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PubMed2003

Extracellular hypothalamic serotonin and plasma amino acids in response to sequential carbohydrate and protein meals.

In previous studies, we showed that carbohydrate and protein ingestion, respectively, increased and decreased hypothalamic extracellular serotonin and the plasma ratio tryptophan over its competitor amino acids (Trp/LNAAs), reflecting serotonin synthesis. Serotonin levels returned towards baseline 2 h after either meal while the ratio remained altered. The question addressed is the ability of serotonin to respond expectedly to a second meal of the alternate nutrient. Rats were fed with sequential meals of either carbohydrates first and then casein 2 h later or in reverse order. Hypothalamic serotonin was measured using microdialysis. Permanent blood sampling allowed to track in parallel plasma amino acids. A carbohydrate meal increased hypothalamic serotonin, so did a subsequent casein meal. Conversely, following a casein meal that reduced serotonin, a carbohydrate meal also decreased it. The plasma ratio Trp/LNAAs was enhanced by a carbohydrate meal and remained high for 2h. A subsequent casein meal reversed this change but the ratio remained higher than basal values. A first casein meal reduced the ratio that was not increased again by a subsequent carbohydrate meal. It is obvious that ingestion of specific nutrients induce long-lasting metabolic and neurochemical variations that prevent subsequent changes to occur. The lack of expected changes to a second meal addresses again the hypothesis of alternate appetites for carbohydrates and proteins driven by serotonin changes.

Amino Acids↗

PubMed2025

Inference of differential kinase interaction networks with KINference.

MOTIVATION: Differential kinase interaction networks (DKINs) are networks containing kinase-substrate links that are differentially active between two conditions. Existing methods are either able to predict condition-agnostic kinase-substrate links or condition-specific differential kinase activity, but do not provide differential kinase-substrate links. Moreover, existing methods for predicting kinase-substrate links usually rely on curated biochemical knowledge. Thus, there is a lack of data-driven DKIN inference methods that are also applicable when prior knowledge is scarce. RESULTS: To address this need, we present KINference. KINference combines computation of a baseline KIN representing the space of all possible kinase-substrate links with filters applied to nodes and edges to identify differentially active subnetworks that are relevant in the context of a specific phosphoproteomics dataset. For the node filters, we rely on functional relevance and differential phosphorylation scores; for the edge filters, we make use of prize-collecting Steiner trees and correlations between phosphorylation sites of kinases and their target proteins. Tests on two phosphoproteomics datasets (kinase inhibition in breast cancer cells, SARS-CoV-2 infection in Calu-3 cells) show that the proposed filters produce significant results in terms of overlap with known interactions between kinases and phosphorylation sites. Furthermore, a case study on the SARS-CoV-2 infection data, suggests a potential host pathway linked to virus replication, showcasing the process of hypothesis generation utilizing DKINs computed by KINference. AVAILABILITY AND IMPLEMENTATION: KINference is available as an R package at https://github.com/bionetslab/KINference and https://doi.org/10.5281/zenodo.15411150. Scripts to reproduce the results are available at https://github.com/bionetslab/KINference-Evaluation-Scripts and https://doi.org/10.5281/zenodo.15424599.

Humans↗

PubMed2003

Effects of adenovirus mediated gene transfer to mouse testis in vivo on spermatogenesis and next generation.

