71.5±10.0) kJ mol-1; TΔS1:1=(-37.57±10.0) kJ mol-1], whereas the second complexation step was found to be endothermic and entropy driven [ΔH2:1=(32.8±4.0) kJ mol-1; TΔS2:1=(68.97±4.0) kJ mol-1]. Moreover, the molecular structure of [UO2(H6L)(NO3)](NO3) (1) was determined by single-crystal X-ray diffraction. Concluding, radiotoxic UVI was separated from a EuIII-containing solution by the calix[4]arene-based ligand in solvent extractions.
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Affiliation(s)
- Anne Bauer
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Astrid Jäschke
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Sebastian Schöne
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Robert Barthen
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Juliane März
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Katja Schmeide
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Michael Patzschke
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Berthold Kersting
- Universität LeipzigInstitute of Inorganic ChemistryJohannisallee 2904103LeipzigGermany
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Jana Oertel
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Vinzenz Brendler
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
| | - Thorsten Stumpf
- Helmholtz-Zentrum Dresden–RossendorfInstitute of Resource EcologyBautzner Landstraße 40001328DresdenGermany), Fax: (+49) 351 260 3553
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25
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Thomas AK, Wieduwild R, Zimmermann R, Lin W, Friedrichs J, Bickle M, Fahmy K, Werner C, Zhang Y. Layer-by-Layer Assembly of Heparin and Peptide-Polyethylene Glycol Conjugates to Form Hybrid Nanothin Films of Biomatrices. ACS Appl Mater Interfaces 2018; 10:14264-14270. [PMID: 29658265 DOI: 10.1021/acsami.8b02014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We investigated the utility of a heparin/peptide-polyethylene glycol conjugate system to build layer-by-layer (LbL) structures, to assemble tailored multilayer-biomatrices for cell culture. The LbL assembly balances the advantages of polyelectrolyte systems and protein-based systems. Human umbilical vein endothelial cells showed distinct responses to the film thickness and structure; the presence, density, and spatial arrangement of a cell adhesion ligand within the nanothin film; and the pretreatment of the film with morphogens. The LbL technique presents a versatile tool for modifying cell culture substrates with defined and diverse biochemical and structural features, for investigating cell-material interactions.
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Affiliation(s)
| | | | - Ralf Zimmermann
- Department of Biofunctional Polymer Materials, Max Bergman Center of Biomaterials , Leibniz Institute of Polymer Research , Dresden 01069 , Germany
| | | | - Jens Friedrichs
- Department of Biofunctional Polymer Materials, Max Bergman Center of Biomaterials , Leibniz Institute of Polymer Research , Dresden 01069 , Germany
| | - Marc Bickle
- High-Throughput Technology Development Studio , Max Planck Institute of Molecular Cell Biology and Genetics , Dresden 01307 , Germany
| | | | - Carsten Werner
- Department of Biofunctional Polymer Materials, Max Bergman Center of Biomaterials , Leibniz Institute of Polymer Research , Dresden 01069 , Germany
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26
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Costanza B, Turtoi A, Bellahcène A, Hirano T, Peulen O, Blomme A, Hennequière V, Mutijima E, Boniver J, Meuwis MA, Josse C, Koopmansch B, Segers K, Yokobori T, Fahmy K, Thiry M, Coimbra C, Garbacki N, Colige A, Baiwir D, Bours V, Louis E, Detry O, Delvenne P, Nishiyama M, Castronovo V. Innovative methodology for the identification of soluble biomarkers in fresh tissues. Oncotarget 2018. [PMID: 29535834 PMCID: PMC5828218 DOI: 10.18632/oncotarget.24366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The identification of diagnostic and prognostic biomarkers from early lesions, measurable in liquid biopsies remains a major challenge, particularly in oncology. Fresh human material of high quality is required for biomarker discovery but is often not available when it is totally required for clinical pathology investigation. Hence, all OMICs studies are done on residual and less clinically relevant biological samples. Here after, we present an innovative, simple, and non-destructive, procedure named EXPEL that uses rapid, pressure-assisted, interstitial fluid extrusion, preserving the specimen for full routine clinical pathology investigation. In the meantime, the technique allows a comprehensive OMICs analysis (proteins, metabolites, miRNAs and DNA). As proof of concept, we have applied EXPEL on freshly collected human colorectal cancer and liver metastases tissues. We demonstrate that the procedure efficiently allows the extraction, within a few minutes, of a wide variety of biomolecules holding diagnostic and prognostic potential while keeping both tissue morphology and antigenicity unaltered. Our method enables, for the first time, both clinicians and scientists to explore identical clinical material regardless of its origin and size, which has a major positive impact on translation to the clinic.
