The Role of Diffusion in Enzyme Kinetics

A discussion is given of the general role of diffusion in enzyme kinetics based upon a rigorous theory for bimolecular association and dissociation steps that was presented previously, and criteria are formulated for the dependence of the over-all rate on medium viscosity. With these criteria it is possible to conclude that a number of enzymes will exhibit no appreciable dependence of over-all rate on the medium viscosity, quite irrespective of the as yet unmeasured rate constants for association and dissociation of enzyme and substrate. The effect of adsorbing the enzyme onto the surface of a much larger spherical colloidal particle is considered with the conclusion that the rate will either remain the same or decrease, and that its sensitivity to medium viscosity will remain the same or increase.     

The Role of Diffusion in Bimolecular Solution Kinetics

An appropriate boundary condition is derived which permits both the bimolecular association and dissociation steps to be simultaneously treated within the framework of the theory of Smoluchowski, Debye, and Collins, and Kimball. Kinetic theory expressions are derived for the intrinsic rate constants. The transient case of the suddenly switched-on reaction is considered as well as the suddenly perturbed equilibrium, but only the time dependence of the rate constants is obtained. The frequency response spectrum for a diffusion-controlled reaction is obtained in the linear approximation and compared with the corresponding Debye relaxation spectrum.     

The Role of Plant Size and Nutrient Concentrations in Associations between Medicago, and Rhizobium and/or Glomus

The aim of this research was to carry out a critical study of the method of obtaining size equivalence between non-symbiotic alfalfa and alfalfa associated with Glomus and/or Rhizobium by applying fixed addition rates of nutrients to the non-symbiotic controls. The experimental design included three nutrient response curves in which the levels of added phosphorus and/or nitrogen were constant during the whole plant growth process: 1) a phosphorus response curve, in order to compare the growth of double symbiotic plants with that of only-Rhizobium inoculated ones; 2) a nitrogen response curve, that consisted of a comparison between the growth of double symbiotic alfalfa and four treatments associated only with Glomus; 3) a phosphorus and nitrogen response curve, to compare the growth of non-inoculated alfalfa with that of double symbiotic plants. Although similar size was achieved among some treatments at harvest, shoot growth over time and nutrient concentrations in tissues differed, indicating that growth equivalence did not mean functional equivalence. A second experimental design was performed taking into account the establishment of microsymbionts for determining the adequate moment to add supplemental phosphorus and/or nitrogen. It included four treatments: a) double symbiotic plants (MR); b) plants inoculated with Rhizobium only (R); c) plants inoculated with Glomus only (M), and d) non-inoculated plants (N). Great similarity in terms of plant growth and nutrient contents in tissues were obtained. Moreover, symbiotic plants were able to produce similar dry matter than non-symbiotic ones under P and N limitations.     

The Effect of Antisite Disorder and Particle Size on Li Intercalation Kinetics in Monoclinic LiMnBO3

In materials containing 1D lithium diffusion channels, cation disorder can strongly affect lithium intercalation processes. This work presents a model to explain the unusual transport properties of monoclinic LiMnBO₃, a material determined by scanning electron microscopy and synchrotron X‐ray diffraction to contain a wide particle size distribution and Mn/Li antisite disorder. First‐principles calculations indicate that Mn occupying Li sites obstruct the 1D lithium diffusion channel along the [001] direction. While channel blockage by the antisites significantly lowers Li mobility in large particles, Li kinetics in small particles and particle surfaces are found to be less sensitive to the presence of antisite disorder. Thus, in an electrode containing a large particle size distribution, smaller particles have higher Li mobility, and the measured Li diffusivity as determined by potentiostatic intermittent titration test varies as a function of particle size. The Li capacity in monoclinic LiMnBO₃ is kinetically controlled by the fraction of large particles with antisite disorder, but is not intrinsically limited. These results strongly suggest that particle nanosizing will significantly enhance the electrochemical performance of LiMnBO₃.     

