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PubMed2006

Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production.

In the post-genome era, it is one challenge to understand the cellular metabolism at the systematic levels. Mathematical modeling of microorganisms and subsequent computer simulation are effective tools for systems biology. In this paper, based on the genome-scale Escherichia coli stoichiometric model iJR904, through the GAMS linear programming package, the in silico maximal succinate yield was estimated to be 1.714 mol/mol glucose. When another two constraints were added, the maximal succinate yield dropped to 1.60 mol/mol glucose. Further analysis substantiated the uniqueness of the flux distribution under such constraints. After comparisons with the metabolic flux analysis (MFA) results computed from the wet experimental data of the three kinds of E. coli, three potential improvement target sites, the glucose phosphotransferase transport system, the pyruvate carboxylase, and the glyoxylate shunt, were identified and selected for the genetic modifications. All the three genetic modified strains showed increased succinate yield. The final strain TUQ19/pQZ6 had a high yield of 1.29 mol succinate/mol glucose and high productivity. The success of the above experiments proved that this in silico optimal succinate production pathway is reasonable and practical. This method may also be used as a general strategy to help enhance the yields of other favorable metabolites in E. coli.

Anaerobiosis↗

PubMed1989

Involvement of nigrotecto-reticulospinal pathways in the iminodipropionitrile (IDPN) model of spasmodic dyskinesias: a 2-deoxy-D-[1-14C]glucose study in the rat.

Chronic administration of iminodipropionitrile (IDPN) to rats causes a persistent behavioral syndrome characterized by lateral and vertical head twitches, random circling, and increased tactile and acoustic startle responses. In order to identify brain areas which are affected in rats manifesting this syndrome, we used the autoradiographic 2-deoxy-D-[1-14C]glucose ([14C]DG) method to map cerebral glucose utilization in IDPN-treated rats. One day after the development of the dyskinetic syndrome, there were significant decreases in local glucose utilization in the substantia nigra pars reticulata (SNr) and compacta (SNc), the dorsal raphe, the superficial and deep layers of the superior colliculus, the inferior colliculi, the interpeduncular nucleus, the medial and dorsolateral geniculate nuclei, and the superior and lateral vestibular nuclei. There were also significant decreases in layer 2 of the cingulate cortex and in the temporal and occipital cortices. In contrast, there were no changes in the motor cortex, the caudate-putamen, the nucleus accumbens, or the median raphe. These findings suggest that deleterious effects of IDPN on the nigrotectal pathways which affect head and neck movements and circling behaviors via the brainstem reticulospinal tracts may play an important role in the IDPN-induced persistent spasmodic dyskinetic syndrome in rats.

Animals↗

PubMed1997

An in vitro model of the kitten retinogeniculate pathway.

An organotypic explant coculture method is described for the developing retinogeniculate pathway of the cat. Retinal explants and thalamic slices containing the dorsal lateral geniculate nucleus (LGN), derived from early postnatal kittens, can be grown in serum-free culture medium for several days. In such cultures, retinal ganglion cells (RGCs) and LGN neurons retained their age-specific morphological features and developed functional connections. Labeling of RGCs and their processes with DiI showed that all three major classes of RGCs (alpha/Y, beta/X, gamma/W) were present in cocultured retinal explants. Retinal axons readily regenerated into thalamic slices and, over time, developed arbors within the LGN. Retrograde labeling from the LGN traced the origin of these axons almost exclusively to alpha-cells in the retina. In vitro intracellular recordings indicated that LGN cells maintained their basic electrophysiological properties in coculture. Current injection generated action potentials, and, at hyperpolarized levels, it led to low-threshold Ca2+ spiking. Regenerated retinal axons also formed functional connections with LGN neurons. Electrical stimulation of the retinal explant elicited excitatory postsynaptic responses (EPSPs) in LGN cells. Drop application of specific glutamate antagonists indicated that EPSPs had both N-methyl-D-aspartate (NMDA) and non-NMDA receptor components. The morphology of the LGN neurons was examined after intracellular injections of biocytin during recording. Labeled cells were very similar to those of early postnatal kittens. Although, in general, they had relatively small soma and simple dendritic branching patterns, a few could be recognized as X- or Y-cells. Thus the coculture model can be used to assay the regenerative propensity of different types of RGCs during development.

Action Potentials↗

PubMed2005

Quantitative mRNA expression analysis of co-stimulatory molecules in sequential biopsies from heart allografts.

