#RealTimeChem Week 2015 Awards and Cook Off prize winners

Hi RealTimeChemists,

Once again I have to say a massive thank you every single chemist out there who took part in #RealTimeChem week. This community only exists because of you and it’s always great fun to witness the massive variety of chemists taking part from all over the world. It was nice to see tweet not just from regulars, but also a lot of newcomers. Welcome to #RealTimeChem I hope you enjoy your stay.

While the week event is over for another year, don’t forget that #RealTimeChem is a 24/7 project, so feel free to keep sharing chemistry whenever you want and engage with your fellow chemists around the world.

I have some very special thank yous to give out this year to the following folks:

  • Andy Brunning of @compoundchem fame. Not only did Andy design all of the graphics for this year, he also provided a really cool infographic competition of his own to celebrate #RealTimeChem Week. I look forward to working with Andy again in the future.
  • Katey Birtcher and all the folks at Elsevier’s SciTechConnect who ran the Blog Carnival this year and promoted the week. Your enthusiasm for the project has really kept me going and I loved the round ups.
  • Nicola Burton, formerly @Elements_UD now @SpaceBambee, thanks greatly for the #RealTimeChem Award badges
  • Kudos to the Royal Society of Chemistry and all my friends at work for supporting the project and also getting on board from time to time.
  • Finally, thanks to Guido Kemeling, Editor-in-Chief of @ChemSusChem, who was kind enough to organise the prizes for the The Great #RealTimeChem Cook Off. Thanks to all the other ladies and gentlemen at WileyVCH for the support as well.

With all of these out of the way, it’s time to get onto this years awards. This was, as ever, ridiculously tough because there were many excellent tweets all deserving a prize. Thankfully, I have a few more prizes to give out this time around!

Below you will find out the results. Drum roll please?


 

RTCWTOW

TOP PRIZE WINNERS

The three tweeters below all win a #RealTimeChem Week 2015 mug of their very own like the below:

Everyone loves a mug right? You can do all kinds of things with them!

BrianWagner

From Wednesday. Brian Wagner (@drummerboy2112) is one of THE chemists to follow on Twitter in my humble opinion and this simple demonstration of Boyle’s Law using a marshmallow, a flask and some suction was arguably the most popular tweet of the whole week in terms of retweets and favourites. Science can be fun and informative both at the same time.

Lauravanlaeren

From Wednesday. Laura van Laeren (@lauravlaeren) strikes again, sharing a lot of great tweets throughout the week, including several pictures of her beautifully painted finger nails. However, it was her starry night flask that caught a lot of attention this year and I couldn’t ignore it’s awesomeness. Pretty colours for the win!

emilyhardy

From Saturday. Speaking of pretty colours, it was National Chemistry Week in the US at the same time, with colours being the big theme. Emily Hardy (@EmilyEHardy) snuck in on the Saturday to show off some fantastic chemiluminescence. Really spectacular.

Don’t forget to DM me your address so I can post your prize to you.

RUNNERS UP

The remaining 9 Pt Awards winners will all get a #RealTimeChem keyring like the one below:

keyring

All winners, DM me your address & I’ll post your key ring to you.


NOTE: Au/Ag award winners. Unfortunately, you don’t get a prize (except the kudos),  but thank you for taking part!


GRTCCO

I was lucky this year to be given some extra prizes for a new competition. The first #RealTimeChem Cook off! There were quite a few entries and below you can find the 6 chosen winners.

The Grumpy Chemist (@Chemistry_Kat) 

Henrik Pedersen (@hacp81)

Victoria Stafford (@ToriaStafford)

Massimo Grillo (@MassimoGrillo63)

Tom Kuntzleman (@pchemstud)

Debbie Mitchell (@heydebigale)

 

All 6 of these tweeters win a copy of “What’s Cooking in Chemistry?: How Leading Chemists Succeed in the Kitchen“.

Send me your address details via DM and the folks at Wiley will send you your prize*!


 

*Book prizes sponsored by @WileyVCH’s society chemistry journals. These are: @ChemEurJ., @ChemistryOpen, @ChemBioChem, @ChemCatChem, @ChemMedChem@ChemElectroChem, @ChemPhysChem, @ChemPlusChem, @ChemSusChem, @EurJIC, and Eur. J. Org. Chem (all journals of ChemPubSoc Europe); @ChemAsianJ, @AsianJOrgChem, and @ChemNanoMat (all journals of the Asian Chemical Editorial Society); and @angew_chem (a journal of @GDCh_aktuell)


 

 

Well, that’s all folks. All awards are now given and #RealTimeChem Week is officially over for this year. Once more, thank you to everyone who took part. May all your chemistry dreams come true.

mischief managed

-Doctor Galactic & The Lab Coat Cowboy-

Joining the dark side of the Force for a week

Hello! I am Clemens, a postdoc at the University of Cambridge, and in this #RealTimeChemInFocus blog post you will follow me, a chemist, doing some “biology” a.k.a. the dark side of the Force.

 

I know it’s weird. Why would a chemist venture into the world of biology in the first place? Honestly, it just happened! Organic chemistry was my first love as an undergrad, even after my final product of a 9-step carbohydrate synthesis decided to spontaneously decompose! I still try holding on to my first love by attempting to solve the Denksport problems of Dirk Trauner’s group and I still admire elegant total syntheses. However, the dark side of the Force has always been strong in me and over the course of my PhD and postdoc, I gradually moved towards chemical biology. I can’t help it; I am simply fascinated how chemistry can give answers to complex problems by probing or perturbing cellular systems. So, without further ado, this is a typical week in my life.

