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[
Worm Breeder's Gazette,
1993]
ceh 6 expression and generation of a knock-out Thomas Burglin, Ron Plasterk*, Gary Ruvkun Dept. of Molecular Biology, Wellman 8, Massachusetts General Hospital, Boston, MA, 02114, USA, and *Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.
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[
The New York Times,
1997]
His tall figure bent over a computer screen in his laboratory at the Massachusetts General Hospital, Dr. Gary Ruvkun rummages through a distant genetic data base for matches to a gene he believes is involved in diabetes. ?You learn how to read these as they are ratcheting by,? he says, while lines of data streak up his screen. ?I think MTV is good training.?
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[
International Worm Meeting,
2003]
Oocyte meiotic maturation is essential to prepare the oocyte for fertilization and embryonic development. During meiotic maturation, C. elegans oocytes undergo nuclear envelope breakdown, cortical rearrangement, and meiotic spindle assembly in a spatially restricted manner such that the most proximal (-1) oocyte matures, is ovulated, and fertilized. Sperm stimulate oocyte meiotic maturation and gonadal sheath cell contraction using the major sperm protein (MSP) as a signaling molecule. The discovery of MSPs signaling role raised the intriguing question of how sperm release MSP to signal oocytes and sheath cells at a distance. The release of MSP from sperm likely occurs through a non-canonical mechanism since spermatozoa do not possess cellular components required in standard models of protein secretion, such as ribosomes, ER, or Golgi. Moreover, MSP does not have a N-terminal leader sequence, and in vitro release does not involve protein processing. Non-canonical or leaderless secretory pathways are widespread, and in general, poorly understood, despite figuring prominently in cell signaling, disease, and host defense. Using specific antibodies, we detect MSP both inside and outside of spermatids and spermatozoa in vitro. MSP release does not require motility or a pseudopod, and does not involve sperm lysis. We observe extracellular MSP up to approximately 90 m away from spermatozoa in the spermatheca, frequently reaching the -1 oocyte. Examination of extracellular MSP reveals it is localized in a graded distribution with the highest levels of MSP adjacent to spermatozoa and lower levels distally. MSP receptors on the -1 oocyte appear to bind and concentrate MSP resulting in a sharp boundary of staining, which is eliminated when trafficking of oocyte membrane proteins is blocked. Confocal microscopy shows extracellular MSP to be punctate. We observe large (~100-200 nM) MSP-staining puncta near spermatids or spermatozoa in the uterus. We speculate that these puncta are MSP-containing vesicles. Using immuno-EM we examined MSP localization in spermatozoa to pinpoint its localization in the cell. In addition to localization of MSP within the pseudopod, we also found MSP located in the cell body. Interestingly, we found a fraction of MSP associated with the plasma membrane of the spermatozoa. Based on these results we propose a model in which spermatids and spermatozoa shed vesicles containing MSP. In this model, MSP-containing vesicles released by spermatozoa in the spermatheca are unstable, forming a diffusible MSP signal that correlates with meiotic maturation rates and MAP kinase activation. Biochemical tests of this model are underway.
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[
Worm Breeder's Gazette,
1991]
Ed Hedgecock came to Tokyo in January for the 2nd seminar on Molecular and Developmental Neurobiology and his cell migration work impressed scientists of other animal field. Sydney Brenner won the Kyoto Prize and came to Japan on 23 of October for receiving the Prize on his fourth visit in this year. He talked with his excellent joke about telescope in Astronomy and microscope in Biology. Sydney is the man who gave the main lecture in the First Meeting of Japan Molecular Biology Society. Iva Greenwald came to Japan for attending the Naito Foundation International Workshop on Morphogenesis Program in early November together with her fiance Gary Struhl. It is true that the relation between Drosophila and Caenorhabditis is very good in U.S. and Japan. Some nematode scientists in Japan got grant from Drosophila project. John Sulston gave the lecture entitled 'The Genome of Caenorhabditis' on 28th of November at the main invited lecture of the Thirteenth Meeting of Japan Molecular Biology Society in Kyoto International Congress Hall. The lecture impressed many Japanese scientists especially his 'The Logical Next Step: Genome Sequencing'. On the 27th night, 34 worm people assembled to the worm party for welcoming to him. Sixteen papers from five labs were presented at the meeting.
