Functional Modeling and Phylogenetic Distribution of Putative Cylindrospermopsin Biosynthesis Enzymes

The alkaloid cylindrospermopsin is the most recently discovered cyanotoxin and has caused epidemic outbreaks of human poisoning. Cylindrospermopsin producing cyanobacteria have in recent times appeared in countries all over the world where they had not been observed previously and, thus, represent a global public health concern. Three putative cylindrospermopsin biosynthesis genes, encoding an amidinotransferase (aoaA), a nonribosomal peptide synthetase (aoaB), and a polyketide synthase (aoaC), have been described. Most cyanotoxins are the product of nonribosomal peptide and polyketide synthesis, but the involvement of an amidinotransferase is novel. In the present study, functional modeling was carried out to gain insight into the mechanism of precursor recruitment in cylindrospermopsin biosynthesis. In addition, the molecular phylogenies of putative cylindrospermopsin biosynthesis genes and producer organisms were determined. The model indicated that AoaA may catalyze the formation of guanidino acetate from glycine and arginine. The catalytic site of the AoaB adenylation domain provided two aspartate residues, instead of the usual one, which may be involved in the binding of the guanidino moiety of guanidino acetate. Molecular phylogenetic analysis grouped cylindrospermopsin producing cyanobacteria into two divergent groups. Although the phylogeny of the cylindrospermopsin biosynthesis genes followed that of the producer organisms, they were less divergent, which may indicate the recent horizontal transfer of these genes. [Reviewing Editor: Dr. Martin Kreitman]     

Comparison Between Tidally Driven Groundwater Flow and Flushing of Animal Burrows in Tropical Mangrove Swamps

Tidal groundwater in a mangrove swamp can return to the mangrove creek by one of two mechanisms: (a) it can either flow through the swamp soil due to the water table difference between the creek and the groundwater in the swamp; or (b) it can flow via tidal flushing of animal burrows. This paper compares the magnitude of these two mechanisms for different regions of a mangrove swamp. Direct groundwater flow rates resulting from water stored in the sediment as a consequence of infiltration, especially during and after tidal inundation, were calculated for every square meter in the surface of a mangrove forest from piezometer data. Flow rates of water due to burrow flushing were determined based on published surveys, by estimating the burrow volume and the percentage of the burrow water that is flushed at each tidal inundation. Although direct groundwater flux was found to decrease further away from the creek compared to close to the creek, it was also found to have a similar range as burrow flushing flow. Specifically, direct groundwater flow ranged from 0.004 to 0.04 m³/m²/day, whilst burrow flushing flux ranged from 0.01 to 0.04 m³/m²/day.Considering the errors involved in the experiments and calculations, these ranges can be considered as being the same and neither of the two processes can be considered as negligible compared to the other. As a consequence, surveys of groundwater processes in mangrove areas, and more generally in swamp and tidal areas where animal burrows are present, will need to consider both mechanisms. Investigations of the influence over flushing mechanisms of different residence times of the water in burrows and in the sediment body would also be recommended in order to establish salt and nutrient budget in mangrove swamps.     

Study of the residues involved in the binding of β1 to β3 subunits in the sodium channel

The voltage-gated sodium channel (VGSC) is a complex, which is composed of one pore-forming α subunit and at least one β subunit. Up to now, five β subunits are known: β1/β1A, β1B, β2, β3, and β4, encoded by four genes (SCN1B∼SCN4B). It is critical to have a deep understanding of the interaction between β1 and β3 subunits, two subunits which frequently appear in many diseases concurrently. In this study, we had screened out the new template of β1 subunit for homology modelling, which shares higher similarity to β3. Docking studies of the β1 and β3 homology model were conducted, and likely β1 and β3 binding loci were investigated. The results revealed that β1–β3 is more likely to form a di-polymer than β1–β1 based on molecular interaction analysis, including potential energy analysis, Van der Waals (VDW) energy analysis and electrostatic energy analysis, and in addition, consideration of the hydrogen bonds and hydrophobic contacts that are involved. Based on these analyses, the residues His122 and Lys140 of β1 and Glu 66, Asn 131, Asp 118, Glu 120, Glu133, Asn135, Ser 137 of β3 were predicted to play a functional role.     

Vascular network remodeling via vessel cooption, regression and growth in tumors

The transformation of the regular vasculature in normal tissue into a highly inhomogeneous tumor specific capillary network is described by a theoretical model incorporating tumor growth, vessel cooption, neo-vascularization, vessel collapse and cell death. Compartmentalization of the tumor into several regions differing in vessel density, diameter and in necrosis is observed for a wide range of parameters in agreement with the vessel morphology found in human melanoma. In accord with data for human melanoma the model predicts that microvascular density (MVD), regarded as an important diagnostic tool in cancer treatment, does not necessarily determine the tempo of tumor progression. Instead it is suggested that the MVD of the original tissue as well as the metabolic demand of the individual tumor cell plays the major role in the initial stages of tumor growth.     

Homology modeling and substrate binding study of Nudix hydrolase Ndx1 from Thermos thermophilus HB8

With homology modeling techniques, molecular mechanics, and molecular dynamics methods, a 3D structure model of Ndx1 is created and refined. This model is further assessed by Profile-3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed and the result indicates that Glu46, Arg88, and Glu90 are three important determinant residues in binding, as they have strong hydrogen bonding interactions and electrostatic interactions with Ap6A. In addition, we further find that three residues, Ser38, Leu39 and Glu46, coordinate enzyme-bound Mg2+ ions in complex N-A. The Glu46 is consistent with the experimental results by Iwai et al., and the other four residues mentioned above may also play vital roles in catalysis of Ndx1.