The ape package written by Emmanuel Paradis is the foundation for phylogenetic analyses in R. Yesterday, Paradis and his coauthors posted a new version (3.2) on the CRAN archive yesterday. There don't seem to be too many new functions, but there are some important bug fixes. One these - preventing calculation of negative state probabilities when reconstructing discrete character states - solves one of the more vexing problems I've had with the ace function. You should definitely get the update if you're doing ancestral reconstruction of discretely coded traits! Now we just need to hope the April 17th upgrade to R 2.9 goes smoothly...
According to the school's Information Technology & Communication department, 3,117 freshmen enrolled in 2007, and 3,113 of them owned their own computer. Nearly all of the machines were laptops, with 72 percent running Windows and 26 percent running Mac OS X (six hardy souls ran Linux).
Labels: open source
Sugarcane genes associated with sucrose content.
Papini-Terzi FS, Rocha FR, Vencio RZ, Felix JM, Branco DS, Waclawovsky AJ, Del Bem LE, Lembke CG, Costa MD, Nishiyama MY Jr, Vicentini R, Vincentz MG, Ulian EC, Menossi M, Souza GM.
ABSTRACT: BACKGROUND: Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges. Sugarcane cultivars differ in their capacity to accumulate sucrose and breeding programs routinely perform crosses to identify genotypes able to produce more sucrose. Sucrose content in the mature internodes reach around 20% of the culms dry weight. Genotypes in the populations reflect their genetic program and may display contrasting growth, development, and physiology, all of which affect carbohydrate metabolism. Few studies have profiled gene expression related to sugarcanes sugar content. The identification of signal transduction components and transcription factors that might regulate sugar accumulation is highly desirable if we are to improve this characteristic of sugarcane plants. RESULTS: We have evaluated thirty genotypes that have different Brix (sugar) levels and identified genes differentially expressed in internodes using cDNA microarrays. These genes were compared to existing gene expression data for sugarcane plants subjected to diverse stress and hormone treatments. The comparisons revealed a strong overlap between the drought and sucrose-content datasets and a limited overlap with ABA signaling. Genes associated with sucrose content were extensively validated by qRT-PCR, which highlighted several protein kinases and transcription factors that are likely to be regulators of sucrose accumulation. The data also indicate that aquaporins, as well as lignin biosynthesis and cell wall metabolism genes, are strongly related to sucrose accumulation. Moreover, sucrose-associated genes were shown to be directly responsive to short term sucrose stimuli, confirming their role in sugar-related pathways. CONCLUSION: Gene expression analysis of sugarcane populations contrasting for sucrose content indicated a possible overlap with drought and cell wall metabolism processes and suggested signaling and transcriptional regulators to be used as molecular markers in breeding programs. Transgenic research is necessary to further clarify the role of the genes and define targets useful for sugarcane improvement programs based on transgenic plants.
As more and more data is being poured into the public sequence databases, an increasingly detailed map is being drawn that relates sequences from different individuals or different species, mainly into what has been known in the field as protein or genomic (DNA) alignments. This is what one can call twenty-first century molecular cartography.
All references to molecular evolution this year should be accompanied with an analogy to Darwin's work, so here is how it works in this case: Darwin's next generation machine, the Beagle, went on a journey to accumulate an enormous variety of specimens that, when compared all together, allowed Darwin to draw the first phylogenetic tree.
Contrary to what one would think, alignments with more sequences are easier to resolve than ones with less sequences, at least when the phylogenetic tree relating the sequences increases in detail, which is almost always. And this is allowing researchers to generate genomic alignments for phylogenetically dense groups of genomes while, in parallel, the protein alignments for the corresponding protein coding genes in these genomes are combined together with more distantly related species. This dense taxon sampling is making the distinction between protein alignments and genomic alignments less and less obvious.
As an example, one can use the highly conserved protein coding exons to anchor the points in the different chromosomes that define stretches of conserved synteny among the genomes, and then align these DNA stretches all together with a genomic aligner. At the same time, one can use the exon boundaries defined in the DNA sequences of the coding genes to help infer the right protein alignment at the aminoacidic level.
A new opportunity is now arising in exploiting the information that is contained separately in the genomic and protein alignments to combine them into a single object representing both. New methods are being developed that will exploit the landmarks that both genomic and protein alignments have correctly place to converge into a single intertwined alignment object. This new type of alignment has in a way already been represented in closely related prokaryotic genomes. But prokaryotic genomes are less interesting for some topics, like alternative splicing, repetitive elements or recombination hotspots. Combined genomic and protein alignments will bring new elements of detail together that have been scattered so far for researchers to study and hopefully some new and brilliant mechanistic explanations of the innards of molecular evolution will arise from them, in the same way that Darwin did two centuries ago.
So a deluge of sequencing data is not really a problem but an opportunity.
Labels: light science
Not surprisingly, given the nature of this blog, I'm pretty favourably disposed towards Google's Linux-based Android platform, even though I don't possess the only phone currently using it, T-Mobile's G1.