Allograft-specific T-cell activation requires two signals, "signal one" via the T-cell receptor and "signal two" via costimulatory pathways. Animal models provide promising data that blockade of costimulatory signals can lead to T-cell anergy and tolerance. We analyzed 72 formalin-fixed and paraffin-embedded sequential heart allograft biopsies from 22 patients by quantitative real-time reverse transcriptase-polymerase chain reaction for the mRNA expression of the costimulatory molecules CD28, CD80, CD86, CD40, and CD154. mRNA expression levels were correlated to histological grade and time-point of rejection. mRNA expression of costimulatory molecules predominantly expressed by antigen-presenting cells (CD80, CD86, CD40), correlated with histological grade of cell-mediated acute rejection. Costimulatory molecules were up-regulated not only during rejection episodes early after transplantation, but also at late occurring rejection. The present results suggest a simultaneous and long-term therapeutical blockade of more than one costimulatory pathway for the prevention of repetitive T-cell mediated acute rejection episodes after heart transplantation.

Adult↗

PubMed2025

Flux-sum coupling analysis of metabolic network models.

Metabolites acting as substrates and regulators of all biochemical reactions play an important role in maintaining the functionality of cellular metabolism. Despite advances in the constraint-based framework for genome-scale metabolic modeling, we lack reliable proxies for metabolite concentrations that can be efficiently determined and that allow us to investigate the relationship between metabolite concentrations in specific metabolic states in the absence of measurements. Here, we introduce a constraint-based approach, the flux-sum coupling analysis (FSCA), which facilitates the study of the interdependencies between metabolite concentrations by determining coupling relationships based on the flux-sum of metabolites. Application of FSCA on metabolic models of Escherichia coli, Saccharomyces cerevisiae, and Arabidopsis thaliana showed that the three coupling relationships are present in all models and pinpointed similarities in coupled metabolite pairs. Using the available concentration measurements of E. coli metabolites, we demonstrated that the coupling relationships identified by FSCA can capture the qualitative associations between metabolite concentrations and that flux-sum is a reliable proxy for metabolite concentration. Therefore, FSCA provides a novel tool for exploring and understanding the intricate interdependencies between the metabolite concentrations, advancing the understanding of metabolic regulation, and improving flux-centered systems biology approaches.

Escherichia coli↗

PubMed2006

Hypoxia-inducible factor-1alpha expression requires PI 3-kinase activity and correlates with Akt1 phosphorylation in invasive breast carcinomas.

Hypoxia-inducible factor-1 alpha (HIF-1alpha) is the regulatory subunit of the heterodimeric transcription factor HIF-1 and the key factor in cellular response to low oxygen tension. Expression of HIF-1alpha protein is associated with poor patient survival and therapy resistance in many types of solid tumors. Insight into HIF-1alpha regulation in solid tumors is important for therapeutic strategies. In this study, we determined the pathophysiological relevance of HIF-1alpha regulation by the oncogenic phosphatidylinositol 3'-kinase (PI 3-kinase)/Akt signaling pathway. We modeled the physiology of hypoxic tumor regions by culturing carcinoma cells under low oxygen tension in the absence of serum. We observed that hypoxic induction of HIF-1alpha protein was decreased by serum deprivation. Overexpression of dominant-active Akt1 restored HIF-1alpha expression, whereas inhibition of PI 3-kinase activity reduced hypoxic HIF-1alpha protein levels to a similar extent as serum deprivation. Immunohistochemical analysis of 95 human breast cancers revealed that lack of Akt1 phosphorylation correlates with low HIF-1alpha levels. To our knowledge, this is the first reported comparison between HIF-1alpha expression and Akt phosphorylation in human carcinomas. We conclude that Akt activity is physiologically relevant for HIF-1alpha expression in breast cancer. This implies that HIF-1alpha function might be therapeutically targeted by inhibition of the PI 3-kinase/Akt pathway.

Breast Neoplasms↗

PubMed2002

Thalamocortical [correction of Thalamcortical] optimization of tactile processing according to behavioral state.

We propose a conceptual model that describes the operation of the main thalamocortical loop of the rat somatosensory system. According to this model, the asynchronous convergence of ascending and descending projections dynamically alters the physiological properties of thalamic neurons in the ventral posterior medial (VPM) nucleus as rats shift between three behavioral states. Two of these states are characterized by distinct modes of rhythmic whisker movements. We posit that these simultaneous shifts in exploratory behavioral strategy and in the physiological properties of VPM neurons allow rats to either (i) optimize the detection of stimuli that are novel or difficult to sense or (ii) process complex patterns of multi-whisker stimulation.

Afferent Pathways↗

PubMed2006

Metabolic flux analysis at ultra short time scale: isotopically non-stationary 13C labeling experiments.

