Phenylpropanoid amides of serotonin accumulate in witches' broom diseased bamboo

Aciculosporium take (Ascomycota; Clavicipitaceae), causes the witches' broom disease in bamboo, particularly Phyllostachys bambusoides. Since it was observed that endogenous indole-3-acetic acid is reduced in the twigs of the diseased bamboo, the symptoms (bushy appearance) may be induced by reduction in auxin levels. Furthermore, two indolic compounds accumulated in diseased twigs, these being identified as N-p-coumaroylserotonin and N-feruloylserotonin by LC-MS, 1H NMR and 13C NMR spectroscopic analyses. N-p-Coumaroylserotonin possesses antifungal activity against A. take.     

Improving conditional random field model for prediction of protein-RNA residue-base contacts

Background: For understanding biological cellular systems, it is important to analyze interactions between protein residues and RNA bases. A method based on conditional random fields (CRFs) was developed for predicting contacts between residues and bases, which receives multiple sequence alignments for given protein and RNA sequences, respectively, and learns the model with many parameters involved in relationships between neighboring residue-base pairs by maximizing the pseudo likelihood function. Methods: In this paper, we proposed a novel CRF-based model with more complicated dependency relationships between random variables than the previous model, but which takes less parameters for the sake of avoidance of overfitting to training data. Results: We performed cross-validation experiments for evaluating the proposed model, and took the average of AUC (area under receiver operating characteristic curve) scores. The result suggests that the proposed CRF-based model without using L₁-norm regularization (lasso) outperforms the existing model with and without the lasso under several input observations to CRFs. Conclusions: We proposed a novel stochastic model for predicting protein-RNA residue-base contacts, and improved the prediction accuracy in terms of the AUC score. It implies that more dependency relationships in a CRF could be controlled by less parameters.     

Origin and possible role of males in hermaphroditic androgenetic Corbicula clams

Hermaphroditic Corbicula leana clams reproduce by androgenesis and have been regarded as simultaneous hermaphrodites. To date, there has been no report on the occurrence of male clams in hermaphroditic Corbicula. In an irrigation ditch in Shiga Prefecture, we found that 78.2% of C. leana specimens were males and 21.8% were hermaphrodites. Microfluorometric analysis revealed that males were diploids and hermaphrodites were triploids. All males produced nonreductional and biflagellate spermatozoa. The sequence analysis of mitochondrial DNA (cytochrome b, 621 bp) for 31 specimens of C. leana showed that four male and nine hermaphrodites shared the same H2 mtDNA haplotype; H1 was detected from 17 males and H3 was detected from one hermaphrodite. Coexisting C. fluminea clams also have haplotypes H1 and H2. Phylogenetic tree by a neighborjoining method based on the partial sequence of cytochrome b revealed that the haplotypes (H1- 3) of C. leana were evidently different from those of dioecious C. sandai (S1 and S2) and C. japonica (J1 and J2). These results suggest that males may be derived from hermaphrodite C. leana clams. The role of males in hermaphroditic populations is unknown. However, if the spermatozoon from a male is able to fertilize an egg from a hermaphrodite and the nuclear genome of the egg is expelled as polar bodies, the sperm nucleus could form a zygote nucleus. This mode of reproduction would allow the replacement of the nuclear genome.     

Loss of protease dimerization inhibition activity of darunavir is associated with the acquisition of resistance to darunavir by HIV-1

Dimerization of HIV protease is essential for the acquisition of protease's proteolytic activity. We previously identified a group of HIV protease dimerization inhibitors, including darunavir (DRV). In the present work, we examine whether loss of DRV's protease dimerization inhibition activity is associated with HIV development of DRV resistance. Single amino acid substitutions, including I3A, L5A, R8A/Q, L24A, T26A, D29N, R87K, T96A, L97A, and F99A, disrupted protease dimerization, as examined using an intermolecular fluorescence resonance energy transfer (FRET)-based HIV expression assay. All recombinant HIV(NL4-3)-based clones with such a protease dimerization-disrupting substitution failed to replicate. A highly DRV-resistant in vitro-selected HIV variant and clinical HIV strains isolated from AIDS patients failing to respond to DRV-containing antiviral regimens typically had the V32I, L33F, I54M, and I84V substitutions in common in protease. None of up to 3 of the 4 substitutions affected DRV's protease dimerization inhibition, which was significantly compromised by the four combined substitutions. Recombinant infectious clones containing up to 3 of the 4 substitutions remained sensitive to DRV, while a clonal HIV variant with all 4 substitutions proved highly resistant to DRV with a 205-fold 50% effective concentration (EC(50)) difference compared to HIV(NL4-3). The present data suggest that the loss of DRV activity to inhibit protease dimerization represents a novel mechanism contributing to HIV resistance to DRV. The finding that 4 substitutions in PR are required for significant loss of DRV's protease dimerization inhibition should at least partially explain the reason DRV has a high genetic barrier against HIV's acquisition of DRV resistance.     

Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase

Glucokinase is a monomeric enzyme that displays a low affinity for glucose and a sigmoidal saturation curve for its substrate, two properties that are important for its playing the role of a glucose sensor in pancreas and liver. The molecular basis for these two properties is not well understood. Herein we report the crystal structures of glucokinase in its active and inactive forms, which demonstrate that global conformational change, including domain reorganization, is induced by glucose binding. This suggests that the positive cooperativity of monomeric glucokinase obeys the "mnemonical mechanism" rather than the well-known concerted model. These structures also revealed an allosteric site through which small molecules may modulate the kinetic properties of the enzyme. This finding provided the mechanistic basis for activation of glucokinase as a potential therapeutic approach for treating type 2 diabetes mellitus.     

Biological activities caused by far-infrared radiation

Contrary to previous presumption, accumulated evidence indicates that far-infrared rays are biologically active. A small ceramic disk that emist far-infrared rays (4–16 m) has commonly been applied to a local spot or a whole part of the body for exposure. Pioneering attempts to experimentally analyze an effect of acute and chronic radiation of far-infrared rays on living organisms have detected a growth-promoting effect in growing rats, a sleep-modulatory effect in freely behaving rats and an insomiac patient, and a blood circulation-enhancing effect in human skin. Question-paires to 542 users of far-infrared radiator disks embedded in bedelothes revealed that the majority of the users subjectively evaluated an improvement of their health. These effects on living organisms appear to be non-specifically triggered by an exposure to far-infrared rays, which eventually induce an increase in temperature of the body tissues or, more basically, an elevated motility of body fluids due to decrease in size of water clusters.     

Structural and molecular interactions of CCR5 inhibitors with CCR5

We have characterized the structural and molecular interactions of CC-chemokine receptor 5 (CCR5) with three CCR5 inhibitors active against R5 human immunodeficiency virus type 1 (HIV-1) including the potent in vitro and in vivo CCR5 inhibitor aplaviroc (AVC). The data obtained with saturation binding assays and structural analyses delineated the key interactions responsible for the binding of CCR5 inhibitors with CCR5 and illustrated that their binding site is located in a predominantly lipophilic pocket in the interface of extracellular loops and within the upper transmembrane (TM) domain of CCR5. Mutations in the CCR5 binding sites of AVC decreased gp120 binding to CCR5 and the susceptibility to HIV-1 infection, although mutations in TM4 and TM5 that also decreased gp120 binding and HIV-1 infectivity had less effects on the binding of CC-chemokines, suggesting that CCR5 inhibition targeting appropriate regions might render the inhibition highly HIV-1-specific while preserving the CC chemokine-CCR5 interactions. The present data delineating residue by residue interactions of CCR5 with CCR5 inhibitors should not only help design more potent and more HIV-1-specific CCR5 inhibitors, but also give new insights into the dynamics of CC-chemokine-CCR5 interactions and the mechanisms of CCR5 involvement in the process of cellular entry of HIV-1.     

The lattice models of neutral multi-alleles in population genetics theory

The aim of this article is to study lattice models of neutral multi-alleles including Ohta-Kimura's step-wise mutation model. We shall show an outline of the construction of a unique strongly continuous non-negative semi-group associated with the infinite dimensional generator and show a general and straightforward method of obtaining the time dependent and equilibrium solutions of all polynomial moments of the gene frequencies. We shall discuss the spectrum of the diffusion processes and as an application we obtain all higher moments of the homozygosity.     

Vasomotor effects of noradrenaline, acetylcholine, histamine, 5-hydroxytryptamine and bradykinin on snake (Trimeresurus flavoviridis) basilar arteries

We investigated the responsiveness of basilar arterial rings isolated from snakes to noradrenaline (NA), acetylcholine (ACh), histamine (His), 5-hydroxytryptamine (5-HT), mammalian bradykinin (BK) and rattlesnake BK. We also examined whether endothelial cells were involved in the responsiveness to ACh, BK, rattlesnake BK and in their resting vascular tone. NA and 5-HT induced concentration-dependent contractions. The cumulative concentration response curves of NA and 5-HT were shifted to the right in parallel by phentolamine (an alpha antagonist) and methiothepin (a 5-HT(1) and 5-HT(2) antagonist), respectively. However, ketanserin (a 5-HT(2) antagonist) had no effect on the cumulative concentration response curve of 5-HT. His, ACh, BK and rattlesnake BK had no effect on resting vascular tone; however, rattlesnake BK and sodium nitroprusside relaxed arteries precontracted by 5-HT. The rattlesnake BK-induced relaxations were almost abolished by L-nitro arginine (L-NA, a nitric oxide synthase inhibitor). L-NA and indomethacin (a cyclooxygenase inhibitor) had no effect on resting vascular tone or on precontracted arteries. These results suggest that alpha and 5-HT(1) receptor subtypes might be important in arterial contraction. Endothelial cells might play an important role in the responsiveness of snake basilar arteries to rattlesnake BK, but they might not be involved in the responsiveness to ACh, BK and in resting vascular tone.