We developed a computer-aided analysis tool for quantitatively determining bioluminescent reporter distributions inside small animals. The core innovations are a body-fitting animal shuttle and a ...statistical mouse atlas, both of which are spatially aligned and scaled according to the animal's weight, and hence provide data congruency across animals of varying size and pose. In conjunction with a multispectral bioluminescence tomography technique capitalizing on the spatial framework of the shuttle, the in vivo biodistribution of luminescent reporters can rapidly be calculated and, thus, enables operator-independent and computer-driven data analysis. We demonstrate its functionality by quantitatively monitoring a bacterial infection, where the bacterial organ burden was determined and validated with the established serial-plating method. In addition, the statistical mouse atlas was validated and compared to existing techniques providing an anatomical reference. The proposed data analysis tool promises to increase data throughput and data reproducibility and accelerate human disease modeling in mice.
2Struc: the secondary structure server Klose, D. P.; Wallace, B. A.; Janes, Robert W.
Bioinformatics,
2010-Oct-15, Letnik:
26, Številka:
20
Journal Article
Recenzirano
Odprti dostop
The defined secondary structure of proteins method is often considered the gold standard for assignment of secondary structure from three-dimensional coordinates. However, there are alternative ...methods. ‘2Struc: The Secondary Structure Server’ has been created as a single point of access for eight different secondary structure assignment methods. It has been designed to enable comparisons between methods for analyzing the secondary structure content for a single protein. It also includes a second functionality, ‘Compare-the-Protein’ to enable comparisons of the secondary structure features from any one method to be made within a collection of nuclear magnetic resonance models, or between the crystal structures of two different proteins. Availability: http://2struc.cryst.bbk.ac.uk Contact: r.w.janes@qmul.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
In this work, we demonstrate the validity of the simplified spherical harmonics equations to approximate the more complicated equation of radiative transfer for modeling light propagation in ...biological tissue. We derive the simplified spherical harmonics equations up to order
N
=
7 for anisotropic scattering and partially reflective boundary conditions. We compare numerical results with diffusion and discrete ordinates transport solutions. We find that the simplified spherical harmonics methods significantly improve the diffusion solution in transport-like domains with high absorption and small geometries, and are computationally less expensive than the discrete ordinates transport method. For example, the simplified
P
3 method is approximately two orders of magnitude faster than the discrete ordinates transport method, but only 2.5 times computationally more demanding than the diffusion method. We conclude that the simplified spherical harmonics methods can accurately model light propagation in small tissue geometries at visible and near-infrared wavelengths, yielding transport-like solutions with only a fraction of the computational cost of the transport calculation.
We present the first tomographic reconstruction algorithm for optical molecular imaging that is based on the equation of radiative transfer. The reconstruction code recovers the spatial distribution ...of fluorescent sources in highly scattering biological tissue. An objective function, which describes the discrepancy of measured near-infrared light with predicted numerical data on the tissue surface, is iteratively minimized to find a solution of the inverse source problem. At each iteration step the predicted data are calculated by a forward model for light propagation based on the equation of radiative transfer. The unknown source distribution is updated along a search direction that is provided by an adjoint differentiation technique.
This note serves as an introduction to two papers by Klose et al.
2,3 and provides a brief review of the latest developments in optical tomography of scattering tissue. We discuss advancements made ...in solving the forward model for light propagation based on the radiative transfer equation, in reconstructing scattering and absorption cross sections of tissue, and in molecular imaging of luminescent sources.
Different types of ibuprofen- and lidocaine-loaded, poly(lactic-co-glycolic acid) (PLGA)-based microparticles and thin, free films of various dimensions were prepared and physico-chemically ...characterized in vitro. The obtained experimental results were analyzed using mathematical theories based on Fick's second law of diffusion. Importantly, the initial drug loadings were low in all cases (4%, w/w), simplifying the mathematical treatment and minimizing potential effects of the acidic/basic nature of the two model drugs on polymer degradation. Interestingly, the type of drug and device geometry strongly affected the resulting release kinetics and relative importance of the involved mass transport mechanisms. For instance, the relative release rate was almost unaffected by the system size in the case of spherical microparticles, but strongly depended on the thickness of thin, free films, irrespective of the type of drug. Ibuprofen and lidocaine release was found to be primarily diffusion controlled from the investigated PLGA-based microparticles for all system sizes, whereas diffusion was only dominant in the case of the thinnest free films. Interestingly, the type of drug did not significantly affect the resulting polymer degradation kinetics. However, ibuprofen release was always much faster than lidocaine release for all system geometries and sizes. This can probably be attributed to attractive ionic interactions between protonated, positively charged lidocaine ions and negatively charged, deprotonated carboxylic end groups of PLGA, hindering drug diffusion. The determined apparent diffusion coefficients of the drugs clearly point out that the mobility of an active agent in PLGA-based delivery systems does not only depend on its own physico-chemical properties and the type of PLGA used, but also to a large extent on the size and shape of the device. This has to be carefully taken into account when developing/optimizing this type of advanced drug delivery systems.
