Deer mouse hemoglobin exhibits a lowered oxygen affinity owing to mobility of the E helix

The deer mouse, Peromyscus maniculatus, exhibits altitude-associated variation in hemoglobin oxygen affinity. To examine the structural basis of this functional variation, the structure of the hemoglobin was solved. Recombinant hemoglobin was expressed in Escherichia coli and was purified by ion-exchange chromatography. Recombinant hemoglobin was crystallized by the hangingdrop vapor-diffusion method using polyethylene glycol as a precipitant. The obtained orthorhombic crystal contained two subunits in the asymmetric unit. The refined structure was interpreted as the aquo-met form. Structural comparisons were performed among hemoglobins from deer mouse, house mouse and human. In contrast to human hemoglobin, deer mouse hemoglobin lacks the hydrogen bond between α1Trp14 in the A helix and α1Thr67 in the E helix owing to the Thr67Ala substitution. In addition, deer mouse hemoglobin has a unique hydrogen bond at the α1β1 interface between residues α1Cys34 and β1Ser128

Aggregation Patterns in Stressed Bacteria

We study the formation of spot patterns seen in a variety of bacterial species when the bacteria are subjected to oxidative stress due to hazardous byproducts of respiration. Our approach consists of coupling the cell density field to a chemoattractant concentration as well as to nutrient and waste fields. The latter serves as a triggering field for emission of chemoattractant. Important elements in the proposed model include the propagation of a front of motile bacteria radially outward form an initial site, a Turing instability of the uniformly dense state and a reduction of motility for cells sufficiently far behind the front. The wide variety of patterns seen in the experiments is explained as being due the variation of the details of the initiation of the chemoattractant emission as well as the transition to a non-motile phase.Comment: 4 pages, REVTeX with 4 postscript figures (uuencoded) Figures 1a and 1b are available from the authors; paper submitted to PRL

Adaptive online deployment for resource constrained mobile smart clients

Nowadays mobile devices are more and more used as a platform for applications. Contrary to prior generation handheld devices configured with a predefined set of applications, today leading edge devices provide a platform for flexible and customized application deployment. However, these applications have to deal with the limitations (e.g. CPU speed, memory) of these mobile devices and thus cannot handle complex tasks. In order to cope with the handheld limitations and the ever changing device context (e.g. network connections, remaining battery time, etc.) we present a middleware solution that dynamically offloads parts of the software to the most appropriate server. Without a priori knowledge of the application, the optimal deployment is calculated, that lowers the cpu usage at the mobile client, whilst keeping the used bandwidth minimal. The information needed to calculate this optimum is gathered on the fly from runtime information. Experimental results show that the proposed solution enables effective execution of complex applications in a constrained environment. Moreover, we demonstrate that the overhead from the middleware components is below 2%

The mechanistic basis of hemoglobin adaptation in the high-flying barheaded goose: insights from ancestral protein resurrection

The bar-headed goose (‘BHG’, Anser indicus) is renowned for its trans-Himalayan migratory flights, and the elevated hemoglobin (Hb)-O2 affinity of this species is thought to make a key contribution to its capacity for powered flight at elevations of ~9000 m. Here we revisit the molecular basis of this text-book example of biochemical adaptation. Previous hypotheses about the molecular basis of the evolved increase in Hb-O2 affinity were tested by engineering BHGspecific mutations into recombinant human Hb. This approach can provide important insights, but one problem with such ‘horizontal’ comparisons – swapping residues between proteins of contemporary species – is that the focal mutations are introduced into a sequence context that may not be evolutionarily relevant. If mutations have context-dependent effects, then introducing BHG-specific substitutions into human Hb may not recapitulate the functional effects of causative mutations on the genetic background in which they actually occurred during evolution (i.e., in the BHG ancestor). An alternative ‘vertical’ approach is to reconstruct and resurrect ancestral proteins to test the effects of historical mutations on the genetic background in which they actually occurred. We used this approach to measure the independent and joint effects of amino acid substitutions that occurred in the reconstructed BHG ancestor. Measuring the additive and nonadditive effects of these substitutions enabled us to address several important evolutionary questions about molecular adaptation: (1) Do each of the substitutions contribute to the increased Hb-O2 affinity? If so, what are their relative effects? (2) Does the sequential order in which they occur make a difference? In other words, do the functional effects of mutations depend on which other substitutions have already occurred

Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

Epistatic interactions between mutant sites in the same protein can exert a strong influence on pathways of molecular evolution. We performed protein engineering experiments that revealed pervasive epistasis among segregating amino acid variants that contribute to adaptive functional variation in deer mouse hemoglobin (Hb). Amino acid mutations increased or decreased Hb-O2 affinity depending on the allelic state of other sites. Structural analysis revealed that epistasis for Hb-O2 affinity and allosteric regulatory control is attributable to indirect interactions between structurally remote sites. The prevalence of sign epistasis for fitness-related biochemical phenotypes has important implications for the evolutionary dynamics of protein polymorphism in natural populations

The mechanistic basis of hemoglobin adaptation in the high-flying barheaded goose: insights from ancestral protein resurrection

