[{"id":183,"date":"2018-06-19T18:47:56","date_gmt":"2018-06-19T18:47:56","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=183"},"modified":"2018-06-19T18:47:56","modified_gmt":"2018-06-19T18:47:56","slug":"sciencegeist-earnest-giralt-uncle-peptide-by-mark-peczuh","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/sciencegeist-earnest-giralt-uncle-peptide-by-mark-peczuh\/","title":{"rendered":"Sciencegeist: Earnest Giralt, Uncle Peptide – by Mark Peczuh"},"content":{"rendered":"

This is the second post from Mark Peczuh<\/a> on the culture of doing science in Spain and, specifically, in Catalunya. (I do owe Mark a big apology for not getting this out sooner.) I really have enjoyed reading this interview with Ernest, and I hope you will too. Lots of great stuff to learn!<\/i><\/p>\n

\u201cThank you to [\u2026] the perpetually avuncular Ernest whom I hope to grow up to be.\u201d<\/p>\n

That\u2019s the sentence thanking Ernest Giralt<\/a> in the acknowledgements of my dissertation. Ernest and my PhD advisor began a collaboration in the late 90\u2019s that involved my thesis project. Ernest\u2019s group used NMR to help us characterize the conformational changes in some \u03b1-helical peptides that occurred when a ligand was bound. During that time he visited our lab for a few weeks at a time. I also spent a few weeks in his lab in the summer of 1997 at the University of Barcelona. My first and strongest impression of Ernest \u2013 beyond his boundless creativity as a scientist \u2013 is the aura of joy that surrounds him. Even though he is always moving at 100 mph and juggling many things, he appears to savor every bit of the process. Whatever he is doing becomes interesting, fun and fulfilling.<\/p>\n


\nErnest Giralt (Image credit: Mark Peczuh)<\/p>\n

Because I enjoy hearing what he has to say on just about anything, and because Xavi Salvatella<\/a> told me he could give me more of the backstory on ICREA and the formation of the research institutes in Catalunya, I bugged him for a lunch meeting and conversation. Over lunch we caught up on family stuff but then we went back to his office to really do the interview. I explained to Ernest the origin of my idea to share the story of Catalan research and how Xavi really opened my eyes to the ICREA and the research institutes that were started by the Generalitat about 10 years ago.<\/p>\n

MP<\/b> Ernest took it from there, starting with the origins of ICREA\u2026<\/p>\n

EG<\/b> The two things, ICREA and the institutes from the Catalan government, are [the] key things. To the best of my knowledge, they were born independently but more or less at the same time. And they\u2019ve been very synergistic.<\/p>\n

The ICREA program was first. In the 1990\u2019s I had co-founded with a colleague an Association of Catalan Scientists for the Promotion of Science. Its objective was to show the connections between science and society. Around that same time, the Generalitiat awarded the Narc\u00eds Monturiol Prize to one of the members of this group, Rolf Tarrach<\/a> [Tarrach won the prize in 1997.]. During the process he had voiced some criticisms of the research situation in Catalunya. Afterwards, the President of Catalunya told him that, if he had ideas about what could be done to improve the situation, he should recommend them. He chose to use our association as a sounding board for discussion and refinement of what would eventually become the ICREA program. I must say that, as usual among a group of scientists, we were not shy with our own criticisms. Together we eventually worked through many of the details to make a plan that we could all support.<\/p>\n

The concept behind ICREA is very simple. The institutions that do research in Catalunya, and really all of Spain, especially at that time, were very old ones \u2013 in particular CSIC on one hand and universities on the other. From the point of view of recruiting new people, these institutions were not agile enough to attract researchers from outside of Catalunya. So the iCREA program was saying, \u201cLet\u2019s invest money in a very meritocratic [way] to select outstanding people and pay the salaries of these scientists.\u201d With the salary in hand a scientist could then knock on the door of these traditional institutions and ask for a position. If they had the salary that they secured in a competitive way, then they would likely look attractive enough for these older institutions to \u201clet in some fresh air.\u201d An infusion of new ideas through new researchers \u2013 new people \u2013 was what we thought CSIC and the universities needed at that time. One year after the other, several investigators have been going into the program over the last 10 years. It\u2019s a competitive, successful program.<\/p>\n

MP<\/b> And what about the parallel development of the institute system?<\/p>\n

EG<\/b> Independent of this, but again around the same time, Andreu Mas-Colell<\/a> [currently Minister of Economy and Knowledge in Catalunya] chose to return to Catalunya to be the Minister of Universities, Research and Information Society. Andreu is a world-famous economist; he was a professor at Berkeley and Harvard, and he is a member of the National Academy of Sciences, one of a small group of international members. One thing that Andreu liked to do was host breakfasts with local scientists, including me. At one of the breakfasts, he reported that an idea was circulating that we should have a research institute system in Catalunya and he wanted to discuss this idea. We discussed at first in abstract how institutes should be created. It became clear to many of us discussing the ICREA program that the new positions could fertilize these new institutes. It was certain, though, that ICREA wasn\u2019t only going to be used for institutes but was to also to be used by universities and CSIC. Areas of investigation for specific institutes were designated through input from a consulting company and the scientific community and also consideration of the potential economic impacts. The IRB was one of the first institutes to get the designation from the Generalitat. These two things \u2013 ICREA and the institutes \u2013 have maintained their support in the Generalitat through changing governments over the past 15 years.<\/p>\n

MP<\/b> But there is another piece to the puzzle \u2013 the story of the Science Park.<\/p>\n

EG<\/b> I have answered your question about Catalunya in general. But now, to complete a triangle, I feel like I should tell you about the science park. This was not in my answer to Catalunya because it is not general. It is specific to the University of Barcelona<\/a> (UB), the oldest, biggest and premier university in Catalunya. We started work on a Science Park about 12-15 years ago. Back then the area housed several other departments at UB, from history to the humanities. These departments decided to move to different campuses in other areas of Barcelona. That meant that a wonderful piece of land near the Diagonal and coincidentally near several science departments like chemistry, physics and biology [was now unused]. Through some collective brainstorming (\u201cun concurso de ideas\u201d), the idea of a science park was selected. UB understood [that] this be a place where basic science research institutes and labs from companies \u2013 both pre-existing companies and spin-offs and start-ups \u2013 would be mixed-up together very intimately. To make it more attractive they would provide shared facilities run by the science park itself for emerging technologies such as proteomics, combinatorial chemistry, and nanosciences. In the meantime, some others have been added, like a transgenic mice facility at the IRB. The philosophy is that each institute can build up facilities, but they have to be open to all.<\/p>\n

Another set of breakfasts was important for this process too. [Like many places, breakfast can be a power-meal in Barcelona.] Marius Rubiralta<\/a>, who was research vice-president of UB at that time, held breakfasts on the first Monday of each month here in the area that would become the science park. Typically we were 8-10 people; half were professors from UB and the other half consisted of the owner of the first pharma, the second pharma, and the third pharma and a rep of all the other companies in Catalunya. This group decided that the first center in the Science Park was to be Institute for Bioactive Molecules. This was the embryo for the science park and also for what was to be[come] the IRB. IRB actually started before the Catalan government decided to make the research institutes. When the Generalitat started the program, we instantly notified them that IRB was a functioning institute already and we were then given the \u201clabel\u201d of the Catalan Research Institute.<\/p>\n

MP<\/b> You were instantly ready to become an investigator at the IRB then, right?<\/p>\n

EG<\/b> Not exactly. When the science park idea was born I was invited to contribute intellectually to the ideas and design and then, afterwards, I was invited to become an investigator in the institute. Being asked to join gave me the same sensation as if I were preparing to jump into a swimming pool that I knew was empty! (Laughter from both of us.) I was moving from the Department of Organic Chemistry at UB \u2013 the department where I had done my PhD studies and had spent all [of] my professional career, except for some parenthetical sabbaticals in France, Scripps, and UCSD. The success of the institute at the time was not a certainty. In some ways, I thought, \u201cThat\u2019s for the others, not for me.\u201d<\/p>\n

MP<\/b> How did you decide?<\/p>\n

EG<\/b> In my case, it was several arguments all together that finally helped me make the decision. The first was the opportunity for interdisciplinary research. At UB we have a great department, but it was too many of the same \u2013 Organic Chemistry everywhere. And we were already at the time already working on several interdisciplinary projects on top of our focus on the synthesis of peptides as protein surface binders. We had already begun doing expression of labeled proteins in E. coli for NMR studies and working on more therapeutic uses of our peptides. I must say IRB was the right fit from the perspective [of] our interdisciplinary research questions. This was the main reason for the move. It was an opportunity for real mixing with scientists from multiple disciplines. The second reason is because I\u2019ve always liked translational science. Here at IRB we\u2019re together with companies, and the opportunity for spin-offs was very attractive. Third, because I was involved in the design of this new institute, I thought joining would be an honest show of support. Any one of the three arguments alone would have been insufficient to compel me to move, but, all together, I knew I had to. But, I was afraid. I didn\u2019t want to lose what I had achieved after so many years in my department at UB.<\/p>\n

MP<\/b> How is research at IRB different?<\/p>\n

EG<\/b> One thing about research is knowing what you want to do. But another thing that is important is how you will do it. What kinds of experiments can answer your question\u2026 that sort of thing. This is the thing that has changed most for my group because to do easy biology in this environment is very, very easy. What I mean is that anyone in my group, even if they have had classical organic training, are able to use a flow cytometer, for example, to measure fluorescence of cells after a few days in the lab. It\u2019s because the facility and the technicians are available for this type of experiment at IRB. My group can now do cell culture, confocal microscopy, [and] we\u2019ve even established a blood-brain barrier model system with epithelial cells and astrocytes isolated from mice. All these were at one time unbelievable experiments for me.<\/p>\n

