Scientific publications

Background: Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorithms to estimate them. Here, we describe a methodology that calculates rates at which light-regulated proteins switch between conformational states. We focus our analysis on the phytochrome family of photoreceptors found in cyanobacteria, plants and many optogenetic tools. Phytochrome proteins change between active (P A) and inactive (P I) states at rates that are proportional to photoconversion cross-sections and influenced by light quality, light intensity, thermal reactions and dimerisation. This work presents a method that can accurately calculate these photoconversion cross-sections in the presence of multiple non-light regulated reactions. Results: Our approach to calculating the photoconversion cross-sections comprises three steps: i) calculate the thermal reversion reaction rate(s); ii) develop search spaces from which all possible sets of photoconversion cross-sections exist, and iii) estimate extinction coefficients that describe our absorption spectra. We confirm that the presented approach yields accurate results through the use of simulated test cases. Our test cases were further expanded to more realistic scenarios where noise, multiple thermal reactions and dimerisation are considered. Finally, we present the photoconversion cross-sections of an Arabidopsis phyB N-terminal fragment commonly used in optogenetic tools. Conclusions: The calculation of photoconversion cross-sections has implications for both photoreceptor and synthetic biologists. Our method allows, for the first time, direct comparisons of photoconversion cross-sections and response speeds of photoreceptors in different cellular environments and synthetic tools. Due to the generality of our procedure, as shown by the application to multiple test cases, the photoconversion cross-sections and quantum yields of any photoreceptor might now, in principle, be obtained. © 2016 The Author(s).

One key aspect of synthetic biology is the development and characterization of modular biological building blocks that can be assembled to construct integrated cell-based circuits performing computational functions. Likewise, the idea of extracting biological modules from the cellular context has led to the development of in vitro operating systems. This principle has attracted substantial interest to extend the repertoire of functional materials by connecting them with modules derived from synthetic biology. In this respect, synthetic biological switches and sensors, as well as biological targeting or structure modules, have been employed to upgrade functions of polymers and solid inorganic material. The resulting systems hold great promise for a variety of applications in diagnosis, tissue engineering, and drug delivery. This review reflects on the most recent developments and critically discusses challenges concerning in vivo functionality and tolerance that must be addressed to allow the future translation of such synthetic biology-upgraded materials from the bench to the bedside. © 2016 Elsevier B.V.

Bis(acetylacetonate)alumo-oxo-tetraphenyldisiloxane-metal(II) dihydrates [(acac)2Al(O–SiPh2–O–SiPh2–O)]2M(H2O)2 (M = Mg, Fe, Co, Ni) were obtained from the corresponding acetyl-acetonate-dihydrates (acac)2M(H2O)2 by reaction with the alumosiloxane [O–Ph2Si–O–SiPh2–O]4Al4(OH)4. These new compounds display two acac ligands at the aluminum atoms as well as disilatrioxy chains linking the two aluminum atoms forming a (Al–O–Si–O–Si–O)2 cycle (X-ray structure analyses). Within this cycle the divalent metal ions M2+, to which two water molecules in trans positions are linked, are installed in almost planar MO4 coordination spheres. Using water free (acac)2Ni a different product forms: both reactants combine in a 2:1 ratio to yield [O–Ph2Si–O–SiPh2–O]4Al4(OH)2O(OH2)Ni2(acac)4. Here, three of the acac ligands were transposed to the aluminum atoms. The nickel atoms are in a distorted octahedral coordination mode from oxygen atoms of the ligands. When iron(III)tris(acetylacetonate) reacts with the alumosiloxane [O–Ph2Si–O–SiPh2–O]3Al2O(OH)Fe2(acac)3 was isolated, in which the two iron atoms still display one of the acac ligands. One of the aluminum atoms is in a tetrahedral oxygen environment, whereas the other is in the center of a trigonal bi-pyramid formed of oxygen atoms either of the siloxane or of acac. The iron atoms have five- or sixfold coordination from oxygen atoms of siloxane, acac, hydroxide or oxide.

Glass coatings are of great interest for biomedical implant application due to their excellent properties. Nowadays they are used in different fields including drug delivery, for bone tissue regeneration or as implant. Nevertheless they can only be applied using high temperatures. Therefore their usage in the field of cardiovascular implant application is still restricted. Accordingly new developments in this field have been carried out to overcome this problem and to coat cardiovascular implants. Here, novel glass-like coatings have been developed and applied using sol-gel technique at moderate temperatures. The biocompatibility and selectivity have been analyzed using human endothelial cells. The obtained results clarify that the developed compositions can either promote or suppress endothelial cell growth only by altering the sintering atmosphere. A later application as thin layer on cardiovascular implants like stents is conceivable.

