Towards NeuroML: model description methods for collaborative modelling in neuroscience.

Biological nervous systems and the mechanisms underlying their operation exhibit astonishing complexity. Computational models of these systems have been correspondingly complex. As these models become ever more sophisticated, they become increasingly difficult to define, comprehend, manage and communicate. Consequently, for scientific understanding of biological nervous systems to progress, it is crucial for modellers to have software tools that support discussion, development and exchange of computational models. We describe methodologies that focus on these tasks, improving the ability of neuroscientists to engage in the modelling process. We report our findings on the requirements for these tools and discuss the use of declarative forms of model description--equivalent to object-oriented classes and database schema--which we call templates. We introduce NeuroML, a mark-up language for the neurosciences which is defined syntactically using templates, and its specific component intended as a common format for communication between modelling-related tools. Finally, we propose a template hierarchy for this modelling component of NeuroML, sufficient for describing models ranging in structural levels from neuron cell membranes to neural networks. These templates support both a framework for user-level interaction with models, and a high-performance framework for efficient simulation of the models.

Kinetic properties of glucosyltransferase adsorbed onto saliva-coated hydroxyapatite.

Results from previous studies have shown that several properties of glucosyltransferase (GTF) adsorbed onto saliva-coated hydroxyapatite beads differ from those of GTF in solution. For example: thermostability, pH-activity dependency, sensitivity to inhibitors. The aim of this study was to compare the kinetics of the adsorbed GTF with its kinetic properties in solution. Hydroxyapatite beads were coated with human parotid saliva (sHA). Following washes, cell-free GTF enzyme from Streptococcus sobrinus 6715 (S. sobrinus 6715) or Streptococcus mutans GS-5 (S. mutans GS-5) was adsorbed onto sHA. The GTF-coated sHA were then incubated with radiolabeled sucrose for intervals of 5-360 minutes and the amount of glucans synthesized in situ by the adsorbed GTF was determined and compared with that produced in solution. The adsorbed GTF (from S. sobrinus 6715) exhibited a sharp increase in glucan production within the first 5 minutes of incubation while surface-bound GTF of S. mutans GS-5 displayed an initial burst of activity within the first 15 minutes of incubation. During the next 6 hours (duration of experiment) the amount of glucan on the beads did not increase with either enzyme. In contrast, the kinetic profile of the two GTFs in solution demonstrated a linear increase in the amount of glucans formed, with no initial burst effect. The results indicate that the rapid formation of glucans by GTF adsorbed onto sHA could have implications for colonization by oral microorganisms on tooth surfaces. The accelerated synthesis of glucan on tooth surfaces may affect the microbiology of the dental plaque, and might also influence the movement of substances, such as acids and antiplaque agents, across the acquired pellicle and dental plaque.

Development and validation of an immunization tracking system in a large health maintenance organization.

Practitioners seeing individual patients and those charged with improving immunization practices in that population need accurate information on the epidemiology of immunizations within the population. To meet this need, we have developed a computer-based record of data required by the National Childhood Vaccine Injury Act of 1986 for all immunizations given to 350,000 enrollees in a large health maintenance organization. In the first eight months of operation, 102,271 immunizations representing 11 separate antigens given to 65,676 enrollees were entered into the database. Comparison of immunizations given and recorded in the medical record with the database shows that the system has high sensitivity, specificity, and positive predictive value, but a relatively low negative predictive value. The database is being used for analysis of current immunization practices for Haemophilus influenzae b vaccine and for research on adverse outcomes of childhood immunizations.

Interactions of delmopinol with constituents of experimental pellicle.

The prolonged retention of an effective chemotherapeutic agent on oral surfaces and in dental plaque aids in plaque control. The objective of this study was to investigate interactions between delmopinol, a morpholinoethanol derivative, and experimental pellicle. Hydroxyapatite beads were coated with different constituents of pellicle (e.g., saliva, carbohydrates, cell-free enzymes, and bacteria). Delmopinol demonstrated a higher affinity for saliva-coated hydroxyapatite (sHA) and for experimental pellicle coated with in situ-synthesized glucans than for untreated hydroxyapatite. High-molecular-weight (MW) dextran but not low-MW dextran interfered with the adsorption of delmopinol to sHA. Delmopinol did not compete with dextran for the same binding sites on sHA, nor did it compete with saliva for the same binding sites on untreated hydroxyapatite. Delmopinol inhibited the activity of cell-free fructosyltransferase adsorbed onto sHA. In addition, synthesis of glucans by Streptococcus mutans adsorbed onto sHA was significantly reduced in the presence of delmopinol.

The effect of delmopinol on glucosyltransferase adsorbed on to saliva-coated hydroxyapatite.