But the goals are the same. We are a molecular recognition group. We want to design molecules that will bind to a target protein and change its function, usually with the intent of interrupting a protein-protein interaction<\/a> (PPI). Its not the \u201cwhat\u201d but the \u201chow\u201d that has changed. This is all from the point of view of the intramural research in my lab. The other thing is now it\u2019s easier to have substantial, meaningful collaborations with other groups on projects of a grander scale. At IRB we have a strong positive pressure to do projects that are synergistic between groups within the institute. This is easy to say but hard work to do. One of the most talented group leaders at the IRB is Eduard Batlle<\/a> who is head of oncology program. He is studying some unique stem cell lines from colon cancer patients. He and I have just advertised for a post-doc who will work 50% in my lab and 50% in his lab. The idea is to work on isolation and chemical modifications of some alkaloids as potential anti-cancer agents. We expect the person to leverage the expertise of both groups, a catalyst of a joint project.<\/p>\n

MP<\/b> So what can you tell me about your latest research?<\/p>\n

EG<\/b> Do you want to hear my dream? Ok. My dream is: you go into my lab with a 3D structure of your favorite protein. You put your finger on one spot on the protein, and my group synthesizes a ligand, typically a cyclic peptide, that will bind very tight and, even more importantly, very specifically to that spot. Now what is our research? We work to understand why the scenario I posed is currently a dream and what we can do to make it a reality. We think that taking into account the dynamics of the proteins is important, so we look at protein dynamics and the \u03bcs-ms timescale. This is an area where huge domains of protein are moving. Until recently we were blind to these motions until relaxation dispersion [NMR] experiments had become available. Now we are not blind. We are discovering that more and more proteins have important dynamic behavior and of course if we tried to do all our design on a frozen structure, it\u2019s difficult to be successful.<\/p>\n

MP<\/b> What is the implication on those movements in a lock and key versus an induced fit model for binding?<\/p>\n

EG<\/b> The implication is significant. Within the lock and key paradigm, if you have a flexible ligand you will have to pay an entropic cost when binding to the target protein. This idea has guided medicinal chemistry for 100 years. It\u2019s based on the assumption that the protein, too, is rigid. But, if you have a protein that is opening and closing with a rigid molecule that is like a \u201cpalo en las ruedas\u201d (stick in the wheels) \u2013 freezing this movement \u2013 then you pay a huge entropic cost on the side of the protein. My view, but I have not been able to prove this experimentally, is that if you could maybe tune the dynamics of the protein with the dynamics of the ligand then both could move together \u2013 a dynamically tight binder.<\/p>\n

My group can now look at the affinity of ligands with proteins in the gas phase and in solution and rank order families to look for the importance of solvation in these interactions. We\u2019d like to understand how solvation plays a role. Molecular recognition at protein surfaces is the focus of the group. We select proteins for investigation not because they are easy to work with or they are good models, but because we are in a biomedical institute so we choose targets that are therapeutically relevant or at least biologically relevant. For instance, we have been working on protein dynamics related to a protein important to schizophrenia and also on amyloid fibrils (Alzheimers), p53 and growth factors related to cancer. Our recent paper<\/a> in Angewandte [It\u2019s the cover graphic!] reports on a peptide that is able to disrupt a PPI important to endocytosis called clathrin-mediated endocytosis. The key is that the peptide (a modified \u03b2-arrestin sequence) must be able to adopt an \u03b1-helical conformation to bind to the target protein \u2013 the \u03b2-appendage domain of the AP2 complex. For one sequence, a diazobenzene is linked to the peptide at two points (alkylation of cysteine thiols) along the peptide spaced three turns apart. The diazobenze is a photo-switch. Irradiation of the peptide with visible light favors the trans form of the diazobenze and consequently the \u03b1-helix (go). Irradiation with UV light switches the diazobenzene to the cis form and the a-helix can not form (stop). The beauty is that the shape of the peptide can be modulated in either direction based on the cis-trans switching of the diazobenzene and the spacing of the linkages to the peptide, whether it\u2019s two or three helix turns. We call them traffic light peptides. Then if you have a cell culture and you add a one of these peptides and you irradiate with the appropriate light (UV or Vis), endocytosis will stop and, when you switch wavelengths, endocytosis will go back again.<\/p>\n

MP<\/b> Do you envision this as a tool compound?<\/p>\n

EG<\/b> Yes, we envision this as a tool for confocal microscopy. On a single cell basis, [a] scientist can choose whether endocytosis is operative or not. And then they can be compared for [determining] what the effects of endocytosed material [are] for example. Therapeutically, we are limited currently because UV-Vis light is poorly absorbed in tissue, but we envision retinopathies, though. Melanoma In the future we envision using the same strategy but with near IR chromophores to help with better tissue penetration.<\/p>\n

MP<\/b> Do you have still have responsibilities at UB?<\/p>\n

EG<\/b> Of course. I love university life, I love my university and I love teaching a lot. One the conditions of coming here [to IRB] was that I could keep this aspect of my academic activity. For example, this year I taught a course on the application of spectroscopy with stereochemistry and conformational analysis to elucidate the configuration and conformation of molecules. Students like this course because it\u2019s like molecular Sudoku, \u201cWhat is a compound that has this MW, with these spectra\u2026,\u201d I participate also on committees for the teaching activities. But my research labs are all at IRB.<\/p>\n

MP<\/b> How do you identify as being a Catalan? You are a son of Barcelona. What kept you here?<\/p>\n

EG<\/b> I am traditional for this point of view. It is a very common practice for people here to live abroad but to come back. When my mother recently passed away (at 92), all four of her sons and her nine grandsons without exception were living in Barcelona. But this doesn\u2019t mean we don\u2019t move. I have lived for periods in France, the US, and the UK; one of my brothers has also lived abroad. One of my sons lived in Italy for several years and another has lived in the US and China. This means we like to go abroad, but we come back. It\u2019s more a question of the style of life. We keep very close to family and friends. I like music. When I was young, say from 16-20 years old, I sang in choir with a group of about 40 singers. That\u2019s been some time ago! Nonetheless, every first Tuesday of the month I have dinner with that group; sometimes we are all 40, and sometimes only 15-20 can make it. I, like the others, sometimes have other plans that can\u2019t be broken or I\u2019m out of town or whatever. I know that if I want, I can go and spend time and talk with those people that I\u2019ve know for all these years and we can sing together if we choose. These roots \u2013 and here when I talk about roots I mean people \u2013 all these people that were my friends when I was 16 and we sang together, or friends I made during the summer when I was young, or friends from school. Many of these people are still around and I can enjoy spending time with them. Of course on top of this is family; once a week while she was still alive, my brothers and I together had lunch with my mother. For me this is very important. It\u2019s about people and relationships.<\/p>\n

MP<\/b> More that a decade after we first met, Ernest continues to inspire and teach me. His life is filled with the same day-to-day challenges as any academic, but he remains focused on what\u2019s important like ideas and relationships. In the end those things provide the greatest joy. Now, just like when I was a grad student, I\u2019m hoping to follow his lead.<\/p>\n","protected":false},"excerpt":{"rendered":"

This is the second post from Mark Peczuh on the culture of doing science in Spain and, specifically, in Catalunya. (I do owe Mark a big apology for not getting this out sooner.) I really have enjoyed reading this interview with Ernest, and I hope you will too. Lots of great stuff to learn! \u201cThank […]<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-183","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/183","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=183"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/183\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=183"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=183"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=183"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":182,"date":"2018-06-19T18:46:58","date_gmt":"2018-06-19T18:46:58","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=182"},"modified":"2018-06-19T18:46:58","modified_gmt":"2018-06-19T18:46:58","slug":"the-jacs-challenge-a-mini-round-up","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/the-jacs-challenge-a-mini-round-up\/","title":{"rendered":"The JACS Challenge – A Mini-Round Up"},"content":{"rendered":"

Originally posted September 30, 2013<\/p>\n

First of all, I wanted to offer a big thank you to everyone who participated. My co-conspirators (CJ<\/a>, See Arr Oh<\/a>, and Stu<\/a>) and I are truly grateful to everyone who took time out of their day to answer our survey questions. We\u2019ve had 401 responses (as of Monday evening at 8pm EST), which, in all honesty, is so much more than we had ever expected. We need to send a special word of thanks to the ever-generous, and awesome, Derek Lowe<\/a> who, I am sure, was the reason that many of those respondents found the survey in the first place.<\/p>\n

I wanted to give a brief run-down of the responses that we received from our first 19 guinea pigs. Not including the four of us, the remaining 15 included: Christopher Cramer<\/a>, a crew from Bruce Turnbull<\/a>, Dr. Rubidium<\/a>, Grant Hill<\/a>, Jessica Breen<\/a>, Marcel Swart<\/a>, Katherine Haxton<\/a>, Aaron Finke<\/a>, Gavin Armstrong<\/a>, Ash Jogalekar<\/a>, Stuart Conway<\/a>, Vikki Cantrill<\/a>, Paul Bracher<\/a>, and Kathy Franz<\/a>.<\/p>\n

