Search

This paper develops L p - L q decay estimates of the gradient of the Stokes semigroup (T (t)) t ≥ 0 generated by the negative of the Stokes operator in exterior Lipschitz domains Ω ⊂ R n , n ≥ 3. More precisely, the L p - L q estimates of ∇ T (t) with optimal rates are proved if p and q satisfy | 1 / p − 1 / 2 | < 1 / (2 n) + ε , | 1 / q − 1 / 2 | < 1 / (2 n) + ε , and p ≤ q ≤ n with some ε > 0 , which should be useful for the study of stability of the several physically relevant flows. As an application, we obtain the existence theorem of global-in-time strong solutions to the three-dimensional Navier–Stokes equations in the critical space L ∞ (0 , ∞ ; L σ 3 (Ω)) provided that the initial velocity is small in the L 3 -norm. [ABSTRACT FROM AUTHOR]

For every linear operator between inner product spaces whose operator norm is less than or equal to one, we show that the restriction to the Möbius gyrovector space is Lipschitz continuous with respect to the Poincaré metric. Moreover, the Lipschitz constant is precisely the operator norm. [ABSTRACT FROM AUTHOR]

We show that the Stokes operator defined on L σ p (Ω) for an exterior Lipschitz domain Ω ⊂ R n (n ≥ 3) admits maximal regularity provided that p satisfies | 1 / p − 1 / 2 | < 1 / (2 n) + ε for some ε > 0. In particular, we prove that the negative of the Stokes operator generates a bounded analytic semigroup on L σ p (Ω) for such p. In addition, L p - L q -mapping properties of the Stokes semigroup and its gradient with optimal decay estimates are obtained. This enables us to prove the existence of mild solutions to the Navier–Stokes equations in the critical space L ∞ (0 , T ; L σ 3 (Ω)) (locally in time and globally in time for small initial data). [ABSTRACT FROM AUTHOR]

We investigate a class of functionals on Möbius gyrovector spaces, which consists of a counterpart to bounded linear functionals on Hilbert spaces. [ABSTRACT FROM AUTHOR]

We investigate a class of functionals on Möbius gyrovector spaces, which consists of a counterpart to bounded linear functionals on Hilbert spaces. [ABSTRACT FROM AUTHOR]

We investigate the Möbius gyrovector spaces which are open balls centered at the origin in a real Hilbert space with the Möbius addition, the Möbius scalar multiplication, and the Poincaré metric introduced by Ungar. In particular, for an arbitrary point, we can easily obtain the unique closest point in any closed gyrovector subspace, by using the ordinary orthogonal decomposition. Further, we show that each element has the orthogonal gyroexpansion with respect to any orthogonal basis in a Möbius gyrovector space, which is similar to each element in a Hilbert space having the orthogonal expansion with respect to any orthonormal basis. Moreover, we present a concrete procedure to calculate the gyrocoefficients of the orthogonal gyroexpansion. [ABSTRACT FROM AUTHOR]

In this study, we show that any finitely generated gyrovector subspace in the Möbius gyrovector space coincides with the intersection of the vector subspace generated by the same generators and the Möbius ball. As an application, we present a notion of orthogonal gyrodecomposition and clarify the relationship with the orthogonal decomposition. [ABSTRACT FROM AUTHOR]

We consider a free boundary problem of the Navier–Stokes equations in the three-dimensional Euclidean space with moving contact line, where the 90 ∘ -contact angle condition is posed. We show that for given T > 0 the problem is local well-posed on (0 , T) provided that the initial data are small. We study the transformed problem in an L p -in-time and L q -in-space setting with 2 < p < ∞ and 3 < q < ∞ satisfying 2 / p + 3 / q < 1 , which provides a weaker setting than the one that was allowed by Wilke (2020) whose case was p = q > 5. [ABSTRACT FROM AUTHOR]

To investigate how the conformational flexibility of subtilisin affects its ability to discriminate between enantiomeric amino acid and ester substrates for the subtilisin-catalyzed reaction in an organic solvent, the flexibility around the active site and the surface of subtilisin was estimated from the mobility of a spin label bound to subtilisin by ESR spectroscopy. Many studies on enzyme flexibility focus on the active site. Both the surface and active site flexibility play an important role in the enantioselectivity enhancement of the enzyme-catalyzed reaction. It was found, however, that the different behavior observed for the enantioselectivity between the amino acid and ester substrates could be correlated with the flexibility around the surface rather than the flexibility at the active site of subtilisin. In other words, for the ester substrates, the greater flexibility around the surface of subtilisin induced by a conformational change resulting from the presence of an additive such as DMSO is essential for the enantioselectivity enhancement. This model is also supported by the Michaelis–Menten kinetic parameters for each enantiomeric substrate. Our findings provide insight into the enantioselectivity enhancement for the resolution of enantiomers for enzyme-catalyzed reactions in organic solvents. [Copyright &y& Elsevier]