PURPOSE: We directly injected DNA into mouse testes in vivo using an adenovirus vector to transfect testicular cells. We then analyzed the transfection efficiency, immunological problems and effects of gene transfer on spermatogenesis and the next generation. In this study we discuss the potential of gene therapy for male infertility. MATERIALS AND METHODS: A replication incompetent human adenovirus serotype 5 contained 2 deletions (E1 and E3 deletions) and was constructed such that the transgene was driven by the chicken beta-actin promoter to promote over expression of the downstream target gene (Lac Z). This adenovirus vector or control solution was injected into the interstitial space (intratesticular injection) or seminiferous tubules (intratubular injection) of the mouse testis. We investigated beta-galactosidase gene expression by X-gal (5-bromo-4-chloro-3-indolyl-beta-d-galactopyranoside) staining, the effects of gene transfer on spermatogenesis by evaluating the frequency of apoptotic cells by the TUNEL method, the inflammatory response on testes by detecting CD4 and CD8 positive cells immunohistochemically, and interleukin (IL)-6 and IL-8 by immunoblot analysis, epididymides sperm motility and the reproductive response of each mouse 3, 7, 14 and 28 days after injection. RESULTS: Intratesticular injection of adenovirus vector resulted in strong transgene expression in Leydig cells. In contrast, intratubular injection resulted in strong expression in Sertoli cells. Transgene expression was not detected in germ cells by either method. The peak of beta-galactosidase activity was on day 7, ie 0.674 +/- 0.20 (intratesticular) and 0.534 +/- 0.22 U (intratubular), and it decreased with time thereafter. The apoptosis index on day 7 was significantly higher in adenovirus injected groups than in noninjected groups, ie 0.46 +/- 0.20 vs 0.10 +/- 0.11 (intratesticular) and 0.78 +/- 0.31 vs 0.24 +/- 0.10 (intratubular). Transfected animals showed a slight mononuclear inflammatory response in the testes composed of CD4 and CD8 positive cells. Adenovirus vector stimulation resulted in the induction of IL-6 and IL-8 secretion in the testis. These immune responses subsided after day 7. There were no significant differences in the percent of motile sperm or the rate of abnormal sperm between the groups on any day after injection. Reproductive ability remained almost normal even after adenovirus mediated gene transfer with no effect observed in offspring. CONCLUSIONS: Our results suggest that although slight spermatogenic damage and inflammatory response caused by these methods may present problems, adenovirus mediated gene transfer may be effective for transfecting testicular somatic cells and applicable for in vivo gene therapy for male infertility in the future.

Adenoviruses, Human↗

PubMed2002

Maximizing spike train coherence or incoherence in the leaky integrate-and-fire model.

We study noise-induced resonance effects in the leaky integrate-and-fire neuron model with absolute refractory period, driven by a Gaussian white noise. It is demonstrated that a finite noise level may either maximize or minimize the regularity of the spike train. We also partition the parameter space into regimes where either or both of these effects occur. It is shown that the coherence minimization at moderate noise results in a flat spectral response with respect to periodic stimulation in contrast to sharp resonances that are observed for both small and large noise intensities.

Journal Article↗

PubMed2003

Noise activated granular dynamics.

We study the behavior of two particles moving in a bistable potential, colliding inelastically with each other and driven by a stochastic heat bath. The system has the tendency to clusterize, placing the particles in the same well at low drivings, and to fill all of the available space at high temperatures. We show that the hopping over the potential barrier occurs following the Arrhenius rate, where the heat bath temperature is replaced by the granular temperature. Moreover, within the clusterized "phase" one encounters two different scenarios: For moderate inelasticity, the jumps from one well to the other involve one particle at a time, whereas for strong inelasticity the two particles hop simultaneously.

Journal Article↗

PubMed2005

Kin interactions and changing social structure during a population outbreak of feral house mice.

Populations of feral house mice (Mus domesticus L.) in Australia undergo multiannual fluctuations in density, and these outbreaks may be partly driven by some change in behavioural self-regulation. In other vertebrate populations with multiannual fluctuations, changes in kin structure have been proposed as a causal mechanism for changes in spacing behaviour, which consequently result in density fluctuations. We tested the predictions of two alternative conceptual models based on kin selection in a population of house mice during such an outbreak. Both published models (Charnov & Finerty 1980; Lambin & Krebs 1991) propose that the level of relatedness between interacting individuals affects their behavioural response and that this changes with population density, though the nature of this relationship differs between the two models. Neither of the models was consistent with all observed changes in relatedness between interacting female mice; however, our results suggested that changes in kin structure still have potential for explaining why mouse outbreaks begin. Therefore, we have developed a variant of one of these conceptual models suggesting that the maintenance of female kin groups through the preceding winter significantly improves recruitment during the subsequent breeding season, and is therefore necessary for mouse outbreaks. We provide six testable predictions to falsify this hypothesis.

Alleles↗

PubMed1991

Hybrid biomechanical assist for acute biventricular failure.