Porous polyethylene (Medpor®) is commonly used in craniofacial reconstructive surgery. Rapid vascularization and tissue incorporation are crucial for the prevention of migration, extrusion, and infection of the biomaterial. Therefore, we analyzed whether surface modification by plasma etching may improve the early tissue response to Medpor®. Medpor® samples were treated in a plasma chamber at low (20 W; LE-PE) and high energy levels (40 W; HE-PE). The samples and non-treated controls were implanted into mouse dorsal skinfold chambers to analyze angiogenesis, inflammation, and granulation tissue formation over 14 days using intravital fluorescence microscopy, histology, and immunohistochemistry. Scanning electron microscopy (SEM) analyses revealed that elevating energy levels of plasma etching progressively increase the oxygen surface content and surface roughness of Medpor®. This did not affect the leukocytic response to the implants. However, LE-PE and HE-PE samples exhibited an impaired vascularization. This was associated with a reduced formation of a collagen-rich granulation tissue at the implantation site. Additional in vitro experiments showed a reduced cell attachment on plasma-etched Medpor®. Thus, plasma etching may not be recommended to improve the clinical outcome of reconstructive interventions using Medpor®. However, it may be beneficial for temporarily implanted polyethylene-based biomedical devices for which tissue incorporation is undesirable.

Lithium aluminum hydride combined with different amounts of aluminum chloride react with cyclopentanol under the formation of compounds with aluminum-oxygen scaffolds and hydrogen or chlorine as terminating substituents at aluminum and cyclopentyl at the oxygen atoms. H6Al4(OC5H9)6 and Cl6Al4(OC5H9)6, both displaying a central aluminum atom almost octahedrally coordinated by oxygen atoms of the cyclopentanolates with three AlH2 or AlCl2 entities bridging three oxygen edges were isolated and fully characterized. The compound dihydrido aluminum cyclopentanolate was isolated together with chloro-hydrido aluminum cyclo-pentanolate as a 6:2 aggregate, [H2Al(OC5H9)]6[H(Cl)Al(OC5H9)]2, displaying alcoholate and hydride bridges in the crystal. Structural isomers of this compound were found in the solid. Mono-hydrides could be isolated in the form of H5Al5(O)(OC5H9)8*OC4H10 and in the form of a hydride/chloride H4.5Cl0.5Al5(O)(OC5H9)8*OC4H10, which is a 1:1 mixture of H5Al5(O)(OC5H9)8 with H4ClAl5(O)(OC5H9)8 in the crystal. In both compounds an oxygen atom is in the center of an Al5 square pyramid. While in the first case the aluminum atom situated at the top of the pyramid has a hydride ligand, in the second case the ligand is a chloride.

When the majority of efforts to control adhesion from surfaces currently focus on a direct modification of the surface, either chemically or physically, perhaps a non-superficial approach where the action occurs underneath the surface can provide a competitive alternative. In this comment we highlight a methodology used to control adhesion from flexible surfaces. This is based on 'semi-closed' flexible microfluidics systems. Three basic functionalities are derived from this methodology. In one case the system is used to improve adhesion; in an extreme opposite case to prevent adhesion and in a somehow intermediate functionality it provides a switchable system in which the surface can be reversibly changed from adhesive to non-adhesive.

Fluid catalytic cracking (FCC), which currently accounts for half of the worldwide petroleum refining efforts, relies on catalytic, aluminosilicate zeolite particles which slowly deactivate. As of yet, this FCC catalyst residue (FC3R) has no commercial outlet, resulting in abundant amounts of landfill-destined refuse. However, this overlooked waste has the right ingredients for the synthesis of some of today's emerging nanomaterials. High-carbon FC3R, sourced from a Uruguayan refinery, was identified as faujasite particles encased in graphitic carbon shells. We show that pulsed laser ablation of raw FC3R produces simultaneous deposition of single-wall carbon nanotubes and silica nanowires through vapour/solid-liquid-solid self-assembly in distinct zones of an oven-laser apparatus. This is an extreme revalorisation and provides a new untapped resource for research and applications in C- and Si-based nanomaterials and mesoscopic physics.

In-stent restenosis (ISR) is one of the most common and serious complications observed after stent implantation. ISR is characterized by the inordinate proliferation of smooth muscle cells (SMC) that leads to narrowing of the blood vessels. To achieve a healthy endothelium, it is critical to selectively enhance the growth of endothelial cells (EC) while suppressing the growth of smooth muscle cells, which is still a major challenge and yet to be achieved. In this study, novel surfaces have been developed to support the selective growth of endothelial cells. Micro- and nanostructured Al2O3 surfaces with unique topographical features were fabricated and tested. Surface characterization and cellular response of endothelial cells (HUVEC) as well as smooth muscle cells (HUVSMC) has been investigated at cellular and molecular levels. A topography driven selective cell response of ECs over SMCs was demonstrated successfully. This selective response of ECs was also analyzed at protein levels in order to understand the basic mechanism.