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Affiliation(s)
- Brunella Costanza
- Metastasis Research Laboratory, GIGA Cancer, University of Liège, Liège, Belgium
| | - Andrei Turtoi
- Metastasis Research Laboratory, GIGA Cancer, University of Liège, Liège, Belgium
| | - Akeila Bellahcène
- Metastasis Research Laboratory, GIGA Cancer, University of Liège, Liège, Belgium
| | - Touko Hirano
- Laboratory for Analytical Instruments, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA Cancer, University of Liège, Liège, Belgium
| | - Arnaud Blomme
- Metastasis Research Laboratory, GIGA Cancer, University of Liège, Liège, Belgium
| | - Vincent Hennequière
- Metastasis Research Laboratory, GIGA Cancer, University of Liège, Liège, Belgium
| | - Eugene Mutijima
- Department of Pathology, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Jacques Boniver
- Department of Pathology, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Marie-Alice Meuwis
- Gastroenterology Department, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Claire Josse
- Center for Human Genetic, Molecular Haemato-Oncology Unit, UniLab, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Benjamin Koopmansch
- Center for Human Genetic, Molecular Haemato-Oncology Unit, UniLab, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Karin Segers
- Center for Human Genetic, Molecular Haemato-Oncology Unit, UniLab, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Takehiko Yokobori
- Division of Integrated Oncology Research, Research Program for Omics-based Medical Science, Gunma University Initiative for Advanced Research, Gunma, Japan
| | - Karim Fahmy
- Metastasis Research Laboratory, GIGA Cancer, University of Liège, Liège, Belgium
| | - Marc Thiry
- Laboratory of Cell Biology, Faculty of Sciences, University of Liège, Liège, Belgium
| | - Carla Coimbra
- Department of Abdominal Surgery, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Nancy Garbacki
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University Hospital, University of Liège, Liège, Belgium
| | - Alain Colige
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University Hospital, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- Mass Spectrometry Laboratory, University of Liège, Liège, Belgium.,GIGA Proteomics Facility, University of Liège, Liège, Belgium
| | - Vincent Bours
- Center for Human Genetic, Molecular Haemato-Oncology Unit, UniLab, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Edouard Louis
- Gastroenterology Department, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Olivier Detry
- Department of Abdominal Surgery, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Department of Pathology, University Hospital (CHU), University of Liège, Liège, Belgium
| | - Masahiko Nishiyama
- Division of Integrated Oncology Research, Research Program for Omics-based Medical Science, Gunma University Initiative for Advanced Research, Gunma, Japan.,Department of Molecular Pharmacology and Oncology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Vincent Castronovo
- Metastasis Research Laboratory, GIGA Cancer, University of Liège, Liège, Belgium
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27
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Sachs S, Geipel G, Bok F, Oertel J, Fahmy K. Calorimetrically Determined U(VI) Toxicity in Brassica napus Correlates with Oxidoreductase Activity and U(VI) Speciation. Environ Sci Technol 2017; 51:10843-10849. [PMID: 28841015 DOI: 10.1021/acs.est.7b02564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Radioecological studies depend on the quantitative toxicity assessment of environmental radionuclides. At low dose exposure, the life span of affected organisms is barely shortened, enabling the transfer of radionuclides through an almost-intact food chain. Lethality-based toxicity estimates are not adequate in this regime because they require higher concentrations. However, increased radionuclide concentration alters its speciation, rendering the extrapolation to the low dose exposure chemically inconsistent. Here, we demonstrate that microcalorimetry provides a sensitive real-time monitor of toxicity of uranium (in the U(VI) oxidation state) in a plant cell model of Brassica napus. We introduce the calorimetric descriptor "metabolic capacity" and show that it correlates with enzymatically determined cell viability. It is independent of physiological models and robust against the naturally occurring fluctuations in the metabolic response to U(VI) of plant cell cultures. In combination with time-resolved laser-induced fluorescence spectroscopy and thermodynamic modeling, we show that the plant cell metabolism is affected predominantly by hydroxo-species of U(VI) with an IC50 threshold of ∼90 μM. The data emphasize the yet-little-exploited potential of microcalorimetry for the speciation-sensitive ecotoxicology of radionuclides.