At the outset, we all (CJ, See Arr OH, Stu, and I) agreed that importance and impact and citations are not equivalent and are also difficult to define. What we were\/are after is an understanding of the following.
\n1) Can chemists agree on what papers are \u201cimportant\u201d?
\n2) Can chemists predict what papers are cited the most?
\n3) Can we identify and agree on papers we want to talk about with chemists (or with non-chemists)
\n4) Is there any overlap between what we find important and what gets cited?
\nAnd, finally
\n5) There\u2019s lots of really cool chemistry out there; what do I (we) miss that other people see?<\/p>\n

Our respondents gave some initial perceptions on how their thought process. In general, there was an opinion that papers from a persons own field would dominate question one (perceived importance) along with titles that included words like \u201cfirst\u201d. Several respondents thought the second question (most citations) would be dominated by \u201cpeople worship\u201d. That is, papers from \u201cbig name\u201d PI\u2019s would be cited the most. Another person thought the best cited papers would include: \u201cAll synthesising things using methods that will undoubtedly have been picked up on by others and further developed.\u201d<\/p>\n

So, how did those predictions play out? And \u2026 what were the answers to our four questions? (1-Which three papers in the issue do YOU think are the most \u2018significant\u2019? 2-Which three papers do you think will have been cited the most to-date? 3-Which three papers would you most want to point out to other chemists? 4-Which three papers would you want to shout about from the rooftops?)<\/p>\n

This pdf<\/a> shows several things. First, it lists the articles from our issue of JACS<\/i> in order of times cited. Second, it shows the number of times each paper was used as a response to one of our questions. Third, there is a comparison between total citations and total responses. There are several results here that I\u2019d like to note:
\n1) Of the 63 papers, there were only 16 not mentioned by any of our respondents.
\n2) The fewest number of citations by any paper on this list is 11. (This seems remarkable. Should<\/i> it be?)<\/p>\n

Let\u2019s have a look at some of the individual papers and their use in the responses (Disclaimer \u2014 I am writing this so I\u2019m going to discuss the papers\/responses that I think are most interesting):<\/p>\n

\u201cFactors that Determine the Protein Resistance of Oligoether Self-Assembled Monolayers \u2212 Internal Hydrophilicity, Terminal Hydrophilicity, and Lateral Packing Density<\/a>\u201d
\nTotal Citations: 325; Total Responses: 4.
\nThis paper addressed issues that many were having at the time and set a precedence for how researchers should construct their self-assembled monolayers. Obviously, there are a lot of chemists who would find this useful to their own research. I think the useful issue is important for determining citation number. I am heartened to see that \u201cuseful\u201d seems to be key in deciding the top three cited papers from this issue.<\/p>\n

\u201cTNA Synthesis by DNA Polymerases<\/a>\u201d
\nTotal Citations: 59; Total Responses: 19.
\nMany of our respondents found this paper interesting due to it\u2019s origin of life (OoL) implications. Seeing as how OoL has come up often among the \u201cgrand challenges\u201d for chemistry, it is somewhat surprising that this study hasn\u2019t been cited more. Are chemists (as a whole) just not that interested in OoL studies? Is this OoL a more recent phenomenon? That is, have most of its citations come in just the last year or two? (This is a question we will be looking to answer in our publication of the larger study.)<\/p>\n

Other Useful<\/u>
\n\u201cEasily Processable Phenylene\u2212Thiophene-Based Organic Field-Effect Transistors and Solution-Fabricated Nonvolatile Transistor Memory Elements<\/a>\u201d
\nTotal Citations: 275; Total Responses: 10 (This one *could* also be helped by \u201cauthor-worship\u201d \u2013 The PI is Tobin Marks).
\n\u201cTransition Metal-Catalyzed Formation of Boron\u2212Nitrogen Bonds:\u2009Catalytic Dehydrocoupling of Amine-Borane Adducts to Form Aminoboranes and Borazines<\/a>\u201d
\nTotal Citations: 258; Total Responses: 2<\/p>\n

Buzzword Bingo<\/u>
\n\u201cSingle-Step in Situ Synthesis of Polymer-Grafted Single-Wall Nanotube Composites<\/a>\u201d
\nTotal Citations: 251; Total Responses: 8
\n\u201cAn Ionic Liquid-Supported Ruthenium Carbene Complex: A Robust and Recyclable Catalyst for Ring-Closing Olefin Metathesis in Ionic Liquids<\/a>\u201d
\nTotal Citations: 251; Total Responses: 14
\n\u201cA Heterocyclic Peptide Nanotube<\/a>\u201d
\nTotal Citations: 171; Total Responses: 15
\n\u201cSolventless Polymerization: Spatial Migration of a Catalyst To Form Polymeric Thin Films in Microchannels<\/a>\u201d
\nTotal Citations: 18; Total Responses: 10<\/p>\n

Firsts<\/u>
\n\u201cFirst Examples of Organophosphorus-Containing Materials for Light-Emitting Diodes<\/a>\u201d
\nTotal Citations: 103; Total Responses: 15
\n\u201cFirst Pseudorotaxane-Like [3]Complexes Based on Cryptands and Paraquat:\u2009Self-Assembly and Crystal Structures<\/a>\u201d
\nTotal Citations: 88; Total Responses: 3.
\n\u201c The First Triple Thiol-thiolate Hydrogen Bond versus Triple Diselenide Bond That Bridges Two Metal Centers<\/a>\u201d
\nTotal Citations: 11; Total Responses: 1<\/p>\n

Things that might show up in a textbook, or in a classroom, or in a conversation between a bunch of dorky chemists<\/u>
\n\u201cOn the Nonpolar Hydration Free Energy of Proteins:\u2009Surface Area and Continuum Solvent Models for the Solute\u2212Solvent Interaction Energy<\/a>\u201d
\nTotal Citations: 129; Total Responses: 3
\n\u201cMechanisms of C\u2212C and C\u2212H Alkane Reductive Eliminations from Octahedral Pt(IV): Reaction via Five-Coordinate Intermediates or Direct Elimination?<\/a>\u201d
\nTotal Citations: 94; Total Responses: 10
\n\u201cTin-Centered Radical and Cation:\u2009Stable and Free<\/a>\u201d
\nTotal Citations: 38; Total Responses: 1
\n\u201cQuantitative Measure for the \u201cNakedness\u201d of Fluoride Ion Sources<\/a>\u201d
\nTotal Citations: 32; Total Responses: 4
\n\u201cA Cationic Guest in a 24+<\/sup> Cationic Host<\/a>\u201d
\nTotal Citations: 31; Total Responses: 5<\/p>\n

Journalism Fodder<\/u>
\n\u201cDiamond Formation by Reduction of Carbon Dioxide at Low Temperatures<\/a>\u201d
\nTotal Citations: 50; Total Responses: 7 (All of which were responses to the \u201ctell non-chemists\u201d question)<\/p>\n

One more curious case<\/u>
\n\u201cPartitioning the Loss in Vancomycin Binding Affinity for d-Ala-d-Lac into Lost H-Bond and Repulsive Lone Pair Contributions<\/a>\u201d
\nTotal Citations: 57; Total Responses: 11
\nA lot of us really \u201cliked\u201d this paper. This is another one of those papers that might not have been \u201ctimely\u201d enough. MRSA<\/a>and other antibiotic resistance bacteria have burst onto the scene much more in recent years. To many of us, this seemed like a great study for chemistry (structure, function, mutation, new function) study as well as a paper that might interest reporters covering antibiotic resistance.<\/p>\n

The Horse Race<\/u>
\nSo \u2026 who did the best picking citations<\/a>?
\nNone of our initial respondents correctly guessed the top 3 cited papers. Our clear winner, however, was Gavin Armstrong. Kathy Franz also put in a very respectable showing! They were the only two to top 600 total citations (between the three articles they chose). In the analysis file<\/a>, I show how respondents picks for each of the questions fared in terms of citations. It is also quite clear that, when asked to pick the most cited articles, chemists are capable of distinguishing papers that will be cited.<\/p>\n

If your still reading, thanks! This is all I\u2019m going to analyze for this post. We do expect to have a more detailed and in depth analysis for the data from the larger survey. These were just things that I found interesting. I\u2019m sure that if I\u2019ve missed anything important, CJ, CRO, and Stu will mention it in the comments. Also, if you see anything interesting, let me know. We had a lot of fun with this survey! And, if you\u2019d like to see more, here are all of our respondents answers<\/a>(with some comments on why they liked the papers they did). Enjoy!<\/p>\n

Thanks
\n-CJ, See Arr Oh, Stu, and Matt<\/p>\n","protected":false},"excerpt":{"rendered":"

Originally posted September 30, 2013 First of all, I wanted to offer a big thank you to everyone who participated. My co-conspirators (CJ, See Arr Oh, and Stu) and I are truly grateful to everyone who took time out of their day to answer our survey questions. We\u2019ve had 401 responses (as of Monday evening […]<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-182","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/182","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=182"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/182\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=182"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=182"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=182"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":181,"date":"2018-06-19T18:46:14","date_gmt":"2018-06-19T18:46:14","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=181"},"modified":"2018-06-19T18:46:14","modified_gmt":"2018-06-19T18:46:14","slug":"sciencegeist-the-jacs-challenge","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/sciencegeist-the-jacs-challenge\/","title":{"rendered":"Sciencegeist: The JACS Challenge"},"content":{"rendered":"

Originally posted September 23, 2013<\/p>\n

What makes a scientific publication good?
\nAs scientists, are we capable of discerning good papers from bad papers?<\/p>\n

These questions were the focus of a recent conversation<\/a> I had on twitter with Stuart Cantrill<\/a>, editor at Nature Chemistry, and bloggers extraordinaire, Chemjobber<\/a> and See Arr Oh<\/a>. This conversation started with the observation that a recent paper<\/a>, containing what might be evidence of scientific misconduct, was generating a lot of buzz<\/a> on-line. Chemists were rightly upset about this alleged impropriety. But, the incident highlighted a different aspect of scientific publishing to me. Precisely:<\/p>\n

