Adaptive tuning of cell sensory diversity without changes in gene expression

In the face of uncertainty, cell populations tend to diversify to enhance survival and growth. Previous studies established that cells can optimize such bet hedging upon environmental change by modulating gene expression to adapt both the average and diversity of phenotypes. Here, we demonstrate that cells can tune phenotypic diversity also using posttranslational modifications. In the chemotaxis network of Escherichia coli, we find, for both major chemoreceptors Tar and Tsr, that cell-to-cell variation in response sensitivity is dynamically modulated depending on the presence or absence of their cognate chemoeffector ligands in the environment. Combining experiments with mathematical modeling, we show that this diversity tuning requires only the environment-dependent covalent modification of chemoreceptors and a standing cell-to-cell variation in their allosteric coupling. Thus, when environmental cues are unavailable, phenotypic diversity enhances the population's readiness for many signals. However, once a signal is perceived, the population focuses on tracking that signal.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

MOTIVATION

Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively.

RESULTS

We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.

AVAILABILITY

The specification of SBML Level 1 is freely available from http://www.sbml.org/

STOCHSIM: modelling of stochastic biomolecular processes

SUMMARY

STOCHSIM is a stochastic simulator for chemical reactions. Molecules are represented as individual software objects that react according to probabilities derived from concentrations and rate constants. Version 1.2 of STOCHSIM provides a novel cross-platform graphical interface written in Perl/Tk. A simple two-dimensional spatial structure has also been implemented, in which nearest-neighbour interactions of molecules in a 2-D lattice can be simulated.

Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis

Coliform bacteria detect chemical attractants by means of a membrane-associated cluster of receptors and signalling molecules. We have used recently determined molecular structures, in conjunction with plastic models generated by three-dimensional printer technology, to predict how the proteins of the complex are arranged in relation to the plasma membrane. The proposed structure is a regular two-dimensional lattice in which the cytoplasmic ends of chemotactic-receptor dimers are inserted into a hexagonal array of CheA and CheW molecules. This structure creates separate compartments for adaptation and downstream signalling, and indicates a possible basis for the spread of activity within the cluster.

A free-energy-based stochastic simulation of the Tar receptor complex

We recently developed a stochastic-based program that allows individual molecules in a cell signalling pathway to be simulated. This program has now been used to model the Tar complex, a multimeric signalling complex employed by coliform bacteria. This complex acts as a solid-state computational cassette, integrating and disseminating information on the presence of attractants and repellents in the environment of the bacterium. In our model, the Tar complex exists in one of two conformations which differ in the rate at which they generate labile phosphate groups and hence signal to the flagellar motor. Individual inputs to the complex (aspartate binding, methylation at different sites, binding of CheB, CheR and CheY) are represented as binary flags, and each combination of flags confers a different free energy to the two conformations. Binding and catalysis by the complex are performed stochastically according to the complete set of known reactions allowing the swimming performance of the bacterium to be predicted. The assumption of two conformational states together with the use of free energy values allows us to bring together seemingly unrelated experimental parameters. Because of thermodynamic constraints, we find that the binding affinity for aspartate is linked to changes in phosphorylation activity. We estimate the pattern of Tar methylation and effective affinity constant of receptors over a range of aspartate levels. We also obtain evidence that both the methylating and demethylating enzymes must operate exclusively on one or other of the two conformations, and that sites of methylation of the complex are occupied in sequential order rather than independently. Detailed analysis of the response to aspartate reveals several quantitative discrepancies between simulated and experimental data which indicate areas for future research.

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/.

CpG distribution patterns in methylated and non-methylated species

To characterize the extent of DNA methylation and its possible biological roles in a wide variety of organisms, we have analyzed gene sequences extracted from the GenBank database. Sequences of both methylated and non-methylated species were used for comparative analysis. The local CpG dinucleotide distribution near the 5' ends of genes as well as the degree of overall CpG suppression/depletion in the entire gene region were examined in all complete gene sequences for each species. We show that the distribution patterns of CpG near the 5' region of genes differ among vertebrates, invertebrates, plants and bacteria. CpG island-like peaks in CpG O/E (observed/expected ratio) were observed not only in methylated species, but also in non-methylated species. In methylated non-vertebrates, overall CpG O/E values were lower, and peaks in the CpG profile of 5' regions were larger than in non-methylated species. We discuss the implications of such biases with respect to DNA methylation.

