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Selection between multiple periodic regimes in a biochemical system: complex dynamic behaviour resolved by use of one-dimensional maps.

We analyse a model biochemical system in which two autocatalytic enzyme reactions are coupled in series, in conditions where multiple stable periodic regimes coexist for the same set of parameter values. We determine how the periodic regimes are reached from different initial conditions. The structure of the attraction basins is generally simple in the case of two coexisting limit cycles (birhythmicity). This structure and the associated behaviour may, however, become highly complex. In particular, the system exhibits enhanced sensitivity to initial conditions when the boundaries of the attraction basins are fractal. In the latter case, it becomes difficult to predict the evolution towards either one of two limit cycles, a phenomenon known as final state sensitivity. We show how these complex phenomena can be explained in a unified and simple manner by means of one-dimensional return maps derived from the time evolution of the model and from fifth degree polynomial equations. We suggest experimental tests of the sensitivity to initial conditions in chemical systems presenting birhythmicity. The physiological significance of the results is discussed with respect to the sensitivity of regulatory systems admitting multiple stable biological rhythms.

Allosteric Regulation↗

A peptidergic basis for sexual behavior in mammals.

Vasopressin (VP) is a peptide neurotransmitter in the limbic system of rats. It is synthesized in the medial amygdaloid nucleus in the presence of sex steroids, transported to other limbic structures such as the hippocampus and septum and secreted there by a calcium-dependent process. In the hippocampus, VP acts on cerebral microvessels and local circuit interneurons. Its excitatory action on the inhibitory interneurons produces near-total shutdown of electrical activity of the efferent fibers of pyramidal cells, the projection neurons of the hippocampus. Stimulation of the medial amygdala and release of the endogenous VP duplicates these effects and, since they are blocked by ventricular application of a VP antagonist, the effects are almost certainly mediated by endogenous VP. Recording from the VP-containing cell bodies or of the hippocampal action of the peptide indicates that the system is selectively involved with the early stages of sexual behavior, specifically those appetitive behaviors that anticipate coitus. Stimulation of the VP cells produces alterations in sexual behavior in a manner consistent with the hypothesis that the medial amygdala organizes the appetitive phase of recognition of an appropriate partner and sexual arousal. This role for the medial amygdala complements the proposed role of nearby structures in the consummatory, reward and learned aspects of sexual behavior. Association between VP, oxytocin (OT) and homologs with sexual behavior is very widespread among vertebrates, including amphibians, reptiles, primates and humans. Humans and other primates display a phenomenon called 'concealed ovulation' that may have played a role in the evolution of social structures. The review concludes with a discussion of possible experimental strategies for evaluating the possible role of VP in concealed ovulation and other conditions in which sexual behavior occurs outside of estrus.

Animals↗

Role of cellular proteinases in acute myocardial infarction. I. Proteolysis in nonischemic and ischemic rat myocardium and the effects of antipain, leupeptin, pepstatin and chymostatin administered in vivo.

To test the hypothesis that cellular proteinases contribute to ischemic myocellular death, measurements were made of tyrosine release (an index of overall proteolysis) from incubated slices of nonischemic and ischemic myocardium obtained at various times after coronary artery occlusion in rats. Proteolysis failed to increase in ischemic myocardium throughout the first 24 hours of occlusion, when irreversible damage develops, indicating that cellular proteinases do not undergo generalized activation in this phase. These data represent the first assessment of myocardial proteolysis throughout the development of ischemic death, and suggest that cellular proteinases do not play a causal role in this process. However, the possibility remains that ischemia selectively accelerates the breakdown of vital proteins, a phenomenon that may not be detected by measuring overall proteolysis. To determine whether future studies on the effects of proteolytic inhibition on infarct size are feasible, the ability of the proteinase inhibitors antipain, leupeptin, pepstatin and chymostatin, given in vivo, to interfere with proteolysis in ischemic myocardium was also evaluated. Leupeptin (10 or 40 mg/kg) inhibited proteolysis in a dose-related fashion (-49 and -72%, respectively, p less than 0.001). Antipain (20 mg/kg) decreased protein breakdown by 60% (p less than 0.001). The combination of antipain (20 mg/kg), leupeptin (40 mg/kg) and pepstatin (5 mg/kg) suppressed proteolysis almost completely at both 15 minutes (-88%, p less than 0.001) and at 6 hours (-72%, p less than 0.05) of ischemia, that is, throughout the development of irreversible injury. These results demonstrate that whatever proteolysis is occurring during acute myocardial infarction is largely mediated by cathepsins A, B, D, L and H and by calcium-activated neutral protease (that is, the enzymes sensitive to the inhibitors used). Because antipain, leupeptin and pepstatin significantly suppress such proteolysis, these agents might be useful in further assessing any potential contribution of cellular proteinases to the production of ischemic myocellular death. In addition, this study provides a new experimental model that affords serial assessments of regional myocardial proteolysis during the evolution of myocardial infarction.

