Nerdy Image: HIV Transactivation Response Element

My research of late has been going well -- recently I've been exploring the behavior of the Transactivation Response (TAR) Element found in Human Immunodeficiency Virus (HIV) using a variety of computational tools.

The TAR element is an essential part of the HIV lifecycle and is found within the RNA genome of this virus. In an infected cell, the interaction between the TAR element and other proteins is responsible for a dramatic increase in the production of viral proteins. The TAR element has also been shown to inhibit programmed cell-death by infected cells, allowing the process of viral replication to continue unabated.

The snapshot I've attached is taken from a simulation I'm running and highlights certain regions of the TAR element, solvated in an environment of water. The isolated spheres are sodium ions.

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Posted 4 months ago

Tuolumne Meadows June 20-21

This trip happened last month but I thought I'd post up a few pictures that Eu-Jin took.

Day 1 - Lembert Dome: Crying Time Again (5.10a) + Direct Northwest Face (5.10c)

Began the day with a leisurely drive from the Evergreen road bivy spot to the Sierra High Country. Decided to head to a familiar favorite: Lembert Dome. The routes on this formation are absolutely classic. Eu-Jin and I started on Crying Time Again (5.10a). It was my third time on the route and it never fails to dissapoint -- just a joy to pick your way through the steep and knobby cruxes on this route. Unfortunately, I also forgot that Crying Time again doesn't get sun until the mid morning. I didn't bring a jacket or windbreaker and by the 2nd pitch, I was shivering pretty hard and my feet were completely numb, making my feet skate all over the place.

After completing Crying Time Again, we went back to the car for some lunch. The weather wasn't looking great so we decided to wait and see if it would start raining. It didn't so we headed out to do Direct Northwest Face (5.10c). I was a bit nervous about this climb. A few years ago I had led the bottom pitches, letting George lead the crux finger crack on pitch 3. I remember the crack being very difficult and I fell while cleaning the nut the protected the crux moves. And the fact that my friend Wendy had fallen off the runout exit slab, separating her shoulder and rolling off the ledge, cemented this route's reputation in my mind.

The route went pretty well. I hesitated a bit on the lower 5.9 pin scar cruxes (a bit harder than I remembered). I set up a belay below the crux finger crack, and psyched myself up. Heading up, I placed a nut to protect the moves, twisted my fingers into the crack, and just motored through (easier than I expected). I reached the piton, clipped it, and let out a whoop. Cory and Laura, watching below, laughed up at me. The exit slab was thought-provoking (climbing above a ledge with nasty fall potential will do that) but it was pretty mellow. I think the moves are pretty height dependent.

Best climbing of the day award goes to Cory and Laura. In about the time it took for Eu-Jin and I to finish one climb (Crying Time Again), Cory and Laura finished two climbs (Northwest Books (5.6) and Direct Northwest Face) and were heading up Crying Time Again for their Lembert Dome Trifecta.

Day 2 - East Cottage Dome: Knobvious (5.10c), Mystery Route (5.10d), Knobnoxious (5.10d), Orange Plasma (5.11a)

The next day began with a nice breakfast and some coffee at the Mobil Station. We wanted to avoid the crowds of people that tend to form around routes in the Supertopo books, so we decided on East Cottage Dome. Pulling into the turnoff we spotted a familiar Stanford alumni license plate on a Subaru Outaback. Hiking through the woods, we caught up to Wendy and Justin and spent an enjoyable day climbing the steep East Cottage dome wall.

Photo Captions (all photos by Eu-Jin Goh)
1. Gearing up in the Lembert parking lot
2. Heading up Direct Northwest Face (5.10c)
3. Heading down after a day's climbing
4. The only picture Eu-Jin would allow me to post ..
5. Consulting the topo. This wasn't staged. I swear!
6. Wendy leading Knobulator (5.10c)
7. Getting psyched!
8. Justin's psyched too!
9. Leading Knobulator
10. Candidate for asianposes.com?
11. Beautiful shot of Cory leading Orange Plasma (5.11a)

                     

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Posted 4 months ago

Ocean beach

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Case study in public art: UCSF's Genentech Hall

UCSF's Genentech Hall is a massive space -- its massive atrium and large windows flood the space with light. One of the cooler aspects of the place is it's attention to detail -- the simple pentagonal shapes on the carpet and on the large hanging lights are abstract representations of the nucleotide bases in DNA, the code of life. It's a great temple for serious science, yet it still manages to be quirky  and fun. The art scattered throughout the building is light and irreverant.

I snapped a few photos of Jean Lowe's "Book and Ideas in an Age of Anxiety" (1994-2006). If you have a chance to visit UCSF's new Mission Bay campus (and manage to sneak in, undetected, past the guard), check it out -- it's on the second floor.

