Mild-to-wild plastic transition is governed by athermal screw dislocation slip in bcc Nb.

Plastic deformation in crystals is mediated by the motion of line defects known as dislocations. For decades, dislocation activity has been treated as a homogeneous, smooth continuous process. However, it is now recognized that plasticity can be determined by long-range correlated and intermittent collective dislocation processes, known as avalanches. Here we demonstrate in body-centered cubic Nb how the long-range and scale-free dynamics at room temperature are progressively quenched out with decreasing temperature, eventually revealing intermittency with a characteristic length scale that approaches the Burgers vector itself. Plasticity is shown to be bimodal across the studied temperature regime, with conventional thermally-activated smooth plastic flow ('mild') coexisting with sporadic bursts ('wild') controlled by athermal screw dislocation activity, thereby violating the classical notion of temperature-dependent screw dislocation motion at low temperatures. An abrupt increase of the athermal avalanche component is identified at the critical temperature of the material. Our results indicate that plasticity at any scale can be understood in terms of the coexistence of these mild and wild modes of deformation, which could help design better alloys by suppressing one of the two modes in desired temperature windows.

An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water.

Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.

Favorable adsorption of capped amino acids on graphene substrate driven by desolvation effect.

The use of graphene-based nanomaterials is being explored in the context of various biomedical applications. Here, we performed a molecular dynamics simulation of individual amino acids on graphene utilizing an empirical force field potential (Amber03). The accuracy of our force field method was verified by modeling the adsorption of amino acids on graphene in vacuum. These results are in excellent agreement with those calculated using ab initio methods. Our study shows that graphene exhibits bioactive properties in spite of the fact that the interaction between graphene and amino acids in a water environment is significantly weaker as compared to that in vacuum. Furthermore, the adsorption characteristics of capped and uncapped amino acids are significantly different from each other due to the desolvation effect. Finally, we conclude that when assessing protein-surface interactions based on adsorption of single amino acids, the minimum requirement is to use capped amino acids as they mimic residues as part of a peptide chain.

Modelling survival and allele complementation in the evolution of genomes with polymorphic loci.

We have simulated the evolution of sexually reproducing populations composed of individuals represented by diploid genomes. A series of eight bits formed an allele occupying one of 128 loci of one haploid genome (chromosome). The environment required a specific activity of each locus, this being the sum of the activities of both alleles located at the corresponding loci on two chromosomes. This activity is represented by the number of bits set to zero. In a constant environment the best fitted individuals were homozygous with alleles' activities corresponding to half of the environment requirement for a locus (in diploid genome two alleles at corresponding loci produced a proper activity). Changing the environment under a relatively low recombination rate promotes generation of more polymorphic alleles. In the heterozygous loci, alleles of different activities complement each other fulfilling the environment requirements. Nevertheless, the genetic pool of populations evolves in the direction of a very restricted number of complementing haplotypes and a fast changing environment kills the population. If simulations start with all loci heterozygous, they stay heterozygous for a long time.

The penna model of biological aging.

This review deals with computer simulation of biological aging, particularly with the Penna model of 1995. They are based on the mutation accumulation theory of half a century ago. The results agree well with demographical reality, and also with the seemingly contradictory influence of predators on the aging of prey.

Simple bit-string model for lineage branching.

We introduce a population dynamics model, where individual genomes are represented by bit strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die, keeping the population constant. An offspring has the same genome as its (randomly chosen) parent, except for a small amount of (also random) mutations. Chance may thus generate a newborn with a genome that is better than that of its parent, and the newborn will have a smaller death probability. When this happens, this individual is a would-be founder of a new lineage. A new lineage is considered created if the number of its live descendants grows above a certain previously defined threshold. The time evolution of populations evolving under these rules is followed by computer simulations and the probability densities of lineage duration and size, among others, are computed. These densities show a scale-free behavior, in accordance with some conjectures in paleoevolution, and suggesting a simple mechanism as explanation for the ubiquity of these power laws.

Social effects in simple computer model of aging.

A simple evolutionary model for biological aging is modified such that it requires a minimum population for survival, like in human society. This social effect leads to a transition between extinction and survival of the species.

CHMP1 is a novel nuclear matrix protein affecting chromatin structure and cell-cycle progression.

