Limited Hydrolysis of Ricin D with Trypsin in the Presence of Sodium Dodecyl Sulfate

An α-amylase which produces both maltotetraose and maltopentaose from starch as the main products was found in the culture filtrate of a strain of Bacillus circulans which was newly isolated from soil. The enzyme was purified to be almost homogeneous on disc electrophoresis in polyacrylamide gel by means of ammonium sulfate fractionation, DEAE-Sepharose column chromatography and Sephadex G-200 gel filtration.

The optimum pH and temperature of the enzyme were around pH 7.0 and around 50°C, respectively. Metal ions such as Hg²⁺, Cu²⁺, Ni²⁺, Zn²⁺, Fe²⁺ and Co²⁺ strongly inhibited the enzyme activity. The molecular weight was about 45,000. The yields of maltotetraose and maltopentaose from potato starch were 30 ~ 40% and 20 ~ 30%, respectively.     

Foraging behavior in stochastic environments

How do temporally stochastic environments affect risk sensitivity in foraging behavior? We build a simple model of foraging under predation risks in stochastic environments, where the environments change over generations. We analyze the effects of stochastic environments on risk sensitivity of foraging animals by means of the difference between the geometric mean fitness and the arithmetic mean fitness. We assume that foraging is associated with predation risks whereas resting in the nest is safe because it is free of predators. In each generation, two different environments with given food amounts and predation risks occur with a certain probability. The geometric mean optimum is independent of food amounts. In most cases of stochastic environments, risk-averse tendency is increased, but in some limited conditions, more risk-prone behavior is favored. Specifically, risk-prone tendency is increased when the variation in food amount increases. Our results imply that the optimal behavior depends on the probability distribution of environmental effects under all selection regimes.     

Dynamic decision-making in uncertain environments II. Allais paradox in human behavior

In both animal and human behavioral repertoires, classical expected utility theory is considered a fundamental element of decision making under conditions of uncertainty. This theory has been widely applied to problems of animal behavior and evolutionary game theory, as well as to human economic behavior. The Allais paradox hinges on the expression of avoidance of bankruptcy by humans, or death by starvation in animals. This paradox reveals that human behavioral patterns are often inconsistent with predictions under the classical expected utility theory as formulated by von Neumann and Morgenstern. None of the many attempts to reformulate utility theory has been entirely successful in resolving this paradox with rigorous logic. We present a simple, but novel approach to the theory of decision making, in which utility is dependent on current wealth, and in which losses are more heavily weighted than gains. Our approach resolves the Allais paradox in a manner that is consistent with how humans formulate decisions under uncertainty. Our results indicate that animals, including humans, are in principle risk-averse. Our restructuring of dynamic utility theory presents a basic optimization scheme for sequential or dynamic decisions in both animals and humans.     

Deletion of Sema3a or plexinA1/plexinA3 Causes Defects in Sensory Afferent Projections of Statoacoustic Ganglion Neurons

Statoacoustic ganglion (SAG) neurons project sensory afferents to appropriate targets in the inner ear to form functional vestibular and auditory circuits. Neuropilin1 (Npn1), a receptor for class 3 semaphorins, is required to generate appropriate afferent projections in SAG neurons; however, the ligands and coreceptors involved in Npn1 functioning remain unknown. Here we show that both plexinA1 and plexinA3 are expressed by SAG neurons, and plexinA1/plexinA3 double mutant mice show defects in afferent projections of SAG neurons in the inner ear. In control mice, sensory afferents of SAG neurons terminate at the vestibular sensory patches, whereas in plexinA1/plexinA3 double mutants, they extend more dorsally in the inner ear beyond normal vestibular target areas. Moreover, we find that semaphorin3a (Sema3a) is expressed in the dorsal otocyst, and Sema3a mutant mice show defects in afferent projections of SAG neurons similar to those observed in plexinA1/plexinA3 double mutants and in mice lacking a functional Npn1 receptor. Taken together, these genetic findings demonstrate that Sema3a repellent signaling plays a role in the establishment of proper afferent projections in SAG neurons, and this signaling likely occurs through a receptor complex involving Npn1 and either plexinA1 or plexinA3.     

A two-step refolding of acid-denatured microbial transglutaminase escaping from the aggregation-prone intermediate

Microbial transglutaminase (MTG) is a monomeric globular enzyme made of 331 amino acid residues. The conformation of MTG was examined over the pH 2.0-6.0 region using circular dichroism (CD) and 1-anilino-8-naphthalenesulfonate (ANS). Under conditions of low ionic strength, a decrease of pH below 4 caused a stepwise unfolding with an intermediate exhibiting specific ANS-binding before full unfolding at pH 2.0. At high ionic strength, the decrease of pH led to only an intermediate without further unfolding. The intermediate corresponds to the molten globule state with a secondary structure similar to the native state but disordered tertiary structures. A pH- and NaCl concentration-dependent phase diagram showed that the fully unfolded state exists only under limited conditions of low pH and a low NaCl concentration. Although a refolding yield by the direct jump to pH 6.0 was low, a two-step refolding with incubation at pH 4.0, where MTG is marginally stable, and a subsequent jump to pH 6.0 improved the yield by suppressing the kinetic traps. We propose that the two-step refolding is useful for improving the yield of larger proteins with a high pI value.     

