Kitano H (1997) Worm Breeder's Gazette "Visualizing the Embryogenesis of C. elegans"

Kitano H

[Worm Breeder's Gazette, 1997]

When Sydney Brenner proposed a new project to investigate C. elegans to the Medical Research Council, he chose it because it is the simplest possible differentiated organism. The decision was right, and now C. elegans is the most well investigated multi-cellular organism. Since the proposal to use this organism as a model organism, a series of research projects on various aspects of this organism were inititated. As a result, the complete cell lineage, neural circuits, and various genes and their functions were identified, and the complete DNA sequencing and the gene expression for each cell at different times in the embryogenesis will be identified in a few years. Despite the fact it is the simplest possible differentiated organism, it is still too complex to understand the dynamics and interactions taking place. Given the abundance of data, we consider that introducing a synthetic approach will further enhance our understanding of the underlying principles of development and behavior of C. elegans. We have started a project which we have named the Perfect C. elegans project, which aims at implementing detailed model of C. elegans on a computer system. As a first step, we have developed a computer graphics visualization system of embryogenesis on C. elegans. The system is based on existing data on the development of C. elegans, and missing information is interpolated using a simulation technique. The current system generates computer graphics images of the embryogenesis of C. elegans up until 500 minutes after the first cell division. The three dimensional (3D) visualization system is an appropriate starting point because it provides a 3D model of C. elegans, so that the cell-cell interaction dynamics, at both the physical and chemical level, can be implemented on top of this model. This would greatly help research on development. The current system is based on the cell lineage and cell location data published in Sulton's papper published in 1983. We are also working on the newer data from the Sanger Centre. It is a non-trivial task to create a reasonably accurate computer graphics image based on the available data because information necessary to create three dimensional models is missing. Following information were available: (1) the complete cell lineage chart, (2) hand-drawing pictures in 2-1/2 dimension (all 28 cells at 100 minutes, 55 out of 180 cells at 200 minutes, 137 out of more than 350 cells at 260 minutes, 156 out of more than 350 cells at 270 minutes, most cells at 430 minutes), qualitative descriptions of the shape of embryo, qualitative description of disparity in the size of divided cells, and general information on migration. In order to create an accurate computer graphics images, we need three dimensional data on the position and shape of the cell in a series of time steps. Obviously, such data is not available. The challenge is to how estimate reasonably accurate cell position data from available information. Our strategy to overcome this problem is to merge simulation with data. First, in order to assure the accuracy of the computer graphics image, cells must be in the position given in the observed data. Second, various simulation techniques are used to fill in the missing information, such as the location of cells not provided in the data. Essentially, this part of the system computes forces between cells, such as the force which pushes back colliding cells (equations not shown). However, if only dynamic simulation is used to decide the position of cells, some cells will not be in the position described in the observed data, because of cell movement. In order to compensate for this discrepancy, the force that a cell is supposed to generate for its movement was estimated using inverse kinematic techniques, and added to the cell's force vector. The motions of the cell are computed as in the case of the motion of objects in a viscous fluid. Along with other simulation techniques, the system creates reasonably realistic 3D computer graphics animation image from the first cell division to about 500 min after the first cell division. Cells are colored by their cell fate, or by their founder cells. Due to the animation capability, movement of the cell can be clearly identified, and helps intuitive understanding of the behaviors of cells during embryogenesis. We are now working on more accurate simulation using newer data sets, as well as implementation of genetic information into the simulation.

Kitano H et al. (1998) Artif Life "The perfect C. elegans project: an initial report."

Luke S, Hamahashi S, Kitano H

[Artif Life, 1998]

The soil nematode Caenorhabditis Elegans (C. elegans) is the most investigated of all multicellular organisms. Since the proposal to use it as a model organism, a series of research projects have been undertaken, investigating various aspects of this organism. As a result, the complete cell lineage, neural circuitry, and various genes and their functions have been identified. The complete C. elegans DNA sequencing and gene expression mapping for each cell at different times during embryogenesis will be identified in a few years. Given the abundance of collected data, we believe that the time is ripe to introduce synthetic models of C. elegans to further enhance our understanding of the underlying principles of its development and behavior. For this reason, we have started the Perfect C. elegans Project, which aims to produce ultimately a complete synthetic model of C. elegans' cellular structure and function. This article describes the goal, the approach, and the initial results of the project.

Onami S et al. (2006) Bioessays "Genome-wide prediction of genetic interactions in a metazoan."