It is now clear dynamic cardiomyoplasty alone will not be able to support patients in severe cardiogenic shock. On the other hand, implantable univentricular electromechanically driven devices for permanent circulatory support are undergoing early clinical trials. Because of the potential for existing or subsequent biventricular failure and to avoid the need to implant two space-occupying mechanical devices, hybrid biomechanical assist devices could have certain advantages. To evaluate the feasibility of supporting profound biventricular failure, utilizing the combination of dynamic cardiomyoplasty and mechanical ventricular assistance, six dogs underwent simultaneous right latissimus dorsi cardiomyoplasty and left heart bypass. Microspheres were embolized into the pulmonary artery resulting in pulmonary hypertension and acutely impairing the right ventricle. The left ventricle was unloaded via a centrifugal Biomedicus pump. To create severe biventricular failure, the aorta was cross-clamped and potassium cardioplegia was infused into the aortic root to achieve a flaccid diastolic arrest of the heart. Infusion of microspheres into the pulmonary artery resulted in a dose-dependent increase in pulmonary artery pressure. Stimulation of the cardiomyoplasty under these conditions showed a 25.9 +/- 7.9% (S.E.M.) (p less than 0.05, paired t-test) increase in mean pulmonary artery flow. There was a corresponding increase of 6.75 +/- 10.6% in the centrifugal pump flow. Following diastolic arrest, the mean pulmonary artery and centrifugal pump flows increased 90.8 +/- 11.5% (p less than 0.001) and 16.4 +/- 12.1%, respectively. These preliminary results suggest this approach could be a useful alternative to patients who require long-term biventricular support.

Acute Disease↗

PubMed2000

Role of aquaporin water channels in pleural fluid dynamics.

Continuous movement of fluid into and out of the pleural compartment occurs in normal chest physiology and in pathophysiological conditions associated with pleural effusions. RT-PCR screening and immunostaining revealed expression of water channel aquaporin-1 (AQP1) in microvascular endothelia near the visceral and parietal pleura and in mesothelial cells in visceral pleura. Comparative physiological measurements were done on wild-type vs. AQP1 null mice. Osmotically driven water transport was measured in anesthetized, mechanically ventilated mice from the kinetics of pleural fluid osmolality after instillation of 0.25 ml of hypertonic or hypotonic fluid into the pleural space. Osmotic equilibration of pleural fluid was rapid in wild-type mice (50% equilibration in <2 min) and remarkably slowed by greater than fourfold in AQP1 null mice. Small amounts of AQP3 transcript were also detected in pleura by RT-PCR, but osmotic water transport was not decreased in AQP3 null mice. In spontaneously breathing mice, the clearance of isosmolar saline instilled in the pleural space ( approximately 4 ml. kg(-1). h(-1)) was not affected by AQP1 deletion. In a fluid overload model produced by intraperitoneal saline administration and renal artery ligation, the accumulation of pleural fluid (approximately 0.035 ml/h) and was not affected by AQP1 deletion. Finally, in a thiourea toxicity model of acute endothelial injury causing pleural effusions and lung interstitial edema, pleural fluid accumulation in the first 3 h ( approximately 4 ml. kg(-1). h(-1)) was not affected by AQP1 deletion. These results indicate rapid osmotic equilibration across the pleural surface that is facilitated by AQP1 water channels. However, AQP1 does not appear to play a role in clinically relevant mechanisms of pleural fluid accumulation or clearance.

Animals↗

PubMedDate not supplied

Assessment of vestibular function by videonystagmoscopy.

Videonystagmoscopy has been used to subjectively observe the responses of the vestibular system in a population of patients with vestibular deficits. These results were compared with those of a control group of healthy, age-matched volunteers. The videonystagmoscopy device is made of one or two CCD cameras mounted on lightproof goggles, allowing a subjective observation of ocular movements on a video monitor. The eye movements, as well as the position of the head in space, can be recorded on videotape. The eyes are illuminated by infrared light emitting diodes placed on each side of the camera lens. The subjects are seated on a manually driven Barany chair. Subjects went through a protocol of passive roll head tilt on each side, followed by a slow, whole body rotation of 180 degrees amplitude, clockwise and counterclockwise, and then a head shaking test (HST). The eyes were subjectively observed, and we focussed on: torsional eye movements during head tilt, nystagmus when the rotation had stopped, and nystagmus induced by HST. With this simple and noninvasive examining procedure, screening of vestibular function at the bedside or during E.N.T. clinical investigations is possible.

Computer Terminals↗

PubMed2006

Climate-driven trends in contemporary ocean productivity.

