Induced pluripotent stem cell-based assays recapture multiple properties of human astrocytes

The majority of the population of glial cells in the central nervous system consists of astrocytes, and impairment of astrocytes causes various disorders. It is useful to assess the multiple astrocytic properties in order to understand their complex roles in the pathophysiology. Although we can differentiate human astrocytes from induced pluripotent stem cells (iPSCs), it remains unknown how we can analyse and reveal the multiple properties of astrocytes in complexed human disease conditions. For this purpose, we tested astrocytic differentiation protocols from feeder-free iPSCs based on the previous method with some modifications. Then, we set up extra- and intracellular assessments of iPSC-derived astrocytes by testing cytokine release, calcium influx, autophagy induction and migration. The results led us to analytic methods with conditions in which iPSC-derived astrocytes behave as in vivo. Finally, we applied these methods for modelling an astrocyte-related disease, Alexander disease. An analytic system using iPSC-derived astrocytes could be used to recapture complexities in human astrocyte diseases.

Cytotoxic Tph subset with low B-cell helper functions and its involvement in systemic lupus erythematosus

T peripheral helper (Tph) cells are thought to contribute to extra-follicular B cell activation and play a pathogenic role in autoimmune diseases. However, the role of Tph subsets is not fully elucidated. Here, we investigate the immunological functions of Tph subsets and their involvement in systemic lupus erythematosus (SLE). We have defined four Tph subsets (Tph1: CXCR3+CCR6-, Tph2: CXCR3-CCR6-, Tph17: CXCR3-CCR6+, and Tph1-17: CXCR3+CCR6+) and performed RNA sequencing after cell sorting. Tph1 and Tph17 subsets express substantial levels of IL21, indicating B cell helper functions. However, Tph2 and Tph1-17 subsets express low IL21. Interestingly, we have found Tph2 subset express high levels of CX3CR1, GZMB, PRF1, GLNY, S1PR5, TBX21, EOMES, ZNF863, and RUNX3, indicating a feature of CD4+ cytotoxic T lymphocytes. In SLE patients, the frequency of Tph1 and Tph2 subsets are significantly increased and positively correlated with SLE disease activity indexes. Tph1 cells expansion has been observed in patients with cutaneous and musculoskeletal manifestations. On the other hand, Tph2 cell expansion has been found in patients with lupus nephritis in addition to the above manifestations. Our findings imply that Tph1 and Tph2 subsets exert distinct immunological functions and are contributed to the complexity of clinical manifestations in SLE.

[Data-driven drug discovery for drug repurposing]

To improve the decreased efficiency of drug discovery and development, drug repurposing (also called drug repositioning) has been expected, that it is a strategy for identifying new medical indications for approved, investigational or suspended drugs. Particularly, according to the rapid expansion of medical and life science data and the remarkable technological progress of AI technology in recent years, the approach of computational drug repurposing has been attracted as one of the applications in data-driven drug discovery. Computational drug repurposing is a method of systematical and strategical research for identifying novel indication candidates and prioritizing the indication candidates based on the various profiles of drugs, genes, and diseases. In this review article, the typical data science techniques for data-driven drug repurposing, 1. drug-target interaction prediction, 2. transcriptomics-based approach by using differentially gene expression profiles, 3. natural language processing and word embedding, and their current status were summarized. We have also introduced a use case of data-driven drug repurposing for the PPARγ/α agonist Netoglitazone that we actually analyzed. In addition, as an excellent successful case of data-driven drug repurposing in recent years, we have also discussed a repurposing case reported by BenevolentAI in 2020, that Baricitinib has been identified as a potential intervention for COVID-19, based on immunomodulatory treatment by its mechanism of action as a JAK1 and JAK2 inhibition.

