Bennett MD et al. (2003) Ann Bot "Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb."

Johnston JS, Bennett MD, Leitch IJ, Price HJ

[Ann Bot, 2003]

Recent genome sequencing papers have given genome sizes of 180 Mb for Drosophila melanogaster Iso-1 and 125 Mb for Arabidopsis thaliana Columbia. The former agrees with early cytochemical estimates, but numerous cytometric estimates of around 170 Mb imply that a genome size of 125 Mb for arabidopsis is an underestimate. In this study, nuclei of species pairs were compared directly using flow cytometry. Co-run Columbia and Iso-1 female gave a 2C peak for arabidopsis only approx. 15% below that for drosophila, and 16C endopolyploid Columbia nuclei had approx. 15% more DNA than 2C chicken nuclei (with gtoreq2280 Mb). Caenorhabditis elegans Bristol N2 (genome size approx. 100 Mb) co-run with Columbia or Iso-1 gave a 2C peak for drosophila approx. 75% above that for 2C C. elegans, and a 2C peak for arabidopsis approx. 57% above that for C. elegans. This confirms that 1C in drosophila is approx. 175 Mb and, combined with other evidence, leads us to conclude that the genome size of arabidopsis is not approx. 125 Mb, but probably approx. 157 Mb. It is likely that the discrepancy represents extra repeated sequences in unsequenced gaps in heterochromatic regions. Complete sequencing of the arabidopsis genome until no gaps remain at telomeres, nucleolar organizing regions or centromeres is still needed to provide the first precise angiosperm C-value as a benchmark calibration standard for plant genomes, and to ensure that no genes have been missed in arabidopsis, especially in centromeric regions, which are clearly larger than once imagined.

Waterston RH et al. (1995) Proc Natl Acad Sci U S A "The genome of Caenorhabditis elegans."

Waterston RH, Sulston JE

[Proc Natl Acad Sci U S A, 1995]

The physical map of the 100-Mb Caenorhabditis elegans genome consists of 17,500 cosmids and 3500 yeast artificial chromosomes (YACs). A total of 22.5 Mb has been sequenced, with the remainder expected by 1998. A further 15.5 Mb of unfinished sequence is freely available online: because the areas sequenced so far are relatively gene rich, about half the 13,000 genes can now be scanned. More than a quarter of the genes are represented by expressed sequence tags (ESTs), All information pertaining to the genome is publicly available in the ACeDB data base.

Marimuthu M et al. (2018) ACS Appl Mater Interfaces "Methylene Blue-Fortified Molybdenum Trioxide Nanoparticles: Harnessing Radical Scavenging Property."

Marimuthu M, Mariya Salomi L, Praveen Kumar B, Veerapandian M, Balamurugan K

[ACS Appl Mater Interfaces, 2018]

Hybrid nanosystem with impeccable cellular imaging and antioxidant functionality is demonstrated. The microwave-irradiation derived molybdenum trioxide nanoparticles (MoO3 NPs) were surface functionalized with cationic dye molecule, methylene blue (MB), which enables superior UV-visible absorbance and fluorescence emission wavelengths potential for bioimaging. Radical scavenging property of the pristine MoO3 NPs and MoO3-MB NPs were studied in vivo using Caenorhabditis elegans as model system. Heat shock induced oxidative stress in the C. elegans was significantly resolved by the MoO3-MB NPs, in agreement with in vitro radical scavenging study by electron paramagnetic resonance spectroscopy. Hybrid nanostructures of MoO3-MB demonstrate synergistic benefits in the intracellular imaging with intrinsic biocompatibility and antioxidant behavior, which can facilitate application as advanced healthcare materials toward bioimaging and clinical therapeutics.

Brenner S et al. (1993) Nature "Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome."