NK1 is a splice variant of the polypeptide growth factor HGF/SF that consists of the N terminal (N) and first kringle (K) domains and retains receptor binding and signalling. While NK1 behaves as a monomer in solution, two independent crystallographic structures have previously shown an identical, tightly packed dimer. Here we report a novel orthorhombic crystal form of NK1 at 2.5 A˚ resolution in which four NK1 protomers are packed in two distinct dimers in the asymmetric unit. Although the basic architecture of the new NK1 dimers is similar to the two described earlier, the new crystal form demonstrates extensive hinge movement between the N and K domain that leads to re-orientation of the receptor-binding sites. The hinge bending is evidence of the paucity of strong interactions between domains within the protomer, in contrast to the extensive interactions between protomers in the dimer. These observations are consistent with domain swapping in the dimer, such that the interdomain interactions of the monomer are replaced by equivalent interprotomer interactions in the dimer and offer a route for protein engineering of NK1 variants which may act as receptor antagonists. [Copyright &y& Elsevier]

Metastable cosmic strings appear in models of new physics with a two-step symmetry breaking G → H → 1, where π1(H) ≠ 0 and π1(G) = 0. They decay via the monopole-antimonopole pair creation inside. Conventionally, the breaking rate has been estimated by an infinitely thin string approximation, which requires a large hierarchy between the symmetry breaking scales. In this paper, we reexamine it by taking into account the finite sizes of both the cosmic string and the monopole. We obtain a robust lower limit on the tunneling factor e − S B even for regimes the conventional estimate is unreliable. In particular, it is relevant to the cosmic string interpretation of the gravitational wave signals recently reported by pulsar timing array experiments. [ABSTRACT FROM AUTHOR]

Consider a free boundary problem of compressible-incompressible two-phase flows with surface tension and phase transition in bounded domains Ω t + , Ω t − ⊂ R N , N ≥ 2 , where the domains are separated by a sharp compact interface Γ t ⊂ R N − 1 . We prove a global in time unique existence theorem for such free boundary problem under the assumption that the initial data are sufficiently small and the initial domain of the incompressible fluid is close to a ball. In particular, we obtain the solution in the maximal L p − L q -regularity class with 2 < p < ∞ and N < q < ∞ and exponential stability of the corresponding analytic semigroup on the infinite time interval. [ABSTRACT FROM AUTHOR]

We present some fundamental results concerning to continuous quasi gyrolinear operators between Möbius gyrovector spaces induced by finite matrices. Such mappings are significant like as operators induced by matrices between finite dimensional Hilbert spaces. This gives a novel approach to the study of mappings between Möbius gyrovector spaces that should correspond to bounded linear operators on real Hilbert spaces. [ABSTRACT FROM AUTHOR]

Tryptic and chymotryptic digestions of a complex between ribosomal protein L2 and the 23S RNA of Bacillus stearothermophilus produced two protected fragments (designated TF and CF). These proteins fragments remained tightly bound to the RNA and were able to rebind specifically to 23S RNA. Amino acid sequence analysis of the isolated fragments revealed that both fragments TF and CF originated from the central half of the protein L2 (positions 60-206 and 58-201) with molecular masses of 15 918 Da and 15 690 Da respectively. From these results it is concluded that the protected central half is the primary RNA-binding region of the protein L2. A combination of these and other results suggests that the N and/or C-terminal (but not the central) regions may be involved in the peptidyltransferase activity of the 50S subunit. [ABSTRACT FROM AUTHOR]

We consider a free boundary problem of compressible–incompressible two-phase flows with phase transitions in general domains of N -dimensional Euclidean space (e.g. whole space; half-spaces; bounded domains; exterior domains). The compressible fluid and the incompressible fluid are separated by either compact or non-compact sharp moving interface, and the surface tension is taken into account. In our model, the compressible fluid and incompressible fluid are occupied by the Navier–Stokes–Korteweg equations and the Navier–Stokes equations, respectively. This paper shows that for given T > 0 the problem admits a unique strong solution on (0 , T) in the maximal L p − L q regularity class provided the initial data are small in their natural norms. [ABSTRACT FROM AUTHOR]

