Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data

BACKGROUND: Over the past decade our laboratory has focused on understanding how soluble cytoskeleton-associated proteins interact with membranes and other lipid aggregates. Many protein domains mediating specific cell membrane interactions appear by fluorescence microscopy and other precision techniques to be partially inserted into the lipid bilayer. It is unclear whether these protein-lipid-interactions are dependent on shared protein motifs or unique regional physiochemistry, or are due to more global characteristics of the protein. RESULTS: We have developed a novel computational program that predicts a protein's lipid-binding site(s) from primary sequence data. Hydrophobic labeling, Fourier transform infrared spectroscopy (FTIR), film balance, T-jump, CD spectroscopy and calorimetry experiments confirm that the interfaces predicted for several key cytoskeletal proteins (alpha-actinin, Arp2, CapZ, talin and vinculin) partially insert into lipid aggregates. The validity of these predictions is supported by an analysis of the available three-dimensional structural data. The lipid interfaces predicted by our algorithm generally contain energetically favorable secondary structures (e.g., an amphipathic alpha-helix flanked by a flexible hinge or loop region), are solvent-exposed in the intact protein, and possess favorable local or global electrostatic properties. CONCLUSION: At present, there are few reliable methods to determine the region of a protein that mediates biologically important interactions with lipids or lipid aggregates. Our matrix-based algorithm predicts lipid interaction sites that are consistent with the available biochemical and structural data. To determine whether these sites are indeed correctly identified, and whether use of the algorithm can be safely extended to other classes of proteins, will require further mapping of these sites, including genetic manipulation and/or targeted crystallography

Coarsening in surface growth models without slope selection

We study conserved models of crystal growth in one dimension [$\partial_t z(x,t) =-\partial_x j(x,t)$] which are linearly unstable and develop a mound structure whose typical size L increases in time ($L = t^n$). If the local slope ($m =\partial_x z$) increases indefinitely, $n$ depends on the exponent $\gamma$ characterizing the large $m$ behaviour of the surface current $j$ ($j = 1/|m|^\gamma$): $n=1/4$ for $1< \gamma <3$ and $n=(1+\gamma)/(1+5\gamma)$ for $\gamma>3$.Comment: 7 pages, 2 EPS figures. To be published in J. Phys. A (Letter to the Editor

High prevalence of scrapie in a dairy goat herd: tissue distribution of disease-associated PrP and effect of PRNP genotype and age

Following a severe outbreak of clinical scrapie in 2006–2007, a large dairy goat herd was culled and 200 animals were selected for post-mortem examinations in order to ascertain the prevalence of infection, the effect of age, breed and PRNP genotype on the susceptibility to scrapie, the tissue distribution of diseaseassociated PrP (PrP$^{\rm d}$), and the comparative efficiency of different diagnostic methods. As determined by immunohistochemical (IHC) examinations with Bar224 PrP antibody, the prevalence of preclinical infection was very high (72/200; 36.0%), with most infected animals being positive for PrP$^{\rm d}$ in lymphoreticular system (LRS) tissues (68/72; 94.4%) compared to those that were positive in brain samples (38/72; 52.8%). The retropharyngeal lymph node and the palatine tonsil showed the highest frequency of PrP$^{\rm d}$ accumulation (87.3% and 84.5%, respectively), while the recto-anal mucosa-associated lymphoid tissue (RAMALT) was positive in only 30 (41.7%) of the infected goats. However, the efficiency of rectal and palatine tonsil biopsies taken shortly before necropsy was similar. The probability of brain and RAMALT being positive directly correlated with the spread of PrP$^{\rm d}$ within the LRS. The prevalence of infection was influenced by PRNP genetics at codon 142 and by the age of the goats: methionine carriers older than 60 months showed a much lower prevalence of infection (12/78; 15.4%) than those younger than 60 months (20/42; 47.6%); these last showed prevalence values similar to isoleucine homozygotes of any age (40/80; 50.0%). Two of seven goats with definite signs of scrapie were negative for PrP$^{\rm d}$ in brain but positive in LRS tissues, and one goat showed biochemical and IHC features of PrP$^{\rm d}$ different from all other infected goats. The results of this study have implications for surveillance and control policies for scrapie in goats

Electron mean free path from angle-dependent photoelectron spectroscopy of aerosol particles

We propose angle-resolved photoelectron spectroscopy of aerosol particles as an alternative way to determine the electron mean free path of low energy electrons in solid and liquid materials. The mean free path is obtained from fits of simulated photoemission images to experimental ones over a broad range of different aerosol particle sizes. The principal advantage of the aerosol approach is twofold. Firstly, aerosol photoemission studies can be performed for many different materials, including liquids. Secondly, the size-dependent anisotropy of the photoelectrons can be exploited in addition to size-dependent changes in their kinetic energy. These finite size effects depend in different ways on the mean free path and thus provide more information on the mean free path than corresponding liquid jet, thin film, or bulk data. The present contribution is a proof of principle employing a simple model for the photoemission of electrons and preliminary experimental data for potassium chloride aerosol particles

