Two-dimensional gel electrophoresis has been used to analyze proteins synthesized during postembryonic development of the nematode Caenorhabditis elegans. This organism is favorable for these studies because it has a limited number of cells, it is genetically well-defined, and its development is currently under investigation in several laboratories. 35S-labeled E. coli was used for continuous and pulse labeling of C. elegans during its four juvenile larval stages and as a gravid adult. After continuous labeling or pulse labeling for 1 hr, 600-800 individual spots can be resolved on a 2D gel using fluorography and 2 weeks of exposure. Proteins that represent 0.0017% of the total sample can be detected. Exposure for 12 weeks reveals only 100 additional spots even though the films are not saturated. It therefore appears that the frequency distribution of proteins decreases significantly beyond these 800 most abundant proteins that can be frationated on an O'Farrell gel. When the patterns of pulse-labeled proteins of the five developmental stages were compared, 113 proteins could be seen to undergo modulation at one or more of the developmental stages. A maximum number of changes was seen in the transition from the L4 to the adult stages when 11% of the total spots either appeared, disappeared, or changed in intensity. As controls, different preparations of the same developmental stage were compared and revealed considerable fluctuation, 2.6-4.8%. These fluctuations are presumed to be due to variations in growth conditions during culture of the organism. Continuous label experiments reveal a distinct set of proteins that undergo turnover and/or modification during development. Some of these proteins are absent in only one stage, indicating that stable proteins are also modulated. But nearly all of the proteins seen in a continuous label are also seen in a pulse label indicating that most of the major proteins are
BMC Evol Biol,
BACKGROUND: Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode Caenorhabditis elegans (CB4856 and CB4858) and the reference genome (N2). RESULTS: The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison.In both CB4856 and CB4858, based on a measure of the strength of selection (ka/ks), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, ka/ks values are smaller in the autosomes than in the X chromosome. In addition, in CB4858, ka/ks values differ between chromosomes. CONCLUSIONS: The clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the ka/ks ratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome.
The authors, Coleman-Hulbert, AL; Johnson, E; Sedore, CA; Banse, SA; Guo, M2; Driscoll, M3; Lithgow, GJ; and Phillips, PC, submit the following correction for 10.17912/micropub.biology.000131
The original text as read &#8220;We assayed lifespan in response to imatinib mesylate exposure in threeCaenorhabditisspecies in triplicate using our previously published workflow (Lucanicet al. 2017a; b). is correct.
The reference Lucanic 2017b et al. is:
Lucanic M, Driscoll M, Plummer WT, Harke J, Chen E, Bhaumik D, Harinath G, Coleman-Hulbert A, Dumas K, Onken B, Johnson E, Fougler A, Guo S, Crist A, Presley M, Xue J, Sedore C, Chamoli M, Change M, Chen M, Angeli S, Royal MA, Willis J, Edgar D, Shobna P, Chao E, Kamat S, Hope J, Ibanez-Ventoso C, Kish J, Guo M, Phillips P, Lithgow G. Standardized protocols from theCaenorhabditisIntervention Testing Program 2013-2016: Conditions and assays used for quantifying the development, fertility and lifespan of hermaphroditicCaenorhabditisstrains. Protoc. Exch. 2017. doi: 10.1038/protex.2016.086.
The following reference is incorrect:
Plummer WT, Harke J, Lucanic M, Chen E, Foulger AC, Onken B, Coleman-Hulbert AL, Dumas KJ, Guo S, Johnson E, Bhaumik D, Xue J, Crist AB, Presley MP, Harinath G, Sedore CA, Chamoli M, Kamat S, Chen MK, Angeli S, Chang C, Willis JH, Edgar D, Royal MA, Chao EA, Shobna P, Garrett T, Ibanez-Ventoso C, Hope J, Kish JA, Guo M, Lithgow GJ, , Phillips PC. Standardized protocols from the Caenorhabditis Intervention Testing Program 2013-2016: Conditions and assays used for quantifying the development, fertility and lifespan of hermaphroditic Caenorhabditis strains. Protoc. Exch. 2017b. 10.1038/protex.2016.086
The authors, Coleman-Hulbert, AL; Johnson, E; Sedore, CA; Banse, SA; Guo, M2; Driscoll, M3; Lithgow, GJ; and Phillips, PC, submit the following correction.
The first reference in the methods paragraph should be (Lucanic et al., 2017; Plummer et al., 2017) and should not be letteredaccordingly.
We assayed lifespan in response to imatinib mesylate exposure in three Caenorhabditis species in triplicate using our previously published workflow (Lucanic et al. 2017a; b).
should be corrected to:
We assayed lifespan in response to imatinib mesylate exposure in three Caenorhabditis species in triplicate using our previously published workflow (Lucanic et al., 2017; Plummer et al., 2017).
J Cell Biol,
We previously described a kinesin-dependent movement of particles in the flagella of Chlamydomonas reinhardtii called intraflagellar transport (IFT) (Kozminski, K.G., K.A. Johnson, P. Forscher, and J.L. Rosenbaum. 1993. Proc. Natl. Acad. Sci. USA. 90:5519-5523). When IFT is inhibited by inactivation of a kinesin, FLA10, in the temperature-sensitive mutant, fla10
, existing flagella resorb and new flagella cannot be assembled. We report here that: (a) the IFT-associated FLA10 protein is a subunit of a heterotrimeric kinesin; (b) IFT particles are composed of 15 polypeptides comprising two large complexes; (c) the FLA10 kinesin-II and IFT particle polypeptides, in addition to being found in flagella, are highly concentrated around the flagellar basal bodies; and, (d) mutations affecting homologs of two of the IFT particle polypeptides in Caenorhabditis elegans result in defects in the sensory cilia located on the dendritic processes of sensory neurons. In the accompanying report by Pazour, G.J., C.G. Wilkerson, and G.B. Witman (1998. J. Cell Biol. 141:979-992), a Chlamydomonas mutant (fla14
) is described in which only the retrograde transport of IFT particles is disrupted, resulting in assembly-defective flagella filled with an excess of IFT particles. This microtubule- dependent transport process, IFT, defined by mutants in both the anterograde (fla10
) and retrograde (fla14
) transport of isolable particles, is probably essential for the maintenance and assembly of all eukaryotic motile flagella and nonmotile sensory cilia.