Prostate-specific antigen in mass screening for carcinoma of the prostate

BACKGROUND

Prostate-specific antigen (PSA) has various advantages over prostatic acid phosphatase (PAP) as a marker for prostate cancer, but its role in prostate cancer mass screening remains controversial. We measured serum PSA in addition to serum PAP determination and digital rectal examination (DRE) in our mass screening program to assess the usefulness of PSA for prostate cancer mass screening.

METHODS

Serum PSA and PAP measurements and DRE were performed in 1249 patients in mass screening for carcinoma of the prostate in 1989 and 1990. Thirteen cancers were diagnosed. We calculated the mean plus standard deviations (2SD) of the PSA and PAP values of men without cancer, and assessed the usefulness of PSA for prostate cancer screening by using these figures as the upper limit of normal.

RESULTS

The number positive for PSA, PAP and DRE were 39, 36 and 48, respectively. If our screening had been performed without DRE, three cancers would have remained undetected, and the number would have been the same if performed without PSA. If the screening had been performed without PAP, on the other hand, no cancers would have remained undetected. The sensitivities of PSA and PAP were 54% and 23%, respectively. The screening detection rate with DRE and PSA was 0.88%, and with DRE and PAP was 0.64%.

CONCLUSIONS

Measurement of serum PSA values with adjustment of the cut-off value was considered more useful than PAP in mass screening for prostate cancer.

Estramustine phosphate for preventing flare-up in luteinizing hormone-releasing hormone analogue depot therapy

The usefulness of estramustine phosphate (ECT) for preventing flare-up in goserelin acetate depot therapy for advanced prostate cancer was studied. Pretreatment with ECT 560 mg daily for 3 weeks almost completely prevented the rise in testosterone level seen in goserelin acetate depot therapy and no signs or symptoms of tumor flare were observed. Long-term ECT completely blocked the rise in luteinizing hormone and testosterone level, but ECT at this dosage was likely to cause complications. The administration of ECT 560 mg daily for 3 weeks prior to goserelin acetate depot therapy was considered sufficient to prevent tumor flare, and its effect was considered to be more marked than that of short-term treatment with antiandrogens.

The colonic neobladder: a stoma-free bladder substitute after radical cystectomy--preliminary results in six patients

We have used a urethral colonic pouch for total bladder replacement in 6 bladder cancer patients after radical cystectomy. The distal ileum, cecum, ascending colon and the right third of the transverse colon were isolated. The cecum and colon were opened along the tenia and a detubulized pouch was created. The ureters were sutured to the terminal ileum. The maximum pressure wave measured ranged 22-58 cmH2O, and the amount of residual urine varied between 0 and 58 ml. All patients were completely continent during the day and slight incontinence at night was observed in 3. By amputating the right colonic artery, the pouch is easily moved to the urethral stump and serves as a low pressure neobladder after cystoprostatectomy.

A case of posttherapeutic sclerotic change of bone metastasis from renal cell carcinoma which proved histopathologically to be complete response

A 60-year-old man with renal cell carcinoma and metastases to the right 7th rib and L2 vertebra (T2N0M1, OSS) was treated with interferon-alpha and the uracil and tegafur combination following nephrectomy. One and a half years later on bone scintigraphy, the abnormal accumulation had disappeared at the L2 vertebra and weakened in its intensity at the right 7th rib. Plain X-ray revealed that the metastatic lesion at the right 7th rib had decreased in size and had been replaced by calcification. The right 7th rib was removed surgically and step-sectioned pathological specimens revealed necrosis with no viable cancer cells.