Specificity of Collybistin-Phosphoinositide Interactions: IMPACT OF THE INDIVIDUAL PROTEIN DOMAINS*

The regulatory protein collybistin (CB) recruits the receptor-scaffolding protein gephyrin to mammalian inhibitory glycinergic and GABAergic postsynaptic membranes in nerve cells. CB is tethered to the membrane via phosphoinositides. We developed an in vitro assay based on solid-supported 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membranes doped with different phosphoinositides on silicon/silicon dioxide substrates to quantify the binding of various CB2 constructs using reflectometric interference spectroscopy. Based on adsorption isotherms, we obtained dissociation constants and binding capacities of the membranes. Our results show that full-length CB2 harboring the N-terminal Src homology 3 (SH3) domain (CB2_SH3+) adopts a closed and autoinhibited conformation that largely prevents membrane binding. This autoinhibition is relieved upon introduction of the W24A/E262A mutation, which conformationally “opens” CB2_SH3+ and allows the pleckstrin homology domain to properly bind lipids depending on the phosphoinositide species with a preference for phosphatidylinositol 3-monophosphate and phosphatidylinositol 4-monophosphate. This type of membrane tethering under the control of the release of the SH3 domain of CB is essential for regulating gephyrin clustering.     

A Murine Model of Stent Implantation in the Carotid Artery for the Study of Restenosis

Despite the considerable progress made in the stent development in the last decades, cardiovascular diseases remain the main cause of death in western countries. Beside the benefits offered by the development of different drug-eluting stents, the coronary revascularization bears also the life-threatening risks of in-stent thrombosis and restenosis. Research on new therapeutic strategies is impaired by the lack of appropriate methods to study stent implantation and restenosis processes. Here, we describe a rapid and accessible procedure of stent implantation in mouse carotid artery, which offers the possibility to study in a convenient way the molecular mechanisms of vessel remodeling and the effects of different drug coatings.     

First record of the goby Buenia affinis Iljin, 1930 (Gobiidae) from the Aegean Sea and Sea of Marmara

Fourteen species of aphids (Hemiptera: Aphidoidea) are recorded as new to Saudi Arabia. These are: Aphis coreopsidis (Thomas, 1878); Aphis illinoisensis Shimer, 1866; Baizongia pistaceae (Linnaeus, 1767); Capitophorus elaeagni (del Guercio, 1894); Dysaphis plantaginea (Passerini, 1860); Eucarazzia elegans (Ferrari, 1872); Geoica lucifuga (Zehntner, 1897); Hayhurstia atriplicis (Linnaeus, 1761); Macrosiphoniella absinthii (Linnaeus, 1758); Macrosiphoniella sanborni (Gillette, 1908); Smynthurodes betae Westwood, 1849; Uroleucon cichorii (Koch, 1855), and Wahlgreniella nervata (Gillette, 1908). Among these, three species, i.e. A. coreopsidis, A. illinoisensis, and W. nervata are alien species.     

On-line preconcentration/determination of zinc from water,biological and food samples using synthesized chelating resin and flame atomic absorption spectrometry

An on-line flow injection pre-concentration-flame atomic absorption spectrometry method was developed to determine trace zinc in water (tap, dam, and well water), biological (hair and nail), and liver samples. As a solid phase extractant, a synthesized new chelating resin, poly(2-thiozylmethacrylamide-co-divinylbenzene-co-2-acrylamido-2-methyl-1-propane sulfonic acid) was used. The resin was characterized by Fourier transform infrared spectroscopy, elemental analysis, and surface area by nitrogen sorption. A pre-concentration factor of 40-fold for a sample volume of 12.6 mL was obtained by using the time-based technique. The detection limit for the pre-concentration method was found to be 2.2 μg L^?1. The precision (as RSD,%) for 10 replicate determinations at the 0.04 μg mL^?1 Zn concentration was 1.2%. The calibration graph using the pre-concentration system for zinc was linear with a correlation coefficient of 0.998 in the concentration range from 0.005 to 0.05 μg mL^?1. The applicability and accuracy of the developed method were estimated by the analysis spiked water, biological, liver samples (83–105%), and also certified reference material TMDA-70 (fortified lake water) and SPS-WW1 Batch 111-Wastewater. The results were in agreement with the certified values.     

Protein structure alignment and fast similarity search using local shape signatures

We present a new method for conducting protein structure similarity searches, which improves on the efficiency of some existing techniques. Our method is grounded in the theory of differential geometry on 3D space curve matching. We generate shape signatures for proteins that are invariant, localized, robust, compact, and biologically meaningful. The invariancy of the shape signatures allows us to improve similarity searching efficiency by adopting a hierarchical coarse-to-fine strategy. We index the shape signatures using an efficient hashing-based technique. With the help of this technique we screen out unlikely candidates and perform detailed pairwise alignments only for a small number of candidates that survive the screening process. Contrary to other hashing based techniques, our technique employs domain specific information (not just geometric information) in constructing the hash key, and hence, is more tuned to the domain of biology. Furthermore, the invariancy, localization, and compactness of the shape signatures allow us to utilize a well-known local sequence alignment algorithm for aligning two protein structures. One measure of the efficacy of the proposed technique is that we were able to perform structure alignment queries 36 times faster (on the average) than a well-known method while keeping the quality of the query results at an approximately similar level.     