Role of interferons (IFNs) in differentiation of T peripheral helper (Tph) cells. 1: Type I IFNs promote differentiation of interleukin-21-producing Tph-like cells

T follicular helper (Tfh) cells and T peripheral helper (Tph) cells produce interleukin (IL)-21 and are thought to contribute to follicular and extra-follicular B cell activation, respectively, in autoimmune diseases. It is known that programmed cell death-1 (PD-1)-positive CXCR5 + Tfh-like cells are differentiated from human naïve CD4 + T cells by IL-12 plus transforming growth factor (TGF)-β. However, it remains unclear what cytokines are required for Tph differentiation. In this study, we found that interferon (IFN)-α and IFN-β reduce the frequency of Tfh-like cells under IL-12 plus TGF-β condition whereas promote generation of PD-1 +CXCR5 -CD4 + T cells and secretion of IL-21, IFN-γ, and CXCL13. Intracellular cytokine staining and T cell-B cell co-culture studies indicated that IFN-α promotes generation of IL-21 +IFN-γ +CXCR5 -CD4 + T cells thereby enhancing B cell helper function. By IFN-α treatment, the mRNA levels of IL21, IFNG, CXCL13, CD244, SLAMF7, GZMB, and PRDM1 were significantly up-regulated but BCL6 mRNA expression was down-regulated, suggesting a Tph-related gene expression pattern. On the other hand, IL-2-neutralization increased mRNA levels of IL21, CXCL13, and CXCR5, retained BCL6, but showed no clear effect on IFNG or PRDM1. RNA sequencing analyses revealed that PD-1 hiCXCR5 -CD4 + T cells prepared from in vitro culture show a Tph-related gene expression pattern similar with that of PD-1 hiCXCR5 - Tph cells obtained from the blood of patients with systemic lupus erythematosus. From our findings, it is highly probable that type I IFNs play a key role in differentiation of Tph cells and trigger Tph cell-expansion in autoimmune diseases.

POS0459 APTAMER-BASED PROTEOMIC SCREENING IN IDENTIFICATION OF PATHOGENIC SIGNAL PATHWAY AND URINARY BIOMARKERS ASSOCIATED WITH HISTOLOGICAL FINDINGS IN LUPUS NEPHRITIS

Background

The current gold standard for the diagnosis and classification, assessment of the severity of lupus nephritis (LN) is a renal biopsy. On the other hand, since the procedure is highly invasive, there is a pressing need to identify biomarkers for predicting the presence and its histological severity of LN. In addition, the background pathogenesis of each histological findings is not clearly understood.

Objectives

The purpose of this study was to elucidate the urine biomarkers for predicting the presence and the severity of histological findings of LN, and to search the pathogenic signal pathway.

Methods

Urine samples from 24 biopsy-proven active LN patients were initially screened for the levels of 1305 distinct human proteins using an aptamer-based-targeted proteomic assay. We developed histological scoring system based on ISN/RPS lesion definitions and classification, NIH activity and chronicity score. Two experienced evaluators assessed the histological scores. Cluster analysis and pathway analysis were performed.

Results

A total of 24 LN patients were included: 20 (83%) had a proliferative histological class (III or IV +/-V), 4 (17%) pure membranous (V). Through cluster analysis, several histological subgroups were extracted according to correlation with each histological finding, and proteins which corelated with each histological scores were analyzed. We focused on two subgroups: one in which including active glomerular histological findings (endocapillary hypercellularity, karyorrhexis, neutrophil infiltration, subendothelial deposits) and the other in which including interstitial histological findings (interstitial inflammation, interstitial fibrosis, tubular atrophy). Histological scores in the former group showed strong positive correlation with protein group which contained 59 proteins (Group A), including CCL21, CXCL10, VCAM1. Histological scores in the latter group corelated with another protein group which contained 85 proteins (Group B), including MCP-1, CCL11. Ingenuity Pathway Analysis showed 16 pathways (PDGF Signaling, Granulocyte Adhesion and Diapedesis, etc) were upregulated in Group A and 11 pathways (IL-17 signaling, Fibrosis signaling pathway, etc) upregulated in Group B. Among group A and group B urine proteins, those showed strong correlation between respective histological findings were validated with ELISA assays.

Conclusion

An aptamer-based-targeted proteomic assay screening by combining with renal histological scoring system suggested several urine proteins can predict the severity and the presence of major renal histological findings, and suggested to be related with the pathogenesis in patients with LN.

