Two distinct heme distal site states define Cerebratulus lacteus mini-hemoglobin oxygen affinity

The nerve tissue hemoglobin of Cerebratulus lacteus (CerHb) is the smallest naturally occurring known hemoglobin. Stabilization of the diatomic bound species (e.g., O(2)) is achieved through a network of hydrogen bonds based on three key residues TyrB10, GlnE7, and ThrE11. The first two residues are typically associated in hemoglobins with enhanced O(2) affinity, related to hydrogen bond stabilization of the heme-bound O(2) resulting in a decrease of the ligand dissociation rates. In contrast to the above observations, the affinity of CerHb for O(2) is only moderate, and the rate of O(2) dissociation is unexpectedly high. To gain insight on the diverse molecular mechanisms controlling ligand affinities, we have analyzed w.t. CerHb and its ThrE11-->Val mutant by means of joint molecular dynamics and quantum mechanics simulation techniques, complementing recent site-directed mutagenesis experiments. Our results suggest that the observed O(2) dissociation rates can only be explained through a dynamic equilibrium between high and low affinity states of the w.t. CerHb heme distal site.     

Computational and Empirical Trans-hydrogen Bond Deuterium Isotope Shifts Suggest that N1–N3 A:U Hydrogen Bonds of RNA are Shorter than those of A:T Hydrogen Bonds of DNA

Density functional theory calculations of isolated Watson–Crick A:U and A:T base pairs predict that adenine ¹³C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, ^2hΔ¹³C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that ^2hΔ¹³C2 is sensitive to hydrogen-bond strength. Calculated ^2hΔ¹³C2 values at a given N1–N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical ^2hΔ¹³C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on ^2hΔ¹³C2 values. Furthermore, ^2hΔ¹³C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that ^2hΔ¹³C2 is context dependent and that this dependence is similar for RNA and DNA. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Factors affecting phase synchronization in integrate-and-fire oscillators

Step changes in input current are known to induce partial phase synchrony in ensembles of leaky integrate-and-fire neurons operating in the oscillatory or “regular firing” regime. An analysis of this phenomenon in the absence of noise is presented based on the probability flux within an ensemble of generalized integrate-and-fire neurons. It is shown that the induction of phase synchrony by a step input can be determined by calculating the ratio of the voltage densities obtained from fully desynchronized ensembles firing at the pre and post-step firing rates. In the limit of low noise and in the absence of phase synchrony, the probability density as a function of voltage is inversely proportional to the time derivative along the voltage trajectory. It follows that the magnitude of phase synchronization depends on the degree to which a change in input leads to a uniform multiplication of the voltage derivative over the range from reset to spike threshold. This analysis is used to investigate several factors affecting phase synchronization including high firing rates, inputs modeled as conductances rather than currents, peri-threshold sodium currents, and spike-triggered potassium currents. Finally, we show that without noise, the equilibrium ensemble density is proportional to the phase response curve commonly used to analyze oscillatory systems. Action Editor: John Rinzel     

Genetic study on the physical properties of Coffea arabica L. wood

The physical characteristics of wood are not usually considered as selection criteria when breeding perennial species that are grown for their fruits or seeds. In the coffee tree, stem breakage during harvesting and lodging during the growth period are major defects in some cultivars. These defects are linked to certain physical and mechanical properties of the wood, such as density or rigidity, which can be characterized by a parameter used in the resistance of materials: the Modulus of Elasticity (MOE). Wood density and the longitudinal MOE were studied on the stems of coffee trees of the species Coffee arabica L., derived from a diallel mating design. The MOE was measured by an acoustic system based on an analysis of the vibrations produced by a blow to the end of a piece of wood of known geometry. The MOE obtained in that way, along with the density of coffee tree stem wood, displayed substantial heritability. A strong link between the average internode length and the yield cumulated over 4 years was detected. Wood density was also correlated to yield and wood elasticity. Classification of parents according to the wood characteristics of their progenies depended on their degree of introgression by the species C. canephora. These traits could therefore be used to measure introgression, possibly as predictors of traits of agronomic interest, and as target traits in the creation of tall C. arabica varieties.

Arbuscular mycorrhizal fungi associated with the Meliaceae on Hainan island, China

Species richness, spore density, frequency of occurrence, and relative abundance of AM fungi were determined in rhizosphere soil samples from nine tropical rainforest sites on Hainan island, south China, and the arbuscular mycorrhizal (AM) status of members of the Meliaceae was examined. All 28 plant taxa investigated (25 species including two varieties of 1 species and three varieties of another) were colonized by AM fungi. The mean proportion of root length colonized was 56% (range 10–95%). Vesicles were observed in 27 and hyphal coils in 26 of the 28 plant taxa. Mycorrhizas were of the Paris-type or intermediate-type, with no Arum-type mycorrhizas observed. Species richness of AM fungi varied from 3 to 15 and spore density from 46 to 1,499 per 100 g rhizosphere soil. Of 33 AM fungal taxa in five genera isolated and identified, 18 belonged to Glomus, 9 to Acaulospora, 1 to Entrophospora, 2 to Gigaspora, and 3 to Scutellospora. Acaulospora and Glomus were the dominant genera identified. Glomus claroideum was the taxon most commonly isolated, with a frequency of occurrence of 56.5% and relative abundance of 10.4%. A positive correlation was found between percentage of root length colonization and species richness. However, there was no correlation between spore density and percentage of root length colonized by AM fungi.     