The aim was to explore the effects of delmopinol, a substituted amino-alcohol compound recently reported as a potential antiplaque agent, on GTF activity in solution and when adsorbed on to sHA. Delmopinol was without a significant effect on GTF activity in solution. In contrast, a reduction in the bound glucans synthesized by the adsorbed GTF was found in the presence of delmopinol. Delmopinol did not displace the adsorbed GTF from the sHA, nor was there significant desorption of glucans from sHA. The total glucan synthesis (bound and unbound) was reduced in the presence of delmopinol. Inhibition of GTF was not reversed by sucrose. Inhibition of GTF activity by delmopinol apparently results from drug-enzyme interaction on the surface of sHA beads. These observations provide further support for the important differences in the properties of adsorbed GTF and GTF in solution, illustrating that GTF-drug interaction differs between enzyme adsorbed to surfaces and enzyme in solution.

Role of a cell surface-associated protein in adherence and dental caries.

Insertional inactivation of the Streptococcus mutans spaP gene was used to construct an isogenic mutant (834) of strain NG8 (serotype c) which lacked the major cell surface-associated protein referred to as P1 (15). Results of several studies suggest that P1 is involved in the adherence of S. mutans to saliva-coated apatite surfaces. With an in vitro model system of hydroxyapatite (HA) beads coated with parotid saliva (PS) and additional HA surfaces coated with PS and in situ-formed glucan, it was observed that mutant 834 adhered poorly to the PS/HA surfaces. In contrast, both parent and mutant strains bound to the PS-glucan/HA surface. Groups of intact and desalivated rats were infected with each strain to determine relative capacities to induce dental caries. Rats were fed a highly cariogenic diet containing 56% sucrose for 3 to 5 weeks. Each strain colonized the rodent model and caused similar levels of smooth-surface caries under these dietary conditions. It was concluded that P1 influences the ability of organisms to adhere to saliva-coated surfaces and possibly affects primary colonization of the oral cavity in the absence of a glucan surface but has no effect on glucan-mediated adherence in vitro or in vivo.

Development of an immunization tracking system in a large health maintenance organization. Group Health Cooperative of Puget Sound.

We have successfully developed a mainframe system for tracking all immunizations administered to enrollees in a large HMO. This system will provide comprehensive immunization records on a population of over 350,000 patients. Data required by the National Childhood Vaccine Injury Act of 1986 are locally entered into terminals, and records of immunization are stored in a database. Preliminary results show that data entry times are practical, but that improvement in data quality is needed. This immunization tracking system will be used for research, and as the foundation of an immunization reminder system under development.

Oncogene alterations in in vitro transformed rat tracheal epithelial cells.

10 derivations of rat tracheal epithelial (RTE) cells, including normal cells, normal primary cultures, 7 tumorigenic cell lines and 1 nontumorigenic cell line transformed in vitro by treatment with 7,12-dimethylbenz[a]anthracene (DMBA), benzo[a]pyrene (BP) and/or 12-O-tetradecanoylphorbol-13-acetate (TPA) were examined for oncogene alterations. No abnormalities of Ha-ras or Ki-ras were seen that were suggestive of amplification, rearrangement or the presence of RFLPs. Analysis of specific-point mutations in Ha-ras using Pst I digestion (codon 12, GGA to GCA) or Ha-ras and Ki-ras using Xba I (codon 61, CAA to CTA) were negative. In one cell line derived by DMBA treatment, changes in the c-myc restriction digest pattern were seen after incubation with Bam HI and Hind III. Northern analysis revealed consistent differences between normal and transformed cells when probed with Ha-ras; c-myc expression was of low intensity, and the expression of Ki-ras could not be detected. Transfection of RTE cell DNAs into NIH/3T3 cells did not result in the appearance of morphologic transformants. The studies suggest that Ha-ras or Ki-ras codon 61 A to T transversions (CAA to CTA) are not associated with the immortal/tumorigenic phenotype in RTE cells transformed by DMBA or TPA, and are in contrast to results reported in some other biological systems.

Consistent oncogene methylation changes in epithelial cells chemically transformed in vitro.

We have examined the restriction digest patterns of CCGG sequences in Kiras, Ha-ras, and c-myc oncogenes in rat tracheal epithelial cells transformed in vitro by 7,12-dimethylbenz(a)anthracene, benzo(a)pyrene/12-O-tetradecanoylphorbol-13-acetate (TPA), or TPA alone. Oncogenes c-myc and Ha-ras in transformed cell lines, compared to normal rat tracheal epithelial cells and untreated primary cultures, had altered Hpa II restriction patterns as demonstrated by hybridizing bands of different molecular weight, or loss of bands. Ki-ras was hypermethylated in all cell derivations, including normal cells. These molecular alterations have not previously been reported for epithelial cells transformed in vitro by polycyclic hydrocarbons and tumor promoters, and suggest common mechanisms of action for agents with diverse molecular targets.