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Affiliation(s)
- Susanne Sachs
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology , Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Gerhard Geipel
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology , Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Frank Bok
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology , Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Jana Oertel
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology , Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology , Bautzner Landstraße 400, 01328 Dresden, Germany
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28
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Sandoval A, Eichler S, Madathil S, Reeves PJ, Fahmy K, Böckmann RA. The Molecular Switching Mechanism at the Conserved D(E)RY Motif in Class-A GPCRs. Biophys J 2017; 111:79-89. [PMID: 27410736 DOI: 10.1016/j.bpj.2016.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/31/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022] Open
Abstract
The disruption of ionic and H-bond interactions between the cytosolic ends of transmembrane helices TM3 and TM6 of class-A (rhodopsin-like) G protein-coupled receptors (GPCRs) is a hallmark for their activation by chemical or physical stimuli. In the bovine photoreceptor rhodopsin, this is accompanied by proton uptake at Glu(134) in the class-conserved D(E)RY motif. Studies on TM3 model peptides proposed a crucial role of the lipid bilayer in linking protonation to stabilization of an active state-like conformation. However, the molecular details of this linkage could not be resolved and have been addressed in this study by molecular dynamics (MD) simulations on TM3 model peptides in a bilayer of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). We show that protonation of the conserved glutamic acid alters the peptide insertion depth in the membrane, its side-chain rotamer preferences, and stabilizes the C-terminal helical structure. These factors contribute to the rise of the side-chain pKa (> 6) and to reduced polarity around the TM3 C terminus as confirmed by fluorescence spectroscopy. Helix stabilization requires the protonated carboxyl group; unexpectedly, this stabilization could not be evoked with an amide in MD simulations. Additionally, time-resolved Fourier transform infrared (FTIR) spectroscopy of TM3 model peptides revealed a different kinetics for lipid ester carbonyl hydration, suggesting that the carboxyl is linked to more extended H-bond clusters than an amide. Remarkably, this was seen as well in DOPC-reconstituted Glu(134)- and Gln(134)-containing bovine opsin mutants and demonstrates that the D(E)RY motif is a hydrated microdomain. The function of the D(E)RY motif as a proton switch is suggested to be based on the reorganization of the H-bond network at the membrane interface.
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Affiliation(s)
- Angelica Sandoval
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stefanie Eichler
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, and Technische Universität Dresden, Dresden, Germany
| | - Sineej Madathil
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Philip J Reeves
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Resource Ecology, and Technische Universität Dresden, Dresden, Germany.
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
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29
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Fischermeier E, Pospíšil P, Sayed A, Hof M, Solioz M, Fahmy K. Dipolar Relaxation Dynamics at the Active Site of an ATPase Regulated by Membrane Lateral Pressure. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201611582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Elisabeth Fischermeier
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
- Nationales Zentrum für Tumorerkrankungen Heidelberg Im Neuenheimer Feld 460 69120 Heidelberg Germany
| | - Petr Pospíšil
- J. Heyrovský Inst. Physical Chemistry of the A.S.C.R. v.v.i. Prague Czech Republic
| | - Ahmed Sayed
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
- Institute for Experimental Physics I Universität Leipzig Linnéstrasse 5 04103 Leipzig Germany
| | - Martin Hof
- J. Heyrovský Inst. Physical Chemistry of the A.S.C.R. v.v.i. Prague Czech Republic
| | - Marc Solioz
- University of Bern Dept. of Clinical Pharmacology Murtenstrasse 35 3008 Bern Switzerland
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
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30
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Fischermeier E, Pospíšil P, Sayed A, Hof M, Solioz M, Fahmy K. Dipolar Relaxation Dynamics at the Active Site of an ATPase Regulated by Membrane Lateral Pressure. Angew Chem Int Ed Engl 2016; 56:1269-1272. [DOI: 10.1002/anie.201611582] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Elisabeth Fischermeier
