1,394 research outputs found
Pulling adsorbed polymers from surfaces with the AFM: stick versus slip, peeling versus gliding
We consider the response of an adsorbed polymer that is pulled by an AFM
within a simple geometric framework. We separately consider the cases of i)
fixed polymer-surface contact point, ii) sticky case where the polymer is
peeled off from the substrate, and iii) slippery case where the polymer glides
over the surface. The resultant behavior depends on the value of the surface
friction coefficient and the adsorption strength. Our resultant force profiles
in principle allow to extract both from non-equilibrium force-spectroscopic
data.Comment: 6 pages, 3 figures; accepted for publication in Europhys. Lett.,
http://www.edpsciences.org/journal/index.cfm?edpsname=ep
Meta-Prediction for Collective Classification
When data instances are inter-related, as are nodes in a social network or hyperlink graph, algorithms for collective classification (CC) can significantly improve accuracy. Recently, an algorithm for CC named Cautious ICA (ICAC) was shown to improve accuracy compared to the popular ICA algorithm. ICAC improves performance by initially favoring its more confident predictions during collective inference. In this paper, we introduce ICAMC, a new algorithm that outperforms ICAC when the attributes that describe each node are not highly predictive. ICAMC learns a meta-classifier that identifies which node label predictions are most likely to be correct. We show that this approach significantly increases accuracy on a range of real and synthetic data sets. We also describe new features for the meta-classifier and demonstrate that a simple search can identify an effective feature set that increases accuracy
Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein
Male-specific proteins have increasingly been reported as targets of positive selection and are of special interest because of the role they may play in the evolution of reproductive isolation. We report the rapid interspecific divergence of cDNA encoding a major acrosomal protein of unknown function (TMAP) of sperm from five species of teguline gastropods. A mitochondrial DNA clock (calibrated by congeneric species divided by the Isthmus of Panama) estimates that these five species diverged 2-10 MYA. Inferred amino acid sequences reveal a propeptide that has diverged rapidly between species. The mature protein has diverged faster still due to high nonsynonymous substitution rates (\u3e25 nonsynonymous substitutions per site per 109 years), cDNA encoding the mature protein (89-100 residues) shows evidence of positive selection (D(n)/D(s) \u3e 1) for 4 of 10 pairwise species comparisons. cDNA and predicted secondary-structure comparisons suggest that TMAP is neither orthologous nor paralogous to abalone lysin, and thus marks a second, phylogenetically independent, protein subject to strong positive selection in free-spawning marine gastropods. In addition, an internal repeat in one species (Tegula aureotincta) produces a duplicated cleavage site which results in two alternatively processed mature proteins differing by nine amino acid residues. Such alternative processing may provide a mechanism for introducing novel amino acid sequence variation at the amino-termini of proteins. Highly divergent TMAP N-termini from two other tegulines (Tegula regina and Norrisia norrisii) may have originated by such a mechanism
Diversity of olfactomedin proteins in the sea urchin
AbstractOlfactomedin (OLF) domain proteins maintain extracellular protein-protein interactions in diverse phyla. Only one OLF family member, amassin-1, has been described from the sea urchin Strongylocentrotus purpuratus, a basal invertebrate deuterostome. Amassin-1 mediates intercellular adhesion of coelomocytes (immunocytes). Here we describe the protein structural features of four additional OLF proteins, the total for the genome being five. Phylogenetically, four of these proteins (the amassins) form a subgroup among previously identified OLF proteins. The fifth OLF protein is within the colmedin subfamily and contains a type II transmembrane domain, collagen repeats, and an OLF domain. Sea urchin OLF proteins represent an intermediate diversification between protostomes and vertebrates. Transcripts of all five OLF family members are in coelomocytes and adult radial nerve tissue. Transcripts for some OLF proteins increase during late larval stages. Transcript levels for amassin-1 increase 1,000,000-fold, coinciding with formation of the adult urchin rudiment within the larval body
The steady state quantum statistics of a non-Markovian atom laser
We present a fully quantum mechanical treatment of a single-mode atomic
cavity with a pumping mechanism and an output coupling to a continuum of
external modes. This system is a schematic description of an atom laser. In the
dilute limit where atom-atom interactions are negligible, we have been able to
solve this model without making the Born and Markov approximations. When
coupling into free space, it is shown that for reasonable parameters there is a
bound state which does not disperse, which means that there is no steady state.
