Calorimetric investigation of the protein-flexible chain polymer interactions and its relationship with protein partition in aqueous two-phase systems

The binding of polyethyleneglycol of molecular mass 1000, 3300 and 6000 and polyethylene-propylene oxide (molecular mass 8400) to lysozyme and ovoalbumin was measured by isothermal calorimetric titration. A binding process was found to be associated with a saturation effect, which suggests a protein-polymer interaction. The proteins showed an affinity for the polymers in the order of 10(2)M(-1) and it decreased with the increase in the polymer molecular mass. The number of polymer molecules bound per protein molecule varied from 0.01 to 0.2 for polyethyleneglycol 1000, 3300 and polyethylene-polypolypropylene oxide 8400, while for polyethyleneglycol 6000 such number got closer to the unity. The enthalpic change associated with the binding was positive in the order of 1 kcal/mol for lysozyme, while ovoalbumin showed values around 2-3 kcal/mol. Entropic changes were also positive with values around 17-20 e.u. for ovoalbumin and 1-7 e.u. for lysozyme. The heat associated with the protein transfer from a buffer to a medium containing the polymer or the salt (a process similar to protein partitioning in aqueous two-phase systems) was obtained. These results allow the direct calculation of the enthalpic change associated with a protein partition process in aqueous two-phase systems without applying the van'tHoff equation. In this way, it is possible to calculate the associated true heat when the protein is transferred from the bottom to the top phase.     

Analyzing the performance of optical multistage interconnection networks with limited crosstalk

Analytical modeling techniques can be used to study the performance of optical multistage interconnection network (OMIN) effectively. MINs have assumed importance in recent times, because of their cost-effectiveness. An N×N MIN consists of a mapping from N processors to N memories, with log ₂ N stages of 2×2 switches with N/2 switches per stage. The interest is on the study of the performance of unbuffered optical multistage interconnection network using the banyan network. The uniform reference model approach is assumed for the purpose of analysis. In this paper the analytical modeling approach is applied to an N×N OMIN with limited crosstalk (conflicts between messages) up to (log ₂ N−1). Messages with switch conflicts satisfying the constraint of (log ₂ N−1) are allowed to pass in the same group, but in case of a link conflict, the message is routed in a different group. The analysis is performed by calculating the bandwidth and throughput of the network operating under a load l and allowing random traffic and using a greedy routing strategy. A number of equations are derived using the theory of probability and the performance curves are plotted. The results obtained show that the performance of the network improves by allowing limited crosstalk in the network.

Indirect effects in ecological interaction networks I. The chain rule approach

A mathematical method for evaluating indirect effects propagated through ecosystems consisting of multiple species is developed. The time-backward expansion of the sensitivity matrix of a system at steady state represents the tracking back of the total effects received by species. Aggregating those portions of the total effect between two species that travel through a common path with various schedules gives the path partitioning of the total effect. From this path partitioning, a chain rule is derived that expresses the indirect effect transmitted through an individual path as the products of direct effects associated with the links constituting the path. The evaluation of indirect effects by this chain rule is applied to example systems to reveal the entire structure of influence propagation through the systems. The results of this application suggest three basic mechanisms through which indirect effects contribute to the complexity and contingency of species interactions: (i) the globalization of influence by bundles of long indirect paths, (ii) the amplification (or reduction) of effects by positive (or negative) cycles, and (iii) the alteration in sign of interactions between a pair of species due to the change in dominance among the effects carried by parallel paths connecting the species.     

Intrinsic disorder in dynein intermediate chain modulates its interactions with NudE and dynactin

The functional diversity of cytoplasmic dynein is in part attributed to multiple interactions between noncatalytic dynein subunits and an array of regulatory proteins. This study focuses on the interaction between the dynein intermediate chain subunit (IC) and a dynein regulator protein (NudE). We use isothermal titration calorimetry and NMR spectroscopy to map their interacting sections to their respective N-terminal domains, which are predicted to form dimeric coiled-coils. Interestingly, the specific residues within IC that interact with NudE are a subset of the bi-segmental binding region reported for p150(Glued), a subunit of the dynein activator protein dynactin. Although the IC binding domains of both NudE and p150(Glued) form dimeric coiled-coils and bind IC at a common site, we observe distinct binding modes for each regulatory protein: 1) NudE binds region 1 of the bi-segmental binding footprint of p150(Glued), whereas p150(Glued) requires regions 1 and 2 to match the binding affinity of NudE with region 1 alone. 2) Compared with unbound IC, NudE-bound IC shows a slight increase in flexibility in region 2, in contrast to the increase in ordered structure observed for p150(Glued)-bound IC (Morgan, J. L., Song, Y., and Barbar, E. (2011) J. Biol. Chem. 286, 39349-39359). 3) Although NudE has a higher affinity for the common binding segment on IC, when all three proteins are in solution, IC preferentially binds p150(Glued). These results underscore the importance of a bi-segmental binding region of IC and disorder in region 2 and flanking linkers in selecting which regulatory protein binds IC.     

