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Behavior [HTML]
...eat avoidance 7. Locomotion 7.1. Quantitation of locomotion rate by counting body bends 7.2. Decreased locomotion on food 7....
....1. Electropharyngeogram recordings 8.2. Pharyngeal pumping rate 8.3. Foraging 9. Egg-laying, males and mating 9.1. Assessin...
Behavior : 1. Introduction
...ve to this than others. Osmolarity and spontaneous reversal rate assays are quite sensitive to plate dryness. Depending on t...
Behavior : 2. Mechanosensation
...ie, unpub. data). Touching animals in the anterior slow the rate of pharyngeal pumping. Another output of the touch circuitr...
...ns of movement can be observed in some strains/animals. The rate of basal foraging is dependent on the RMD motorneurons and ...
Behavior : 3. Osmotic avoidance
...inal assay, described in an updated format below, tests the rate at which C. elegans will cross an osmotic barrier on the su...
...rmal NGM agar, a region of low osmolarity. In practice, the rate at which animals escape is dependent on several parameters....
...of animals in the ring versus the size of the ring, and the rate of diffusion of the osmotic barrier. The assay is dependent...
....4. Running assays with limited numbers of animals The rate at which animals encounter the osmotic barrier is important...
Behavior : 6. Thermal responses
... calculated for each video frame. Typically, we use a frame rate of 1-5 Hz. High frame rates are suitable if one wants to ca...
...High frame rates are suitable if one wants to calculate the rate of bending waves, which will emerge as the high frequency c...
Behavior : 7. Locomotion
...clearly define the direction of locomotion at this sampling rate. Convert this record to instantaneous turning rate vs. time, R ( t ). This is done by computing the (minimum) ...
...7.1 7. Locomotion 7.1. Quantitation of locomotion rate by counting body bends Contributed by Niels Ringstad and Bo...
...ed, not glossy, appearance. Plates for measuring locomotory rate in the absence of bacteria are also incubated at 37°C. ...
... larval stage) are tested. For well-fed animals, locomotory rate is measured by gently picking 5 animals from plates with am...
Behavior : 8. Feeding
...edu/Worm_labs/Avery/MiniRig/ . 8.2. Pharyngeal pumping rate Pumping rate are measured by counting visible movements of the grinder. ...
Behavior : 9. Egg-laying, males and mating
...s that accumulate inside an adult is a function both of the rate of egg production and the rate of egg-laying. If you want to use this assay to quantify di...
...g hatched larvae therefore does not necessarily reflect the rate at which eggs have been laid; it is skewed by this damage t...
...ur strain undergoes embryonic development at about the same rate as does N2. Pick a few early 1 or 2 cell embryos and follow...
...n some species of parasitic nematodes, it appeared that the rate of release of chitinase into culture medium could be used a...
Behavior : 10. Assays of C. elegans reproductive behaviors
...rching behavior. Mate-searching is assayed by measuring the rate at which isolated males leave a food spot in the Leaving As...
...flections of laboratory lights on the agar surface. Leaving rate is calculated as the probability of leaving per hour, PL. P...
...say. To control for fluctuations in conditions, the leaving rate of experimental animals should be compared to that of wild ...
Natural variation and population genetics of Caenorhabditis elegans [HTML]
...ns The level and pattern of genetic diversity depend on the rate and pattern of mutation, which can be measured after accumu...
...ved molecular diversity in wild isolates, then the mutation rate and pattern in MA lines, and compare them to reveal the act...
...tion accumulation lines of a fitness measure (the intrinsic rate of increase) after 214 generations ( Vassilieva et al., 200...
...ave the same mitochondrial DNA sequence as N2. The mutation rate and pattern of mitochondrial DNA were assessed in mutation ...
Natural variation and population genetics of Caenorhabditis elegans : 2. Phenotypic diversity
...genic bacterium Bacillus thuringiensis in terms of survival rate, infection levels, pumping rate and evasion behavior ( Schulenburg and Muller, 2004 ). Resi...
...As with DNA evolution, the effect of random mutation on the rate and pattern of phenotypic variation can then be compared wi...
... time. This laboratory “fitness” decreases at a rate of about 0.1% per generation in mutation accumulation lines...
...re 2 ). Knowing the fitness decrease the molecular mutation rate and the proportion of constrained nucleotides as estimated ...
The measurement and analysis of age-related changes in Caenorhabditis elegans [HTML]
...ive. Some measurements are highly quantitative, such as the rate of pharyngeal pumping or the amount of a biochemical produc...
The measurement and analysis of age-related changes in Caenorhabditis elegans : 2. Age-related changes in C. elegans
...croscope ( Avery and Thomas, 1997 ). The pharyngeal pumping rate reaches a maximum of approximately 300 pumps per minute in ...
...ference(s) Behavioral Pharyngeal pumping Decrease in rate Dissecting scope Yes No Croll et al., 1977 Hosono et al., 1...
...w et al., 2006 Body movement Progressive decrease in rate and coordination Dissecting scope Yes No Bolanowski et al.,...
... Yes/No Murakami et al., 2005 Defecation Decrease in rate Disecting scope Yes No Croll et al., 1977 Bolanowski et al....
