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After the class, I felt this strange movement in my stomach. I immediately ran to the training wall. I needed to forget about my guts…

Biological linguists develop new ontologies for richer, and cross-database searches

During most of the 1990s, a linguistic chasm divided the worlds of flies, worms, mice, and other model organisms. People in one world remained largely ignorant about related genes and proteins being studied in the others, in part because each group stored data using its own peculiar vocabulary. Even within a single organism, a search for genes involved in “translation” might not pull up those described using the term “protein synthesis”, and vice versa…

The Scientist: Your Database Is Talking; Is Anybody Listening?

Background

Regular exercise reduces cardiovascular and metabolic disease partly through improved aerobic fitness. The determinants of exercise-induced gains in aerobic fitness in humans are not known. We have demonstrated that over 500 genes are activated in response to endurance-exercise training, including modulation of muscle extracellular matrix (ECM) genes. Real-time quantitative PCR, which is essential for the characterization of lower abundance genes, was used to examine 15 ECM genes potentially relevant for endurance-exercise adaptation. Twenty-four sedentary male subjects undertook six weeks of high-intensity aerobic cycle training with muscle biopsies being obtained both before and 24 h after training. Subjects were ranked based on improvement in aerobic fitness, and two cohorts were formed (n=8 per group): the high-responder group (HRG; peak rate of oxygen consumption increased by +0.71+/-0.1 L min-1; p<0.0001) while the low-responder group (LRG; peak rate of oxygen consumption did not change, +0.17+/-0.1 L min-1, ns). ECM genes profiled included the angiopoietin 1 and related genes (angiopoietin 2, tyrosine kinase with immunoglobulin-like and EGF-like domains 1 (TIE1) and 2 (TIE2), vascular endothelial growth factor (VEGF) and related receptors (VEGF receptor 1, VEGF receptor 2 and neuropilin-1), thrombospondin-4, alpha2-macroglobulin and transforming growth factor beta2.

Results

neuropilin-1 (800%; p<0.001) and VEGF receptor 2 (300%; p<0.01) transcript abundance increased only in the HRG, whereas levels of VEGF receptor 1 mRNA actually declined in the LRG (p<0.05). TIE1 and TIE2 mRNA levels were unaltered in the LRG, whereas transcription levels of both genes were increased by 2.5-fold in the HRG (p<0.01). Levels of thrombospondin-4 (900%; p<0.001) and alpha2-macroglobulin (300%, p<0.05) mRNA increased substantially in the HRG. In contrast, the amount of transforming growth factor beta2 transcript increased only in the HRG (330%; p<0.01), whereas it remained unchanged in the LRG (-80%).

Conclusions

We demonstrate for the first time that aerobic training activates angiopoietin 1 and TIE2 genes in human muscle, but only when aerobic capacity adapts to exercise-training. The fourfold-greater increase in aerobic fitness and markedly differing gene expression profile in the HRG indicates that these ECM genes may be critical for physiological adaptation to exercise in humans. In addition, we show that, without careful demonstration of physiological adaptation, conclusions derived from gene expression profiling of human skeletal muscle following exercise may be of limited value. We propose that future studies should (a) investigate the mechanisms that underlie the apparent link between physiological adaptation and gene expression and (b) use the genes profiled in this paper as candidates for population genetic studies.

BMC Biology: Modulation of extracellular matrix genes reflects the magnitude of physiological adaptation to aerobic exercise training in humans

While coming back home I was reading one of my favourite books. This chapter always gets deep into my mind:

Why?

The adventure doesn’t have date nor age.
Two months, the same mountain. Why?
I think about the dusk with Hermann Buhl at the summit and the odyssey when we descended with Julie. But not only this.
Why, then? Why a mountain can give men knowledge and dimensions of which they don’t even have idea?
How many times will we return to K2? Every time a new facet shines in the crystal. Every step, is a step towards unlimited new possibilities.
Julie simply says: “Where I go, everything is possible”.
I say: “Where everything is possible, I go”. Because of this, we are together…

- Kurt Diemberger
The Endless Knot: K2, Mountain of Dreams and Destiny

Never stop exploring…

Early this morning, Beto and I finally found the correct path for the running trail from Güero’s house to Villa Alpina.

We left the car at the end of the graveyard and entered the usual trail following to the right of the big hill we ran some days ago. We used our instinct to go around this big mountain and entered a river gorge, following its uphill stream to guide ourselves towards Villa Alpina. As soon as we could imagine we were reaching a small village below our desired goal. We were beginning to feel thirsty, but the proximity to the summit brought us more energy to burn.

After 1 hour 23 minutes, an aproximate distance of 13 kilometers and a rise level of almost 900 meters, we reached Villa Alpina with more than a happy face. Full of laughs, we shaked our hands and psyched up for the descent.

It was still early and we thought of looking for a more direct descent route. I guess we haven’t had enough adventure yet…

And we actually found it! We managed to cut a little bit the route by going more directly into the woods. We arrived to the car 1 hour after beginning the descent. We drank lots of water and ate some sweet cookies.

We were ready to celebrate, so we headed to Coyoacán for a well deserved breakfast and our favourite mocha coffee. We talked about the completed objective and started planning the next one. We never stop bringing new ideas…

By noon I arrived home and Cova called. He asked me to go bouldering to Chiluca. I didn’t thought it twice, I accepted immediately. The rest of the afternoon is easy to guess… We had an excellent time and even managed to create some interesting new problems…

Here is our finished trail running route, drawn thanks to the Google Earth software:

Even tough sometimes it has been difficult to keep up the habit of writing, I’ve managed to share a lot of the things that I enjoy the most. I hope some of you have enjoyed them too…

It doesn’t have to be fun to be fun…

After some work in the morning, Fer arrived to my place and we bought some sushi rolls for lunch. I’ve never tasted the rice from Superama‘s sushi bar, I really liked it (thanks to Fer’s suggestion ).

Beto & Lula called and invited us to join them in “el tour del sur”. We spent the rest of the afternoon walking in Coyoacán, drinking coffee, reading books, watching bonsai trees, laughing and relaxing a lot.

Then, the big almost-full moon rised…

By yesterday evening, Beto and I managed to ran into full adventure while continuing the search for a trail to Villa Alpina from Güero’s house.

We didn’t got into the correct path, but found a beautiful landscape: an enormous 45-degree hill without trail that led us to some boulders near the top of it. The night caught us up there and somehow we found the way back through another hill.

After some crazy minutes sliding and falling down the mountain, we reached the car and shaked hands with that particular grin in our faces…

During the coffee break, my eyes focused on the reality of what was supposed to be an interesting problem. No such thing…

After recovering from the disturbing confusion, the class ended and I departed to do some laps at the training wall. It was raining slightly, so I avoided using chalk for grabbing the wet handholds. No soapy wall and nice grip!

Just getting older & remembering the good times at the gaming console…