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[
RNA Biol,
2019]
Worm biologists from the United States, Canada, and the United Kingdom gathered at the Colorado State University Todos Santos Center in Baja California Sur, Mexico, April 3-5, 2019 for the Todos Santos Small RNA Symposium. Meeting participants, many of whom were still recovering from the bomb cyclone that struck a large swath of North America just days earlier, were greeted by the warmth and sunshine that is nearly ubiquitous in the sleepy seaside town of Todos Santos. With only 24 speakers, the meeting had the sort of laid-back vibe you might expect amongst the palm trees and ocean breeze of the Pacific coast of Mexico. The meeting started with tracing the laboratory lineages of participants. Not surprisingly, the most common parental lineages represented at the meeting were Dr. Craig Mello, Dr. Gary Ruvkun, and Dr. Victor Ambros, whom, together with Dr. Andy Fire and Dr. David Baulcombe, pioneered the small RNA field. In sad irony, on the closing day of the meeting, participants were met with the news of Dr. Sydney Brenner's passing. By establishing the worm, <i>Caenorhabditis elegans</i>, as a model system Dr. Brenner paved the way for much of the research discussed here.
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Berriman, Matt, Howe, Kevin, Kersey, Paul, Stein, Lincoln, Harris, Todd, Sternberg, Paul, Schedl, Tim
[
International Worm Meeting,
2015]
WormBase has existed for 15 years and has evolved in many ways. The new website is fully operational and has made the process of adding new data types, displays, and tools easier. Behind the scenes we are piloting an overhaul of the underlying database infrastructure to allow us to handle the ever increasing data, have the website perform faster, and allow more frequent updates of information. This is a critical time for the project, as we face considerable pressure from two directions. The first is that our funders really want us to do more with less. We are responding to this by leading the way in making curation (the process of extracting information from papers and data sets into computable form) more efficient using a new version of Textpresso (to be released later this calendar year); by discussing with other model organism information resources ways to work together to be more efficient and inter-connected; and by seeking additional sources of funding. The second, delightful, pressure is an increase in data and results generated by the C. elegans and nematode communities. While we are handling this increase by changes in our software for curation, the database infrastructure, and the website, we do need your help. Many of you have helped us over the last few years to identify data in your papers or by sending us data directly. We now need you to help with a few types of information by submitting the data via specially designed, user-friendly forms that ensure good quality and the use of standard terminology. In particular, we have a large backlog of uncurated information associating alleles with phenotypes. We pledge to make this process as painless as possible, and to improve WormBase's description of phenotypes with your feedback, starting at this meeting at the WormBase booth, workshops and posters. With your help, continual improvement of our efficiency, and additional sources of funding, we are optimistic that we can do much more with even somewhat less effort.Consortium: Paul Davis, Michael Paulini, Gary Williams, Bruce Bolt, Thomas Down, Jane Lomax, Todd Harris, Sibyl Gao, Scott Cain, Xiaodong Wang, Karen Yook, Juancarlos Chan, Wen Chen, Chris Grove, Mary Ann Tuli, Kimberly Van Auken, D. Wang, Ranjana Kishore, Raymond Lee, John DeModena, James Done, Yuling Li, H.-M. Mueller, Cecilia Nakamura, Daniela Raciti, Gary Schindelman.
