485 research outputs found
Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
A new theoretical survey of proteins' resistance to constant speed stretching
is performed for a set of 17 134 proteins as described by a structure-based
model. The proteins selected have no gaps in their structure determination and
consist of no more than 250 amino acids. Our previous studies have dealt with
7510 proteins of no more than 150 amino acids. The proteins are ranked
according to the strength of the resistance. Most of the predicted top-strength
proteins have not yet been studied experimentally. Architectures and folds
which are likely to yield large forces are identified. New types of potent
force clamps are discovered. They involve disulphide bridges and, in
particular, cysteine slipknots. An effective energy parameter of the model is
estimated by comparing the theoretical data on characteristic forces to the
corresponding experimental values combined with an extrapolation of the
theoretical data to the experimental pulling speeds. These studies provide
guidance for future experiments on single molecule manipulation and should lead
to selection of proteins for applications. A new class of proteins, involving
cystein slipknots, is identified as one that is expected to lead to the
strongest force clamps known. This class is characterized through molecular
dynamics simulations.Comment: 40 pages, 13 PostScript figure
Computational design of a homotrimeric metalloprotein with a trisbipyridyl core
Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2'-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala)3]2+ complexes at the interface between monomers. X-ray crystallographic analysis of the homotrimer showed that the design process had near-atomic-level accuracy: The all-atom rmsd between the design model and crystal structure for the residues at the protein interface is âŒ1.4 Ă
. These results demonstrate that computational protein design together with genetically encoded noncanonical amino acids can be used to drive formation of precisely specified metal-mediated protein assemblies that could find use in a wide range of photophysical applications.</p
Floristic analysis of a high-speed railway embankment in a Mediterranean landscape
We analyzed the floristic composition of a 4.5 km-long segment of a high-speed railway in Lazio, central Italy, which travels on an artificial embankment through an intensively-farmed landscape. In total, 287 vascular plant species were recorded. The life-form distribution was found to be similar to that of the regional species pool, with high percentages of therophytes (38%) and phanerophytes (13%). In the chorological spectrum the Mediterranean floristic element prevailed (44%), while alien species were 8% of the flora. The phytosociological spectrum showed a high diversity of characteristic species from the class Stellarietea mediae or its subordinate syntaxa (26%), and in particular from the order Thero-Brometalia (Mediterranean, sub-nitrophilous annual communities). Species from forest syntaxa had a relatively high diversity (9%). These results suggest that the ecological filtering provided by the Mediterranean regional climate controlled species assemblage even in a completely artificial habitat, preventing floristic homogenization: the flora of the studied railway section is only partially »ruderalized«, while it keeps strong links with the regional (semi-) natural plant communities. However, in contrast to what is observed in central and north Europe, the railway sides studied in the present paper do not seem to represent a refugial habitat for rare species from grassland communities, mainly because in Italy semi-natural dry grasslands are still widely represented
Factors Associated with HIV/AIDS Diagnostic Disclosure to HIV Infected Children Receiving HAART: A Multi-Center Study in Addis Ababa, Ethiopia
BACKGROUND: Diagnostic disclosure of HIV/AIDS to a child is becoming an increasingly common issue in clinical practice. Nevertheless, some parents and health care professionals are reluctant to inform children about their HIV infection status. The objective of this study was to identify the proportion of children who have knowledge of their serostatus and factors associated with disclosure in HIV-infected children receiving HAART in Addis Ababa, Ethiopia. METHODS: A cross-sectional study was conducted in five hospitals in Addis Ababa from February 18, 2008-April 28, 2008. The study populations were parents/caretakers and children living with HIV/AIDS who were receiving Highly Active Antiretroviral Therapy (HAART) in selected hospitals in Addis Ababa. Univariate and multivariate logistic regression analysis were carried out using SPSS 12.0.1 statistical software. RESULTS: A total of 390 children/caretaker pairs were included in the study. Two hundred forty three children (62.3%) were between 6-9 years of age. HIV/AIDS status was known by 68 (17.4%) children, 93 (29%) caretakers reported knowing the child's serostatus two years prior to our survey, 180 (46.2%) respondents said that the child should be told about his/her HIV/AIDS status when he/she is older than 14 years of age. Children less than 9 years of age and those living with educated caregivers are less likely to know their results than their counterparts. Children referred from hospital's in-patient ward before attending the HIV clinic and private clinic were more likely to know their results than those from community clinic. CONCLUSION: The proportion of disclosure of HIV/AIDS diagnosis to HIV-infected children is low. Strengthening referral linkage and health education tailored to educated caregivers are recommended to increase the rate of disclosure
Isotopic, geophysical and biogeochemical investigation of submarine groundwater discharge : IAEA-UNESCO intercomparison exercise at Mauritius Island
Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Environmental Radioactivity 104 (2012): 24-45, doi:10.1016/j.jenvrad.2011.09.009.Submarine groundwater discharge (SGD) into a shallow lagoon on the west coast of Mauritius Island (Flic-en-Flac) was
investigated using radioactive (3H, 222Rn, 223Ra, 224Ra, 226Ra, 228Ra) and stable (2H, 18O) isotopes and nutrients. SGD
intercomparison exercises were carried out to validate the various approaches used to measure SGD including radium and radon
measurements, seepage-rate measurements using manual and automated meters, sediment bulk conductivity and salinity surveys.
