Naaman Kam et al. (2003) International Worm Meeting "Computer Modeling, Simulation and Analysis of C. elegans Development"

David Harel, Naaman Kam, Michael J Stern, E Jane Albert Hubbard, Amir Pnueli

[International Worm Meeting, 2003]

Na'aman Kam et al. (2004) East Coast Worm Meeting "COMPUTER MODELING, SIMULATION AND ANALYSIS OF C. elegans VULVAL INDUCTION"

Jasmin Fisher, Amir Pnueli, David Harel, E Jane Albert Hubbard, Na'aman Kam, Michael J Stern

[East Coast Worm Meeting, 2004]

We have been developing a new approach to modeling biological phenomena, focusing on the signaling events that influence vulval fate specification in C. elegans . Our motivation is the striking similarity between the methods and logic of developmental genetics with the languages and tools used in the design of complex computerized systems. Vulval precursor cell (VPC) fate specification is an excellent system to test our approach for two reasons: (1) the mechanisms underlying this process are sufficiently understood to allow meaningful models to be created; and (2) the multiple known inputs that determine fate output create a complexity that can adequately challenge the efficacy of the modeling approach. Developmental genetic data are difficult to make tractable for simulation and analysis by computers ("formalize"), since they are often in a condition-result form in which the precise mechanisms linking the conditions (eg. mutated genes) and the results (eg. phenotypes) are not fully established. We are using two complementary languages, statecharts and live sequence charts (LSCs) , which describe system behaviors using time-constrained logical constructs. Here we present our model of VPC fate specification using the language of LSCs and the Play-Engine tool. The Play-Engine allows data and mechanistic models to be entered by the manipulation of a graphical user interface (GUI) that resembles the pictorial models that biologists draw ( play in ). The GUI also functions as a dynamic pictorial model that depicts computer-executed simulations ( play out ). Using these tools, we have succeeded in representing various types of data commonly obtained in VPC specification experiments, the variability of biological results, cell movement events, and the interdependence of biological behavior and anatomical structure. The model is easily extendable, either by including additional VPC specification data, by linking together GUIs that represent other developmental processes, or by creating links to models in the complementary language of statecharts . The construction and analysis of our model of VPC fate specification has enhanced our understanding of this biological process in several ways. At the simplest level, we have transformed biological data and mechanisms into a database of executable statements of system behavior. Beyond this, however, our modeling has revealed inconsistencies between the "rules" and the actual data in these established papers, and has highlighted interesting gaps in our understanding of this system that we have begun to investigate experimentally.

Naaman Kam et al. (2005) International Worm Meeting "A computational model of vulval fate specification"

Hillel Kugler, E Jane Albert Hubbard, Naaman Kam, Amir Pnueli, Michael J Stern, David Harel

[International Worm Meeting, 2005]

We have developed a computational model of vulval precursor cell (VPC) fate specification. This model is capable of reproducing essentially all of the experimental observations reported in a subset of papers that form the basis of our initial understanding of this process. Since this model is mechanism-based, it is also capable of predicting outcomes of new experiments. Our results demonstrate that the development of such computational models can be helpful in integrating the complex, dynamic behaviors of biological systems. The generic nature of the tool and methodologies used for this project enables the natural extension of our model to other aspects of C. elegans biology. We used the language of LSCs and the Play-Engine tool to build a model that dynamically recapitulates the experiments presented in three seminal papers [Sternberg and Horvitz (1986); Sternberg (1988); Sternberg and Horvitz (1989)]. Our model is driven by biological mechanisms inferred from results reported in these papers as well as several more recent papers. The Play-Engine allows both experiments and mechanistic hypotheses to be entered in a user-friendly manner via the manipulation of a graphical user interface (GUI). The GUI also reflects the dynamic representation of the computer-executed simulations. In constructing the model, we represented all of the biological behaviors and phenomena referred to in these papers including developmental time, cell movements, gradient formation, cell fate assumption, variable biological outcomes, and inter- and intra-cellular signaling. The model enables the user to perform all experimental perturbations described in these papers, including cell ablations and genetic manipulations. The construction and analysis of our model of VPC fate specification enhanced our understanding of this biological process in several ways. First, we identified mechanistic gaps that have not been investigated. One such mechanism governs the movements of the VPCs that allow them to replace one another according to their developmental hierarchy. Second, constructing the model provided unexpected insights into the biology of this system, such as the dynamics and prioritization of fate assumption. These insights have instigated a number of experiments whose results will further enhance the model and our understanding of this process.