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
- Nationales Zentrum für Tumorerkrankungen Heidelberg Im Neuenheimer Feld 460 69120 Heidelberg Germany
| | - Petr Pospíšil
- J. Heyrovský Inst. Physical Chemistry of the A.S.C.R. v.v.i. Prague Czech Republic
| | - Ahmed Sayed
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
- Institute for Experimental Physics I Universität Leipzig Linnéstrasse 5 04103 Leipzig Germany
| | - Martin Hof
- J. Heyrovský Inst. Physical Chemistry of the A.S.C.R. v.v.i. Prague Czech Republic
| | - Marc Solioz
- University of Bern Dept. of Clinical Pharmacology Murtenstrasse 35 3008 Bern Switzerland
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf Institute of Resource Ecology Bautzner Landstrasse 400 01328 Dresden Germany
- Technische Universität Dresden Biotechnology Center Tatzberg 47-49, 01307 Dresden Germany
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31
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Liu J, Falke S, Drobot B, Oberthuer D, Kikhney A, Guenther T, Fahmy K, Svergun D, Betzel C, Raff J. Analysis of self-assembly of S-layer protein slp-B53 from Lysinibacillus sphaericus. Eur Biophys J 2016; 46:77-89. [PMID: 27270294 DOI: 10.1007/s00249-016-1139-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/29/2016] [Accepted: 05/12/2016] [Indexed: 10/21/2022]
Abstract
The formation of stable and functional surface layers (S-layers) via self-assembly of surface-layer proteins on the cell surface is a dynamic and complex process. S-layers facilitate a number of important biological functions, e.g., providing protection and mediating selective exchange of molecules and thereby functioning as molecular sieves. Furthermore, S-layers selectively bind several metal ions including uranium, palladium, gold, and europium, some of them with high affinity. Most current research on surface layers focuses on investigating crystalline arrays of protein subunits in Archaea and bacteria. In this work, several complementary analytical techniques and methods have been applied to examine structure-function relationships and dynamics for assembly of S-layer protein slp-B53 from Lysinibacillus sphaericus: (1) The secondary structure of the S-layer protein was analyzed by circular dichroism spectroscopy; (2) Small-angle X-ray scattering was applied to gain insights into the three-dimensional structure in solution; (3) The interaction with bivalent cations was followed by differential scanning calorimetry; (4) The dynamics and time-dependent assembly of S-layers were followed by applying dynamic light scattering; (5) The two-dimensional structure of the paracrystalline S-layer lattice was examined by atomic force microscopy. The data obtained provide essential structural insights into the mechanism of S-layer self-assembly, particularly with respect to binding of bivalent cations, i.e., Mg2+ and Ca2+. Furthermore, the results obtained highlight potential applications of S-layers in the fields of micromaterials and nanobiotechnology by providing engineered or individual symmetric thin protein layers, e.g., for protective, antimicrobial, or otherwise functionalized surfaces.
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Affiliation(s)
- Jun Liu
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany.,Bioengineering Faculty, Sichuan University of Science and Engineering, Huixing Rd., Xueyuan Street 180, Zigong, 643000, Sichuan, China
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Bjoern Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany
| | - Dominik Oberthuer
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany.,Center for Free-Electron Laser Science (CFEL), DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Alexey Kikhney
- EMBL Hamburg, European Molecular Biology Laboratory, Notkestr. 85, 22607, Hamburg, Germany
| | - Tobias Guenther
- Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany
| | - Dmitri Svergun
- EMBL Hamburg, European Molecular Biology Laboratory, Notkestr. 85, 22607, Hamburg, Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Johannes Raff
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany. .,Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany.
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Ruiz-Gómez G, Hawkins JC, Philipp J, Künze G, Wodtke R, Löser R, Fahmy K, Pisabarro MT. Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics. PLoS One 2016; 11:e0154046. [PMID: 27123592 PMCID: PMC4849758 DOI: 10.1371/journal.pone.0154046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/07/2016] [Indexed: 12/25/2022] Open
Abstract
Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.