Disclosure of Interests

Kazuoto Hiramoto: None declared, Shuntaro Saito: None declared, Hironari Hanaoka: None declared, Katsuya Suzuki: None declared, Jun Kikuchi: None declared, Hiroyuki Fukui: None declared, Ryo Takano Employee of: Mitsubishi Tanabe Pharma Corporation Sohyaku, Fumihiko Miyoshi Employee of: Mitsubishi Tanabe Pharma Corporation Sohyaku, Noriyasu Seki Employee of: Mitsubishi Tanabe Pharma Corporation Sohyaku, Kunio Sugahara Employee of: Mitsubishi Tanabe Pharma Corporation Sohyaku, Yuko Kaneko: None declared, Tsutomu Takeuchi: None declared.

Safety and efficacy of a hyperaemic agent, intracoronary nicorandil 4mg, for invasive physiological assessments during fractional flow reserve measurement

Background

Fractional flow reserve (FFR) is one of most reliable index for the determining the functional severity coronary artery stenosis. Adenosine is the most commonly used agent for maximal hyperaemia. However, adenosine can cause chest discomfort, bronchial hyper-reactivity, and atrioventricular block. The aim of this study is to evaluate the safety and efficacy of intracoronary nicorandil as an alternative hyperaemic agent for FFR.

Methods and results

We enrolled consecutive 82 patients (87 lesions) who underwent FFR measurement in our center from Nov. 2018. We compared three groups; intravenous infusion of adenosine (150 μg/kg/min); and adenosine added intracoronary nicorandil 2mg; and intracoronary nicorandil 4mg. Mean FFR value was 0.83±0.09, 0.82±0.09, 0.82±0.08, There was a strong correlation among three groups (R2>0.9). Mean cyclic change in FFR was 0.026±0.023, 0.019±0.010, 0.016±0.014, respectively, cyclic change was smallest in intracoronary nicorandil 4mg group (vs ATP; p<0.001, vs ATP + nicorandil 2mg; p<0.001). By Wilcoxon test, mean FFR value of nicorandil 4mg was significant lower than ATP (p=0.0021), and equal to ATP + nicorandil 2mg (p=0.98).

Conclusions

Intracoronary nicorandil 4mg is a simple, safe, and effective way to induce steady-state hyperaemia for FFR.

Figure 1

Funding Acknowledgement

Type of funding source: None

Changes in the pattern of cytokine production from peripheral blood mononuclear cells in patients with rheumatoid arthritis treated with infliximab and their relation to plasma arginase activity

AIM

The aim of this study was to quantify the production of T-cell cytokines from the peripheral blood mononuclear cells (PBMCs) of RA patients before and after treatment with anti-tumor necrosis factor (TNF)-α infliximab (IFX).

METHOD

We stimulated the PBMCs of RA patients (n = 24) in vitro and quantified the cytokines in the culture supernatant using enzyme-linked immunosorbent assay.

RESULTS

Unexpectedly, the cytokines tested, interferon (IFN)-γ, interleukin (IL)-4 and IL-17, were all found to have increased, rather than decreased, after the treatment. When the patients were divided into two groups according to the plasma activity of arginase, which is implicated in the immune-suppressive function of myeloid-derived suppressor cells, the substantial increase in the cytokine production ex vivo was only detected in the group in which the arginase activity was decreased after the treatment with IFX. In fact, although the ex vivo production of IL-21 increased along with the other cytokines, the plasma concentration of IL-21 decreased significantly after IFX treatment.

CONCLUSION

It is important to exercise caution in interpreting ex vivo cytokine production data, in that they can be negatively influenced by the immune-suppressive mechanisms that prevent excessive inflammation. Thus, to analyze the T-cell response accurately, T-cell markers that are detectable in the serum or plasma need to be discovered. The concentrations of IFN-γ, IL-4 and IL-17 were all below detection limits, but that of IL-21 was detectable in the plasma and inversely correlated with the production of IL-21 ex vivo. This may indicate the involvement of Th17 response in the pathogenesis of RA.

A novel method predicting clinical response using only background clinical data in RA patients before treatment with infliximab

OBJECTIVES

The aim of the present study was to generate a novel method for predicting the clinical response to infliximab (IFX), using a machine-learning algorithm with only clinical data obtained before the treatment in rheumatoid arthritis (RA) patients.

METHODS

We obtained 32 variables out of the clinical data on the patients from two independent hospitals. Next, we selected both clinical parameters and machine-learning algorithms and decided the candidates of prediction method. These candidates were verified by clinical variables on different patients from two other hospitals. Finally, we decided the prediction method to achieve the highest score.