SGD measurements using benthic chambers placed on the floor of the Flic-en-Flac Lagoon showed discharge rates up to 500
cm/day. Large variability in SGD was observed over distances of a few meters, which were attributed to different
geomorphological features. Deployments of automated seepage meters captured the spatial and temporal variability of SGD with
a mean seepage rate of 10 cm/day. The stable isotopic composition of submarine waters was characterized by significant
variability and heavy isotope enrichment and was used to predict the contribution of fresh terrestrially derived groundwater to
SGD (range from a few % to almost 100 %). The integrated SGD flux, estimated from seepage meters placed parallel to the
shoreline, was 35 m3/m day, which was in a reasonable agreement with results obtained from hydrologic water balance
calculation (26 m3/m day). SGD calculated from the radon inventory method using in situ radon measurements were between 5
and 56 m3/m per day. Low concentrations of radium isotopes observed in the lagoon water reflected the low abundance of U and
Th in the basalt that makes up the island. High SGD rates contribute to high nutrients loading to the lagoon, potentially leading to
eutrophication. Each of the applied methods yielded unique information about the character and magnitude of SGD. The results
of the intercomparison studies have resulted a better understanding of groundwater-seawater interactions in coastal regions. Such
information is an important pre-requisite for the protection management of coastal freshwater resources.The
financial support provided by the IOC and IHP of UNESCO for travel arrangements, and by the IAEAâs Marine
Environment Laboratories for logistics is highly acknowledged. MAC and MEG were supported in part by the US
National Science Foundation (OCE-0425061 and OCE-0751525). PPP acknowledges a support provided by the EU
Research & Development Operational Program funded by the ERDF (project No. 26240220004), and the Slovak
Scientific Agency VEGA (grant No. 1/108/08). The International Atomic Energy Agency is grateful to the
Government of the Principality of Monaco for support provided to its Marine Environment Laboratories
Correlations among biodiversity, biomass and other plant community parameters using the phytosociological approach: A case study from the south-eastern Alps
The present study deals with the grassland complex of communities which may be found on the limestones in the southeastern
Alps; these communities show in fact a particular interest for their high biodiversity degree and for their importance
for the traditional land-use economy of the south-European mountain regions. Phytosociological releveÂŽs corresponding to
well-defined plant associations have been used in order to get information on the relationships among plant species diversity,
biomass, chorotypes, pollination types, functional strategies and soil characteristics. The analysis was carried out both along
an altitudinal and a soil evolution gradient. The analysis of the correlations among the variables and the application of the
principal component analysis shows a positive correlation between soil parameters and biomass, eurichory, anemogamy and
C- and R-strategies; on the contrary, a negative correlation among stenochory, entomogamy and S-strategy with the soil
evolution seems to be present. This article shows how the phytosociological approach can be used to get information and
knowledge on the correlations between several variables useful to understand the complex nature of the plant communities in
order to support management plans
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