My three days at the European Symposium on Biological and Organic Chemistry (ESBOC) did not start in the most auspicious way. Or, again, maybe they did. Well, Friday the 17^th, the day of my departure, is a day of bad luck in Italy, much like Friday 13^th is in many other countries (it may not sound like it given my name, but I am indeed Italian), and my stopover at Birmingham New Street station to catch my connection to Newtown (Powys), Wales, certainly got my heart pumping.

To make a long story short, my apparently comfortable fifteen-minute leeway between my arrival from London Euston and my departure to (seemingly unknown in Birmingham) Newtown got eaten away by a mostly fruitless search for ‘my’ platform in a station, which, I later found out, is undergoing significant redevelopment — and is not very passenger-friendly. After a few minutes’ queue to reach the information desk, I got sent by the guy behind it to “platform 5b”, when I probably had something like seven minutes left to spare. After about five minutes of frantic soul-searching while pacing on a platform that just didn’t seem right, and that was at once platform 5, platform 5a and platform 5b, I grabbed my trusty trolley by the neck, ran up the stairs to the main concourse, then to the closest display panel, and finally down the stairs to platform 6b, as a train moved slowly past it. Was it my train? Was it pulling in? Was it pulling out? Well, suffice to say that, much to my relief, I made it to Newtown on time to catch the minibus meant to take all ESBOC participants arriving by train to the conference venue at Gregynog, a relatively isolated location about 8 km of narrow, windy road away from the town.

View of Gregynog. Courtesy of Dr. James Redman.

Gregynog… It is actually a beautiful country house surrounded by 750 acres of (beautiful, it behooves to stress) gardens and woods sitting right in the middle of Wales. It was donated to the University of Wales in 1960 by its owner, the late Miss Margaret Davies, as an arts center. As I started looking for my room, a friendly and slightly surprised member of staff exclaimed, “Room G2? It’s one of our two best rooms sir!” Wow, time to let my hair down, if I hadn’t just had it cut rather short, that is. The room was actually very nice and comfy, and I had something like half an hour to unpack before the conference reception and presentation.

This year’s annual conference was the 47^th of the series, as this symposium was first organized here at Gregynog in 1967 by Professor Cedric Hassall of University College, Swansea. At the time, it was called Gregynog Natural Products Symposium, a name changed to European Symposium In Bio-Organic Chemistry in 1971, to become the present-day European Symposium on Biological and Organic Chemistry only in 2011. This year’s chair, Professor Kai Johnsson of EPFL Lausanne, Switzerland, could actually not be present, as his wife is expecting a baby imminently, so the role of hosts was entrusted to the capable hands of the Chairman of the Steering Committee, Professor Tim Bugg of the University of Warwick, and of the Treasurer and Secretary, Dr. James Redman of Cardiff University.

Cover of the program of the 1967 Gregynog Natural Products Symposium.Courtesy of Dr. James Redman.

The title of this year’s symposium was “Chemical Probes for Cellular Processes”, a subject that elicited an excellent response of corporate and non-corporate sponsors and, according to Professor Bugg, the most international attendance of the symposium to date. This year’s ESBOC had 60 participants from eight different countries affiliated to both academic institutions and industry. The program included 18 lectures by invited speakers, ten of them plenary and two ‘named’, and it also included a 12-strong poster session. Among the scheduled speakers were Nature Protocols’s own authors Ben Cravatt of the Scripps Research Institute, Edward Tate of Imperial College London, and Carsten Schultz of EMBL Heidelberg. All the talks, which included lectures by ‘industry’ speakers Dr. Ivan Correa of New England Biolabs and Dr. Keith Wood of Promega, were up my alley, so to speak, as they were generally given by chemists who applied their skills to attempt to answer biological questions, exactly my research background.

Participants of the 1969 Gregynog Natural Products Symposium. Cedric Hassall is the second person on the left seated. Courtesy of Professor Timothy Bugg.

It wasn’t just that I understood the talks in their entirety, which is undoubtedly a big plus, but I actually really enjoyed them. The symposium was small enough that no talks needed to be scheduled at the same time, so I was able to attend all of them. The lectures spanned subjects like applying bioluminescence to the study of intracellular interactions or the imaging of fatty acids, activity-based protein profiling, phage selection of peptides with different bio-relevant properties, the synthesis of riboswitches to control gene expression, the expansion of the SNAP-tag tool box, and fluorescence-based approaches to investigate nucleic acid structure. Talking about activity-based protein profiling, unfortunately Professor Ben Cravatt, who was supposed to give the first day’s Royal Society of Chemistry Bio-Organic Group Lecture entitled “Activity-based proteomics: applications for enzyme and inhibitor discovery”, could not be present, due to a family commitment, but he was replaced by post-doc Ken Hsu from his lab, who, despite the short notice and an 8-hour jetlag — Scripps is in San Diego, California — gave a wonderful talk on the use of activity-based protein profiling on serine hydrolases for the discovery of bioactive lipid networks by chemoproteomics and metabolomics.