Na'aman Kam et al. (2002) European Worm Meeting "A GUI depicting VPC specification Formal Modeling, Simulation and Analysis of C. elegans Development"

Rami Marelly, David Harel, Na'aman Kam, Albert Hubbard, Irun R Cohen, Amir Pnueli, Michael J Stern

[European Worm Meeting, 2002]

Hillel Kugler et al. (2007) International Worm Meeting "Modeling C. elegans vulval cell fate specification."

Naaman Kam, David Harel, Michael J. Stern, Lara Appleby, Amir Pnueli, E. Jane Albert Hubbard, Hillel Kugler

[International Worm Meeting, 2007]

We are testing the feasibility of applying a rule-based, logic-driven approach to modeling biology based on state-of-the-art methods and tools from software and system engineering. The model is assembled from short logical statements that each describe a small part of how the system works. These descriptions of the various snippets of biology are termed scenarios. There are two sets of scenario statements in our model. One set describes the rules we have inferred about how the system works; these propel model simulation. Since these are generalized rules of behavior, the model is predictive. The second set of scenario statements describes actual experimental outcomes; these can be used to test whether the rule-based model is consistent with the data upon which it is based. An attractive feature of this approach is that scenario-based models are assembled similarly to the manner in which we build our understanding of biology from sets of experiments that address specific aspects of a biological process. The model can be built, altered, tested, and extended in a modular fashion, recapitulating the iterative processes of hypothesis testing and data analysis. We tested the feasibility of this approach by modeling a subset of the data pertaining to C. elegans vulval precursor cell (VPC) fate specification. The model covers a wide range of behaviors - anatomical, cellular and genetic. We present a rigorously tested dynamic model that is both usable and extendable. Simulations can be run and analyzed dynamically in detail under varying conditions. We first tested the model by seeing if it could reproduce all of the data of the pre-1990 data set from which many of the underlying rules were inferred. Our modeling methodology is also useful for testing competing hypotheses. Multiple hypotheses can be represented and stored within the same model by introducing the subset of variant rules that distinguish them. The variant models can then be tested for their consistency with the known set of pertinent data to help understand their differences. We applied this feature to probe the sequential versus graded signaling hypotheses given our pre-1990 data set. Systematic testing then identified the actual experimental results that were not consistent with each hypothesis. The construction and testing of our dynamic model raised important testable hypotheses. Our work demonstrates that the traditional hypothesis-experiment cycle can be supplemented by the construction and use of executable dynamic models, creating a more powerful cycle of hypothesis-modeling-testing-experiment.

Schein JE et al. (1997) International C. elegans Meeting "POSITIONING OF ESSENTIAL GENES IN THE lin-3 - let-60 INTERVAL"

Franz NW, Rose AM, Janke DL, Bilkhu N, Baillie DL, Schein JE

[International C. elegans Meeting, 1997]