Effect of phorbol esters on clonal cultures of human, hamster, and rat respiratory epithelial cells.

The effect of the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) on the growth of epithelial cells from rat, hamster, and human respiratory tract has been measured by monitoring colony formation and cross-linked envelope formation in culture. TPA and its active derivatives stimulated colony formation of rat tracheal epithelial cells but did not stimulate cross-linked envelope formation. Tracheal epithelial cells from the hamster and human bronchial epithelial cells were inhibited from forming colonies by these agents. This inhibitory effect was also dependent on concentration. In the rat, the stimulation of cells to enter cell division induced by TPA decayed with time after removal of primary cells from the trachea, while in hamster and human cells, the inhibitory effect of TPA was independent of time. Although TPA inhibited colony formation in hamster and human cells, it did not elicit the same responses with respect to cross-linked envelopes. Hamster tracheal epithelial cells did not form cross-linked envelopes in response to TPA, whereas human bronchial cells did. A comparison was made of the response to TPA in cells from the human bronchi of 24 individuals; the extent of inhibition of colony formation induced by TPA varied by 130-fold. These results show that normal cells from these species vary in biological response to tumor promoters, implying that selective induction of terminal differentiation in normal cells may not be a universal mechanism of action of tumor promoters.

Teaching interactive signing in a dialogue situation to mentally retarded individuals.

Verbal prompts, modeling, physical guidance, positive reinforcement, fading, and chaining procedures were used to teach two nonverbal individuals, one severely and one moderately mentally retarded, an interactive signing dialogue in a naturalistic snack time setting. Both were required to initiate signed communication and to respond to signed communication with either action or manual signing. Using a multiple probe design across three dialogue situations, each client was successively taught his role in each dialogue with a staff member serving as his partner. After both trainees had mastered a dialogue role, signing competency was formally probed as they interacted with their staff partner in a maintenance situation and with the other trainee in a generalization situation. Results showed that clients could learn to use signed communication in each dialogue situation but that extensive training was required. Data also indicated that only partial generalization to the client-client situation occurred.

Changes in stem cell populations of rat tracheal epithelial cell cultures at an early stage in neoplastic progression.

The development of transformed colonies and concomitant changes in proliferative and nonproliferative cell compartments were studied in rat tracheal epithelial (RTE) cell cultures following exposure to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Primary RTE cells were plated onto 3T3 feeder layers and treated with MNNG (0.25 micrograms/ml) or solvent. Seven days later, the feeder cells were removed to select for enhanced growth variants, which are the transformants of the RTE cell system, usually scored 5 weeks after carcinogen exposure. Most of the RTE cell colonies, which originally formed during the first 7 days of culture, disappeared within 2 weeks after feeder cell removal in control and MNNG-treated cultures. In control cultures, about 3% of the original colonies persisted, while in MNNG-treated cultures, a larger percentage (approximately 9%) of the colonies persisted. These percentages remained constant from 3 to 7 weeks. Based on colony size, cell density, and cell morphology, the persistent colonies were classified into transformed colonies (large colony size, high cell density, high nuclear:cytoplasmic ratio) and untransformed colonies (small size, low cell density, low nuclear:cytoplasmic ratio). In the MNNG-treated cultures, about 50% of all persistent colonies showed transformed morphology. Their frequency remained unchanged between 3 and 7 weeks of culture. In contrast, only 10 to 15% of the persistent colonies in control cultures showed transformed morphology at 3 weeks, but that proportion increased steadily between 3 and 7 weeks. These data suggest that, in control cultures, transformed colonies developed spontaneously as a function of time within untransformed colonies. Autoradiographic studies with [3H]thymidine showed that labeling indices in the early "normal" RTE cell colonies between Days 4 and 7 of culture were very high, ranging between 75 and 90%. In contrast, the labeling indices of persistent colonies, both those without and those with transformed morphology, were low, i.e., between 18 and 25%, indicating that a major proportion of cells was either noncycling or cycling very slowly. The relative compartment sizes of cells with stem cell characteristics and of cells with characteristics of transformed stem cells were estimated before and after transformed colonies appeared.(ABSTRACT TRUNCATED AT 400 WORDS)

Heterogeneity in responses of human and rodent respiratory epithelial cells to tumor promoters in culture.