Contributing roughly half of the biosphere's net primary production (NPP), photosynthesis by oceanic phytoplankton is a vital link in the cycling of carbon between living and inorganic stocks. Each day, more than a hundred million tons of carbon in the form of CO2 are fixed into organic material by these ubiquitous, microscopic plants of the upper ocean, and each day a similar amount of organic carbon is transferred into marine ecosystems by sinking and grazing. The distribution of phytoplankton biomass and NPP is defined by the availability of light and nutrients (nitrogen, phosphate, iron). These growth-limiting factors are in turn regulated by physical processes of ocean circulation, mixed-layer dynamics, upwelling, atmospheric dust deposition, and the solar cycle. Satellite measurements of ocean colour provide a means of quantifying ocean productivity on a global scale and linking its variability to environmental factors. Here we describe global ocean NPP changes detected from space over the past decade. The period is dominated by an initial increase in NPP of 1,930 teragrams of carbon a year (Tg C yr(-1)), followed by a prolonged decrease averaging 190 Tg C yr(-1). These trends are driven by changes occurring in the expansive stratified low-latitude oceans and are tightly coupled to coincident climate variability. This link between the physical environment and ocean biology functions through changes in upper-ocean temperature and stratification, which influence the availability of nutrients for phytoplankton growth. The observed reductions in ocean productivity during the recent post-1999 warming period provide insight on how future climate change can alter marine food webs.

Animals↗

PubMed1990

Mechanism and regulation of intestinal phosphate absorption.

Proper absorption of inorganic phosphate (Pi) from the lumen of the small intestine is of great importance for the achievement of Pi homeostasis. Although due to intralumenal H+ and Pi concentrations, Pi probably can be absorbed as H2PO4- by passive means in the duodenum, transepithelial transport of HPO4(2)- requires uptake from the lumen by an active transport system. The latter has been identified in many species as a Na(+)-Pi cotransport system at the brush-border membrane of the enterocyte. Although it is still a matter of debate whether the intestinal Na+ gradient-driven Pi transport system is electrogenic or electroneutral, there is agreement that the transporter accepts H2PO4- and HPO4(2)- alike. Recently, two laboratories independently isolated a Na(+)-Pi-binding protein which has been tentatively identified as part of the Na(+)-Pi cotransport system. Movement of Pi from the cytosol across the basolateral membrane into the interstitial space has only been preliminarily characterized as transfer by facilitated diffusion. Na(+)-Pi cotransport across the brush-border membrane is under control by the active vitamin D metabolite, 1,25-dihydroxyvitamin D3 (1,25-(OH)2D3). The sterol increases the intrinsic activity, i.e. the number and/or mobility of Na(+)-Pi carriers through genomic and probably also nongenomic actions. In addition, the rate of Na(+)-gradient-driven Pi transport can be enhanced by the hormone also through reduction of transmembrane Na+ fluxes so that more energy for translocation becomes available from the transmembrane Na+ gradient. Evidence is accumulating that thyroid hormones as well as glucocorticoids, apart from stimulating vitamin D-independent Pi uptake, potentiate the effect of 1,25-(OH)2D3 on Na(+)-Pi cotransport across the brush-border membrane.

Animals↗

PubMed2004

Transcriptional regulation of Msx2 in the AERs of developing limbs is dependent on multiple closely spaced regulatory elements.

In developing limb buds, Msx2 transcripts are expressed in the apical ectodermal ridge (AER) and in various regions of the limb mesenchyme. To identify DNA sequences responsible for Msx2 expression in the AER, we characterized the expression of LacZ reporter constructs driven by chicken Msx2 regulatory sequences in transgenic mice. We have identified a 55-bp enhancer that can direct AER-specific reporter gene expression. This 55-bp enhancer contains three elements that are evolutionary conserved among five vertebrate Msx2 genomic sequences. AER expression of reporter constructs in transgenic mice is lost or reduced when mutations are introduced into each of these three regions. Moreover, changing the relative orientation by reverse complementing one of the three elements also results in loss of expression, suggesting that the relative orientations of transcription factor binding is important. To identify the transcription factor(s) binding to these elements, we conducted one-hybrid screening and identified Dlx5 and Sox11. Both Dlx5 and Sox11 are expressed in the AER, and the proteins encoded by these genes bind to separate conserved elements, supporting their possible roles in regulating Msx2 expression.