RESULTS

The combination of multilayer perceptron algorithm (neural network) and nine clinical parameters shows the best accuracy performance. This method could predict the good or moderate response to IFX with 92% accuracy. The sensitivity of this method was 96.7%, while the specificity was 75%.

CONCLUSIONS

We have developed a novel method for predicting the clinical response using only background clinical data in RA patients before treatment with IFX. Our method for predicting the response to IFX in RA patients may have advantages over the other previous methods in several points including easy usability, cost-effectiveness and accuracy.

Nationwide epidemiological survey of 169 patients with adult Still's disease in Japan

OBJECTIVES

A nationwide survey was conducted to assess the number of patients, clinical aspects, treatment, and prognosis of adult Still's disease (ASD) in Japan.

METHODS

A primary questionnaire was sent to randomly selected medical institutions in order to estimate the number of patients. We sent a secondary questionnaire to the same institutions to characterize the clinical manifestations and treatment of ASD.

RESULTS

The estimated prevalence of ASD was 3.9 per 100,000. Analysis of 169 patients showed a mean age at onset of 46 years. The main clinical symptoms were fever, arthritis, and typical rash in agreement with previous surveys. Oral glucocorticoids were used to treat 96% of the patients, while methotrexate was used in 41% and biological agents were used in 16%. Lymphadenopathy and macrophage activation syndrome were significantly associated with increased risk of relapse (P < 0.05, each). Patients who achieved remission after tocilizumab therapy had significantly longer disease duration (6.2 years) than patients who did not (1.9 years) (p < 0.05).

CONCLUSIONS

The 2010-2011 nationwide survey of ASD identified important changes in treatment and improvement of prognosis compared with previous surveys.

Evaluation of Parkinson disease and Alzheimer disease with the use of neuromelanin MR imaging and (123)I-metaiodobenzylguanidine scintigraphy

BACKGROUND AND PURPOSE

Progressive changes in the substantia nigra pars compacta and locus ceruleus of patients with Parkinson disease and Alzheimer disease visualized by neuromelanin MRI and cardiac postganglionic sympathetic nerve function on (123)I-metaiodobenzylguanidine scintigraphy have not been fully evaluated. We compared the diagnostic value of these modalities among patients with early Parkinson disease, late Parkinson disease, and Alzheimer disease.

MATERIALS AND METHODS

We compared contrast ratios of signal intensity in medial and lateral regions of the substantia nigra pars compacta and locus ceruleus with those of the tegmentum of the midbrain and the pons, respectively, by use of neuromelanin MRI in patients with early Parkinson disease (n = 13), late Parkinson disease (n = 31), Alzheimer disease (n = 6), and age-matched healthy control subjects (n = 20). We calculated heart-to-mediastinum ratios on (123)I-metaiodobenzylguanidine scintigrams after setting regions of interest on the left cardiac ventricle and upper mediastinum.

RESULTS

The signal intensity of the lateral substantia nigra pars compacta on neuromelanin MRI was significantly reduced in early and late Parkinson disease, and that of the medial substantia nigra pars compacta was gradually and stage-dependently reduced in Parkinson disease. The signal intensity of the locus ceruleus was obviously reduced in late Parkinson disease. Signal reduction was not significant in the substantia nigra pars compacta and locus ceruleus of patients with Alzheimer disease. The heart-to-mediastinum ratio on (123)I-metaiodobenzylguanidine scintigrams was stage-dependently reduced in Parkinson disease and normal in Alzheimer disease. The signal intensity ratios in substantia nigra pars compacta and locus ceruleus on neuromelanin MRI positively correlated with the heart-to-mediastinum ratio on (123)I-metaiodobenzylguanidine scintigrams.

CONCLUSIONS

Both neuromelanin MRI and (123)I-metaiodobenzylguanidine scintigraphy can help to evaluate disease progression in Parkinson disease and are useful for differentiating Parkinson disease from Alzheimer disease.

