Consortia,the importance of their study for phytocoenology

An idea is given of consortia, that is of elementary units of biocoenoses composed of single species of autotrophic plants and organisms intimately connected with them, chiefly heterotrophs. The dependence of different forms of interrelations between plants and organisms consortially connected with them is discussed.     

Sulfhydryl-reactive, cleavable, and radioiodinatable benzophenone photoprobes for study of protein-protein interaction

The major task in proteomics is to understand how proteins interact with their partners. The photo-cross-linking technique enables direct probing of protein-protein interaction. Here we report the development of three novel sulfhydryl-reactive benzophenone photoprobes of short "arm" length, each with a substitution of either amino, iodo, or nitro at the para-position, rendering the benzophenone moiety directly radioiodinatable. Their potential for study of protein-protein interaction was assessed using the inhibitory subunit of rod cGMP phosphodiesterase (PDEgamma) and the activated transducin alphasubunit (G alpha t-GTPgammaS) as a model system. These photoprobes proved to be stable at neutral pH and dithiothreitol-cleavable in addition. The PDEgamma constructs derivatized at the C-terminal positions with these probes could be readily purified, had unaltered PDEgamma functional activity, and were shown to photo-cross-link to G alpha t-GTPgammaS with an efficiency as high as 40%. Additionally, the amino benzophenone probe was radioiodinated, facilitating sensitive detection of label transfer. The uniquely combined features of these benzophenone photoprobes promise robust and flexible methods for characterization of protein-protein interaction, either by mass spectrometry when a nonradioactive label is available or by autoradiography when using radioiodinated derivatives.     

Use of the antibiotic, olivomycin, for the cytochemical study of chromatin]

The possibility to use the antibiotic olivomycin for fluorescence cytochemistry of chromatin properties has been shown. It is found that the binding of olivomycin to nuclei reveals the functional state of chromatin and changes in the course of its activation. The essential condition for the application of the method described is the use of ethanol-aceton fixative. When other fixatives are used, in particular 70% ethanol, olivomycin binding reflects differences in nuclear DNA amount, rather than those in chromatin properties. The advantages of the method described, in comparison with the commonly used technique, are associated with the high affinity of olivomycin to DNA, absence of olivomycin binding with RNA, simplicity of the staining procedures , and with rather a high stability of complexes formed between olivomycin and DNA.     

Candida albicans, a distinctive fungal model for cellular aging study

The unicellular eukaryotic organisms represent the popular model systems to understand aging in eukaryotes. Candida albicans, a polymorphic fungus, appears to be another distinctive unicellular aging model in addition to the budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe. The two types of Candida cells, yeast (blastospore) form and hyphal (filamentous) form, have similar replicative lifespan. Taking the advantage of morphologic changes, we are able to obtain cells of different ages. Old Candida cells tend to accumulate glycogen and oxidatively damaged proteins. Deletion of the SIR2 gene causes a decrease of lifespan, while insertion of an extra copy of SIR2 extends lifespan, indicating that like in S. cerevisiae, Sir2 regulates cellular aging in C. albicans. Interestingly, Sir2 deletion does not result in the accumulation of extra-chromosomal rDNA molecules, but influences the retention of oxidized proteins in mother cells, suggesting that the extra-chromosomal rDNA molecules may not be associated with cellular aging in C. albicans. This novel aging model, which allows efficient large-scale isolation of old cells, may facilitate biochemical characterizations and genomics/proteomics studies of cellular aging, and help to verify the aging pathways observed in other organisms including S. cerevisiae.     

Ramachandran free-energy surfaces for disaccharides: trehalose, a case study

We present calculated potential of mean force surfaces for rotation about phi, psi dihedral angles of the alpha(1<-->1)alpha-glycosidic linkage in the disaccharide trehalose (alpha-D-Glc-(1<-->1)-alpha-D-Glc) in both vacuum and aqueous solution. The effects of aqueous solvation upon the alpha(1<-->1)alpha-glycosidic linkage are investigated through comparison of the vacuum and aqueous solution free-energy surfaces. These surfaces reveal that trehalose is restricted to a single minimum-energy conformation in both vacuum and solution. The exceptional rigidity of this disaccharide in solution may provide a molecular rationale for the antidesiccant properties of trehalose glasses.     