Table Detection in Invoice Documents by Graph Neural Networks

This is the author accepted manuscript. The final version is available from IEEE via the DOI in this record.Tabular structures in documents offer a complementary dimension to the raw textual data, representing logical or quantitative relationships among pieces of information. In digital mail room applications, where a large amount of administrative documents must be processed with reasonable accuracy, the detection and interpretation of tables is crucial. Table recognition has gained interest in document image analysis, in particular in unconstrained formats (absence of rule lines, unknown information of rows and columns). In this work, we propose a graph-based approach for detecting tables in document images. Instead of using the raw content (recognized text), we make use of the location, context and content type, thus it is purely a structure perception approach, not dependent on the language and the quality of the text reading. Our framework makes use of Graph Neural Networks (GNNs) in order to describe the local repetitive structural information of tables in invoice documents. Our proposed model has been experimentally validated in two invoice datasets and achieved encouraging results. Additionally, due to the scarcity of benchmark datasets for this task, we have contributed to the community a novel dataset derived from the RVL-CDIP invoice data. It will be publicly released to facilitate future research.European Unio

INTERACTION OF RESEARCH AND SUBJECTS IN SOCIAL INTERVENTION STUDIES

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74684/1/j.1749-6632.1973.tb47621.x.pd

Influence of Hydrodynamic Interactions on the Adsorption Process of Large Particles

We have studied the adsorption process of non-Brownian particles on a line incorporating hydrodynamic interactionsa and we have numerically analyzed their effect on typical relevant quantities. We compare our model to the ballistic deposition model (BM) and address the limitations of BM in experimental situations. The results obtained can explain some differences observed between recent experiments and BM predictions.Comment: 10 pages, LaTeX. 4 Figures upon reques

Experimental Bovine Spongiform Encephalopathy in Squirrel Monkeys:The Same Complex Proteinopathy Appearing after Very Different Incubation Times

Incubation periods in humans infected with transmissible spongiform encephalopathy (TSE) agents can exceed 50 years. In humans infected with bovine spongiform encephalopathy (BSE) agents, the effects of a “species barrier,” often observed when TSE infections are transmitted from one species to another, would be expected to increase incubation periods compared with transmissions of same infectious agents within the same species. As part of a long-term study investigating the susceptibility to BSE of cell cultures used to produce vaccines, we inoculated squirrel monkeys (Saimiri sp., here designated SQ) with serial dilutions of a bovine brain suspension containing the BSE agent and monitored them for as long as ten years. Previously, we showed that SQ infected with the original “classical” BSE agent (SQ-BSE) developed a neurological disease resembling that seen in humans with variant CJD (vCJD). Here, we report the final characterization of the SQ-BSE model. We observed an unexpectedly marked difference in incubation times between two animals inoculated with the same dilution and volume of the same C-BSE bovine brain extract on the same day. SQ-BSE developed, in addition to spongiform changes and astrogliosis typical of TSEs, a complex proteinopathy with severe accumulations of protease-resistant prion protein (PrP(TSE)), hyperphosphorylated tau (p-tau), ubiquitin, and α-synuclein, but without any amyloid plaques or β-amyloid protein (Aβ) typical of Alzheimer’s disease. These results suggest that PrP(TSE) enhanced the accumulation of several key proteins characteristically seen in human neurodegenerative diseases. The marked variation in incubation periods in the same experimental TSE should be taken into account when modeling the epidemiology of human TSEs

Do bioresorbable polyesters have antimicrobial properties?

Biodegradable and bioresorbable polyesters (BBPEs) are a widespread class of aliphatic polymers with a plethora of applications in the medical field. Some reports speculate that these polymers have intrinsic antibacterial activity as a consequence of their acidic degradation by-products. The release of organic acids as a result of the hydrolytic degradation of BBPEs in vivo and the resulting pH drop could be an effective inhibitor of the growth of pathogens in the local environment adjacent to BBPE-based devices. However, there is no clear and conclusive evidence in the literature concerning the antibacterial activity of BBPE to support or refute this hypothesis. In this communication we address this point through an assessment of the antibacterial properties of six well-established commercially available BBPEs. Agar diffusion assays and optical density measurements at 600 nm were performed on all the polymer samples to characterize the growth of bacteria and any potential inhibition over an incubation period of 24 h. The results indicated that BBPEs do not possess an intrinsic and immediate antibacterial activity, which is consistent with the clear mismatch between the time-scales for bacterial growth and the rate of degradation of the polyesters

Lifetime of d-holes at Cu surfaces: Theory and experiment

We have investigated the hole dynamics at copper surfaces by high-resolution angle-resolved photoemission experiments and many-body quasiparticle GW calculations. Large deviations from a free-electron-like picture are observed both in the magnitude and the energy dependence of the lifetimes, with a clear indication that holes exhibit longer lifetimes than electrons with the same excitation energy. Our calculations show that the small overlap of d- and sp-states below the Fermi level is responsible for the observed enhancement. Although there is qualitative good agreement of our theoretical predictions and the measured lifetimes, there still exist some discrepancies pointing to the need of a better description of the actual band structure of the solid.Comment: 15 pages, 7 figures, 1 table, to appear in Phys. Rev.