The Mosquito Net (1912) by John Singer Sargent. Licensed under Public Domain via Wikimedia Commons

The Mosquito Net (1912) by John Singer Sargent. Licensed under Public Domain via Wikimedia Commons

 

We all know how pesky mosquitoes can be. Did you know that the ability of a mosquito to find a suitable host to feed is due to thermotaxis? This behavior, being attracted/repelled due to high/low temperature, is seen in other organisms as well such as Drosophila melanogaster and Caenorhabditis elegans. 

However, the behaviour is more pronounced among blood-feeding pests (kissing bugs, bedbugs, Ticks, and mosquitoes including Aedes aegypti). Aedes aegypti is a vector for many flaviviral diseases (Dengue fever, Yellow fever, etc.) Until now, it was well established that thermotaxis requires specific thermosensors that activate the sensory signals for a subsequent flight response in a mosquito. However, how exactly they function was not resolved.

ResearchBlogging.orgIn a recent paper by Corfas and Vosshall [1] describe the use of zinc-finger nuclease-mediated genome editing method to identify the role of two receptors TRPA1 and GR19 in Aedes aegypti‘s attraction to heat. It was found that these receptors help the mosquito to identify the host for feeding (in the temperature range of 43-50 deg Celcius), however they avoid surfaces that exhibit above 50 deg Celcius. [Read the recent editorial on genome editing in Genome Biology]

The sequence (923 residues long) of this receptor (Uniprot id: Q0IFQ4) has at least five transmembrane regions that are approximately 20-25 residues long. A cursory glance at homologous sequences shows that it shares 37% sequence identity with the a de novo designed protein (PDB id:2xeh).

The homology modeled structure showing coiled coil region (residues 189-338). Although, the eLife paper does not talk about structure, I felt that this paper deserves a mention here. The reason is the structural biology/bioinformatics possibilities with this novel target. It is a suitable target for designing inhibitors that would potentially act as mosquito repellents.

Also, combined with the method described in my previous post on mutating transmembrane proteins as a method of making them crystallize, I guess the 3D structure of this important protein will come to light sooner!

Homology modeled region of TRPA1, from ModBase

Homology modeled region of TRPA1 (189-338), from ModBase

 

References:

  1. Corfas RA, & Vosshall LB (2015). The cation channel TRPA1 tunes mosquito thermotaxis to host temperatures. eLife, 4 PMID: 26670734
  2. Greppi, Chloe and Budelli, Gonzalo and Garrity, Paul A (2015). Some like it hot, but not too hot. eLife, 4
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I am sharing this guest post of mine that was published in Cell’s Crosstalk: Biology in 3D Blog. Yes, the journal Cell!

Here is the link: http://www.cell.com/crosstalk/why-do-i-blog-about-structural-bioinformatics

Enjoy!

Why Do I Blog about Structural Bioinformatics?:Biology in 3D

When someone says that they have a blog, the stereotypical response would be, “About your travels?” or “Hmmm … Recipes … Must be a delicious blog!” And when one confesses that said blog is about scientific research, the jaw drops. I presume it has to do with the notion that blogging science is not that much fun!

Two things inspired me to become a blogger: (1) an amazing community of scientific bloggers at Research Blogging, who inspired me with their wonderful posts; and (2) my view that structural biology and structural bioinformatics are not getting the exposure they deserve. Thus inspired and motivated, I begun blogging about four years ago, and was able to channel some of my thoughts and energy into my blog, called Getting to Know Structural Bioinformatics.

Guest author and blogger
Raghu Yennamalli

Why do I blog? Blogging is fun! For me, blogging is about sharing with the world recent research and tidbits on structural biology and bioinformatics. Most importantly, it is about sharing the excitement that I feel after reading a paper. In some sense, blogging about research is similar to a journal club, where I am able to share the latest research with my peers. However, unlike a journal club, the audience for my blog is the entire world.

Blogging is also dynamic and interactive, because it allows me to engage in conversation with others (specifically students) when they weigh in with their comments. Below I highlight some of the best practices that I’ve developed over the years that help me with balancing my research, teaching, and personal responsibilities with my blogging.

