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Worm Breeder's Gazette,
1983]
Use of Colloidal Gold Particles in EM We have been using a simple and inexpensive procedure to produce colloidal gold particles of a uniform size (5 nm) which can be conjugated directly to proteins. Gold particles serve as excellent electron dense markers for use in electron microscopy. Preparation of Colloidal Gold Particles by Ultrasonics 1. Dilute 0.1 ml of 1% gold chloride [ H(AuCl4) ] in 50 ml dH20. 2. Make solution neutral with 0.2M K2CO3. 3. Immediately before sonication, add 0.5 ml of 100% ethanol as a catalyst. 4. Carry out sonication at 20 Kc and 125 W by immersing a flat-end probe approximately 1 cm under the surface of the gold solution. 5. After about 2-5 min, the solution attains a pinkish color with maximum intensity at A = 520 nm. Note: To prevent the solution from heating up during sonication, keep it cool in an ice water bath. This helps prevent the formation of larger gold particles. Store at 4 C. Preparation of Gold Labelled Protein 1. Mix 1mg of purified protein with 5ml of colloidal gold solution and incubate for 15 min at room temperature with mixing. 2. Add 10mg BSA, mix, and incubate for another 5 min to prevent aggregation of gold-protein complexes. 3. Add NaCl (100g/l) to make a final concentration of 10g/l. 4. Centrifuge at 1700 g for 20 min to remove excess BSA. 5. Centrifuge supernatant from step 4 at 60,000 g for 15 min to bring down gold labelled protein, leaving unlabelled protein in the supernatant. 6. Pellet should be a loosely packed, dense red sediment and can be resuspended in 0.5 to 1.0 ml of desired buffer. Use undiluted.
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Worm Breeder's Gazette,
1983]
We have been applying hybridoma technology to our research by generating monoclonal antibodies (MAb's) against C. elegans sperm. We have produced 10 mAb's in our lab and have obtained 2 others from Susie Strome at Boulder. Seven of these mAb's target antigens present on the cell surface. We have been purifying monoclonal antibodies from ascites fluid by DEAE Affi-Gel blue chromatography (supplied by Bio-Rad). Although yields have been lower than ideal (40-60%), these antibodies are free of all contaminants except mouse transferrin. Membrane lipid flow and directed movement of pseudopod surface components on sperm was previously reported by Roberts and Ward (J. Cell Bio. 92: 113-120). We have evidence that the movement of antigen-antibody complexes may be due to a continual flow of membrane lipid (see Bretscher, 1976, Nature 260: 21-23) from the tip of the pseudopod back toward the cell body. Bretscher's lipid flow model of membrane movement predicts that membrane components which diffuse slowly are displaced by the lipid stream whereas those which diffuse rapidly effectively escape lipid flow. Because the rate of diffusion is related to molecular weight, large complexes (e.g. antibody- crosslinked membrane proteins) would be swept along more rapidly than individual molecules (e.g.- unbound membrane proteins). We have tested this prediction by comparing clearance rates of various sized complexes form the cell pseudopod. On sperm, relatively small antigen- mAb complexes clear from the pseudopod surface slowly (2-3 min) while larger, cross-linked antigen-mAb-2 antibody complexes are cleared more rapidly (30-45 seconds). Using mAb's conjugated directly to colloidal gold particles (CGP), we have obtained evidence that new surface antigens are preferentially inserted at the tips of pseudopodial projections and then move rearward toward the cell body pseudopod junction (Pavalko and Roberts, C. elegans Meeting Abstracts, 1983). This observation predicts that there must be a pool of antigen in the cytoplasm which would be available for insertion into the membrane. Labelling thin sections of spermatozoa with CGP conjugates of mAb's 11, 63, and 56 (each of which bind to the cell surface in indirect immunofluorescence assays) reveals antigen on the surface (plasma membrane, exposed face of fused membranous organelles and MO contents). In addition, these antibodies label the cytoplasmic laminar membranes and the pseudopod cytoplasm. Many of the gold particles in the cytoplasm lie just beneath the plasma membrane suggesting that they are bound to antigens that were destined for insertion onto the surface. Because there are no vesicles in the cytoplasm, the mechanism which transports these antigens is unknown. We will be trying to characterize the antigens targeted by the mAb's and to solve the question of how they are shuttled around the cell.