• A 226-bp TE was inserted into the coding region of CCD4 and interrupts its expression in yellow-flowered petunia. • The insertion contains a premature stop codon and could form secondary structures in hairpin RNA. • The transformants of CCD4a showed carotenoid degradation in corollas. Petunia is a popular commercial bedding plant that comes in many colors, but there are no petunia cultivars with deep yellow petals. The carotenoid degradation gene carotenoid cleavage dioxygenase (CCD4) was isolated from white and yellow-flowered petunia and we found the 226-bp insertion of a non-autonomous transposable element tourist-like miniature-inverted repeat (MITE) in the coding region of CCD4 only in yellow cultivars. The insertion interrupts gene expression because of a premature stop codon after the TE insertion and could form secondary structures in hairpin RNA that could then be processed into a mature miRNA. Here, the normal function of CCD4 isolated from a white cultivar was introduced to a yellow cultivar. The transformants showed more fading pale-yellow flowers and carotenoid content was decreased. These results indicate that transformed CCD4 expression promoted carotenoid degradation and the lack of CCD4 expression results in more carotenoid accumulation in wild-type yellow-flowered petunia. [ABSTRACT FROM AUTHOR]

The asymmetric dark matter (ADM) scenario solves the baryon-dark matter coincidence problem when the dark matter (DM) mass is of O 1 GeV. Composite ADM models based on QCD-like strong dynamics are particularly motivated since the strong dynamics naturally provides the DM mass of O 1 GeV and the large annihilation cross-section simultaneously. In those models, the sub-GeV dark photon often plays an essential role in transferring the excessive entropy in the dark sector into the visible sector, i.e., the Standard Model sector. This paper constructs a chiral composite ADM model where the U(1)D gauge symmetry is embedded into the chiral flavor symmetry. Due to the dynamical breaking of the chiral flavor symmetry, the model naturally provides the masses of the dark photon and the dark pions in the sub-GeV range, both of which play crucial roles for a successful ADM model. [ABSTRACT FROM AUTHOR]

We show some Cauchy–Bunyakovsky–Schwarz type inequalities related to the Möbius operations in complex inner product spaces which are extensions of a similar type inequality obtained recently, and we discuss some properties. [ABSTRACT FROM AUTHOR]

In this article, we show two fundamental features of the restriction of Möbius operations to the real numbers, that is, a Cauchy type inequality and a criterion for convergence of series. [ABSTRACT FROM AUTHOR]

Mimosinase degrades the non-protein amino acid mimosine and is thought to have evolved from cystathionine β-lyase (CBL) via gene duplication. However, no study has, to date, compared the molecular characteristics of mimosinase and CBL. We therefore cloned mimosinase and CBL from the Mimosoideae subfamily member Mimosa pudica (Mp) and explored the molecular relationship between mimosinase and CBL for the first time. The recombinant Mp mimosinase degraded both mimosine and cystathionine with a much higher turnover number (kcat) for mimosine compared with cystathionine, and Mp CBL utilized only cystathionine as a substrate. The critical residues implicated in the substrate binding of Arabidopsis thaliana CBL (Tyr-127, Arg-129, Tyr-181, and Arg-440) were highly conserved in both Mp mimosinase and CBL. However, homology modeling and molecular simulation of these enzymes predicted variations in the residues that interact with substrates. A mutation experiment on Mp mimosinase revealed that the disruption of a disulfide bond in the vicinity of the pyridoxal-5′-phosphate domain increased the enzyme's preference toward cystathionine. Treatment of Mp mimosinase with a disulfide-cleavage agent also decreased mimosinase activity. Furthermore, mutation near the conserved binding residue altered the substrate preference between mimosine and cystathionine. Molecular dynamics simulations of Mp mimosinase suggested a closer coordination of the residues that interact with mimosine at the active site compared with cystathionine, indicating a more compact pocket size for mimosine degradation. This study thus may provide new insights into the molecular diversification of CBL, a C–S lyase, into the C–N lyase mimosinase in the Mimosoideae subfamily. [ABSTRACT FROM AUTHOR]

