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[
Worm Breeder's Gazette,
1994]
We are making sets of cDNA filters which are blotted with high-density grids of plaques of the some 4,400 cDNA clones most of which has been tag-sequenced as described above. The set consists of 3 nylon membrane filters (12 x 8.5 cm) on each of which cDNA clones from 15 or 16 of 96 well plate stocks are gridded as below using a home-made apparatus. We are intended to make the filters available to the worm community. Anyone who are interested in trying the filters, send your request to us at (e-mail) ykohara@ddbj.nig.ac.jp or (Fax) +81-559-75-6240.
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[
BMC Bioinformatics,
2010]
BACKGROUND: Graph drawing is one of the important techniques for understanding biological regulations in a cell or among cells at the pathway level. Among many available layout algorithms, the spring embedder algorithm is widely used not only for pathway drawing but also for circuit placement and www visualization and so on because of the harmonized appearance of its results. For pathway drawing, location information is essential for its comprehension. However, complex shapes need to be taken into account when torus-shaped location information such as nuclear inner membrane, nuclear outer membrane, and plasma membrane is considered. Unfortunately, the spring embedder algorithm cannot easily handle such information. In addition, crossings between edges and nodes are usually not considered explicitly. RESULTS: We proposed a new grid-layout algorithm based on the spring embedder algorithm that can handle location information and provide layouts with harmonized appearance. In grid-layout algorithms, the mapping of nodes to grid points that minimizes a cost function is searched. By imposing positional constraints on grid points, location information including complex shapes can be easily considered. Our layout algorithm includes the spring embedder cost as a component of the cost function. We further extend the layout algorithm to enable dynamic update of the positions and sizes of compartments at each step. CONCLUSIONS: The new spring embedder-based grid-layout algorithm and a spring embedder algorithm are applied to three biological pathways; endothelial cell model, Fas-induced apoptosis model, and C. elegans cell fate simulation model. From the positional constraints, all the results of our algorithm satisfy location information, and hence, more comprehensible layouts are obtained as compared to the spring embedder algorithm. From the comparison of the number of crossings, the results of the grid-layout-based algorithm tend to contain more crossings than those of the spring embedder algorithm due to the positional constraints. For a fair comparison, we also apply our proposed method without positional constraints. This comparison shows that these results contain less crossings than those of the spring embedder algorithm. We also compared layouts of the proposed algorithm with and without compartment update and verified that latter can reach better local optima.
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[
Lab Chip,
2013]
This paper reports on the development of a lens-less and image-sensor-less micro-electro-fluidic (MEF) approach for real-time monitoring of the locomotion of microscopic nematodes. The technology showed promise for overcoming the constraint of the limited field of view of conventional optical microscopy, with relatively low cost, good spatial resolution, and high portability. The core of the device was microelectrode grids formed by orthogonally arranging two identical arrays of microelectrode lines. The two microelectrode arrays were spaced by a microfluidic chamber containing a liquid medium of interest. As a nematode (e.g., Caenorhabditis elegans) moved inside the chamber, the invasion of part of its body into some intersection regions between the microelectrodes caused changes in the electrical resistance of these intersection regions. The worm's presence at, or absence from, a detection unit was determined by a comparison between the measured resistance variation of this unit and a pre-defined threshold resistance variation. An electronic readout circuit was designed to address all the detection units and read out their individual electrical resistances. By this means, it was possible to obtain the electrical resistance profile of the whole MEF grid, and thus, the physical pattern of the swimming nematode. We studied the influence of a worm's body on the resistance of an addressed unit. We also investigated how the full-frame scanning and readout rates of the electronic circuit and the dimensions of a detection unit posed an impact on the spatial resolution of the reconstructed images of the nematode. Other important issues, such as the manufacturing-induced initial non-uniformity of the grids and the electrotaxic behaviour of nematodes, were also studied. A drug resistance screening experiment was conducted by using the grids with a good resolution of 30 x 30 m(2). The phenotypic differences in the locomotion behaviours (e.g., moving speed and oscillation frequency extracted from the reconstructed images with the help of software) between the wild-type (N2) and mutant (
lev-8) C. elegans worms in response to different doses of the anthelmintic drug, levamisole, were investigated. The locomotive parameters obtained by the MEF grids agreed well with those obtained by optical microscopy. Therefore, this technology will benefit whole-animal assays by providing a structurally simple, potentially cost-effective device capable of tracking the movement and phenotypes of important nematodes in various microenvironments.