The measurement and analysis of age-related changes in Caenorhabditis elegans : 3. Conclusions
...nce lifespan appear to control processes that determine the rate of age-related degenerative changes and do not appear to sp...
... of reproductive aging. These three processes determine the rate of progeny production and the total number of progeny gener...
Nematode genome evolution [HTML]
... in the Nematoda 4.5. Identifying "parasitism genes" 5. The rate of evolution in nematodes 6. Summary 7. Acknowledgements 8....
Nematode genome evolution : 2. Evolution of genome size
...). The compact nature of nematode genomes may due to a high rate of large, spontaneous deletions ( Witherspoon and Robertson...
Nematode genome evolution : 3. The evolution of chromosome number and structure
.... Alternatively, the arms may simply have a higher mutation rate, since the high recombination rate may provoke substitutions ( Cutter and Payseur, 2003 ), whi...
...e deleterious mutations, resulting in a faster substitution rate and rate of chromosomal rearrangement ( Charlesworth, 1992 ; Cutter ...
...repeat-rich "arms" that have a ~7-fold higher recombination rate ( Barnes et al., 1995 ; C. elegans Sequencing Consortium, 1...
...ve DNA. Barnes et al. (1995) noticed that the recombination rate in most C. elegans autosomes differs by a factor of ~7̵...
Nematode genome evolution : 4. Evolution of gene content
...C. elegans chromosomes probably results from the arms' high rate of rearrangement ( Stein et al., 2003 ). C. elegans is not ...
Nematode genome evolution : 5. The rate of evolution in nematodes
...10.1895/wormbook.1.15.1 5. The rate of evolution in nematodes Mushegian et al. (1998) compared ...
...ologs. Nematode rRNA genes also seem to have a substitution rate that is 2-3 times that of other animal phyla ( Aguinaldo et...
...tke et al., 2004 )! To accurately estimate the evolutionary rate in nematodes, ideally we would divide the number of mutatio...
...ated from the subset of genes that have evolved at the same rate in all animals (for example, see Stein et al., 2003 ). Unfo...
Molecular evolution inferences from the C. elegans genome [HTML]
...ls in the nuclear genome are thought to arise at an average rate per generation that is comparable to the single-nucleotide rate ( Denver et al., 2004b ), although it is now unclear whethe...
...b ; Denver et al., 2000 ) inference of the average mutation rate across the genome. The most recent incarnation of this work...
...icates an average per-generation single-nucleotide mutation rate in the nuclear genome of 2.7 × 10 −9 ( Denver e...
...is result holds, in light of the most recent point-mutation rate estimates. Denver et al. (2004b) estimated that an average ...
Molecular evolution inferences from the C. elegans genome : 3. Recombination
...stitution (K A ) does not strongly correlate with crossover rate once the substitution rate at synonymous sites (K S ) is properly accounted for (inclu...
...7 ; Stein et al., 2003 ), consistent with a higher mutation rate in regions experiencing elevated crossover rates. However, ...
...ty along the length of chromosomes with respect to mutation rate, based on ∼400 detected mutations ( Denver et al., 20...
...proteins encoded in chromosomal centers (i.e. low crossover rate regions) tend to be more highly conserved across taxa ( C. ...
Molecular evolution inferences from the C. elegans genome : 4. Natural Selection
...0 ). Dividing K A by K S provides a metric that relates the rate of change at amino acid-changing sites relative to the rate expected for putatively neutrally evolving synonymous sites...
...t to reflect differences among loci in the underlying local rate of mutation that could, in itself, give rise to differences...
...others use a phylogenetic tree to generate lineage-specific rate estimates separately for each branch in the tree ( Figure 1...
Molecular evolution inferences from the C. elegans genome : 5. Genetic Drift
...populations not in terms of census size but in terms of the rate of genetic change due to drift ( Charlesworth, 2009 ). Sinc...
Intermediary metabolism [HTML]
...uring development and aging 6.1. Development Metabolic rate measured as oxygen consumed or heat produced per unit time ...
...by a steep decrease as worms reach adulthood. The metabolic rate then gradually decreases as the worms traverse this final s...
...an be used for energy production and gluconeogenesis. After hatching, the activity of isocitrate lyase progressively decreases, ...
... 2002b ), consistent with an overall reduction of metabolic rate. This appears to be caused by the reduced activities of the...
Intermediary metabolism : 7. Influence of external factors on intermediary metabolism
...perature ( Klass, 1977 ), whereas development and metabolic rate show a positive correlation within an acceptable physiologi...
...striction lowers ROS production by decreasing the metabolic rate ( Sohal and Weindruch, 1996 ; Lakowski and Hekimi, 1998 ). ...
... potential increases and more electrons tend to leak as the rate of reduction of oxygen to water by complex IV decreases ( K...
... of SKN-1 signaling on metabolic activity and the metabolic rate studies of Houthoofd and co-workers (2002a ; 2002c ; 2003 ;...
The C. elegans intestine [HTML]
...ugh int9) has two cells. The basic form of the intestine at hatching is shown schematically at the bottom of Figure 2 . A schema...
The C. elegans intestine : 3. Intestinal morphogenesis and patterning
...rotation increases to approximately 180° by the time of hatching ( Sulston and Horvitz, 1977 ) but may be variable (See Worm...