Positive Affect and Cognitive Restoration: Investigating the Role of Valence and Arousal

Positive moods are thought to restore self-control resources following depletion. However, it is not well understood whether this effect is due to affective valence (pleasantness), arousal (activation), or a combination of both. Across four studies, we set out to investigate the role of positive moods on cognitive and behavioral measures of self-regulation in an ego-depletion paradigm. In studies 1 and 2, we independently manipulated affective valence and arousal and assessed self-regulation with a Stroop task. Results did not suggest a restorative effect of either on cognitive resources. In study 3, we employed both behavioral (the ‘handgrip task’) and cognitive (Stroop) assessments of self-regulation. Again, no significant effect of mood was observed on the Stroop task. Additionally, participants did not persist significantly longer on the handgrip task following a positive mood induction. Finally, in study 4, high vs. low states of arousal were manipulated and self-regulation was assessed via pre- and post-manipulation Stroop performance. In study 4, Stroop performance improved slightly more across time points for those in the high arousal condition than for those in the low arousal condition. Therefore, across four studies, we failed to find a consistent pattern of results suggesting that positive moods restore cognitive resources.     

The Role of Colony Size on Tunnel Branching Morphogenesis in Ant Nests

Many ant species excavate nests that are made up of chambers and interconnecting tunnels. There is a general trend of an increase in nest complexity with increasing population size. This complexity reflects a higher ramification and anastomosis of tunnels that can be estimated by the meshedness coefficient of the tunnelling networks. It has long been observed that meshedness increases with colony size within and across species, but no explanation has been provided so far. Since colony size is a strong factor controlling collective digging, a high value of the meshedness could simply be a side effect of a larger number of workers. To test this hypothesis, we study the digging dynamics in different group size of ants Messor sancta. We build a model of collective digging that is calibrated from the experimental data. Model''s predictions successfully reproduce the topological properties of tunnelling networks observed in experiments, including the increase of the meshedness with group size. We then use the model to investigate situations in which collective digging progresses outward from a centre corresponding to the way tunnelling behaviour occurs in field conditions. Our model predicts that, when all other parameters are kept constant, an increase of the number of workers leads to a higher value of the meshedness and a transition from tree-like structures to highly meshed networks. Therefore we conclude that colony size is a key factor determining tunnelling network complexity in ant colonies.     

A Role for Giantin in Docking COPI Vesicles to Golgi Membranes

We have previously shown that p115, a vesicle docking protein, binds to two proteins (p130 and p400) in detergent extracts of Golgi membranes. p130 was identified as GM130, a Golgi matrix protein, and was shown to act as a membrane receptor for p115. p400 has now been identified as giantin, a Golgi membrane protein with most of its mass projecting into the cytoplasm. Giantin is found on COPI vesicles and pretreatment with antibodies inhibits both the binding of p115 and the docking of these vesicles with Golgi membranes. In contrast, GM130 is depleted from COPI vesicles and inhibition of the GM130 on Golgi membranes, using either antibodies or an NH₂-terminal GM130 peptide, inhibits p115 binding and vesicle docking. Together these results suggest that COPI vesicles are docked by giantin on the COPI vesicles and GM130 on Golgi membranes with p115 providing a bridge.     

Revisiting the Role of Cystic Fibrosis Transmembrane Conductance Regulator and Counterion Permeability in the pH Regulation of Endocytic Organelles

Organellar acidification by the electrogenic vacuolar proton-ATPase is coupled to anion uptake and cation efflux to preserve electroneutrality. The defective organellar pH regulation, caused by impaired counterion conductance of the mutant cystic fibrosis transmembrane conductance regulator (CFTR), remains highly controversial in epithelia and macrophages. Restricting the pH-sensitive probe to CFTR-containing vesicles, the counterion and proton permeability, and the luminal pH of endosomes were measured in various cells, including genetically matched CF and non-CF human respiratory epithelia, as well as cftr^+/+ and cftr^−/− mouse alveolar macrophages. Passive proton and relative counterion permeabilities, determinants of endosomal, lysosomal, and phagosomal pH-regulation, were probed with FITC-conjugated transferrin, dextran, and Pseudomonas aeruginosa, respectively. Although CFTR function could be documented in recycling endosomes and immature phagosomes, neither channel activation nor inhibition influenced the pH in any of these organelles. CFTR heterologous overexpression also failed to alter endocytic organellar pH. We propose that the relatively large CFTR-independent counterion and small passive proton permeability ensure efficient shunting of the proton-ATPase–generated membrane potential. These results have implications in the regulation of organelle acidification in general and demonstrate that perturbations of the endolysosomal organelles pH homeostasis cannot be linked to the etiology of the CF lung disease.     

