Computer simulation of surface-induced aggregation of ferritin.

Models are presented describing the transient mass-transport limited adsorption and cluster growth of ferritin at a solid surface. Computer simulations are carried out on a hexagonal lattice using a computer model that can be characterized as a two-dimensional stochastic cellular automaton allowing different rules regarding association, lateral interaction and dissociation to be incorporated in the model. The fractal dimensions of individual clusters were extracted from simulated aggregates and for similar rules found to be consistent with literature values on reversible diffusion-limited aggregation in two dimensions. The distribution of clusters versus free surface were shown to be affected by neighbor-dependent association probability. Low fractal dimension clusters were generated by a combination of strong lateral cohesion and neighbor-dependent dissociation to the bulk. By comparing computer simulated aggregation to experimental electron micrographs of adsorbed ferritin layers it is suggested that neighbor-dependent association, neighbor-dependent dissociation and lateral interactions are important factors in the complex dynamics of adsorbed protein layers.     

Molecular and morphometric analyses identify new lineages within a large Eumida (Annelida) species complex

We report on two new lineages of the Eumida sanguinea complex from Great Britain and describe one of them as a new species using a multilocus approach, including the mitochondrial DNA COI-5P and the nuclear markers ITS (ITS1, 5.8S rRNA and ITS2) and 28S rRNA. The molecular analysis placed Eumida mackiei sp. nov. in a monophyletic clade with 19.1% (COI), 10.1% (ITS) and 1.7% (28S) mean distance to its nearest neighbour. Molecular diagnoses were also applied to nine lineages within the E. sanguinea complex. This was complemented with morphometric data employing multivariate statistical analysis and the incorporation of statistical dissimilarities against three other described species from the complex. Eumida mackiei sp. nov. can be distinguished from E. notata and E. maia by the larger distance between the eyes and differences in morphometric proportions mainly in the dorsal and ventral cirri as well as in the prostomial appendages. E. sanguinea sensu stricto failed to produce a cluster of its own in the morphometric analysis, probably due to juvenile bias. Integrative taxonomy provided strong evidence to formally describe a new cryptic species that can now be used in biomonitoring or other relevant ecological research.     

Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation

The signal produced by fluorescence in situ hybridization (FISH) often is inconsistent among cells and sensitivity is low. Small DNA targets on the chromatin are difficult to detect. We report here an improved nick translation procedure for Texas red and Alexa Fluor 488 direct labeling of FISH probes. Brighter probes can be obtained by adding excess DNA polymerase I. Using such probes, a 30?kb yeast transgene, and the rp1, rp3 and zein multigene clusters were clearly detected.     

FracMod: A computational tool for assessing IMRT field modulation

The authors develop and investigate a user-friendly computational tool (FracMod) to quantify modulation complexity in planned IMRT fields.FracMod comprises a graphical user interface and variogram fractal dimension (FD) analysis tool developed by the authors using MATLAB^®, and made freely available at http://www.medphysfiles.com/index.php. FracMod is investigated for its ability to identify overly-modulated dynamic IMRT fields designed for prostatic carcinoma treatments. A set of 5 prostate alone plans and 5 prostate plus pelvic node plans were used to choose FD cut-points that ensure no false positives in distinguishing between moderate and high field modulation. IMRT quality control (QC) was performed on all the treatment fields using Varian^® Portal Dosimetry and MapCHECK?. Receiver operating characteristic analysis was used to quantitatively compare the classification performance of FD and the number of monitor units (MUs). The effect of dose rate on the average leaf pair opening (ALPO) and the number of MUs delivered was also investigated.The variogram FD performed better than the number of MUs in identifying overly-modulated fields.FD thresholds >2.15 for prostate alone and >2.20 for prostate plus pelvic nodes correctly identified 75% and 100% of the high modulation fields, respectively, with no false positives. With appropriate cut-points, MapCHECK? identified the most highly modulated IMRT fields, whereas Varian^® Portal Dosimetry could not. As expected, ALPO decreases with increasing modulation and increasing dose rate.FracMod is a user-friendly tool that allows one to accurately quantify and identify overly-modulated IMRT fields at the treatment planning stage before they are sent for patient-specific QC.     

Atomistic details of effect of disulfide bond reduction on active site of Phytase B from Aspergillus niger: A MD Study

The molecular integrity of the active site of phytases from fungi is critical for maintaining phytase function as efficient catalytic machines. In this study, the molecular dynamics (MD) of two monomers of phytase B from Aspergillus niger, the disulfide intact monomer (NAP) and a monomer with broken disulfide bonds (RAP), were simulated to explore the conformational basis of the loss of catalytic activity when disulfide bonds are broken. The simulations indicated that the overall secondary and tertiary structures of the two monomers were nearly identical but differed in some crucial secondary–structural elements in the vicinity of the disulfide bonds and catalytic site. Disulfide bonds stabilize the β-sheet that contains residue Arg66 of the active site and destabilize the α-helix that contains the catalytic residue Asp319. This stabilization and destabilization lead to changes in the shape of the active–site pocket. Functionally important hydrogen bonds and atomic fluctuations in the catalytic pocket change during the RAP simulation. None of the disulfide bonds are in or near the catalytic pocket but are most likely essential for maintaining the native conformation of the catalytic site.

Abbreviations

PhyB - 2.5 pH acid phophatese from Aspergillus niger, NAP - disulphide intact monomer of Phytase B, RAP - disulphide reduced monomer of Phytase B, Rg - radius of gyration, RMSD - root mean square deviation, MD - molecular dynamics.     

Effect of weight loss and exercise on angiogenic factors in the circulation and in adipose tissue in obese subjects

Background:

Vascular growth is a prerequisite for adipose tissue (AT) development and expansion. Some AT cytokines and hormones have effects on vascular development, like vascular endothelial growth factor (VEGF‐A), angiopoietin (ANG‐1), ANG‐2 and angiopoietin‐like protein‐4 (ANGPTL‐4).

Methods:

In this study, the independent and combined effects of diet‐induced weight loss and exercise on AT gene expression and proteins levels of those angiogenic factors were investigated. Seventy‐nine obese males and females were randomized to: 1. Exercise‐only (EXO; 12‐weeks exercise without diet‐restriction), 2. Hypocaloric diet (DIO; 8‐weeks very low energy diet (VLED) + 4‐weeks weight maintenance diet) and 3. Hypocaloric diet and exercise (DEX; 8‐weeks VLED + 4‐weeks weight maintenance diet combined with exercise throughout the 12 weeks). Blood samples and fat biopsies were taken before and after the intervention.

Results:

Weight loss was 3.5 kg in the EXO group and 12.3 kg in the DIO and DEX groups. VEGF‐A protein was non‐significantly reduced in the weight loss groups. ANG‐1 protein levels were significantly reduced 22‐25% after all three interventions (P < 0.01). The ANG‐1/ANG‐2 ratio was also decreased in all three groups (P < 0.05) by 27‐38%. ANGPTL‐4 was increased in the EXO group (15%, P < 0.05) and 9% (P < 0.05) in the DIO group. VEGF‐A, ANG‐1, and ANGPTL‐4 were all expressed in human AT, but only ANGPTL‐4 was influenced by the interventions.

Conclusions:

Our data show that serum VEGF‐A, ANG‐1, ANG‐2, and ANGPTL‐4 levels are influenced by weight changes, indicating the involvement of these factors in the obese state. Moreover, it was found that weight loss generally was associated with a reduced angiogenic activity in the circulation.