SwissPKcdw - A clinical data warehouse for the optimization of pediatric dosing regimens.

Clinical trials have been performed mainly in adults and accordingly the necessary information is lacking for pediatric patients, especially regarding dosage recommendation for approved drugs. This gap in information could be filled with results from pharmacokinetic (PK) modeling, based on data collected in daily clinical routine. In order to make this data accessible and usable for research, the Swiss Pharmacokinetics Clinical Data Warehouse (SwissPKcdw ) project has been set up, including a clinical data warehouse (CDW) and the regulatory framework for data transfer and use within. Embedded into the secure BioMedIT network, the CDW can connect to various data providers and researchers in order to collaborate on the data securely. Due to its modularity, partially containerized deployment and open-source software, each of the components can be extended, modified, and re-used for similar projects that require integrated data management, data analysis, and web tools in a secure scientific data and information technology (IT) environment. Here, we describe a collaborative and interprofessional effort to implement the aforementioned infrastructure between several partners from medical health care and academia. Furthermore, we describe a real-world use case where blood samples from pediatric patients were analyzed for the presence of genetic polymorphisms and the results were aggregated and further analyzed together with the health-related patient data in the SwissPKcdw .

Oxidative stress-associated shape transformation and membrane proteome remodeling in erythrocytes of end stage renal disease patients on hemodialysis.

This study was designed to evaluate the oxidative stress status of erythrocytes and its association with cellular ultrastructure and membrane proteome modifications in patients with end stage renal disease (ESRD) on hemodialysis (HD). For that purpose, we studied red blood cells' (RBCs) modifications in twelve non-diabetic ESRD patients that were responsive in erythropoietin therapy. Intracellular ROS levels were measured by fluorometry, RBCs ultra-structure was examined by electron microscopy, while the membrane proteome by electrophoresis and immunoblotting. Compared to the healthy subjects, the uremic RBCs exhibited significantly increased ROS accumulation. Dialysis partially ameliorated the basal ROS levels but triggered cellular sensitivity to exogenous oxidative stimuli. Common membrane modifications involved loss, aggregation, fragmentation and carbonylation of critical components as well as over-expression of stress markers. HD significantly contributed to membrane proteome remodeling, especially for aquaporin-1, peroxiredoxin-2 and ubiquitinated proteins. The intracellular redox status and the closely associated membrane modifications seemed to be related to membrane instability, loss of surface area through vesiculation, echinocytosis and stomatocytosis. Our data evinced a network of interactions among the uremic toxins, the RBCs membrane composition and the cellular shape modifications in ESRD, which is developed around a core of oxidative provocations and cellular responses.

Near-UV circular dichroism reveals structural transitions of vimentin subunits during intermediate filament assembly.

In vitro assembly of vimentin intermediate filaments (IFs) proceeds from soluble, reconstituted tetrameric complexes to mature filaments in three distinct stages: (1) within the first seconds after initiation of assembly, tetramers laterally associate into unit-length filaments (ULFs), on average 17 nm wide; (2) for the next few minutes, ULFs grow by longitudinal annealing into short, immature filaments; (3) almost concomitant with elongation, these immature filaments begin to radially compact, yielding approximately 11-nm-wide IFs at around 15 min. The near-UV CD signal of soluble tetramers exhibits two main peaks at 285 and 278 nm, which do not change during ULF formation. In contrast, the CD signal of mature IFs exhibits two major changes: (1) the 278-nm band, denoting the transition of the tyrosines from the ground state to the first vibrational mode of the excited state, is lost; (2) a red-shifted band appears at 291 nm, indicating the emergence of a new electronic species. These changes take place independently and at different time scales. The 278-nm signal disappears within the first minute of assembly, compatible with increased rigidity of the tyrosines during elongation of the ULFs. The rise of the 291-nm band has a lifetime of approximately 13 min and denotes the generation of phenolates by deprotonation of the tyrosines' hydroxyl group after they relocalize into a negatively charged environment. The appearance of such tyrosine-binding "pockets" in the assembling filaments highlights an essential part of the molecular rearrangements characterizing the later stages of the assembly process, including the radial compaction.

Understanding the changes in the circular dichroism of light harvesting complex II upon varying its pigment composition and organization.

In this work we modeled the circular dichroism (CD) spectrum of LHCII, the main light harvesting antenna of photosystem II of higher plants. Excitonic calculations are performed for a monomeric subunit, taken from the crystal structure of trimeric LHCII from spinach [Liu, Z. F., Yan, H. C., Wang, K. B., Kuang, T. Y., Zhang, J. P., Gui, L. L., An, X. M., and Chang, W. R. (2004) Nature 428, 287-292]. All of the major features of the CD spectrum above 450 nm are satisfactorily reproduced, and possible orientations of the Chl and carotenoid transition dipole moments are identified. The obtained modeling parameters are used to simulate the CD spectra of two complexes with altered pigment composition: a mutant lacking Chls a 611-612 and a complex lacking the carotenoid neoxanthin. By removing the relevant pigment(s) from the structure, we are able to reproduce their spectra, which implies that the alteration does not disturb the overall structure. The CD spectrum of trimeric LHCII shows a reversed relative intensity of the two negative bands around 470 and 490 nm as compared to monomeric LHCII. The simulations reproduce this reversal, indicating that it is mainly due to interactions between chromophores in different monomeric subunits, and the trimerization does not induce observable changes in the monomeric structure. Our simulated spectrum resembles one of two different trimeric CD spectra reported in literature. We argue that the differences in the experimental trimeric CD spectra are caused by changes in the strength of the monomer-monomer interactions due to the differences in detergents used for the purification of the complexes.