Monday

Although I am not a particular fan of Monday mornings, this Monday morning is one of the toughest of the year! I just came back from an exciting week featuring the ISACS16 conference in Zurich and a 3-day music festival in Austria (Figure 1). It made me realize how similar festivals and conferences are. Long days, short nights, meeting new people and listening to some raw talent all day long.

Figure 1: A tough start to this week after a conference & festival double feature last week.

Figure 1: A tough start to this week after a conference & festival double feature last week.

Don’t get me wrong, I enjoyed it a lot, but it took a lot of energy out of me and getting up for the obligatory Monday morning group meeting at 9 a.m. is tough. I get coffee and arrive on time, a miracle! After the meeting, which is held in the Chemistry department, I postpone my plans to go to the Cancer Research UK (CRUK) Cambridge Institute, where the biology projects of our group happen, for one day and take some time to recover. After all, I missed a lot of science in the last week, as my RSS feed and email client tell me (Figure 2). Even better, I have to analyze some exciting sequencing data, which were generated in my absence. Having multiple, diverse projects running in parallel is one of the great things about being a chemical biologist. As my computer does all the hard work, aligning millions of reads to a reference genome, all I need to do is drink coffee and use the software correctly. The latter is something I am still struggling with (Figure 2). Nevertheless, at the end of the day I get everything analyzed and the results tell me that I am all set for writing my first manuscript as a postdoc! I also managed to catch up with my emails and the RSS feed so it’s time to cycle home and get some much-needed rest!

Figure 2: Clearly, I haven't figured out how to take screenshots on a mac…

Figure 2: Clearly, I haven’t figured out how to take screenshots on a mac…

Tuesday

Another morning and it is time to head to the CRUK Cambridge Institute (Figure 3), where I will spend the rest of my working week.

Figure 3: The CRUK Cambridge institute and yes, we do have the occasional sunshine here in the UK.

Figure 3: The CRUK Cambridge institute and yes, we do have the occasional sunshine here in the UK.

I am not sure how many of you fellow chemists have ever set food in a hardcore biology working environment, so let me give you a short tour. Things here are a lot cleaner and the number of fume hoods is sadly kept to a bare minimum. They are mostly used for “dangerous” phenol-chloroform extractions of nucleic acids. Being thrown into a new working environment, I always look out for things I recognize or can relate to. Lab coats are mandatory and even wearing eye protection is reinforced (Figure 4). You can also spot the occasional TLC chamber (everybody loves TLC chambers), although they are often used for a completely different purpose than analyzing your reactions.

Figure 4: Familiar sights for a chemist in a biology lab.

Figure 4: Familiar sights for a chemist in a biology lab.

Once you are feeling more comfortable in the world of biology, you might even find more similarities to your familiar chemistry lab. For working with tissue cultures, we have special hoods that remind me a lot of glove boxes. Instead of using an airlock you are using ethanol to decontaminate everything before placing it inside the hood. Of course, once you put your thoroughly washed hands inside, your nose starts to itch. Another similarity to the familiar glove box; you have to keep the place spotless as contamination with evil bacteria or yeast will spoil not only your cells, but could affect the cultures of a whole lot of other people (Figure 5). This scenario is especially bothersome, when you have worked for months creating a cell line for a particular disease you’re studying, only to find it contaminated and yourself right back at the start of your project.

Figure 5: Things you do not want find in your mammalian cell cultures! (https://www.microscopyu.com/articles/livecellimaging/livecellmaintenance.html)

Figure 5: Things you do not want find in your mammalian cell cultures! (https://www.microscopyu.com/articles/livecellimaging/livecellmaintenance.html)

Unfortunately for you, I won’t culture any cells this week, so I can’t show of my recently acquired and still embarrassingly clumsy skills, but I encourage anyone who’s curious to give it a go. It is surprisingly simple to culture mammalian cells like HeLa or HEK293 and as a chemist you have enough skills in your repertoire to learn it quickly. Because you have to work carefully and be gentle with the cells, I always picture myself handling tert-BuLi, which freaks me out, but my cells seem to appreciate the gentle treatment.

The plan for the week is to continue with a project I stopped working on before my week abroad. To cut a rather long story short, we identified some potential protein targets in a screen and are now keen on validating these hits. To get an independent confirmation, we need to clone all  28 proteins of interest (P.O.I.) into a transfection vector and express them inside the cell as a tagged version, in order to confirm the interaction by Western blot. That should suffice to give you a rough idea, and the rest of my day is spent planning everything and diluting 56 primers to the right concentrations. By the time night falls, my pipetting thumb has had a good workout!

Wednesday

I spent my PhD in an enzyme-engineering lab, so I did my fair share of cloning and from my experience I can tell you everything starts approximately like this:

Figure 6: Every good cloning starts with a successful PCR. The tricky thing is where to go from there.

Figure 6: Every good cloning starts with a successful PCR. The tricky thing is where to go from there.

For the current task at hand it is a bit trickier. For half of our P.O.I.s we were lucky and could obtain the cDNA – that is the complementary DNA synthesized from the corresponding messenger RNA – in the form of E. coli glycerol stocks that carry a vector containing the cDNA. For these proteins, cloning is easy: isolate the plasmid from the E. coli precultures and simply amplify the cDNA with the correct primers. We use primers that have 5’ and 3’ overhangs, which allow us to subclone the amplified cDNAs into the Gateway cloning system (Figure 7, http://scienceftw.wikia.com/wiki/Gateway_cloning).

Figure 7: Step-by-step workflow of Gateway cloning.

Figure 7: Step-by-step workflow of Gateway cloning.