Structural comparison of F1-ATPase: interplay among enzyme structures, catalysis, and rotations

F(1)-ATPase, a rotary motor powered by adenosine triphosphate hydrolysis, has been extensively studied by various methods. Here, we performed a systematic comparison of 29 X-ray crystal structures of F(1)-complexes, finding fine interplay among enzyme structures, catalysis, and rotations. First, analyzing the 87 structures of enzymatic αβ-subunits, we confirmed that the two modes, the hinge motion of β-subunit and the loose/tight motion of the αβ-interface, dominate the variations. The structural ensemble was nearly contiguous bridging three clusters, αβ(TP), αβ(DP), and αβ(E). Second, the catalytic site analysis suggested the correlation between the phosphate binding and the tightening of the αβ-interface. Third, addressing correlations of enzymatic structures with the orientations of the central stalk γ, we found that the γ rotation highly correlates with loosening of αβ(E)-interface and β(DP) hinge motions. Finally, calculating the helix 6 angle of β, we identified the recently observed partially closed conformation being consistent with β(HC).     

Acid-induced Molten Globule State of a Prion Protein: CRUCIAL ROLE OF STRAND 1-HELIX 1-STRAND 2 SEGMENT*

The conversion of a cellular prion protein (PrP^C) to its pathogenic isoform (PrP^Sc) is a critical event in the pathogenesis of prion diseases. Pathogenic conversion is usually associated with the oligomerization process; therefore, the conformational characteristics of the pre-oligomer state may provide insights into the conversion process. Previous studies indicate that PrP^C is prone to oligomer formation at low pH, but the conformation of the pre-oligomer state remains unknown. In this study, we systematically analyzed the acid-induced conformational changes of PrP^C and discovered a unique acid-induced molten globule state at pH 2.0 termed the “A-state.” We characterized the structure of the A-state using far/near-UV CD, 1-anilino-8-naphthalene sulfonate fluorescence, size exclusion chromatography, and NMR. Deuterium exchange experiments with NMR detection revealed its first unique structure ever reported thus far; i.e. the Strand 1-Helix 1-Strand 2 segment at the N terminus was preferentially unfolded, whereas the Helix 2-Helix 3 segment at the C terminus remained marginally stable. This conformational change could be triggered by the protonation of Asp¹⁴⁴, Asp¹⁴⁷, and Glu¹⁹⁶, followed by disruption of key salt bridges in PrP^C. Moreover, the initial population of the A-state at low pH (pH 2.0–5.0) was well correlated with the rate of the β-rich oligomer formation, suggesting that the A-state is the pre-oligomer state. Thus, the specific conformation of the A-state would provide crucial insights into the mechanisms of oligomerization and further pathogenic conversion as well as facilitating the design of novel medical chaperones for treating prion diseases.     

α2-antiplasmin positively regulates endothelial-to-mesenchymal transition and fibrosis progression in diabetic nephropathy

Molecular Biology Reports - Diabetic nephropathy (DN), is microvascular complication of diabetes causes to kidney dysfunction and renal fibrosis. It is known that hyperglycemia and advanced...     

Evolution of gamete size in primitive taxa without mating types

An ESS model to better understand the evolutionary dynamics of a primitive non-mating type gamete size was developed with reference to the PBS (Parker, Baker and Smith’s) theory, which was based on total numbers of zygotes formed and the zygote survival rates. We did not include mating types since it has been suggested that primitive mating systems did not have mating types. As input parameters, we used experimental data on gamete motility of marine green algae. Based on hard sphere collision mechanics, we detailed the fertilization kinetics of gametes that swim in water prior to fusing with their partners through a set of coupled, non-linear differential equations. These equations were integrated numerically using typical values of the constant parameters. To estimate the relative zygote survival rate, we used a function that is sigmoid in shape and examined some evolutionarily stable strategies in mating systems that depend on optimizing values of the invasion success ratio.     

Life cycle replacement by gene introduction under an allee effect in periodical cicadas

Periodical cicadas (Magicicada spp.) in the USA are divided into three species groups (-decim, -cassini, -decula) of similar but distinct morphology and behavior. Each group contains at least one species with a 17-year life cycle and one with a 13-year cycle; each species is most closely related to one with the other cycle. One explanation for the apparent polyphyly of 13- and 17-year life cycles is that populations switch between the two cycles. Using a numerical model, we test the general feasibility of life cycle switching by the introduction of alleles for one cycle into populations of the other cycle. Our results suggest that fitness reductions at low population densities of mating individuals (the Allee effect) could play a role in life cycle switching. In our model, if the 13-year cycle is genetically dominant, a 17-year cycle population will switch to a 13-year cycle given the introduction of a few 13-year cycle alleles under a moderate Allee effect. We also show that under a weak Allee effect, different year-classes ("broods") with 17-year life cycles can be generated. Remarkably, the outcomes of our models depend only on the dominance relationships of the cycle alleles, irrespective of any fitness advantages.