Animals↗

Magnetic resonance imaging in the assessment of disease activity in multiple sclerosis.

Magnetic resonance imaging (MRI) has been shown to be a good method of visualizing the lesions in MS. We have studied several applications of MRI to the evaluation of patients and experimental models. In diagnosis, MRI is the most sensitive test for the demonstration of dissemination of lesions in space. Pathological correlation studies show that MRI reliably measures the extent of chronic demyelination. Experimental studies show that MRI detects acute inflammatory lesions and measures their evolution. MRI also is a reliable measure of the extent of the MS process, serial MRI scans detect evidence of disease activity in MS not always disclosed by clinical evaluation. MRI will have an enormous future impact on the evaluation of patients in clinical studies and in understanding the evolution of pathological processes.

Humans↗

Electronic structure study of the high-pressure vibrational spectrum of FeS2 pyrite.

Plane-wave density functional calculations are used to investigate the pressure dependence of the geometry and Gamma-point phonons of FeS(2) pyrite up to 150 GPa. The linear response method is employed to calculate the vibrational properties. Raman-active modes are in excellent agreement with the experimental data available up to 50 GPa,(1) and we predict the evolution with pressure of the IR-active modes for which no high-pressure spectroscopic data have been reported so far. Over the wide pressure range investigated here, all vibrational frequencies depend nonlinearly on pressure; their pressure dependence is quantified by determining the full set of mode Grüneisen parameters and their pressure derivatives.

Journal Article↗

Raman spectra of ionic liquids: a simulation study of AlF3 and its mixtures with NaF.

Theoretical Raman spectra of the melts of NaF/AlF3 mixtures have been obtained from computer simulations in order to examine how the Raman spectra reflect the coordination structure around the Al3+ ions. The Raman spectra, both polarized and depolarized, are calculated from a model for the dependence of the polarizability of the system on the ionic coordinates which was inspired by electronic structure calculations of the polarizabilities of ions in a condensed-phase environment. The shapes of the spectra and their evolution with composition in the mixtures conform remarkably well to those seen experimentally, and we discuss the relationship between the bands seen in the spectra and the vibrational modes of the AlFn(3-n) coordination complexes which are found in the melts. Finally, we calculate quantities which relate to the degree of cross-linking between these coordination complexes and their lifetimes.

Journal Article↗

An integrated theory of ageing in the nematode Caenorhabditis elegans.

Numerous theories of ageing have been proposed, and many have been tested experimentally, particularly using nematode models such as Caenorhabditis elegans. By combining those theories of ageing that remain plausible with recent findings from studies of C. elegans life span mutants, an integrated theory of ageing has been devised. This is formed from 3 interconnected elements: the evolutionary theory of ageing, the oxidative damage theory of ageing, and a nonadaptive programmed ageing theory. This tripartite theory of ageing gives rise to a number of predictions that may be tested experimentally.

Aging↗

[Diffusion-weighted magnetic resonance tomography: a highly promising MR technic for the early recognition of cerebral ischemia].

PURPOSE: The aim of this study was to show the temporal and spatial evolution of ischaemia over time using diffusion-weighted magnetic resonance imaging, and to correlate the extent of ischaemia with the postmortem infarct size after 24 hours. MATERIAL AND METHODS: In 8 rats focal cerebral ischaemia was induced by intravascular occlusion of the middle cerebral artery. The evolution of the ischaemic lesion was examined over 180 min with an experimental MR scanner. RESULTS: Diffusion-weighted magnetic resonance imaging displayed a hyperintense area in the lateral part of the putamen as early as 5 min after the onset of ischaemia. The mean volume of ischaemia on diffusion mapping after 5 min was 62.5 +/- 12.9 microliters and increased to 224.4 +/- 48.5 microliters after 180 min. This correlated well with the corrected infarct volume at postmortem examination (194.0 +/- 23.1 microliters, r = 0.72, p < 0.05) using the TTC staining. CONCLUSION: Diffusion-weighted magnetic resonance imaging is a reliable tool in the early diagnosis of cerebral ischaemia. Due to the non-invasiveness this method can be used for therapy monitoring and might help to develop new therapeutic strategies.

