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First Segment (first + segment)

Distribution by Scientific Domains

Life Sciences	60%

Selected Abstracts

Experimental validation of metabolic pathway modeling

FEBS JOURNAL, Issue 13 2008
An illustration with glycolytic segments from Entamoeba histolytica
In the search for new drug targets in the human parasite Entamoeba histolytica, metabolic control analysis was applied to determine, experimentally, flux control distribution of amebal glycolysis. The first (hexokinase, hexose-6-phosphate isomerase, pyrophosphate-dependent phosphofructokinase (PPi -PFK), aldolase and triose-phosphate isomerase) and final (3-phosphoglycerate mutase, enolase and pyruvate phosphate dikinase) glycolytic segments were reconstituted in vitro with recombinant enzymes under near-physiological conditions of pH, temperature and enzyme proportion. Flux control was determined by titrating flux with each enzyme component. In parallel, both glycolytic segments were also modeled by using the rate equations and kinetic parameters previously determined. Because the flux control distribution predicted by modeling and that determined by reconstitution were not similar, kinetic interactions among all the reconstituted components were experimentally revised to unravel the causes of the discrepancy. For the final segment, it was found that 3-phosphoglycerate was a weakly competitive inhibitor of enolase, whereas PPi was a moderate inhibitor of 3-phosphoglycerate mutase and enolase. For the first segment, PPi was both a strong inhibitor of aldolase and a nonessential mixed-type activator of amebal hexokinase; in addition, lower Vmax values for hexose-6-phosphate isomerase, PPi -PFK and aldolase were induced by PPi or ATP inhibition. It should be noted that PPi and other metabolites were absent from the 3-phosphoglycerate mutase and enolase or aldolase and hexokinase kinetics experiments, but present in reconstitution experiments. Only by incorporating these modifications in the rate equations, modeling predicted values of flux control distribution, flux rate and metabolite concentrations similar to those experimentally determined. The experimentally validated segment models allowed ,in silico experimentation' to be carried out, which is not easy to achieve in in vivo or in vitro systems. The results predicted a nonsignificant effect on flux rate and flux control distribution by adding parallel routes (pyruvate kinase for the final segment and ATP-dependent PFK for the first segment), because of the much lower activity of these enzymes in the ameba. Furthermore, modeling predicted full flux-control by 3-phosphoglycerate mutase and hexokinase, in the presence of low physiological substrate and product concentrations. It is concluded that the combination of in vitro pathway reconstitution with modeling and enzyme kinetics experimentation permits a more comprehensive understanding of the pathway behavior and control properties. [source]

Evaluation of one- and two-equation low- Re turbulence models.

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 12 2003
Axisymmetric separating, Part I, swirling flows
Abstract This first segment of the two-part paper systematically examines several turbulence models in the context of three flows, namely a simple flat-plate turbulent boundary layer, an axisymmetric separating flow, and a swirling flow. The test cases are chosen on the basis of availability of high-quality and detailed experimental data. The tested turbulence models are integrated to solid surfaces and consist of: Rodi's two-layer k,, model, Chien's low-Reynolds number k,, model, Wilcox's k,, model, Menter's two-equation shear-stress-transport model, and the one-equation model of Spalart and Allmaras. The objective of the study is to establish the prediction accuracy of these turbulence models with respect to axisymmetric separating flows, and flows of high streamline curvature. At the same time, the study establishes the minimum spatial resolution requirements for each of these turbulence closures, and identifies the proper low-Mach-number preconditioning and artificial diffusion settings of a Reynolds-averaged Navier,Stokes algorithm for optimum rate of convergence and minimum adverse impact on prediction accuracy. Copyright © 2003 John Wiley & Sons, Ltd. [source]

A scaleworm's setal snorkel

INVERTEBRATE BIOLOGY, Issue 2 2000
Bruno Pernet
Abstract. Setae of the first segment of the marine annelid Sthenelais berkeleyi (family Sigalionidae) are arranged in the shape of an antero-dorsally directed tube. When the worm is in resting position buried in sediment, this setal tube projects slightly from the sediment surface. A current of water is drawn into it by cilia on the parapodia of the first segment. The water is then diverted to a pair of lateral spaces between the body wall and elytra, moved posteriorly in these spaces along the length of the body by segmental cilia, and eventually exits posteriorly or ventrally. This flow permits the worm to respire while remaining buried and immobile for long periods of time, waiting for prey to move over the sediment near it. Setae of the first segment are probably used as snorkels in some other infaunal sigalionids as well. [source]

Protective mechanisms of the common fibular nerve in and around the fibular tunnel: A new concept

CLINICAL ANATOMY, Issue 6 2009
Ramadan M. El Gharbawy
Abstract The most frequent site at which the common fibular nerve is affected by compression, trauma, traction, masses, and surgery is within and around the fibular tunnel. The aim of this study was to determine whether there were protective mechanisms at this site that guard against compression of the nerve. Twenty-six lower limbs of 13 preserved adult cadavers (11 males and two females) were used. Proximal to the entrance of the tunnel, three anatomical configurations seemed to afford the required protection for the nerve: reinforcement of the deep fascia; tethering of the common fibular nerve to both the tendon of the biceps femoris and the reinforced fascia; and the particular arrangement of the deep fascia, fibular head, and soleus and gastrocnemius muscles. At the entrance of the tunnel, contraction of the first segment of fibularis longus muscle could afford the required protection. In the tunnel, contraction of the second and third segments of fibularis longus muscle could guard against compression of the nerve. The tough fascia on the surface of fibularis longus muscle and the fascial band within it, which have long been accused of compression of the nerve, may actually be elements of the protective mechanisms. We conclude that there are innate, anatomical protective mechanisms which should be taken into consideration when decompressing the common fibular nerve. To preserve these mechanisms whenever possible, the technique should be planned and varied according to the underlying etiology. Clin. Anat. 22:738,746, 2009. © 2009 Wiley-Liss, Inc. [source]

A critical review of ontogenetic development in Terebellidae (Polychaeta)

ACTA ZOOLOGICA, Issue 4 2010
André R. S. Garraffoni
Abstract Garraffoni, A.R.S. and Lana, P.C. 2009. A critical review of ontogenetic development in Terebellidae (Polychaeta). ,Acta Zoologica (Stockholm) 91: 390,401. This study reviews the ontogenetic variability of the head, the first segments and the uncini in Terebellidae, based on primary literature and development series of four terebellid species. We test hypotheses on character homologies and indicate informative characters for future phylogenetic analyses. The prostomium, identified as the region above the prototroch band of the larva, in addition to being the region of origin of the buccal tentacles, contains a series of nerves originating from the cerebrum. The peristomium, which contains the mouth, is innervated by the stomogastric nerve and consists of upper and lower lips and an internal pharynx. The loss of the first notochaetae and neurochaetae in the course of development is a recurrent pattern in terebellids. The claviform chaetae disappear with age and growth, and can be used to define the larval stage. Chaetogenesis shows that the long shaft-shaped manubrium and posterior process develop from different regions. The uncini terminology ,double rows' was reinterpreted and renamed ,inverted rows', which better reflects the inversion of chaetal positions during ontogenetic development. [source]