... int5 beginning from approximately 350 cells until at least hatching and perhaps this is what makes int5 different from the othe...
...nthesis and patterned cell/nuclear divisions At the time of hatching, the L1 intestine has 20 cells, each with a single diploid ...
...being produced by an extra round of division shortly before hatching ( Hong et al., 1998 ; Kostic and Roy, 2002 ; Fukuyama et al...
The C. elegans intestine : 4. Structure of an intestinal cell
...icrovilli. Knockouts of act-5 cause lethality shortly after hatching. The mutant intestinal cells retain normal polarity and hav...
...rine binding protein) is widespread in the embryo but after hatching, most GEM-4 is located in the intestinal brush border ( Chu...
The C. elegans intestine : 5. Function: towards a molecular physiology of the intestine
...of cdr-1 is exclusively in the intestine in all stages post-hatching. The CDR-1 protein is highly hydrophobic, appears novel and...
The C. elegans intestine : 6. Transcriptional control in the intestine
...ed late in embryogenesis and analyzed immediately following hatching: the mtl-2 metallothionein gene ( Moilanen et al., 1999 ), ...
Cell division [HTML]
...sm into oocytes ( Figure 1 ). Since depletion relies on the rate of embryo production instead of protein half-life, the kine...
...ryonic lethality due to developmental defects that preclude hatching. ...
Cell division : 4. Pronuclear migration
...onucleus moves ~ 12 μm towards the posterior at a slow rate (~ 3.5 μm/min). As it approaches the sperm pronucleus,...
... moving an additional 10 μm at ~5-10 times its initial rate ( Figure 4 ; Albertson, 1984 ; O'Connell et al., 2000 ). Th...
...ion later than its female counterpart and travels at a slow rate of ~ 3.5 μm/min till it meets the oocyte pronucleus ne...
...nucleus moves towards the embryo anterior at a uniform slow rate. The oocyte pronucleus initially moves towards the embryo p...
Cell division : 5. Centrosome assembly and duplication
...support partial assembly of mitotic centrosomal asters, the rate of centrosomal microtubule nucleation is severely compromis...
...01 ). However, chill and rewarm experiments reveal that the rate of centrosomal microtubule nucleation is highly compromised...
Cell division : 7. Kinetochore assembly
...In MIS embryos, kinetochore assembly occurs but at a slower rate and to a reduced extent relative to wild-type. (Yellow) ...
Cell division : 9. Chromosome segregation
...uggests that the central spindle normally acts to limit the rate of pole separation. However, in embryos in which G protein ...
... still elongate ( Colombo et al., 2003 ) albeit at a slower rate, indicating that other spindle intrinsic forces contribute ...
Cell division : 10. Cytokinesis
...ting myosin phosphatase; inhibition of Rho-kinase slows the rate of furrow ingression but does not prevent furrow assembly o...
Obesity and the regulation of fat metabolism [HTML]
... (food consumption) and energy expenditure (basal metabolic rate, i.e. biochemical processes required to maintain cellular v...
Obesity and the regulation of fat metabolism : 2. C. elegans fat
...yes do not produce any adverse effects on C. elegans growth rate, brood-size, pharyngeal pumping, dauer (a larval hibernatio...
Obesity and the regulation of fat metabolism : 3. Metabolic pathways
...lation in adults (see Figure 4 ). Measurements of metabolic rate, as assessed by CO 2 release, biochemical activity assessme...
...tes dauer formation. In adults, DAF-16 reduces reproductive rate, enhances lifespan and causes fat accumulation. The C. eleg...
...ause feedback inhibition of acyl-CoA carboxylase (ACC), the rate-limiting enzyme of fatty acid synthesis. ACC inhibition res...
Obesity and the regulation of fat metabolism : 7. Neuroendocrine fat and feeding regulatory pathways
...re viable but have excess fat accumulation, reduced feeding rate (see section 7.4 ) and reduced rate of progeny production ( Sze et al., 2000 ). Genetic analysi...
...., 2004 ; Sawin et al., 2000 ). Serotonin modulates pumping rate. tph-1 mutant animals display reduced pumping rate while animals exposed to excess serotonin or imipramine, a ...
...tors alters fat deposits without adversely affecting growth rate or viability ( Ashrafi et al., 2003 ). Mammalian counterpar...
... pump in the presence and absence of food; however, pumping rate is modulated by food availability ( Avery and Horvitz, 1990...
Reverse genetics [HTML]
...lusions from a negative RNAi experiment; the false negative rate is about 30% over all genes, and varies depending on the ti...
...ckground, plate configuration, etc) to find the highest hit rate and fastest screening time. Carrying out these controls wil...
Reverse genetics : 5. RNAi feeding on agar plates
...ng bleached embryos directly onto feeding plates instead of hatching them into starved L1s first is not recommended because it i...
...imals/well due to embryos sticking together. Also, variable hatching rates between bleached preparations will cause inter-experi...
Reverse genetics : 7. Construction and screening of deletion mutant libraries to generate C. elegans gene knockouts
...en.lab.nig.ac.jp/c.elegans/ index.jsp . 7.1.3. Success rate of the strategy A key feature of these protocols is that th...
... the library can easily be increased to improve the success rate and average number of alleles obtained per gene. At Yale we...