We, as a scientific community, generate many thousands of research articles a year. In my ideal world, research publications should be an ongoing conversation to better understand our world. Most of that conversation does occur in the literature. For a healthy discipline, shouldn\u2019t that conversation be happening outside of the literature as well? This dialogue certainly happens at conferences and within research groups and in general-interest articles. Shouldn\u2019t these conversations also be taking place in the on-line world as well? Between blogs and social media, there are some powerful methods for enabling real-time communication with scientists all over the world! Shouldn\u2019t some topics be so vital and interesting to our field that we want to discuss them immediately? Even if they aren\u2019t within our chosen sub-discipline? Shouldn\u2019t we collectively be talking about some research as much as we discuss research misconduct?<\/p>\n

With these topics on my mind, I asked Stu, (paraphrasing) \u201cAs an editor, can you recognize a paper that should garner broader discussion, and how do you effectively share *good* papers?\u201d We went on to have a broader conversation about how any of us (seriously, we\u2019re all experts in chemistry here) recognize a \u201cworthy\u201d paper. Finally, in a fit of genius, Stu asked, \u201cIf we were all given the same 10year old copy of JACS1<\/sup>, would we pick out the same \u2018top 5\u2032 papers?\u201d Stu\u2019s hypothesis for this question, which the rest of us agreed with, was: I doubt it!<\/p>\n

So we set forth to find out! We sent out emails to a broad range of chemists (grad students, professors, editors, journalists, professionals) asking if they\u2019d like to be involved in our experiment. Could they (we) choose the best papers from a 10 year old issue of JACS<\/a>?<\/p>\n

Best or good or important are judgements that are entirely subjective! So we asked four very specific questions:<\/p>\n

1) Which three papers in the issue do YOU think are the most \u2018significant\u2019 (your own definition of \u2018significant\u2019 is what is important here)?
\n2) Without looking up the numbers<\/b>, which three papers do you think will have been cited the most to-date?
\n3) Which three papers would you most want to point out to other chemists?
\n4) Which three papers would you want to shout about from the rooftops (i.e., tell anybody about, not just chemists)?<\/p>\n

None of these questions really get at what it means to be important. They are just ways to describe how we perceive importance. Even question number 2, which evokes an easily retrieved metric, doesn\u2019t necessarily prove a paper\u2019s \u201cworth\u201d. But, are we (scientists! chemists!) even able to figure out which articles would get cited the most?<\/p>\n

Our esteemed panel of experts have weighed in with their thoughts. How well would you do in the JACS Challenge? We\u2019ll be back in one week with our respondents answers along with an analysis of their answers and thoughts.<\/p>\n

But, first, we\u2019d love to hear from you! How would you<\/b> answer these four questions?! We have set up a survey<\/a> on Survey Monkey in order to compile more answers. We plan on using your anonymous responses to try to glean some generalized trends about the way chemists view a study\u2019s \u201cimportance\u201d for a publication that we are preparing. We\u2019d love to hear your thoughts on how you tried to analyze these papers here in the comments of this post!<\/p>\n

Are you chemist-enough? You\u2019ve got the questions<\/a>! You\u2019ve got the issue of JACS<\/a>! Put your expertise on the line!!<\/p>\n

We\u2019re looking forward to hearing from you!<\/p>\n

Survey link: HERE<\/a><\/p>\n

\u2013 See Arr Oh, Chemjobber, Stu, and Matt<\/p>\n

1<\/sup>This could have just as easily involved an issue of Angewandte Chemie or other journal. We chose JACS because it was the first journal that popped up (in considering journals that is a standard of quality and broad applicability among all chemists) and also because \u201cThe JACS Challenge\u201d had such a nice ring to it!<\/p>\n","protected":false},"excerpt":{"rendered":"

Originally posted September 23, 2013 What makes a scientific publication good? As scientists, are we capable of discerning good papers from bad papers? These questions were the focus of a recent conversation I had on twitter with Stuart Cantrill, editor at Nature Chemistry, and bloggers extraordinaire, Chemjobber and See Arr Oh. This conversation started with […]<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-181","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/181","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=181"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/181\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=181"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=181"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=181"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":180,"date":"2018-06-19T18:45:41","date_gmt":"2018-06-19T18:45:41","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=180"},"modified":"2018-06-19T18:45:41","modified_gmt":"2018-06-19T18:45:41","slug":"sciencegeist-interview-with-xavier-salvatella-by-mark-peczuh","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/sciencegeist-interview-with-xavier-salvatella-by-mark-peczuh\/","title":{"rendered":"Sciencegeist: Interview with Xavier Salvatella – by Mark Peczuh"},"content":{"rendered":"

Originally posted June 5, 2013<\/p>\n

This is the first of several posts from Mark Peczuh<\/a> that I am hosting. In this post, Mark interviews Xavier Salvatella on his research (protein-protein interactions and their implications for disease) and why he works\/lives in Barcelona. Enjoy!<\/i><\/p>\n

\u201cIt is a bit like Janelia Farm on the Diagonal\u201d<\/b><\/p>\n

We met, unexpectedly, at the entrance to his building in the Barcelona Science Park on the University of Barcelona campus. His building is literally in the shadow of Camp Nou, the home stadium of the famed Football Club of Barcelona<\/a>better known simply as \u201cBar\u00e7a\u201d. He was hurriedly arriving to make our appointment in the same way I was. Although it has been a few years, I instantly recognized Xavier Salvatella<\/b> by his characteristic gait with the torso slightly askew and the welcoming smile. Xavier had reluctantly agreed to be the subject of my first interview \u2013 a guinea pig. I am currently in Barcelona on a Fulbright Fellowship. As part of this fellowship I will be interviewing interesting scientists here in order to understand the practice of science\/research in the context of place.<\/p>\n


\nXavier Salvatella (Image Credit: Mark Peczuh)<\/p>\n

MP: So tell me about your research.<\/b>
\nWe have two sides of the lab<\/a>. One side has been focusing on methods development to characterize the flexibility of proteins. Everybody is aware of the importance of flexibility, but it\u2019s very hard to characterize. Right now only simulations are undergoing a revolution. [This revolution] is based on a change of approach on how computers are built. Rather than building supercomputers that can do many different tasks, people have said, \u201cPerhaps it\u2019s better to build them for a specific task.\u201d Computers have been optimized to do molecular dynamics on a much longer time scale, up to microseconds. The simulations still cannot be done with very large and complex flexible proteins and many things can not be studied with simulation.<\/p>\n

MP: I\u2019m expecting you to tell me something about how your group uses NMR as a tool for characterizing dynamics of proteins. How does the time scale of the experiment \u2013 either simulations or NMR \u2013 fit with the dynamics of the protein?<\/b>
\nThat\u2019s a good question. By NMR you can look at dynamic processes at any time scale. Processes from nanoseconds, using relaxation times, to seconds or more, by doing experiments in real time, can be studied. Simulations can only look at the fastest time scales but there are many, interesting, dynamic processes that are so slow that they\u2019re beyond the current reach of simulations. The encouraging thing is that on the fastest time scales, there is good agreement between the two. This has led to improvement of both of the methods (NMR and simulation).<\/p>\n

MP: Where do protein dynamics come into play in biochemistry? Protein-protein interactions, catalysis, what?<\/b>
\nProtein dynamics are definitely important to catalysis, but we\u2019re focused on protein associations \u2013 either protein-protein interactions (PPIs) or protein oligomerization. Usually when PPIs are modeled via docking, they\u2019re treated as two rigid bodies and the complementarity of their surfaces is interrogated. In reality, however, the two proteins are fluctuating; they are flexible. When they associate, there are often subtle conformational rearrangements in both proteins. We\u2019ve been collaborating with a computational team at the Barcelona Supercomputing Facility regarding this. We reported earlier this year on a strategy to improve prediction of binding partners and docking modes between ubiquitin and several of its partners<\/a>. The task of ubiquitin is to bind proteins. If you try to predict complexes with it you have to take into account the flexibility. We used NMR experiments to define a conformational ensemble for ubiquitin; this is a collection of all the conformations that have a certain probability of being populated by the protein. It\u2019s multimodal, and when all the conformers are probed in the simulation, you get accurate complexes. The collection of conformers agrees with the experimental data better than the crystal structure. So protein flexibility, when accounted for by conformational ensembles, improves the performance of docking methods.<\/p>\n

MP: What about the other side of the lab?<\/b>
\nThe other side of the lab is working on a project that also involves a question related to PPIs because it involves the association of a protein with itself. Flexibility often makes proteins more probable to aggregate and form plaques as a consequence of that flexibility. We are interested in this relationship: more flexibility \u2013 more aggregation, more flexibility \u2013 faster aggregation, different types of flexibility \u2013 different types of aggregates, these sorts of questions. But we were using a protein that is not particularly important to biomedicine.<\/p>\n