This method is neat, because it uses a recombinase instead of restriction enzymes and the main objective is to bring your insert into the entry vector for the Gateway system. From there, you can use another recombinase and insert your cDNA into a whole bunch of different vectors that carry appropriate tags and also allows transfecting mammalian cells! Compared to 10 years ago, when I first tackled a cloning problem, this protocol is a piece of cake.

As I started the E. coli precultures from the glycerol stocks before I left yesterday, my day consists of isolating the plasmid, doing the PCR reactions, and purifying the inserts. Sounds like a walk in the park, but it takes time (a lot of pipetting again). By the end of the day, I got 12 out of 28 cDNAs ready to insert them into the entry vector. It was clearly a successful day and I leave the lab happy for my weekly basketball game!

Thursday

Today, I start the cloning of the P.O.I.s we couldn’t obtain from the cDNA in the convenient E. coli glycerol stock form. This cloning is a lot trickier, as we have to prepare our own cDNA. For this, we isolate the total RNA from HeLA cells, which involves a phenol-chloroform extraction (so dangerous!) in a real hood (so happy!). Next, we use a poly dT primer that – at least in theory – is expected to hybridize with all mRNAs in the cell as they carry a complementary poly A tail. Creating an RNA-DNA duplex allows us to reverse transcribe the whole transcriptome and generate our sought-after cDNAs. In principle, we should have our P.O.I. cDNAs in there as well, however there is no easy way of determining the concentration and whether they were fully reverse transcribed in the first place. Nevertheless, we take the crude reaction as a template for some PCR reactions. Given that we are working with a complex mixture, I start a gradient PCR – which probes annealing temperatures between 50 and 70 degrees – and hope for the best. A few hours later, I load the first 48 out of 96 PCR reactions onto an agarose gel (Figure 8), and after size separation take a look at the gel under UV light! Hurray, for 4 of 6 targets we amplified something (Figure 8). I check, whether they have the right size, which they all do, and purify them. The second batch looks equally good, which means that combined with the inserts I amplified yesterday, I got 25 out of 28 constructs ready for the recombination reaction. That’s pretty awesome and I call it a day!

Figure 8: Loading of my agarose gel on the left (hoping), results on the right (celebrating).

Figure 8: Loading of my agarose gel on the left (hoping), results on the right (celebrating).

 

Friday

It’s Friday! And it’s a special Friday, as we are invited to our bosses place for a British “summer” BBQ. I prepared some salmon-spinach roles yesterday night, but they really looked ugly so I didn’t dare taking a picture. With the BBQ coming up later in the afternoon, it will also be a short day in the lab, which suits me, as all I need to do is finishing the first stage of my cloning efforts.

To insert my cDNAs into the Gateway entry vector, all I need to do is mix the vector with my PCR products. I then add the recombinase enzyme that swaps the standard insert – a gene encoding for a toxic protein that prevents growth of false positives – with my cDNAs. After incubating the reaction for an hour at room temperature, I thaw some chemically competent E. coli cells, which I will use for the upcoming transformation. These bacteria are suspended in a buffer-DMSO mixture, conditions that promote plasmid uptake through the cell membrane when heated to 42 degrees Celsius for a short time (about a minute). This procedure is a bit cruel as it kills most of the bacteria; after all they don’t like the DMSO too much. However, some bacteria that took up the plasmid during the heat shock survive and they are allowed to recover at 37 degrees Celsius in a rich medium for half an hour. Next, they are pelleted by centrifugation and resuspended in 100 μL of medium. The E. coli suspension is finally spread onto LB agar plates that have the right antibiotic (kanamycin) in them, which ensures the plasmid is amplified while the bacteria happily divide. Normally, you would incubate at 37 degrees Celsius overnight, which will give you good-sized colonies; however, with the BBQ and the weekend coming up, I just place them on my bench, where they will incubate at room temperature over the weekend, delaying the growth by about two days (Figure 9).

Figure 9: My prize after a week of cloning! Grow E. coli, grow!

Figure 9: My prize after a week of cloning! Grow E. coli, grow!

All there’s left to do: Head home, get the ugly salmon-spinach roles out of the fridge, cycle to my bosses place and enjoy a burger and some beer at the BBQ. Obviously, rain begins to fall as soon as the BBQ starts, but hey, that’s life in the UK after all.

 Figure 10: A proper British “Summer” BBQ in the rain.


Figure 10: A proper British “Summer” BBQ in the rain.

Author biography:

ClemensClemens Mayer is a postdoc, working at the University of Cambridge under the supervision of Prof. Shankar Balasubramanian. He was born in Graz, where he completed his undergrad in 2008. Subsequently, he moved to Zurich to pursue his Ph.D. in the field of enzyme engineering. In 2014 he joined the University of Cambridge, where he is currently investigating the role of RNA structures in biological processes. Passions include coffee, basketball, the accumulation of useless knowledge, being a geek, and dreading the English summer.


If you are interested in writing a guest post for #RealTimeChemInFocus, please get in touch with @RealTimeChem on Twitter.

RealTimeChem Live Tweeting UK Public Attitudes to Chemistry launch – 1st June 2015

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Hello everybody,

I have some slightly different news to report today. I am pleased to announce that @RealTimeChem will be live tweeting from London on Monday 1st June at the launch of the results of the Royal Society of Chemistry’s research into UK Public Attitudes to Chemistry. You’ll be able to follow tweets about the event under the hashtag #chemperceptions. The launch will also be covered on YouTube in the form of a live stream starting at 3pm BST. 

You can find more information on the RSC’s website. This research represents the first national, in-depth study into what the UK public thinks and feels about the topics of chemistry, chemists and chemicals. I have had the privilege of participating in this project at various stages, in part due to my involvement with #RealTimeChem as well as working for the RSC, and I will say that the results are fascinating. I look forward to the discussions that this will spark among the community!

