Go Mendel!

Today’s Google Doodle celebrates what would have been the 189th birthday of Gregor Mendel. Mendel is known as the founder of the science of genetics for his works with pea plants.

Although, inheritance of traits in most microorganisms is mostly remarkably non-Mendelian, Mendel's concept of transmissible genes has been the starting point that led to the identification of DNA as the primary genetic information carier. It allowed for the discovery of the biochemical structure of genes, an understanding of how DNA stores and regulates the flow of genetic material, and ultimately the development of techniques that allow for the manipulation of DNA.

EHEC

Enterohaemorrhagic E. coli (EHEC), can cause severe foodborne disease. Symptoms of an infection include abdominal cramps and diarrhoea that may progress to bloody diarrhoea (haemorrhagic colitis). In a small proportion of patients (particularly young children and the elderly), the infection may lead to a life-threatening disease, such as haemolytic uraemic syndrome (HUS). HUS is characterized by acute renal failure, haemolytic anaemia and thrombocytopenia.

EHEC is transmitted to humans primarily through consumption of contaminated foods, such as raw or undercooked ground meat products and raw milk. Its significance as a public health problem was recognized in the early eighties, following an outbreak in the USA. Since early May 2011, an increased incidence of EHEC infections has been observed in North Germany. Cases reported from other European countries had traveled to this area. This particular  E. coli O104:H4 strain seems to be particularly virulent and is resistant to most β-Lactam antibiotics.  Unfortunately,  as of 31 May 2011, more than 30 patients in Germany have died of EHEC induced HUS. There seems to be an association between the outbreak the consumption of raw cucumbers, tomatoes, and leaf salad vegetable sprouts. I am not sure what the Google Insights graph below exactly tells us... but it is kind of interesting to see that for a while the "web search interest" of EHEC approached Lady Gaga's.

Evidence of "extra" terrestrial life?

NASA will hold a news conference at 11 a.m. PST on Thursday, Dec. 2, to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life. Astrobiology is the study of the origin, evolution, distribution and future of life in the universe.

Very exciting stuff! I have a gut feeling that this story involves Arsenic.

If it turns out that Felisa Wolfe was right after all she will have to grow a large beard ASAP.... because she will be a f**$#!? new Darwin.
 

UPDATE:

Now most of the media dust has settled, some of us might have actually read the Science paper. I admire the "progressive" attitude of this team of scientist. I think they have found a cool bug that is unusually resistant to As, but I am both a bit disappointed and alarmed by some of the presented evidence.

One of the things that struck me was how the Felisa and her team aim to show that the genomic DNA contains As in place of P.

Their mass spectrometry analysis seems to reveal only very little As relative to carbon. The study lacks some controls (e.g. other genomic DNA incubated with As medium) to rule out that the small amounts of As result from carry over during DNA extraction and purification.

UPDATE II:

A good but slightly virulent post by Rosie Redfield. Rosie shares (and does a good job explaining) my doubts about the As being covalently bound into nucleotides and describes a few other potential weaknesses of this paper.

Robert Krulwich: Why Can't We Walk Straight?

Try as you might, you can't walk in a straight line without a visible guide point, like the Sun or a star. 

In this cool animation, Robert Krulwich, a correspondent for NPR's Science Desk shows that while you might think you're walking straight, a map of your route would reveal you are doomed to walk in circles.

Random Blog Post

"Any one who considers arithmetical methods of producing random digits is, of course, in a state of sin. For, as has been pointed out several times, there is no such thing as a random number — there are only methods to produce random numbers, and a strict arithmetic procedure of course is not such a method".  (John von Neumann [1951] Various techniques used in connection with random digits. National Bureau of Standards, Applied Math Series, 11:36-38. )

Nevertheless, I added a "Random Blog Post" button.

Tree time!

My favorite dendrograms (randomly ordered)

The first-known sketch by Charles Darwin of an evolutionary tree describing the relationships among groups of organisms (Notebook B: Transmutation of species, 1837-1838). This tree figure, with the most ancestral species at the bottom and their descendants branching off, reveals that Darwin understood all plants and animals are related. Above this tree Darwin wrote firmly, "I think."