Fat-Tailed Fluctuations in the Size of Organizations: The Role of Social Influence

Organizational growth processes have consistently been shown to exhibit a fatter-than-Gaussian growth-rate distribution in a variety of settings. Long periods of relatively small changes are interrupted by sudden changes in all size scales. This kind of extreme events can have important consequences for the development of biological and socio-economic systems. Existing models do not derive this aggregated pattern from agent actions at the micro level. We develop an agent-based simulation model on a social network. We take our departure in a model by a Schwarzkopf et al. on a scale-free network. We reproduce the fat-tailed pattern out of internal dynamics alone, and also find that it is robust with respect to network topology. Thus, the social network and the local interactions are a prerequisite for generating the pattern, but not the network topology itself. We further extend the model with a parameter that weights the relative fraction of an individual''s neighbours belonging to a given organization, representing a contextual aspect of social influence. In the lower limit of this parameter, the fraction is irrelevant and choice of organization is random. In the upper limit of the parameter, the largest fraction quickly dominates, leading to a winner-takes-all situation. We recover the real pattern as an intermediate case between these two extremes.     

Quantitative analysis of the isolated GAAA tetraloop/receptor interaction in solution: a site-directed spin labeling study

The GNRA (N: any nucleotide; R: purine) tetraloop/receptor interaction is believed to be one of the most frequently occurring tertiary interaction motifs in RNAs, but an isolated tetraloop/receptor complex has not been identified in solution. In the present work, site-directed spin labeling is applied to detect tetraloop/receptor complex formation and estimate the free energy of interaction. For this purpose, the GAAA tetraloop/receptor interaction was chosen as a model system. A method was developed to place nitroxide labels at specific backbone locations in an RNA hairpin containing the GAAA tetraloop. Formation of the tetraloop/receptor complex was monitored through changes in the rotational correlation time of the tetraloop and the attached nitroxide. Results show that a hairpin containing the GAAA tetraloop forms a complex with an RNA containing the 11-nucleotide GAAA tetraloop receptor motif with an apparent Kd that is strongly dependent on Mg2+. At 125 mM MgCl2, Kd = 0.40 +/- 0.05 mM. The corresponding standard free energy of complex formation is -4.6 kcal/mol, representing the energetics of the tetraloop/receptor interaction in the absence of other tertiary constraints. The experimental strategy presented here should have broad utility in quantifying weak interactions that would otherwise be undetectable, for both nucleic acids and nucleic acid-protein complexes.     

UNC-10在致密核心囊泡分泌过程中的作用

Rim是囊泡分泌活性区中的重要组成蛋白,它与细胞分泌和突触可塑性相关．在秀丽隐感线虫中只存在一种编码Rim的基因即unc-10．我们的研究发现,在线虫中Rim的基因突变unc-10(md1117)会导致致密核心囊泡的分泌缺陷．在活体中,unc-10突变虫系的神经多肽分泌显著下降．此外,在主要分泌致密核心囊泡的ALA神经元内,钙光解释放促发的快相分泌也比野生型减少．运用全内反射荧光显微成像技术,我们观察在unc-10缺失的情况下ALA 神经元中致密核心囊泡的锚定过程,结果显示在细胞膜附近停留的囊泡数目减少,表明囊泡锚定受到阻碍．上述试验结果表明,UNC-10能够影响致密核心囊泡的分泌过程,其机制可能是影响了囊泡的锚定过程．     

Lifting without Seeing: The Role of Vision in Perceiving and Acting upon the Size Weight Illusion

Background

Our expectations of an object''s heaviness not only drive our fingertip forces, but also our perception of heaviness. This effect is highlighted by the classic size-weight illusion (SWI), where different-sized objects of identical mass feel different weights. Here, we examined whether these expectations are sufficient to induce the SWI in a single wooden cube when lifted without visual feedback, by varying the size of the object seen prior to the lift.

Methodology/Principal Findings

Participants, who believed that they were lifting the same object that they had just seen, reported that the weight of the single, standard-sized cube that they lifted on every trial varied as a function of the size of object they had just seen. Seeing the small object before the lift made the cube feel heavier than it did after seeing the large object. These expectations also affected the fingertip forces that were used to lift the object when vision was not permitted. The expectation-driven errors made in early trials were not corrected with repeated lifting, and participants failed to adapt their grip and load forces from the expected weight to the object''s actual mass in the same way that they could when lifting with vision.