Phorbol ester tumor promoters enhance the ability of primary normal rat tracheal epithelial cells to form colonies in a time-dependent fashion. The potency of phorbol derivatives in inducing this effect is relative to their potency as tumor promoters in mouse epidermis. Agents which do not interact with the putative TPA receptor are not effective. In contrast, both hamster tracheal and human bronchial epithelial cells are inhibited from forming colonies by phorbol esters. The sensitivity of human cells varied among individuals but could not be related to age, smoking history, or presence of a cancerous condition. These results bear some similarity to those of Harris et al. where levels of BP-DNA binding were measured in organ cultures of human bronchus. An interindividual variation of 120-fold was observed in 37 specimens of human bronchus, however, no correlation was apparent between levels of binding and whether the specimens were from patients with cancer. It would be of interest to determine if there is a relationship between carcinogen metabolism or binding and the ability to respond to promoters in specimens from normal and lung cancer patients. It is conceivable that lung cancer arises in individuals that have rare peculiarities in carcinogen metabolism combined with peculiarities in their responses to promoters present in cigarette smoke. Several conclusions can be drawn from these data. Species vary in response to tumor promoting agents, and the type of response may be a result of the biochemical events which are triggered by interaction with protein kinase C or another cellular receptor. Both responses, that of enhanced growth of epithelial cells observed in the rat, or that of inhibition of growth (induction of terminal differentiation) seen in human and hamster epithelial cells are consistent with proposed mechanisms by which tumor promoters may function. A general enhancement of cell proliferation may lead to fixation or expansion of genetic damage in initiated cells, while induction of terminal differentiation in normal cells could lead to expanded cell proliferation in initiated cells resistant to differentiation controls. This indicates that both responses may be useful in detecting environmental promoting agents. In light of these studies perhaps the hamster trachea may more closely mimic the responses of the human bronchus than does the rat. This is consistent with observations of the difficulty in transforming hamster tracheal epithelium (Dr. Brooke Mossman, personal communication) and human bronchial epithelium compared with rat tissue.(ABSTRACT TRUNCATED AT 400 WORDS)

Inhibition of transformation of primary rat tracheal epithelial cells by retinoic acid.

The effect of retinoic acid (RA) on N-methyl-N'-nitro-N-nitrosoguanidine-induced transformation of primary cultures of rat tracheal epithelial cells was investigated. RA inhibited transformation of rat tracheal epithelial cells by up to 95% at concentrations of 3.3 to 33 nM which did not substantially affect cell survival. The inhibitory effect of RA on transformation was concentration dependent and was also dependent upon timing and duration of treatment. Treatment with RA for only 1 week following N-methyl-N'-nitro-N-nitrosoguanidine exposure diminished the transformation frequency by 30 to 57%, although longer treatment times were more effective. Because RA was able to inhibit transformation effectively at concentrations which were not substantially inhibitory to colony-forming efficiency of rat tracheal epithelial cells, the mechanism of inhibition of cell transformation does not seem to be related to cytotoxic effects of RA known to occur at high RA concentrations.

Enhanced induction of the anchorage-independent phenotype in initiated rat tracheal epithelial cell cultures by the tumor promoter 12-O-tetradecanoylphorbol-13-acetate.

The purpose of the studies reported here was to compare the response of noninitiated and initiated primary rat tracheal epithelial (RTE) cell cultures to the mouse skin tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA). The endpoints measured were number of cells per culture, colony-forming efficiency, subculturability, and colony formation in soft agarose. Primary RTE cell cultures were exposed on Day 1 to either 0.2% dimethyl sulfoxide, or to 0.1 micrograms per ml of N-methyl-N'-nitro-N-nitroso-guanidine (MNNG). Thereafter, the same cultures were exposed twice weekly from Days 6 to 30 to either 0.2% dimethyl sulfoxide or to TPA (10 pg/ml). Sequential exposure to MNNG and TPA did not increase the number of viable cells per culture beyond that seen in MNNG-exposed cultures. Determination of the frequency of colony-forming cells 10 days after the end of the initiation-promotion treatment (Day 40 of culture) revealed a marked enhancement in colony-forming efficiency of treated cultures compared to dimethyl sulfoxide-exposed control cultures. However, sequential exposure to MNNG and TPA had an additive or slightly more than additive effect on the colony-forming efficiency of RTE cells exposed to MNNG or TPA only. Treatment of the primary cultures with MNNG alone or TPA alone increased the subculturability of RTE cells to a similar extent. The sequential exposure to MNNG followed by TPA appeared to have an additive effect on the frequency of subculturability. The most pronounced effect of the sequential MNNG-TPA exposure as compared to single-agent exposure was a marked enhancement of the anchorage-independent (ag+) phenotype. Of the cultures treated with MNNG followed by TPA, over 50% were ag+ at 60 days. In contrast, of the cultures treated either with MNNG alone or with TPA alone, only 3% were ag+ on Day 60. (All control cultures were ag-.) Colony-forming efficiency in soft agarose also increased disproportionately between 60 and 120 days in initiated-promoted cultures. These experiments indicate that the major effect of the tumor promoter TPA on initiated RTE cell cultures is to enhance the appearance of the late ag+-phenotype.