Intrinsic connectivity reveals functionally distinct cortico-hippocampal networks in the human brain

Episodic memory depends on interactions between the hippocampus and interconnected neocortical regions. Here, using data-driven analyses of resting-state functional magnetic resonance imaging (fMRI) data, we identified the networks that interact with the hippocampus—the default mode network (DMN) and a “medial temporal network” (MTN) that included regions in the medial temporal lobe (MTL) and precuneus. We observed that the MTN plays a critical role in connecting the visual network to the DMN and hippocampus. The DMN could be further divided into 3 subnetworks: a “posterior medial” (PM) subnetwork comprised of posterior cingulate and lateral parietal cortices; an “anterior temporal” (AT) subnetwork comprised of regions in the temporopolar and dorsomedial prefrontal cortex; and a “medial prefrontal” (MP) subnetwork comprised of regions primarily in the medial prefrontal cortex (mPFC). These networks vary in their functional connectivity (FC) along the hippocampal long axis and represent different kinds of information during memory-guided decision-making. Finally, a Neurosynth meta-analysis of fMRI studies suggests new hypotheses regarding the functions of the MTN and DMN subnetworks, providing a framework to guide future research on the neural architecture of episodic memory.

Episodic memory depends on interactions between the hippocampus and interconnected neocortical regions. This study uses network analyses of intrinsic brain networks at rest to identify and characterize brain networks that interact with the hippocampus and have distinct functions during memory-guided decision making.     

Radial migration of DNA molecules in cylindrical flow. III. Circles and the effect of non-gaussian polymer statistics.

We have previously shown that DNA will migrate radially inward in a concentric-cylinder shear flow apparatus. We assumed gaussian chain statistics, and we considered only linear molecules. In this paper, we extend the analysis to closed circular molecules, and we consider non-gaussian statistics for both linears and circles. We find that, in good solvents, the inward radial migration velocity is more sensitive to the molecular weight than M5/2, which we previously reported for gaussian chains. Furthermore, linears migrate radially inward 8 times faster than do circles of the same molecular weight. This suggests the possibility of separating linear from circular DNA in solution.     

Dealing with limited overlap in estimation of average treatment effects

Estimation of average treatment effects under unconfounded orignorable treatment assignment is often hampered by lack ofoverlap in the covariate distributions between treatment groups.This lack of overlap can lead to imprecise estimates, and canmake commonly used estimators sensitive to the choice of specification.In such cases researchers have often used ad hoc methods fortrimming the sample. We develop a systematic approach to addressinglack of overlap. We characterize optimal subsamples for whichthe average treatment effect can be estimated most precisely.Under some conditions, the optimal selection rules depend solelyon the propensity score. For a wide range of distributions,a good approximation to the optimal rule is provided by thesimple rule of thumb to discard all units with estimated propensityscores outside the range [0.1,0.9].     

Passive forces in mammalian skeletal muscle: a freely-jointed and worm-like chain.

The passive mechanical properties of whole muscle in active and nonactive states are compared. The experimental results are presented as stress-strain curves, which are analyzed in the framework of the current theoretical background [viz. the freely-jointed chain model (FJCM) and the worm-like chain model (WLCM)] in a semi-quantitative fashion. This analysis shows that both models can explain the mechanical behavior of whole muscle in non-active state. In the active state, the presence of crossbridges alters the mechanical response, leading to a markedly different behavior, as expected. A discussion of the mechanisms involved and the interpretation of the parameters required for the fitting of the stress-strain curves is also presented.     