Animals↗

Theoretical investigation on 1H and 13C NMR chemical shifts of small alkanes and chloroalkanes.

Using density functional theory (DFT) with the B3LYP, PBE, and PBE0 exchange-correlation functionals as well as the Moller-Plesset second-order perturbation theory (MP2) combined with a series of rather extended basis sets, 1H and 13C chemical shifts of small alkanes and chloroalkanes (with different numbers of chlorine atoms on specific positions) have been simulated and compared to experimental data. For the 1H chemical shifts, theory tends to reproduce experiment within the limits of the experimental errors. In the case of 13C chemical shift, the differences between theory and experiment increase monotonically with the number of chlorine atoms and exhibit a deviation from additivity. This behavior is related to the saturation of the experimental 13C chemical shifts with the number of chlorine atoms, whereas the evolution is mostly linear at both DFT and MP2 levels of approximation. This difference has been traced back to the relativistic spin-orbit coupling effects, which are exalted as a result of the enhancement of the s character of the C atom when increasing the number of linked Cl atoms. Thus, it was demonstrated that not only electron correlation but also relativistic effects have to be considered for estimating the 13C chemical shifts when several Cl atoms are directly attached to the C atom. Linear (theory/experiment) regressions have then been performed for the different types of C atoms, i.e., bearing one, two, and three Cl atoms, with excellent correlation coefficients. The linear correlation relationships so obtained can then serve to predict and facilitate the interpretation of the nuclear magnetic resonance spectra of more complex compounds. Furthermore, by investigating the basis set effects, the correlation between the chemical shifts calculated using the 6-311 + G(2d,p) basis set and the more extended 6-311 + G(2df,p) and aug-cc-pvtz basis sets is excellent, demonstrating that the choice of the 6-311 + G(2d,p) basis set for calculating the 1H and 13C chemical shifts is relevant.

Journal Article↗

Regional and laminar distribution of cortical neurons projecting to either superior or inferior colliculus in the hedgehog tenrec.

Retrograde tracer substances were injected into either the inferior or the superior colliculus in the Madagascan hedgehog tenrec, Echinops telfairi (Insectivora), to reveal the laminar and regional distribution of corticotectal cells and to correlate the labeled areas with architectural data. The tenrecs, taken from our breeding colony, have one of the least differentiated cerebral cortices among mammals, and experimental investigations of such brains are important for the understanding of the evolution and intrinsic organization of the more highly differentiated cerebral cortex in other placental mammals. Following injections into the inferior colliculus, cortical neurons were labeled bilaterally, with an ipsilateral predominance. Most labeled cells were found in the caudolateral hemisphere, area 4 as defined by Rehkämper (1981); some were in the somatosensorimotor cortex, as defined in a previous study. The labeled neurons in area 4 were located in layers V and VI, forming two bands of cells separated from each other by a poorly labeled interspace. A further subdivision of this presumed auditory region could not be achieved. This entire area was also weakly labeled following tracer injections into the superior colliculus. The labeled cells, however, were restricted to layer V of the ipsilateral side. The most consistent sites of labeled cells following injections into the superior colliculus were found in layer V of the ipsilateral caudomedial hemisphere, Rehkämper's caudal area 3, and the transitional zone adjacent to the retrosplenial cortex. This area is small in comparison to the entire region that was found in this study to project to the superior colliculus. The superior colliculus also receives projections from the ipsilateral sensorimotor and cingulate cortices. The latter projections are particularly striking in comparison to other mammals because they originate from along the entire rostrocaudal extent of the cingulate/retrosplenial region.

Afferent Pathways↗

Biological Parts in Yeast Synthetic Biology: From Regulatory Elements to Predictive Design Platforms.

Yeasts, particularly Saccharomyces cerevisiae, are important eukaryotic chassis for synthetic biology because of their tractable genetics, versatile toolkits, and broad utility in metabolic engineering and functional genomics. Progress in this field has been driven by biological parts that enable programmable control of gene expression and cellular behavior. Early efforts focused mainly on promoters, terminators, and other regulatory elements for tuning individual genes. However, as engineering expanded to multigene pathways, genetic circuits, and dynamic regulatory systems, the limits of part-centric design became clear. Part performance is often shaped by genomic context, chromatin state, host physiology, and interactions with other components, which restricts modularity and predictability. In response, yeast synthetic biology is shifting toward integrated design frameworks combining multilayer regulation, standardized assembly, automated experimentation, and computational modeling. This review provides an integrated perspective on the evolution of biological parts across DNA-, RNA-, and protein-level regulation, connecting these advances with assembly frameworks, biofoundries, and machine learning to trace the trajectory from part-centric engineering toward predictive, system-level design in yeast synthetic biology.