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Affiliation(s)
- Gloria Ruiz-Gómez
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg, Dresden, Germany
- * E-mail: (GRG); (MTB)
| | - John C. Hawkins
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg, Dresden, Germany
| | - Jenny Philipp
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - Georg Künze
- Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Robert Wodtke
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Reik Löser
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - M. Teresa Pisabarro
- Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg, Dresden, Germany
- * E-mail: (GRG); (MTB)
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Hassan W, Fahmy K, Hassan M, Zaghloul S, Hasan EI. Long-term clinical outcomes up to 7- year results of intracoronary stand-alone bolus administration of eptifibatide during coronary intervention (ice) study. Interv Cardiol 2016. [DOI: 10.4172/interventional-cardiology.1000542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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34
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Abusharkh SE, Erkut C, Oertel J, Kurzchalia TV, Fahmy K. The role of phospholipid headgroup composition and trehalose in the desiccation tolerance of Caenorhabditis elegans. Cryobiology 2015. [DOI: 10.1016/j.cryobiol.2015.10.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Fahmy K, Gonzalez A, Arafa M, Peixoto P, Bellahcène A, Turtoi A, Delvenne P, Thiry M, Castronovo V, Peulen O. Myoferlin plays a key role in VEGFA secretion and impacts tumor-associated angiogenesis in human pancreas cancer. Int J Cancer 2015; 138:652-63. [PMID: 26311411 DOI: 10.1002/ijc.29820] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 01/14/2023]
Abstract
Pancreatic ductal adenocarcinoma is one of the most deadly forms of cancers with no satisfactory treatment to date. Recent studies have identified myoferlin, a ferlin family member, in human pancreas adenocarcinoma where its expression was associated to a bad prognosis. However, the function of myoferlin in pancreas adenocarcinoma has not been reported. In other cell types, myoferlin is involved in several key plasma membrane processes such as fusion, repair, endocytosis and tyrosine kinase receptor activity. In this study, we showed that myoferlin silencing in BxPC-3 human pancreatic cancer cells resulted in the inhibition of cell proliferation in vitro and in a significant reduction of the tumor volume in chick chorioallantoic membrane assay. In addition to be smaller, the tumors formed by the myoferlin-silenced cells showed a marked absence of functional blood vessels. We further demonstrated that this effect was due, at least in part, to an inhibition of VEGFA secretion by BxPC-3 myoferlin-silenced cells. Using immunofluorescence and electron microscopy, we linked the decreased VEGFA secretion to an impairment of VEGFA exocytosis. The clinical relevance of our results was further strengthened by a significant correlation between myoferlin expression in a series of human pancreatic malignant lesions and their angiogenic status evaluated by the determination of the blood vessel density.
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Affiliation(s)
- Karim Fahmy
- Metastasis Research Laboratory, GIGA-Cancer, University of Liege, Liege, Belgium
| | - Arnaud Gonzalez
- Metastasis Research Laboratory, GIGA-Cancer, University of Liege, Liege, Belgium
| | - Mohammad Arafa
- Department of Pathology, Faculty of Medicine, University of Mansoura, Mansoura, Egypt
| | - Paul Peixoto
- Metastasis Research Laboratory, GIGA-Cancer, University of Liege, Liege, Belgium
| | - Akeila Bellahcène
- Metastasis Research Laboratory, GIGA-Cancer, University of Liege, Liege, Belgium
| | - Andrei Turtoi
- Metastasis Research Laboratory, GIGA-Cancer, University of Liege, Liege, Belgium
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, Liege, Belgium
| | - Marc Thiry
- Laboratory of Cell Biology, GIGA-R, University of Liege, Liege, Belgium
| | - Vincent Castronovo
- Metastasis Research Laboratory, GIGA-Cancer, University of Liege, Liege, Belgium
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA-Cancer, University of Liege, Liege, Belgium
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Ander M, Subramaniam S, Fahmy K, Stewart AF, Schäffer E. A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology. PLoS Biol 2015; 13:e1002213. [PMID: 26271032 PMCID: PMC4535883 DOI: 10.1371/journal.pbio.1002213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/26/2015] [Indexed: 11/24/2022] Open
Abstract
Repair of DNA breaks by single-strand annealing (SSA) is a major mechanism for the maintenance of genomic integrity. SSA is promoted by proteins (single-strand-annealing proteins [SSAPs]), such as eukaryotic RAD52 and λ phage Redβ. These proteins use a short single-stranded region to find sequence identity and initiate homologous recombination. However, it is unclear how SSAPs detect homology and catalyze annealing. Using single-molecule experiments, we provide evidence that homology is recognized by Redβ monomers that weakly hold single DNA strands together. Once annealing begins, dimerization of Redβ clamps the double-stranded region and nucleates nucleoprotein filament growth. In this manner, DNA clamping ensures and secures a successful detection for DNA sequence homology. The clamp is characterized by a structural change of Redβ and a remarkable stability against force up to 200 pN. Our findings not only present a detailed explanation for SSAP action but also identify the DNA clamp as a very stable, noncovalent, DNA-protein interaction.