The lin-3 - let-60 interval of the right arm of chromosome IV contains thirteen essential gene mutations and 22 overlapping sequenced cosmids. The Sanger Center has nearly finished sequencing the entire interval. Analysis of cosmid sequences shows over one hundred potential coding regions. Of the coding regions with proposed protein function, more than 50% have strong homology to human genes. Most notably, the putative genes include three phosphatases, four protein kinases, a kinesin, and a cluster of histones. C. elegans strains carrying sequenced cosmids (in extrachromosomal arrays) have been constructed (see abstract for D. Janke et al., this meeting) and will be used in rescue experiments involving the essential genes in this interval. lin-3 and let-60(ras), the two genes bracketing this interval, were previously placed on the physical map by others. One of the remaining eleven essential genes has been already positioned to a cosmid: let-70(ubc2) (in collaboration with Mei Zhen and Peter Candido). By the time of the meeting, we anticipate that several of the remaining mutations will have been positioned to cosmids. This work is being funded by a grant from the Medical Research Council to Ann Rose and David Baillie and by a grant from the Natural Sciences & Engineering Research Council to David Baillie.

Na'aman Kam et al. (2002) East Coast Worm Meeting "Formal Modeling, Simulation and Analysis of C. elegans Development"

David Harel, E Jane Albert Hubbard, Na'aman Kam, Michael J Stern, Irun R Cohen, Amir Pnueli, Rami Marelly, Hillel Kugler

[East Coast Worm Meeting, 2002]

The field of developmental genetics is entering a new phase, in which the synthesis of information from many sources will be necessary to gain a deeper understanding of how various tissues, cells, biochemical interactions and genetic networks collaborate to form a functional organism. The purpose of this project is to model and rigorously simulate and analyze a particular biological system the C. elegans egg-laying system using languages, methodologies and tools developed by computer scientists for the reliable development of highly reactive computerized systems. The model will incorporate existing anatomical, genetic and biochemical data pertaining to the development and function of (i) the gonad, (ii) the vulva, (iii) the uterine and vulval musculature, and (iv) the hermaphrodite specific neurons (HSNs). We concentrate on an object-oriented approach using the visual language of statecharts for specifying behavior, and tools such as Rhapsody for model execution and analysis. In previous work, we have successfully applied this language and tool to the biological phenomenon of T cell activation. The T cell activation model served as a feasibility test and integrated phenomena associated with cell-cycle control, cell fate, cell behavior and location. We are now in the midst of a far more ambitious effort, involving more complex biological phenomena that will incorporate additional aspects of development, including cell fate acquisition, cell migration, axon guidance, and apoptosis. In principle, our model will eventually handle virtually all aspects of development, ultimately allowing our results to be extended to and used by the entire C. elegans community, and will apply to other systems too.

Stewart HI et al. (1996) West Coast Worm Meeting "Rescue of New Essential Genes on LGIII(left), in the Nematode Caenorhabditis elegans."

Stewart HI, Franz NW, Barbazuk BW, Baillie DL, Ha TT

[West Coast Worm Meeting, 1996]

We utilized trangenic strains containing cosmids, sequenced by the sequencing consortium, to rescue the lethal phenotype of several essential genes (See presentation by Diana Janke et al, this session). The rescued genes are positioned on LGIII(left) balanced by the duplication sDp3(see poster; Stewart et al, this session). A set of overlapping deficiencies was utilized to define areas within which to focus our rescue attempts). PCR analysis was utilized to further define the end points of these deficiencies, facilitating our analysis ( see poster ; Norm Franz et al, this session). We concentrated our analysis on areas to the right of dpy-17, in the interval between dpy-17 to dpy-19. Lethals mapping to sDf125 that were not rescued by sDp8 are presented in a poster by Nigel O'Niel et al, this session. We have rescued several essential genes. Our rescues will facilitate the functional analysis of these new genes. These rescues have also helped us to align and correlate the physical and genetic maps. Our estimates are that there will be more than two essential genes per cosmid. A total of 202 recessive lethal mutations have been generated, using EMS as a mutagen. We intend to make molecular assignments of all of these elements, through our cosmid rescue experiments. As we have estimated that there is only a 28% saturation of the area for essential genes, we will be generating more recessive lethal genes, to facilitate this analysis. This work has been funded by grants from the National Institute of Health (N.I.H.), U. S.A. to Ann Rose; D. Riddle and David Baillie and Canadian Genome and Advanced Technologies (C.G.A.T.), Canada to Ann Rose and David Baillie.

