Steve Koch › Comments

More time? ;-) currently away from proper connection but have some ideas mainly around making partial ons an easier choice - Cameron Neylon from Android

Cookies. You should bring cookies. (Translation for Cam: biscuits.) :-) - Bill Hooker

It's all about ultrasound. I even have a nifty movie where you can see the sound waves coming from the transducer. - Andy Maloney

small world Steve - some things are easier to do with vesicles than monolayers - another tool to keep in mind - Jean-Claude Bradley

They had Swine Flu too, and you should check that out if you want. - Anthony Salvagno

Swine Flu doesn't have the timelessness and staying power that T4 and E. coli do. You picked well. - Steve Koch

I have coli and rhinovirus on my desk but I agree. That t4 is a must have... - Cameron Neylon from Android

Great job, Anthony! - Steve Koch

Langmuir, Vol. 13, No. 9. (1 April 1997), pp. 2457-2462. The concept of toposelectively modified vesicles (toposomes) is presented. The application of an electric field vector constitutes a method by which these objects can be created. The effect of millisecond electric field pulses on giant (10200 mum) vesicles composed of either one of two polymerizable lipids was studied in the unpolymerized and partially polymerized states. It was found that the behavior of the vesicles depended strongly on the fluidity of the membrane. For N,N-dimethyl-N,N-bis[2-(tetradeca-2,4-trans,trans-dienoyl)oxyethyl]ammonium bromide (C-14, Tm = 20.5 oC) in the unpolymerized state, large (several microns) hole formation was observed in the direction of one of the electrodes followed by resealing. In the partially polymerized state, a similar puncturing was observed, but instead of resealing, the hole remained stable for 90 s. For N,N-dimethyl-N,N-bis[2-(octadeca-2,4-trans,trans-dienoyl)oxyethyl]ammonium... - Steve Koch

Jean-Claude linked to this article on 'Andy's ultrasound / liposome thread':http://friendfeed.com/andymal... . Interesting paper on being able to create relatively stable pores in giant vessicles at specific locations using electric field pulses. Read the introduction but only skimmed the rest. - Steve Koch

FINALLY was able to log in to the wiki with openID...couldn't get it to work multiple days / tried with firefox. Then (and I know this is the unthinkable to many of you), I tried IE and it worked first try. Going back to firefox, was able to login with openID. Not sure what that was all about. Perhaps a broken cookie? - Steve Koch

Yes, had problems with cookies on Firefox and having things take forever to time out. Flushing the cache usually works but then you lose all the memory of what you've done and where you've been... - Cameron Neylon

All of their notebook entries were outstanding. This was their final lab, and they still had the energy to keep up the excellent work. Definitely very strong talents for this sort of thing--willing to spend the energy on taking the photos and writing the detailed descriptions of methods. - Steve Koch from Bookmarklet

ditto Bill - since the results are linked to raw data errors are far less dangerous than traditional publication, where you pretty much have to trust that the authors did not make any mistakes - Jean-Claude Bradley

Old news, but I've had to search for this article multiple times, so figured I'd better bookmark it. - Steve Koch

Another example of a good unintended consequence of using ONS in undergraduate lab courses. He is a star student and did outstanding work. Clearly has a successful research career ahead of him. It's only anecdotal evidence, but I have to think that the fact that he's linking to his ONS coursework means that he's likely to be more open with his future research (when he's able to). - Steve Koch from Bookmarklet

Steve - I think your guidance is right on track. Those who are learning to work openly (to whatever degree) are at a significant advantage for finding positions with groups who value that approach - but they are also qualified for traditional "closed" positions with the added benefit of being able to show their potential future employer what they are capable of doing in their public... more... - Jean-Claude Bradley

@Michael: John Callow (an undergraduate math and physics major at UNM) developed a really interesting algorithm for analyzing his Millikan data that I hadn't seen before. I thought I'd point it out to you because (a) it's interesting and (b) I wondered if you'd seen this kind of analysis done in some other area of math or science. I'm linking to his final report...if you want to take a look, you can scroll down to the "algorithm for finding most likely value of e" section. - Steve Koch from Bookmarklet

Oh, definitely no need for him to look up the paper, the trick I mentioned is used pretty often, and I'll bet it was first used hundreds of years ago. What he's done is much more interesting and orginal! - Michael Nielsen

From Alex Andrego's open notebook - Steve Koch from Bookmarklet

FF doesn't meet all your requirements but it does seem to work well compared to the specialized services - at least in some fields - Jean-Claude Bradley