Marked induction of c-Maf protein during Th17 cell differentiation and its implication in memory Th cell development

Until recently, effector T helper (Th) cells have been classified into two subsets, Th1 and Th2 cells. Since the discovery of Th17 cells, which produce IL-17, much attention has been given to Th17 cells, mainly because they have been implicated in the pathogenesis of various inflammatory diseases. We have performed transcriptome analysis combined with factor analysis and revealed that the expression level of c-Maf, which is considered to be important for Th2 differentiation, increases significantly during the course of Th17 differentiation. The IL-23 receptor (IL-23R), which is important for Th17 cells, is among putative transcriptional targets of c-Maf. Interestingly, the analysis of c-Maf transgenic Th cells revealed that the overexpression of c-Maf did not lead to the acceleration of the early stage of Th17 differentiation but rather to the expansion of memory phenotype cells, particularly with Th1 and Th17 traits. Consistently, mouse wild-type memory Th cells expressed higher mRNA levels of c-Maf, IL-23R, IL-17, and IFN-γ than control cells; in contrast, Maf(-/-) memory Th cells expressed lower mRNA levels of those molecules. Thus, we propose that c-Maf is important for the development of memory Th cells, particularly memory Th17 cells and Th1 cells.

Geranylgeranyl-pyrophosphate regulates secretion of pentraxin 3 and monocyte chemoattractant protein-1 from rheumatoid fibroblast-like synoviocytes in distinct manners

OBJECTIVES

We previously reported that 10 mg/day of simvastatin significantly reduced clinical scores of rheumatoid arthritis (RA) in active RA patients with hypercholesterolemia. In this study, we have investigated the mechanism by which simvastatin inhibits the production of the mediators of inflammation, such as pentraxin 3 (PTX3) and monocyte chemoattractant protein-1 (MCP-1), from fibroblast-like synoviocytes (FLS) derived from patients with RA.

METHODS

FLS from RA patients were cultured with 0-10 μM simvastatin for 24 h. ELISA and real-time PCR were used to quantitate the protein level and the mRNA level of PTX3 and MCP-1, respectively.

RESULTS

Simvastatin both reduced the secretion of PTX3 and MCP-1 in FLS cultures and inhibited their mRNA expression in these cells. The effects of simvastatin were all completely reversed in the presence of mevalonic acid or geranylgeranylpyrophosphate, but not in the presence of farnesyl-pyrophosphate. The geranylgeranyl transferase inhibitor GGTI-298 and the Rho kinase inhibitor Y-27632 inhibited the production of PTX3 but not of MCP-1.

CONCLUSIONS

Although simvastatin inhibited the production of PTX3 and MCP-1 in RA FLS, the mechanisms were quite different. It inhibits PTX3 production in a Rho-dependent manner but MCP-1 production in a Rho-independent manner. These results shed light on novel aspects of the anti-inflammatory mechanisms of simvastatin and may prove its important role in the treatment of rheumatic diseases.

Analysis of cytokine production patterns of peripheral blood mononuclear cells from a rheumatoid arthritis patient successfully treated with rituximab

We had a rheumatoid arthritis (RA) patient resistant to multiple drugs and who developed panniculitis due to etanercept treatment, then responded fairly well to rituximab. Intracellular staining of cytokines in the peripheral blood mononuclear cells before and after rituximab administration revealed that the cytokine production, representative of T-helper (Th)1-, Th2-, and Th17-type responses, decreased abruptly after the treatment. Interestingly, this timing coincided with that of the manifestation of the beneficial effect. This relationship may provide useful insight into the mechanism of action of the drug and hence about the pathogenesis of RA.

Vasculo-Behçet's disease with non-traumatic subcapsular hematoma of the kidney and aneurysmal dilatations of the celiac and superior mesenteric arteries

We report a patient with vasculo-Behçet's disease treated successfully with a high dose of prednisolone. In 2002, the patient was diagnosed with vasculo-Behçet's disease. He was admitted to our hospital because of sudden-onset right lower back pain in June 2006. Upon admission, abdominal angiography revealed aneurysmal dilatations of the celiac and superior mesenteric arteries. He was treated promptly with high-dose prednisolone, after which the aneurysms displayed no further enlargement. As we believe this case to be quite rare, we report this case with a literature review in support of this characterization.

