Difference between revisions of "Worm numbers"
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Here is a summary table of interesting numbers pertaining to ''C. elegans'': | Here is a summary table of interesting numbers pertaining to ''C. elegans'': | ||
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− | + | '''Worm Volumes''' | |
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+ | |30 - 50 picoliters = 30,000 - 50,000 cubic microns = (3*10^-5)-(5*10^-5) cubic millimeters | ||
==Worm Volume== | ==Worm Volume== |
Revision as of 17:48, 13 July 2012
This page is intended to become a collection ground for useful and interesting numbers about C. elegans biology. These numbers include things such as the average volume and mass (calculated estimates) of an adult hermaphrodite, larval stage, or embryo. Some of these numbers are well established facts whereas others are estimations, with a description of the method for calculating or estimating provided.
The Numbers
Here is a summary table of interesting numbers pertaining to C. elegans:
The Genome
Size of genome: | 100,272,276 bp |
%GC Content: | 35% |
Number of GC base pairs: | 35,537,772 |
%AT Content: | 65% |
Number of AT base pairs: | 64,734,504 |
Mass of a haploid genome: | 103 femtograms (1.03 * 10^-13 grams) |
Volume of a haploid genome: | 0.1 cubic microns = 0.1 femtoliters = 100 attoliters |
Worm Volumes
Volume of an embryo: | 30 - 50 picoliters = 30,000 - 50,000 cubic microns = (3*10^-5)-(5*10^-5) cubic millimeters
Worm VolumeBased on these images from Worm Atlas (www.wormatlas.org):
Volume of a single L1 larva = ~80 picoliters = ~0.000080 cubic millimeters = ~80,000 cubic microns Volume of a single L2 larva = ~135 picoliters = ~0.000135 cubic millimeters = ~135,000 cubic microns Volume of a single L3 larva = ~300 picoliters = ~0.0003 cubic millimeters = ~300,000 cubic microns Volume of a single L4 larva = ~800 picoliters = ~0.0008 cubic millimeters = ~800,000 cubic microns Volume of a single Adult hermaphrodite = ~2.2 nanoliters = ~0.0022 cubic millimeters = ~2,200,000 cubic microns
L1: 50,000 - 200,000 cubic microns L2: 200,000 - 400,000 cubic microns L3: 500,000 - 900,000 cubic microns L4: 900,000 - 2,000,000 cubic microns Hence, the calculations above appear to be roughly lower limits on the size of each stage. Worm MassAssuming the worm has a density close to that of water (1 gram per milliliter) these are estimates of mass: Mass of a single Embryo = ~35 nanograms Mass of a single L1 larva = ~80 nanograms Mass of a single L2 larva = ~135 nanograms Mass of a single L3 larva = ~300 nanograms Mass of a single L4 larva = ~800 nanograms Mass of a single Adult hermaphrodite = ~2.2 micrograms
Dry weight of a single Embryo = ~11 nanograms Dry weight of a single L1 larva = ~24 nanograms Dry weight of a single L2 larva = ~41 nanograms Dry weight of a single L3 larva = ~90 nanograms Dry weight of a single L4 larva = ~240 nanograms Dry weight of a single Adult hermaphrodite = ~660 nanograms
Protein mass of a single Embryo = ~5.3 nanograms Protein mass of a single L1 larva = ~12 nanograms Protein mass of a single L2 larva = ~20.3 nanograms Protein mass of a single L3 larva = ~45 nanograms Protein mass of a single L4 larva = ~120 nanograms Protein mass of a single Adult hermaphrodite = ~330 nanograms
RNA mass of a single Embryo = ~350 picograms RNA mass of a single L1 larva = ~800 picograms RNA mass of a single L2 larva = ~1.35 nanograms RNA mass of a single L3 larva = ~3 nanograms RNA mass of a single L4 larva = ~8 nanograms RNA mass of a single Adult hermaphrodite = ~22 nanograms
mRNA mass of a single Embryo = ~10.5 picograms mRNA mass of a single L1 larva = ~24 picograms mRNA mass of a single L2 larva = ~40.5 picograms mRNA mass of a single L3 larva = ~90 picograms mRNA mass of a single L4 larva = ~240 picograms mRNA mass of a single Adult hermaphrodite = ~660 picograms
AMP = 347.2 grams per mole in polymer form (i.e. minus one water molecule, 18 grams per mole): AMP = 329.2 grams per mole Average mass of polymer-NMP = 321.5 grams per mole
Number of polymer NMPs of a single Embryo = ~20 billion Number of polymer NMPs of a single L1 larva = ~45 billion Number of polymer NMPs of a single L2 larva = ~76 billion Number of polymer NMPs of a single L3 larva = ~170 billion Number of polymer NMPs of a single L4 larva = ~450 billion Number of polymer NMPs of a single Adult hermaphrodite = ~1,236 billion