...rocedure have been varied to improve efficiency and success rate. Thus, these methods differ from those of others in a numbe...
...iner. 7.2.3.2.1. Special cooler for freezing worms The rate at which worms cool during freezing is critical for their v...
Introduction to nematode evolution and ecology [HTML]
... data (taxa or sequences) which show a significantly higher rate in nematodes than in other taxa. In the relative-rate test, the distance (amount of change, corrected for superim...
...g to nematodes could be long for different reasons: (1) the rate of nucleotide change is higher in nematodes than in other t...
...ue after all), or (3) both (i.e., Coelomata is true and the rate is higher in nematodes). One legitimate method for testing ...
...od for testing for significant LBA is to conduct a relative-rate test; one can then discard data (taxa or sequences) which s...
Gene duplications and genetic redundancy in C. elegans [HTML]
...n either Drosophila or yeast. It has been proposed that the rate of duplication of a gene is of the same order of magnitude ...
...lication of a gene is of the same order of magnitude as the rate of mutation per nucleotide site, emphasising the enormous p...
Gene duplications and genetic redundancy in C. elegans: 1. Gene duplications and genetic redundancy
... segments of the autosomal arms ( Rubin et al., 2000 ). The rate of origin of gene duplicates in C. elegans over the past fe...
...Conery, 2000 ). Lynch and Conery (2000 ) propose a per-gene rate of duplication of 0.02 per million years for C. elegans , c...
... of 0.02 per million years for C. elegans , compared with a rate of 0.002 duplications per gene per million years in Drosoph...
...ed exactly the same figure for C. elegans , compared with a rate of only 0.0014 for Drosophila ( Gu, 2003 ). Given the range...
Egg-laying [HTML]
...tract C. elegans hermaphrodites are self-fertile, and their rate and temporal pattern of egg-laying are modulated by diverse...
Egg-laying: 1. A description of egg-laying behavior
...-distributed random variables with different characteristic rate constants ( Zhou et al., 1998 ). Thus, the timing of egg-la...
...gg-laying ( Horvitz et al., 1982 ). Finally, the egg-laying rate in the presence of abundant food is significantly higher th...
...ultiple regulatory mechanisms. The modulation of egg-laying rate by food abundance appears to require the neuropeptides enco...
...2002 ; Fujiwara et al., 2002 ). Mutations in egl-4 slow the rate of egg-laying on food and render animals insensitive to foo...
Egg-laying: 2. Functional roles of egg-laying circuitry components
...ion of the HSNs results in a strong reduction in egg-laying rate, and many egg-laying defective mutants have abnormal HSN de...
...g the HSNs are still capable of modulating their egg-laying rate in response to food abundance, suggesting that humoral or o...
...accumulute fewer unlaid eggs, suggesting that their overall rate of egg-laying is elevated ( Bany et al., 2003 ). The questi...
Egg-laying: 3. Perspectives
...ture investigation is how sensory information modulates the rate of egg-laying. The structure of the C. elegans nervous syst...
Heterotrimeric G proteins in C. elegans [HTML]
...ith G βγ and receptor to terminate signaling. The rate of G protein activation can be enhanced by the guanine-nucl...
...y the guanine-nucleotide exchange factor, RIC-8 , while the rate of GTP hydrolysis can be enhanced by RGS proteins such as E...
Heterotrimeric G proteins in C. elegans : 1. Introduction
... subunit ( Tall et al., 2003 ; Reynolds et al., 2005 ). The rate of GTP hydrolysis can be enhanced by RGS proteins (regulato...
..., 2003 ). GSA-1 and EGL-30 are required for viability after hatching ( Brundage et al., 1996 ; Korswagen et al, 1997 ). GSA-1 , ...
Heterotrimeric G proteins in C. elegans : 2. Gαs
... gametogenesis, hermaphrodite genital morphogenesis, growth rate and morphogenesis of the epithelium, as determined in large...
...n ( Moorman and Plasterk, 2002 ). For growth and locomotion rate, ACY-1 appears to be the major effector of GSA-1 since null...
Heterotrimeric G proteins in C. elegans : 5. Gαo
...en definitively identified, GOA-1 likely affects locomotion rate by negatively regulating the acetylcholine release pathway ...
...alat et al., 1995 ). Exogenous serotonin reduces locomotion rate by reducing acetylcholine release at neuromuscular junction...
Biogenic amine neurotransmitters in C. elegans [HTML]
...codes a tyrosine hydroxylase responsible for catalyzing the rate-limiting step in the synthesis of dopamine (see Figure 1 ; ...
...behavior. Well-fed, wild-type animals slow their locomotion rate when they encounter a bacterial lawn and this “basal ...
... either backing or by accelerating their forward locomotion rate ( Rose and Rankin, 2001 ). Upon repeated tapping of the pla...
...dopamine in response to a bacterial lawn to slow locomotion rate. The slowing defect of dop-3 mutants is rescued by mutation...
Biogenic amine neurotransmitters in C. elegans : 5. Serotonin
...otion behavior. Food-deprived animals slow their locomotion rate dramatically when they encounter a bacterial lawn and this ...
...whereas well-fed animals often simply slow their locomotion rate. Serotonin signaling thus provides a mechanism to ensure th...
