Read more carefully

I was kind of complaining on my own that the other person give me a clone without telling me enough information. I have to went to the website and double-check the sequences she gave me. I do see a little difference from the database of the sequence, the stop codon. But it doesn't matter much so I don't need to worry about it.

But then I have to go on to design the cut site to pop this insert out and transfer it to another vector. The two cutting site she left on the VNTI molecule, on purpose, which is suggesting me to use those two, are definitely not good choices. I found a PsiI cutting site right at both ends of the insert on the vector. So this should be perfect.

I went to Barb and ask her to order this enzyme. I can't borrow it from other lab, it seems to be rarely used by researchers. We could not find it on Roche, but finally on NE. Barb ask me what's this for. I explained to her, it's actully she taking care of this clone to some part. Barb said there is actually a SfiI on it, if she remember correctly.

I went back to check. I know the insert I put here is a little bit out of the region of start and stop codon. I went to the website and marked the feature sequences. Then I found it's said there! SfiI site!

If I had read carefully, I would not need to waste so much time looking for the best cutting sites and bother people around. I hate this.

A lesson for myself: Be patient and read carefully!

Listening to Seminars

I like to go to seminars and meetings. To me seminars and key-note talks are more worthwhile to go because from those I could hear a full story, while the 20'-30' doesn't really benefit you much in an overview of that specific field, rather than browsing through the result of the speaker's work.

I make notes whatever talks I went to, like when I go to audit a class. David even asked me once if it (making notes) did anything at all, you would forget it anyway if you don't go back. Actually it's very true.

Today I am thinking I should trace up a little bit whatever talks I went to, I mean if they are somehow interesting or let me learn something. I am making a Wiki myself, specific to my interest.

Just make a note for myself to remind me doing that, since I am such a forgetful person. This is what a graduate student should do.

My night dreams

I make a lot of dreams in the night. It's like my dreams in the night are even more colorful and interesting than my life in the day.

You know what I dreamed of the night before last night?

In the dream, I was very familiar with Barack Obama. I was chatting with him like a friend. Then it comes to the moment that someone (He was well-dressed and I talked to the person too before knowing he is actually the one to decide the president.) announce the next president of America. It's Obama! I was very happy and went to congratulate to him. Shaking hands with him, I said: You should tell NIH to increase the funding to researches!

And then I switched to other dreams.

Oh my god, how can I come to a dream like this? I'm not caring much about the campaign. Except for that I can't avoid to hear those stuff on TV when it comes to a news channel.

Comment on a little paper

To my interest I just went to pubmed to look for the most recent articles on Kv2.1 channel. It turns out our lab's just came to the second. I went to the first one, read the introduction part which could help me to know about Kv2.1 channel in the nervous system. But the overall research is really nothing interesting.

The authors are trying to compare the native Ik current in hippocampus and the in-vitro current expressed by the cloned Kv2.1 gene. How can such a comparison make any significance??? Do you know how exactly is Kv2.1 functioning as an ion channel? How many auxilary subunits might it use? How many signaling molecules it might get through in order to be able to function normally? This doesn't mean anything!

In the introduction they draw people to understand that Kv2.1 makes up the majority of Ik currents. It would be more interesting if they try to pull out another channel gene may have a significant role in making the Ik current. Or they find that this channel doesn't play the "major" role any more because of making an auxilary subunit or another gene defective. Any way, I don't like it at all. I should not waste my time commenting about it. But let me start to critisize every paper I met.

My comment on Deepika's one blog article

It is believed by the evolutionist(?) that evolution keep the organisms with higher evolvability. Evolution is not really continuous process, there is a phenomenon called evolutionary stasis.  

Evolution is decided by selection (natural, or environmental) and all kinds of constraints such as physical, physiological, developmental and genetic constraints.  

Emm.... Will those mechanisms be able to exist is still a question... Bacteria can evolve fast because they are single cell organisms, they don't really need to worry that if you change you neck then the brain had to be changed as well. Mutations can easily be adopted by the cells because of the high degree of evolution freedom. But higher organisms have their own way of adopting large genetical changes: sexual reproduction can exchange the whole genome material. This way they still have high evolvability. For those multicellular organisms which abandon sexual behavior will have short evolution future (except for one species).  

Oh, I have a phone call.  

I'm back. Wow, I wrote a lot.