High concentration simvastatin induces apoptosis in fibroblast-like synoviocytes from patients with rheumatoid arthritis

OBJECTIVE

We previously reported that 10 mg/day of simvastatin significantly reduced clinical scores of rheumatoid arthritis (RA) in patients with active RA with hypercholesterolemia. We have also reported that a certain pharmacological concentration of simvastatin, i.e., 0.05-0.1 microM, inhibits the production of interleukin 6 (IL-6) and IL-8 and the cell proliferation induced by tumor necrosis factor-alpha (TNF-alpha) in fibroblast-like synoviocytes (FLS) derived from patients with RA in vitro. We investigated other effects of simvastatin on FLS from the standpoint of cell viability and apoptosis.

METHODS

RA FLS were cultured with or without 0.05-50 microM simvastatin for 48 h. Cell viability was determined using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Apoptosis was measured by flow cytometric analysis using propidium iodide and annexin-V. Caspase-3 and -9 activities were analyzed by colorimetric assays.

RESULTS

High concentrations of simvastatin, i.e., 1.0-50 microM, reduced cell viability and induced prominent apoptosis in FLS in a dose-dependent manner. The apoptosis induced by simvastatin was caspase-3- and caspase-9-dependent. These effects were completely reversed in the presence of mevalonic acid or geranylgeranyl-pyrophosphate, but not in the presence of farnesyl-pyrophosphate. Further, a geranylgeranyl transferase inhibitor and a RhoA kinase inhibitor mimicked the effect of simvastatin.

CONCLUSION

These data, together with our previous report, suggest that low (pharmacological range) and high concentrations of simvastatin affect FLS differently: (1) at a low concentration, it inhibits IL-6 and IL-8 production and the cell proliferation of FLS induced by TNF-alpha (2) at high concentrations, it induces apoptosis in FLS. Understanding this dose-dependent biphasic effect of simvastatin may prove important for its clinical applications in the treatment of RA.

Comparative study of circadian oscillatory network models of Drosophila

The circadian clock of Drosophila is a model pathway for research in biological clock mechanisms, both with traditional experimental approaches and with emerging systems biology approaches utilizing mathematical modeling and in silico computer simulation. Dynamic diurnal oscillations are achieved by the complex interaction of components as a system, and mathematical reconstruction has proven to be an invaluable means of understanding such systematic behavior. In this study, we implemented eight published models of the Drosophila circadian clock in Systems Biology Markup Language (SBML) for comparative systems biology studies using E-Cell Simulation Environment version 3, to examine the system-level requirements for the clock mechanism to be robust, by calculating the period and amplitude sensitivity coefficients with simulation experiments. While all models were generally robust as determined by the network topology of the oscillatory feedback loop structure, existing models place relatively strong emphasis on transcription regulation, although this is a limitation on robustness. We suggest that more comprehensive modeling including protein phosphorylation, polymerization, and nuclear transport with regard to amplitude sensitivity will be necessary for understanding the light entrainment and temperature compensation of circadian clocks.

A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria

In the cyanobacterium, Synechococcus elongatus, most promoters are regulated by a circadian clock under continuous light (LL) conditions. Nevertheless, the basic circadian oscillation is primarily generated by alternating KaiC phosphorylation/dephosphorylation reactions at the posttranslational level. Indeed, the KaiC phosphorylation cycle was recently reconstituted in vitro by incubating KaiA, KaiB, and KaiC proteins with ATP. However, the molecular dynamics of this chemical oscillation and the mechanism that drives the circadian transcription/translation rhythms remain unknown. In this report, the KaiC phosphorylation cycle and the gene regulatory network in the cyanobacterial circadian system have been modeled. The model reproduces the robust KaiC phosphorylation cycle in the absence of de novo gene expression as is observed in vitro, as well as its coupling to transcriptional/translational feedback in LL conditions in vivo. Moreover, the model is consistent with most previous experiments, including various combinations of genetic knockout or overexpression of kai genes. It also predicts that multiple KaiC phosphorylation states and dynamic Kai protein interactions may be required for the cyanobacterial circadian system.

E-Cell 2: Multi-platform E-Cell simulation system

A new version of the E-Cell simulation system,which runs on Windows as well as Linux, has been released as free software under the terms of the GNU General Public License.

E-CELL: software environment for whole-cell simulation

MOTIVATION

Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico.

RESULTS

E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering.

AVAILABILITY

The E-CELL software is available upon request.

SUPPLEMENTARY INFORMATION

The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://e-cell.org/.