Characterization of nascent HDL particles and microparticles formed by ABCA1-mediated efflux of cellular lipids to apoA-I

The nascent HDL created by ABCA1-mediated efflux of cellular phospholipid (PL) and free (unesterified) cholesterol (FC) to apolipoprotein A-I (apoA-I) has not been defined. To address this issue, we characterized the lipid particles released when J774 mouse macrophages and human skin fibroblasts in which ABCA1 is activated are incubated with human apoA-I. In both cases, three types of nascent HDL containing two, three, or four molecules of apoA-I per particle are formed. With J774 cells, the predominant species have hydrodynamic diameters of approximately 9 and 12 nm. These discoidal HDL particles have different FC contents and PL compositions, and the presence of acidic PL causes them to exhibit alpha-electrophoretic mobility. These results are consistent with ABCA1 located in more than one membrane microenvironment being responsible for the production of the heterogeneous HDL. Activation of ABCA1 also leads to the release of apoA-I-free plasma membrane vesicles (microparticles). These larger, spherical particles released from J774 cells have the same PL composition as the 12 nm HDL and contain CD14 and ganglioside, consistent with their origin being plasma membrane raft domains. The various HDL particles and microparticles are created concurrently, and there is no precursor-product relationship between them. Importantly, a large fraction of the cellular FC effluxed from these cells by ABCA1 is located in microparticles. Collectively, these results show that the products of the apoA-I/ABCA1 interaction include discoidal HDL particles containing different numbers of apoA-I molecules. The cellular PLs and cholesterol incorporated into these nascent HDL particles originate from different cell membrane domains.     

Epigallocatechin gallate increases the formation of cytosolic lipid droplets and decreases the secretion of apoB-100 VLDL

Epigallocatechin gallate (EGCG) increases the formation of cytosolic lipid droplets by a mechanism that is independent of the rate of triglyceride biosynthesis and involves an enhanced fusion between lipid droplets, a process that is crucial for their growth in size. EGCG treatment reduced the secretion of both triglycerides and apolipoprotein B-100 (apoB-100) VLDLs but not of transferrin, albumin, or total proteins, indicating that EGCG diverts triglycerides from VLDL assembly to storage in the cytosol. This is further supported by the observed increase in both intracellular degradation of apoB-100 and ubiquitination of the protein (indicative of increased proteasomal degradation) in EGCG-treated cells. EGCG did not interfere with the microsomal triglyceride transfer protein, and the effect of EGCG on the secretion of VLDLs was found to be independent of the LDL receptor. Thus, our results indicate that EGCG promotes the accumulation of triglycerides in cytosolic lipid droplets, thereby diverting lipids from the assembly of VLDL to storage in the cytosol. Our results also indicate that the accumulation of lipids in the cytosol is not always associated with increased secretion of VLDL.     

Increased sphingomyelin content impairs HDL biogenesis and maturation in human Niemann-Pick disease type B

We previously reported that human Niemann-Pick Disease type B (NPD-B) is associated with low HDL. In this study, we investigated the pathophysiology of this HDL deficiency by examining both HDL samples from NPD-B patients and nascent high density lipoprotein (LpA-I) generated by incubation of lipid-free apolipoprotein A-I (apoA-I) with NPD-B fibroblasts. Interestingly, both LpA-I and HDL isolated from patient plasma had a significant increase in sphingomyelin (SM) mass ( approximately 50-100%). Analysis of LCAT kinetics parameters (V(max) and K(m)) revealed that either LpA-I or plasma HDL from NPD-B, as well as reconstituted HDL enriched with SM, exhibited severely decreased LCAT-mediated cholesterol esterification. Importantly, we documented that SM enrichment of NPD-B LpA-I was not attributable to increased cellular mass transfer of SM or unesterified cholesterol to lipid-free apoA-I. Finally, we obtained evidence that the conditioned medium from HUVEC, THP-1, and normal fibroblasts, but not NPD-B fibroblasts, contained active secretory sphingomyelinase (S-SMase) that mediated the hydrolysis of [(3)H]SM-labeled LpA-I and HDL(3). Furthermore, expression of mutant SMase (DeltaR608) in CHO cells revealed that DeltaR608 was synthesized normally but had defective secretion and activity. Our data suggest that defective S-SMase in NPD leads to SM enrichment of HDL that impairs LCAT-mediated nascent HDL maturation and contributes to HDL deficiency. Thus, S-SMase and LCAT may act in concert and play a crucial role in the biogenesis and maturation of nascent HDL particles.     

Inhibition of lipid synthesis through activation of AMP kinase: an additional mechanism for the hypolipidemic effects of berberine

The alkaloid drug berberine (BBR) was recently described to decrease plasma cholesterol and triglycerides (TGs) in hypercholesterolemic patients by increasing expression of the hepatic low density lipoprotein receptor (LDLR). Using HepG2 human hepatoma cells, we found that BBR inhibits cholesterol and TG synthesis in a similar manner to the AMP-activated protein kinase (AMPK) activator 5-aminoimidazole-4-carboxamide 1-beta-ribofuranoside (AICAR). Significant increases in AMPK phosphorylation and AMPK activity were observed when the cells were incubated with BBR. Activation of AMPK was also demonstrated by measuring the phosphorylation of acetyl-CoA carboxylase, a substrate of AMPK, correlated with a subsequent increase in fatty acid oxidation. All of these effects were abolished by the mitogen-activated protein kinase kinase inhibitor PD98059. Treatment of hyperlipidemic hamsters with BBR decreased plasma LDL cholesterol and strongly reduced fat storage in the liver. These findings indicate that BBR, in addition to upregulating the LDLR, inhibits lipid synthesis in human hepatocytes through the activation of AMPK. These effects could account for the strong reduction of plasma TGs observed with this drug in clinical trials.