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Affiliation(s)
- Marcel Ander
- Nanomechanics Group, Biotechnology Center, TU Dresden, Dresden, Germany
| | | | - Karim Fahmy
- Division of Biophysics, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - A. Francis Stewart
- Department of Genomics, Biotechnology Center, TU Dresden, Dresden, Germany
| | - Erik Schäffer
- Nanomechanics Group, Biotechnology Center, TU Dresden, Dresden, Germany
- Cellular Nanoscience, Center for Plant Molecular Biology (ZMBP), Universität Tübingen, Tübingen, Germany
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Abusharkh SE, Erkut C, Oertel J, Kurzchalia TV, Fahmy K. The role of phospholipid headgroup composition and trehalose in the desiccation tolerance of Caenorhabditis elegans. Langmuir 2014; 30:12897-12906. [PMID: 25290156 DOI: 10.1021/la502654j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Anhydrobiotic organisms have the remarkable ability to lose extensive amounts of body water and survive in an ametabolic state. Distributed to various taxa of life, these organisms have developed strategies to efficiently protect their cell membranes and proteins against extreme water loss. Recently, we showed that the dauer larva of the nematode Caenorhabditis elegans is anhydrobiotic and accumulates high amounts of trehalose during preparation to harsh desiccation (preconditioning). Here, we have used this genetic model to study the biophysical manifestations of anhydrobiosis and show that, in addition to trehalose accumulation, dauer larvae dramatically reduce their phosphatidylcholine (PC) content. The chemical composition of the phospholipids (PLs) has key consequences not only for their interaction with trehalose, as we demonstrate with Langmuir-Blodgett monolayers, but also, the kinetic response of PLs to hydration transients is strongly influenced as evidenced by time-resolved FTIR spectroscopy. PLs from preconditioned larvae with reduced PC content exhibit a higher trehalose affinity, a stronger hydration-induced gain in acyl chain free volume, and a wider spread of structural relaxation rates of their lyotropic transitions and sub-headgroup H-bond interactions. The different hydration properties of PC and phosphatidylethanolamine (PE) headgroups are crucial for the hydration-dependent rearrangement of the trehalose-mediated H-bond network. As a consequence, the compressibility modulus of PLs from preconditioned larvae is about 2.6-fold smaller than that from non-preconditioned ones. Thus, the biological relevance of reducing the PC:PE ratio by PL headgroup adaptation should be the preservation of plasma membrane integrity by relieving mechanical strain from desiccated trehalose-containing cells during fast rehydration.
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Affiliation(s)
- Sawsan E Abusharkh
- Biophysics Division, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf , PF 510119, D-01314 Dresden, Germany
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Abstract
The folding of DNA into arbitrary two- and three-dimensional shapes, called DNA origami, represents a powerful tool for the synthesis of functional nanostructures. Here, we present the first approach toward the paramagnetic functionalization of DNA origami nanostructures by utilizing postassembly coordination with Eu(3+) ions. In contrast to the usual formation of toroidal dsDNA condensates in the presence of trivalent cations, planar as well as rod-like DNA origami maintain their shape and monomeric state even under high loading with the trivalent lanthanide. Europium coordination was demonstrated by the change in Eu(3+) luminescence upon binding to the two DNA origami. Their natural circular dichroism in the Mg(2+)- and Eu(3+)-bound state was found to be very similar to that of genomic DNA, evidencing little influence of the DNA origami superstructure on the local chirality of the stacked base pairs. In contrast, the magnetic circular dichroism of the Mg(2+)-bound DNA origami deviates from that of genomic DNA. Furthermore, the lanthanide affects the magnetic properties of DNA in a superstructure-dependent fashion, indicative of the existence of superstructure-specific geometry of Eu(3+) binding sites in the DNA origami that are not formed in genomic DNA. This simple approach lays the foundation for the generation of magneto-responsive DNA origami nanostructures. Such systems do not require covalent modifications and can be used for the magnetic manipulation of DNA nanostructures or for the paramagnetic alignment of molecules in NMR spectroscopy.