Lentebloesem (Spring Blossom) 1987; the Dutch painter René Daniels depicts his own oeuvre as a branched tree, which leaves are formed by the titles of his previous paintings.

Ribosomal RNA gene based phylogenetic tree by Carl Woese (1987) illustrating the three-domain classification system.

W. Ford Doolittle’s reticulated tree, or net, stresses the importance of horizontal gene transfer in archaeal and bacterial evolution.

NDM-1

Louis-Ferdinand Célin once said “Even diseases have lost their prestige, there aren't so many of them left. Think it over... no more syphilis, no more clap, no more typhoid... antibiotics have taken half the tragedy out of medicine.”

He didn’t anticipate carbapenem resistant Enterobacteriaceae coming into existence.

Bacterial genome size & base composition

Browsing through the currently available microbial genomes in Genbank I noticed that it is remarkably easy to make some highly illustrative graphs. E.g. plotting the G+C percentage of a complete genome against the total size of the genome reveals a remarkable trend.

In the early sixties it was first noted that “Among bacteria the mean G+C content of DNA varies approximately from 25 to 75%, and this range extends over the range of the mean G+C content of DNA of higher organisms” (Sueoka, 1962).
Currently, the mean G+C content for sequenced bacterial genomes deposited in Genbank is 48.3% and ranges from 74.9% (Anaeromyxobacter dehalogenans 2CP-C) to 16.6 % (Candidatus Carsonella ruddii PV).
The figure above shows the “linear” correlation between bacterial genome size and base composition.
An adaptive explanation for this apparent correlation could be the fact that synthesis of GTP and CTP is energetically more expensive than ATP and TTP (Rocha & Danchin, 2002). In addition, the central role of ATP in cellular metabolism results in a greater availability relative to other nucleotides. Under resource limiting conditions, this could drive microbial genomes to drift towards AT-richness.
Another possible explanation is DNA repair. Small (reduced) genomes often lack genes involved in DNA repair machineries (Moran, 2002) allowing accumulation of point mutations. Experiments have shown that the most frequent random mutation occurring in cells is C to T (or G to A), due to the deamination of Cytosine to form Uracil, which is subsequently replicated as Thymidine (Glass et al., 2000). Thus in the absence of DNA repair mechanisms, genomes might become more AT-rich.

References
Glass JI, Lefkowitz EJ, Glass JS, Heiner CR, Chen EY, Cassell GH. 2000. The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature 407:757-762.
Moran NA. 2002. Microbial minimalism: Genome reduction in bacterial pathogens. Cell 108:583-586.
Rocha EPC, Danchin A. 2002. Base composition bias might result from competition for metabolic resources. Trends Genet 18:291–294.
Sueoka N. 1962. On genetic basis of variation and heterogeneity of DNA base composition. PNAS 48:582-592.

Fallible Design

The basic concept of intelligent design comes in two parts and is as simple as it is satisfying for those unwilling to think deeply about the natural world, science, or the nature of religion. 1) Nature is so perfectly integrated that it must have been designed just as we see it. 2) While some aspects of nature might have changed (evolved) over time, others are so complex that they must always have existed in the form we find them in today, and must have been created by an "intelligent designer".

This part can be largely attributed to Michael Behe (Lehigh University), who claims that certain biochemical processes are "irreducibly complex". They involve multiple proteins, and without any one of them the overall pathway would not work. Like the good old ... eye.
It is quite needless to say that both parts of ID are spectacularly wrong, but it is not a bad thing to preach to the choir every now and then. The choir can enjoy reading about the wonders of biology and human stupidity. Enfin. A notably elegant ID rebuttal appeared recently in PNAS. In “Footprints of nonsentient design inside the human genome” John Avise (University of California) provides entertaining examples of the human genomes incredible imperfection.

Lies, Damn Lies and Medical Research