The Polycomb-group (PcG) is a diverse set of proteins required for maintenance of gene silencing during development. In a screen for conserved partners of the PcG protein Polycomblike (Pcl), we have identified a new protein, human CHMP1 (CHromatin Modifying Protein; CHarged Multivesicular body Protein), which is encoded by an alternative open reading frame in the PRSM1 gene and is conserved in both complex and simple eukaryotes. CHMP1 contains a predicted bipartite nuclear localization signal and distributes as distinct forms to the cytoplasm and the nuclear matrix in all cell lines tested. We have constructed a stable HEK293 cell line that inducibly overexpresses CHMP1 under ecdysone control. Overexpressed CHMP1 localizes to a punctate subnuclear pattern, encapsulating regions of nuclease-resistant, condensed chromatin. These novel structures are also frequently surrounded by increased histone H3 phosphorylation and acetylation. CHMP1 can recruit a PcG protein, BMI1, to these regions of condensed chromatin and can cooperate with co-expressed vertebrate Pcl in a Xenopus embryo PcG assay; this is consistent with a role in PcG function. In combination, these observations suggest that CHMP1 plays a role in stable gene silencing within the nucleus.

CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins.

A multivesicular body is a vesicle-filled endosome that targets proteins to the interior of lysosomes. We have identified a conserved eukaryotic protein, human CHMP1, which is strongly implicated in multivesicular body formation. Immunocytochemistry and biochemical fractionation localize CHMP1 to early endosomes and CHMP1 physically interacts with SKD1/VPS4, a highly conserved protein directly linked to multivesicular body sorting in yeast. Similar to the action of a mutant SKD1 protein, overexpression of a fusion derivative of human CHMP1 dilates endosomal compartments and disrupts the normal distribution of several endosomal markers. Genetic studies in Saccharomyces cerevisiae further support a conserved role of CHMP1 in vesicle trafficking. Deletion of CHM1, the budding yeast homolog of CHMP1, results in defective sorting of carboxypeptidases S and Y and produces abnormal, multi-lamellar prevacuolar compartments. This phenotype classifies CHM1 as a member of the class E vacuolar protein sorting genes. Yeast Chm1p belongs to a structurally-related, but rather divergent family of proteins, including Vps24p and Snf7p and three novel proteins, Chm2p, Chm5p and Chm6p, which are all essential for multivesicular body sorting. These observations identify the conserved CHMP/Chmp family as a set of proteins fundamental to understanding multivesicular body sorting in eukaryotic organisms.

Genetic characterization of a large, historically significant Utah kindred with facioscapulohumeral dystrophy.

In 1950, Tyler and Stephens reported a remarkable kindred affected with facioscapulohumeral dystrophy (FSHD), consisting of 1249 descendants of a man who emigrated to Utah in 1840. Members of this kindred are still seen in our clinic and, to our knowledge, no member had been tested for deletions at the FSHD1A locus on chromosome 4q35, the common chromosomal rearrangement associated with FSHD. We have identified 971 additional members of this kindred who either were not included in or unborn at the time of the report by Tyler and Stephens, and have identified 120 living members as affected by history or by examination. Members of this kindred contribute to a disease prevalence of nearly 1:15 000 in the Utah/southern Idaho region. We have demonstrated that affected members carry a disease-associated 20 kb deletion allele at the FSHD1A locus. This allele is the same size in multiple, distantly-related branches of the kindred, confirming the meiotic stability of the FSHD1A deletion. This large, genetically homogeneous population of patients represents a unique resource with which to study current questions about FSHD, including the possibilities of anticipation and parental transmission effects.

Spin domains generate hierarchical ground state structure in J = +/-1 spin glasses.

Unbiased samples of ground states were generated for the short-range Ising spin glass with J(ij) = +/-1, in three dimensions. Clustering the ground states revealed their hierarchical structure, which is explained by correlated spin domains, serving as cores for macroscopic zero energy "excitations."

Computer simulations for biological aging and sexual reproduction.

The sexual version of the Penna model of biological aging, simulated since 1996, is compared here with alternative forms of reproduction as well as with models not involving aging. In particular we want to check how sexual forms of life could have evolved and won over earlier asexual forms hundreds of million years ago. This computer model is based on the mutation-accumulation theory of aging, using bits-strings to represent the genome. Its population dynamics is studied by Monte Carlo methods.