Deepak, I think I was just using terminology incorrectly. I was assuming Facebook = social networking. - Steve Koch

I'm skeptical - Steve Koch from Bookmarklet

I understand that the context will be lost without more introduction but I'm still constructing the how and why I do experiments for each notebook entry. Hopefully this will generate a template for my notebook entries that will allow anyone to be able to reproduce what I do if they want. - Andy Maloney

Steve - what you are talking about reminds me of the "snapshot" approach we are trying to use. Where an archive contains a copy of every document as it existed on that day. Andy Lang has already written some code for this - if you want it could be modified slightly to work on any similar systems: http://onsarchive.wikispaces.com/ - Jean-Claude Bradley

I don't know if it actually has higher concentration of deuterium (or 18-O) (or 3-H for that matter) than does regular Vodka. But it does sound delicious. - Steve Koch from Bookmarklet

Wow, that's really weird. - Ruchira S. Datta

What is strangest to me about this story is how did a supervisor get all the other authors to go with the fake results ? - Pedro Beltrao

This is my review of a recent PLoS ONE article I read. I think people on FriendFeed will be most interested by how well the PLoS commenting system worked for me. I love it! Also, this is my first stab at a "Research Blogging" post, and if you're interested in microtubules, the results of the paper are pretty interesting. - Steve Koch from Bookmarklet

Science2.0 at work - beautiful - Jean-Claude Bradley

All STM publishers everywhere please take note, this is the way it's supposed to work in the 21st C: any journal that does not have this functionality is a glamor magazine, not an instrument of scientific communication. Reading Steve's post gives me a happy that I don't think I can describe in words. - Bill Hooker

I have no idea if this is the best workaround for Blogger not using trackbacks. - Steve Koch

Abstract: The EMBO journal (5 November 2009) The motor protein kinesin has two heads and walks along microtubules processively using energy derived from ATP. However, how kinesin heads are coordinated to generate processive movement remains elusive. Here we created a hybrid nanomachine (DNA-kinesin) using DNA as the skeletal structure and kinesin as the functional module. Single molecule imaging of DNA-kinesin hybrid allowed us to evaluate the effects of both connect position of the heads (N, C-terminal or Mid position) and sub-nanometer changes in the distance between the two heads on motility. Our results show that although the native structure of kinesin is not essential for processive movement, it is the most efficient. Furthermore, forward bias by the power stroke of the neck linker, a 13-amino-acid chain positioned at the C-terminus of the head, and internal strain applied to the rear of the head through the neck linker are crucial for the processive movement. Results also show that the... - Steve Koch

This is a fascinating paper by Miyazono, Hayashi, Karagiannis, Harada, and Tadakuma. There is a lot of information in the paper, and it is a system that is completely new to me, so it's going to take me a lot more reading time to fully understand their constructs and the results. So, at this point, I can only give a cursory summary. The paper is investigating the same issues as 'Yildiz... more... - Steve Koch

The EMBO journal (5 November 2009) The motor protein kinesin has two heads and walks along microtubules processively using energy derived from ATP. However, how kinesin heads are coordinated to generate processive movement remains elusive. Here we created a hybrid nanomachine (DNA-kinesin) using DNA as the skeletal structure and kinesin as the functional module. Single molecule imaging of DNA-kinesin hybrid allowed us to evaluate the effects of both connect position of the heads (N, C-terminal or Mid position) and sub-nanometer changes in the distance between the two heads on motility. Our results show that although the native structure of kinesin is not essential for processive movement, it is the most efficient. Furthermore, forward bias by the power stroke of the neck linker, a 13-amino-acid chain positioned at the C-terminus of the head, and internal strain applied to the rear of the head through the neck linker are crucial for the processive movement. Results also show that the... - Steve Koch

This is a fascinating paper by Miyazono, Hayashi, Karagiannis, Harada, and Tadakuma. There is a lot of information in the paper, and it is a system that is completely new to me, so it's going to take me a lot more reading time to fully understand their constructs and the results. So, at this point, I can only give a cursory summary. The paper is investigating the same issues as 'Yildiz... more... - Steve Koch