So, please tune in and follow #chemperceptions on the 1st June, I will be tweeting all day using the hashtag (whilst also keeping up with all of your wonderful #RealTimeChem of course!) so feel free to take part in the discussion as it unfolds.

-Doctor Galactic-

Chemistry: Lost in Translation (sort of)

I’m Jason Hoshikawa, a 2nd year PhD student in the Kitagawa Lab at Kyoto University in Kyoto, Japan.My main area of focus is polymer synthesis and heterogenous catalysis using porous coordination polymers (PCPs).

The thing about working in the sciences (and maybe the arts too) is that we generally work in a multi-cultural environment. During my undergrad and Masters in the US, I was the native surrounded by foreign students. It was a wonderful experience. Many of the members of that group were from India, specifically from around the Hyderabad area. This turned out nicely for me because Indian food is my favorite food. When I entered my first research lab as an undergrad, I was assigned to work with a woman that makes the most amazing food. She quickly learned the key to motivating me to work hard in the lab. If I worked late enough, she would bring me dinner. I miss those dinners more than you can imagine.

Kyoto University's clocktower. - Image Courtesy of Wikipedia.

Kyoto University’s clock tower – Image Courtesy of Wikipedia.

But, now, I live in Japan where I am the foreign student surrounded by natives. Aside from learning about chemistry, I’ve learned a lot about myself. This is not the first time I’ve lived in Japan, but this time it’s very different from my previous experiences.

More than the simple difference in culture between the US and Japan, the other bit of context that may be important is that the Chemistry Department at my previous university is relatively small compared to our department at Kyoto University. The change in environment was quite significant. Going from a department where everyone basically knows everyone else to a department where there are simply too many people to know hardly anyone outside one’s own research group was rather shocking.

In my research group, all of the students are assigned various jobs. Most students are assigned to manage an instrument or two, and some students, like myself, are assigned to administrative roles. I have two administrative roles, actually. Firstly, I am the lab manager. I’m responsible for the general day-to-day operation of the lab (i.e., the room where experiments are performed). I purchase all the expendables (e.g., gloves, vials, pipette tips, glassware, weigh paper, etc). In a separate (but related) administrative role, I’m also responsible for buying all of the solvents (both regular and deuterated) and common reagents (acids, bases, metal salts, etc). Basically, I buy everything except specific reagents that only one or two people would use, and instrument-specific expendables.

An average day

In our lab, we work Monday through Saturday, and the layout of my day is basically the same, unless there is something special that requires me to leave early.

My alarm is set for 07:00. The actual time that I wake up varies seasonally. I don’t have blackout curtains in my room, and Japan doesn’t observe summer time (which I’m happy about), so right now, the sun rises at around 05:00. During the summer, I wake up often before my alarm, but during the winter, I can usually sleep until my alarm wakes me up.

I like to leave my apartment at 08:45 so that I can get to the bus stop early enough to get a seat on the 09:00 bus. The trip to campus takes about 10 mins. If you’d like to see the area around where I live on the bus ride to campus, watch the video below.

I take breakfast at the bakery on campus. They have a lovely breakfast set for Â¥270, and I usually add to that a donut (Â¥151). While I eat breakfast, I like to look at twitter, reddit or Instagram, while listening to a podcast. My work day starts between 09:30 and 10:00. Everyone usually gets in during this time, and we generally think of 10:00 as the start of our workday. The first work period is 10:00 to 12:30. During this time I like to look over new ASAPs in my RSS reader, and then try to write for an hour, or look up papers. Then at 12:30 we have an hour for lunch. My hearing is not so good, so I tend to eat lunch by myself in the office rather than going to the cafeteria with everyone else. I used to go, but it’s just so noisy that I can’t really hear anyone. So, I sit at my desk and watch the PBS Newshour (@pbsnewshour) on YouTube.

After lunch is the second work period that runs from about 13:30 to 19:30. During this block of time, I like to do heavy synthetic work. I try to start reactions, end reactions, and do work up during this period. If at all possible, I try to do all synthesis related work during that six hours.

Dinner from 19:30 to 20:00. After dinner, I try to focus mainly on characterization. After 20:00, the number of students starts to decrease, and it’s easier to make reservations on the instruments. I can use them in peace and quiet.

I generally go home on one of the two busses in the 22:00-hour. Once home, I decompress by taking a shower and reading until I fall asleep. With that ideal in mind, here is reality…

An average week

Saturday

I like to think of my week starting on a Saturday. The reason is because that it’s the last day of the research week. I go through and take inventory of the lab in order to figure out what I need to order. It’s not as involved as it may sound. It usually occupies the first work period. I have lists of everything so I can check through quickly, and for most things, I can stand in one spot and just look around the room while marking off my list. The solvents are easy too. I open the cabinet and count the bottles remaining.

I place the orders by writing them into the order notebooks for each of the suppliers. In Japan, representatives from manufactures and suppliers come around several times a day to collect the orders, and then they deliver them directly. Each lab manages its own finances, so as long as one isn’t buying and NMR spectrometer, there is almost no red tape.

Figure 1

Figure 1

On this particular day, I spent most of it cleaning as my workbench was a complete disaster (Figure 1). Also, I didn’t want to start any reactions because the reactions that wanted/needed to do I did not want to leave running unchecked on Sunday.

Sunday

Sunday is the one day a week off that we have. I treasure those days. Getting to sleep in late, and getting to do what I want all day is a luxury I try not to squander. However, there are still practical things that must be done. As if cleaning my workbench wasn’t enough, I clean my apartment and do laundry. I also cook lunch and dinner for the next seven day period. I try to do as much pleasure reading as I can because during the rest of the week, I read mainly research related materials. It’s a nice break.