Regulatory evolution

Sean B. Carroll is the key biologist in this topic. He even has his own website: http://www.seanbcarroll.com/

This may he published a "paper" here: http://web.ebscohost.com.ezproxy.hsclib.sunysb.edu/ehost/detail?vid=2&hid=8&sid=4f39dc57-3dba-46a0-8f96-cc1a7a5b842f%40SRCSM2
which is really a great thesis on this topic.

Got an idea to describe regulatory evolution and structural evolution

Everytime getting aware of something. I would like to discuss it with someone to make sure that I got it right. Here in McKinnon lab, it's definitely going to be Shian-ren. Today I discussed with her about the role of regulatory evolution on the small scale and structural evolution on the larger scale amongst the living beings. I just got the reminder to myself that actually this small scale and large scale is actually not only limited to the vertical dimension of species, but it's also on the horizontal dimension of traits. For example, morphological traits.

The existance of a trait would be structural evolution, or the big morphological changes. But the more complex, detailed evolution of a trait would be regulatory. How to say, oh, like the transportation tools, said me. Having Shian-ren being there clarifying something, all in a sudden this great example come into my brain. I can't wait to telling her about this, because it's so great analogy for me.

Yes, look, even though a car can have a speed range from 0 to 100 MPH, it can never arrive hundreds of MPH like the plane. Without structural evolution into plane, this high speed could never happen. However, within the category of car, there can be lot of changes across different brands or even inside a brand; these are regulatory evolution.

Wow, good, I can give this example on my proposal defense.

Neuronal activity dephosphorylate and translocate Kv2.1 ion channel:

04 Nature: "Regulation of ion channel localization and phosphorylation by neuronal" activityhttp://www.nature.com/neuro/journal/v7/n7/full/nn1260.html
Voltage-dependent Kv2.1 K⁺ channels, which mediate delayed rectifier Kv currents (I_K), are expressed in large clusters on the somata and dendrites of principal pyramidal neurons, where they regulate neuronal excitability.

Very good review: "Localization of Voltage-Gated Ion Channels IN Mammalian Brain" in Annual review of physiology
http://arjournals.annualreviews.org/doi/full/10.1146/annurev.physiol.66.032102.113328?cookieSet=1

The exam

http://en.wikipedia.org/wiki/List_of_regions_in_the_human_brain

Too many thing to memorize... :(

The Motor Lab

This is a very interesting lab. http://motorlab.neurobio.pitt.edu/index.php

Especially the multimedia of robot arms controlled by cortical neuron activity. But my main argu is that because of the plasticity of the brain, you don't really need to train the person prior to implement the robot arm, nor to put the source electrode at any specific area of the brain.

It's really great to hear the Evinger have invited Dr. Schwartz to come. I am so looking forward to that. I think I have a lot to discuss with him.

Very interesting multimedia to watch here: http://motorlab.neurobio.pitt.edu/multimedia.php

The best knowledge collection of visual system

http://webvision.med.utah.edu/

Should be interesting to know

Title: Regulation of the timing of MNTB neurons by short-term and long-term modulation of potassium channels

I know some families of potassium channel are important in auditory function. Especially the ones in the hair cells. But this is something I didn't know.

http://www.sciencedirect.com.ezproxy.hsclib.sunysb.edu/science?_ob=ArticleURL&_udi=B6T73-4FXV7BJ-3&_user=334567&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000017318&_version=1&_urlVersion=0&_userid=334567&md5=bb2dd706f5fc02dee27cde9d9097e1ed

Abstract

The firing patterns of neurons in central auditory pathways encode specific features of sound stimuli, such as frequency, intensity and localization in space. The generation of the appropriate pattern depends, to a major extent, on the properties of the voltage-dependent potassium channels in these neurons. The mammalian auditory pathways that compute the direction of a sound source are located in the brainstem and include the connection from bushy cells in the anteroventral cochlear nucleus (AVCN) to the principal neurons of the medial nucleus of the trapezoid body (MNTB). To preserve the fidelity of timing of action potentials that is required for sound localization, these neurons express several types of potassium channels, including the Kv3 and Kv1 families of voltage-dependent channels and the Slick and Slack sodium-dependent channels. These channels determine the pattern of action potentials and the amount of neurotransmitter released during repeated stimulation. The amplitude of currents carried by one of these channels, the Kv3.1b channel, is regulated in the short term by protein phosphorylation, and in the long term, by changes in gene expression, such that the intrinsic excitability of the neurons is constantly being regulated by the ambient auditory environment.