Polyacrylamide gel electrophoretic patterns of chicken serum in acute inflammation induced by intramuscular injection of turpentine

To develop a method to detect hidden inflammation using serum protein in chickens, changes in serum proteins with acute inflammation were analyzed using a turpentine-induced inflammation model. Inflammation in the pectoral muscle of a 14-wk-old White Leghorn became apparent 3 h after the injection of turpentine and became more severe thereafter. Coincident with the development of inflammation, changes in serum proteins were analyzed by electrophoresis on polyacrylamide gradient gels. The electrophoretic patterns were divided into 21 segments. Two of these segments increased remarkably. These were located near the center of the electrophoretic pattern and were identified as transferrin due to iron staining, correlation of movement against a commercial transferrin sample in SDS-PAGE, and immunoblotting. These results suggest that transferrin may serve as a marker for inflammation in chicken.

Purification and identification of a serum protein increased by anthelmintic drugs for Dirofilaria immitis in dogs

Polyacrylamide gel electrophoretic analysis of canine serum protein has revealed that the administration of anthelmintics elicits an increase in a certain serum protein. This protein, named PT60, was partially purified by ammonium sulfate fractionation and preparative electrophoresis. The purified PT60 gave a single band with the molecular size of 53 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis under non-reducing conditions. After reduction with 2-mercaptoethanol, two bands appeared at 35 kDa and 17 kDa, indicating that PT60 consists of two subunits which are linked with each other by disulfide bonds. PT60 had the capacity to bind to hemoglobin. In an immunodiffusion test, an antiserum against PT60 cross-reacted with canine haptoglobin (Hp). N-terminal amino acid sequences of two PT60 subunits were identical to those of alpha and beta subunits of canine Hp, respectively. Thus, PT60 was identified as Hp.

[Colorimetric study of color reproduction in porcelain-fused-to-metal restoration. The application of Kubelka-Munk theory in porcelain mixtures]

To get a more natural and harmonious color of porcelain-fused-to-metal restorations, an objective and precise systematic method from shade selection to color evaluation is needed. Thus, the absorption and scattering coefficients were determined to develop a CCM system for porcelain-fused-to-metal restorations. The Kubelka-Munk Theory was applied on the dental porcelain, opaque, dentin, and enamel. From these data, we predicted the color of the porcelain mixtures from the both coefficients. From the results of comparing the spectral curves and analyzing the color differences between measured values and predicted values of porcelain mixtures, the following was analysed; 1. In opaque, spectral curves of the predicted and measured values were exactly alike and the mean dE between two values was 0.39. 2. In dentin, the spectral curved of the predicted and measured values were exactly alike, and the mean dE was 1.13. The measured values indicated a slight increase in the level of chroma and lightness. 3. In enamel, the spectral curves were exactly alike and the mean dE was 1.16. The measured values indicated a slight decrease in the level of lightness. Therefore, it was possible to predict the color of opaque, dentin and enamel porcelain mixtures, by applying the Kubelka-Munk Theory.

Enhancement of 5-hydroxytryptamine-induced contraction of the guinea pig ileum by a new sulfur compound, tripropylsulfonium bromide

In the presence of tripropylsulfonium bromide (TPS) (1 X 10(-4) g/ml), a new compound, the phasic contraction of the isolated guinea pig ileum to 5-hydroxytryptamine (5-HT) (5 X 10(-7) g/ml) was consistently enhanced ("TPS effect"). TPS alone increased moderatley the spontaneous movement of the ileum. When the contraction height was calculated as the percentage of that to 5-HT alone, such was observed in the "TPS effect" to be 167.1 +/- 3.6% (mean +/- S.E., n = 80). TPS did not enhance the contraction due to acetylcholine or histamine. The "TPS effect" remained unaffected in the presence of dibenzyline (1 X 10(-7) g/ml), was abolished by morphine(1 X 10(-6) g/ml), tetrodotoxin (2 X 10(-8) g/ml) adenosine (3 X 10(-6) g/ml) and atropine (1 X 10(-7) g/ml) and was not observed under anoxic conditions. Eserine (1 X 10(-8) g/ml) strengthened the "TPS effect" markedly. It is concluded that this effect may be the result of the potentiating effect of TPS on the action of 5-HT through the M receptors, possibly by the facilitation of the acetylcholine-liberation from the nervous tissue.