Hermaphrodite cell-fate specification [HTML]
...image. Figure 4. Male and hermaphrodite L1 larvae. At hatching, male and hermaphrodite larvae are anatomically identical a...
Hermaphrodite cell-fate specification : 4. Epidermal cell fates
...s and the male sensory rays from the lateral hypodermis. At hatching, there are 85 hypodermal nuclei that are derived from only ...
...ated by divisions of the H , V and T cells ( Figure 7 ). At hatching, there are eight seam cells along the each side of the anim...
...ates ( Zhao et al., 2002 ). 4.2. Ventral hypodermis At hatching, the nuclei of six ventrolateral P cells lie along each sid...
...ay to the right side of the embryo, where it is found after hatching ( Figure 1 ; Sulston et al., 1983 ). In hermaphrodites, the...
Nomarski images for learning the anatomy, with tips for mosaic analysis [HTML]
...ally likely when using extrachromosomal arrays, even if the rate of loss is within what is generally accepted as suitable fo...
Nomarski images for learning the anatomy, with tips for mosaic analysis : 2. The tutorial
... Although the B cells of the sexes are indistinguishable at hatching, the B cell of a male becomes much more prominent during th...
...egion, and the gonad of either sex dramatically grows after hatching to take up a large volume of the region. In hermaphrodites,...
...f the hyp7 syncytium, but it did not start out that way. At hatching, the 12 P cells, the progenitors of the Pn.p nuclei, are no...
Germline chromatin [HTML]
...t disappears, H3methK4 remains absent from PGCs until after hatching, and even then does not return if the embryos hatch into a ...
...portant cells, and continued absence from PGC birth through hatching requires the Nanos orthologues NOS-1 and NOS-2 . Both the a...
Germline chromatin : 5. Completing the cycle: the zygote
...fluences the stability of the imprint in the offspring. The rate of disappearance of the imprint could theoretically be dete...
...nce of the imprint could theoretically be determined by its rate of replacement by S-phase histone H3, which is a suitable s...
Karyotype, ploidy, and gene dosage [HTML]
...ustering results from long-range variation in recombination rate, with a metric (ratio of physical distance to genetic dista...
Karyotype, ploidy, and gene dosage: 4. Tetraploids, triploids and haploids
...ids). Tetraploid egg viability was lower, with 87 % of eggs hatching compared to > 99 % for diploids. Triploids were also gen...
...bryonic inviability in their broods, with only 15 % of eggs hatching, which presumably results from the production of many aneup...
Karyotype, ploidy, and gene dosage: 5. Aneuploids
... hermaphrodites with a dumpy body morphology, slower growth rate and lower fertility than normal 2A;2X hermaphrodites ( Hodg...
Acetylcholine [HTML]
..., 2001 ). 4.3. Sources of choline If choline is indeed rate-limiting for acetylcholine synthesis under some circumstanc...
Acetylcholine : 9. ACh-mediated behaviors
...in the regulation of the oscillator circuit controlling the rate of wave initiation: in addition to their uncoordinated move...
....e., cha-1 and unc-17 ) mutants have a dramatically reduced rate of wave initiation. 9.2. Egg laying Egg laying behavio...
...scle (via the EAT-2 receptor) to control pharyngeal pumping rate ( McKay et al., 2004 ). Wild-type animals pump >250/min;...
...nts ( Rand and Russell, 1984 ) are related to their reduced rate of pharyngeal pumping. In addition, a number of other ACh r...
Germline survival and apoptosis [HTML]
...ber of apoptotic cells will be influenced by changes in the rate of corpse engulfment. When analyzing germ cell apoptosis, i...
...ell corpse formation and removal directly. In addition, the rate at which corpses are generated is theoretically determined ...
...obability that oogenic germ cells will die, but also by the rate at which germ cells are produced. It is therefore important...
...ll number, analysis of the mitotic index or determining the rate of egg laying ( Gartner et al., 2004 ; Methods in cell biol...
Germline survival and apoptosis : 6. cep-1 (p53/p63) and the regulation of DNA damage-induced germ cell apoptosis
...e to radiation, and showed the highest spontaneous mutation rate. In contrast, clk-2 alleles are less sensitive to ionizing ...
Mitochondrial genetics [HTML]
...mains an important challenge. The C. elegans mtDNA mutation rate has been estimated using a series of mutation accumulation ...
...letion mutations were detected, corresponding to a measured rate approximately 100-fold higher than previous indirect estima...
...election may occur in a natural context. The mtDNA mutation rate can be increased by environmental agents or by mutation of ...
Mitochondrial genetics: 9. mtDNA and aging
... Mitochondrial functions influence and possibly control the rate of aging ( Dillin et al., 2002 ) and conversely, aging affe...
...hosphate:tRNA transferase (gro-1( e2400 ) , abnormal growth rate), produces a Clk (biological clock abnormal) phenotype char...
Genetic balancers [HTML]
...7 progeny). Brood size in heterozygotes ~200, with 100% egg hatching. Handling: Easy to manipulate. Heterozygous male stocks mat...
...es). Growth characteristics: Homozygous inviable. ~100% egg hatching, but 25% arrest. Handling: Easy to manipulate. Males carryi...