alpha-fetoprotein binding specificity for arachidonate, bilirubin, docosahexaenoate, and palmitate. A spin label study

A dianionic spin label, 1-L-glutamate-5-N-(1-oxyl-2,2,6,6-tetramethyl-4-aminopiperidinyl)-i,4-dinitrobenzene, has been used to probe the relative binding specificity of a single anionic ligand site on bovine alpha-fetoprotein (AFP) to arachidonate, bilirubin, docosahexaenoate, and plamitate. The binding isotherm of the spin label with AFP, as shown by a Scatchard plot, indicates the presence of a single high affinity binding site. The site-site relationship of the four endogenous ligands, arachidonate, bilirubin, docosahexaenoate, and palmitate, was determined by studying their effectiveness in competing for this anionic ligand binding site on AFP. Scatchard plots of the spin label in the presence of 1 to 3 molar equivalents of arachidonate, bilirubin, and docosahexaenoate and up to 6 molar equivalents of palmitate have been determined. The effectiveness of the four endogenous ligands in displacing the spin label from its primary binding site is bilirubin greater than or equal arachidonate approximately equal to docosahexaenoate greater than palmitate. These results indicate that polyunsaturated essential fatty acids and bilirubin share a high affinity binding site on AFP. We propose that the function of this anionic ligand binding site on AFP is for the transport of bilirubin and polyunsaturated fatty acids in fetal serum, as well as for the cross-placental transfer of this metabolite and of essential fatty acids.     

Approaches for treatment of aortic arch aneurysm,a numerical study

Aortic arch aneurysm is a complex pathology which requires coverage of one or more aortic arch vessels. In this study we explore the hemodynamic behavior of the aortic arch in aneurysmatic and treated cases with three currently available treatment approaches: Surgery Graft, hybrid Stent-Graft and chimney Stent Graft. The analysis included four models of the time-dependent fluid domains of aneurysmatic arch and of the surgery, hybrid and chimney endovascular techniques. Dimensions of the models are based on typical anatomy, and boundary conditions are based on typical physiological flow.The simulations used computational fluid dynamics (CFD) methods to delineate the time-dependent flow dynamics in the four geometric models.Results of velocity vectors, flow patterns, blood pressure and wall shear stress distributions are presented.The results delineate disturbed and recirculating flow in the aortic arch aneurysm accompanied with low wall shear stress and velocities, compared to a uniformly directed flow and nominal wall shear stress (WSS) in the model of Surgery graft. Out of the two endograft procedures, the hybrid procedure clearly exhibits better hemodynamic performances over the chimney model, with lower WSS, lower pressure drop and less disturbed and vortical flow regions. Although the chimney procedure requires less manufacturing time and cost, it is associated with higher risk rates, and therefore, it is recommended only for emergency cases. This study may shed light on the hemodynamic factors for these complications and provide insight into ways to improve the procedure.     

Methods for the study of amphipod swimming: behavior,morphology, and fluid dynamics

A thorough hydrodynamic approach to the study of swimming in amphipods demands a multipronged attack. A possible first step would be to gather swimming behavior data and determine the biomechanics and kinematics of pleopod beat. This requires careful observation of the swimming modes, swimming speeds, body positions and other aspects of behavior and limb motion that are crucial to swimming. Secondly, it is important to describe the morphology of the body and swimming appendages. Detailed drawings of body shape and design, skeletomusculature, condylic structure, and setal density and distribution on the pleopods and pereopods, are the tools required to ascribe hydrodynamic function to specific limb and body morphology. Finally, the information gathered from behavioral observations bolstered by functional morphology studies is applied to fluid dynamic calculations of drag, lift, and thrust. The theoretical calculations are then compared with empirical determinations of drag, wake generation, vortex shedding frequency, and flow patterns around an amphipod. The fluid dynamic facet of this research is the most challenging and requires an excellent grasp of the fundamental concepts of fluid flow and access to some highly technical equipment. The proposed tripartite approach for the study of amphipod swimming is by no means an exhaustive review of all the techniques that can be employed to quantify amphipod swimming. It will nevertheless permit a rigorous and systematic study of amphipod swimming.     

Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis

Osteoporosis, a highly heritable disease, is characterized mainly by low bone-mineral density (BMD), poor bone geometry, and/or osteoporotic fractures (OF). Copy-number variation (CNV) has been shown to be associated with complex human diseases. The contribution of CNV to osteoporosis has not been determined yet. We conducted case-control genome-wide CNV analyses, using the Affymetrix 500K Array Set, in 700 elderly Chinese individuals comprising 350 cases with homogeneous hip OF and 350 matched controls. We constructed a genomic map containing 727 CNV regions in Chinese individuals. We found that CNV 4q13.2 was strongly associated with OF (p = 2.0 × 10⁻⁴, Bonferroni-corrected p = 0.02, odds ratio = 1.73). Validation experiments using PCR and electrophoresis, as well as real-time PCR, further identified a deletion variant of UGT2B17 in CNV 4q13.2. Importantly, the association between CNV of UGT2B17 and OF was successfully replicated in an independent Chinese sample containing 399 cases with hip OF and 400 controls. We further examined this CNV's relevance to major risk factors for OF (i.e., hip BMD and femoral-neck bone geometry) in both Chinese (689 subjects) and white (1000 subjects) samples and found consistently significant results (p = 5.0 × 10⁻⁴ −0.021). Because UGT2B17 encodes an enzyme catabolizing steroid hormones, we measured the concentrations of serum testosterone and estradiol for 236 young Chinese males and assessed their UGT2B17 copy number. Subjects without UGT2B17 had significantly higher concentrations of testosterone and estradiol. Our findings suggest the important contribution of CNV of UGT2B17 to the pathogenesis of osteoporosis.     

Affordable compensator for IMRT delivery designed for low-and-middle income countries,a Monte Carlo study

We propose a novel cost-effective compensator that can be used to facilitate access to IMRT in low-and-middle income countries. The compensator has the advantages of simplicity, less downtime, increased reliability and less impact on treatment quality from patient motion during treatment. Moreover, the system can be used with either a cobalt-60 unit or linear accelerator. In this Monte Carlo study, the dosimetric properties of the new compensator design have been evaluated. Results were obtained for different field sizes of cobalt teletherapy machine, and the dose was scored at 0.5 cm depth in a water phantom. The effects of compensator thickness, filling material type and shape, and field size were identified. Furthermore, the percentage depth dose and beam profiles for various field sizes and at different depths were obtained. Beam profiles show no significant signature of the beads relative to a solid compensator; in addition, they exhibit a better flatness while preserving symmetry for all field sizes. A reusable bead-based compensator appears to be feasible, and provides dose distribution similar to a solid compensator with low cost and no hazards. Our results avail the ongoing efforts to expand the reach to IMRT in low- and middle-income countries.     

K-35, a fluorescent probe for albumin study: Optical properties

Fluorescent probe N-(carboxyphenyl)imide of 4-(dimethylamino)naphthalic acid, K-35, is used as an indicator of structural changes of human serum albumin molecules in pathology. The probe occupies albumin binding pockets where the probe environment is of very high polarity; probably, the pockets contain protein polar groups and also water molecules. At the same time the rather small Stokes shift of K-35 fluorescence spectrum shows that the polar group motion is one-two orders of magnitude lower than the mobility of polar molecules in polar fluids. K-35 fluorescence decay in HSA can be described as a sum of three exponentials with time constants close to τ₁ = 9 ns; τ₂ = 3.6 ns and τ₃ = 1.0 ns. The difference between excitation maxima of these three decay components shows that the environment of these three species of K-35 molecules has been different before excitation. Different τ values are probably a consequence of nonidentical structure of several binding sites, or the binding site(s) can have variable conformation.     

Phagocytosis, an alternative model system for the study of cell adhesion

Cell adhesion encompasses a variety of cell-cell and cell-matrix adhesive interactions. Whereas ligation of most adhesion receptors activate Rho-family GTP-binding proteins and the subsequent reorganization of the actin cytoskeleton, the molecular mechanisms involved remain poorly understood. Because phagocytosis is a spatially restricted adhesion process, it represents a simplified model system to investigate the spatio-temporal regulation of the signalling pathways that link surface adhesion receptors, small GTPases and the actin cytoskeleton. This review highlights some of the similarities between the formation and maintenance of adhesive contacts and phagocytic uptake and discusses why the study of phagocytosis can help understand more complex adhesion processes.