C-terminal interaction is essential for surface trafficking but not for heteromeric assembly of GABA(b) receptors.

Assembly of fully functional GABA(B) receptors requires heteromerization of the GABA(B(1)) and GABA(B(2)) subunits. It is thought that GABA(B(1)) and GABA(B(2)) undergo coiled-coil dimerization in their cytoplasmic C termini and that assembly is necessary to overcome GABA(B(1)) retention in the endoplasmatic reticulum (ER). We investigated the mechanism underlying GABA(B(1)) trafficking to the cell surface. We identified a signal, RSRR, proximal to the coiled-coil domain of GABA(B(1)) that when deleted or mutagenized allows for surface delivery in the absence of GABA(B(2)). A similar motif, RXR, was recently shown to function as an ER retention/retrieval (ERR/R) signal in K(ATP) channels, demonstrating that G-protein-coupled receptors (GPCRs) and ion channels use common mechanisms to control surface trafficking. A C-terminal fragment of GABA(B(2)) is able to mask the RSRR signal and to direct the GABA(B(1)) monomer to the cell surface, where it is functionally inert. This indicates that in the heteromer, GABA(B(2)) participates in coupling to the G-protein. Mutagenesis of the C-terminal coiled-coil domains in GABA(B(1)) and GABA(B(2)) supports the possibility that their interaction is involved in shielding the ERR/R signal. However, assembly of heteromeric GABA(B) receptors is possible in the absence of the C-terminal domains, indicating that coiled-coil interaction is not necessary for function. Rather than guaranteeing heterodimerization, as previously assumed, the coiled-coil structure appears to be important for export of the receptor complex from the secretory apparatus.

A novel site on the Galpha -protein that recognizes heptahelical receptors.

Specific domains of the G-protein alpha subunit have been shown to control coupling to heptahelical receptors. The extreme N and C termini and a region between alpha4 and alpha5 helices of the G-protein alpha subunit are known to determine selective interaction with the receptors. The metabotropic glutamate receptor 2 activated both mouse Galpha(15) and its human homologue Galpha(16), whereas metabotropic glutamate receptor 8 activated Galpha(15) only. The extreme C-terminal 20 amino acid residues are identical between the Galpha(15) and Galpha(16) and are therefore unlikely to be involved in coupling selectivity. Our data reveal two regions on Galpha(16) that inhibit its coupling to metabotropic glutamate receptor 8. On a three-dimensional model, both regions are found in a close proximity to the extreme C terminus of Galpha(16). One module comprises alpha4 helix, alpha4-beta6 loop (L9 Loop), beta6 sheet, and alpha5 helix. The other, not described previously, is located within the loop that links the N-terminal alpha helix to the beta1 strand of the Ras-like domain of the alpha subunit. Coupling of Galpha(16) protein to the metabotropic glutamate receptor 8 is partially modulated by each module alone, whereas both modules are needed to eliminate the coupling fully.

Protein isoaspartyl methyltransferase protects from Bax-induced apoptosis.

Protein L-isoaspartyl methyltransferase (Pimt) is a highly conserved enzyme utilising S-adenosylmethionine (AdoMet) to methylate aspartate residues of proteins damaged by age-related isomerisation and deamidation. We have been particularly interested in this enzyme since addition of the compound CGP3466 to primary rat astroglia cell cultures resulted in an upregulation of Pimt at the mRNA level, as shown here by semi-quantitative RT-PCR. CGP3466 is a compound related to the anti-Parkinson's drug R-(-)-deprenyl, which has been shown to protect from neural apoptosis induced by trophic factor withdrawal [Tatton et al., 1994. J. Neurochem. 63, 1572]. The pro-apoptotic gene Bax is required in the cascade of events following withdrawal [Deckwerth et al., 1996. Neuron 17, 401]. We therefore investigated whether Pimt overexpression was able to affect Bax-induced apoptosis in primary mouse cortical neurons. Our results show that Pimt is indeed able to protect from Bax-induced apoptosis. Furthermore, this activity is not restricted to brain-specific cell types, since the same effect is also demonstrated in COS1 cells. In addition, mutational analysis suggests that the protective effect is dependent on the adenosine methionine-binding motif, which is well conserved in protein methyltransferases, and that a mutation destroying this motif crucially affects cytoskeletal structures of the cell.

