On the structural differences between markers and genomic AC microsatellites

AC microsatellites have proved particularly useful as genetic markers. For some purposes, such as in population biology, the inferences drawn depend on the quantitative values of their mutation rates. This, together with intrinsic biological interest, has led to widespread study of microsatellite mutational mechanisms. Now, however, inconsistencies are appearing in the results of marker-based versus non-marker-based studies of mutational mechanisms. The reasons for this have not been investigated, but one possibility, pursued here, is that the differences result from structural differences between markers and genomic microsatellites. Here we report a comparison between the CEPH AC marker microsatellites and the global population of AC microsatellites in the human genome. AC marker microsatellites are longer than the global average. Controlling for length, marker microsatellites contain on average fewer interruptions, and have longer segments, than their genomic counterparts. Related to this, marker microsatellites show a greater tendency to concentrate the majority of their repeats into one segment. These differences plausibly result from scientists selecting markers for their high polymorphism. In addition to the structural differences, there are differences in the base composition of flanking sequences, marker flanking regions being richer in C and G and poorer in A and T. Our results indicate that there are profound differences between marker and genomic microsatellites that almost certainly affect their mutation rates. There is a need for a unified model of mutational mechanisms that accounts for both marker-derived and genomic observations. A suggestion is made as to how this might be done.

Estrogen receptor: Structural differences and potential implications on selectivity examined by the GRID/CPCA approach

Selective Estrogen Receptor Modulators ( SERMs) have been developed, but the selectivity towards the subtypes ( ER or ER is not well understood. Based on three-dimensional structural properties of ligand binding domains, a model that takes into account this aspect was developed via molecular interaction fields and consensus principal component analysis (GRID/CPCA).

Spectroscopic Study on the Structural Differences of Thermally Induced Cross-Linking Segments in Emeraldine Salt and Base Forms of Polyaniline

This paper reports the spectroscopic study on the structural differences of thermally induced cross-linking segments in polyaniline in its emeraldine salt (PANI-ES) and base (PANI-EB) forms. Casting films of PANI-ES (ES-film) and PANI-EB (EB-film) were prepared and heated at 150 degrees C under atmospheric air for 30 min. Raman spectra excited at 632.8 nm of heated ES-film presented the characteristic bands of phenazine-like structures at 1638, 1392, and 575 cm(-1), whereas EB-film showed lower relative intensities for these bands. The lower content of phenazine-like segments in heated EB-film is related to residual polaronic segments from preparation procedures, as revealed by Raman. This statement was confirmed by a sequence of thermal and doping experiments in both films. Quantum-chemical calculations by density functional theory (DFT) and time-dependent density functional theory (TD-DFT) showed that the phenazine-like structure presents the intense Raman band at 1350 cm(-1) due to heterocycle breathing mode, and the non-phenazine-like structure (substituted hydrophenazine-type) presents higher energy for HOMO-LUMO transition, indicating the lack of conjugation in the heterocycle compared with the phenazine-like structure. According to experimental and theoretical data reported here, it is proposed that only thermally treated PANI-ES presents phenazine-like rings, whereas PANI-EB presents heterocyclic non-aromatic structures.

Structural differences between the bladder dome and trigone revealed by mRNA expression analysis of cold-cut biopsies

To establish the mRNA expression profiles of selected genes involved in bladder contractility and epithelial permeability in the bladder dome and trigone in order to evaluate the use of cold-cut biopsies for comparative quantitative studies into the anatomical differences between these two bladder regions.

A new approach to detect structural differences in lung parenchyma using digital image analysis

Morphometric investigations using a point and intersection counting strategy in the lung often are not able to reveal the full set of morphologic changes. This happens particularly when structural modifications are not expressed in terms of volume density changes and when rough and fine surface density alterations cancel each other at different magnifications. Making use of digital image processing, we present a methodological approach that allows to easily and quickly quantify changes of the geometrical properties of the parenchymal lung structure and reflects closely the visual appreciation of the changes. Randomly sampled digital images from light microscopic sections of lung parenchyma are filtered, binarized, and skeletonized. The lung septa are thus represented as a single-pixel wide line network with nodal points and end points and the corresponding internodal and end segments. By automatically counting the number of points and measuring the lengths of the skeletal segments, the lung architecture can be characterized and very subtle structural changes can be detected. This new methodological approach to lung structure analysis is highly sensitive to morphological changes in the parenchyma: it detected highly significant quantitative alterations in the structure of lungs of rats treated with a glucocorticoid hormone, where the classical morphometry had partly failed.

