rayna.s – Australian Science

“Do what it takes to solve the problem, and no more”: a small talk with ‘Bunnie’ Huang

rayna.s — Sun, 10 Feb 2013 08:44:37 +0000

As a Free & Open Source Software (FOSS) geek, I was really looking very much forward to anything coming out from the linux.conf.au, better known as LCA. And for a huge bouquet of surprises, this year’s edition was one.

Andrew “bunnie” Huang (@bunniestudios) at LCA2013: “Do what it takes to solve the problem, and no more”. Photo by @kinshasha on Twitter

Along with Radia Perlman and Bdale Garbee, there was Andrew ‘bunnie’ Huang. He is a very interesting person, and his activities go beyond just-basic-nerdiness. Huang happens to be the person responsible for the jailbreaking of Microsoft’s Xbox360, something he wrote a book about in 2003. Moreover, he holds a PhD in engineering from the MIT. What I really like Bunnie for is all his great coverage of Chinese manufacturing, while sourcing suppliers for Chumby. Chumby is a gem: a totally open and hackable device designed from the ground up complete with open source hardware. This embedded computer provides internet access through a WiFi connection, and is able to run a wide range of software widgets once connected. The hardware being open, everyone willing to use Chumby is encouraged to get into the device and make it his/her own.

You may be blinking a bit thinking “OMG, how come I don’t know this guy!

Cite this article:
Stamboliyska R (2013-02-10 08:44:37). "Do what it takes to solve the problem, and no more": a small talk with 'Bunnie' Huang. Australian Science. Retrieved: Apr 29, 2024, from http://australianscience.com.au/interviews/do-what-it-takes-to-solve-the-problem-and-no-more-a-small-talk-with-bunnie-huang/

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The post “Do what it takes to solve the problem, and no more”: a small talk with ‘Bunnie’ Huang appeared first on Australian Science.

Bacon Fans United: The Pig Genome Sequenced

rayna.s — Sat, 17 Nov 2012 00:28:42 +0000

Breeding healthier and meatier piggies has been one of the many scientific challenges of the past decades; creating more reliable models to study human diseases is another. The swine disease model is indeed much better to use when studying human disorders than the (thus far) widely used murine models. Although pigs reproduce slower than mice and are more expensive to take care of, they are more similar to humans when it comes to anatomy and physiology. These common grounds have allowed the development of accurate swine models for diabetes, cystic fibrosis or retinitis pigmentosa (a cause of blindness). In its issue of 15 November, Nature published the fully sequenced and annotated pig genome. This is a major achievement, and will allow considerable progress to be made on both the yummy and the healthy fronts.

Sus scrofa domestica, by its official name, originates from South-East Asia and then went on a visit to Europe. A closer examination of the sequenced pig genome consistently shows a clear and deep split between Asian and European wild boars rooting some 1 My ago. More precisely, the analysis allowed to date the split between the two lineages in the mid-Pleistocene (1.6–0.8 My ago), a divergence the authors explain with possible colder climate prompting isolation between populations across Eurasia.

Demographic history of wild boars. Image from Groenen et al. (Nature, 2012). The default mutation rate for human (μ) was used, and the generation time (g) was estimated to 5 years. The Last Glacial Maximum (LGM) is highlighted in grey. WBnl, wild boar Netherlands; WBit, wild boar Italy; WBNch, wild boar north China; WBSch, wild boar south China.

As the authors explain it:

Our demographic analysis on the whole-genome sequences of European and Asian wild boars revealed an increase in the European population after pigs arrived from China. During the Last Glacial Maximum (LGM; ~20,000 years ago), however, Asian and European populations both suffered population bottlenecks. The drop in population size was more pronounced in Europe than Asia, suggesting a greater impact of the LGM in northern European regions and probably resulting in the observed lower genetic diversity in modern European wild boar.

Noticeably, pigs have been faithful companions to humans for 10,000 years now. Breeding piggies and selecting for some particular features of theirs has had an important impact on the swine genome. Authors thus identified a wide range of genes and gene families to have undergone fast-paced evolution. Immunity-related genes, already known to be actively evolving in Mammals, were for instance part of this subset, and further analysis revealed evidence for specific gene duplications and gene-family expansions. Lastly, a significant expansion of the porcine olfactory receptor gene family was described. The authors explain it by the importance smell has for pigs when scavenging for food.