We have shown previously that perturbation of origin firing in chromosome replication causes DNA lesions and triggers DNA damage checkpoint control, which ensures genomic integrity by stopping cell cycle progression until the lesions are repaired or by inducing cell death if they are not properly repaired. This was based on the observation that the temperature-sensitive phenotype of orc1-4 and orc2-1 mutants required a programmed action of the RAD9-dependent DNA damage checkpoint. Here, we report that DNA lesions in the orc mutants are induced much more quickly and frequently within the rRNA gene (rDNA) locus than at other chromosomal loci upon temperature shift. orc mutant cells with greatly reduced rDNA copy numbers regained the ability to grow at restrictive temperatures, and the checkpoint response after the temperature shift became weak in these cells. In orc2-1 cells, completion of chromosomal duplication was delayed specifically on chromosome XII, where the rDNA array is located, and the delay was partially suppressed when the rDNA copy number was reduced. These results suggest that the rDNA locus primarily signals abnormalities in the initiation program to the DNA damage checkpoint and that the rDNA copy number modulates the sensitivity of this monitoring function. [ABSTRACT FROM AUTHOR]

It is remarkable that the matter fields in the Standard Model (SM) are apparently unified into the SU(5) representations. A straightforward explanation of this fact is to embed all the SM gauge groups into a simple group containing SU(5), i.e., the grand unified theory (GUT). Recently, however, a new framework "fake GUT" has been proposed. In this new framework, the apparent matter unification can be explained by a chiral gauge group G, G ⊃ SU(5). We emphasize that the SM matter fields are not necessarily embed- ded into the chiral representations to explain the apparent unification. In this paper, we discuss details of concrete realizations of the fake GUT model. We first study the model based on SU(5) × U(2)H, where SU(3)c in the SM is from SU(5) while SU(2)L× U(1)Y are from the diagonal subgroups of SU(5) × U(2)H. We also extend this model to the one based on a semi-simple group, SU(5) × SU(3)H, so that U(2)H is embedded in SU(3)H. We also show that this framework predicts rather different decay patterns of the proton, compared to the conventional GUT. [ABSTRACT FROM AUTHOR]

Acetate kinase catalyzes the reversible magnesium-dependent phosphoryl transfer from ATP to acetate to form acetyl phosphate and ADP. Here, we report functional and some structural properties of cold-adapted psychrotrophic enzyme; acetate kinase with those from mesophilic counterpart in Escherichia coli K-12. Recombinant acetate kinase from Shewanella sp. AS-11 (SAK) and E. coli K-12 (EAK) were purified to homogeneity following affinity chromatography and followed by Super Q column chromatography as reported before []. Both purified enzymes are shared some of the common properties such as (similar molecular mass, amino acid sequence and similar optimum pH), but characterized shift in the apparent optimum temperature of specific activity to lower temperature as well as by a lower thermal stability compared with EAK. The functional comparisons reveal that SAK is a cold adapted enzyme, having a higher affinity to acetate than EAK. In the acetyl phosphate and ADP-forming direction, the catalytic efficiency ( k/ K) for acetate was 8.0 times higher for SAK than EAK at 10 °C. The activity ratio of SAK to EAK was increased with decreasing temperature in both of the forward and backward reactions. Furthermore, the activation energy, enthalpy and entropy in both reaction directions that catalyzed by SAK were lower than those catalyzed by EAK. The model structure of SAK showed the significantly reduced numbers of salt bridges and cation-pi interactions as compared with EAK. These results suggest that weakening of intramolecular electrostatic interactions of SAK is involved in a more flexible structure which is likely to be responsible for its cold adaptation. [ABSTRACT FROM AUTHOR]

The acetate kinase from the Antarctic psychrophilic Shewanella sp. AS-11 (SAK) has a significantly higher catalytic efficiency at low temperatures when compared with that from mesophilic Escherichia coli K-12 (EAK). To examine the stability and conformational flexibility of SAK and EAK, steady state intrinsic fluorescence studies were performed. EAK contains only one Trp at a position 46, while SAK contains two Trps at positions 46 and 388. From the fluorescence emission spectra, quenching with acrylamide, Cs and I at different temperatures and denaturation with guanidine-HCl, it was revealed that the SAK bears more flexible and unstable structure than that of EAK. Substrate-induced conformational changes reflect that SAK reached transition state through more conformational changes than EAK. In combination of our thermodynamic studies on the enzymatic reaction and present research findings, it can be concluded that these structural features of SAK may contribute to its high catalytic efficiency at low temperatures. [ABSTRACT FROM AUTHOR]

Abstract: We investigate solvation dynamics of organogel utilizing ps–ns fluorescence spectroscopy. The organogel studied in this Letter comprises bis(2-ethylhexyl) sulfosuccinate (AOT) and p-chlorophenol in the m-xylene solvent, that produce an organogel architecture with self-assembly. Within the organogel, an emitting probe, coumarin 153 (C153), is embedded. We then obtain dynamic response functions of solvation derived from the time-resolved fluorescence spectra of C153. We propose that total energy of the C153–organogel system relaxes with a relaxation time of 3.9ns, whereas the entire rearrangement of the organogel structure around C153 is achieved with that of 6.1ns, respectively. [Copyright &y& Elsevier]

Describes the purification and some properties of novel antimicrobial peptides (AMP) from Fagopyrum esculentum, which have a potent and wide antimicrobial activity against various pathogens. Methods used for purification; Concentration of peptides required for 50 percent inhibition of the growth of plant pathogenic fungi and Gram-positive and -negative bacteria.