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[
Worm Breeder's Gazette,
1986]
Schwartz and Cantor (Cell 37, 67-75 (1984) and Carle and Olson (NAR 12, 5647-5664, 1984) have devised an orthogonal field agarose gel system that allows the separation of large DNA molecules (>2000 kb). A recent modification of the method by Carle et al. (Science 232, 65- 68, 1986) allows these separations to be obtained using a conventional gel box by periodically reversing the field. Control of the switch times through a microcomputer is convenient and allows the switch time to be varied at will during the run. This is important as the switch time controls the range of sizes that can be separated in a given run. Chris Bond of the MRC electronics laboratory designed and built an extremely convenient switch box employing Mosfett power bridges, which have an excellent response time and a long life time. Details of the set up I'm using are available to anyone interested (see also Carle and Olson's Science paper). To make high molecular weight (chromosomal?) DNA from C. elegans, I am currently using pure populations of L1's as starting material. These are embedded in 0.5% agarose in 0.125 M EDTA 0.125 M Tris pH9 and then lysed by overlayering with 1% sarcosyl, 1 mg/ml proteinase K and 7% -ME as described by Carle and Olson (1985) for yeast. Without restriction of the lysed worms very little ethidium stained material enters the gel under a variety of conditions with the exception of some low molecular weight material, assumed to be degraded RNA, and 2 or 3 ethidium stained bands with a mobility corresponding to about 100 kb but of unknown origin. After digestion with any of a series of restriction enzymes large amounts of DNA enter the gel. Two enzymes, NotI and SfiI which both have 8 bp recognition sequences composed entirely of G:C pairs yield a smear extending from about 100 kb to more than 1000 kb. A few distinct bands are visible against the background smear but it is impossible to directly estimate the number of fragments present. From parallel experiments using digests of random cosmid clones, NotI sites are estimated to occur every 600-700 kb on average, predicting be less than 150 bands. SfiI sites are slightly more frequent. After BglI digest, a 6 bp recognition site enzyme that does not cut within the ribosomal repeat sequence (Ellis et al. NAR 14, 2345-2364, 1986), most DNA appears to be about 50-150 kb although bands are visible at 300 and 350-400 kb and a single distinct band is present with a mobility between that of yeast chromosomes XI (~700 kb) and X. This band hybridizes strongly and specifically with an rDNA probe provided by R. Fishpool, and places an upper limit of 100 rDNA of 7.2 kb repeats. Current efforts are being directed toward using this methodology to characterize genome rearrangements in the
sma-1 region of LGV. I am also trying to identify the free duplication fragments mnDp30 and eDp6 in unrestricted DNA preps. The methodology may provide a level of resolution intermediate between that of cytogenetics and the cosmid mapping.
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[
Front Cell Dev Biol,
2022]
Axon-dendrite formation is a crucial milestone in the life history of neurons. During this process, historically referred as "the establishment of polarity," newborn neurons undergo biochemical, morphological and functional transformations to generate the axonal and dendritic domains, which are the basis of neuronal wiring and connectivity. Since the implementation of primary cultures of rat hippocampal neurons by Gary Banker and Max Cowan in 1977, the community of neurobiologists has made significant achievements in decoding signals that trigger axo-dendritic specification. External and internal cues able to switch on/off signaling pathways controlling gene expression, protein stability, the assembly of the polarity complex (i.e., PAR3-PAR6-aPKC), cytoskeleton remodeling and vesicle trafficking contribute to shape the morphology of neurons. Currently, the culture of hippocampal neurons coexists with alternative model systems to study neuronal polarization in several species, from single-cell to whole-organisms. For instance, <i>in vivo</i> approaches using <i>C. elegans</i> and <i>D. melanogaster,</i> as well as <i>in situ</i> imaging in rodents, have refined our knowledge by incorporating new variables in the polarity equation, such as the influence of the tissue, glia-neuron interactions and three-dimensional development. Nowadays, we have the unique opportunity of studying neurons differentiated from human induced pluripotent stem cells (hiPSCs), and test hypotheses previously originated in small animals and propose new ones perhaps specific for humans. Thus, this article will attempt to review critical mechanisms controlling polarization compiled over decades, highlighting points to be considered in new experimental systems, such as hiPSC neurons and human brain organoids.