MP: And then?<\/b>
\nThe story is quite funny, actually. Shortly after I had arrived at the IRB, while we were in the midst of the methods development project, my wife\u2019s friend asked me to describe our research to her. The incident coincided with a real effort on our part to try and adapt our research to what we have here [at the IRB]. I realized that it would be attractive to get into a biomedical problem. Rather than working only on the methods for their own sake, we wanted to apply the methods to an important protein. I was explaining our research about aggregation to her when she said, \u201cI have a family member that has a disease that is similar to this, it\u2019s called Kennedy\u2019s disease<\/a>.\u201d I looked up Kennedy\u2019s disease on Wikipedia and found out it\u2019s a rare familial genetic disease of which not much is known. But it had to do with aggregation of a protein called androgen receptor, a protein that is responsible for the male phenotype. In the cytosol it is in an inactive state and then upon binding testosterone large conformational changes occur. This leads to translocation into the nucleus and the protein then acts as a transcription factor to upregulate specific genes.<\/p>\n

MP: Wow. So it was a project that was perfectly suited to your program, right?<\/b>
\nYes. Around that same time there was a call by Catalan funding agency that targeted rare diseases. So I quickly wrote up an application and got about 400.000 euros<\/a> (shared with two other groups) to work on the androgen receptor aggregation project \u2013 [in order] to characterize how it aggregates, etc.<\/p>\n

MP: Isn\u2019t androgen receptor linked to prostate cancer too?<\/b>
\nYes, it is also the main target in prostate cancer. The normal state of prostate cells is to be turned \u201con\u201d via testosterone through the androgen receptor. Unless there is constant activation by testosterone, the cells will go into apoptosis. So a common pharmacological treatment for prostate cancer is to stop the activation of androgen receptor. But in a certain fraction of patients that undergo this therapy, [after] two to three years, they stop responding to the treatment. This recurrence is called castration resistant prostate cancer. Here the receptor is able to activate itself even in the absence of testosterone. We\u2019re trying to look into this process using our methods. The reason being that the protein sequences (via sequencing of the patients\u2019 DNA) for the androgen receptors have mutations. They are all in a domain that is totally flexible, and there are many hints that this is the domain that drugs should really target. So crystallography can\u2019t give much information here but our NMR methods can\u2026.and do, because we can look at these \u201cintrinsically disordered\u201d proteins.<\/p>\n

MP: So it\u2019s methods development to look at protein flexibility and its implications for aggregation and the application of the methods to therapeutically important proteins?<\/b>
\nYes, and the upside is that, if you look at the IRB website we have five research program areas: chemistry and molecular pharmacology, structural and computational biology, cell and developmental biology, oncology, and molecular medicine. Out of those five, three or four of the program areas are in this one project. These two projects related to androgen receptor \u2013 Kennedy\u2019s disease and prostate cancer \u2013 have been well received by my colleagues and students.<\/p>\n

MP: I haven\u2019t asked about the IRB itself. How would you describe it?<\/b>
\nFor me, right now, the reasons I joined IRB<\/a> were that I could solve two [problems]. It was here I knew I would \u201cbe where I belong.\u201d I am from here and I have friends and I like to live here. And there was a place I could [perform] the type of research I wanted with the resources that I think are necessary. Because the two things happened in the same place, I took [the position]. It was very pragmatic.<\/p>\n


\n(Image Source: Institute for Research in Biomedicine<\/a>)<\/p>\n

MP: What resources, maybe beyond the obvious instrumentation, etc.?<\/b>
\nAt the IRB, all the resources necessary to ask broad, impactful questions are provided. In return there is an expectation that investigators are ambitious about their science; big ideas are encouraged. By design, there is no process for tenure at the IRB, and investigators are reviewed every five years. This creates a certain urgency or an intensity that that defines the environment here. It is quite effective for motivating everyone.<\/p>\n

MP: It sounds like Janelia Farm on the Diagonal.<\/b>
\nYes, it is a bit like Janelia Farm on the Diagonal. (La Diagonal is a huge boulevard in Barcelona where the IRB is located.) When I left to do a post-doc in Cambridge, I thought, \u201cI am going to a great place in a very important group who try to solve huge fundamental problems. I will not be able to do this in Barcelona ever so I may as well enjoy it and if I do well I will look for positions elsewhere \u2013 in the US or the UK to run a research group.\u201d And then, I realized it was possible to do it here in Barcelona at the IRB, so I applied to the job and I got it.<\/p>\n

MP: What made this possible?<\/b>
\nThere is another virtual institution, called iCREA<\/a> that hired me from Cambridge to work at the IRB; they gave me a salary for five years. Let me give you some background. Before I left for Cambridge, there were two places where you could do research: as a university professor or as a CSIC investigator. CSIC is a national research institute all across Spain \u2013 it\u2019s similar to the CNRS in France \u2013 one institution devoted to many different types of research. But there was [an] interesting development in Catalu\u00f1a around the time when I left [for Cambridge] in which the government decided that those two institutions were not appropriate for doing cutting edge, high impact research for many reasons \u2013 the rigidity of the hiring system, tenure \u2013 which can cause people to relax, bureaucracy, etc. etc. etc. Two instruments were created by the Catalan government to solve this problem. One is the creation of iCREA; it is a very small agency that recruits good scientists and negotiates a salary with them and assesses their performance every 3-5 years. This instrument is open to all institutions (universities, CSIC) as a way to support salaries for their staff. This was a way that many talented scientists have moved [back] to Barcelona. The big thing is that the selection of the iCREA researchers is done by committees of experts that couldn\u2019t care less about anything except the quality of the science of the applicants. There was a huge emphasis on that. Each year there is a huge competition for 20 positions in iCREA. I was brought in to the IRB on a (now discontinued) junior iCREA program. In parallel to this was the creation of centers of excellence. The government created a number of research institutes of varying sizes in areas of science that were considered important to Catalu\u00f1a. Of the many centers that were created, IRB is one of the biggest. They are totally different than a university or CSIC \u2013 more intensity, more resources. Both university faculty and CSIC researchers can be investigators at an institute along with iCREA researchers\u2026 or in fact \u201cno ones\u201d \u2013 investigators that are sponsored directly by the institute. We have all of these varieties at IRB. These two instruments have been very successful, so successful that the competition is quite intense. They have changed the panorama completely \u2013 now we have in Catalu\u00f1a research centers that are top quality in Europe, top quality in the world.<\/p>\n

There\u2019s something about this neighborhood of Barcelona that encompasses Camp Nou and the IRB. The motto of Bar\u00e7a is visible from an arial view of the stadium, \u201cM\u00e9s que un club (More than a club).\u201d Perhaps the same can be said for the IRB, \u201cM\u00e9s que un institut.\u201d<\/p>\n


\nImage from Google Maps. A<\/b> indicates the Institute for Research in Biomedicine.<\/p>\n

*Name: Xavier Salvatella
\nPosition: Investigator at the Institute for Research in Biomedicine (IRB) in Barcelona.
\nResearch: Characterizing the flexibility of proteins and the implications of this flexibility for biology
\nImportant: Married, father of son Lluc (2 years) and daughter Maria (4 months)
\nWhy Barcelona? I am from here and I have friends [here] and I like to live here
\nWhy IRB? And [in Barcelona] there was a place I could [do] the type of research I wanted [and] where there [were] resources that I think are necessary [for that research]. Because the two things happened in the same place, I took [the position]. It was very pragmatic.
\nQuirky: [I have] a peculiar fascination with pens and personal office supplies.<\/p>\n","protected":false},"excerpt":{"rendered":"

Originally posted June 5, 2013 This is the first of several posts from Mark Peczuh that I am hosting. In this post, Mark interviews Xavier Salvatella on his research (protein-protein interactions and their implications for disease) and why he works\/lives in Barcelona. Enjoy! \u201cIt is a bit like Janelia Farm on the Diagonal\u201d We met, […]<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-180","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/180","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=180"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/180\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=180"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=180"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=180"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":179,"date":"2018-06-19T18:45:02","date_gmt":"2018-06-19T18:45:02","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=179"},"modified":"2018-06-19T18:45:02","modified_gmt":"2018-06-19T18:45:02","slug":"sciencegeist-guest-writer-mark-peczuh","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/sciencegeist-guest-writer-mark-peczuh\/","title":{"rendered":"Sciencegeist: Guest Writer: Mark Peczuh"},"content":{"rendered":"

Originally posted June 5, 2013<\/p>\n

Over the next several weeks, I am going to be hosting posts written by Mark Peczuh<\/a> (pronounced PEEzee \u2013 thanks to some brilliant translation of Hungarian at Ellis Island). Mark is an associate professor of chemistry at the University of Connecticut. His research group synthesizes molecules that are used to better understand how proteins interact with sugars. In order to do this, they make sugar molecules with seven-membered rings (instead of the natural six-membered \u2013 as in glucose \u2013 or five-membered \u2013 as in fructose). Some of you may know Mark from Twitter<\/a>.<\/p>\n


\nMark Peczuh (Photo Credit: UConn Chemistry<\/a>)<\/p>\n

Mark is currently on a Fulbright Fellowship in Barcelona. He is working with Toni Planas<\/a> of the Institute of Chemistry of Sarria<\/a> at the University of Ramon Llull. Toni is an expert in (and one of the founders of) a field that develops proteins called glycosynthases (proteins that synthesize sugars). Mark and Toni are hoping that they can coax some of the proteins (that Toni works with) to synthesize some sugars with seven-membered rings (that Mark studies).<\/p>\n

Mark contacted me recently to see if I would host some interviews he is conducting with scientists in and around Barcelona. Mark is interested in exploring how the practice of research relates to the context of the place in which the research is being done. Of course, I jumped at the chance. I am really looking forward to seeing what Mark and his interviewees have to say! The first interview, which will be posted later this evening, is with Xavier Salvatella<\/a>, and I know you\u2019ll all enjoy it!<\/p>\n