Monday

I had run out of a ligand that I need to make several of the MOFs that I use. To start the process, I perform a Suzuki-Miyaura coupling reaction. I use the reaction to couple an arylbromide with an arylboronic acid.

Figure 2

Figure 2

Figure 2 shows the progression of the reaction. In the upper left is the start of the reaction. The brown color is from the palladium(II) acetate that I’m using as the catalyst. The upper right shows the reaction mixture right before I stop the reaction. The palladium has formed palladium black over the course of the reaction. During the catalytic cycle, palladium(0) is formed, and in this oxidation state, if two palladium(0) atoms bump into each other, they can begin to form palladium nano particles, which kills the catalyst. Basically, the reaction is over. The lower right shows the result after liquid-liquid extraction. Many people try to get rid of the palladium black, but I find it too much trouble to deal with, plus I always end up with a lower yield. I prefer to just let most of it get clumped onto the magnesium sulfate that I used to dry the organic extract, and if it still persists after filtration, it will be stopped by the column when I purify by chromatography. In the lower right is the nice white powder that I obtain after purification.

Incidentally, I love watching the condenser of the rotavap.

Tuesday

It’s lab clean up day! Every Tuesday morning, everyone gets together and cleans the lab. At my university, every lab is responsible for taking out the trash and the recycling. The cleaning staff are only responsible for common areas. The labs are our responsibility. This is an average load of refuse for a week (Figure 3):

Figure 3

Figure 3

The product from the previous reaction has a methyl group attach to a phenyl ring. This methyl group can be easily oxidized to a carboxylic acid. A synonymous reaction would be that of turning toluene into benzoic acid. The method I prefer is heating the starting material in a hydrothermal vessel in the presence of about 30% nitric acid (Figure 4).

Figure 4

Figure 4

This reaction makes me nervous because it heats nitric acid to 170 ℃. The product of this reaction, aside from the carboxylic acid, is a lot of nitric oxide gas. I made a video showing the opening of the vessel after the reaction.

Wednesday

After the ligand has been purified, it’s time to make the PCPs. The PCPs that I use are made of a mix of ligands. That means I combine more than one ligand to form the framework in the hopes of altering the pore surface functionality. I made two different PCPs on this day. One is a copper(II)-based PCP, and it’s synthesized in two steps.

In the first step, one set of ligands are combined with a copper(II) salt. This is then stirred for two days. The video below shows the mixing of reagents at the beginning of the reaction.

The other MOF is aluminium(III)-based. It’s a one step reaction that performed in a glass vial in the oven at 120 ℃. Unfortunately, that’s all I can say about those projects until they are published!

Thursday

I spent most of this day performing spectroscopy. Of all the spectroscopic techniques, NMR is my favorite. I fell in love with NMR the first day I had ever heard of it.

Figure 5

Figure 5

Our NMR lab (Firgure 5) has three spectrometers, all made by JEOL. In the foreground is the 400 MHz, behind that is the 600 MHz (my workhorse), and in the back on the right side is a 500 MHz. The sample that I was measuring that day was of a polymer that I had synthesized. I was doing a full set of characterization, so I set up a whole set of experiments: 1-D 1H and 13C, COSY, HSQC and I measured relaxation t1 with a double pulse experiment.

Figure 6

Figure 6

The sample (Figrue 6) was dissolved in benzene-d6, and I was was worried that since this sample would be running for 3 or 4 days that the solvent would slowly evaporate, so I sealed it rather than using a cap.

Friday

I realized that I forgot to add the group meeting schedule to my calendar. I’m presenting on Monday of the next week. There’s two things you should know about me. First, I have a terrible memory. If my Google calendar doesn’t remind me about important things like group meetings, I will surely forget them. Of course this isn’t a fail proof system because I have to remember to put these important reminders into the calendar first!

Normally, I do it right when I get the e-mail from the boss with the schedule for the next month. Somehow, I forgot.

The second thing is, I really hate making presentations. I often wish I could pay someone to do it for me. In some ways, I think this might make me a failure as a scientist (Editor’s note: Far from it!) While I love using my computer, I hate being chained to it. That’s how I feel when I have to sit and work on a presentation, or poster, or paper. I would much rather just work in the lab. However, I realize that it doesn’t work that way. My results, success or failure, are meaningless unless I report them.

However true that may be, making presentations is still probably my least favorite thing to do in science. And so, since I forgot, I spent most of the Friday and Saturday compiling data and making figures and putting together a presentation.

Maybe next week won’t be so crazy.

Yeah, that’s what I always tell myself.

Author biography:

wLT3vNAF_400x400Jason Hoshikawa is a 2nd year PhD student working in the Kitagawa Lab at Kyoto University under Assoc. Prof. Takashi Uemura. He was born in Dallas, Texas. After working in the television and radio industry as a high-power transmitter engineer, he started his undergrad education at the University of Hawaii at Manoa, but returned to Texas to finish his BS in Chemistry (2010) and MSc in Organic Chemistry (2012) at the University of North Texas under Prof. Mohammad A Omary. After being awarded a Japanese Government Scholarship for Research Students (2013) he entered the Graduate School of Engineering at Kyoto University to complete his PhD studies.

You can follow Jason on Twitter (@ChemistInJapan), on YouTube (https://www.youtube.com/user/ChemistInJapan), and Instagram (@ChemistInJapan).

The weekly adventures of a jolly chemist

In this world there are two kind of postdocs: some are hired for a specific project and are focused on that, others are jolly helping here and there. I am, ladies and gentleman, a jolly.