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[
International C. elegans Meeting,
1985]
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[
International C. elegans Meeting,
1983]
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J Cell Biochem,
1989]
We have examined the mechanism of membrane protein insertion in the ameboid spermatozoa of Caenorhabditis elegans using two monoclonal antibodies which recognize the same set of eight sperm-specific polypeptides. Previous electron microscopic studies demonstrated that these antibodies label surface and cytoplasmic populations of antigen. Cells whose surface antigen had been removed by proteolysis were able to localize new membrane protein insertion at the tips of pseudopodial projections. C. elegans sperm do not contain the protein synthesizing machinery needed for delivery of new membrane to the cell surface. It has, therefore, been of interest to determine how localized membrane assembly occurs. Here we have determined the subcellular location of each of these eight polypeptides. A closely positioned doublet of bands around 97 kD (comprising 40% of the total antigen in sperm) represents surface (larger member of doublet) and cytoplasmic (lower member) forms of protein. Proteolysis of live cells eliminated this surface form from immunoblots but did not affect the cytoplasmic protein. When cells were allowed to reinsert new protein following removal of the enzyme, this surface form was regenerated. Since sperm are unable to synthesize new protein, this higher molecular weight species may arise from a posttranslational modification of proteins in the cytoplasmic pool. We present evidence suggesting that the surface protein is generated from this cytoplasmic pool by addition of fatty acid. Fatty acid acylation would account for both the observed decrease in electrophoretic mobility of the surface form and provide increased hydrophobicity to the protein which may allow for its insertion into the lipid bilayer.
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Cell Motil Cytoskeleton,
1988]
Caenorhabditis elegans sperm are nonflagellated cells that lack actin and myosin yet can form pseudopods to propel themselves over solid substrates. Surface-attached probes such as latex beads, lectins, and antimembrane protein monoclonal antibodies move rearward over the dorsal pseudopod surface of sessile cells. Using monoclonal antibodies against membrane proteins of C. elegans sperm to examine the role of localized membrane assembly and rearward flow in crawling movement, we determined that substrates prepared by coating glass with antimembrane protein antibodies, but not naked glass or other nonmembrane-binding proteins, promote sperm motility. Sperm locomotion is inhibited in a concentration-dependent fashion when cells are bathed with soluble antimembrane protein monoclonal antibodies but not with antimouse Ig antibodies or a monoclonal antibody against a sperm cytoplasmic protein. Our results suggest that C. elegans sperm crawl by gaining traction with substrate- attached ligands via their surface proteins and by using the motor that moves those proteins rearward on unattached cells to pull the entire cell forward. Continuous insertion of new proteins at the front of the cell and their subsequent adhesion to the substrate allows this process to continue.
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[
International C. elegans Meeting,
1985]
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J Cell Biol,
1986]
During the development of pseudopodial spermatozoa of the nematode, Caenorhabditis elegans, protein synthesis stops before differentiation is completed. Colloidal gold conjugates of monoclonal antibody SP56, which binds to the surface of spermatozoa, and TR20, which recognizes the major sperm cytoplasmic protein (MSP), were used to label thin sections of testes embedded in Lowicryl K4M in order to follow polypeptides from their synthesis early in spermatogenesis to their segregation to specific compartments of the mature cell. Both antigens are synthesized in primary spermatocytes and are assembled into a unique double organelle, the fibrous body-membranous organelle (FB-MO) complex. However, the antigens are localized in different regions of this FB-MO complex. As described in detail, the assembly of proteins into the FB-MO complex allows both membrane and cytoplamsic components to be concentrated in the spermatids after meiosis. Then, the stepwise disassembly of this transient structure ensures delivery of each component to its final destination in the mature spermatozoan: MSP filaments in the fibrous body depolymerize, releasing MSP into the cytoplasm and the membranous organelles fuse with the plasma membrane, delivering SP56 antigen to the surface.
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[
International C. elegans Meeting,
1985]
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BMC Bioinformatics,
2017]
BACKGROUND: High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing. Because, errors may reduce the accuracy of subsequent de novo assembly, error correction is necessary prior to assembly. However, existing correction methods still face trade-offs among correction power, accuracy, and speed. RESULTS: We develop a novel overlap-based error correction algorithm using FM-index (called FMOE). FMOE first identifies overlapping reads by aligning a query read simultaneously against multiple reads compressed by FM-index. Subsequently, sequencing errors are corrected by k-mer voting from overlapping reads only. The experimental results indicate that FMOE has highest correction power with comparable accuracy and speed. Our algorithm performs better in long-read than short-read datasets when compared with others. The assembly results indicated different algorithms has its own strength and weakness, whereas FMOE is good for long or good-quality reads. CONCLUSIONS: FMOE is freely available at https://github.com/ythuang0522/FMOC .