Macrae A, Venkatesh B, Elgar G, Aparicio S, Sandford R, Brenner S

[Nature, 1993]

Cloning and sequencing techniques now allow us to characterize genes directly instead of having to deduce their properties from their effects. This new genetics reaches its apotheosis in the plan to obtain the complete DNA sequence of the human genome, but this is far beyond the capacity of present sequencing methods. Small 'model' genomes, 'such as those of Escherichia coli (4.7 megabases (Mb) and yeast (14 Mb), or even those of Caenorhabditis elegans (100 Mb) and Drosophila (165 Mb), are better scaled to existing technology. The yeast genome will contain genes with functions common to all eukaryotic cells, and those of simple multicellular organisms may throw light on the genetic specification of more complex functions. However, vertebrates differ in their morphology and development, so the ideal model would be a vertebrate genome of minimum size and complexity but with maximum homology to the human genome. Here we report the characterization of the small genome (400 Mb) of the tetraodontoid fish, Fugu rubripes. A random sequencing approach supported by gene probing shows that the haploid genome contains 400 Mb of DNA, of which more that 90% is unique. This genome is 7.5 times smaller than the human genome and because it has a similar gene repertoire it is the best model genome for the discovery of human genes.

Yaniv SP et al. (2012) Curr Biol "Axon regrowth during development and regeneration following injury share molecular mechanisms."

Issman-Zecharya N, Podbilewicz B, Yaniv SP, Schuldiner O, Oren-Suissa M

[Curr Biol, 2012]

BACKGROUND: The molecular mechanisms that determine axonal growth potential are poorly understood. Intrinsic growth potential decreases with age, and thus one strategy to identify molecular pathways controlling intrinsic growth potential is by studying developing young neurons. The programmed and stereotypic remodeling of Drosophila mushroom body (MB) neurons during metamorphosis offers a unique opportunity to uncover such mechanisms. Despite emerging insights into MB -neuron axon pruning, nothing is known about the ensuing axon re-extension. RESULTS: Using mosaic loss of function, we found that the nuclear receptor UNF (Nr2e3) is cell autonomously required for the re-extension of MB -axons following pruning, but not for the initial growth or guidance of any MB neuron type. We found that UNF promotes this process of developmental axon regrowth via the TOR pathway as well as a late axon guidance program via an unknown mechanism. We have thus uncovered a novel developmental program of axon regrowth that is cell autonomously regulated by the UNF nuclear receptor and the TOR pathway. CONCLUSIONS: Our results suggest that UNF activates neuronal re-extension during development. Taken together, we show that axon growth during developmental remodeling is mechanistically distinct from initial axon outgrowth. Due to the involvement of the TOR pathway in axon regeneration following injury, our results also suggests that developmental regrowth shares common molecular mechanisms with regeneration following injury.

Coulson AR (1996) Biochem Soc Trans "The Caenorhabditis elegans genome project. C. elegans Genome Consortium."

Coulson AR

[Biochem Soc Trans, 1996]

A number of projects are underway that have as their goal the complete analysis and understanding of the genomes of a variety of organisms. The most advanced of these (as of mid-1995) for a multicellular organism is the Caenorhabditis elegans genome project. To date, 20 Mb of the 100 Mb genome has been fully sequenced, and completion is expected in 1998. In addition to providing an invaluable resource for the C. elegans community, and beyond, experience gained from mapping and sequencing of this genome has led to the formulation of a scheme that could produce a coherent, near-complete 'sequence map' of the human genome in a 5 year period.

Sallam AA et al. (2013) Eur J Med Chem "Indole diterpene alkaloids as novel inhibitors of the Wnt/-catenin pathway in breast cancer cells."

El Sayed KA, Sallam AA, Meyer SA, Foudah AI, Gissendanner CR, Ayoub NM

[Eur J Med Chem, 2013]