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Image source

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How Have Marsupials Evolved?

rayna.s — Thu, 08 Nov 2012 00:18:59 +0000

The phylogenetic relationships between two orders of marsupials have been intesively debated. Authors benefited from recent sequencing projects which provided two marsupial genomes: this of the South American opossum (Monodelphis domestica) and the one of a kangaroo, the Australian tammar wallaby (Macropus eugenii). Retroposons are suitable and homoplasy-free markers: their insertion sites are random; parallel insertions or exact excisions are very rare.

Thus, if one finds a retroposon in the homologous genomic loci of both species this indicates a common ancestry; on the contrary: if the marker is missing in one of the species, it means prior divergence. Moreover, one retroposon can insert into another: this situation is called transposition into transposition. These nested mobile elements insertions provide precious information about the relative times during which given retroposon families integrated into genomes: young elements can insert into older ones, but the reciprocal is impossible.

After complete screening of the opposum and kangaroo genomes, authors found ~8,000 and ~4,000 nested retroposon insertions, respectively. Then, the frequencies and time scales of SINEs (Short INterspersed Elements) were calculated (using TinT software) and 3 groups identified:

SINEs specific to the lineage leading to opossum => phylogenetically informative markers present in the opossum lineage;
SINEs specific to the lineage leading to kangaroo => phylogenetically informative markers present in the kangaroo lineage;
SINEs active in both species => phylogenetically informative markers present in both lineages .

Also, ~220,000 genomic loci containing retroposons were detected using three different strategies. After screening and experimental confirmation, a total of ~440 marsupial sequences were aligned and analyzed to reveal 53 informative markers. Ten of those confirmed again the monophyly of marsupials. The other 43 phylogenetically informative retroposon markers provide significant support for most of the basal splits within marsupials.

Phylogenetic tree of marsupials derived from retroposon data.

Authors did not find any loci containing elements present in opossum plus Paucituberculata but absent in kangaroo, which would have supported the alternative of a close relationship between Didelphimorphia and Paucituberculata. They screened for markers that would support the alternative hypothesis of Paucituberculata being the sister to all marsupials: experimental verification showed that all of the putative elements were also present in the order Paucituberculata (Rhyncholestes), thus supporting the monophyly of marsupials, but not the basal divergence.

Furthermore, 13 of the original 53 markers were present in the South American Microbiotheria and the 4 Australasian orders but not in either Didelphimorphia or Paucituberculata: this significantly supports the monophyly of Australidelphia. The branch separating Australidelphia from Didelphimorphia and Paucituberculata is one of the strongest supported as well. Nevertheless, poor fossil record from South America, Antarctica, and Australia does not allow to assess Australidelphian early realtionships and biogeography.

Two competing hypotheses exist regarding Microbiotheria: the latter are either excluded from the Australasian order (based on nuclear protein-coding genes) or embeded into it (completely or partially based on mitochondrial data). No reliable marsupial phylogeny is established up to now. In the present study, authors provide evidence for 4 independent diagnostic retroposon insertions which allow to place Microbiotheria within South America marsupials. Thus, authors propose the new name Euaustralidelphia for the monophyletic grouping of the four Australasian orders Notoryctemorphia, Dasyuromorphia, Peramelemorphia, and Diprotodontia. In total, 18 out of the initial 53 retroposon markers provide significant support for the monophyly of each of the five multi-species marsupial orders.

Authors conclude: “the retroposon marker system identified a clear separation between the South American and Australasian marsupials. Thus, the current findings support a simple paleobiogeographic hypothesis, indicating only a single effective migration from South America to Australia, which is remarkable given that South America, Antarctica, and Australia were connected in the South Gondwanan continent for a considerable time.”

Nilsson MA, Churakov G, Sommer M, Tran NV, Zemann A, Brosius J, & Schmitz J (2010). Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS biology, 8 (7) PMID: 20668664

(This was originally published on the author’s personal blog. Image is from the original article.)

Cite this article:
Stamboliyska R (2012-11-08 00:18:59). How Have Marsupials Evolved?. Australian Science. Retrieved: Apr 29, 2024, from http://australianscience.com.au/genetics/how-have-marsupials-evolved/

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