A single-sided NMR approach to study structural differences of bovine articular tissue

This thesis work has been developed in collaboration between the Department of Physics and Astronomy of the University of Bologna and the IRCCS Rizzoli Orthopedic Institute during an internship period. The study aims to investigate the sensitivity of single-sided NMR in detecting structural differences of the articular cartilage tissue and their correlation with mechanical behavior. Suitable cartilage indicators for osteoarthritis (OA) severity (e.g., water and proteoglycans content, collagen structure) were explored through four NMR parameters: T2, T1, D, and Slp. Structural variations of the cartilage among its three layers (i.e., superficial, middle, and deep) were investigated performing several NMR pulses sequences on bovine knee joint samples using the NMR-MOUSE device. Previously, cartilage degradation studies were carried out, performing tests in three different experimental setups. The monitoring of the parameters and the best experimental setup were determined. An NMR automatized procedure based on the acquisition of these quantitative parameters was implemented, tested, and used for the investigation of the layers of twenty bovine cartilage samples. Statistical and pattern recognition analyses on these parameters have been performed. The results obtained from the analyses are very promising: the discrimination of the three cartilage layers shows very good results in terms of significance, paving the way for extensive use of NMR single-sided devices for biomedical applications. These results will be also integrated with analyses of tissue mechanical properties for a complete evaluation of cartilage changes throughout OA disease. The use of low-priced and mobile devices towards clinical applications could concern the screening of diseases related to cartilage tissue. This could have a positive impact both economically (including for underdeveloped countries) and socially, providing screening possibilities to a large part of the population.

Synthesis and structural properties of patellamide a derivatives and their copper(II) compounds

The synthesis, characterization and copper(II) coordination chemistry of three new cyclic peptide ligands, PatJ(1) (cyclo-(Ile -Thr- (Gly)Thz-lle-Thr(Gly)Thz)), PatJ(2) (cyclo-(Ile-Thr(Gly)Thz-(D)-Ile-Thr-(Gly)Thz)), and PatL (cyclo-(Ile-Ser-(Gly)Thz-Ile-Ser(Gly)Thz)) are reported. All of these cyclic peptides and PatN (cyclo-(Ile-Ser(Gly)Thz-Ile-Thr-(Gly)Thz)) are derivatives of patellamide A and have a [24]azacrown-8 macrocyclic structure. All four synthetic cyclic peptides have two thiazole rings but, in contrast to patellamide A, no oxazoline rings. The molecular structure of PatJ1, determined by X-ray crystallography, has a saddle conformation with two close-to-co-parallel thiazole rings, very similar to the geometry of patellamide D. The two coordination sites of PatJ1 with thiazole-N and amide-N donors are each well preorganized for transition metal ion binding. The coordination of copper(II) was monitored by UV/Vis spectroscopy, and this reveals various (meta)stable mono- and dinuclear copper(II) complexes whose stoichiometry was confirmed by mass spectra. Two types of dinuclear copper(II) complexes, [Cu-2(H4L)(OH2)(n)](2+) (n = 6, 8) and [Cu-2(H4L)(OH2)(n)] (n=4, 6; L=PatN, PatL, PatJ1, PatJ2) have been identified and analyzed structurally by EPR spectroscopy and a combination of spectra simulations and molecular mechanics calculations (MM-EPR). The four structures are similar to each other and have a saddle conformation, that is, derived from the crystal structure of PatJ(1) by a twist of the two thiozole rings. The small but significant structural differences are characterized by the EPR simulations.

Structural bioinformatics study of cyclin-dependent kinases complexed with inhibitors

The present work describes molecular models for the binary complexes CDK9, CDK5 and CDK1 complexed with Flavopiridol and Roscovitine. These structural models indicate that the inhibitors strongly bind to the ATP-binding pocket of CDKs and the structural comparison with the complexes CDK2:Flavopiridol and CDK2:Roscovitine correlates the structural differences with differences in inhibition of these CDKs by the inhibitors. These structures open the possibility of testing new inhibitor families, in addition to new substituents for the already known lead structures such as flavones and adenine derivatives.

Structural aspects and floristic similarity among tropical dry forest fragments with different management histories in northern Minas Gerais, Brazil

In order to produce useful knowledge to the initiatives of protection and management of forest fragments, more specifically for tropical dry forests which suffer with frequent anthropic activities, and due to the lack of specific studies, this article aimed describe the structure and the floristic similarity among three areas of dry forest with different management histories. The study was developed in Capitão Enéas municipality, Northern Minas Gerais, Brazil, where three fragments were evaluated, being one in regeneration for 30 years, another submitted to occasional fire and the third with selective cut in small scale. The sampling was developed through the point quarter method considering all the alive phanerophyte individuals with circumference at breast height (CBH) > 15 cm. In the three fragments, 512 individuals, distributed in 60 species, 47 genera, and 23 families were sampled. The most representative families were Fabaceae (26), Anacardiaceae (4), Bignoniaceae (3) and Combretaceae (3). However, fourteen families were represented by only one species. Only eight species were common to all fragments - Myracrodruon urundeuva standed out with 26.9% of all sampled individuals - while a great number of species were exclusive of each fragment. The floristic and structural differences between the fragments are possibly related to the history and intensity of management in each area besides the topography variations and the presence or absence of limestone outcrops. These results show the importance of each fragment, indicating that the loss of anyone would cause negative impacts on the regional flora and consequently to the associated biodiversity.