Unknown identification using reference mass spectra. Quality evaluation of databases.

The high success of the "uncertified" mass spectrometry spectral collection started in 1956 demonstrated qualitatively that a partial reference mass spectrum, even one measured routinely, can be of real value. Correct matchings were still possible despite reference errors, which almost never led to close matches that were incorrect. This study shows quantitatively that the number of different compounds, not the number of peaks in a spectrum, is by far the most important determinant of database efficiency for identifying a "global" unknown. A statistical evaluation of matching performance shows that only 6, 12, and 18 peaks in a reference spectrum are 13%, 67%, and 96%, respectively, as valuable as hundreds of peaks. Also, a separately measured second spectrum of the same compound is 50% as valuable as the first. Database expansion that tripled the number of possible wrong answers only reduced the proportion of correct identifications by 5%. Corrections of a mass or abundance error in each of six reference spectra increase the database matching performance by as much as the addition of one spectrum of a new compound. A new "matching quality index" based statistically on these values indicates that the largest database is also by far the most effective for matching unknowns.

The chimpanzee as a model of human benign prostatic hyperplasia.

PURPOSE: The etiology and natural history of benign prostatic hyperplasia (BPH), the most common benign disease in aging men, remain obscure. The canine BPH model has serious limitations but other animal BPH models have not been identified. We evaluated whether the chimpanzee, man's closest primate relative, developed spontaneous BPH. MATERIALS AND METHODS: A cross-sectional analysis of a colony (White Sands Research Center) that contained 700 chimpanzees was undertaken by sampling 63 male and female (controls) chimpanzees 8 to 35 years old. The presence of spontaneous BPH was evaluated by assessing pathological and clinical variables, including prostate volume, serum prostate specific antigen, presence of histological BPH, serum androgens and estradiol, and urodynamics studies. RESULTS: The chimpanzee had evidence of spontaneous histological BPH, and incidence and grade increased with age. Spontaneous BPH was manifested by increased prostate volume, higher serum prostate specific antigen, higher stromal/epithelial ratio and decreased urinary flow rates. As in man, serum androgens did not correlate with BPH in the chimpanzee. CONCLUSIONS: Male chimpanzees developed spontaneous histological BPH at the same relative point in their life cycle as humans which resulted clinically in larger prostates and decreased urinary flow rates. Serum hormone levels did not appear to correlate with BPH. A better understanding of the chimpanzee BPH model may lead to new therapeutic strategies for BPH in man.

Fragmentation of percolation clusters in general dimensions.

The scaling behavior for binary fragmentation of critical percolation clusters in general dimensions is investigated by Monte Carlo simulation as well as by exact series expansions. We obtain values of critical exponents lambda and phi describing the scaling of the fragmentation rate and the distribution of cluster masses produced by binary fragmentation. Our results for lambda and phi in two to nine dimensions agree with the conjectured scaling relation sigma=1+lambda-phi by Edwards and co-workers [Phys. Rev. Lett. 68, 2692 (1992); Phys. Rev. A 46, 6252 (1992)], which in turn excludes the other scaling relations suggested by Gouyet (for d=2), and by Roux and Guyon [J. Phys. A 22, 3693 (1989)], where sigma is the crossover exponent for the cluster numbers in percolation theory.

Periodicity-dependent stiffness of periodic hydrophilic-hydrophobic heteropolymers.

From extensive Monte Carlo simulations of a Larson model of perfectly periodic heteropolymers (PHP) in water, a striking stiffening is observed as the period of the alternating hydrophobic and hydrophilic blocks is shortened. At short period and low temperature needlelike conformations are the stable conformations. As temperature is increased thermal fluctuations induce kinks and bends. At large periods compact oligomeric globules are observed. From the generalized Larson prescription, originally developed for modeling surfactant molecules in aqueous solutions, we find that the shorter the period is the more stretched the PHP is. This novel effect is expected to stimulate polymer synthesis and trigger research on the rheology of aqueous periodic heteropolymer solutions.