Selecting the paper

The main way I find articles that I want to blog about is by scouring through the table of contents of the journals I am interested in. Sometimes I also hear about exciting protein structures via friends and other blogs that I follow. I try to have a balanced approach and highlight structural work on systems that are “hot topics” as well as papers that just captured my interest and fancy.

In the early days of my blogging, I was trying to collate and compile tools and techniques that would come in handy for students working with protein structures. I wanted my blog to be a handy place for myself and others to find tips and tricks. Over time, the range of topics and papers I cover has broadened, and although I still cover a lot of method development work, I cover other topics as well. In general, once I make up my mind about the paper I want to blog about, I start reading it, give myself some time to soak in the method and outcome of the paper, and try to think critically as to what possible gaps or methods that the authors could have done to make the paper better. Alternatively, I also analyze the paper’s novelty with respect to structural bioinformatics.

Composing the blog post

I should confess that the monthly posts in Protein Spotlight by Vivienne Baillie Gerritsen are my inspiration while composing posts. I love her writing style and also the manner in which artwork is included in every post, to make it fun to read. Like Protein Spotlight, blogs have the advantage of including other multimedia items, for example using animated gifs and YouTube videos that make the post much easier for the reader. So, I start finding an appropriate image from an art database that best fits the topic (of course, giving credit where it is due). When it is about a tool/software, I figure the best approach is to use said tool/software and include a “first-hand” experience of how I perceived it. Also, I try to include an additional tidbit or information that the authors mention in passing.

Balancing things

With an active teaching and research schedule, finding time to blog does become a challenge. I try to make it a fun process, so that it does not feel cumbersome. If one looks at the frequency of my posts, I try to maintain at least one post per month. Looking at others’ blogs at Research Blogging, I realize that one post a month is a low turnout, and I try to post as frequently as possible. Sometimes, the problem is sheer lack of time or not finding exciting enough material to blog about. However, this does not mean that exciting research is not out there. The key is to find a balance between blogging and other duties. I have had discussions with other bloggers who blog on other nonscience topics, and we observed that the main turnoff in blogging is when one delves deeper and over time a particular post becomes “work.” Maneuvering that roadblock is key to maintaining a successful blog.

In the end, as at the beginning, it all comes down to having fun and sharing with the world my excitement about the type of scientific research I enjoy. I think this is probably the feeling others who blog share as well, and I can see it in some of the blogs I follow, such as the following:


Raghu Yennamalli completed his PhD in Computational Biology and Bioinformatics in 2008 from Jawaharlal Nehru University. He conducted postdoctoral research at Iowa State University, University of Wisconsin-Madison, and Rice University. Currently, he is an Assistant Professor at Jaypee University of Information Technology. He can be contacted at ragothaman AT gmail DOT com.

In the 90s morphing of two unrelated images was popular and mostly it was used for entertainment purposes. For example: the famous video of Michael Jackson’s pop hit “Black or White”.

Courtesy: Google

Courtesy: Google

This morphing method was also used to analyze changes in protein motions, like in domain rearrangement. A popular webserver, where you can get an animated gif of your protein’s motion (assuming you have two distinct conformations), is the Morph server (http://www2.molmovdb.org/) from Gerstein’s Lab. In many cases this gave us insight of how the protein could dynamically change from one form to another.

ResearchBlogging.orgThe change in structural forms of a protein is not a trivial problem. We would need to generate ensembles of protein structures for many purposes. 1) Understand conformational transition paths, 2) Generating more realistic receptors for docking 3) in turn understand the flexible and rigid parts of the protein, and few other applications.

Till now, one could use Normal mode analysis and Molecular Dynamics methods to generate ensemble. It is here that ConTemplate tries to bring in fresh perspective to generate an ensemble of structures.

ConTemplate mines the PDB for existing structures and gives the user a set of possible conformations. The main presumptions are that for any given PDB structure, it has more than one available structure, and there are additional conformations available for proteins that undergo major conformational changes.