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[
Worm Breeder's Gazette,
1986]
We have been using Maynard Olson's one-dimensional field-reversal gels (an improvement on Schwartz-Cantor orthogonal gels; see below) to look at large pieces of DNA. This technique is potentially useful for worm breeders in several ways. First, it may be possible to separate small free duplications from worm chromosomes, making quick clone mapping or region-specific libraries possible. Second, restriction enzymes that cut worm DNA infrequently can be used to determine the structure of DNA in a large region; specifically, they can be used to find breakpoints of chromosomal aberrations. Third, resolution can be improved over normal gels in the 10-50 kb range. Intact (>2Mb) DNA was prepared (see below) from SP957, a strain carrying mnDp30 balanced by a deficiency. On gels that resolve a 1.6 Mb yeast chromosome, mnDp30 is excluded from the gel (using a probe kindly supplied by Barbara Meyer). We were not particularly surprised, as 1.6 MB is about one-eighth of a chromosome, about the genetic size of mnDp30. (Contrary to Olson, we find that DNA larger than a certain cutoff size remains at the origin; he probably did not see this phenomenon because he used nothing larger than yeast chromosomes.) The eight-base recognition sequence enzymes NotI and SfiI both cut worm DNA into a smear of fragments ranging in size from about 50 kb to about 300 kb (and a small amount of DNA of very high molecular weight). This range is somewhat smaller than was predicted based on the AT content of worm DNA. Getting a complete digest can be difficult if there is very much DNA; nevertheless, we do see bands on Southerns, and we are looking for the eT1 breakpoint using probes linked to unc- 86.Technical Section Intact worm DNA: Prepare nuclei suspended in agarose as follows. Freeze worms at -80 C (or in liquid nitrogen) in a buffered solution containing 1mM spermidine, 5mM EDTA, and 1% NP40. Grind the frozen worms in a mortar until powdered. Scrape the powder into a microfuge tube and let thaw on ice. Spin in a microfuge for 1 second to pellet debris and transfer the sup to a new tube. Spin for 10 minutes at 5 C to pellet nuclei and discard sup. Resuspend pellet in the same buffer without detergent and add and mix in quickly an equal volume of 50mM EDTA 1% agarose, melted and cooled to 55 C. Let the agarose harden and slice the plug into convenient sized pieces. Add a ml of your favorite SDS-proteinase K solution and incubate at 65 C for an hour. Soak the slices in several changes of TE. Store them at 5 C in TE. To digest, soak a slice in the appropriate enzyme buffer containing 1mM of the protease inhibitor PMSF, and then change the buffer and add enzyme. Before trying to load the slice into a gel well, it helps to soak it in TE containing dye, so you can find it if you drop it. Field reversal electrophoresis: First read Carle, Frank, and Olson, Science 232, 65, 1986. Initially we reversed the field using a computer-controlled apparatus built by Leon Avery and MF. Plans are available on request. The disadvantage of this arrangement is that the computer is tied up for the entire run of the gel. Now we are using a switching apparatus with an integral microprocessor built by MF. We are still experimenting with conditions--for the latest, give us a call.
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[
Worm Breeder's Gazette,
1994]
MEF-2 ,(formyocyte-enhancer-binding-factor), is a muscle-restricted, sequence-specific transcription factor known to participate in the regulation of many muscle genes. In vertebrates, MEF-2 binding sites have been demonstrated for both terminally expressed gene products (such as muscle creatine kinase) and MyoD Family members (MyoD and myogenin). Recent results suggest that MEF-2 may play a more important role in myogenic cell fate determination than originally thought. Expression of certain isoforms of MEF-2 occurs in early muscle precursors during development in mouse, Xenopus, and Drosophila. In Drosophila, expression of a MEF-2 clone occurs prior to expression of the MyoD Family homolog nautilus and occurs in cells that are precursors for visceral and skeletal muscle cells (Brenda Lilly and Eric Olson). MEF-2 is a member of a larger group of transcription factors that are know as the MADS Family (MCM1, Agamous, Deficiens, and Serum response factor). MADS Family members share a conserved domain spanning about 55 amino acids at the amino terminal end of the protein. The MADS domain is involved in both dimerization and DNA binding of these transcription factors. The conservation of the MADS domain makes these genes good targets for PCR cloning; so we did. We used degenerate oligonucleotides in RT-PCR reactions of worm total RNA. The clones isolated are listed below; they each are related to MEF-2 and demonstrate that MADS box proteins are present in worms. The sequence results suggest as many as five different MEF-2 gene products. We are presently screening a C. elegans cDNA library with the partial sequence of MEF-2 initially obtained and are also attempting to amplify flanking sequences of the same partial sequence of MEF-2 .We want to know when and where these genes are expressed and how their expression is related to myogenesis in the worm.