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Affiliation(s)
- Lars Opherden
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf , P.O.B. 510119, 01314 Dresden, Germany
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Petrovska I, Nüske E, Munder MC, Kulasegaran G, Malinovska L, Kroschwald S, Richter D, Fahmy K, Gibson K, Verbavatz JM, Alberti S. Filament formation by metabolic enzymes is a specific adaptation to an advanced state of cellular starvation. eLife 2014; 3:eLife.02409. [PMID: 24771766 PMCID: PMC4011332 DOI: 10.7554/elife.02409] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/10/2014] [Indexed: 01/20/2023] Open
Abstract
One of the key questions in biology is how the metabolism of a cell responds to changes in the environment. In budding yeast, starvation causes a drop in intracellular pH, but the functional role of this pH change is not well understood. Here, we show that the enzyme glutamine synthetase (Gln1) forms filaments at low pH and that filament formation leads to enzymatic inactivation. Filament formation by Gln1 is a highly cooperative process, strongly dependent on macromolecular crowding, and involves back-to-back stacking of cylindrical homo-decamers into filaments that associate laterally to form higher order fibrils. Other metabolic enzymes also assemble into filaments at low pH. Hence, we propose that filament formation is a general mechanism to inactivate and store key metabolic enzymes during a state of advanced cellular starvation. These findings have broad implications for understanding the interplay between nutritional stress, the metabolism and the physical organization of a cell.
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Affiliation(s)
- Ivana Petrovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Matthias C Munder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Liliana Malinovska
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sonja Kroschwald
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology, Helmholtz Institute Dresden-Rossendorf, Dresden, Germany
| | - Kimberley Gibson
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jean-Marc Verbavatz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Ander M, Subramaniam S, Fahmy K, Stewart AF, Schäffer E. A Single-Strand Annealing Protein Clamps DNA to Detect Homology. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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41
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Sayed A, Zhang Y, Fahmy K. Peptide-Based Approach to Study Cytosolic Domain Interactions in a Bacterial Copper-Transporting ATPase. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Abstract
While life requires water, many organisms, known as anhydrobiotes, can survive in the absence of water for extended periods of time. Although discovered 300 years ago, we know very little about the fascinating phenomenon of anhydrobiosis. In this paper, we summarize our previous findings on the desiccation tolerance of the Caenorhabditis elegans dauer larva. A special emphasis is given to the role of trehalose in protecting membranes against desiccation. We also propose a simple mechanism for this process.
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Affiliation(s)
- Cihan Erkut
- Max Planck Institute of Molecular Cell Biology and Genetics; Dresden, Germany
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44
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Lucks C, Rossberg A, Tsushima S, Foerstendorf H, Fahmy K, Bernhard G. Formic acid interaction with the uranyl(vi) ion: structural and photochemical characterization. Dalton Trans 2013; 42:13584-9. [DOI: 10.1039/c3dt51711j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Erkut C, Penkov S, Khesbak H, Vorkel D, Verbavatz JM, Fahmy K, Kurzchalia TV. Trehalose renders the dauer larva of Caenorhabditis elegans resistant to extreme desiccation. Curr Biol 2011; 21:1331-6. [PMID: 21782434 DOI: 10.1016/j.cub.2011.06.064] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 06/13/2011] [Accepted: 06/30/2011] [Indexed: 11/29/2022]
Abstract
Water is essential for life on Earth. In its absence, however, some organisms can interrupt their life cycle and temporarily enter an ametabolic state, known as anhydrobiosis [1]. It is assumed that sugars (in particular trehalose) are instrumental for survival under anhydrobiotic conditions [2]. However, the role of trehalose remained obscure because the corresponding evidence was purely correlative and based mostly on in vitro studies without any genetic manipulations of trehalose metabolism. In this study, we used C. elegans as a genetic model to investigate molecular mechanisms of anhydrobiosis. We show that the C. elegans dauer larva is a true anhydrobiote: under defined conditions it can survive even after losing 98% of its body water. This ability is correlated with a several fold increase in the amount of trehalose. Mutants unable to synthesize trehalose cannot survive even mild dehydration. Light and electron microscopy indicate that one of the major functions of trehalose is the preservation of membrane organization. Fourier-transform infrared spectroscopy of whole worms suggests that this is achieved by preserving homogeneous and compact packing of lipid acyl chains. By means of infrared spectroscopy, we can now distinguish a "dry, yet alive" larva from a "dry and dead" one.