For the dataset created for ConTemplate the maximum RMSD between two structures of the same protein is 5 Angstroms. 69.2% of the proteins have less than 1 Angstroms RMSD. Thus, the method uses an interesting three-step process:

  1. using the query it searches for structural equivalents using GESAMT aligner. Here using the structural alignment sequence alignments are generated.
  2. it runs BLAST to identify additional conformations for all structural equivalents obtained in step 1. A representative template is identified
  3. Finally, Modeller is used to build model structures using this template in various conformations.

The advantage of ConTemplate is that it yields a more relevant set of conformations for the query protein. I tried running a query to the server and I would say that I got some interesting results. Screenshot below:

contemplate

Superposition of models created in ConTemplate for PDB id; 1ECE

Superposition of models created in ConTemplate for PDB id; 1ECE

References:
Narunsky A, Nepomnyachiy S, Ashkenazy H, Kolodny R, & Ben-Tal N (2015). ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure. Structure (London, England : 1993), 23 (11), 2162-70 PMID: 26455800

ResearchBlogging.orgReblogging this blog post

http://loonylabs.org/2015/11/24/protein-structure-biotechnology-personalized-medicines/

Professor Meiering and her colleagues were able to incorporate both structure and function into the design process by using bioinformatics to leverage information from nature. They then analyzed what they made and measured how long it took for the folded, functional protein to unfold and breakdown.

Using a combination of biophysical and computational analyses, the team discovered this kinetic stability can be successfully modeled based on the extent to which the protein chain loops back on itself in the folded structure. Because their approach to stability is also quantitative, the protein’s stability can be adjusted to naturally break down when it is no longer needed.

Reference:

Broom A, Ma SM, Xia K, Rafalia H, Trainor K, Colón W, Gosavi S, & Meiering EM (2015). Designed protein reveals structural determinants of extreme kinetic stability. Proceedings of the National Academy of Sciences of the United States of America, 112 (47), 14605-10 PMID: 26554002

 

Fire, by Giuseppe Arcimboldo. 1566 Oil on wood, 67 x 51 cm Kunsthistorisches Museum, Vienna

Fire, by Giuseppe Arcimboldo.
1566
Oil on wood, 67 x 51 cm
Kunsthistorisches Museum, Vienna
The allegory of Fire combines objects that are more or less directly related to fire in a bizarre profile head. The cheek is formed by a large firestone, the neck and chin are formed by a burning candle and an oil lamp, the nose and ear are contoured by firesteels; a blond moustache is formed by a crossed bundle of wood shavings for kindling, the eye is an extinguished candle stub, the forehead area is a wound-up fuse, the hair of the head forms a crown of blazing logs. The breast is composed of fire weapons: mortar and canon barrels together with the respective gunpowder shovel and a pistol barrel.

In protein engineering studies, mutating a residue to increase thermostability without affecting the activity of the protein/enzyme is a major consideration for researchers. The laborious method is list the number of possible mutations and then finding out the stability and activity for each mutant, one after another.

This method becomes more time consuming if the protein is a membrane proteins and especially determining their 3D structure. I like to call membrane proteins as “diva” proteins. The reason being that they are high maintenance and tend to be picky about what conditions require for them to crystallize. It has been reported that when thermostability is introduced in membrane proteins, their solubility increases, thus increasing the chances of getting a good crystal for diffraction. [1]

ResearchBlogging.org

Not everyone could avail high-throughput mutation experiments to screen for thermostable membrane proteins. Here is where Bioinformatics based analysis comes to help in faster screening and selecting a few mutants among the hundreds that can be tested experimentally. In the recent issue of Biophysical Journal, Sauer et al have come up with two methods to identify potential “thermoadaptive” sequences. [2]

The first method or global method, involves generating a heatmap of amino acid frequency differences between the thermophilic and mesophilic sequences. So, residues that are either most represented or less represented are identified.

The second method or pairwise method, involves pairwise comparison of thermophilic and mesophilic sequences and identify the differences.