I’m Vittorio Saggiomo, a postdoc in the BioNanoTechnology group at the University of Wageningen (in the sunny, sunny Netherlands). As a jolly, I’m working on PDMS microfluidics chips, coacervate micelles and (quite a lot) of devices with chemical sensors for soil, animal food, and recently, malaria vectors.

As I tend to swear a lot, in this blogpost I’ve censored myself changing the word f*ck with frak (Doctor Galactic: I’m partial to frell myself).

Vit1

Fig 1. Example of the research going on in my university…

Fig 2. Mosquito farm

Monday starts like all my Mondays: the alarm clock buzzing on my night table, me thinking that it’s Sunday morning and relaxing a little bit more in the bed. Between 10 and 15 minutes later I finally realize that it’s not Sunday and I have to rush to the university. Welcome, first frak of the week.

Our building is probably the only laboratory in the whole of the Netherlands that is uphill (here it’s called “the mountain”) and when I’m late I try to bike as fast as I can. Entering the corridor of the building is like finishing the marathon, with coworkers cheering me up and giving me water. In a chaos of people screaming my name I finally enter my office with only 30/45 minutes of delay. Then I usually need 10/15 minutes to recover from the high speed biking uphill, and to get my heartbeat on a human level and to try to breath again.

Turn on my computer, 20/30 unread email, 10/15 “frak I completely forgot about this” and “oh for frak’s sake” and finally I’m in the lab, my acetone smelling kingdom.

I devote the first two days of the week on synthesis. We are trying to control the core of the coacervate micelle (very huge 100 nm micelles with a soft core of chocolate (ok, maybe not chocolate, but still a soft core) for incorporating and releasing drugs on command (hopefully our command). I put a couple of reactions on the notes of Metallica and/or AC/DC.

I spend the rest of the day supervising (or trying my best to) two master students.

Fig 3. Fairy dust synthesis

Tuesday is purification day. I love column chromatography, I find it extremely zen and relaxing. And it gives me an awesome excuse not to do anything else -“come on dude, I cannot stop my column, I’ll come to you later”-. TLC, rotavap, NMR, and then i can choose between: “fraking hell, why you don’t want to work?”, “what the frak are you?”, “for frak sake, who on earth is doing a 2 h proton NMR?”.

Then I try not to get mad at one master student because he believes that his column didn’t work because the size of the capillaries is wrong. Between a colloquium and a coworker that MUST show you at least 10 youtube videos the day passes quite easily. Tuesday after work is also squash night with my boss. Perfect for stress reliever and for legs related injuries.

Fig 4. The eye of Sauron

Wednesday is PDMS and devices day. Since I came in this lab I have fallen in love with PDMS, an extremely nice polymer for making microfluidics chips, stamps for microcontact printing and bouncing balls. I spend most of the day playing around with PDMS, using different crosslinkers, checking the swelling and the stability, pressure and so on. We are currently applying for a patent on a discovery we made last year and now are waiting to publish it. Usually on a Wednesday I also discuss a little bit with the boss. It happens more or less randomly, but most of the time it is on Wednesday. My boss’ office is between my lab and my office and when I walk from one place to the other I can clearly hear someone screaming my name.

The discussion goes often like this (I’m currently working on many different projects and I’m extremely picky on which new project I can accept):

Boss: Maybe we can do this…

Me: No.

Boss: Yes.

Me: No.

Boss: Yes.

Me: No.

Boss: Yes.

Me: No.

The discussion can go on for hours. The first that lowers his eyes loses.

When I’m finally back in the lab I can start soldering wires, checking resistances and programming Arduino and Raspberry Pi. It’s not chemistry but it’s quite entertaining.

Fig 5. Maybe a pinch more crosslinker.

Fig 6. Maybe even more crosslinker.

 

Fig 7. Pinky microfluidics.

Thursday is terminator day. The day of the machines. Now NMR, now fluorimeter, now AFM. The synthesis of new sensor would be useless without some in-depth characterization. In this day the amount of fraks climbs to the top. Swearing at a random machine is one of my favorite hobbies. When Skynet finally takes control of the world I will be one of the first to be murdered (or enslaved). The time lost in understanding why a machine is not properly working is way more than the time used for the real analysis. Today is also a day of squash with my colleagues. Time for shoulder related injuries.

Fig 8. 8-bit AFM.

Friday is group meeting day. I usually clean a little bit in the lab, write down the stuff I did in the week and program what I’ll do the following week. The group meeting starts after lunch and no one knows when it will end, but usually we finish very, very late. Beer, alcohol and junk food are more than welcome during the discussions. BBQ in summer time. We also use 10 minutes of our time collectively swearing at a random referee number 3.

Fig 9. Group meeting.

Saturday and Sunday I try to read some literature, writing/correcting/rewriting papers,grant, patents and blog posts.

….and from my side, that’s all folks. Feel free to contact me for info, news, fun or just for swearing together.

 

Author biography:

Vit

Dr. Vittorio Saggiomo is a post doc, working at the University of Wageningen under Professor Aldrick Velders. He was born in Naples (Italy) where earning an M.Sc in Organic Chemistry in 2007. He then moved to Kiel (Germany) pursuing a Ph.D. working on Dynamic Combinatorial Chemistry. In 2010 he moved to Groningen for his first post doc in the field of Systems Chemistry, before heading to Wageningen. Find about more about him at: www.vsaggiomo.com/

Blogs at Labsolutely (http://www.labsolutely.org/) & creates videos on Youtube (https://www.youtube.com/user/vsaggiomo)

 

A week in the life of a Radical Chemist

G’day! Welcome to the inaugural #RealTimeChemInFocus post, where I aim to give you a bit of an insight into the world of a radical chemist. Radical in the sense that I work with free radicals (molecules or atoms with an unpaired electron), not my political/social leanings. Read on for an introduction to our work on respiratory disease and atmospheric pollutants as I walk you through a typical week in the life of an organic chemistry PhD student.