                     

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Working from Boulder ...

Why don't my simulations behave as well as Benny does?

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Benny is tired

Benny is lucky. He gets to sleep. I get to work.

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The best part of fake graduation is ... the cake!

I can't believe that Dennis drove two of these bad boys up from Portos' bakery down in LA. The other one is an ice cream cake courtesy of Sam, Doris, and Bryan. Yum!

     

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Caltrain, bird's eye view

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Posted 5 months ago

Alpinists Jonny Copp and Micah Dash lost along with filmmaker Wade Johnson

Was saddened to hear that Jonny Copp, Micah Dash, and their filmmaker Wade Johnson were lost in an apparent avalanche while attempting an unclimbed route on Mt. Edgar in the Sichuan province of China. I didn't know these guys personally, only following them through climbing films and print articles but their exploits always served as a source of inspiration. The closest to either of them I ever got was seeing Micah giving a wonderful slide show when he swung through Stanford.

One thing that strikes me about these guys was their unquestioned passion for climbing and their humility. Unlike the top athletes in other professional sports, Micah and Jonny pursued climbing out of an overriding passion to see what was around the next corner. They certainly didn't do it for the financial rewards. Like most professional climbers, they were probably lucky to scrape a modest living together confronting some of the most dangerous conditions in the world.

Inevitably after a tragedy such as this, armchair alpinists emerge from the woodwork to question the motivations of those who've died. Micah and Jonny have been called reckless and foolhardy --- one internet pundit even called them "selfish". Though they can't speak from themselves, perhaps it's best that they explain themselves in their own words. These two videos probably do the best job exploring why they did what they did, in their own words.

"Longway" by Jonny Copp

Excerpt from "The Sharp End", produced by Wade Johnson

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Posted 5 months ago

Trip Report: South By Southwest, Hotline, EPIC!

As many of you know, my climbing partner Justin and I epiced on our trip to Yosemite a few weeks ago. Here's a trip report for that weekend. Pictures are all from Justin's camera.

Day 1: Justin and I met up with Cory and Laura at the rockpiles bivy outside of Yosemite on the 140. Our objective for the day was "South by Southwest", a classic 5.11a that ascends to the summit of Lower Cathedral Spire. Depending on how fast we moved, we were also thinking about running up "Braille Book" (5.8) on Higher Cathedral rock.

South By Southwest, first climbed by the late Walt Shipley and Keith Reynolds in 1993, is a beautiful and exposed route to the an aesthetic summit. The first two pitch is forgettable, but you quickly get to the business: a short 5.10d finger crack to an exposed hanging belay, followed by a wonderful 5.11a traverse. Protection is super solid and the climbing is great. Cory and Laura climbed ahead of us and Cory did an amazing job making the 5.10d and 5.11a sections look effortless. Justin also did a great job leading the stout and tiring moves right off of the belay before crusing through the 5.11a underclinging section. I'm always amazed at how easy the people I climb with make things look!

The four of us gained th summit with impressive views of El Capitan and the rest of Yosemite Valley. It's a great little summit and well worth the effort. On the way down, we decided not to go for Braille Book. It was hot, and the hike up the approach gully had really drained us --- a dip in the cool, snow-melt fed waters of the Merced seemed more and more enjoyable. On the way to the bridge, we bumped into a friendly bear and met a guy who had just soloed the Muir wall -- impressive!

We then made our way for beer and pizza at the Curry pizza deck -- a great way to end a nice day of climbing. Over pizza, Justin convinced me to give Hotline (5.12a) a try. I was somewha anxious, but he assured me that we could easily aid through the hard stuff. Plus, the third pitch is reputed to be the best 5.10 handcrack in all of Yosemite Valley --- even Ron Kauk has called Hotline the definition of classic. It was hard to pass up!

Day 2: After a cup of coffee and breakfast at Degnan's, we headed up to the valley rim on Highway towards Hotline on Elephant rock. Ordinarily, Hotline is approached by crossing the Merced river. However, during peak snowmelt, the river is hard / impossible to cross so the recommended approach starts from the valley rim and heads down a steep canyon towards the river. The approach was heinous, like skiing down a steep slope where every step sent showers of dirt and pebbles downhill. To top it all off, poison oak was everywhere!

The climb itself was beautiful. Justin made short work of the difficult and strenous fingercrack crux of the first pitch. When I followed him, it felt a lot harder than "5.10c." The next pitch is the hardest part of the climb -- 5.11d fingers, followed by a 5.12a traverse. Since neither of us was strong enough to climb it free, Justin aided through it. I was pretty impressed at how easy he made it look! I made a feeble attempt to follow the pitch free but eventually resorted to pulling on gear and tension-traversing through the 5.12 section.