The bar-headed goose (‘BHG’, Anser indicus) is renowned for its trans-Himalayan migratory flights, and the elevated hemoglobin (Hb)-O2 affinity of this species is thought to make a key contribution to its capacity for powered flight at elevations of ~9000 m. Here we revisit the molecular basis of this text-book example of biochemical adaptation. Previous hypotheses about the molecular basis of the evolved increase in Hb-O2 affinity were tested by engineering BHGspecific mutations into recombinant human Hb. This approach can provide important insights, but one problem with such ‘horizontal’ comparisons – swapping residues between proteins of contemporary species – is that the focal mutations are introduced into a sequence context that may not be evolutionarily relevant. If mutations have context-dependent effects, then introducing BHG-specific substitutions into human Hb may not recapitulate the functional effects of causative mutations on the genetic background in which they actually occurred during evolution (i.e., in the BHG ancestor). An alternative ‘vertical’ approach is to reconstruct and resurrect ancestral proteins to test the effects of historical mutations on the genetic background in which they actually occurred. We used this approach to measure the independent and joint effects of amino acid substitutions that occurred in the reconstructed BHG ancestor. Measuring the additive and nonadditive effects of these substitutions enabled us to address several important evolutionary questions about molecular adaptation: (1) Do each of the substitutions contribute to the increased Hb-O2 affinity? If so, what are their relative effects? (2) Does the sequential order in which they occur make a difference? In other words, do the functional effects of mutations depend on which other substitutions have already occurred

The simplicity project: easing the burden of using complex and heterogeneous ICT devices and services

As of today, to exploit the variety of different "services", users need to configure each of their devices by using different procedures and need to explicitly select among heterogeneous access technologies and protocols. In addition to that, users are authenticated and charged by different means. The lack of implicit human computer interaction, context-awareness and standardisation places an enormous burden of complexity on the shoulders of the final users. The IST-Simplicity project aims at leveraging such problems by: i) automatically creating and customizing a user communication space; ii) adapting services to user terminal characteristics and to users preferences; iii) orchestrating network capabilities. The aim of this paper is to present the technical framework of the IST-Simplicity project. This paper is a thorough analysis and qualitative evaluation of the different technologies, standards and works presented in the literature related to the Simplicity system to be developed

Predictable convergence in hemoglobin function has unpredictable molecular underpinnings

To investigate the predictability of genetic adaptation, we examined the molecular basis of convergence in hemoglobin function in comparisons involving 56 avian taxa that have contrasting altitudinal range limits. Convergent increases in hemoglobin-oxygen affinity were pervasive among high-altitude taxa, but few such changes were attributable to parallel amino acid substitutions at key residues.Thus, predictable changes in biochemical phenotype do not have a predictable molecular basis. Experiments involving resurrected ancestral proteins revealed that historical substitutions have context-dependent effects, indicating that possible adaptive solutions are contingent on prior history. Mutations that produce an adaptive change in one species may represent precluded possibilities in other species because of differences in genetic background

Predictable convergence in hemoglobin function has unpredictable molecular underpinnings

To investigate the predictability of genetic adaptation, we examined the molecular basis of convergence in hemoglobin function in comparisons involving 56 avian taxa that have contrasting altitudinal range limits. Convergent increases in hemoglobin-oxygen affinity were pervasive among high-altitude taxa, but few such changes were attributable to parallel amino acid substitutions at key residues.Thus, predictable changes in biochemical phenotype do not have a predictable molecular basis. Experiments involving resurrected ancestral proteins revealed that historical substitutions have context-dependent effects, indicating that possible adaptive solutions are contingent on prior history. Mutations that produce an adaptive change in one species may represent precluded possibilities in other species because of differences in genetic background

Sub-nanosecond signal propagation in anisotropy engineered nanomagnetic logic chains

Energy efficient nanomagnetic logic (NML) computing architectures propagate and process binary information by relying on dipolar field coupling to reorient closely-spaced nanoscale magnets. Signal propagation in nanomagnet chains of various sizes, shapes, and magnetic orientations has been previously characterized by static magnetic imaging experiments with low-speed adiabatic operation; however the mechanisms which determine the final state and their reproducibility over millions of cycles in high-speed operation (sub-ns time scale) have yet to be experimentally investigated. Monitoring NML operation at its ultimate intrinsic speed reveals features undetectable by conventional static imaging including individual nanomagnetic switching events and systematic error nucleation during signal propagation. Here, we present a new study of NML operation in a high speed regime at fast repetition rates. We perform direct imaging of digital signal propagation in permalloy nanomagnet chains with varying degrees of shape-engineered biaxial anisotropy using full-field magnetic soft x-ray transmission microscopy after applying single nanosecond magnetic field pulses. Further, we use time-resolved magnetic photo-emission electron microscopy to evaluate the sub-nanosecond dipolar coupling signal propagation dynamics in optimized chains with 100 ps time resolution as they are cycled with nanosecond field pulses at a rate of 3 MHz. An intrinsic switching time of 100 ps per magnet is observed. These experiments, and accompanying macro-spin and micromagnetic simulations, reveal the underlying physics of NML architectures repetitively operated on nanosecond timescales and identify relevant engineering parameters to optimize performance and reliability.Comment: Main article (22 pages, 4 figures), Supplementary info (11 pages, 5 sections