A unique observation was that the the selected list of amino acids did not overlap from either of the methods and the global method identified potential mutants in the N-terminal domain of the test case and the pairwise method identified the potential C-terminal mutants only. This could be a case of thermostabilization for the protein tested, i.e., BsTetL – Tetracycline transporter from Bacillus subtilis.

The caveat is that there should be enough available sequences for identification of potential mutants, in any protein family. This does not, on the outset, seem like a limitation. Since, we have abundant protein sequences available and steadily increasing.

The main selling point is the speed of identifying the mutations given a particular target sequence, and its applicability in membrane protein crystallization. However, their success rate was 26-30%. Here, success indicates both thermostable mutant and maintaining the tetracycline resistance activity.

References:

  1. Mancusso R, Karpowich NK, Czyzewski BK, & Wang DN (2011). Simple screening method for improving membrane protein thermostability. Methods (San Diego, Calif.), 55 (4), 324-9 PMID: 21840396
  2. Sauer DB, Karpowich NK, Song JM, & Wang DN (2015). Rapid Bioinformatic Identification of Thermostabilizing Mutations. Biophysical journal, 109 (7), 1420-8 PMID: 26445442
bioasphalt_des_moines_waveland_trail_finished

Image Courtesy: i.bnet.com

Biofuel prodcution involves removing Lignin from the biomass, in fact efficient removal so that Lignin and its by-products do not inhibit the enzymatic process that follows. But, what happens to the Lignin? Well, it can used in laying roads and thus creating bioasphalt.

Usually, after the sugars, cellulose, and other more useful materials have been extracted from plant matter to make biofuels or paper, the leftover lignin is tossed aside and burned. In principle, the economics are therefore promising: Paper companies could profit from what had been a waste product, and biofuel makers could similarly use the proceeds of selling lignin to bring down fuel production costs.

FYI, Lignin looks something like this.

Lignin. Image Courtesy: Wikimedia Commons

Lignin. Image Courtesy: Wikimedia Commons

Read more here
 R. Chris Williams, a materials engineer at the Iowa State University Institute for Transportation, has developed a way to turn lignin-rich stover, leftover from biofuel production, into bioasphalt. The Iowa team uses a process called fast pyrolysis that turns plant waste into a charcoal-like fertilizer, natural gas, and an oily mixture that can be made into bioasphalt.
If you live in Iowa, you could see the bioasphalt paved bike path in Des Moines as the article mentions.
Update: My friend Ethy, pointed out that the bike trail (~1 mile long) between University Avenue and Franklin Avenue, on the west side of Glendale Cemetery has this bioasphalt bike path. See map below. Link: http://www.news.iastate.edu/news/2010/oct/bioasphalt
Google Maps

Google Maps

ResearchBlogging.org
Bourzac, K. (2015). Inner Workings: Paving with plants Proceedings of the National Academy of Sciences, 112 (38), 11743-11744 DOI: 10.1073/pnas.1509010112

Reading one paper in a decent way takes a lot of time, which I realized in the past few months where I am strapped for time! Hopefully the dry phase ends sooner.

Came across this “Science blogging” article/podcast in Nature newsletter and thought of sharing it here. Enjoy!

The challenges of science blogging for established professors and young PhD students.

Whether you’re a PhD student or an established professor, being able to communicate your research is an important part of your career development. You will, at some point, have to persuade that funding body to give you some money, or that supervisory committee to grant you that PhD. Other times, you might have to work with politicians and the media to help them access your research. All these conversations, whether oral or in writing, require good communication skills.

Many of these will be done in a written format and blogging can be a great way to practice those writing skills.

Suzi Gage is writing up her PhD thesis. Three years ago, this was a gargantuan challenge that she was unsure of how to tackle. To prepare, she started blogging. “I really feel like the blogging has helped so much. When I sit down at a blank page, I know that I can write 1000 words. They might not be good words, but I know that I can turn them into something better.” Now she’s a well-established, award-winning science blogger, writing about epidemiology on Sifting the evidence, hosted by the Guardian.