The next day’s ‘marquee’ talk, the Cedric Hassall Lecture (“In vivo selective optical imaging of tiny tumors to rationally designed activatable fuorescence probes”), was to be given instead by Professor Yasutero Urano, of the University of Tokyo. Except that Yasutero was not the speaker’s first name. As he initiated his talk, Professor Urano pointed out that his name is actually YasuterU, and went on to speculate that the tendency of his European colleagues to spell it with an “O” must be due to an understandable mental association between himself and Elvis CostellO. Well, to be honest, I did not see much of a physical resemblance between Professor Urano and Elvis Costello, not least because the former is obviously much younger. The association was made clearer, however, by the thunderous applause that greeted the end of Urano’s lecture. A really impressive talk, even for an outsider like myself.

Professor Urano had described his laboratory’s work on synthesizing and testing probes that become fluorescent only when taken up by tumor cells, a strategy that would prospectively enhance surgeons’ ability to literally see cancerous tissues when operating. Urano’s research group had used two main approaches to achieve their goal. In one, pH-sensitive fluorescent probes are fused to an antibody specific to membrane receptors that are highly expressed on the surface of tumor cells. Upon endocytosis, the low-pH environment of the cell lysosome causes activation of the probe, which thus becomes fluorescent. In the second, the probe is fluorescently inactive as long as it remains bound to an appended peptide group, which can however be cleaved by GGT, a peptidase highly expressed on the surface of tumor cells. Upon cleavage of the peptide bond, the newly fluorescent and highly hydrophobic probe concentrates first on the cell membrane, and, eventually, inside the cell, to highlight that cell’s unhealthy state. What did I say? Really impressive.

As ESBOC drew towards its end, I even found out how Gregynog is pronounced correctly. Two competing schools of thought seemed to take shape on the matter at the conference. According to participants with Welsh connections, the pronunciation in southern Wales would be something like Greg-EYE-nog, whereas people in northern Wales may actually pronounce it Greg-E-nog. Unfortunately Gregynog is almost in the dead center of Wales… Mystery solved on Saturday night, however, when we ESBOC participants were entertained by the charming music of Welsh harp player and folk singer Siân James, clearly a reliable source on all things Welsh. To my untrained ear, she pronounced the locale “Greg-e-nog”, making a slight clicking sound with her tongue when she uttered the second and third g’s of the word.

What can I say? My experience at ESBOC was excellent all around. The place was fantastic, the talks outstanding, the participants friendly and chatty, and my ‘contacts’, Professor Bugg and Dr. Redman, always helpful. Even the food was terrific. Word on the street was that Gregynog had recently hired a new German chef, and everyone was raving about him. Ok, I am Italian, but I have to admit that he really knew his stuff. On Sunday the weather too smiled on us, with a gloriously sunny day; too bad that we were about to leave and that strolling around the grounds had been scheduled for the day before. Oh well, not bad for a conference two train and one minibus ride away that started on a Friday the seventeenth…

Well, the last bit of important information concerns next year’s ESBOC at Gregynog: ESBOC 2014 will take place on 16–18 May, and it will be organized by next year’s scientific chair, Dr. José Luis Mascareñas of the Universidade de Santiago de Compostela, in Spain. The title of that conference will be “Biological Applications of Supramolecular Chemistry”. Make time to go, if you can.

So I’m back… Well, I have actually been back for a little while already, as this year’s Mathematical and Statistical Aspects in Molecular Biology (MASAMB) meeting was held last April 11th and 12th.

Mission accomplished, it is fair to say. The idea was for me to acquaint myself face-to-face with research areas — bioinformatics and statistical genetics — which Nature Protocols has always covered, and in which it hopes to be even more active in the near future. For sure, over a day and a half I had the opportunity to attend a total of 25 presentations divided into five sessions: statistical bioinformatics, computational cell biology, next-generation sequencing, systems biology, and evolution. I will not claim to have understood everything I heard, but all presentations were stimulating and thought-provoking. Given my background in ‘wet’ chemistry and biochemistry, I guess it was no surprise that I found it easier to follow the biological side of the talks than the parts that dealt with mathematical and computational models, but I am now much more familiar with the landscape in this research area.

My attendance of MASAMB, as I discovered on site, was primarily made possible by the engaging and amiable host of this year’s MASAMB, Dr. Michael Stumpf of Imperial College, via the intercession of my email contact, Dr. Louise English. During one of the poster sessions, Michael explained to me that one of the main goals of MASAMB is to provide PhD students and post-docs with a workshop-like venue in which to present their own research in an environment that is more ‘intimate’ and less intimidating than the average meeting. Students and post-docs are those most encouraged to present their work, Michael added, and most of the conference speakers belong to this category.

Besides the scientific quality of the presentations, I was quite impressed with how well they were timed and organized. Each talk was to last 20 minutes, including eventual questions from the audience, and not a single presentation out of 25 went long, while the switch between speakers always ran smoothly and quickly. I found this to be quite the impressive feat, both in terms of the technical prowess of the meeting organizers and of the scholarliness of the young — and one would assume generally relatively inexperienced — speakers.