Conclusions/Significance

Vision appears to be crucial for the detection, and subsequent correction, of the ostensibly non-visual grip and load force errors that are a common feature of this type of object interaction. Expectations of heaviness are not only powerful enough to alter the perception of a single object''s weight, but also continually drive the forces we use to lift the object when vision is unavailable.     

The Role of Body Size in Mating Interactions of the Sexually Cannibalistic Fishing Spider Dolomedes triton

Some arachnids display extreme sexual size dimorphism (SSD) with adult females being several times larger than adult males. One explanation for SSD in species that exhibit pre‐copulatory sexual cannibalism (female attack, kill and consumption of the male prior to mating) is that smaller males may be less likely victims of predatory attacks by females. However, in some sexually cannibalistic species SSD is relatively moderate (i.e. males are similar in size to females) suggesting benefits of large male body size. Here, I report the results of an experiment designed to explore the ramifications of body size in mating interactions of the sexually cannibalistic, North American fishing spider (Dolomedes triton). Results suggest that male size does not influence courtship behavior, the likelihood of being attacked, or the male's ability to secure a mounting. However, large males were superior at gaining copulations once mounted. Sexual cannibalism may also be predicated on female size. Female condition (mass/cephalothorax area) did not explain any of these behaviors from the copulatory sequence, however, females with a smaller cephalothorax area were more likely to attack courting males. Finally, analysis of the ratio of female size to male size showed that when SSD is weak males are more likely to escape attacks and mate successfully. Results are discussed in light of several hypotheses for sexual cannibalism, and the benefits of large male body size illustrated here are put forth as potential explanations for the relatively moderate extent of SSD found in this sexually cannibalistic species.     

Counterion collapse and the effect of diamines on bacteriorhodopsin

A recent report of electrical measurements on oriented bacteriorhodopsin in gels [(1986) FEBS Lett. 195, 164 168] concluded that low concentrations of diamines reversed the direction of the proton pump. Calculations are presented which show that in low diamine concentrations, charge displacements of the counterion atmosphere in the direction opposite to proton pumping are expected following H+ ejection. It is also shown that the effect will be sharply reduced by raising the diamine concentration or by adding excess salt, as was observed. Hence it is not necessary to conclude that diamines reverse the direction of the proton pump itself.     

The Probabilistic Niche Model Reveals the Niche Structure and Role of Body Size in a Complex Food Web

The niche model has been widely used to model the structure of complex food webs, and yet the ecological meaning of the single niche dimension has not been explored. In the niche model, each species has three traits, niche position, diet position and feeding range. Here, a new probabilistic niche model, which allows the maximum likelihood set of trait values to be estimated for each species, is applied to the food web of the Benguela fishery. We also developed the allometric niche model, in which body size is used as the niche dimension. About 80% of the links in the empirical data are predicted by the probabilistic niche model, a significant improvement over recent models. As in the niche model, species are uniformly distributed on the niche axis. Feeding ranges are exponentially distributed, but diet positions are not uniformly distributed below the predator. Species traits are strongly correlated with body size, but the allometric niche model performs significantly worse than the probabilistic niche model. The best-fit parameter set provides a significantly better model of the structure of the Benguela food web than was previously available. The methodology allows the identification of a number of taxa that stand out as outliers either in the model''s poor performance at predicting their predators or prey or in their parameter values. While important, body size alone does not explain the structure of the one-dimensional niche.     

Counterion displacement in the molecular evolution of the rhodopsin family

The counterion, a negatively charged amino acid residue that stabilizes a positive charge on the retinylidene chromophore, is essential for rhodopsin to receive visible light. The counterion in vertebrate rhodopsins, Glu113 in the third transmembrane helix, has an additional role as an intramolecular switch to activate G protein efficiently. Here we show on the basis of mutational analyses that Glu181 in the second extracellular loop acts as the counterion in invertebrate rhodopsins. Like invertebrate rhodopsins, UV-absorbing parapinopsin has a Glu181 counterion in its G protein-activating state. Its G protein activation efficiency is similar to that of the invertebrate rhodopsins, but significantly lower than that of bovine rhodopsin, with which it shares greater sequence identity. Thus an ancestral vertebrate rhodopsin probably acquired the Glu113 counterion, followed by structural optimization for efficient G protein activation during molecular evolution.