Biofoundry↗

Atrial natriuretic factor: specific binding to renal glomeruli during the development of two-kidney, one clip hypertension in the rat.

Blood pressure (BP), atrial and plasma concentrations of atrial natriuretic factor (ANF), hematocrit and renal glomerular ANF receptors were studied during the development of hypertension in two-kidney, one clip (2-K, 1C) rats and were compared with normotensive controls. Plasma ANF was elevated in the 2-K, 1C group in all stages of hypertension, even after 3 weeks when BP, although higher than in sham-operated animals, had not yet reached arbitrarily-set hypertensive levels. At this time, hematocrit was higher in the hypertensive rats than in the controls, but the difference later disappeared. Lower atrial ANF concentrations were observed in the 2-K, 1C group at week 3, but only in the right atrium. No difference in ANF levels was noted in either the left or right atrium between hypertensive and normotensive animals 5 and 7 weeks after clipping. The glomerular ANF receptor population was markedly smaller in the clipped left kidney of 2-K, 1C rats during all stages of hypertension, and in the untouched right kidney at 5 and 7 weeks after surgery, but was larger in the non-clipped right kidney in the pre-hypertensive phase (3 weeks). It is concluded that receptor density changes during the evolution of high BP in the 2-K, 1C Goldblatt model of experimental hypertension. Our data suggest that the increases and decreases in density of renal glomerular ANF receptors may play a role in the differential handling of sodium by the clipped and non-clipped kidney during the various stages of development of 2-K, 1C hypertension in the rat.

Animals↗

Apoptosis and rejection in rat intestinal transplantation: correlation with FK506 doses and donor specific bone marrow infusions.

BACKGROUND: Our purpose was to investigate the occurrence and the evolution of apoptosis of enterocytes during acute and chronic rejection in an experimental model of allogeneic heterotopic small bowel transplantation (SBTx). METHODS: Forty-five rats were divided in 10 experimental groups according to the dose of FK506 administration and donor bone marrow infusions (DBMI). Groups 1 and 2 did not received BMI. Groups 3 and 4 received 150x106 cells at day 0, groups 5 and 6 received 75x106 cells at days 0-4, groups 7 and 8 received 75x106 cells at days 4 and 10, and groups 9 and 10 received 30x106 cells at days 4, 10, 15, 20, and 25. Animals of groups 1, 3, 5, 7, and 9 were immunosuppressed with 0.5 mg/kg FK 506, although the remaining groups with 1 mg/kg FK 506, from day 0 to 4 after transplant. Fragment end labeling of DNA was used to detect apoptosis. RESULTS: The number of apoptotic cells detected was highest at day 15 (184+/-154) and then progressively decreased thereafter (day 30=159+/-197; day 45=80+/-167; day 60=0). The number of apoptotic enterocytes was found increased during mild (151+/-108) and moderate (281+/-161) allograft rejection, although a low apoptotic rate was observed in cases without rejection (59+/-13) and during severe (53+/-131) and chronic rejection (46+/-136). Furthermore the number of labeled cells was found inversely correlated with fibrosis (P<0.0001). There was no correlation between apoptosis and the presence or absence of DBMI; however, at day 15 rats receiving 1 mg/day of FK 506 had a significantly lower number of apoptotic cells detected (127+/-103 vs. 233+/-174; P<0.02). CONCLUSIONS: In this study the number of apoptotic cells correlated positively with mild and moderate rejection episodes. In case of severe and chronic rejection a low apoptotic rate was found due probably to extensive necrosis and fibrosis of the mucosa. These data suggest an important role of apoptosis in acute and chronic intestinal rejection in a rat model of intestinal transplantation. Determination of apoptosis in allografts might represent an early sign of small bowel rejection and a useful marker in defining the degree of rejection and its outcome/prognosis.

Animals↗

Post-copulatory sexual selection and female fitness in Scathophaga stercoraria.