The effects of muscle stretching and shortening on isometric forces on the descending limb of the force-length relationship

The purpose of this study was to examine the effects of stretching and shortening on the isometric forces at different lengths on the descending limb of the force-length relationship. Cat soleus (N = 10) was stretched and shortened by various amounts on the descending limb of the force-length relationship, and the steady-state forces following these dynamic contractions were compared to the isometric forces at the corresponding muscle lengths. We found a shift of the force-length relationship to greater force values following muscle stretching, and to smaller force values following muscle shortening. Shifts in both directions critically depended on the magnitude of stretching/shortening and the final muscle length. We confirm recent findings that the steady-state isometric force following some stretch conditions clearly exceeded the maximal isometric forces at optimum muscle length, and that force enhancement was associated with an increase in the passive force, i.e., a passive force enhancement. When the passive force enhancement was subtracted from the total force enhancement, forces following stretch were always equal to or smaller than the isometric force at optimum muscle length. Together, these findings led to the conclusions: (a). that force enhancement is composed of an "active and a "passive" component; (b). that the "passive" component of force enhancement allows for forces greater than the maximal isometric forces at the muscle's optimum length; and (c). that force enhancement and force depression are critically affected by muscle length and stretch/shortening amplitude.     

Intrinsic bent DNA colocalizes with the sequence involved in the Nd-sD mutation in the Bombyx mori fibroin light chain gene

Multiple sequence alignments of the Bombyx mori fibroin light chain gene (fib-L) from hybrids and from Chinese and Japanese strains demonstrated that 51.6% of the fib-L third intron is conserved. One of these conserved segments, 41 bp long, contains the sequence CGTTATTATACATATT, which is duplicated in the B. mori Nd-s(D) mutant. In the present work, electrophoretic mobility assays and computational analyses revealed a major peak of intrinsic bent DNA within the segment that undergoes breakage in the previously-described Nd-s(D) mutation. This result suggested that this intrinsically-curved region might mediate DNA cleavage and enhance recombination events in the third intron of the Bombyx mori fib-L gene.     

Predicting the voluntary arm forces in FES-assisted standing up using neural networks

 For individuals with paraplegia, standing up requires activation of paralyzed leg muscles by an artificial functional electrical stimulation (FES) controller and voluntary control of arm forces by the individual. Any knowledge of such voluntary control, particularly its prediction, could be used to design more effective FES controllers. Therefore, artificial neural network models were developed to predict voluntary arm forces from measured angular positions of the ankle, knee, and hip joints during FES-assisted standing up in paraplegia. The training data were collected from eight paraplegic subjects in repeated standing-up trials, and divided into two categories for training and validation. The predictions of the models closely followed both the training and validation data, showing good accuracy and generalization. The comparison of the models showed that, although there are striking similarities among the voluntary controls adopted by different subjects, each subject develops his/her own `personal strategy' to control the arm forces, which is consistent from trial to trial. The level of consistency was dependent on the experience in using FES, injury level, body weight, and other subject-specific parameters. Received: 5 January 1999 / Accepted in revised form: 29 January 2001     

Conformational transitions in a model polymer chain with secondary and tertiary structures

The confonnational properties of a simulated polymer chain with secondary and tertiary structures are calculated. The calculation is carried out by a Monte-Carlo procedure for a chain on the cubic lattice consisting of 64 links with Zimm-Bragg parameters s = 0.8–1.3, σ = $\text{1}\text{64}$ and an energy of attraction between links ? = 0–1.0.Different confonnational transitions are investigated: helix-coil, coil-globule, coil-crystal, globule-crystal. It is shown that in all cases formation (or destruction) of a crystal-like structure occurs as a Jump-like transition.The results obtained for a model chain are discussed in relation with confonnational transitions in globular pioteins.     

Implicit associations with social status: the effects of relationship involvement

The study tested the proposition that relationship involvement influences the implicit responses of women to high- and low-status professions. It was hypothesized that when a high-involvement context was primed, women would have more positive implicit associations with high-status occupations than when a low-involvement context was primed. In contrast, when a high-involvement context was primed, women would have more negative associations with low-status occupations than when a low-involvement context was primed. To test the hypothesis, 123 female participants received a high or low relationship involvement prime. Then the participants completed a single category implicit associations test designed to measure the participants' associations with either high- or low-status occupations. As predicted, the relationship involvement prime influenced the positivity of associations made with high- and low-status occupations. The study pointed to the possibility that persons possess evolutionary-based implicit associations.     