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Affiliation(s)
- Cihan Erkut
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
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Barkleit A, Tsushima S, Savchuk O, Philipp J, Heim K, Acker M, Taut S, Fahmy K. Eu3+-Mediated Polymerization of Benzenetetracarboxylic Acid Studied by Spectroscopy, Temperature-Dependent Calorimetry, and Density Functional Theory. Inorg Chem 2011; 50:5451-9. [DOI: 10.1021/ic102292j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Astrid Barkleit
- Institute of Radiochemistry, Helmholtz-Zentrum Dresden-Rossendorf e.V., P.O. Box 510119, 01314 Dresden, Germany
- Division of Radiochemistry, Department of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany
| | - Satoru Tsushima
- Institute of Radiochemistry, Helmholtz-Zentrum Dresden-Rossendorf e.V., P.O. Box 510119, 01314 Dresden, Germany
| | - Olesya Savchuk
- Institute of Radiochemistry, Helmholtz-Zentrum Dresden-Rossendorf e.V., P.O. Box 510119, 01314 Dresden, Germany
| | - Jenny Philipp
- Institute of Radiochemistry, Helmholtz-Zentrum Dresden-Rossendorf e.V., P.O. Box 510119, 01314 Dresden, Germany
| | - Karsten Heim
- Institute of Radiochemistry, Helmholtz-Zentrum Dresden-Rossendorf e.V., P.O. Box 510119, 01314 Dresden, Germany
| | - Margret Acker
- Central Radionuclide Laboratory, Technische Universität Dresden, 01062 Dresden, Germany
| | - Steffen Taut
- Central Radionuclide Laboratory, Technische Universität Dresden, 01062 Dresden, Germany
| | - Karim Fahmy
- Institute of Radiochemistry, Helmholtz-Zentrum Dresden-Rossendorf e.V., P.O. Box 510119, 01314 Dresden, Germany
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Khesbak H, Savchuk O, Tsushima S, Fahmy K. The Role of Water H-Bond Imbalances in B-DNA Substate Transitions and Peptide Recognition Revealed by Time-Resolved FTIR Spectroscopy. J Am Chem Soc 2011; 133:5834-42. [DOI: 10.1021/ja108863v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Fahmy K, Siebert F, Tavan P. Structural investigation of bacteriorhodopsin and some of its photoproducts by polarized Fourier transform infrared spectroscopic methods-difference spectroscopy and photoselection. Biophys J 2010; 60:989-1001. [PMID: 19431812 DOI: 10.1016/s0006-3495(91)82136-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The direction of selected IR-transition moments of the retinal chromophore of bacteriorhodopsin (BR) and functional active amino acid residues are determined for light- and dark-adapted BR and for the intermediates K and L of the photocycle. Torsions around single bonds of the chromophore are found to be present in all the investigated BR states. The number of twisted single bonds and the magnitude of these torsions decreases in the order K, L, light-adapted BR, dark-adapted BR. In the last, only the C(14)-C(15) single bond is twisted. The orientation of molecular planes and chemical bonds of such protein side chains, which are perturbed during the transition of light-adapted BR to the respective intermediates, are deduced and the results compared with the current three dimensional model of BR. Trp 86 and Trp 185 are found to form a rigid part of the protein, whereas Asp 96 and Asp 115 perform molecular rearrangements upon formation of the L-intermediate.
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Affiliation(s)
- K Fahmy
- Institut für Biophysik und Strahlenbiologie der Universität Freiburg, Albertstrasse 23, D-7800 Freiburg i. Brsg
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50
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Tsushima S, Brendler V, Fahmy K. Aqueous coordination chemistry and photochemistry of uranyl(vi) oxalate revisited: a density functional theory study. Dalton Trans 2010; 39:10953-8. [DOI: 10.1039/c0dt00974a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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