Also \u2026 A big congrats to Mark on being awarded (read: earning) this Fulbright Fellowship. The Fulbright is a very prestigious, and highly competitive award, meant to foster academic relationships between scholars in the U.S. and scholars in Europe. While some Fulbright\u2019s involve both research and teaching, Mark is on a full research scholarship. This is a very exciting time for Mark, though I know he is missing his family like crazy! I wish him all the best during his fellowship!<\/p>\n","protected":false},"excerpt":{"rendered":"

Originally posted June 5, 2013 Over the next several weeks, I am going to be hosting posts written by Mark Peczuh (pronounced PEEzee \u2013 thanks to some brilliant translation of Hungarian at Ellis Island). Mark is an associate professor of chemistry at the University of Connecticut. His research group synthesizes molecules that are used to […]<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-179","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/179","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=179"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/179\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=179"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=179"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=179"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":178,"date":"2018-06-19T18:44:28","date_gmt":"2018-06-19T18:44:28","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=178"},"modified":"2018-06-19T18:44:28","modified_gmt":"2018-06-19T18:44:28","slug":"sciencegeist-alchemy-vs-chemistry-same-as-it-ever-was","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/sciencegeist-alchemy-vs-chemistry-same-as-it-ever-was\/","title":{"rendered":"Sciencegeist: Alchemy vs Chemistry: Same as it ever was"},"content":{"rendered":"

Originally posted May 17, 2013<\/p>\n

\u2026 The more things change, the more they stay the same.<\/p>\n

I\u2019m currently reading The Secrets of Alchemy<\/i><\/a> by Lawrence Principe. It\u2019s a really enjoyable book, and I\u2019ve learned so many things from it. I hope to share some of my favorites. But, I\u2019ve just read a bit of Principe\u2019s research in the book that seems poignant for my profession (chemistry) in these times. (In any book, there is always some bit: character, place, situation, or story that seems very relevant to some part of your life \u2026 and this book is no different).<\/p>\n

On communication issues:<\/p>\n

Let no man trouble to explore this art
\nIf he can\u2019t understand the aims and jargon
\nOf alchemists \u2013 and if he does, then
\nHe is a pretty foolish sort of man
\nBecause this art and science is, said he,
\nIndeed a mystery in a mystery<\/p>\n

And so I conclude: since God in heaven
\nWill not permit alchemists to explain
\nHow anyone may discover this stone,
\nMy best advice is this \u2013 let it alone<\/p><\/blockquote>\n

From Chaucer\u2019s Canterbury Tales<\/i><\/p>\n

On chemical employment:
\nPrincipe writes about Pieter Brueghel\u2019s drawing Alghemist<\/i>, which is a play on words for a Dutch phrase meaning \u201ceverything is lost.\u201d This work, and other art that followed, reprises the themes of the chemist toiling away while putting his family into the poor house. The labor demands and consumes infinite time and treasure while returning little to nothing.<\/p>\n

These are just a few of the recurring historical themes that appear in the book, and I hope to be able to share more of this. But, if you are interested in the history of chemistry\/chymystry\/alchemy go out and buy it.<\/p>\n","protected":false},"excerpt":{"rendered":"

Originally posted May 17, 2013 \u2026 The more things change, the more they stay the same. I\u2019m currently reading The Secrets of Alchemy by Lawrence Principe. It\u2019s a really enjoyable book, and I\u2019ve learned so many things from it. I hope to share some of my favorites. But, I\u2019ve just read a bit of Principe\u2019s […]<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-178","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/178","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=178"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/178\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=178"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=178"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=178"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":177,"date":"2018-06-19T18:43:56","date_gmt":"2018-06-19T18:43:56","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=177"},"modified":"2018-06-19T18:43:56","modified_gmt":"2018-06-19T18:43:56","slug":"sciencegeist-movie-blood","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/sciencegeist-movie-blood\/","title":{"rendered":"Sciencegeist: Movie Blood"},"content":{"rendered":"

Originally posted April 18, 2013<\/p>\n

\u201cIf it bleeds, we can kill it\u201d \u2013 Major Dutch Schaefer<\/a>
\n(This post is an entry in See Arr Oh<\/a>\u2018s Chemistry at the Movies<\/a> Blog Carnival)<\/i><\/p>\n

When Dutch and his band of military mercenaries went stalking the Predator in the jungles of South America, they had no idea what they were going up against. Bio-adaptive camouflage. Laser-based weaponry. Infrared vision. These guys were screwed. Not even Apollo Creed<\/a> or Jesse \u201cThe Body\u201d Ventura<\/a> had any hope of surviving!<\/p>\n

<\/p>\n

So, yeah. This alien is pretty bad-ass. But probably my favorite anatomical feature (ahem) of this thing is its blood. The Predator has this really cool luminescent blood. Being that I\u2019m a nerd (check), that I really enjoy sci-fi (check \u2026 really, people, I\u2019m just a statistic), and that I\u2019m a bioinorganic chemist (that means that I study metals in biology, and, specifically, that I study metals in proteins, and, more specifically, that I study hemoglobin and myoglobin, which are the proteins that give the red color to blood and muscles\/meat). In fact, one of my primary research goals is to study how proteins like hemoglobin and myoglobin affect the chemistry (gas storage storage capacity, reactivity) of the metal complex that it contains. In the lab, that means that I replace the heme in hemoglobin and myoglobin with non-biological metal complexes and see what happens! So, when it comes to alien blood in the movies, I tend to geek out and try to figure out how that blood might \u201cnaturally\u201d occur. The fun part about this is that, while our understanding of biology is limited to how it works on Earth, there are nearly limitless possibilities for how biology might work on another planet.<\/p>\n

Blooooooooood<\/b><\/p>\n

Before we get too much into speculating on alien blood, I thought that a little primer blood and the cardiovascular system might be worthwhile. The main function of these, carrying oxygen to the rest of the body, is one of the reasons why our blood is red. (Actually distributing molecular\/cellular nutrients, energy, and defense throughout the body IS the purpose of the cardiovascular system.) But, back to blood and oxygen. For humans (and animals and insects and many bacteria, fungi, and protists) we use the energy stored in the O2<\/sub> bonds to supply the energy we need to be active and maintain life. Many of you should be familiar with the chemical reaction depicting respiration:
\nC6<\/sub>H12<\/sub>O6<\/sub> + 6O2<\/sub> \u2013> 6CO2<\/sub> + 6H2<\/sub>O + Energy
\nIn this reaction, oxygen is a critical component, along with glucose, for supplying energy to our bodies. As with many things in Nature, life isn\u2019t this simple as this reaction. This seemingly simple chemical equation is the sum of many different biological and chemical processes that occur. But, the point still stands, oxygen is necessary for our life because life found a way to propagate and evolve through exploiting energy stored in oxygen. To do this, Nature had had come up with a means for storing oxygen, transporting it, and extracting its energy. Nature does this, here on Earth, through the use of metal complexes that are associated with proteins.<\/p>\n

In terms of oxygen storage and transport, the proteins myoglobin and hemoglobin are used. Each of these proteins contains a heme complex (shown in the picture below on the upper right). Heme is a compound that is made up of a porphyrin (protoporphyrin IX to be precise) that contains a central iron ion. Heme is attached to these proteins (either hemoglobin or myoglobin) through an interaction between the iron and a one of the protein\u2019s histidine amino acids. Heme on it\u2019s own is purple\u2019ish in color and is clumps up in solid form when you try to put it into water. However, when it is in hemoglobin or myoglobin, and an oxygen is bound to the iron, it is reddish in color and the protein keeps it soluble in water.<\/p>\n

<\/p>\n

So why does (our) Nature use these hemes anyway? Turns out that heme are probably a second-thought or one-off when it comes to evolution. It is likely that they are the not-so-distant chemical (and evolutionary) cousins of another molecule that Nature found useful, chlorophyll. Chlorophyll, shown in the image above on the upper left, is used in photosynthesis. The light that chlorophyll absorbs ultimately leads to the electron removal and energy required for plants (and algae and cyanobacteria) to convert water and carbon dioxide into O2<\/sub> and glucose (the opposite of the chemical reaction shown above). If you take a closer look at the structures of chlorophyll and heme (bottom of the above image), you will see that their structures have some very important similarities. In fact, in their basic architectures, they differ by only one double bond (and two hydrogens), as highlighted in red.<\/p>\n

Current estimates put the accumulation of atmospheric O2<\/sub> at around 2.4 billion years ago, indicating the probability that biosynthesis of chlorophyll was occurring at or prior to that time. (ref<\/a>) The genes for hemoglobin started appearing roughly 600 million years after that (by best estimates). (ref<\/a>) And, in what should be obvious from looking at their chemical structures, heme and chlorophyll do share a common biosynthetic pathway. (ref<\/a>) Nature evolved chlorophyll, which helped produce O2<\/sub>, and then used that same biosynthetic pathway to create heme for the purpose of utilizing that O2<\/sub>. Nature uses one basic molecular framework in order to produce and exploit O2<\/sub>. Pretty cool.<\/p>\n

So, we have red blood because Nature started making O2<\/sub> with chlorophyll. There is no reason why any other planet would constrain evolution to selecting for chlorophyll and heme biosynthesis. It happened on Earth because of the available materials (magnesium and iron) as well as some primitive biosynthetic pathway. If other species on some distant planet have similar circulatory systems, there is no reason why they would have to have the same kind of blood as we have! This is a bug in our Earth-designed life.<\/p>\n