Porous, poly(lactic-
co-glycolic acid) (PLGA)-based microparticles were prepared using a water-in-oil-in-water (W/O/W) solvent extraction/evaporation technique. Lidocaine was used as a model drug and ...different-sized particle fractions were obtained by sieving. The physicochemical properties of the devices and changes thereof upon exposure to phosphate buffer pH 7.4 were studied using optical and scanning electron microscopy, size exclusion chromatography (SEC), differential scanning calorimetry (DSC), gravimetric analysis and in vitro drug release measurements. In contrast to non-porous microparticles of identical composition, the relative drug release rate was found to decrease with increasing system size. SEC, DSC and gravimetric analysis showed that the degradation rate of the polymer increased with increasing microparticle dimension, indicating that autocatalytic effects play an important role even in small and highly porous PLGA-based microparticles. However, these effects were much less pronounced than in non-porous devices. Importantly, they were overcompensated by the effects of the increasing diffusion pathway lengths with increasing system dimension. Thus, high initial microparticle porosities do not only lead to increased drug mobilities, but can also fundamentally alter the underlying mass transport mechanisms.
Animal models recapitulating COVID-19 are critical to enhance our understanding of SARS-CoV-2 pathogenesis. Intranasally inoculated transgenic mice expressing human angiotensin-converting enzyme 2 ...under the cytokeratin 18 promoter (K18-hACE2) represent a lethal model of SARS-CoV-2 infection. We evaluated the clinical and virological dynamics of SARS-CoV-2 using two intranasal doses (10
and 10
PFUs), with a detailed spatiotemporal pathologic analysis of the 10
dose cohort. Despite generally mild-to-moderate pneumonia, clinical decline resulting in euthanasia or death was commonly associated with hypothermia and viral neurodissemination independent of inoculation dose. Neuroinvasion was first observed at 4 days post-infection, initially restricted to the olfactory bulb suggesting axonal transport via the olfactory neuroepithelium as the earliest portal of entry. Absence of viremia suggests neuroinvasion occurs independently of transport across the blood-brain barrier. SARS-CoV-2 tropism was neither restricted to ACE2-expressing cells (e.g., AT1 pneumocytes), nor inclusive of some ACE2-positive cell lineages (e.g., bronchiolar epithelium and brain vasculature). Absence of detectable ACE2 protein expression in neurons but overexpression in neuroepithelium suggest this as the most likely portal of neuroinvasion, with subsequent ACE2 independent lethal neurodissemination. A paucity of epidemiological data and contradicting evidence for neuroinvasion and neurodissemination in humans call into question the translational relevance of this model.
The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their ...associated experimental metadata. All entries undergo validation and curation procedures to ensure completeness, consistency and quality of the data included. A web-based interface enables users to browse and query sample types, sample conditions, experimental parameters and provides spectra in both graphical display format and as downloadable text files. The entries are linked, when appropriate, to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional classification database and the CATH fold classification database, as well as to literature citations. The PCDDB is available at: http://pcddb.cryst.bbk.ac.uk.
Determining distributed exchange couplings is important for understanding the properties of synthetic magnetic molecules. Such distributions can be determined from pulsed dipolar spectroscopy (PDS) ...data, but this is challenging due to the similar influence of both exchange and dipolar couplings on such data. In this work we introduce two models that aim to identify these two contributions to the spin-spin couplings from frequency-domain PDS data of shape-persistent molecules having either two Cu(
ii
) ions, or a Cu(
ii
) ion and a nitroxide radical as the paramagnetic moieties. The first model assumes correlated Lorentzian or Gaussian exchange and dipole-dipole coupling distributions whose parameters are the model's unknowns. The second model relies on prior knowledge of the distance distribution and by performing Tikhonov regularization along the exchange coupling dimension yields the latter distribution model-free. Both models were able to differentiate between the absence and the presence of exchange interaction, to determine the coupling regime (ferro- or antiferromagnetic) and to estimate the distribution shape. In contrast, calculations within the exchange resilient model of the neural network analysis implemented in DeerAnalysis2018 were not able for our data to identify exchange couplings and return correct distance distributions. However, the generic model was able to identify and separate the strongly curved intermolecular background in the relaxation-induced dipolar modulation enhancement (RIDME) experiments. Our analysis revealed that in such systems exchange coupling may be present up to at least 3.3 nm in π-conjugated systems involving Cu(
ii
)-PyMTA, while it is negligible for distances
r
≥ 4.5 nm between Cu(
ii
) ions and
r
≥ 3.8 nm between a Cu(
ii
) ion and an unpaired electron of a nitroxide radical. Disruption of the π-conjugation between the ligand of the Cu(
ii
) complex and the nitroxide leads to negligible exchange coupling at distances
r
≥ 2.6 nm in the corresponding Cu(
ii
)-TAHA-nitroxide ruler. Overall, for cases with known distance distributions, the presented analysis techniques allow to determine distributions of exchange couplings from PDS data.
Novel approaches to quantitatively analyse distributed exchange couplings are described and tested on experimental data sets for stiff synthetic molecules.
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