Kitano H, Onami S

[Bioessays, 2006]

Genetic interactions provide information about genes and processes with overlapping functions in biological systems. For Saccharomyces cerevisiae, computational integration of multiple types of functional genomic data is used to generate genome-wide predictions of genetic interactions. However, this methodology cannot be applied to the vastly more complex genome of metazoans, and only recently has the first metazoan genome-wide prediction of genetic interactions been reported. The prediction for Caenorhabditis elegans was generated by computationally integrating functional genomic data from S. cerevisiae, C. elegans and Drosophila melanogaster. This achievement is an important step toward system-level understanding of biological systems and human diseases. BioEssays 28: 1087-1090, 2006. (c) 2006 Wiley Periodicals, Inc.

Zeyu Zheng et al. (2006) East Asia C. elegans Meeting "Towards a quantitative 4D analysis of early embryogenesis using subcellular GFP markers"

Takafumi Konishi, Fumio Motegi, Asako Sugimoto, Nobuko Uodome, Zeyu Zheng

[East Asia C. elegans Meeting, 2006]

One of the challenges for analyses of developmental process is that manipulation of gene function can affect not only fate of cells but also their location, size, movement and developmental timings. Therefore, to understand the genes function comprehensively, 4-dimensional (= 3-dimension + time) description of cellular information is crucial. The C. elegans embryo is one of the best model systems for the 4D analysis of developmental processes, because of its transparency and invariant cell lineage, as well as amenability to genetic and cellular manipulations. Recent advancement of 4D-microscopy and computer technology has led to the development of several approaches to 4D data analysis (1-5), mainly focusing on nuclear divisions and lineage analysis. Here, to study cellular dynamics of early embryogenesis in C. elegans at a higher spatiotemporal resolution, we aim to establish a new 4D image analysis algorithm by incorporating GFP markers that highlight specific subcellular components. We have been testing GFP markers available in the community (e.g., histone, β-tubulin, and γ-tubulin), and also constructing potentially useful new markers. We will present our progress on the optimization of fluorescent 4D image capturing with a high-speed laser scanning confocal microscope, and the algorithms for quantitative analysis of the 4D datasets. 1. Bao, Z., et al. (2006) PNAS 103, 2707-2712. 2. Hamahashi, S., Onami, S. and Kitano, H. (2005) BMC Bioinformatics 6, 125-140. 3. Heid P., Voss E. and Soll D. (2002) Developmental Biology 245, 329-347. 4. Schnabel R., et al. (2006) Developmental Biology 294, 438-431. 5. Bischoff M. and Schnabel R. (2006) Developmental Biology 294, 432-444.

Hamahashi S et al. (2005) BMC Bioinformatics "Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking."

Onami S, Hamahashi S, Kitano H

[BMC Bioinformatics, 2005]

BACKGROUND: The ability to detect nuclei in embryos is essential for studying the development of multicellular organisms. A system of automated nuclear detection has already been tested on a set of four-dimensional (4D) Nomarski differential interference contrast (DIC) microscope images of Caenorhabditis elegans embryos. However, the system needed laborious hand-tuning of its parameters every time a new image set was used. It could not detect nuclei in the process of cell division, and could detect nuclei only from the two- to eight-cell stages. RESULTS: We developed a system that automates the detection of nuclei in a set of 4D DIC microscope images of C. elegans embryos. Local image entropy is used to produce regions of the images that have the image texture of the nucleus. From these regions, those that actually detect nuclei are manually selected at the first and last time points of the image set, and an object-tracking algorithm then selects regions that detect nuclei in between the first and last time points. The use of local image entropy makes the system applicable to multiple image sets without the need to change its parameter values. The use of an object-tracking algorithm enables the system to detect nuclei in the process of cell division. The system detected nuclei with high sensitivity and specificity from the one- to 24-cell stages. CONCLUSIONS: A combination of local image entropy and an object-tracking algorithm enabled highly objective and productive detection of nuclei in a set of 4D DIC microscope images of C. elegans embryos. The system will facilitate genomic and computational analyses of C. elegans embryos.

Thomas JH et al. (1994) Worm Breeder's Gazette "lin-36, a Class B Synthetic Multivulva Gene, Encodes a Novel Protein"

Thomas JH, Horvitz HR

[Worm Breeder's Gazette, 1994]

lin-36, a Class B Synthetic Multivulva Gene, Encodes a Novel Protein Jeffrey H. Thomas and H. Robert Horvitz, HHMI, Dept. Biology, MIT, Cambridge, MA 02139, USA

Sun J et al. (2013) Exp Parasitol "Parasitism of secondary-stage juvenile of Heterodera glycines and four larva stages of Caenorhabditis elegans by Hirsutella spp."