...mnC1[ dpy-10 unc-52 ]; mnDpx ). Growth characteristics: Egg hatching nearly 100%. About 20% of these arrest development as early...
Male development [HTML]
...t some essential male cell fates are already established at hatching 4. Multiple pattern formation mechanisms specify cell fates...
...t some essential male cell fates are already established at hatching. The male mating structures arise from three important sets...
Male development: 3. Male and hermaphrodite embryogenesis are similar but some essential male cell fates are already established at hatching
...t some essential male cell fates are already established at hatching Male and hermaphrodite embryos generate the same set of cel...
Germline proliferation and its control [HTML]
...ng embryogenesis, and only begin active proliferation after hatching. Continued germline mitoses take place in a somatic gonadal...
... cell (PGC), which divides once during embryogenesis. After hatching, the two PGCs begin their post-embryonic divisions to gener...
Germline proliferation and its control: 2. Course of germline proliferation
... called Z2 and Z3 , which do not divide further until after hatching ( Sulston et al., 1983 ). About halfway through the first l...
Epidermal morphogenesis [HTML]
...und in the Cell biology section of WormBook. At the time of hatching, the C. elegans epidermis is almost entirely composed of sy...
Epidermal morphogenesis : 3. Movements of ventral neuroblasts
... the posterior cleft and progress towards the anterior. The rate and timing of individual neuroblast movements have not been...
Epidermal morphogenesis : 6. Embryonic elongation
...56; m/hour until ~600 minutes ( McKeown et al., 1998 ). The rate of elongation is highly reproducible and late C. elegans em...
.... In such mutants elongation appears to proceed at a normal rate until the two-fold stage when it ceases. The mechanism by w...
Methods in cell biology [HTML]
...imizing the specimen geometry to maximize the heat transfer rate with the coolant used. Increasing the heat transfer rate is often best achieved by minimizing the size of the specim...
...y because the higher water content does affect the freezing rate. Place the flat side of a second Type B holder (300 m) on t...
...lowing protocol for conventional EM: Stage Temp. or warming rate Duration (hrs) Total time (hrs) T1 − 90° C 72 72 ...
Gene expression changes associated with aging in C. elegans [HTML]
... and function, but most importantly, increase the mortality rate as a function of time” ( Finch, 1990 ). The etiology ...
...proposed to accumulate with age, either due to an increased rate of production, or because of decreased repair or clearance,...
...t source and targets of damage are, or if there is a common rate limiting step for aging in a given organism or tissue. C. e...
Gene expression changes associated with aging in C. elegans : 4. What have we learned?
...metabolic, consistent with biochemical studies of metabolic rate in long-lived strains ( Van Voorhies and Ward, 1999 ). Prot...
Gene expression changes associated with aging in C. elegans [HTML]
... and function, but most importantly, increase the mortality rate as a function of time” ( Finch, 1990 ). The etiology ...
...proposed to accumulate with age, either due to an increased rate of production, or because of decreased repair or clearance,...
...t source and targets of damage are, or if there is a common rate limiting step for aging in a given organism or tissue. C. e...
Gene expression changes associated with aging in C. elegans : 4. What have we learned?
...metabolic, consistent with biochemical studies of metabolic rate in long-lived strains ( Van Voorhies and Ward, 1999 ). Prot...
Sperm motility and MSP [HTML]
...assembly at its base produce a treadmilling motion, and the rate of treadmilling correlates precisely with the rate of crawling ( Roberts and King, 1991 ). Manipulation of the...
Sperm motility and MSP : 6. Reconstituted MSP polymerization system
...omote MSP filament assembly in vitro . The maximum observed rate of fiber growth is similar to the rate of sperm crawling, suggesting that all of the relevant comp...
Evolution of development in nematodes related to C. elegans [HTML]
... ; Sommer and Sternberg, 1994 ). If the gonad is ablated at hatching, a normal vulva forms in the absence of any gonadal tissue....
...induction by the somatic gonad. After ablation of Z(1,4) at hatching, no vulva formation is seen. However, if Z(1,4) and P8.p ar...
Genetic mapping and manipulation: Chapter 1-Introduction and basics [HTML]
... and 20 ° C) is pretty much the only way to control the rate of worm growth and development. Higher temperatures (20 &de...
...ratures (20 ° C to 25 ° C) can further expedite the rate of development but can cause a drop in fertility and poor h...
Genetic mapping and manipulation: Chapter 1-Introduction and basics : 7. Setting up crosses
...our crosses to get a feeling for the normal progression and rate of the process . Otherwise, you could possibly mistake male...
C. elegans network biology: a beginning [HTML]
...e set of full-length cDNAs ( Reboul et al., 2003 ), and the rate of novel sequences identified has reached diminishing retur...
C. elegans network biology: a beginning : 3. Network connections: interactome
...in-protein interactions ( Li et al., 2004 ). The validation rate of the interactome map was estimated at ~70% by retesting l...
C. elegans network biology: a beginning : 4. Network perturbations: phenome
...al., 2004 ; Qiu et al., 2005 ). The actual off-target error rate in vivo will depend on factors such as cooperativity betwee...
Cell-cycle regulation [HTML]
...he S phase marker rnr :: gfp . Thus, cki-1 Kip1 function is rate limiting for S phase entry, particularly in cells that ente...