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[
Commun Biol,
2020]
Non-invasive and label-free spectral microscopy (spectromicroscopy) techniques can provide quantitative biochemical information complementary to genomic sequencing, transcriptomic profiling, and proteomic analyses. However, spectromicroscopy techniques generate high-dimensional data; acquisition of a single spectral image can range from tens of minutes to hours, depending on the desired spatial resolution and the image size. This substantially limits the timescales of observable transient biological processes. To address this challenge and move spectromicroscopy towards efficient real-time spatiochemical imaging, we developed a grid-less autonomous adaptive sampling method. Our method substantially decreases image acquisition time while increasing sampling density in regions of steeper physico-chemical gradients. When implemented with scanning Fourier Transform infrared spectromicroscopy experiments, this grid-less adaptive sampling approach outperformed standard uniform grid sampling in a two-component chemical model system and in a complex biological sample, Caenorhabditis elegans. We quantitatively and qualitatively assess the efficiency of data acquisition using performance metrics and multivariate infrared spectral analysis, respectively.
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Fang, Yuan-Sheng, Sternberg, Paul, DeWeese, Michael, Holman, Hoi-Ying, Holman, Elizabeth, Chen, Liang
[
International Worm Meeting,
2021]
Non-invasive and label-free spectral microscopy (spectromicroscopy) techniques can provide quantitative biochemical information complementary to genomic sequencing, transcriptomic profiling, and proteomic analyses. However, spectromicroscopy techniques generate high-dimensional data; acquisition of a single spectral image can range from tens of minutes to hours, depending on the desired spatial resolution and the image size. This substantially limits the timescales of observable transient biological processes. To address this challenge and move spectromicroscopy towards efficient real-time spatiochemical imaging, we developed a grid-less autonomous adaptive sampling method. Our method substantially decreases image acquisition time while increasing sampling density in regions of steeper physico-chemical gradients. When implemented with scanning Fourier Transform infrared spectromicroscopy experiments, this grid-less adaptive sampling approach outperformed standard uniform grid sampling in a two-component chemical model system and in a complex biological sample, Caenorhabditis elegans. We quantitatively and qualitatively assess the efficiency of data acquisition using performance metrics and multivariate infrared spectral analysis, respectively.
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[
International C. elegans Meeting,
1995]
Twelve contigs of cosmids and yeast artificial chromosomes (YACs) span more than 95Mb of the 100Mb C.elegans genome. 650 markers link the physical and genetic maps.Hybridisation of tag-sequenced cDNA clones to a map-representative set of YACs indicates that the map incorporates in excess of 99.8% of genes. The map is accessible in ACeDB. We (S.C.) are investigating the representation by bacterial artificial chromosomes (BACs) of regions of the genome not represented by cosmids. Two grids of YACs, of 958 clones ('Poly2') and 223 clones ('Suppoly') are available on request. The latter represents regions of the genome that have been characterised or better defined since the selection of clones for the former. Cosmid clones and YAC grids are available from the Sanger Centre (requests to alan@sanger.ac.uk; FAX 01223 494919). YAC clones and 'cm' series cDNA clones are available from the Sanger Centre or Washington University (rw@nematode. wustl.edu; FAX 314 362 2985).
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[
Worm Breeder's Gazette,
1987]
clones analyzed = 17545 clones in contigs = 17092 contigs = 680 % genome in contigs = 89. 5 mean contig size (Kb) = 105 contigs >200Kb = 79 unattached clones = 453 maximum % genome in unattached clones = 19. 3 As we indicated at Cold Spring Harbor, Bob Waterston has constructed a C. in a yeast artificial chromosome (YAC) vector. The mean insert size is 100-150 Kb. 2100 YAC's have been isolated and gridded and we have started using them as probes to make joins in the cosmid map. In addition, a limited number of replicas of the grid are available from the Medical Research Council (MRC). First reports are good, in that a number of people have found positives with their probes. We are not entirely clear how best to use the YAC's thus identified; however, since many individual walking efforts, as well as generalized closure of the map, are going to revolve around this grid for a time, the more information that we can collect about it the better. We would, therefore, like to send replicas to those labs that are interested in probing them and ask in return to be given the hybridization data that you collect. YAC's of interest to you are available from either St. Louis or the MRC. The part of the current map marked by cloned genes or polymorphisms is summarized in the following table. Contigs on each chromosome are ordered in three blocks: (1) unknown position; (2) known physical position (by in situ hybridization); (3) known genetic but unknown physical position. Because of the distortion of the genetic map relative to the physical map, there is no systematic way to unite (2) and (3); but as linkage proceeds, everything will move into (2).