The WHO estimates that roughly 7 million deaths per year are caused by exposure to air pollution. It is now well known that living in highly polluted areas makes you more susceptible to maladies such as respiratory disease, allergy, asthma and even death. My PhD aims to work out the underlying chemical processes, or chemical entities, responsible for these biological effects. Using a bottom-up approach, we expose simple biomolecules to pollutant gases and see what kind of havoc they wreak.

The week begins with an outline of the research tasks ahead and, like most, this is one dominated by organic synthesis. For us, this is purely a means to an end. Each peptide we wish to study is carefully designed with respect to amino acid sequence and composition. As we work on gram scale, it is typically more cost effective to synthesise these peptides in-house. That means grunt work and grunt work means coffee, lots and lots of coffee.1

Past me had the foresight to prepare the compound I needed before end of year closure. Present me lacked memory of events before end of year closure.

Past me had the foresight to prepare the compound I needed before end of year closure. Present me lacked memory of events before end of year closure.

 

Synthesising each peptide involves protection of the amino acids, a coupling reaction, followed by extraction/washing and purification. Building up larger peptides, such as tri- or tetra-peptides, also involves deprotection and another coupling/work-up. To work efficiently, I often do two or three reactions simultaneously. Each reaction uses the same solvent, reagents and work-up procedure so this saves a lot of time.

 

 

 

 

A fairly epic prank by Aaron’s group members, who replaced all of the posters in the building the morning of his talk - this is one of about four different versions

A fairly epic prank by Aaron’s group members, who replaced all of the posters in the building the morning of his talk – this is one of about four different versions

The end of the week brings a busy day. Friday means more coffee (#FilterFriday!), our department’s organic chemistry seminar and, today, our group meeting and a couple of  radical reactions. These experiments are the true focus of my PhD – new, original research, delving into the effects atmospheric pollutants may have on our body. That means its time to take those peptides prepared earlier in the week and treat them with some ‘pollution’, today it will be nitrogen dioxide (NO2•).

Huge quantities of nitrogen dioxide are produced in China, where air pollution is now a part of daily life – via NASA (http://www.nasa.gov/topics/earth/features/KnowYourEarth/Air_prt.htm)

Every time you drive your car you are emitting not only carbon dioxide but also nitrogen oxides (collectively referred to as NOx gases) such as NO2•. This is one of the most abundant radicals in our atmosphere and has been implicated in respiratory disease, being toxic by inhalation. Once upon a time we obtained gas cylinders of pure nitrogen dioxide. As Australia does not produce it locally, they were shipped from overseas but sadly the freight costs are exorbitant and it can be surprisingly difficult to convince a ship captain to receive a cylinder of toxic NO2• gas. Tyranny of distance strikes again. We now produce our own nitrogen dioxide in the lab.

While chemistry is famous for beautiful colours, the field of organic chemistry is typically characterised by white solids, colourless oils and clear solutions. Peptide chemistry doubly so. My favourite chemical reaction, for reasons now obvious, is the classic reaction between copper and concentrated nitric acid. Nitric acid is slowly dripped over solid copper metal (such as the copper penny above), producing a brown noxious gas – our pollutant, nitrogen dioxide. The copper is converted from Cu0 to Cu2+, forming a gorgeous, bright blue solution of copper nitrate. Meanwhile, the nitrogen dioxide passes through a drying tube and is condensed as a liquid which allows us to react a known quantity with our peptides.

Once we have treated our peptides with this simulated pollution, we go through a painstaking process of identifying each product that is formed. This involves repeated HPLC purifications and characterisation with analytical techniques including HRMS, MS/MS, multi-dimensional NMR and, when I’m lucky, X-ray crystallography. Our results so far show that nitrogen dioxide and ozone are a destructive force, modifying residues or cleaving peptide chains. For a nice article on our latest research check out “Nitrogen dioxide and ozone: a sinister synergy” via Chemistry World or the accompanying paper  published in Organic and Biomolecular Chemistry.

Over the last few years I have taken great pleasure in becoming a part of the online chemistry community. In particular, the burgeoning #RealTimeChem community is extremely welcoming, friendly and engaging. Whether it’s talking about the latest Nature paper, whingeing about that guy who just lined up 6 hours worth of samples on the NMR queue or asking for tips about how to get that postdoc you’ve always wanted – there’s something for chemists of all kinds. A PhD can sometimes be quite a solitary experience and I love having the opportunity to engage with passionate, creative and ambitious people from all around the globe. Get on there, #RealTimeChem and tweet me some time.

 

Thankfully, I live in Melbourne, Australia’s coffee mecca (sorry Sydney), surrounded by multiple coffee roasters.

Author Biography:
lgamon
Luke Gamon is in the final year of his PhD in chemistry at The University of Melbourne, Australia. Under the supervision of A/Prof Uta Wille, he is currently investigating the effects of pollution on biological molecules. Passions include coffee, baking sourdough, photography, sci-comm and board games.
Blogs at A Radical Approach lukegamon.wordpress.com

icon320x320Follow: @lgamon

Could more be done to teach young chemists the right ethics?

Disclaimer: As always this is just my opinion. In fact, this blog post is more of a stream of consciousness that I’ve had today more than a structured argument. Please feel free to discuss this issue with me on Twitter (@doctor_galactic) or in the comments section.

Do young scientists need more guidance on scientific ethics?

Do young scientists need more guidance on scientific ethics?