Animals↗

PubMed2003

Anomalous roughening in experiments of interfaces in Hele-Shaw flows with strong quenched disorder.

We report experimental evidence of anomalous kinetic roughening in the stable displacement of an oil-air interface in a Hele-Shaw cell with strong quenched disorder. The disorder consists of a random modulation of the gap spacing that is transverse to the growth direction (tracks). Experiments were performed by varying the average interface velocity and the gap spacing, and measuring the scaling exponents. The following values of the scaling exponents were obtained; beta approximately 0.50, beta* approximately 0.25, alpha approximately 1.0, alpha(loc) approximately 0.5, and z approximately 2. When there is no fluid injection, the interface is driven solely by capillary forces, and a higher value of beta of approximately beta=0.65 is measured. The presence of multiscaling and the particular morphology of the interfaces, characterized by large height differences that follow a Lévy distribution, confirms the existence of anomalous scaling. From a detailed study of the motion of the oil-air interface, we show that the anomaly is a consequence of different local velocities on the tracks plus the coupling in the motion between neighboring tracks. The anomaly disappears at high interface velocities, weak capillary forces, or when the disorder is not sufficiently persistent in the growth direction. We have also observed the absence of scaling when the disorder is very strong or when a regular modulation of the gap spacing is introduced.

Journal Article↗

PubMed2003

X-ray structure and circular dichroism of pure rotamers of bis[guanosine-5'-monophosphate(-1)](N,N,N',N'-tetramethylcyclohexyl-1,2-diamine)platinum(II) complexes that have R,R and S,S configurations at the asymmetric diamine.

The use of a sterically hindered diamine ligand (Me(4)DACH) has allowed for the first time, the isolation and characterization, both in the solid state (X-ray crystallography) and in solution (circular dichroism), of pure DeltaHT rotamers of [Pt(Me(4)dach)(5'-GMP)(2)] (compounds 1 and 2 for R,R and S,S configurations of the Me(4)DACH ligand, respectively). Comparison of the CD spectra obtained for each rotamer, which differ only in the chirality of the Me(4)DACH ligand (R,R or S,S) or in the chirality of the HT conformation (Delta or Lambda), allowed us to conclude that, in the 200-350 nm range, the contributions to the overall CD spectrum that stem from diamine chirality and diamine-induced chirality of platinum d--d transitions or from sugar chirality are negligible relative to the exciton chiral coupling that occurs for pi-pi* transitions of the cis guanines. Accurate molecular structures of 1.10 D(2)O and 2.14 D(2)O (conventional crystallographic agreement indexes R(1) convergent to 2.07 % and 2.18 %, respectively) revealed that the crystallized rotamers have a DeltaHT conformation that is in agreement with all previously reported X-ray structures of [Pt(diamine)(nucleos(t)ide)(2)] complexes. This conformation allows the 5'-phosphate to be located in proximity to the Me(4)DACH ligand so that (P)O...HC(N) hydrogen-bond interactions exists in both complexes. For both structures, the canting of the guanine planes on the coordination plane is right-handed (R; canting angle (Phi) of 80.9 degrees and 73.2 degrees, respectively); this indicates that the canting direction is driven by the HT conformation chirality (Delta for both compounds) and not by the chirality of the carrier ligand (different for the two compounds). Density functional theory analysis of the conformational space as a function of Phi indicated a good agreement between the computed and experimental structures. The increase in energy for Phi values below 65 degrees and 55 degrees (for 1 and 2, respectively) is mainly due to the short intramolecular contacts between C(8)H and the cis N-Me groups on the same side of the platinum coordination plane.

Antineoplastic Agents↗

PubMed2004

Defining pathways of loss and secretion of chemical messengers from astrocytes.