Cell-cycle regulation: 4. Cell-Cycle regulation in development
...sor cells appear to contain a 2n DNA content at the time of hatching and go through a DNA synthesis phase before initiating mito...
The cuticle [HTML]
...cuticle is synthesized at the end of embryogenesis prior to hatching and then prior to molting at the end of each larval stage. ...
The cuticle : 6. Collagen biosynthetic pathway
... of imino-rich (25% proline and hydroxyproline) collagen is rate-limited by the slow cis-trans proline isomerization, and re...
X-Chromosome dosage compensation [HTML]
...( Plath et al., 2002 ). Male flies double the transcription rate of their single X chromosome ( Meller and Kuroda, 2002 ). H...
...one X chromosome. Male fruit flies double the transcription rate of their single X chromosome. Hermaphrodite worms half the ...
The phylogenetic relationships of Caenorhabditis and other rhabditids [HTML]
... unreliable. Complicating this issue, there is considerable rate heterogeneity among different lineages for some genes (e.g....
...re assumed. A general time-reversible model (accounting for rate heterogeneity across sites with some fraction of invariant ...
Chemosensation in C. elegans [HTML]
...nt of attractant, it pirouettes frequently. By changing the rate of pirouettes, the animal makes long movements in the right...
... suppressed ( Dusenbery, 1980b ; Miller et al., 2005 ). The rate of pirouettes then returned to baseline through rapid adapt...
Pristionchus pacificus genetic protocols [HTML]
...ing the samples inside the box. This ensures a slow constat rate of cooling. Place the box at − 80°C for at least ...
...antage. However, the injection of morpholinos causes a high rate of lethality in the P. pacificus F1 progeny (about 50%).Whe...
Ethanol.pdf [preprint PDF]
...rain isolated in Hawaii) than N2. These differences in the rate of development of acute tolerance were found to be due to ...
...e of npr-1. When these isolates were tested, the relative rate of adaptation to ethanol was predicted in all cases by the...
The biology and genome of Heterorhabditis bacteriophora [HTML]
... bacteria in a pulsatile and staggered manner at an average rate of 1 cell released every 2 minutes. The regurgitation induc...
...released in a pulsatile and staggered manner, at an average rate of 1 release bacter/2 minutes for more than 5 hours. Like m...
Ethanol [HTML]
...train isolated in Hawaii) than N2. These differences in the rate of development of acute tolerance were found to be due to a...
...le of npr-1 . When these isolates were tested, the relative rate of adaptation to ethanol was predicted in all cases by the ...
Synaptic function [HTML]
...ate ( Clark et al., 1997 ). GTP-bound dynamin appears to be rate limiting for endocytosis as increasing the GTP-bound form o...
... RNAi treated worms, supporting the notion that clathrin is rate limiting. Adaptor complexes can remain associated with syna...
Imaging the activity of neurons and muscles [HTML]
...as have a binning feature that lets the user increase frame rate at the expense of resolution. For imaging of activity, this...
... duration of the event, while the slope is a measure of the rate of calcium entry, the biological interpretation of the two ...
Mechanism and regulation of translation in C. elegans [HTML]
...s or RNAs that interact with a subset of mRNAs. The overall rate of protein synthesis as well as the translational efficienc...
Mechanism and regulation of translation in C. elegans : 3. Structural features of mRNA that affect translational efficiency
...other 3'-terminal element, the poly(A) tract, increases the rate of translational initiation in yeast and plants due to the ...
Oscheius tipulae [HTML]
...XO males like C. elegans . The X chromosome non-disjunction rate of the reference strain CEW1 is lower than that of C. elega...
Oscheius tipulae : 6. Developmental biology
...alent in C. elegans , or are at least not found at the same rate. In contrast, Hypoinduced phenotypes have proven difficult ...
Control of oocyte meiotic maturation and fertilization [HTML]
...mpetent sperm defective ( spe ) mutants restores the normal rate of oocyte maturation when sperm are plentiful (~2.5 maturat...
Control of oocyte meiotic maturation and fertilization : 3. Control of ovulation
...ath contractions, which includes an increase in contraction rate and intensity during ovulation, and it induces spermathecal...
Germline genomics [HTML]
...ady state levels of mRNAs; they do not directly address the rate at which a transcript is synthesized or degraded. The C. el...
Germline genomics : 4. Integration of germline functional genomic data
...ession, perhaps because the germ line has a relatively high rate of mRNA production and/or because the germ line is one of t...
Transformation and microinjection [HTML]
...3%) can increase worm adhesion but will also increase their rate of drying out (see below). Injection oil. Series 700 ...
Transformation and microinjection : 4. DNA transformation: Creating repetitive extrachromosomal arrays by microinjection
...enotype or if large genomic fragments are used, the success rate can be lower). All that is needed is a plate of well-fed he...
Isolation of C. elegans and related nematodes [HTML]
...for the embryonic stages, which can only be retrieved after hatching). The number of individuals in the original sample can be m...
Strongyloides spp. [HTML]
...t of the host in faeces either before and, or shortly after hatching depending on the species. Parasitic females are usually con...
Neuropeptides [HTML]
...l., 1984 ). The decision to enter reproductive growth after hatching is dependent on the activity of DAF-2 , an insulin-like rec...