Back to the Movies!<\/b><\/p>\n

OK. More Fi and less Sci. I hear ya.<\/p>\n

Predator<\/u><\/p>\n

<\/p>\n

Getting back to our friend, The Predator \u2026 The Predator has glowing (luminescent) blood. Actually, in some scenes, it\u2019s blood is shown as black. Let\u2019s think about what is going on here. Luminescence occurs when energy (maybe in the form of heat maybe in the form of light) is absorbed by a molecule and then re-emitted as light. (This is the process that goes on in glow sticks. When you \u201ccrack\u201d a glow stick, it initiates a chemical reaction, which puts out energy. This energy is absorbed by another fluorescent molecule inside of the glow stick, which, in turn, converts the energy into the fluorescent light that we see.) In the case of The Predator, one of two things may be happening. In scenario one, his body produces heat, which is absorbed by some molecule in his blood and emitted from that molecule as light. In scenario two, his blood only glows when exposed to energy in the form of light. The question is: Why do we only see his blood when he is bleeding? Why can\u2019t we see it glowing through his body? If the blood is only luminescent upon absorption of light, that could explain it. If, however, their blood was luminescent due to an energy transfer process, then, perhaps, the luminescent light might not pass through their skin. (Our own tissue, by the way, will absorb most visible light.)<\/p>\n

What kinds of molecules might be involved in this process? These glowing molecules could be organic compounds (i.e. no metals) or they could have inorganic (i.e. have metals). We know that the predator\u2019s blood is highly luminescent. That is, you can REALLY see it. Therefore, it must have a very high concentration of luminescent compound in it. So, either The Predator relies on a high concentration of an organic molecule, that happens to be luminescent, or the metal complex that it requires to carry oxygen also happens to be luminescent. (Because I\u2019m writing this post, I\u2019m going to speculate that it\u2019s got a metal in it!) Zinc porphyrins happen to be luminescent. But, their glowing is diminished by the presence of oxygen. Other luminescent metals compounds include those of iridium (ref<\/a>) and ruthenium (ref<\/a>) So, perhaps The Predator comes from a planet formed in the aftermath of a supernova, which would be necessary for large scale production of either of these two metals. (Like I said \u2026 I enjoy this a little too much).<\/p>\n

Vulcan Blood<\/u><\/p>\n


\nThis awesome image was blatantly stolen from \u201cmicathemineral\u201d who wrote a great post<\/a> on the biology of Vulcan blood.<\/p>\n

In Star Trek lore, Vulcans (Spock is a Vulcan) have green blood<\/a>. Actually, it is green when it is oxygenated and rust-colored when it is not carrying oxygen. Also, it is copper-based. So \u2026 how the heck would this happen? Turns out that we have copper-based blood here on Earth too. The hemocyanin proteins<\/a> are the oxygen carrying proteins in many shellfish. There are no special molecular appendages (like heme) in these proteins. The copper atoms (there are two in hemocyanin) are kept in close proximity to one another through their interaction with six histidine amino acids. These proteins are colorless when there is no oxygen bound and blue when they are carrying oxygen. (A twitter discussion<\/a> of Vulcan blood, started by Biochem Belle<\/a> was the original inspiration to write this post. And in the discussion, we talked about the comparison between Vulcan blood and shellfish blood). Now, just because the copper-based hemocyanin proteins are blue does not mean that all copper-based oxygen storage proteins would be blue as well. By slightly changing the protein architecture, you can greatly affect the physical and chemical properties of that protein. In this<\/a>study, Yi Lu performed single mutations on a copper protein. These single mutations dramatically changed the redox properties (i.e. the energy required to change the charge on the copper ion) as well as the color of the protein. So, I can imagine that specific mutations to a hemocyanin-type protein could produce dramatic changes in color. In fact, I would imagine that tuning the color from blue to green would be relatively easy! (Famous last words) As an example of how this might be possible, the Tolman Group<\/a> at Minnesota synthesized a compound<\/a> containing three copper atoms with two bridging sulfur atoms (see image below). This molecule is dark green in color.<\/p>\n


\n(Image modified from JACS<\/a><\/i>)<\/p>\n

Alien<\/u><\/p>\n

The aliens in Alien and Aliens have very acidic blood. If these creatures use H+<\/sup> gradients in order to store electrochemical energy, like a battery, that could make a lot of sense. (We do this at a much smaller scale in our mitochondria.)<\/p>\n

Avatar<\/u><\/p>\n

The Na\u2019vi of James Cameron\u2019s imagination have red blood. They also breath an atmosphere that is similar<\/a> to Earth\u2019s. The main difference is that their atmosphere has a very high content of carbon dioxide, xenon, and H2<\/sub>S. The humans who go to Pandora can\u2019t breath the air because that level of CO2<\/sub> is toxic. And the H2<\/sub> would reek to high heaven. So, all indications are that the Na\u2019vi have an O2<\/sub> storage system similar to what we terrestrial creatures have.<\/p>\n

The blood\u2019s run out<\/b><\/p>\n

See what I mean \u2026 I enjoy this stuff \u2026
\ntl;dr
\n\":)\"<\/p>\n

There really is a world of possibility out there for protein color (and blood color). And, part of my research is to expand on the types of metal complexes we normally associate as being protein. I guess you could say I\u2019m trying to make up my own alien blood in the lab (if you like that sort of thing). So (a request), if you\u2019ve got some cool metal compounds, and you are interested in what they might look like (and react like) while inside of a protein, send them my way. We\u2019ll do some unnatural things with Nature!<\/p>\n","protected":false},"excerpt":{"rendered":"

Originally posted April 18, 2013 \u201cIf it bleeds, we can kill it\u201d \u2013 Major Dutch Schaefer (This post is an entry in See Arr Oh\u2018s Chemistry at the Movies Blog Carnival) When Dutch and his band of military mercenaries went stalking the Predator in the jungles of South America, they had no idea what they […]<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-177","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/177","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=177"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/177\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=177"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=177"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=177"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":176,"date":"2018-06-19T18:43:20","date_gmt":"2018-06-19T18:43:20","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=176"},"modified":"2018-06-19T18:43:20","modified_gmt":"2018-06-19T18:43:20","slug":"sciencegeist-tryptophan-and-sleepiness","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/sciencegeist-tryptophan-and-sleepiness\/","title":{"rendered":"Sciencegeist: Tryptophan and Sleepiness"},"content":{"rendered":"

Originally posted November 16, 2012<\/p>\n

Someone asked about tryptophan and sleepiness earlier \u2026 So I am adding some of the slides from my Chemistry of Cooking Thanksgiving lecture. This is certainly not the final or complete word on the subject, but I thought people might enjoy it anyway.<\/p>\n

Here<\/a> are the slides<\/p>\n

Cheers<\/p>\n","protected":false},"excerpt":{"rendered":"

Originally posted November 16, 2012 Someone asked about tryptophan and sleepiness earlier \u2026 So I am adding some of the slides from my Chemistry of Cooking Thanksgiving lecture. This is certainly not the final or complete word on the subject, but I thought people might enjoy it anyway. Here are the slides Cheers<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-176","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/176","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=176"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/176\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=176"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=176"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=176"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":175,"date":"2018-06-19T18:42:38","date_gmt":"2018-06-19T18:42:38","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=175"},"modified":"2018-06-19T18:42:38","modified_gmt":"2018-06-19T18:42:38","slug":"sciencegeist-foodchem-thanksgiving-blogging-carnival","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/sciencegeist-foodchem-thanksgiving-blogging-carnival\/","title":{"rendered":"Sciencegeist: #FoodChem Thanksgiving Blogging Carnival"},"content":{"rendered":"

Originally posted November 16, 2012<\/p>\n

Thanks to the CENtral Science<\/a> blogging crew for putting this together! Rachel has been aggregating<\/a> the incoming links. Go and have a read. Some great stuff here!<\/i><\/p>\n

Thanksgiving is meant to be a time of gratitude. It is a day set aside to remember all that we have been blessed with and all that we are grateful for. Thanksgiving is a time to celebrate the season\u2019s harvests, a time to recall the first harvest of the original European settlers to America.<\/p>\n

Well, that\u2019s what Thanksgiving is supposed to be.<\/p>\n

What Thanksgiving is, however, is something entirely different. It is a day when we pretend to care about the Detroit Lions and Dallas Cowboys. It is a day when we remember just how much we dislike our relatives\u2019 politics. It is a day when you drink one too many high balls and your grandfather starts making boilermakers with Canadian Club and Bud Light. And, it is a day of overeating.<\/p>\n

When we sit down to lunch\/dinner\/leftovers, we are committing ourselves and confirming our faith in the glory of starch. Mashed potatoes. Sweet potatoes. Stuffing. Gravy. Corn. Dinner rolls. Cranberry sauce. Pumpkin pie. Our communal platters are awash in starch. We are bathed in its glory. And we pray that we never again have to succumb to Dr. Atkins and his damned diet.<\/p>\n

Thanksgiving is a holiday because it is the one day where we don\u2019t have to believe that starch is evil. Sure, it makes us sleepy (its seriously not the tryptophan). Sure, we put on some weight (but our bodies are just preparing themselves for winter, right?).<\/p>\n

So let\u2019s take a closer look at the chemistry behind our true national obsession. Starch is a really long molecule. Starch is a really long molecule that is made out of a single, small molecule that repeats itself, hand-in-hand, over a thousand times. That single small molecule is glucose. You all know glucose, it is sweet and delightful and makes our world a better place.<\/p>\n

<\/p>\n

Now, if you take one glucose molecule and attach it to a second molecule and repeat this process a thousand times, you get one giant starch molecule.<\/p>\n