But it's hard to tell just how well it's doing against the iPhone, say. If any one knows, it's T-Mobile, so I was interested to receive this morning some tantalising tidbits from Richard Warmsley, head of Internet and Entertainment at T-Mobile UK.
Despite being pressed by me, he wouldn't get into specifics (now, there's a surprise) about sales, saying only that they had exceeded expectations. But he did reveal that according to their market research, G1s were selling at 70-80% the rate of iPhones. Even allowing for margins of error and any tendency to talk up such numbers, this suggests a healthy uptake.
Labels: open source
Study leader Dr Mike Modo, from the Institute of Psychiatry at King's College London, said: "This works really well because the stem cell-loaded particles can be injected through a very fine needle and then adopt the precise shape of the cavity.
"In this process the cells fill the cavity and can make connections with other cells, which helps to establish the tissue."
He said over a few days they were able to see cells migrating along the scaffold particles and forming a primitive brain tissue that interacts with the host brain.
Labels: light science
Labels: scientific talk
By re-sequencing a handful of candidate genes from previous genome-wide association studies, University of Cambridge and Roche 454 researchers have identified four rare variants and one common variant in an antiviral gene called IFIH1 that protect against type 1 diabetes or T1D. Since the variants appear to curb the gene's activity, the team proposes that functional IFIH1 may contribute to T1D.
The Atacama desert lies on the western edge of South America, covering much of northern Chile and parts of Argentina. It is the closest one can get to Mars while remaining grounded on Earth. High atop the Socompa volcano on the Eastern edge of the Atacama desert, the atmosphere is thin, the ultraviolet radiation is intense, and the climate is dry. Nevertheless, the improbable has been found: life. Near the rim of the 19,850-foot-high Socompa volcano, researchers from the University of Colorado at Boulder's Alpine Microbial Observatory found a thriving, complex microbial community that appears to be supported by gases emanating from volcanic vents around the rim.
The Atacama desert is the driest place on Earth. Weather stations in the Antofagasta region of Chile average one millimeter of precipitation per year, and a number of weather stations in the Atacama have never recorded rainfall throughout their entire operational life. The extreme climate there is often compared to the surface of Mars. It is believed to be so similar that a Science article, published in 2003, used it in an attempt to re-create the experiments that Viking One and Two performed on the Martian surface. It is also a proving ground for equipment that NASA plans to send to Mars one day. Given the geologic similarities, the discovery of life in such a hostile place suggests that life could exist elsewhere as well.
Labels: light science
So this is actually old-ish news, but I saw this press release about paper published last year describing the ability of the fungus Gliocladium roseum to naturally synthesizes diesel compounds. The paper from Gary Strobel @Montana State and collaborators describes that G. roseum produces volatile hydrocarbon on cellulose media. Extracts from the host plant (Eucryphia cordifolia) were also able to support growth of the fungus alone. This production of products have been dubbed “myco-diesel”. G. roseum is an endophyte of E. cordifolia I wonder what kinds of advantages it might provide for the fungus or the plant to produce these hydrocarbons.
I wonder if it is better to focus on these organisms that have already evolved a way to make these hydrocarbons directly from cellulose rather than the multistep process of making easy to process sugars from different starting plant materials and then ethanol or other hydrocarbons from yeast or bacteria growing on that sugar. Growth rates, amenability to grow in bioreactors, etc certainly are considerations in building production systems, but I wonder whether these kind of finding represent inroads to solving our problems or if they are peripheral to the current bioengineering approaches that are underway.
Some of the earlier press releases I had missed it seems:
* Rainforest fungus makes diesel
* Diesel Fuel From a Tree Fungus?
* Google news
G. A. Strobel, B. Knighton, K. Kluck, Y. Ren, T. Livinghouse, M. Griffin, D. Spakowicz, J. Sears (2008). The production of myco-diesel hydrocarbons and their derivatives by the endophytic fungus Gliocladium roseum (NRRL 50072) Microbiology, 154 (11), 3319-3328 DOI: 10.1099/mic.0.2008/022186-0
Labels: light science
A little detective work traced the problem to default date format conversions and floating-point format conversions in the very useful Excel program package. The date conversions affect at least 30 gene names; the floating-point conversions affect at least 2,000 if Riken identifiers are included. These conversions are irreversible; the original gene names cannot be recovered.
Labels: scientific talk
200409 200412 200501 200502 200503 200504 200505 200506 200507 200508 200509 200510 200511 200512 200601 200602 200603 200604 200605 200606 200607 200608 200609 200610 200611 200612 200701 200702 200703 200704 200705 200707 200708 200709 200710 200711 200712 200801 200802 200803 200804 200805 200806 200807 200808 200809 200810 200811 200812 200901 200902 200903 200904 200905 200906 200907 200908 200909 200912 201001 201002 201003 201004 201007 201009 201011 201102
Subscribe to Posts [Atom]