Optimization of bovine serum albumin sorption and recovery by hydrogels

Aqueous two-phase systems are composed of aqueous solutions of either two water-soluble polymers, usually polyethylene glycol (PEG) and dextran (Dx), or a polymer and a salt, usually PEG and phosphate or sulfate. Partitioning of proteins in such systems provides a powerful method for separating and purifying mixtures of biomolecules by extraction. If one of the phase forming polymers is a crosslinked gel, then the solution-controlled gel sorption may be considered as a modification of aqueous two-phase extraction. Since PEG/dextran systems are widely used in aqueous two-phase extraction and dextran gels (Sephadex) are common chromatographic media, we choose a PEG/dextran gel system as a model system in this study. The partitioning behavior of pure bovine serum albumin (BSA) in PEG/dextran gel systems is investigated to see the effects of variations in PEG and NaCl concentrations on the partition coefficient K. By making use of the Box-Wilson experimental design, K is shown to be maximized at 9.8 (%, w/w) PEG and 0.2 M NaCl concentrations, respectively, as 182.     

FPV: fast protein visualization using Java 3D

MOTIVATION: Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D((TM)) are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison. RESULTS: In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could. AVAILABILITY: EPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/     

Age,growth and sexual development of solenette,Buglossidium luteum (Risso, 1810), in the central Aegean Sea

Age, growth, spawning period and maturity of the solenette (Buglossidium luteum Risso, 1810) were studied in the central Aegean Sea to provide fisheries managers with essential data for science‐based management. A total of 1220 samples were collected by trawl hauls from July 2004 to June 2007 in ?zmir Bay (Turkey). Sample sizes ranging from 5.3 to 11.6 cm total length were composed of 46% females, 32% males and 22% immature individuals, with a female to male ratio of 1 : 0.7. Age composition stages of the females were from I to IV, and males between I and III. The length–weight relationship was calculated as W = 0.0101L^3.008 for all samples. Estimated von Bertalanffy growth parameters were L = 13.30 cm, t_o = ?0.440 year and k = 0.481 year^?1, with a growth performance index of 1.93 (?’). The spawning period began in April and continued until July. Lengths at first maturity of females and males were 8.1 and 7.9 cm total length, respectively. Both sexes matured at the age of 2 years.     

Investigation of the VDR gene polymorphisms association with susceptibility to colorectal cancer

The effects of 1,25-dihydroxyvitamin D3 are mediated by binding to a specific intracellular vitamin D receptor (VDR), which has been identified in a variety of tissues. Certain polymorphisms in the VDR gene have been associated with various neoplasms. For this purpose, we studied whether VDR TaqI or FokI genotype are associated with serum 25-hydroxyvitamin D3 in 52 controls and 26 patients with colorectal cancer. Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP), and agarose gel electrophoresis tecniques were used to detect these polymorphisms. We measured 25-hydroxyvitamin D3 serum levels by ELISA. The frequencies of the FF, Ff and ff genotypes were 73.1%, 11.5%, 15.4% in colorectal cancer patients and 38.5%, 59.6%, 1.9% in healthy controls, respectively. We observed the T allele in 50% and 58.7%, and the t allele in 50% and 41.3% of colorectal cancer patients and the control group, respectively. In patients with colorectal cancer who have TT genotype, serum 25-hydroxyvitamin D3 level was lower than those with Tt/tt genotype (p:0.016). The frequency of subjects with TTFf or TtFf genotype in colorectal cancer patients was very low compared with all other genotypes (OR = 0.112; 95%CI 0.030-0.419). These data suggest that VDR TtFf or TTFf genotypes may protect against colorectal carcinogenesis. However, further studies are necessary to confirm these findings.     

Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework

Species abundance distributions (SADs) follow one of ecology's oldest and most universal laws – every community shows a hollow curve or hyperbolic shape on a histogram with many rare species and just a few common species. Here, we review theoretical, empirical and statistical developments in the study of SADs. Several key points emerge. (i) Literally dozens of models have been proposed to explain the hollow curve. Unfortunately, very few models are ever rejected, primarily because few theories make any predictions beyond the hollow-curve SAD itself. (ii) Interesting work has been performed both empirically and theoretically, which goes beyond the hollow-curve prediction to provide a rich variety of information about how SADs behave. These include the study of SADs along environmental gradients and theories that integrate SADs with other biodiversity patterns. Central to this body of work is an effort to move beyond treating the SAD in isolation and to integrate the SAD into its ecological context to enable making many predictions. (iii) Moving forward will entail understanding how sampling and scale affect SADs and developing statistical tools for describing and comparing SADs. We are optimistic that SADs can provide significant insights into basic and applied ecological science.