Number of mRNAs of a single Embryo = ~20 million Number of mRNAs NMPs of a single L1 larva = ~45 million Number of mRNAs NMPs of a single L2 larva = ~76 million Number of mRNAs NMPs of a single L3 larva = ~170 million Number of mRNAs NMPs of a single L4 larva = ~450 million Number of mRNAs NMPs of a single Adult hermaphrodite = ~1,236 million DNA NumbersFrom the WS231 release notes of WormBase, the C. elegans genome has the following number of bases: A 32,367,418 Total 100,272,276 This means that there are 35,537,772 GC base pairs (35.4% of the genome) and 64,734,504 AT base pairs (64.6% of the genome). Genome VolumeKnowing that a single complete turn of DNA is approximately 3.4 nanometers in length (34 Ångstroms), 2 nanometers in width (20 Ångstroms), and is about 10 base pairs (bp)(and therefore 1 base pair is .34 nanometers long (3.4 Ångstroms)), we can deduce the volume of a single base pair of DNA to be roughly 1 cubic nanometer (1 nm^3): Assuming a base pair is like a short cylinder with volume: Volume = (pi)*(radius)^2*(height) Volume = (~3.14)*(~1nm)^2*(~.34nm) Volume of 1 base pair = ~1 cubic nanometer Therefore: No. of bp -> Volume 1bp -> 1 cubic nanometer So, a single haploid genome of C. elegans (~100Mb) would be approximately 0.1 cubic microns and a diploid genome approximately 0.2 cubic microns. Volume of sphere = (4/3)*(pi)*(radius)^3 Haploid genome radius = ~0.29 microns Diploid genome radius = ~0.36 microns That is the smallest sphere that the haploid and diploid genomes, respectively, could pack into. We are, of course, ignoring proteins, RNA molecules, and any other small molecules, so the cell nuclei must be significantly larger. For polyploid nuclei, like those of the intestine, the nuclei must be substantially larger. So, Volume of the adult intestinal (32-ploid) genomes = ~3.2 cubic microns Genome MassMolar mass of dNMPs: dAMP = 331.2 grams per mole in polymer form (i.e. minus one water molecule, 18 grams per mole): dAMP = 313.2 grams per mole Average mass of polymer-dNMP = 308.5 grams per mole An AT base pair = 615.4 grams per mole The C. elegans haploid genome is ~100Mb (100,272,276 bp to be exact) with (as noted above) 35,537,772 GC base pairs and 64,734,504 AT base pairs, hence the total molar mass of the genome is: [AT base pair molar mass]*[No. of AT base pairs] + [CG base pair molar mass]*[No. of CG base pairs] (615.4g/mol)(64,734,504bp) + (618.4g/mol)(35,537,772bp) = 39,837,613,761.6 + 21,976,558,204.8 Molar mass of C. elegans genome = 61,814,171,966.4 grams per mole Mass of C. elegans genome = 61,814,171,966.4 / Avagadro's number (6.022 * 10^23) Mass of C. elegans genome = 103 * 10^-15 grams = 103 femtograms (fg) There are 959 somatic nuclei in a single adult hermaphrodite, and so there are roughly 197.6 picograms (assuming each somatic nuclei is diploid) of somatic genomic DNA that can be isolated from a single adult hermaphrodite, not including sperm, oocytes or other germline nuclei. This also does not account for the fact that some of the 959 somatic nuclei are polyploid, such as intestinal nuclei. A single C. elegans hermaphrodite can give rise to approximately 300 progeny from ~300 oocytes and ~300 sperm, ~150 of each from each gonad arm (see Worm Atlas [4]). As a first order approximation of the number of genomes contributed from the (non-somatic) germline, let's say there are 600 haploid genomes (or 300 diploid genomes) present at any given moment in a mature adult hermaphrodite. These genomes would total to about 61.8 picograms of genomic DNA. Added to the total soma-derived genomic DNA gives us a rough grand total of: Total amount of genomic DNA from a single C. elegans adult hermaphrodite: ~260 picograms Again, this is not accounting for polyploidy in special cases; therefore this number is likely an underestimate. Considering the polyploidy of the intestinal cells (30-34 nuclei each with 32 genomes [5]), (let's assume 32 intestinal nuclei for simplicity) and assuming all other somatic nuclei are diploid, that gives us 937 diploid somatic nuclei and 32 intestinal nuclei at 32-ploid. This gives us an updated estimate of: Total amount of genomic DNA from a single C. elegans adult hermaphrodite: ~360 picograms |