Changes in liver glycogen and lipid metabolism during transient graft-versus-host (GvH) and graft-versus-leukemia (GvL) reactivity

We investigated the influence of transient graft-versus-leukemia (GvL) and graft-versus-host reactivity (GvH) following allogeneic immune cell transfer on the glycogen and lipid metabolism in the liver of affected mice to better understand the underlying mechanism of these phenomena. As model we used a well established adoptive cellular immunotherapy (ADI) system. This involves transfer of in situ activated anti-tumor immune spleen lymphocytes (ISPL) from the tumor-resistant mouse strain B10.D2 (H-2(d), M1s(b)) into 5 Gy sublethally irradiated syngeneic ESb-MP lymphoma-bearing DBA/2 (H-2(d), M1s(a)) mice. Experiments were performed by transfer of ISPL from B10.D2 into DBA/2 tumor-bearing mice (GvL effect on liver metabolism) and into DBA/2 non-tumor-bearing mice (GvH effect on liver metabolism). Our results show that glycogen in hepatocytes decreased dramatically 5 days after ISPL transfer, which coincided with a high increase of large fat granules. 8 days after ISPL transfer, livers started to re-express glycogen and to decrease their lipid content. Normalization of both parameters was seen after day 30. These changes were qualitatively similar in both GvL and GvH. Measurement of activity of the liver marker enzymes, GOT and GPT, in the sera of animals subjected to GvL or GvH, showed peak values also at day 5, coinciding with the loss of glycogen. Quantitative differences were seen, however, in that much higher levels were reached in GvL than in GvH. Immune system recovery from irradiation damage and liver regeneration after immune cell mediated liver damage are likely explanations for the reversibility of the metabolic changes and for the lack of GVH disease and mortality in this new and effective cellular cancer immunotherapy model.

Activated endothelial cells induce apoptosis in lymphoma cells

We have previously shown that the arrest or regression of mouse liver metastases formed by lacZ-transduced ESbL T lymphoma cells (ESbL-lacZ) is associated with the stimulation of nitric oxide (NO) production by liver endothelial cells in sis. Here we studied in vitro the NO-mediated cytotoxicity against ESbL-lacZ target cells using well-characterized bovine endothelial cells (BEG) as effector cells. It was found that the co-culture of BEC with human TNF-alpha caused an increase of NO synthesis which could be completely blocked by the treatment with inducible NO synthase (iNOS) inhibitor N-G-monomethyl-L-arginine (NMMA). Incubation of activated BEC with metastatic lymphoma cells led to the death of the latter cells as evidenced by staining with propidium iodide and FAGS analysis. This cytotoxicity was considerably reduced after pretreatment of BEC with NMMA. Cytotoxic effects were also demonstrated after incubation of tumor cells with NO donor glycerol trinitrate (GTN). Non-activated BEC were not able to produce NO and showed a substantially lower level of cytotoxicity. The anti-tumor cytotoxicity exerted by activated BEC includes the stimulation of apoptosis in metastatic lymphoma cells which is mediated to a large extent by NO. These data reveal a novel role of endothelial cells in the elimination of metastatic cells through the induction of programmed cell death.

In situ downregulation of VLA-4 integrin cell surface expression during lymphoma growth and liver metastasis

The role of VLA-4 integrin in liver metastasis of lymphoma cells was investigated. ESbL-lacZ lymphoma cells in vitro exhibited high surface expression of VLA-4, adhered to CS-1 fibronectin and VCAM-1 and cell adhesion was inhibited by anti-VLA-4 MAb PS/2. When injected in vivo, however, PS/2 did not interfere with spontaneous liver metastasis and had no effect on survival. Ex vivo analysis of VLA-4 surface expression was facilitated by a new reisolation method for tumor and host cells derived from metastatic target organs. Freshly ex vivo isolated tumor cells from metastatic livers revealed VLA-4 surface downregulation as early as 3 days after tumor injection, which continued during the course of metastasis. VLA-4 downregulation in liver metastasis was also seen at the mRNA transcriptional level. Primary tumor cells showed similar VLA-4 downregulation suggesting that the in vivo phenotype was induced by the microenvironment at the primary tumor site. In support of this hypothesis, re-isolated tumor cells from metastatic livers recovered the high VLA-4 expression in host-depleted cell cultures. This study suggests that VLA-4 expression on tumor cells can be modulated in situ during tumor growth and metastasis formation.