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[
Semin Cell Dev Biol,
2023]
If mitochondria are the powerhouses of the cell, then mitochondrial dynamics are the power grid that regulates how that energy output is directed and maintained in response to unique physiological demands. Fission and fusion dynamics are highly regulated processes that fine-tune the mitochondrial networks of cells to enable appropriate responses to intrinsic and extrinsic stimuli, thereby maintaining cellular and organismal homeostasis. These dynamics shape many aspects of an organism's healthspan including development, longevity, stress resistance, immunity, and response to disease. In this review, we discuss the latest findings regarding the mechanisms and roles of mitochondrial dynamics by focussing on the nematode Caenorhabditis elegans. Whole live-animal studies in C. elegans have enabled a true organismal-level understanding of the impact that mitochondrial dynamics play in homeostasis over a lifetime.
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[
International C. elegans Meeting,
1991]
The C. elegans physical map has been assembled with a combination of cosmid and yeast artificial chromosome (YAC) clones. In the first phase, cosmid clone overlaps were detected using a high resolution fingerprinting technique. This produced a map with more than 700 contigs. Next, YACs were used to link together the multiple cosmid contigs via hybridization of the YACs to colony grids of representative cosmids. By the time this approach reached its practical limits, the map had been reduced to about 170 contigs. The current phase has involved detecting overlaps between protruding YAC clones at the ends of existing contigs, and also between small cosmid contigs and YACs. End sequence from the clones was obtained by using flanking vector primers either on total yeast genomic DNA for YACs or miniprep DNA for cosmids. PCR was then used to get unique hybridization probes. Hybridizing YACs were checked by PCR to confirm overlaps. From these efforts, the map now contains less than 90 contigs. Through the supporting evidence of genetic and physical information from other sources, more than 85 Mb of the assembled DNA has been assigned to chromosomes in 35 large contigs. Since C. elegans genes are preferentially located in the centers of chromosomes and the continuity of the map is greatest in these locations, all but a few coding sequences are now covered by contigs. The results of the physical map effort are available to the community in three forms: The database can be accessed either via network or modem from several locations throughout the world; a colony grid of 958 YACs, genomically ordered at the time of selection, has been prepared in a postcard sized array and replicas have been distributed to interested labs; YACs and cosmid clones covering any region are available upon request.
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[
International C. elegans Meeting,
2001]
The sequencing of the entire C. elegans genome has facilitated the ability to investigate gene function and gene interactions on a global scale. Advances in whole genome screening technology, in particular DNA microarrays, enable investigators to analyse the expression profiles of thousands of gene sequences simultaneously. This, combined with the genetic data available for C. elegans , makes the technique extremely powerful. DNA microarrays have been produced following protocols originally developed in the laboratory of P. Brown (Stanford, CA). Our arrays are composed of approx. 1kb genomic DNA fragments corresponding to each of the 19,000 predicted C. elegans ORFs. The microarrays were generated by robotically gridding each of these fragments onto poly-lysine coated glass slides. The complete complement of fragments was arrayed on two slides, and includes various controls. The microarrays are being used to compare steady-state RNA populations expressed by animals with different genetic backgrounds or physiologies by differential hybridisation of cDNAs. The cDNAs used in the experiments are labelled with either a Cy3 or Cy5 fluorescent tag, incorporated during reverse transcription. Fluorescence hybridisation signals are detected by confocal laser scanning; the resulting data are expressed as two-colour ratios. We are presently optimising a number of parameters affecting array gridding, RNA labelling, hybridisation and data analysis. We have developed a core database for analysing array data using the GeneSpring™ (Silicon Genetics) commercial software package. GeneSpring™ allows the user to perform hierarchical clustering, correlate data across multiple experiments and view data graphically. The Sanger Centre is developing additional software suites that will facilitate array data handling and analysis, including a web based browser. Microarrays produced at the Sanger Centre will be made available as a scientific resource for members of the UK research community, and the data obtained will be freely accessible to all. We are grateful to Stuart Kim and members of his laboratory for providing reagents and advice.