The third pitch was amazing -- a 150 foot handcrack that seemed to go on forever. No wonder it's such a classic! Justin was gracious enough to give me the lead and I was happy to lead through this amazing crack. I then flailed my way up the next 5.9 section --  I definitely need to improve on my wide crack technique. Thankfully Justin, master of the old-school, burly, and wide cracks that characterize Yosemite climbing was there to give me pointers, patiently waiting as I groveled up the crack. The last 5.9 pitch was Justin's and he easily floated. We then rapped the route, arriving at our packs at around 2pm.

Here's the first fateful decision that eventually led to our epic and forced bivouac. Having gone through the poison oak once, we somehow formulated a crackpot plan. Instead of going back uphill the way we came, we'd head down towards the river. Our plan was simple: we'd try and find a place to cross and hitchhike back to our car which was at the valley rim. If we couldn't find a place to cross, we'd just keep going until we hit the bridge some 3 miles away. One way or the other, we'd get across and hitch a ride back. At the time, the plan seemed reasonable. Our belays high up on Hotline had given us a commanding view of the river and we spied a few places where the river widened into calm pools.

We started down and arrived at the Merced pretty quickly. Unfortunately, the 'calm' pools that we thought we had seen from the belay were actually raging with snowmelt. Undiscouraged, we started hiking towards the bridge. Unfortunately, our path was choked with poison oak, thicker than we had passed through on the way down. Our 'plan' was quickly unravelling. After negotiating the rough, poison-oak choked terrain on the riverbank, we came a place where the river split into three streams, flowing around several small islands.

The first stream wasn't too bad and Justin swam across pretty easily. We set up a Tyrolean traverse between the island and the bank, shuttling our gear across. At this point, we were all very optimistic. The flow wasn't really that bad, and we were confident that we could negotiate the other two. We quickly packed up our gear, and started wading through the second crossing. Unfortunately, the flow on the far side of the island was strong. After much deliberation, we decided that it was foolhardy to attempt a crossing, especially as darkness was falling and we were soaked from wading and swimming in the river. The section of river was no more than 40 feet across.

Given the circumstances, we thought it best to bivy on the island. It was our first forced bivy and we spent it huddled in the dirt next to a fire we had built to stave off the cold. I spent the night with my legs stuffed into my backpack and one of our ropes for a pillow. Not the best of circumstances, but we made the best of it. The most maddening thing was listening to traffic on the far side of the river all night long -- the road was literally 100 yards away.

Day 3: We woke up the next day eager to get out of there and back to civilization. We knew that people were expecting us and that they'd probably be worried. We swam back across the river and began walking towards the bridge. Unfortuntely, the rugged terrain was so steep that we couldn't pass through. Swallowing our pride, we realized that we would have to hike back the way we came. Our shortcut has cost us an entire day.

We reluctantly started back, even trying to cross the river once more at another point. Eventually, we were resigned to the long hike back up. I was thirsty beyond belief. The 90 degree temperatures, lack of water and food, were beginning to take their toll. Desperate, I filled up my Nalgene with water from the Merced and drank it. The risk of contracting giardia was worth it if it kept me going. Justin did without. We ate the last of our trail mix (our only food) and hiked back up.

Arriving at our car, we found a note from the Yosemite Search and Rescue (YOSAR) --- we had been reported missing and overdue. We drove back down to the Valley floor, stopped off. I ran into the shop and bought two scoops of ice cream and 2 liters of gatorade. We called YOSAR and told them that we were all right before calling our friends to tell them that we were safe.

A stop by Taqueria El Agave in Oakland, our traditional post-climbing stop, finished off a somewhat-longer than expected weekend.

Aside: This experience made us realize how lucky we are to have friends that care -- as soon as Justin and I were overdue, they sprung into action, calling around, figuring out what climb we were on, notifying the search and rescue squad, and working to find out where we were. We later found out that YOSAR had sent some people down the gully to see if they could find us. Having not found us, they were on the verge of initiating a much larger and wider search before we called them. Thanks to them, and the great community of Stanford friends who were all worried --- sorry for that! =)

1. Cory leading on South By Southwest (5.11a)
2. Admiring the view on the summit of Lower Cathedral Spire
3. Justin and I
4. Laura and I
5. A small brown bear by the El Cap bridge
6. Can't beat taking a bath in the river ..
7. Justin aiding through the 5.11d + 5.12a section of Hotline
8. The best 5.10 handcrack in the Valley!
9. Justin leading the last 5.9 pitch
10. The Merced, raging from snowmelt. Not calm at all!
11. Vince does not like poison oak
12. Justin negotiating the first crossing
13. Success!
14. Shuttling gear across via a Tyrolean traverse
15. Can we make it across? My smile seems optimistic!
16. Back at the car, safe and sound
17. The island in front of the tower was our home for the night

                                 

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Posted 5 months ago