Synthetic Biology on the Radio

Definitely worth listening to the RadioLab show episode “So-Called Life”. The second act describes some “MIT bioengineering kids” who engineered sweet smelling E.coli. I’m sure some of them interviewed hang out at OWW, like Reshma. The sound effects for gene exchange and “The BioEngineers song” at the end of the 2nd act is definitely worth listening to. Still trying to find a link to the song itsself.

The third act talks with founder of Codon Devices, George Church, and Craig. They describe George “as Santa Clause as played by Clark Gable.”

We salute a show singing the praises of mighty microbes.

New Saccharomyces resequencing assembly

SGRP LogoDavid Carter at the Sanger Centre emailed a message that new assemblies of Saccharomyces strain resequencing project have been posted including a new three-way alignment of S. bayanus-S.paradoxus-S.cerevisiae. This updates the Dec 2007 release.

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Scrambled Genomes

Though less Fungal (and more fungal, if you’ll grant me that) than most of the stories we cover, a recent analysis of the Diplonema papillatum mitochondria genome sequence is interesting nonetheless. The genome consists of over 100 chromosomes, each roughly 6 kilobasepairs (kbp) or 7 kbp in size. However, each chromosome contains only a short (less than 500 bp) gene encoding region. It appears that genes are scrambled, where modular genetic units are dispersed across many chromosomes. Curiously, despite having discontigous genes, cDNA sequencing identifies contiguous and properly ordered mRNA. So just how are scrambled genes expressed and asssembled?

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Comparing development

PZ Meyers has a post summarizing of an older paper from Elliot Meyerowitz (2002) that comapares plant and animal development. In particular there is are some major themes summarized about how plants and animals form patterns and cell to cell signaling as part of development. What’s missing is what we’ve learned about within group comparisons where there are multiple lineages of single-celled and multicelled forms like choanozoa/metazoa (See M. brevicolis genome paper) and green algae (Volvox-Chlamydomonas comparisons are forthcoming, but see Chlamydomonas genome paper).

I hope some of our work will provide more data to include in the comparison of fungal, animal, and plant development in the not too distant future.

Cryptococcus species deliniation

ResearchBlogging.org What delineates species boundaries in fungi? Much work has been done on biological and phylogenetic species concepts in fungi. Some concepts are reviewed in Taylor et al 2006 and in Taylor et al 2000, and applications can be seen in several pathogens such as Paraccocidiodies, Coccidioides, and the model filamentous (non-pathogenic) fungus Neurospora.

A paper in Fungal Genetics and Biology on species definitions in Cryptococcus neoformans from multi-locus sequencing seeks to provide additional treatment of the observed diversity. A large study of 117 Cryptococcus isolates were examined through multi-locus sequencing (6 loci) and identified two monophyletic lineages within C. neoformans varieties that correspond to var. neoformans and var. grubii. However within the C. gattii samples they identified four monophyletic groups consistent with deep divergences observed from whole genome trees for two strains of C. gattii, MLST, and AFLP studies. By first defining species, we can now test whether any of the species groups have different traits including prevalence in clinical settings and in nature.

BOVERS, M., HAGEN, F., KURAMAE, E., BOEKHOUT, T. (2007). Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2007.12.004

Art with Fungi

Ganoderma
I had the pleasure of meeting Phil Ross, a SF area artist, last night at the BABS Darwin Day Celebration. He has been growing fungi in a variety of different ways to make living art in an project called ‘Pure Culture‘. He is using Ganoderma lucidum (a Polyporales fungus, which is being sequenced in Taiwan) grown in molds (plaster, not the other kind of molds) to create some fantastic shapes including a recreation of a photo of a drop of milk splashing as seen to the right.

[Corrected: Brain was not in gear, Ganoderma is not an Agaricales, but a Polyporales basidiomycete fungus.]

Next next-gen sequencing technology

I’m not at AGBT, but Jonathan and Anthony both have coverage of Pacific Biosciences’s new sequencing technology that uses detection of DNA polymerase activity to determine sequence.  I believe some of the details are in the paper “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures“, but I’ve not had a chance to read it.

Phytopathogenic Fungi: what have we learned from genome sequences?

ResearchBlogging.orgA review in Plant Cell from Darren Soanes and colleagues summarizes some of the major findings about evolution of phytopathogenic fungi gleaned from genome sequencing highlighting 12 fungi and 2 oomycetes. By mapping evolution of genes identified as virulence factors as well as genes that appear to have similar patterns of diversification, we can hope to derive some principals about how phytopathogenic fungi have evolved from saprophyte ancestors.

They infer from phylogenies we’ve published (Fitzpatrick et al, James et al) that plant pathogenic capabilities have arisen at least 5 times in the fungi and at least 7 times in the eukaryotes. In addition they use data on gene duplication and loss in the ascomycete fungi (Wapinski et al) to infer there large numbers of losses and gains of genes have occurred in fungal lineages.

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Neurospora speciation through experimental evolution

ResearchBlogging.orgDettman, Anderson, and Kohn recently published a paper in BMC Evolutionary Biology on reproductive experimental evolution in two Neurospora crassa populations evolved under different selective conditions. This is a great study that complements work published last year in Nature on experimental evolution in Saccharomyces cerevisiae populations. Neurospora populations were evolved under high salt and low temperature and were started from either high diversity (interspecific crosses, N. crassa vs N. intermedia) or low diversity (intraspecific cross, two N. crassa isolates D143 (Louisiana, USA)and D69 (Ivory Coast)) as described in Figure 1. The experimentally evolved populations were then tested for asexual and sexual fitness (they were taken through complete meiotic cycle throughout the experiment to avoid insure there was selection on the sexual reproduction pathway.

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