Partial abstract: The motor protein kinesin has two heads and walks along microtubules processively using energy derived from ATP. However, how kinesin heads are coordinated to generate processive movement remains elusive. Here we created a hybrid nanomachine (DNA-kinesin) using DNA as the skeletal structure and kinesin as the functional module. Single molecule imaging of DNA-kinesin hybrid allowed us to evaluate the effects of both connect position of the heads (N, C-terminal or Mid position) and sub-nanometer changes in the distance between the two heads on motility. Our results show that although the native structure of kinesin is not essential for processive movement, it is the most efficient. Furthermore, forward bias by the power stroke of the neck linker, a 13-amino-acid chain positioned at the C-terminus of the head, and internal strain applied to the rear of the head through the neck linker are crucial for the processive movement. Results also show that the internal strain coordinates both ... - Steve Koch

Abstract: Kinesin advances 8 nm along a microtubule per ATP hydrolyzed, but the mechanism responsible for coordinating the enzymatic cycles of kinesin's two identical motor domains remains unresolved. Here, we have tested whether such coordination is mediated by intramolecular tension generated by the "neck linkers," mechanical elements that span between the motor domains. When tension is reduced by extending the neck linkers with artificial peptides, the coupling between ATP hydrolysis and forward stepping is impaired and motor's velocity decreases as a consequence. However, speed recovers to nearly normal levels when external tension is applied by an optical trap. Remarkably, external load also induces bidirectional stepping of an immotile kinesin that lacks its mechanical element (neck linker) and fuel (ATP). Our results indicate that the kinesin motor domain senses and responds to strain in a manner that facilitates its plus-end-directed stepping and communication between its two motor domains. - Steve Koch from Bookmarklet

This is an article by Yildiz, Tomishige, Gennerich, and Vale where they carry out two important studies of dimeric human kinesin-1. First, they systematically change the length between the two kinesin heads by adding in proline residues between the neck linker and the coiled-coil. They show a number of interesting results from these constructs. First, the processivity (in terms of... more... - Steve Koch

The motor protein kinesin has two heads and walks along microtubules processively using energy derived from ATP. However, how kinesin heads are coordinated to generate processive movement remains elusive. Here we created a hybrid nanomachine (DNA-kinesin) using DNA as the skeletal structure and kinesin as the functional module. Single molecule imaging of DNA-kinesin hybrid allowed us to evaluate the effects of both connect position of the heads (N, C-terminal or Mid position) and sub-nanometer changes in the distance between the two heads on motility. Our results show that although the native structure of kinesin is not essential for processive movement, it is the most efficient. Furthermore, forward bias by the power stroke of the neck linker, a 13-amino-acid chain positioned at the C-terminus of the head, and internal strain applied to the rear of the head through the neck linker are crucial for the processive movement. Results also show that the internal strain coordinates both ... - Steve Koch

See Cameron's friendfeed link: http://friendfeed.com/cameron... - Steve Koch

comment = {Found via another user's citeulike posting (http://www.citeulike.org/user...). Have only read the abstract. Interesting to note that heavy water stiffens proteins relative to normal water.} Biophys. J., Vol. 82, No. 6. (1 June 2002), pp. 3246-3253. The effects of heavy water (D2O) on internal dynamics of proteins were assessed by both the intrinsic phosphorescence lifetime of deeply buried Trp residues, which reports on the local structure about the triplet probe, and the bimolecular acrylamide phosphorescence quenching rate constant that is a measure of the average acrylamide diffusion coefficient through the macromolecule. The results obtained with several protein systems (ribonuclease T1, superoxide dismutase, [beta]-lactoglobulin, liver alcohol dehydrogenase, alkaline phosphatase, and apo- and Cd-azurin) demonstrate that in most cases D2O does significantly increase the rigidity the native structure. With the exception of alkaline phosphatase, the kinetics of the... - Steve Koch

Went back and reskimmed this paper. From their conclusions: "In summary, the present study demonstrates that D2O significantly increases the rigidity of most protein structures, the effect being generally amplified by temperature as well as by the destabilization of the folded state." - Steve Koch

From Mackenzie Cowell on friendfeed: http://friendfeed.com/100idea... - Steve Koch

Sad, just sad - Deepak Singh

what is so harmful about having your research referenced by another? if it is cited, it can bring attention and acclaim to the original. if it is not properly cited, then that is itself the problem - Mike Chelen

is anyone an active member? - Alejandro Montenegro

in the category of try anything once - Jean-Claude Bradley

I think the compatibility of IP and ONS is a very interesting topic - Steve Koch has an agreement with his research office that might make it partially compatible - Jean-Claude Bradley

Steve - hopefully we'll discuss that a bit at the ONS session in NC - Jean-Claude Bradley

From Shirley Wu on FriendFeed http://friendfeed.com/shwu... - Steve Koch