The complete amino acid sequence of ribosomal protein L2 from the moderate thermophile Bacillus stearothermophilus has been determined. This has been achieved by the sequence analysis of peptides derived by enzymatic digestion with Staphylococcus aureus protease, trypsin and chymotrypsin, as well as by chemical cleavage with o-iodosobenzoic acid. The protein contains 275 amino acid residues and has a calculated molecular mass of 30201 Da. Comparison of this sequence with sequences of the corresponding proteins from Escherichia coli and from spinach and tobacco chloroplasts reveals that 60% of the residues of protein L2 from B. stearothermophilus are identical to those of the protein from E. coli and 45% are identical to those found in the two chloroplast proteins. There are extended regions of totally conserved sequence at positions 54-58 (GGGHK), 81-86 (EYDPNR), and 224-230 (MNPVDHP) in all four proteins. [ABSTRACT FROM AUTHOR]

Inorganic pyrophosphatase (PPase) catalyses the hydrolysis reaction of inorganic pyrophosphate to phosphates. Our previous studies showed that manganese (Mn) activated PPase from the psychrophilic bacterium Shewanella sp. AS-11 (Mn-Sh-PPase) has a characteristic temperature dependence of the activity with an optimum at 5 °C. Here we report the X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy structural analyses of Sh-PPase in the absence and presence of substrate analogues. We successfully determined the crystal structure of Mn-Sh-PPase without substrate and Mg-activated Sh-PPase (Mg-Sh-PPase) complexed with substrate analogue (imidodiphosphate; PNP). Crystallographic studies revealed a bridged water placed at a distance from the di-Mn centre in Mn-Sh-PPase without substrate. The water came closer to the metal centre when PNP bound. EPR analysis of Mn-Sh-PPase without substrate revealed considerably weak exchange coupling, whose magnitude was increased by binding of substrate analogues. The data indicate that the bridged molecule has weak bonds with the di-Mn centre, which suggests a 'loose' structure, whereas it comes closer to di-Mn centre by substrate binding, which suggests a 'well-tuned' structure for catalysis. Thus, we propose that Sh-PPase can rearrange the active site and that the 'loose' structure plays an important role in the cold adaptation mechanism. [ABSTRACT FROM AUTHOR]

We investigated changes in starch content and starch metabolic enzyme activities in developing and postharvest squash of distinct species, Cucurbita maxima and Cucurbita moschata, which accumulate high and low levels of starch, respectively. The total activity of starch phosphorylase in developing fruits significantly correlated (r = 0.99) to the amount of starch among Cucurbita species (C. maxima, C. moschata and C. pepo). Separable activity of a plastidial L‐form phosphorylase in C. maxima fruit markedly increased corresponding with starch accumulation. We isolated two genes (CmPhoL1 and CmPhoH1) encoding an L‐form and a cytosolic H‐form phosphorylase from C. maxima fruit. The expression of CmPhoL1 in the fruit dramatically increased at the beginning of starch accumulation. Recombinant CmPhoL1 enzyme showed similar kinetic parameters in both glucan synthesis and phosphorolysis: this enzyme can catalyze the invertible reaction in vitro depending on the concentration of substrates. These results suggest that CmPhoL1 plays a role in the starch accumulation process during squash development, but the aid of other starch synthetic enzymes may be required for in vivo glucan synthesis reaction by CmPhoL1. An importance of plastidial starch phosphorylase in the starch accumulation in the fruit organ was indicated. [ABSTRACT FROM AUTHOR]