Colloidal gas aphrons (CGA): dispersion and structural features

Colloidal gas aphrons (CGA) have previously been defined as surfactant stabilized gas microbubbles and characterized for a number of surfactants in terms of stability, gas holdup and bubble size even though there is no conclusive evidence of their structure (that is, orientation of surfactant molecules at the gas–liquid interface, thickness of gas–liquid interface, and/or number of surfactant layers). Knowledge of the structure would enable us to use these dispersions more efficiently for their diverse applications (such as for removal of dyes, recovery of proteins, and enhancement of mass transfer in bioreactors). This study investigates dispersion and structural features of CGA utilizing a range of novel predictive (for prediction of aphron size and drainage rate) and experimental (electron microscopy and X-ray diffraction) methods. Results indicate structural differences between foams and CGA, which may have been caused by a multilayer structure of the latter as suggested by the electron and X-ray diffraction analysis.

Commercial thickeners used by patients with dysphagia: rheological and structural behaviour in different food matrices

In order to achieve a safe swallowing in patients with dysphagia, liquids must be thickened. In this work, two commercial starch based thickeners dissolved in water, whole milk, apple juice and tomato juice were studied. The thickeners were Resource®, composed of modified maize starch and Nutilis®, composed of modified maize starch and gums. They were formulated at two different concentrations corresponding to nectar- and pudding-like consistencies. Influence of composition, concentration and food matrix on rheological properties and structure of the resulting pastes were analysed. Viscoelastic measurements and microscopic observations of the thickeners dissolved in water revealed structural differences due to the presence of gums. When the thickeners were dissolved in the other food matrices significant statistical interactions were found between the matrix and the thickener-type in both the viscoelastic and flow parameters. The most relevant differences were observed for the nectar-like consistency with Nutilis® thickener in milk and apple juice. These samples had lower zero viscosity values and higher loss tangent values, that corresponded to weaker structured systems. Light microscopy images showed that the matrix formed by swollen starch granules was interrupted by the presence of gums. The structure of the matrices in pudding-like formulations became more continuous irrespectively of the matrix employed, and also differences in viscoelasticity among samples diminished. Although differences were observed in zero shear viscosity values among samples, the viscosity of the beverages at 50 s−1 – commonly used as a reference for swallowing – was similar for all samples regardless of the matrix used.

Structural basis for selective inhibition of purine nucleoside phosphorylase from Schistosoma mansoni: Kinetic and structural studies

Selectivity plays a crucial role in the design of enzyme inhibitors as novel antiparasitic agents, particularly in cases where the target enzyme is also present in the human host. Purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) is an attractive target for the discovery of potential antischistosomal agents. In the present work, kinetic studies were carried out in order to determine the inhibitory potency, mode of action and enzyme selectivity of a series of inhibitors of SmPNP. In addition, crystallographic studies provided important structural insights for rational inhibitor design, revealing consistent structural differences in the binding mode of the inhibitors in the active sites of the SmPNP and human PNP (HsPNP) structures. The molecular information gathered in this work should be useful for future medicinal chemistry efforts in the design of new inhibitors of SmPNP having increased affinity and selectivity. (C) 2010 Elsevier Ltd. All rights reserved.

Structural and functional leaf traits of two Gochnatia species from distinct growth forms in a sclerophyll forest site in Southeastern Brazil

O gênero Gochnatia é comumente encontrado em diferentes fitofisionomias do Cerrado do Estado de São Paulo, crescendo desde ambientes mais abertos até áreas florestais mais fechadas. Aqui foram comparadas a anatomia foliar e alguns parâmetros ecofisiológicos de duas espécies do gênero Gochnatia, uma arbustiva (Gochnatia barrosii Cabrera) e a outra arbórea (Gochnatia polymorpha (Less.) Cabrera), ambas ocorrendo em área de cerradão na Estação Ecológica de Assis, SP. Encontraram-se diferenças estruturais qualitativas entre as espécies, com G. barrosii apresentando folhas anfiestomáticas, com epiderme unisseriada e G. polymorpha apresentando folhas hipoestomáticas, com epiderme múltipla ou hipoderme, na face adaxial. Além disso, as folhas de G. barrosii apresentaram menores valores para a espessura dos tecidos (com exceção da epiderme na face abaxial) e da folha em relação a G. polymorpha. Foram observadas diferenças na assimilação de CO2 tanto em base de área quanto de massa seca foliar, além de diferenças na área foliar específica, sendo esta maior em G. barrosii. Apesar das folhas de G. barrosii possuírem estrutura bem menos escleromorfa do que as folhas de G. polymorpha, não foram encontradas diferenças na eficiência do uso de água. Os resultados sugerem que espécies de formas distintas de crescimento de um mesmo gênero possuem características foliares diferenciadas para lidar com as variações ambientais a que são submetidas.

Structural bioinformatics study of cyclin-dependent kinases complexed with inhibitors

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)