A novel approach to (13)C metabolic flux analysis (MFA) is presented using cytosolic metabolite pool sizes and their (13)C labeling data from an isotopically non-stationary (13)C labeling experiment (INST-CLE). The procedure is demonstrated with an E. coli wild type strain grown at fed batch conditions. The intra cellular labeling dynamics are excited by a sudden step increase of the (13)C portion in the substrate feed. Due to unchanged saturation of the substrate uptake system, the metabolic fluxes remain constant during the following sampling time period of only 16s, in which 20 samples are taken by an automated rapid sampling device immediately stopping metabolism by methanol quenching. Subsequent cell disruptive sample preparation and LC-MS/MS enabled simultaneous determination of pool sizes and mass isotopomers of intra cellular metabolites requiring detection limits in the nM range. Based on this data the new computational flux analysis tool 13CFLUX/INST is used to determine the intra cellular fluxes based on a complex carbon labeling network model. The measured data is in good agreement with the model predictions, thus proving the applicability of the new isotopically non-stationary (13)C metabolic flux analysis (INST-(13)C-MFA) concept. Moreover, it is shown that significant new information with respect to flux identifiability, non-measurable pool sizes, data consistency, or large storage pools can be taken from the novel kind of experimental data. This offers new insight into the biological operation of the metabolic network in vivo.

Bioreactors↗

PubMed2004

Differential kinetochore requirements for establishment and maintenance of the spindle checkpoint are dependent on the mechanism of checkpoint activation in Saccharomyces cerevisiae.

The spindle checkpoint in the yeast Saccharomyces cerevisiae is an intracellular signal transduction pathway comprised of two branches that inhibit two different mitotic transitions in cells treated with benzimidazole drugs such as nocodazole. The kinetochore is an integral component of the MAD2 branch of the spindle checkpoint pathway. Current models propose that the kinetochore is required for both the establishment and maintenance of the spindle checkpoint but a role for the kinetochore in the maintenance of spindle checkpoint in yeast has never been directly tested. We used a temperature sensitive ndc10-1 mutant to inactivate kinetochores before and after arresting cells in mitosis to determine the role of kinetochores in the establishment and maintenance of the spindle checkpoint. We show that both establishment and maintenance requires kinetochore function in response to spindle damage induced by benzimidazole drugs. Excess expression of the Mps1 protein kinase causes wild type cells and ndc10-1 cells to arrest in mitosis. Unlike the spindle checkpoint arrest activated by benzimidazoles, this arrest can be maintained independently of kinetochores. The arrest induced by excess Mps1p is independent of BUB2. Therefore, mitotic arrest induced by excess Mps1p expression is due to the action of the MAD2 branch of the spindle checkpoint pathway and excess Mps1p acts downstream of the kinetochore.

Carrier Proteins↗

PubMed2005

Left ventricular hypertrophy and angiotensin II receptor blocking agents.

Angiotensin II plays a significant role in cell growth and proliferation in model systems and in humans. Numerous studies have shown that left ventricular hypertrophy (LVH) increases the risk of coronary heart disease, congestive heart failure, stroke or transient ischemic attack; all-cause deaths, and sudden death. The use of angiotensin-converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs) has provided beneficial effects on LVH regression and on cardiac remodeling in the presence of hypertension and heart failure. The new class of ARBs appears to provide cardioprotective effects that are similar to those of the ACE inhibitors. Most of the beneficial effects provided by these agents appear to be related to a more complete blockade of the angiotensin II type 1 (AT1) receptor. However, costimulation of the angiotensin II type 2 (AT2) receptor appears to increase nitric oxide and thus causes some bradykinin-like effects. Evidence for the role of angiotensin II in promoting LVH as well as abnormal regulation of the angiotensin II signal transduction pathways in model systems and in humans has been reviewed. Secondly, the mechanisms for the beneficial effects of angiotensin II receptor blockers studied in model systems and in humans, including possible involvement in the formation of reactive oxygen species by mononuclear cells, are presented. Finally, results from large-scale interventions such as the Losartan Intervention For Endpoint reduction (LIFE) study, as well as an overview of the Valsartan Antihypertensive Long-term Use Evaluation (VALUE) trial involving the use of ARB in high-risk patients, are presented.

Angiotensin II↗

PubMed1996

Vigabatrin and carbamazepine have different efficacies in the prevention of status epilepticus induced neuronal damage in the hippocampus and amygdala.