Protein crystallization and subsequent X-ray diffraction analysis of the three-dimensional structure are necessary for elucidation of the biological functions of proteins and effective rational drug design. Therefore, controlling protein crystallization is important to obtain high resolution X-ray diffraction data. Here, a simple microfluidic method using chips with 10 and 50 μm high crystallization chambers to selectively form suitable single protein crystals for X-ray analysis is demonstrated. As proof of concept, three different types of proteins: lysozyme, glucokinase from Pseudoalteromonas sp. AS-131 (PsGK), and NADPH-cytochrome P450 oxidoreductase–heme oxygenase complex were crystallized. We demonstrate that the crystal growth orientation depends on the height of the crystallization chamber regardless of the protein type. Our results suggest that the confined micro space induces the protein molecules to adhere to a specific crystal face and affects the growth kinetics of each crystal face. The present microfluidic-based protein crystallization method can reform a suitable single protein crystal for X-ray analysis from aggregates of needle-shaped protein crystals. [ABSTRACT FROM AUTHOR]

Isoprene emission from plants is very sensitive to environmental temperature both at short-term and long-term scales. Our previous study demonstrated suppression of isoprene emission by cold temperatures in a high emitting tropical tree Ficus septica and revealed a strong correlation of emission to isoprene synthase (IspS) protein levels. When challenged with decreasing daily temperatures from 30 to 12 °C, F. septica completely stopped isoprene emission at 12 °C, only to recover on the second day after re-exposure to 30 °C. Here, we explored this regulation of isoprene emission in response to environmental temperature by a comprehensive analysis of transcriptome data, gene expressions and metabolite pools of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. MEP pathway genes and metabolites dynamics did not support substrate-level limitations as major control over observed basal emission, but transcriptome data, network inferences and putative regulatory elements on IspS promoter suggested transcriptional regulation of IspS gene through circadian rhythm and phytohormone signalling processes. Expression levels of 29 genes involved in these pathways were examined by quantitative real-time PCR. We propose that temperature controls over basal isoprene emission at a time-scale of hours to few days are regulated by phytohormone-mediated transcriptional modulation of IspS gene under synchronization by the circadian clock. [ABSTRACT FROM AUTHOR]

Tropical trees account for most emissions of isoprene, a reactive biogenic volatile organic compound into the atmosphere. The Guenther 1993 (G-93) model is the most widely used algorithm for predicting isoprene emissions by leaves of terrestrial plants. Several studies have reported on the poor performance of the G-93 model in predicting emissions from tropical tree species. To improve the performance of the G-93 model in tropical regions, we carried out diurnal leaf-scale observations of tropical trees Casuarina equisetifolia and Ficus septica outdoors. We developed an iterative method that uses mutual and repetitive step-by-step optimization of the G-93 parameters for temperature ( C T ) and light ( C L ) variables using best fit practices, named “Ping-Pong” optimization. Using temperate tree species (Poplar) for comparison, we show that emissions from C . equisetifolia and F . septica had a diversion from predictions of the G-93 formula, especially at high temperatures and high light intensities during mid-day, whilst emissions from temperate tree species were fairly captured by G-93. Results demonstrate that our optimized formulas greatly improved capturing of high light and temperature responses of emission profiles from tropical trees whilst it also performed well for poplar species. Parameterization of the G-93 formula greatly improved its performance on predicting diurnal isoprene emission from tropical trees C . equisetifolia and F . septica ; explaining 81–96% of variation up from 73 to 77% explained by default G-93. We propose that there is a need to optimize the G-93 model to more accurately predict regional emissions from tropical ecosystems. [ABSTRACT FROM AUTHOR]

[Display omitted] • We discovered a ricefish species from a river in central Sulawesi. • This river shares estuarine waters with another river where its sister species occurs. • These two species are genetically isolated despite freshwater drainage connectivity. • Coalescent-based demographic inference demonstrated that they are of lake-origin. • They are probably relic species left in these rivers due to lost dispersal ability. Sulawesi is a biodiversity hotspot for ricefishes (Adrianichthyidae), with many species endemic to the central part of this island in single ancient lakes or lake systems. Frequent vicariance by lake fragmentation since the Pliocene may be largely responsible for diversification in this family. In this study, we demonstrate that not only lacustrine species but also riverine species in this area are also deeply divergent even within a single river system. A mitochondrial phylogeny revealed that a ricefish population newly discovered from Cerekang River is sister to Oryzias dopingdopingensis Mandagi, Mokodongan, Tanaka, & Yamahira, another riverine species endemic to Doping-doping River. However, the Cerekang Oryzias was genetically isolated from O. dopingdopingensis , despite that Cerekang River and Doping-doping River share a connection across estuarine waters. This separation was supported by phylogenomic trees and population genetic structure analyses based on genome-wide single nucleotide polymorphisms. Coalescent-based demographic inference demonstrated that the ancestral population of these two riverine ricefishes had experienced a substantial population decrease and subsequently diverged into two sub-populations. Because the Cerekang Oryzias was also morphologically distinguished from O. dopingdopingensis , we described it as a new species, O. landangiensis. We infer that O. landangiensis and O. dopingdopingensis are of lake-origin and are relic species which were left in these rivers after the lake disappeared, and that they have lost their dispersal ability when inhabiting the ancient lake. The lost dispersal ability possibly contributed to the formation of the biodiversity hotspot for this fish group on this island. [ABSTRACT FROM AUTHOR]