Sun J, Xie H, Xiang M, Liu X, Qiu J

[Exp Parasitol, 2013]

The fungi Hirsutella rhossiliensis and Hirsutella minnesotensis generally parasitize only plant-parasitic nematodes in nature but parasitize the bacterivorous nematode Caenorhabditis elegans on agar plates. To establish a model system for studying the interaction between fungi and nematodes, we compared the parasitism of the first- to fourth-stage larvae (L1-L4) of C. elegans and second-stage juvenile (J2) of Heterodera glycines by twenty isolates of Hirsutella spp. Although parasitism differed substantially among isolates, both H. minnesotensis and H. rhossiliensis parasitized a higher percentage of H. glycines J2s than of C. elegans larvae. Parasitism of C. elegans L1s was correlated with parasitism of H. glycines J2s. Parasitism of C. elegans by H. rhossiliensis and H. minnesotensis was negatively correlated with larva size and motility, i.e., parasitism was higher for the younger stages. The C. elegans L1 is recommended for studying parasitism of nematodes by H. rhossiliensis and H. minnesotensis.

Fei YJ et al. (2000) J Biol Chem "A novel H(+)-coupled oligopeptide transporter (OPT3) from Caenorhabditis elegans with a predominant function as a H(+) channel and an exclusive expression in neurons."

Leibach FH, Romero MF, Krause MW, Huang W, Ganapathy V, Fei YJ, Liu JC

[J Biol Chem, 2000]

We have cloned and functionally characterized a novel, neuron-specific, H(+)-coupled oligopeptide transporter (OPT3) from Caenorhabditis elegans that functions predominantly as a H(+) channel. The opt3 gene is approximately 4.4 kilobases long and consists of 13 exons. The cDNA codes for a protein of 701 amino acids with 11 putative transmembrane domains. When expressed in mammalian cells and in Xenopus laevis oocytes, OPT3 cDNA induces H(+)-coupled transport of the dipeptide glycylsarcosine. Electrophysiological studies of the transport function of OPT3 in Xenopus oocytes show that this transporter, although capable of mediating H(+)-coupled peptide transport, functions predominantly as a H(+) channel. The H(+) channel activity of OPT3 is approximately 3-4-fold greater than the H(+)/peptide cotransport activity as determined by measurements of H(+) gradient-induced inward currents in the absence and presence of the dipeptide using the two-microelectrode voltage clamp technique. A downhill influx of H(+) was accompanied by a large intracellular acidification as evidenced from the changes in intracellular pH using an ion-selective microelectrode. The H(+) channel activity exhibits a K(0.5)(H) of 1.0 microM at a membrane potential of -50 mV. At the level of primary structure, OPT3 has moderate homology with OPT1 and OPT2, two other H(+)-coupled oligopeptide transporters previously cloned from C. elegans. Expression studies using the opt3::gfp fusion constructs in transgenic C. elegans demonstrate that opt3 gene is exclusively expressed in neurons. OPT3 may play an important physiological role as a pH balancer in the maintenance of H(+) homeostasis in C. elegans.

Imadzu H et al. (1994) Worm Breeder's Gazette "Two Tropomyosins Expressed in Body Wall and the Third Did In Pharynx of Caenorhabditis elegans"

Kagawa H, Sakube Y, Imadzu H

[Worm Breeder's Gazette, 1994]

TWO TROPOMYOSINS EXPRBSSBD IN BODY WALL AND THE THIRD DID IN PHARYNX OF CAENORHABDDITIS ELEGANS. H. Imadzu, Y. Sakube and H. gagawa. Department of Biology, Faculty of Science, Okayama University, Okayama, 700 Japan.

Wilson PA et al. (1982) Parasitology "Strongyloides ratti (homogonic): the time-course of early migration in the generalized host deduced from experiments in lactating rats."

Steven GE, Simpson NE, Wilson PA

[Parasitology, 1982]

Unsuckled mother rats given a 1 h suckling stimulus 3 h after subcutaneous injection of an exact dose of homogonic Strongyloides ratti allow fewer worms to develop in their intestines by day 9 than nulliparous rats (Wilson & Simpson, 1981). This effect is studied in more detail in terms of the length of time between weaning and stimulus (W leads to S) and injection and stimulus (I leads to S). It was observable with a W leads to S of 30 h but this and a period of 5 h were less effective than 24 h. With W leads to S constant at 24 h, significantly more worms developed in mothers when I leads to S was 24 h compared to 3 h and 10 h (P less than 0.005). The data, combined with those from nulliparous controls, are presented as a measure of the change with time of numbers of larvae in that compartment of the system which gives access to the stimulated mammary gland. It is argued that the particular compartment is the local lymph node draining the injection site and that the kinetics deduced are applicable to migration in the rat in general.