The present study compares the efficacy of carbamazepine (20 mg/kg/day) and vigabatrin (250 mg/kg/day) in preventing hippocampal and amygdaloid damage in the perforant pathway stimulation model of status epilepticus in the rat. One group of rats received a combination of the drugs. Drug treatments were started one week before the stimulation and continued for two weeks thereafter. Gallyas silver impregnation and somatostatin immunohistochemistry were used to detect neuronal damage. All drug treatments were equally effective in decreasing the number and severity of seizures during electrical stimulation. In the vigabatrin group, the damage to the hilar somatostatin-immunoreactive (SOM-ir) neurons and hippocampal CA3c pyramidal cells was less severe than in the vehicle (SOM-ir, P < 0.01; CA3c, P < 0.05) and carbamazepine (SOM-ir, P < 0.01; CA3c, P < 0.05) groups. In the carbamazepine and combination groups, the severity of neuronal damage in the hippocampus did not differ from that in vehicle-treated animals. The amygdaloid neurons were not protected by any of the treatments. Our results show that even though vigabatrin and carbamazepine treatments had similar anticonvulsant efficacy during the perforant pathway stimulation, only vigabatrin but not carbamazepine decreased seizure-induced neuronal damage. Vigabatrin decreased neuronal damage in the hippocampus but not in the amygdala. These results demonstrate that different brain regions and neuronal networks may be protected unequally by different anticonvulsants.

Amygdala↗

PubMed1992

Polyethylene glycol enhanced refolding of bovine carbonic anhydrase B. Reaction stoichiometry and refolding model.

Polyethylene glycol (PEG) inhibited aggregation during refolding of bovine carbonic anhydrase B (CAB) through the formation of a nonassociating PEG-intermediate complex. Stoichiometric concentrations of PEG were required for complete recovery of active protein during refolding at aggregating conditions. For example, a PEG (Mr = 3350) to CAB molar ratio ([PEG]/[CAB]) of 2 was sufficient to inhibit aggregation during refolding at 1.0 mg/ml (33.3 microM) protein and 0.5 M guanidine hydrochloride. In addition, the PEG concentration required for enhancement was dependent upon the molecular weight and only molecular weights between 1000 and 8000 were effective in inhibiting aggregation. In the presence of PEG, the rate of refolding was the same as that observed for refolding without the formation of associated species. Refolding in the presence of PEG resulted in the rapid formation of a PEG complex with the molten globule first intermediate, and this PEG-intermediate complex did not aggregate. The CAB refolding kinetics in the presence of PEG were determined and used to develop a model of the PEG enhanced refolding pathway. The mathematical model was validated by independent activity measurements of CAB refolding. This model predicted that PEG enhanced refolding of CAB occurred by a specific interaction of PEG with the molten globule first intermediate to form a nonassociating complex which continued to fold at the same rate as the first intermediate. The predicted pathway and binding properties of PEG indicate that PEG enhanced refolding may be analogous to chaperonin mediated protein folding.

Animals↗

PubMed2006

Representing, storing and accessing molecular interaction data: a review of models and tools.

One important aim within systems biology is to integrate disparate pieces of information, leading to discovery of higher-level knowledge about important functionality within living organisms. This makes standards for representation of data and technology for exchange and integration of data important key points for development within the area. In this article, we focus on the recent developments within the field. We compare the recent updates to the three standard representations for exchange of data SBML, PSI MI and BioPAX. In addition, we give an overview of available tools for these three standards and a discussion on how these developments support possibilities for data exchange and integration.

Computational Biology↗

PubMed2003

Consideration of a unified model of amygdalar associative functions.

This paper considers issues arising from presentations by Barry Everitt and Gorica Petrovich concerning amygdalar involvement in appetitive conditioning. Studies reported by these researchers are beginning to unravel the distribution of associative functions among amygdalar nuclei and their efferent targets. The main issue addressed here concerns how to integrate the information from studies of appetitive conditioning with conclusions from studies of other forms of associative learning, including pavlovian fear conditioning and instrumental conditioning. Most students of this issue will agree that no prima facie integration is readily apparent in current scholarship. Although we do not here provide the definitive integration, we do attempt to take some preliminary, broad-brush steps towards that goal.

Amygdala↗

PubMed2000

IFN-gamma is necessary but not sufficient for anti-CD40 antibody-mediated inhibition of the Th2 response to Schistosoma mansoni eggs.