Nucleoside diphosphate kinase isolated from psychrophilic Pseudoalteromonas sp. AS-131 (ASNDK) was expressed in Escherichia coli and purified to homogeneity. Comparing to mesophilic NDK isolated from Pseudomonas aeruginosa, ASNDK exhibited highly elevated thermolability: E. coli expression at 37 °C as a denatured insoluble form, 30 °C lower optimum temperature of enzymatic activity, and greatly reduced heat stability with 38 °C lower Tm value, fourfold higher Km and reduced Kcat/Km by 0.4-fold upon reaction temperature increase from 20 to 37 °C. The subunit structure of ASNDK was suggested to be dimer, as in NDKs isolated from moderate halophiles. [ABSTRACT FROM AUTHOR]

Mn ions influence the activity, temperature dependence, and thermostability of the psychrophilic Shewanella-PPase ( Sh-PPase), and are required to function in cold environments. The functional characteristics of Sh-PPase on activation with Mn ions are possibly related to conformational changes in the molecule. In this study, conformational changes of Sh-PPase on activation with Mn ions were analyzed in solution by fluorescence spectroscopy analysis of intrinsic tryptophan residues, 1-anilino-8-naphthalene sulfonate fluorescence, and circular dichroism spectroscopy. For Sh-PPase, Mn ions did not affect the flexibility of the tryptophan residues and secondary structure of the enzyme. However, the microenvironment of the tryptophan residues and surface area of Sh-PPase were more hydrophilic on activation with Mn ions. These results indicate that activation with Mn ions causes conformational changes around the aromatic amino acid residues and affects the hydrophobicity of the enzyme surface, which results in conformational changes. Substrate-induced conformational changes reflect that metal-free Sh-PPase in solution indicated an open structure and will be a close structure when binding substrate. In combination of our spectroscopic analyses on Sh-PPase, it can be concluded that activation with Mn ions changes some conformation of Sh-PPase molecule in solution. [ABSTRACT FROM AUTHOR]

The structural feature of unfolding intermediate of pokeweed anti-viral protein (PAP) was characterized using time-resolved fluorescence spectroscopic methods to elucidate protein folding/unfolding process. CD and fluorescence spectra consistently demonstrated that the unfolding of PAP completed at 4 M of guanidine hydrochloride (GuHCl). The fluorescence resonance energy transfer (FRET) and time-resolve fluorescence depolarization analysis of Trp208 and Trp237 located in the C-terminal domain of PAP suggested that peculiar unfolding intermediate populated before reaching to the unfolding state. The FRET distance of Trp237 to Tyr182 was extended to more than 28 Å with keeping the compact conformation in the unfolding intermediate state populated in the presence of 2 M GuHCl. On the other hand, Trp208 maintained the energy transfer pair with Tyr72 near the active site, although the rotational freedom was increased a little. There results suggest that the most distinguished structural feature of the unfolding intermediate of PAP is the separation of C-terminal domain from N-terminal domain. FRET and fluorescence depolarization studies also showed that C-terminal domain would be more separated to liberate the segmental motions of Trp208 and Trp237 distinctly at the unfolding state. [ABSTRACT FROM AUTHOR]

Abstract: A comparison of the primary structures among psychrophilic, mesophilic, and thermophilic subtilases revealed that the turn between the β8 and β9 strands (β8–β9 turn, BPN′ numbering) of psychrophilic subtilases are more flexible than those of their mesophilic and thermophilic counterparts. To investigate the relationship between structure of this turn and enzyme activity as well as thermostability of mesophilic subtilisin Carlsberg (sC), we analyzed 6 mutants of sC with a single, double, or triple Gly or Ala substitutions for Pro210Thr211Asn212 at the β8–β9 turn. Among the single Gly substitutions, the P210G substitution most significantly (1.5-fold) increased the specific activity on N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide (AAPF) substrate and 12-fold decreased the thermostability. All mutants tested showed the increased k cat for the AAPF substrate and reduced thermostability compared with the wild-type sC. The k cat values of the P210G, P210G/T211G, and P210G/T211G/N212G mutants were 1.5-, 1.7-, and 1.8-fold higher than that of the wild-type sC. There were significant positive correlations between k cat and thermal inactivation rates as well as k cat and K m of the wild-type and mutants. These results demonstrate that the structure of β8–β9 turn, despite its distance from the active site, has significant effects on the catalytic rate and thermostability of sC through a global network of intramolecular interactions and suggest that the lack of flexibility of this turn stabilizes the wild-type sC against thermal inactivation in compensation for some loss of catalytic activity. [Copyright &y& Elsevier]

