L'évolution biologique de mon nom

For the heck of it, I did a BLAST query with my name. BLAST is a fast search algorithm to look up biological sequences in massive databases. The amino acid abbreviations corresponding to the letters my name have arisen throughout millions of years of evolution to find themselves in.... a protein from a bacterial pathogen of plants called Botryotinia fuckeliana (MVRTVNSMIT). Pretty cool eh? The second best (MARTINNMSSSIT) hit is a protein fragment from Coprococcus comes, another dirty sounding name.

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Pour le plaisir, j'ai fait une recherche de bases de données avec mon nom. Plus précisement, les abbreviations d'acides aminés (les monomeres de protéines) qui forment les lettres de mon nom. Il s'avere que quelques especes ont evolué d'une maniere a ce que les lettre de mon nom apparaissent dans leur proteines. Ok, ce n'est pas 100% exact, mais presque! La plus apparentée est Botryotinia fuckeliana (serieux!), une bacterie pathogene de plantes. Voir les resultats ci-apres:

>ref|XP_001548570.1| hypothetical protein BC1G_12965 [Botryotinia fuckeliana B05.10] gb|EDN18616.1| hypothetical protein BC1G_12965 [Botryotinia fuckeliana B05.10] Length=672 GENE ID: 5429089 BC1G_12965 | hypothetical protein [Botryotinia fuckeliana B05.10] Score = 31.2 bits (66), Expect = 13 Identities = 8/10 (80%), Positives = 9/10 (90%), Gaps = 0/10 (0%) Query 1 MARTINSMIT 10 M RT+NSMIT Sbjct 658 MVRTVNSMIT 667 >ref|ZP_03798050.1| hypothetical protein COPCOM_00304 [Coprococcus comes ATCC 27758] gb|EEG91380.1| hypothetical protein COPCOM_00304 [Coprococcus comes ATCC 27758] Length=330 Score = 29.5 bits (62), Expect = 42 Identities = 9/13 (69%), Positives = 10/13 (76%), Gaps = 3/13 (23%) Query 1 MARTINSM---IT 10 MARTIN+M IT Sbjct 241 MARTINNMSSSIT 253

GPU in mass spec analysis

Go figure... The main economical pressure for video card (Graphics Processing Unit-GPU) development is computer games on high-def monitors. Well, as it turns out, some really bright people have put the hardware in them to use for elucidating tertiary (3D) structures in computational biology. A very impressive work, have a read (read the paper here)

Another wonder of biodiversity

As you may know, there are more species living in tropical rain forests than anywhere else in the world. They make up less than 2% of the earth's surface (less than 6% of the earth's land mass).

• More than 20 percent of the world oxygen is produced in the Amazon Rainforest.
  
• More than half of the world's estimated 10 million species of plants, animals and insects live in the tropical rainforests. One-fifth of the world's fresh water is in the Amazon Basin.
  
• At least 80% of the developed world's diet originated in the tropical rainforest.
  
• A single pond in Brazil can sustain a greater variety of fish than is found in all of Europe's rivers.
  
• A 25-acre plot of rainforest in Borneo may contain more than 700 species of trees - a number equal to the total tree diversity of North America.
  
• More than 2,000 species of fish have been identified in the Amazon Basin - more species than in the entire Atlantic Ocean
  

While surfing the net, I stumbled upon this "ancient chinese remedy" called Dong Chong and some mumbo jumbo marketing video:

One of the active compounds comes from Cordyceps, a endoparasitic fungus that preys on insects. In fact, there are thousands of cordyceps species, each one "preying" on specific insect species. It is estimated that a square kilometer of rainforest harbors more than 30,000 different species of insect: imagine the whole ecosystem? Insects make up most of the macroscopic biodiversity on the planet. Parasites and predators are well established in such ecosystems to control populations, ensuring no one species is too common. Cordyceps fungi are a beautiful example, as you can see from these screenshots taken from BBC's planet Earth series. They (like many parasitic organisms) can alter the infected insect's behavior to make them climb higher or anything that might give the fungus an evolutionary advantage.

Mise a jour

Bonjour la gang,

Si ca fait quelque temps que je n'ai rien mis a jour, c'est qu'il ne se passe pas grand chose! On est au creux de l'hiver, et je commence a trouver ca long. Disons que c'est beaucoup plus long quand il fait 8 degres dans la maison. Le doctorat se met en branle: la je me concentre sur l'elaboration de ma methodologie en vue des resultats que je veux obtenir.

Sinon, tout va bon train. Je devrais retourner au Quebec en Aout pour une petite visite, qui risque d'etre la derniere avant une douzaine de mois. Je trouve ca un peu platte de visiter le Canada pendant mes vacances lorsqu'il y a tant de recoins a explorer en Océanie. Par contre, le Quebec me manque (surtout la poutine et la biere!) et ca va me faire du bien revoir le monde. 

Aujour'hui c'etait le 3e match de "State of Origin", le match des etoiles du rugby australien en quelquesorte. C'est les joueurs d'origine du Queensland qui affrontent ceux du New South Wales dans 3 matchs decisifs. Le perdant doit porter le drapeau de l'autre etat sur le plus gros pont de la ville! Les Maroons du Queensland ont perdu le dernier match, mais il est un peu sans but (mise a part l'honneur) car les gars on gagné les 2 matchs precedents, etablissant donc un record de 4 années victorieuses successives. C'est la fete a Brisbane ce soir!

Je suis chez nous avec un verre de Jacobs Creek Shiraz-Cabernet (le Jacobs Creek est une des marques les plus courantes ici, et aussi l'une des moins bonnes). Le Jacobs Creek du Quebec est meilleur!

A la prochaine