O'Neil NJ et al. (1996) West Coast Worm Meeting "SYSTEMATIC HIGH RESOLUTION MAPPING OF ESSENTIAL GENES IN THE sDf125 REGION BY TRANSGENIC RESCUE."

Kuervers LM, Baillie DL, Vatcher GP, O'Neil NJ

[West Coast Worm Meeting, 1996]

We have demonstrated that transgenic rescue is an effective method for high resolution mapping of essential genes. Our lab is constructing a map of essential genes on LGIII left. We have divided the left end of the central cluster into manageable regions which are defined by overlapping deficiencies and duplications. These regions are determined physically by PCR testing the deficiencies to determine endpoints (see N.Franz et al. abstract, this meeting). Into these regions, we have mapped a set of EMS induced lethals and maternal effect lethals. (see abstracts by H. Stewart et al. and G. Vatcher and D. Baillie, this meeting). One such region is defined by sDf125 and sDp8. This region spans 340 000 base pairs and is completely covered by nine cosmids. Within this region there are 75 putative genes predicted by Genefinder. We have used a sytematic approach to rescue essential genes within the sDf125 region with transgenic cosmids from the library created by J. Schein, D. Janke and The Ha as part of a CGAT grant to Ann Rose and David Baillie (see abstracts by J.Schein et al. and D. Janke et al., this meeting) To date this method has proven very successful. At least 8 genes have been completely rescued in this region by this approach. These transgenic rescues map these genes to 40 kB (one cosmid) resolution as opposed to the 340 kB resolution of the deficiency and duplication data. This is almost a ten-fold increase in resolution and reduces the number of ORFs which may be responsible for the gene function. The next step will be the subcloning of cosmids with which we have rescued essential genes. This will directly corellate the lethal or maternal effect lethal phenotype to the appropriate ORF. We have already begun the subcloning of cosmid C05D11 (see G.Vatcher and D.Baillie abstract, this meeting). This project is funded by a CGAT grant to Ann Rose and David Baillie.

O'Neil NJ et al. (1997) International C. elegans Meeting "ANALYSIS OF THE sDf127 REGION BY TRANSGENIC RESCUE."

O'Neil NJ, Vatcher GP, Kuervers LM, Baillie DL

[International C. elegans Meeting, 1997]

We have demonstrated that transgenic rescue is an effective method for high resolution mapping of essential genes. Our lab is constructing a map of essential genes on LGIII left. We have divided the region between dpy-17 and unc-36 into manageable regions that are defined by overlapping deficiencies and duplications. These regions are determined physically by PCR testing the deficiencies to determine endpoints. Into these regions, we have mapped a set of EMS induced lethal and maternal effect lethal mutations (See abstract H.Stewart et al., this meeting). One such region is defined by sDf127 and sDp8. This region spans 340 000 base pairs and is completely covered by ten cosmids. Within this region there are 75 putative genes predicted by Genefinder. To date, we have mapped 14 essential genes into this region. We have used a sytematic approach to rescue these essential genes with cosmid transgenics from the library created as part of a CGAT grant to Ann Rose and David Baillie (See abstract by D. Janke et al., this meeting) To date this method has proven very successful. At least 8 genes have been completely rescued in this region utilizing this approach. These transgenic rescues map these genes to 40 kB (one cosmid) as opposed to the 340 kB resolution of the deficiency and duplication data. This is almost a ten-fold increase in resolution and reduces the number of coding sequences which may be responsible for the gene function. The next step will be to subclone the cosmids with which we have rescued essential gene mutations. This will directly corellate the lethal or maternal effect lethal phenotype to the appropriate coding sequence. We have already begun the subcloning of the cosmids C05D11 (see abstract by G.Vatcher et al., this meeting), C31H11 and C16A3. This project is funded by a grant from the Medical Research Council of Canada to Ann Rose and David Baillie.