It is becoming evident that glia, and astrocytes in particular, are intimately involved in neuronal signaling. Astrocytic modulation of signaling in neurons appears to be mediated by the release of neuroactive compounds such as the excitatory amino acid glutamate. Release of these transmitters appears to be driven by two different processes: (1) a volume regulatory response triggered by hypo-osmotic conditions that leads to the release of osmotically active solutes from the cytoplasm into the extracellular space, and (2) intracellular calcium-dependent vesicle-mediated excytotic release. The regulatory volume decrease may be mediated by any of several different pathways that increase membrane permeability, thus allowing osmolytes to travel down their concentration gradient into the extracellular space. Such pathways include anion channels, hemichannels, P2X receptor channels, and transporters or multidrug resistance proteins. The excytotic release process may use calcium triggered synaptic like vesicle fusion or alterations in constitutive vesicle trafficking to the membrane. Determining the contribution of any of these release mechanisms requires agents that can be used to specifically block pathways of interest. Currently, many of the pharmacological compounds being used exhibit a great deal of cross-reactivity between several of these pathways. For example, the popular anion channel inhibitor 5-nitro-2-(3-phenyl-propylamino)benzoic acid (NPPB) is an efficient blocker of both hemichannels and vesicle loading. This demonstrates the need to more fully characterize the activities of the agents currently available and to choose pathway blockers carefully when designing experiments.

Animals↗

PubMed1982

The bioenergetics of denitrification.

In anaerobically grown Paracoccus denitrificans the dissimilatory nitrate reductase is linked to the respiratory chain at the level of cytochromes b. Electron transport to nitrite and nitrous oxide involves c-type cytochromes. During electron transport from NADH to nitrate one phosphorylation site is passed, whereas two sites are passed during electron transport from NADH to oxygen, nitrite and nitrous oxide. The presentation of a respiratory chain as a linear array of electron carriers gives a misleading picture of the efficiency of energy conservation since the location of the reductases is not taken into account. For the reduction of nitrite and nitrous oxide, protons are utilized from the periplasmic space, whereas for the reduction of oxygen and nitrate, protons are utilized from the cytoplasmic side of the inner membrane. Evidence for two transport systems for nitrate was obtained. One is driven by the proton motive force; this system is used to initiate nitrate reduction. The second system is a nitrate-nitrite antiport system. A scheme for proton translocation and electron transport to nitrate, nitrite, nitrous oxide and oxygen is presented. The number of charges translocated across the membrane during flow of two electrons from NADH is the same for all nitrogenous oxides and is 67-71% of that during electron transfer to oxygen via cytochrome o. These findings are in accordance with growth yield studies. YMAX electron values determined in chemostat cultures for growth with various substrates and hydrogen acceptors are proportional to the number of charges translocated to these hydrogen acceptors during electron transport.

Adenosine Triphosphate↗

PubMed1997

Dynamics of the neural discharge in snail neurons.

Spike trains recorded under weak sinusoidal driving from central neurons of Lymnaea stagnalis appear quite irregular and envisage the possibility of an underlying chaotic process. Therefore, the sequences of interspike intervals are analyzed in the framework of non-linear dynamics. Since, for several reasons, these sequences are rather short, the analysis is performed by using methods of non-linear forecasting. To reject the null hypothesis that the original time series is a realization of a linear stochastic process with the same autocorrelation function, the results obtained on the original data are compared with those from surrogate data sets. Some 'non-linear' predictability occurs only in narrow regions of the space of stimulus parameters and the frequency of perturbation is critical in determining it. Moreover, it is shown that such behavior can be qualitatively mimicked by the FitzHugh-Nagumo model driven by a weak sinusoidal signal plus noise. It is argued that the narrowness of the non-linear predictability regions renders quite unlikely the detection of deterministic dynamics in the activity of these neurons.

Action Potentials↗

PubMed2004

Integrated lithographic membranes and surface adhesion chemistry for three-dimensional cellular stimulation.

The complex spatiotemporal organization of cellular and molecular interactions dictates the physiological function of cells. These behaviors are indications of an integrated response to a three-dimensional cellular environment and anchored in cell adhesion on scaffolds. Here, we are able to control interconnected structural, mechanical, and chemical stimuli by dictating the cellular environment through chemical surface modifications, soft lithography, and mechanical deformation. Control of these variables is obtained through the use of an elastomeric membrane chemically modified for cell adhesion with a pressure-driven cell-stretching device which creates a pattern of forces similar to those encountered in physiological environments. Further, the integration of lithographic methods and chemical patterning allows the introduction of space- and time-dependent parameters by combining mechanical stimulation, biochemical regulation, and scaffolding design. The method is applied to stimulate single cells and cell populations to examine cellular response with spatiotemporal control. This research provides the capacity to probe biological patterns and tissue formation under the influence of mechanical stress.

Animals↗