Hypertrophic pulmonary osteoarthropathy with positive antinuclear antibodies: case report

A male Afro-descendant patient, 57 years old, complaining of polyarticular involvement and weight loss for 18 months, with a load of 13.5 pack years of smoking. On physical examination there was pain on palpation of the right knee and right leg, with signs of inflammation on the knee. We also observed digital clubbing in all fingers. Antinuclear antibodies (ANA) and anti-Sm antibodies were positive. X-rays of the legs and arm showed cortical thickening of long bones. The computed tomography demonstrated a large mass located in the middle lobe of the right lung. The anatomopathological study revealed a bronchial adenocarcinoma. The history of polyarticular involvement associated with positive anti-Sm and ANA antibodies could lead to an erroneous diagnosis of systemic lupus erythematosus. Considering the bad consequences of delayed diagnosis in this patient, the medical team should be alerted for suspecting and look for a lung cancer under these circumstances.

Modeling formalisms in Systems Biology

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.

Is cerebellar volume related to bipolar disorder?

BACKGROUND

Recent data suggest that cerebellum influences emotion modulation in humans. The findings of cerebellar abnormalities in bipolar disorder (BD) are especially intriguing given the link between the cerebellum emotional and behavioral regulation. The purpose of this study was to evaluate cerebellar volume in patients with euthymic BD type I compared to controls. Moreover, we investigated the possible relationship between cerebellar volume and suicidal behavior.

METHODS

Forty-patients with euthymic BD type I, 20 with and 20 without history of suicide attempt, and 22 healthy controls underwent an MRI scan. The participants were interviewed using the Structured Clinical Interview with the DSM-IV axis I (SCID-I), the Hamilton Depression Rating Scale (HDRS), the Young Mania Rating Scale (YMRS) and the Barratt Impulsiveness Scale (BIS-11).

RESULTS

Groups were age, gender and years of schooling-matched. The left cerebellum (p=0.02), right cerebellum (p=0.02) and vermis (p<0.01) were significantly smaller in the BD group; however, there were no volumetric differences between the BD subjects with and without suicidal attempt. There was no correlation between cerebellar measurements and clinical variables.

LIMITATIONS

The main strength is that our sample consisted of patients with euthymic BD type I without any comorbidities, however, these results cannot establish causality as the cross-sectional nature of the study.

CONCLUSIONS

Our findings suggest that the reduction in cerebellar volumes observed in BD type I might be a trait-related characteristic of this disorder. Additional studies with larger samples and subtypes of this heterogeneous disorder are warranted to determine the possible specificity of this cerebellar finding.

A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways

The present study addresses the regulatory network of Escherichia coli and offers a global view of the short- and long-term regulation of its metabolic pathways. The regulatory mechanisms responsible for key metabolic activities and the structure behind such mechanisms are detailed. Most metabolic functions are dependent on the activity of transcriptional regulators over gene expression - the so-called long-term regulation. However, enzymatic regulation - the so-called short-term regulation - often overlays transcriptional regulation and even, in particular metabolic pathways, enzymatic regulation may prevail. As such, understanding the balance between these two types of regulation is necessary to be able to predict and control cell responses, specifically cell responses to the various environmental stresses.