Explaining the visible and near-infrared circular dichroism spectra of light-harvesting 1 complexes from purple bacteria: a modeling study.

In this work, we investigate the origin and characteristics of the circular dichroism (CD) spectrum of various light-harvesting 1 (LH1) complexes. The near-infrared (NIR) CD signal of these core antennae is strongly nonconservative, and the nature of this nonconservativity is under examination in this paper. So far, on the basis of the high-resolution structures of LH2, we have been able to model the absorption and CD spectra in the bacteriochlorophyll (BChl) Q(Y) and Q(X) regions of LH2 (Georgakopoulou et al., Biophys. J. 2002, 82, 2184-2197), as well as in the carotenoid region (Georgakopoulou et al., Biophys. J. 2004, 87, 3010-3022). We proceed by applying the same modeling method in order to reproduce the LH1 spectra. We assume a ring of dimers in a perfect circular arrangement with 16-fold symmetry, and account for all excitonic interactions within the ring. Because LH1 complexes exhibit Q(Y) and Q(X) CD signals of very low intensity, higher transitions can easily affect these regions. Therefore, we expand the model and take into account also the Soret and carotenoid transitions. We can now understand the shape of the absorption and CD spectra and contemplate the structure of the LH1 complex. The latter is similar to LH2 in that it is a very symmetric ring dominated by excitonic interactions. The larger number of symmetry and the bigger diameter of LH1, combined with small rotations of the BChl transition dipole moments, are responsible for the display of CD signals that are very low in intensity. The interaction of the Q(Y) with the carotenoid transitions results in complete loss of the conservativity. Interaction energies between all the pigments in the ring are calculated, and their values are in good accordance with what is reported in the literature.

Investigation of the effects of different carotenoids on the absorption and CD signals of light harvesting 1 complexes.

Absorption and circular dichroism (CD) spectra of light-harvesting (LH)1 complexes from the purple bacteria Rhodobacter (Rba.) sphaeroides and Rhodospirillum (Rsp.) rubrum are presented. The complexes exhibit very low intensity, highly nonconservative, near-infrared (NIR) CD spectra. Absorption and CD spectra from several mutant and reconstituted LH1 complexes, with the carotenoid neurosporene and the precursor phytoene replacing the wild-type (WT) carotenoids, are also examined. The experiments show that the position of the carotenoid bands as well as the bacteriochlorophyll (BChl)/carotenoid ratio affect the NIR CD spectra: bluer bands and larger ratios make the NIR CD signal more conservative. Modeling results that support this finding are presented. This study, combined with the theoretical approach of the companion paper, where modeling of such complexes is presented and discussed in detail, provide a complete explanation of the origin of the nonconservative NIR CD spectra of LH1 and B820.

Investigations of intermediates appearing in the reassociation of the light-harvesting 1 complex of Rhodospirillum rubrum.

We investigated the temperature-mediated reassociation of the B820 subunit of Rs. rubrum to form a light-harvesting 1 complex (LH 1). By combining several spectroscopic techniques with global spectral data analysis fitting, we present evidence for the occurence of two spectral intermediates that appear during the reassociation process. At high temperatures, halfway the reassociation reaction, a prominent intermediate appears that has an absorption maximum around 850 nm, a fluorescence maximum around 860-867 nm, a high anisotropy (0.3 to 0.4) and a circular dichroism spectrum with three or four bands with alternating signs. At lower temperatures, more towards the end of the reassociation process, a second intermediate tends to appear that has an absorption maximum around 860 nm, a fluorescence maximum around 885 nm, a medium to high anisotropy (0.1 to 0.3) and a circular dichroism spectrum with two bands with alternating signs. The latter circular dichroism spectrum has a blueshifted zero-crossing compared to the spectrum of the LH 1 complex. Both intermediates have the spectroscopic features of a small oligomer. In the Q(y) region, the fluorescence anisotropy of both intermediates slightly increases at longer excitation wavelengths, indicative for energy transfer among the pigments within the intermediate oligomers.

Absorption and CD spectroscopy and modeling of various LH2 complexes from purple bacteria.

The absorption (OD) and circular dichroism (CD) spectra of LH2 complexes from various purple bacteria have been measured and modeled. Based on the lineshapes of the spectra we can sort the LH2 complexes into two distinguishable groups: "acidophila"-like (type 1) and "molischianum"-like (type 2). Starting from the known geometric structures of Rhodopseudomonas (Rps.) acidophila and Rhodospirillum (Rsp.) molischianum we can model the OD and CD spectra of all species by just slightly varying some key parameters: the interaction strength, the energy difference of alpha- and beta-bound B850 bacteriochlorophylls (BChls), the orientation of the B800 and B850 BChls, and the (in)homogeneous broadening. Although the ring size can vary, the data are consistent with all the LH2 complexes having basically very similar structures.