The injection of Schistosoma mansoni eggs into the footpads of mice results in a localized Th2 cytokine response and tissue eosinophilia. We examined whether treatment with CD40-activating Abs would block the development of Th2 cytokine responses and eosinophilic tissue pathology in this model. Seven days after C57BL/6 mice were injected with eggs and the FGK45 anti-CD40 Ab, Ag-specific synthesis of IL-4, IL-5, and IL-13 in lymph node culture was reduced (>10-fold) relative to control mice treated with eggs and rat IgG. In contrast, IFN-gamma and IL-12 were increased in both culture supernatants and in the serum. Similar changes in lymph node cytokine mRNA were observed in vivo, and tissue eosinophilia was reduced nearly 20-fold. Th2 cytokine responses in anti-CD40-treated IFN-gamma-/- and IL-12 p40-/- C57BL/6 mice were unaffected, although anti-CD40 induced high levels of systemic and local IFN-gamma production in both wild-type and IL-12 p40-/- mice. We conclude that CD40-activating treatments strongly reverse the immune phenotype generated in response to a classic, Th2-biasing stimulus and stimulate IFN-gamma through a novel IL-12-independent pathway. This model for Th1-deviating immune therapy may have relevance to the treatment of Th2-dependent diseases in general.

Animals↗

PubMed2001

Activation of the nuclear factor-kappaB is a key event in brain tolerance.

The transcription factor nuclear factor-kappaB (NFkappaB) is an ubiquitously expressed inducible regulator of a broad range of genes and plays a pivotal role in cell death and survival pathways. Three models of brain tolerance (ischemic, epileptic, and polyunsaturated fatty acid-induced preconditioning), known to confer resistance to neurons against ischemia or status epilepticus, were used to determine whether NFkappaB mediated the late preconditioning. A sublethal 3 min ischemia, a dose of 5 mg/kg kainic acid (KA5) or 500 nmol of linolenic acid (LIN500) led to a rapid increase of NFkappaB DNA-binding activity and nuclear translocation of p65 and p50 subunits of NFkappaB in neurons. Pretreatment with the NFkappaB inhibitor diethyldithiocarbamate or kappaB decoy DNA blocked the increased DNA-binding activity and the nuclear translocation of NFkappaB and abolished the neuroprotective effects of different delayed preconditionings against severe ischemia or epilepsy. The inhibition of NFkappaB observed in rats preconditioned with 3 min ischemia, KA5 or LIN500 treatments compared with ischemic or epileptic controls was correlated with the prevention of the inducible degradation of the inhibitory protein IkappaBalpha. Preconditioning probably inhibits the activation of NFkappaB by interfering with a pathway that leads to the direct transcriptional activation of IkappaBalpha by NFkappaB itself. The present work provides evidence that activation of NFkappaB is a crucial step in the signal transduction pathway that underlies the development of brain tolerance and may open new strategies in the prevention of cerebral diseases, such as ischemia or epilepsy.

Active Transport, Cell Nucleus↗

PubMed2006

Hepatocytes--the choice to investigate drug metabolism and toxicity in man: in vitro variability as a reflection of in vivo.

The pharmaceutical industry is committed to marketing safer drugs with fewer side effects, predictable pharmacokinetic properties and quantifiable drug-drug interactions. Drug metabolism is a major determinant of drug clearance and interindividual pharmacokinetic differences, and an indirect determinant of the clinical efficacy and toxicity of drugs. Progressive advances in the knowledge of metabolic routes and enzymes responsible for drug biotransformation have contributed to understanding the great metabolic variations existing in human beings. Phenotypic as well genotypic differences in the expression of the enzymes involved in drug metabolism are the main causes of this variability. However, only a minor part of phenotypic variability in man is attributable to gene polymorphisms, thus making the definition of a normal liver complex. At present, the use of human in vitro hepatic models at early preclinical stages means that the process of selecting drug candidates is becoming much more rational. Cultured human hepatocytes are considered to be the closest model to human liver. However, the fact that hepatocytes are located in a microenvironment that differs from that of the cell in the liver raises the question: to what extent does drug metabolism variability observed in vitro actually reflect that of the liver in vivo? By comparing the metabolism of a model compound both in vitro and in vivo in the same individual, a good correlation between the in vitro and in vivo relative abundance of oxidized metabolites and the hydrolysis of the compound was observed. Thus, it is reasonable to consider that the variability observed in human hepatocytes reflects the existing phenotypic heterogeneity of the P450 expression in human liver.

Anti-Inflammatory Agents, Non-Steroidal↗

PubMed2006

Resources for integrative systems biology: from data through databases to networks and dynamic system models.

In systems biology, biologically relevant quantitative modelling of physiological processes requires the integration of experimental data from diverse sources. Recent developments in high-throughput methodologies enable the analysis of the transcriptome, proteome, interactome, metabolome and phenome on a previously unprecedented scale, thus contributing to the deluge of experimental data held in numerous public databases. In this review, we describe some of the databases and simulation tools that are relevant to systems biology and discuss a number of key issues affecting data integration and the challenges these pose to systems-level research.

Animals↗