Semantic annotation of biological concepts interplaying microbial cellular responses

BACKGROUND

Automated extraction systems have become a time saving necessity in Systems Biology. Considerable human effort is needed to model, analyse and simulate biological networks. Thus, one of the challenges posed to Biomedical Text Mining tools is that of learning to recognise a wide variety of biological concepts with different functional roles to assist in these processes.

RESULTS

Here, we present a novel corpus concerning the integrated cellular responses to nutrient starvation in the model-organism Escherichia coli. Our corpus is a unique resource in that it annotates biomedical concepts that play a functional role in expression, regulation and metabolism. Namely, it includes annotations for genetic information carriers (genes and DNA, RNA molecules), proteins (transcription factors, enzymes and transporters), small metabolites, physiological states and laboratory techniques. The corpus consists of 130 full-text papers with a total of 59043 annotations for 3649 different biomedical concepts; the two dominant classes are genes (highest number of unique concepts) and compounds (most frequently annotated concepts), whereas other important cellular concepts such as proteins account for no more than 10% of the annotated concepts.

CONCLUSIONS

To the best of our knowledge, a corpus that details such a wide range of biological concepts has never been presented to the text mining community. The inter-annotator agreement statistics provide evidence of the importance of a consolidated background when dealing with such complex descriptions, the ambiguities naturally arising from the terminology and their impact for modelling purposes.Availability is granted for the full-text corpora of 130 freely accessible documents, the annotation scheme and the annotation guidelines. Also, we include a corpus of 340 abstracts.

A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information

BACKGROUND AND SCOPE

Recently, a number of methods and tools have been proposed to allow the use of genome-scale metabolic models for the phenotype simulation and optimization of microbial strains, within the field of Metabolic Engineering (ME). One of the limitations of most of these algorithms and tools is the fact that only metabolic information is taken into account, disregarding knowledge on regulatory events.

IMPLEMENTATION AND PERFORMANCES

This work proposes a novel software tool that implements methods for the phenotype simulation and optimization of microbial strains using integrated models, encompassing both metabolic and regulatory information. This tool is developed as a plug-in that runs over OptFlux, a computational platform that aims to be a reference tool for the ME community.

AVAILABILITY

The plug-in is made available in the OptFlux web site (www.optflux.org) together with examples and documentation.

The effects of aging on dopaminergic neurotransmission: a microPET study of [11C]-raclopride binding in the aged rodent brain

Rodent models are frequently used in aging research to investigate biochemical age effects and aid in the development of therapies for pathological and non-pathological age-related degenerative processes. In order to validate the use of animal models in aging research and pave the way for longitudinal intervention-based animal studies, the consistency of cerebral aging processes across species needs to be evaluated. The dopaminergic system seems particularly susceptible to the aging process, and one of the most consistent findings in human brain aging research is a decline in striatal D2-like receptor (D2R) availability, quantifiable by positron emission tomography (PET) imaging. In this study, we aimed to assess whether similar age effects can be discerned in rat brains, using in vivo molecular imaging with the radioactive compound [(11)C]-raclopride. We observed a robust decline in striatal [(11)C]-raclopride uptake in the aged rats in comparison to the young control group, comprising a 41% decrement in striatal binding potential. In accordance with human studies, these results indicate that substantial reductions in D2R availability can be measured in the aged striatal complex. Our findings suggest that rat and human brains exhibit similar biochemical alterations with age in the striatal dopaminergic system, providing support for the pertinence of rodent models in aging research.

Surveillance of norovirus infections in the state of Rio De Janeiro, Brazil 2005-2008