Penitrems are indole diterpene alkaloids best known for their BK channel inhibition and tremorgenic effects in mammals. In a previous study, penitrems A-F (1-5), their biosynthetic precursors, paspaline (6) and emindole SB (7), and two brominated penitrem analogs 8 and 9 demonstrated promising in vitro antiproliferative, antimigratory, and anti-invasive effects in the MTT (MCF-7 and MDA-MB-231), wound-healing, and Cultrex BME cell invasion (MDA-MB-231) assays, respectively. The study herein reports the novel ability of penitrem A to suppress total -catenin levels in MDA-MB-231 mammary cancer cells. Nine new penitrem analogs (10-18) were semisynthetically prepared, in an attempt to identify pharmacophores correlated with BK channel inhibition and tremorgenicity of penitrems and decrease their toxicity. The degree of BK channel inhibition was assessed using the nematode Caenorhabditis elegans, and in vivo tremorgenic EC was calculated using CD-1 male mice following an Up-and-Down Procedure (UDP). Although new analogs were generally less active than parent compound 1, some showed no BK channel inhibition or tremorgenicity and retained the ability of penitrem A (1) to suppress total -catenin levels in MDA-MB-231 cells. Paspaline (6) and emindole SB (7), both lacking BK channel inhibition and tremorgenicity, represent the simplest indole diterpene skeleton that retains the antiproliferative, antimigratory and total -catenin suppressing effects shown by the more complex penitrem A (1).

Korhonen PK et al. (2019) Gigascience "Common Workflow Language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data."

Young ND, Korhonen PK, Hall RS, Gasser RB

[Gigascience, 2019]

BACKGROUND: Here, we created an automated pipeline for the de novo-assembly of genomes from PacBio long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (100 Mb), Drosophila melanogaster (138 Mb) and Plasmodium falciparum (23 Mb) directly from publicly accessible nucleotide sequence data sets, and assessed the quality of the assemblies against curated reference genomes. BACKGROUND: We showed a dependency of the accuracy of assembly on sequencing technology and GC content, and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses. CONCLUSIONS: This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse data sets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes.

Ghedin E et al. (2007) Science "Draft genome of the filarial nematode parasite Brugia malayi."

Wortman JR, Lustigman S, Spiro D, Tallon L, Li W, Barton GJ, Salzberg SL, Jin J, Parkinson J, White O, Feldblyum T, Pertea M, Shumway M, Miranda-Saavedra D, Kumar S, Ma D, Wang S, McCarter JP, Williams SA, Fraser-Liggett C, Slatko B, Haas B, Johnson NM, Estes CF, Koo H, Poole C, Nutman TB, Crabtree J, Sluder AE, Unnasch TR, Zhao Q, Wei AD, Foster JM, Williams DJ, Mitreva M, Schatz M, Ghedin E, McReynolds L, Schobel S, Amedeo P, Maina CV, Stanke M, Saunders L, Peregrin-Alvarez JM, Caler E, Smith K, Laney S, Guiliano DB, Komuniecki R, Allen JE, Weil G, Dimmic MW, Delcher AL, Angiuoli SV, Blaxter ML, Lindblom TH, Creasy T, El-Sayed NM, Scott AL, Ren Q, Zhang Y, Pop M, Ganatra M, Li BW, Daub J, Korf I, Gregory WF, Crawford MJ, Martin DM, Carlow CK, Ware J

[Science, 2007]

Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the approximately 90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict approximately 11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during approximately 350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.

Whitton C et al. (2004) Mol Biochem Parasitol "A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics."

Daub J, Blaxter M, Quail M, Ganatra M, Hall N, Ware J, Whitton C, Slatko B, Foster J, Barrell B

[Mol Biochem Parasitol, 2004]

Comparative nematode genomics has thus far been largely constrained to the genus Caenorhabditis, but a huge diversity of other nematode species, and genomes, exist. The Brugia malayi genome is approximately 100 Mb in size, and distributed across five chromosome pairs. Previous genomic investigations have included definition of major repeat classes and sequencing of selected genes. We have generated over 18,000 sequences from the ends of large-insert clones from bacterial artificial chromosome libraries. These end sequences, totalling over 10 Mb of sequence, contain just under 8 Mb of unique sequence. We identified the known Mbo I and Hha I repeat families in the sequence data, and also identified several new repeats based on their abundance. Genomic copies of 17% of B. malayi genes defined by expressed sequence tags have been identified. Nearly one quarter of end sequences can encode peptides with significant similarity to protein sequences in the public databases, and we estimate that we have identified more than 2700 new B. malayi genes. Importantly, 459 end sequences had homologues in other organisms, but lacked a match in the completely sequenced genomes of Caenorhabditis briggsae and Caenorhabditis elegans, emphasising the role of gene loss in genome evolution. B. malayi is estimated to have over 18,500 protein-coding genes.