Abstract: Novel antimicrobial peptides (AMP), designated Cy-AMP1, Cy-AMP2, and Cy-AMP3, were purified from seeds of the cycad (Cycas revoluta) by a CM cellulofine column, ion-exchange HPLC on SP COSMOGEL, and reverse-phase HPLC. They had molecular masses of 4583.2Da, 4568.9Da and 9275.8Da, respectively, by MALDI–TOF MS analysis. Half of the amino acid residues of Cy-AMP1 and Cy-AMP2 were cysteine, glycine and proline, and their sequences were similar. The sequence of Cy-AMP3 showed high homology to various lipid transfer proteins. For Cy-AMP1 and Cy-AMP2, the concentrations of peptides required for 50% inhibition (IC50) of the growth of plant pathogenic fungi, Gram-positive and Gram-negative bacteria were 7.0–8.9μg/ml. The Cy-AMP3 had weak antimicrobial activity. The structural and antimicrobial characteristics of Cy-AMP1 and Cy-AMP2 indicated that they are a novel type of antimicrobial peptide belonging to a plant defensin family. [Copyright &y& Elsevier]

Abstract: β-Galactosidases (EC 3.2.1.23; β-Gals) consist of several isoforms which have different activity levels against native and synthetic substrates and play an important role in cell wall metabolism during fruit growth and ripening. In this study, we isolated three new β-Gal cDNA clones, PaGAL2, PaGAL3 and PaGAL4, from the fruit of ripening avocado in addition to the AV-GAL1 clone previously obtained. The expression patterns of these genes during fruit ripening were quite different. The AV-GAL1 transcript, which was solely found in the fruit, accumulated with fruit ripening. PaGAL2 transcript, which was detected in leaves, shoots, roots and fruit, showed a constant level throughout fruit ripening. The level of PaGAL3 transcript in control fruit, which was not detected in root but only in other tissues, increased markedly at 2 days after treatment (DAT) (air treatment) and dropped quickly at 4DAT in fruit. The transcript was not detectable at 6DAT and thereafter. The PaGAL4 transcript was detected in all tissues except for the fruit. In order to investigate the role of ethylene, on the regulation of β-Gal expression, pre-ripe fruit were treated with either ethylene or its inhibitor 1-methylcyclopropene (1-MCP). Exogenous ethylene promoted AV-GAL1 expression but severely suppressed PaGAL3 expression. Ethylene also affected the activities of fractionated β-Gal isozymes in a differential manner. Among the three isozymes, the increase in AV-GAL III activity with fruit softening were promoted by exogenous ethylene and delayed by 1-MCP. However, no apparent changes in the activities were observed in the other two isozymes. Based on the results obtained, it seems that AV-GAL1, which may encode AV-GAL III, is important for postharvest fruit softening while PaGAL2, PaGAL3 and PaGAL4 may be involved in galactose metabolism of cells or cell walls during development and ripening. [Copyright &y& Elsevier]

Investigates the amino acid sequence and antimicrobial activity of chitin-binding peptides, Pp-AMP 1 and Pp-AMP 2, from Japanese bamboo shoots (Phyllostachys pubescens). Structural features of the chitin-binding peptides; High degree of homology shown by the peptides to mistletoe toxins.

Describes the purification and properties of two novel chitin-binding antimicrobial peptides from Tulipa gesneriana L. using chitin affinity chromatography. Characteristic properties of antimicrobial peptides; Antimicrobial activity of these two antimicrobial peptides against various pathogenic microorganisms; Function of antimicrobial peptides as self-defense against infection by various harmful pathogens.

Focuses on a study which evaluated the localization of glutathione peroxidase in the photoreceptor cells and the retinal pigment epithelial cells of Wistar and Royal college of Surgeons dystrophic rats. Materials and methods used; Results of the study; Conclusion.