Whether sexual selection increases or decreases female fitness is determined by the occurrence and relative importance of sexual-conflict processes and the ability of females to choose high-quality males. Experimentally enforced polyandry and monogamy have previously been shown to cause rapid evolution in the yellow dung fly Scathophaga stercoraria. Flies from polyandrous lines invested more in reproductive tissue, and this investment influenced paternity in sperm competition, but came at a cost to immune function. While some fitness consequences of enforced polyandry or monogamy have been examined when flies mate multiply, the consequences for female fitness when singly copulated remain unexplored. Under a good-genes scenario females from polyandrous lines should be of higher general quality and should outperform females from monogamous lines even with a single copulation. Under sexual conflict, costly adaptations will afford no advantages when females are allowed to mate only once. We investigate the lifetime reproductive success and longevity of females evolving under enforced monogamy or polyandry when mating once with males from these selection regimes. Females from polyandrous lines were found to have lower fitness than their monogamous counterparts when mating once. They died earlier and produced significantly fewer eggs and offspring. These results suggest that sexual conflict probably drove evolution under enforced polyandry as female fitness did not increase overall as expected with purely good-genes effects.

Animals↗

Structural modifications in the swelling of inhomogeneous microgels by light and neutron scattering.

Small-angle neutron scattering and dynamic light scattering have been used to study the thermodynamics of swelling and the associated structure modifications of highly cross-linked temperature-sensitive poly (N-isopropylacrylamide) [poly(NIPAM)] microgels in D2O. A particle core-shell model is proposed, with the core containing most of the cross-linker molecules. The Flory-Rehner theory, with the inclusion of a concentration dependent Flory solvency parameter, successfully describes the experimental swelling, despite the inhomogeneous character of the particles. Interestingly, the shell evolution with temperature controls the whole particle swelling, exerting an external pressure over the core, which in turn influences its size during the swelling process. Scaling laws for the correlation lengths were found with respect to temperature and polymer concentration. Finally, it has been encountered that for the collapsed microgel states, the particle surface seems to have a fractal character.

Journal Article↗

Wavelength selection of rolling-grain ripples in the laboratory.

We have performed an experimental study, at very high resolution, of the wavelength selection and the evolution of rolling-grain ripples. A clear distinction is made between the flat sand bed instability and the ripple coarsening. The observation of the initial wavelength for the rolling-grain ripples is only possible close to the threshold for movement which imposes a constraint on the parameters. Moreover, we have proposed a law for the selection of the unstable wavelength under the latter constraint. Our results suggest that the initial wavelength depends on the amplitude of oscillation, the grain diameter, and the Stokes layer. Besides, during the coarsening, we observe no self-similarity of the ripple shape and for few cases a logarithmic growth of the wavelength.

Journal Article↗

Quantum information processing with large nuclear spins in GaAs semiconductors.

We propose an implementation for quantum information processing based on coherent manipulations of nuclear spins I=3/2 in GaAs semiconductors. We describe theoretically an NMR method which involves multiphoton transitions and which exploits the nonequidistance of nuclear spin levels due to quadrupolar splittings. Starting from known spin anisotropies we derive effective Hamiltonians in a generalized rotating frame, valid for arbitrary I, which allow us to describe the nonperturbative time evolution of spin states generated by magnetic rf fields. We identify an experimentally observable regime for multiphoton Rabi oscillations. In the nonlinear regime, we find Berry phase interference.

Journal Article↗

Thoroughly sampling sequence space: large-scale protein design of structural ensembles.

Modeling the inherent flexibility of the protein backbone as part of computational protein design is necessary to capture the behavior of real proteins and is a prerequisite for the accurate exploration of protein sequence space. We present the results of a broad exploration of sequence space, with backbone flexibility, through a novel approach: large-scale protein design to structural ensembles. A distributed computing architecture has allowed us to generate hundreds of thousands of diverse sequences for a set of 253 naturally occurring proteins, allowing exciting insights into the nature of protein sequence space. Designing to a structural ensemble produces a much greater diversity of sequences than previous studies have reported, and homology searches using profiles derived from the designed sequences against the Protein Data Bank show that the relevance and quality of the sequences is not diminished. The designed sequences have greater overall diversity than corresponding natural sequence alignments, and no direct correlations are seen between the diversity of natural sequence alignments and the diversity of the corresponding designed sequences. For structures in the same fold, the sequence entropies of the designed sequences cluster together tightly. This tight clustering of sequence entropies within a fold and the separation of sequence entropy distributions for different folds suggest that the diversity of designed sequences is primarily determined by a structure's overall fold, and that the designability principle postulated from studies of simple models holds in real proteins. This has important implications for experimental protein design and engineering, as well as providing insight into protein evolution.

Amino Acid Sequence↗