<\/p>\n

Surely you\u2019ve noticed that starch, itself, is not pleasant to eat. In my home, the cornstarch resides in a clear container right next to another clear container that stores our powdered sugar. (Genius, right?) The two powders may look similar, but their tastes are entirely different. And potatoes, which are called pomme du terre<\/i> (apple of the earth) in french, are mostly just big balls of starch. (You won\u2019t be catching me eating a potato like an apple any time soon).<\/p>\n

How is it that this unpleasing molecule plays such a big role in the food that we eat? And, why are these foods so enjoyable?<\/p>\n

It turns out that starch doesn\u2019t just hang around on its own. Many molecules of starch cluster together and hang out in \u201ccrystals\u201d. One way to think about a starch crystal is to imagine a sheet of paper. Take that sheet of paper and cut it into very skinny strips. (Each of those strips represents a single starch molecule). Now take those strips and crumple them up into a ball. This is what a starch crystal looks like.<\/p>\n

<\/p>\n

As you know, starch, in its resting state, is \u201ctough\u201d. It feels a little bit gritty in your mouth. (Again, think of corn starch or a raw potato.) What happens to that starch crystal as you cook it constitutes one of the most important transitions in cooking.<\/p>\n

As you start to heat a starch crystal in water, the molecules of water begin to seep into the interior of the crystal and it swells. As it continues to swell, individual chains of starch start to leach out of the crystal and into solution. This process proceeds until a molecular mesh is created within the water. When you are cooking with starch, this is what you are going for. Gelation. You want your starch crystals to swell, leach some of their contents, and mesh. This \u201csoftens\u201d the starch and makes the liquid feel \u201cthicker\u201d. Of course, this process can be carried out for too long of a time and the starch crystals deflate. If this happens, all of the hard work you have been putting into cooking your starch will be destroyed.<\/p>\n

<\/p>\n

All of this is particularly important when making gravy. When preparing gravy, you have two basic starch sources that you can use. Wheat starch (aka flour) and Vegetable starch (aka corn starch or potato starch or other). There are some differences between the gravies made with these. Corn starch gravy tends to have a more clear appearance and is less likely to clump. Gravies made with flour tend to have a richer flavor, are more cloudy in appearance, and have a greater tendency to clump. However, there are several methods that you can take such that you don\u2019t make clumpy gravy. 1) Mix your starch in cold water before adding it to the drippings from the roasted turkey. Then add the liquid slowly to the hot drippings. In the case of flour, adding it too quickly to the hot liquid causes gluten formation (think bread) and the formation of clumps. Adding the starch slowly to the pan keeps the starch crystals dispersed in the gravy. 2) Coat the starch in oil (clarified butter) before adding it to the hot drippings. The coating of oil controls the swelling of the starch crystal. It keeps it from rupturing. It also adds a deeper flavor to your gravy.<\/p>\n

In preparation of next weekend, I may have to cut back on my starch consumption. I am fully planning to be taken in by the magic of Thanksgiving dinner and the glory of starch. I do this in full knowledge that when the clock turns midnight next Thursday and the spell is broken, I will most likely turn into a potato.<\/p>\n","protected":false},"excerpt":{"rendered":"

Originally posted November 16, 2012 Thanks to the CENtral Science blogging crew for putting this together! Rachel has been aggregating the incoming links. Go and have a read. Some great stuff here! Thanksgiving is meant to be a time of gratitude. It is a day set aside to remember all that we have been blessed […]<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-175","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/175","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=175"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/175\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=175"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=175"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=175"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":174,"date":"2018-06-19T18:42:02","date_gmt":"2018-06-19T18:42:02","guid":{"rendered":"http:\/\/edspace.american.edu\/hartingslab\/?p=174"},"modified":"2018-06-19T18:42:02","modified_gmt":"2018-06-19T18:42:02","slug":"sciencegeist-chemcoach-carnival","status":"publish","type":"post","link":"https:\/\/edspace.american.edu\/hartingslab\/2018\/06\/19\/sciencegeist-chemcoach-carnival\/","title":{"rendered":"Sciencegeist: #ChemCoach Carnival"},"content":{"rendered":"

Originally posted October 25, 2012<\/p>\n

\n

See Arr Oh is hosting a ChemCoach blogging carnival<\/a> over at his site. The hope is that someone, somewhere will find some useful helps and hints as they are pushing for their degrees in chemistry.<\/p>\n

So \u2026 Here goes \u2026<\/p>\n

Your Current Job<\/b> I am an assistant professor of chemistry at American University. No, really, I am. They actually gave me my own lab and let me teach this stuff. I have proof. Here<\/a> and here<\/a>.<\/p>\n

What do you do in a standard work day?<\/b> I think, one of the recurring themes from this blogging carnival is that there is no standard work day. Recently I\u2019ve been devoting 95% of my waking hours to two grants that I am writing. But, I also teach. (Normally, it\u2019s two classes a semester. But, I have this semester off for a research release!) I have undergraduates who work with me in lab. I do research on my own. I maintain a budget for my expenses. I write. I mentor. I serve on committees (at the university, college, and department level). I try to help the university improve their reputation in the sciences. I also drink a lot of Coca-cola.<\/p>\n

What kind of school\/training\/experience helped you to get here?<\/b> As many of you know. It is no easy task landing a tenure track professorship. That doesn\u2019t mean that I worked harder than everyone else to get here, or that I am naturally brilliant, or anything like that. What I\u2019m trying to get at is that getting a TT job requires some amount of luck. Having served on faculty search committees and having gone through the process myself, there is a lot of what goes on that makes even getting an interview a complete crapshoot. But, there are certainly things you can do to prepare yourself. Number 1: Publish. A lot. A wise person once said \u201cFaculty search committees may be dumb. They may not be able to read very well. But they can certainly count.\u201d A good publication record implies that you know how to get research accomplished and that you understand how to craft a research program. This may not be true. But it is certainly an indicator. Number 2: Get your own funding. Whenever we go through applications for our search committee, people who have their own funding (most likely a postdoctoral fellowship) go right to the top of the pile. Universities want to see that you can write and be awarded external funding. In fact, I would say that getting external funding is my primary requirement, at the moment, for moving up the tenure ladder. Number 3: Brand yourself and your research. Become \u201cTHE\u201d expert in your specialty within your sub-discipline. And it is not just important to be an expert. It is MORE important to bee seen by others as THE expert.<\/p>\n

So that\u2019s how I got the job. What training was important for what I actually do? My research experience (from undergraduate, to PhD, to postdoc) informs what I do everyday in the projects that I choose and the manner in which I train the undergraduates in my lab. I was never truly prepared for teaching. Sure, I was a TA in graduate school. But that doesn\u2019t count. Making lesson plans and crafting lectures is an enormous task. Having gone through this, I have am infinitely more respectful for the work that K-12 teachers and professional lecturers do every day. For most postdocs transitioning into a tenure track position, that first course that you teach is a trial by fire. Thankfully, I\u2019ve found my own little niche in my teaching style.<\/p>\n

How does chemistry inform your work?<\/b> Obviously, I am constantly teaching the theory and practice of chemistry. In order to be relevant to my students and in my research and to the granting agencies, I need to be keenly focused and aware and of the current trends in chemistry. This focus, however, must be grounded in what the field has developed over the course of its history. That is to say, I read a lot. I suppose that I could say that reading is the one single thing that I do every day. No matter what other things I have on my plate. I am always reading.<\/p>\n

Finally, a unique, interesting, or funny anecdote about your career<\/b> It was my first semester of lecturing. Actually, it was within the first two months of my first semester lecturing. As I said earlier, I really didn\u2019t know what I was doing. In order to cover that blemish, I would do a lot of demonstrations. Because, everybody loves demos \u2026 and who really wants to listen to me talk for an hour and fifteen minutes?<\/p>\n

I was teaching the first semester of general chemistry. We were covering reactions and were specifically talking about combustion. Now \u2026 our building is \u2026 well \u2026 old. Perhaps old isn\u2019t the right word. What I mean to say is that our building doesn\u2019t have the most up to date air handling system. The hoods are just OK. And the lecture hall certainly doesn\u2019t have any fume hoods. But, I\u2019m teaching combustion. And how can you teach combustion without burning something. So, I decide to burn some magnesium strips. Its a really nice reaction. There is a brilliant white flame. And, importantly, there is almost no smoke. Win-win! So, I start setting up my demo. There are no lab tables in the lecture hall. Only an old desk. So, I place a ring stand on the dest. Place a watch glass on the ring stand. Add some magnesium to the watch glass. Light the torch. Start the reaction. It is all going beautifully until the watch glass cracks and shatters. The (burning) magnesium strips fall onto the desk \u2026 which has a plastic top. The desk bursts into flames. Thankfully I have my wits about me. I run and get the fire extinguisher before the smoke gets out of hand. I put the fire out quickly. Only the fire extinguisher is particulate-based. A haze from the extinguisher fills the room. And sets off the fire alarm.<\/p>\n

And that\u2019s why the department chair calls me Smokey.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

Originally posted October 25, 2012 See Arr Oh is hosting a ChemCoach blogging carnival over at his site. The hope is that someone, somewhere will find some useful helps and hints as they are pushing for their degrees in chemistry. So \u2026 Here goes \u2026 Your Current Job I am an assistant professor of chemistry […]<\/p>\n","protected":false},"author":2625,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":{"0":"post-174","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-uncategorized","7":"czr-hentry"},"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/174","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/users\/2625"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/comments?post=174"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/posts\/174\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/media?parent=174"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/categories?post=174"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/hartingslab\/wp-json\/wp\/v2\/tags?post=174"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}]