Anthelmintic drugs [HTML]
...anide, 100 μM, had no effect on either embryonation or hatching in Heligmosomoides polygyrus. Therefore the efficacy of thi...
Somatic sex determination [HTML]
...atic gonadal primordium ( Mathies et al., 2004 ), and after hatching, tra-1 and fkh-6 redundantly control gonadal cell prolifera...
Embryological variation during nematode development [HTML]
...s in nematodes is more variable than the final product, the hatching juvenile, would predict. While unexpectedly large genetic d...
The C. elegans pharynx: a model for organogenesis [HTML]
...ear to secrete vesicles through these processes just before hatching, at each larval molt and during feeding. The nature of the ...
Introduction to the germ line [HTML]
...L3: germline proliferation, survival and differentiation At hatching, the gonad comprises the primordial germ cells ( Z2 and Z3 ...
Pristionchus pacificus genomics: from genetics to genome sequence [HTML]
... including C. elegans . However, we observe a divergence in hatching time with respect to the molt between these species, sugges...
Genomics and biology of the nematode Caenorhabditis briggsae [HTML]
...s since the split between C. briggsae and C. elegans . This rate is dramatically higher than that of mouse and human, which ...
Profiling C. elegans gene expression with DNA microarrays [HTML]
...umber of specifically expressed genes with a relatively low rate of false positives. Drawbacks, however, include the technic...
Spermatogenesis [HTML]
...evident. The ife-1 gene is not shown, but it slows down the rate of spermatogenesis and also affects spermatozoa. The next t...
The sensory cilia of Caenorhabditis elegans [HTML]
...∼ 1.3 μm s -1 ) to give rise to the intermediate rate of motor-IFT-particle transport observed ( ∼ 0.7 _...
SNPs: Introduction and two-point mapping [HTML]
...iability. On average the database contains a false positive rate of ∼ 5%. Also very useful is the “sequence̶...
Translational control of maternal RNAs [HTML]
...re for post-initiation repression, which bypasses the often rate-limiting step of translation initiation. 2.2. Control ...
Asymmetric cell division and axis formation in the embryo [HTML]
... The founder cells each display a characteristic cell cycle rate and lineage: The AB lineage produces hypodermis, neurons, a...
Genomic overview of protein kinases [HTML]
...nase pseudogenes are from these families, indicating a high rate of gene turnover. A similar expansion is seen in C. briggsa...
Essential genes [HTML]
...l and sterile RNAi phenotypes adjusted for a false negative rate of 22% and 86% genome coverage; Kamath et al., 2003 ) Scree...
Overview of gene structure [HTML]
...o not overlap existing WormBase genes and an RT-PCR success rate of 55% confirms a subset of the novel genes ( Wei et al., 2...
LIN-12/Notch signaling in C. elegans [HTML]
...evelopment and disease have been identified at a prodigious rate ( Gridley, 2003 ; Harper et al., 2003 ; Hansson et al., 200...
C. elegans and volatile anesthetics [HTML]
...are resistant to volatile anesthetics and have an increased rate of complex I dependent oxidative phosphorylation (Morgan an...
Transposons in C. elegans [HTML]
...sposons and the regions of higher chromosomal recombination rate ( Duret et al., 2000 ; Rizzon et al., 2003 ). Whether these...
Ubiquitin-mediated pathways in C. elegans [HTML]
...UbcD10; Ubc84D UBE2L1; UBE2L3/ UBCH7; UBE2L6 reduced growth rate and brood size (mut) Fay et al., 2003 ubc-19 ? - - - unheal...
Transgenic solutions for the germline [HTML]
... to specific stages ( Merritt et al., 2008 ). Note that the rate of H2B turnover during germline development is not known an...
Immunohistochemistry [HTML]
...g drops of 20 mM glutaraldehyde (TOXIC). Add the drops at a rate of 100 ul per 5 minutes until up to 1 ml of glutaraldehyde ...
Electrophysiological recordings from the pharynx [HTML]
...t al., 1995 ) and provide information on parameters such as rate of pharyngeal pumping, duration of each pump (i.e. time bet...
Biology and genome of Trichinella spiralis [HTML]
...T. spiralis SL1-based library produced a much lower passing rate than other species. This can imply that either the SL1 sequ...
Reporter gene fusions [HTML]
...ans experiments suggests that GFP S65T matures at a similar rate in the worm, as do CFP and YFP variants. The red fluorescen...
Heterologous expression of C. elegans ion channels in Xenopus oocytes [HTML]
... then filtered (filtering frequency depends on the sampling rate, see the "Axon Guide" for more information) and recorded us...
Genetic mapping and manipulation: Chapter 3-Three-point mapping with genetic markers [HTML]
...to pick more worms than is anticipated to be necessary. The rate-limiting step for all genetics is growth of the animals, an...
The sensory cilia of Caenorhabditis elegans [HTML]
...∼ 1.3 μm s -1 ) to give rise to the intermediate rate of motor-IFT-particle transport observed ( ∼ 0.7 _...
Ionotropic glutamate receptors: genetics, behavior and electrophysiology [HTML]
...Interestingly, mechanical stimulation of the tail slows the rate of pharyngeal pumping in adult worms; and mutations in both...
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