This bound state does not exist when gravity is included, and in that case the
system reaches a steady state. We develop equations of motion for the two-time
correlation in the presence of pumping and gravity in the output modes. We then
calculate the steady-state output energy flux from the laser.Comment: 14 pages (twocloumn), 6 figure
Confinement Effects on the Kinetics and Thermodynamics of Protein Dimerization
In the cell, protein complexes form relying on specific interactions between
their monomers. Excluded volume effects due to molecular crowding would lead to
correlations between molecules even without specific interactions. What is the
interplay of these effects in the crowded cellular environment? We study
dimerization of a model homodimer both when the mondimers are free or tethered
to each other. We consider a structured environment: Two monomers first diffuse
into a cavity of size and then fold and bind within the cavity. The folding
and binding are simulated using molecular dynamics based on a simplified
topology based model. The {\it confinement} in the cell is described by an
effective molecular concentration . A two-state coupled folding
and binding behavior is found. We show the maximal rate of dimerization
occurred at an effective molecular concentration M which is a
relevant cellular concentration. In contrast, for tethered chains the rate
keeps at a plateau when .
For both the free and tethered cases, the simulated variation of the rate of
dimerization and thermodynamic stability with effective molecular concentration
agrees well with experimental observations. In addition, a theoretical argument
for the effects of confinement on dimerization is also made
Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1''-phosphate dephosphorylation by a conserved domain of nsP3.
The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 A resolution. The structure of this "X" domain, seen in many single-stranded RNA viruses, reveals a three-layered alpha/beta/alpha core with a macro-H2A-like fold. The putative active site is a solvent-exposed cleft that is conserved in its three structural homologs, yeast Ymx7, Archeoglobus fulgidus AF1521, and Er58 from E. coli. Its sequence is similar to yeast YBR022W (also known as Poa1P), a known phosphatase that acts on ADP-ribose-1''-phosphate (Appr-1''-p). The SARS nsP3 domain readily removes the 1'' phosphate group from Appr-1''-p in in vitro assays, confirming its phosphatase activity. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1''-p
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A moderate increase in dietary zinc reduces DNA strand breaks in leukocytes and alters plasma proteins without changing plasma zinc concentrations.
BackgroundFood fortification has been recommended to improve a population's micronutrient status. Biofortification techniques modestly elevate the zinc content of cereals, but few studies have reported a positive impact on functional indicators of zinc status.ObjectiveWe determined the impact of a modest increase in dietary zinc that was similar to that provided by biofortification programs on whole-body and cellular indicators of zinc status.DesignEighteen men participated in a 6-wk controlled consumption study of a low-zinc, rice-based diet. The diet contained 6 mg Zn/d for 2 wk and was followed by 10 mg Zn/d for 4 wk. To reduce zinc absorption, phytate was added to the diet during the initial period. Indicators of zinc homeostasis, including total absorbed zinc (TAZ), the exchangeable zinc pool (EZP), plasma and cellular zinc concentrations, zinc transporter gene expression, and other metabolic indicators (i.e., DNA damage, inflammation, and oxidative stress), were measured before and after each dietary-zinc period.ResultsTAZ increased with increased dietary zinc, but plasma zinc concentrations and EZP size were unchanged. Erythrocyte and leukocyte zinc concentrations and zinc transporter expressions were not altered. However, leukocyte DNA strand breaks decreased with increased dietary zinc, and the level of proteins involved in DNA repair and antioxidant and immune functions were restored after the dietary-zinc increase.ConclusionsA moderate 4-mg/d increase in dietary zinc, similar to that which would be expected from zinc-biofortified crops, improves zinc absorption but does not alter plasma zinc. The repair of DNA strand breaks improves, as do serum protein concentrations that are associated with the DNA repair process. This trial was registered at clinicaltrials.gov as NCT02861352
Methods of Preparing Three-Dimensional, Macroscopic Assemblages of Carbon Fibrils and the Products Obtained Thereby
A method of making randomly oriented carbons fibrils having a cylindrical constant diameter with c-axes perpendicular to their cylindrical axis, which are free of pyrolytically deposited carbon, with a diameter of between 3.5 and 70 nanometers, by dispersing carbon fibrils in a medium and separating them from the medium, by filtration or evaporation to form a porous mat or sheet
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