Professor Jon Butterworth is an established experimental physicist, splitting his time between the Large Hadron Collider in Geneva and teaching at UCL. He blogs at Life and physics, also hosted by the Guardian. “We wanted to share the excitement of the thing [LHC].”

Science blogging challenges for young scientists

Audience

Your audience could include fellow students, potential employers and your supervisors. Therefore, think carefully about how you portray and express yourself, “particularly if you’re blogging under your own name,” says Suzi. There is a fine line between voicing your opinion and becoming a trouble maker, so it’s worth understanding where that line is. Our advice: don’t cross it.

Evidence

“My blogs came under a lot of attention from those who disagreed with what I was saying… everything I said I had to back up,” says Suzi. This is the case for anyone who is blogging about science, really, but it’s especially true for young scientists as they don’t have a decade-long research career and reputation to back them up. Do your research, interview scientists in the field and be 100% positive that what you are saying is correct, or can be backed up if it is opinion.

Bosses

Suzi is fortunate in that she has had supportive bosses who understand and agree with what she is doing. “But I don’t take the micky,” she says. As a young scientist, your priority should be your research, so don’t let your hobby take over. Suzi suggests combining the two: if you have to read a paper for your literature review, why not write up a lay summary for it at the same time? This is a good test to see if you have really understood it: if your audiences understand what you’ve written, you’re off to a flying start.

Goals

Are your science communication efforts a hobby, or are they something more? “This is a question that might come up in a job interview,” says Jon, and one that you should be prepared to answer. If you’re interviewing for a postdoc position, make sure that your potential employer understands that this is a hobby, that you’re organised and that your blogging won’t interfere with your work. If it isn’t a hobby, and you’re considering becoming a journalist, think carefully about applying for a postdoc, it might not be the right thing for you.

Sounding boards

“Two heads are better than one.” Wise words that apply to science blogging (as well as many other things!) When you run dry on ideas, or you’re not sure if one will work, use a friend or colleague as a sounding board. They’ll be able to help you think through your ideas, or maybe even give you new ones. It’s always useful to get another set of eyes on your work, just to check for grammatical and spelling errors.

Networks

“If you don’t think you have time to do a blog entirely by yourself….” approach a network that is already on the go, says Suzi. “That’s a great way to practice writing and see if it’s the kind of thing that you want to do,” she says. Setting up a blog for your lab can also be an option. “You don’t just have to cover the science, you can also talk about the PhD life.” Some good examples are The Mental Elf (mental health research, policy and guidance), Speakers of Science (science communication), Naturejobs (science careers), Climate Snack (environmental science) and others.

Science blogging challenges for an established scientist

Audience

The audience of an established researcher will be mixed. It might include your students and others that work for you, colleagues or “directors of labs in the US and Switzerland, leaders in the field and within government departments,” says Jon. They will each be judging your written words with their role in mind. You can never keep everyone happy, but try not to upset the same group of people two posts in a row!

Impact

What you say not only affects you, but it could also impact on your colleagues, policy, funding bodies and research decisions. Consider what you write, and how you write it, very carefully. “It does cramp your style a little bit,” says Jon, but don’t let that take all the enjoyment out of it.

Trust

Maintain the trust of your colleagues. As a senior scientist, you’ll be privy to meetings and experimental results that are not to be shared with the media. So don’t share them. Simple. If you do, you’ll risk being blacklisted from those meetings. Jon, as a researcher at the LHC, was part of several meetings that discussed confidential results, and he had to make sure that his colleagues trusted him not to spill the beans. “I don’t want to be shut out of the room for those [meetings],” says Jon.

Location

Don’t write a corporate blog, that’s Jon’s advice. Jon feels that a blog is a space where you can express your own personality and views (in a sensible way). If you have to walk a corporate tight-rope, he says it might not be worth it.

Responsibility

“You have a position of influence that you have to be conscious of when you’re writing,” says Jon. Accept your responsibility as a professor and a blogger: be polite, considerate of colleagues and your science, and a nice person!