1,574 research outputs found
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 [] which are linearly unstable and develop a mound
structure whose typical size L increases in time (). If the local
slope () increases indefinitely, depends on the exponent
characterizing the large behaviour of the surface current (): for and for
.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), 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 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 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 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 in brain but positive
in LRS tissues, and one goat showed
biochemical and IHC features of PrP 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
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
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
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
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A facility to remotely assemble radioisotope thermoelectric generators
Radioisotope Thermoelectric Generators (RTGs) are electrical power sources that use heat from decaying radioisotopes to directly generate electrical power. The RTG assembly process is performed in an inert atmosphere inside a large glovebox, which is surrounded by radiation shielding to reduce exposure to neutron and gamma radiation from the radioisotope heat source. In the past, allowable dose rate limits have allowed direct, manual assembly methods; however, current dose rate limits require a thicker radiation shielding that makes direct, manual assembly infeasible. To minimize RTG assembly process modifications, telerobotic systems are being investigated to perform remote assembly tasks. Telerobotic systems duplicate human arm motion and incorporate force feedback sensitivity to handle objects and tools in a human-like manner. A telerobotic system with two arms and a three-dimensional (3-D) vision system can be used to perform remote RTG assembly tasks inside gloveboxes and cells using unmodified, normal hand tools
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