A 4-year (2005-2008) norovirus (NoV) surveillance study was conducted in the state of Rio Janeiro, Brazil, to demonstrate the role of these viruses in outbreaks and sporadic cases of acute gastroenteritis. A cohort of 1,687 fecal samples was obtained from patients with gastroenteritis; 324 were rotavirus-positive. Of the remainder 1,363 rotavirus-negative samples, 1,087 samples were tested for NoV RNA in this study. The study enrolled 267 outpatients from Municipal Public Health Centers and 820 inpatients, whose samples were obtained by active surveillance in Public Hospitals. Fecal samples were tested by reverse transcription (RT) followed by polymerase chain reaction (PCR) using the MON 431-434 set of degenerate primers for NoV GI and GII detection, and there were 35.1% (381/1,087) positive samples for NoV, consisting of 30.2% (248/820) and 49.8% (133/267) from inpatient and outpatient, respectively. Children infected by NoV had significantly more frequent mucus in feces, vomiting and fever. No seasonal pattern in NoV infections was observed in patients admitted to hospital; however, two peaks of NoV infections were observed from ambulatory cases, suggesting that there was an occurrence of outbreaks in those time periods. Molecular characterization revealed GII to be the most prevalent genogroup, totaling 96.3% (104/108) of all sequences analyzed, and GII.4 was the genotype detected most frequently (80.7%), followed by GII.6, 3, 14, 7, and 8. Two GI strains, GI.2 and GI.3, were also observed. The number of outbreaks and sporadic cases described in this study highlights the need to implement diagnosis of NoV in surveillance laboratories.

AIBench: a rapid application development framework for translational research in biomedicine

Applied research in both biomedical discovery and translational medicine today often requires the rapid development of fully featured applications containing both advanced and specific functionalities, for real use in practice. In this context, new tools are demanded that allow for efficient generation, deployment and reutilization of such biomedical applications as well as their associated functionalities. In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research in the domain of translational biomedicine. AIBench incorporates a powerful plug-in engine, a flexible scripting platform and takes advantage of Java annotations, reflection and various design principles in order to make it easy to use, lightweight and non-intrusive. By following a basic input-processing-output life cycle, it is possible to fully develop multiplatform applications using only three types of concepts: operations, data-types and views. The framework automatically provides functionalities that are present in a typical scientific application including user parameter definition, logging facilities, multi-threading execution, experiment repeatability and user interface workflow management, among others. The proposed framework architecture defines a reusable component model which also allows assembling new applications by the reuse of libraries from past projects or third-party software.

OptFlux: an open-source software platform for in silico metabolic engineering

Background

Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications.

Results

OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes.

OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms.

The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph.

Conclusions

The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community.

Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models.

Oxidative stress and mitochondrial dysfunction in atherosclerosis: mitochondria-targeted antioxidants as potential therapy

Chronic and acute overproduction of reactive oxygen species (ROS) under pathophysiologic conditions forms an integral part of the development of cardiovascular diseases (CVD), and in particular atherosclerosis. These ROS are released from different sources, such as xanthine oxidase, lipoxygenase, nicotinamide adenine dinucleotide phosphate oxidase, the uncoupling of nitric oxide synthase and, in particular, mitochondria. Endothelial dysfunction, characterized by a loss of nitric oxide (NO) bioactivity, occurs early on in the development of atherosclerosis, and determines future vascular complications. Although the molecular mechanisms responsible for mitochondria-mediated disease processes are not clear, oxidative stress seems to play an important role. In general, ROS are essential to cell function, but adequate levels of antioxidant defenses are required in order to avoid the harmful effects of excessive ROS production. Mitochondrial oxidative stress damage and dysfunction contribute to a number of cell pathologies that manifest themselves through a range of conditions. This review considers the process of atherosclerosis from a mitochondrial perspective, and assesses strategies for the targeted delivery of antioxidants to mitochondria that are currently under development. We will provide a summary of the following areas: the cellular metabolism of reactive oxygen species (ROS) and its role in pathophysiological processes such as atherosclerosis; currently available antioxidants and possible reasons for their efficacy and inefficacy in ameliorating oxidative stress-mediated diseases; and recent developments in mitochondrially-targeted antioxidants that concentrate on the matrix-facing surface of the inner mitochondrial membrane in order to protect against mitochondrial oxidative damage, and their therapeutic potential as a treatment for atherosclerosis.