Carbon monoxide-binding cytochromes in the respiratory chain of the thermophilic bacterium PS3 grown with sufficient or limited aeration

The effects of aeration on the growth and cytochrome patterns of thermophilic bacterium PS3 were studied; bacteria grown with strong aeration synthesized cytochromes c, b, and aa3, while those grown with low aeration, showing non-exponential growth, synthesized higher amounts of cytochromes c and b including o, and a lower amount of cytochrome a (a3). The CO-difference spectra indicated that the terminal oxidase was cytochrome aa3 for high aeration conditions and the cytochrome o for low aeration conditions. Cytochrome o can be solubilized by Triton X-100 from the membrane fraction of bacteria grown under oxygen-limited conditions. The carbon monoxide complex of cytochrome o, obtained by exposing this extract to CO, was photolyzed and the subsequent rebinding of CO was analyzed; it followed first order kinetics with a rate constant of around 8 s-1 at 25 degrees C. At liquid nitrogen temperature, CO-rebinding did not occur. The CO-difference spectrum of purified cytochrome oxidase sample from the bacteria grown with strong aeration (Sone, N., et al. (1979) FEBS Lett. 106, 39-42) revealed the presence of a small amount of a cytochrome o-like pigment besides cytochrome aa3. Analysis of the CO complexes of these chromophores showed rate constants of 29-30 s-1 for cytochrome aa3 and 35-42 s-1 for the o-like pigment, indicating that the cytochrome o-like pigment contaminating the purified cytochrome oxidase preparation was not typical cytochrome o.     

Intrinsic rate of natural increase in Neotropical forest mammals: relationship to phylogeny and diet

Summary The relationship of diet and phylogeny to the intrinsic rate of population increase (r _max) was examined in a sample of 39 mammalian species that live in Neotropical forests. Diets of species did not predict their r _max, contrary to published predictions based on associations between basal metabolic rate and diet and between basal metabolic rate and r _max. Phylogeny did however, apparently because life history characteristics and susceptibility to predation vary predictably with phylogeny and with one another.     

Packing of the polynucleosome chain in interphase chromosomes: evidence for a contribution of crowding and entropic forces

In the crowded intranuclear environment, entropic depletion forces between macromolecules are expected to be strong. A review of simulations of linear polymers leads to several predictions about probable conformations of a polynucleosome chain in these conditions. These include a globular conformation, variable compaction due to different local rigidity or curvature of the mosaic of isochores, satellite sequences, and nucleosomes containing different histone variants, and the possibility that chromosomes represent separate phases like those seen in heterogeneous particle mixtures by experiment and simulation. Experimental results which show that macromolecular crowding alone, in the absence of exogenous cations, can stabilise interphase chromosomes and cause self-association of polynucleosome chains are presented. Together, these considerations suggest that macromolecular crowding and entropic forces are major factors in packing polynucleosome chains in vivo.     

A method for estimating the rejection coefficient-molecular weight relationship of ultrafiltration membrane for a chain polymer by using gel permeation chromatography

An improved method is presented for estimating rejection coefficient-molecular weight relationship of an ultrafiltration membrane for a polydisperse chain polymer. It is based on the basic idea using gel permeation chromatography originally developed by Cooper and Van Derveer. The method, in which peak spreading of an elution curve of the polymer was taken into consideration, is available for evaluating the relationship over a wide range of the molecular weight through only one experiment in analyses of the retentate and filtrate.     

Shape-memory effects in biopolymer networks with collagen-like transient nodes

In this article we study shape-memory behavior of hydrogels, formed by biodegradable and biocompatible recombinant telechelic polypeptides, with collagen-like end blocks and a random coil-like middle block. The programmed shape of these hydrogels was achieved by chemical cross-linking of lysine residues present in the random coil. This led to soft networks, which can be stretched up to 200% and "pinned" in a temporary shape by lowering the temperature and allowing the collagen-like end blocks to assemble into physical nodes. The deformed shape of the hydrogel can be maintained, at room temperature, for several days, or relaxed within a few minutes upon heating to 50 °C or higher. The presented hydrogels could return to their programmed shape even after several thermomechanical cycles, indicating that they remember the programmed shape. The kinetics of shape recovery at different temperatures was studied in more detail and analyzed using a mechanical model composed of two springs and a dashpot.