I imagine that by now most of the chemistry community is aware of the “Dorta affair” that has been recently exposed by ChemBark. In brief, a recently published article in the journal Organometallics contained a rather suspcious note in its supporting information that seemed to suggest that the principal investigator was asking his student to fabricate elemental analysis data (the actual supporting information can be found here).

This line will probably lead to a "meme". Please just don't. Do something with cats instead.

This line will probably lead to a “meme”. Please just don’t. Do something with cats instead.

How this note, which appears on page 12, came to be, what it actually means and how it got through the peer review process are all under investigation. Unsurprisingly, this issue has sparked a huge amount of debate. As for my own two pence on the issue, I’m reserving judgement until all of the facts have been fully revealed. Let’s just say it does not look good, at all. I will say that I hope that everyone stays professional as distinctly dislike “witch hunts” and “personal assassinations”. So far, the authors have not defended themselves and they should have the opportunity to do so. The paper is currently I believe being withdrawn.

All in all though seeing something like this in a published work reminds me of a song by Tim Vine and should sound “Alarm Bells”:

Science in general is receiving an ever increasing amount of scrutiny concerning just how widespread fraud is, be it plagiarism, deception, bribery, sabotage, professorial misconduct or simply making shit up. A lot of this is likely a symptom of the “publish or perish” culture that seems to have a vice-like grip on the scientific world. Research-oriented universities put pressure on scholars, particularly those early in their careers, to publish as much as possible. This can detract from the amount of time that they have to actually teach and train undergraduates and postgraduates. Universities largely don’t seem to hire on teaching/mentoring ability, but rather by apparent research prowess. This approach can be detrimental to creating the next generation of scientists.

Anyway, all of this leads to some questions (and the point of this already rambling blog post); from where do we new chemists learn our scientific ethical compass? And could we do more to teach chemists (and scientists in general) the correct ethics?

PhD comics has a comic covering most things in your PhD and a lot of them are very accurate.

One imagines that the biggest influence on your ethical choices as a student of the sciences are your teachers, lecturers and subsequently your PhD supervisor. Let’s go straight to the example of PhD students. I’ve certainly worked for senior chemists who were ethical and always encouraged the right sort of behaviour. But, what if they hadn’t? What if you do have a supervisor who encourages you to do something that is not ethically correct? Most of us would say that we’d cry foul and say no. However, clearly this is not the case for all of us. It seems that would probably go along what our supervisor suggests, PhD’s are stressful, supervisors often want results all the time, corners may be cut and it may seem all perfectly innocent and reasonable if your supervisor says it’s okay. They are your direct boss. This is the person you work for after all, they are your scientific mentor.

Of course it’s perfectly possible that a supervisor can be ethically perfect and a student can still do things that are not. In which case it is still the supervisors responsiblity to: a) spot this and b) stamp it out.

By the time you get to being a PhD student you should have already developed a strong idea of the ethical rights and wrongs of science. You should feel empowered enough to say no if you are asked to do something that you know is wrong. This empowerment and the ideals should come from the top down at your University (that place of learning that you’re spending a huge amount of money to attend). They should have provided you with ethical guidelines and a structure by which to report any ethical problems that you run into. However, is what you get from your University on this subject adequate?

I posted the following question on Twitter to my chemistry based followers (of which I have quite a few these days!):

The response so far have ranged from PhDs being given full courses (even at the undergraduate level) to practically nothing at all. In my own experience, I don’t recall any formal courses or talks being made at my University on this subject, at least not any that were mandatory or weren’t so perfunctory that I actually could remember them. Like a lot of universities mine ran “doctoral workshops”, but attendance at these was never truly enforced, they are merely suggestions. This can vary wildly from insitution to instuition, and from supervisor to supervisor. Yet, it really shouldn’t. There should be some kind of set standard level of training. The general impression given during a PhD is that your laboratory work comes first and everything else is secondary and should happen off your own back. In part, I feel like this is actually okay sometimes, after all, every PhD students should take responsibility for their own career and personal development.

Take this place. Not that hot on the ethics. At least it’s only a Disney film.

The question becomes, are universities giving PhD students the tools to do this? I have only good things to say about the supervisors I have worked for, but I cannot say the same for the institutions I have worked at. I haven’t written a blog post on my experiences with university administrations (mainly because it brings up bad memories and I think it’s time to let bygones be bygones), but suffice to say that I have generally felt, at times, like those higher up have an “out of sight, out of mind” attitude toward postgraduates.

At my postgraduate university the grand sum of ethics training for PhD student was a handbook to read and a form to sign. It’s all in there of course, in black and white, the “do’s and don’ts” and the consequences and processes, but these are just words on a page. It’s something you read, sign a piece of paper to say that you have read it and then, probably, never read again. That’s it. All ethic’d up for 3-4 years. The same kind of forms and hand books come out again at Post Doctoral stage.

I think that universities should take more responsibility for ensuring that students are adequately equipped to understand and follow the ethical guidelines of science. That students feel empowered enough to take a stand and report unethical behaviour and recognise that a good scientist is an ethical scientist. It is something that should be drilled into those learning science from the moment they enter an institution of higher learning until the day that they leave it (preferably before this). I’d advocate training courses at undergraduate, postgraduate and post doctoral levels, giving case studies, advice and information about the procedures in place at the university to deal with ethical issues.

This should really form only a small part of an all around more adequate training for postgraduate students at all higher education institutions. So that PhD students are better equipped for their future careers. Currently, it’s a complete lottery in terms of the amount and quality of extra training and support that are available to postgraduates and this should not be the case.

Going back to the title of this blog post; could more be done to teach young chemists the right ethics?

Yes.

-The Lab Coat Cowboy-