This year’s MASAMB conference attendance was about 110, toward the high-end of the average, but it still felt quite ‘cozy’ for participants and reporters alike (well, for the only reporter, me). Speakers were mostly from UK institutions (e.g., Imperial College, UCL, University of Glasgow, University of Warwick, University of Bristol, Cancer Research UK, Brunel University, University of Manchester, University of Sheffield and the University of Reading), but there was also a significant representation of researchers from other European countries, including Cyprus (University of Cyprus), Germany (EMBL Heidelberg), Austria (Center for Integrative Bioinformatics and the University of Veterinary Medicine), Switzerland (ETH-Zürich), Poland (Polish Academy of Sciences), and Finland (Aalto University).

If I were a young scientist being trained in computational biology or bioinformatics in a European institution, I would try my best to attend MASAMB, and apply to either give an oral presentation or present a poster on my own research. Talking about posters, the poster count for this year’s conference was 35, which, according to Michael Stumpf’s concluding remarks, included “not a single stinker!” The high quality of the pool made it all the more impressive for the winners of this year’s best poster competition: Ann Babtie, Dominic Smith and Phoebe Jones from Imperial College for “A moment expansion approach for stochastic simulation and inference” and Agnes Jonas from the University of Veterinary Medicine of Vienna for “Modelling allele frequency trajectories of experimental evolution with fruit flies”. On presenting the awards, Stumpf remarked how pleasantly impressed he was that three of the four recipients were women, even though the vast majority of entrants were men. Well, you heard it, if you’re not just a young scientist, but also a woman, it’s time to do your best to attend the upcoming MASAMBs and extend the flattering gender-slanted tradition.

Well, attending MASAMB XXIII was an excellent experience, which would not have been nearly as pleasant or useful if it weren’t for the current and former members of the Stumpf laboratory. Aside from Michael himself, I had the opportunity to meet and converse (about science and everything else) with research fellows Tina Toni and Sarah Filippi, post-doc Juliane Liepe, graduate students Ann Babtie, Adam McLean and Delphine Rolando, and former Stumpf group member (now a post-doc at the University of Cyprus) Kamil Erguler. I sincerely thank them for their invaluable help and for making me feel very welcome. I feel Nature Protocols and I have now an ‘in’ into the world of bioinformatics research, and I look forward to receiving news and feedback on how Nature Protocols can be of more help to researchers in this field — right Juliane?

One last bit of information: the general preference is for the yearly MASAMB meeting to take place in the UK for two consecutive years, then somewhere else in Europe, before returning to these shores. Tentatively, MASAMB 2014 will take place at the University of Sheffield, a venue that was preferred by this year’s participants to the other two candidates, Warsaw and UCL. Stay tuned…

Last night I went to a public lecture at the University of Surrey organised by the Royal Society of Chemistry. Professor Ian Wilson spoke on the topic: “Mapping the Phenome: The analytical chemistry of life”.

I receive email alerts of talks like this, and was alerted by the fact that this was a topic that I was interested in (I have a past as a natural products chemist, and I edit quite a lot of metabolomics protocols), and that it was going to be happening in Guildford (which is closer to where I live than London is!).

The first comment to make is that this was a public lecture, so it was pitched at the level of an intelligent, interested person who had not necessarily had any formal scientific training. This talk was definitely a success; whenever I looked at the other people around me they were attentive and smiling.

The title of the talk mentions the phenome which, I suppose, looks at different phenotypes (as apposed to genotypes). As we know, organisms are somehow a product of their genome and their environment, and the point where I laughed and laughed was when he referred to the compounds that the organism is exposed to as being the “exposome”.

One part of the phenotype of an organism is its metabolome, and that was the main focus of the talk.  The title could equally easily have been: “Metabolomic analysis of urine” or perhaps “Pisse prophets of the past, present and future”.

Woodcut showing a wheel and chart that classify urine samples, shown in the blog: “Medium Aevum”.

Professor Wilson had a wooden rack for screw-top test-tubes which he opened and sniffed during the first part of his talk. He concluded this act by drinking one of them! While they all looked they might possibly be urine, they were in fact: coffee, pepsi, two strengths of tea, and scotch. He drank the scotch, apparently.

For the rest of the talk, he showed a lot of NMR spectra from urine samples of mice, rats and humans:

600 MHz 1H NMR spectrum of control rat urine, displaying hundreds of resolved peaks

… and Principle Component Analysis plots:

I know, I know, it is actually from a protocol for NMR of plants, but it is the nicest image that I can find in our content that looks like what Prof. Wilson showed in the talk.

At no point did he get bogged down with how the samples were prepared, what NMR was, or even what principle component analysis involved. What he emphasised was pattern recognition, and how you could start to see patterns in the NMR spectra for different mouse types, treatment groups, or people with different diets.

There was a feeling of optimism that this type of analysis would ultimately result in clinicians being better able to choose for each patient the best drug out of an array of possible treatments (i.e. the one most likely to help, and least likely to cause harmful side effects), because clinicians would be able to determine which pattern-group the patient belonged to.

With the advent of technologies that have made large-scale genome sequencing projects possible and since a stream of high-throughput biological assays have been developed to collect, for instance, data on proteomics, metabolomics and gene expression, the need for ever more advanced, powerful and sophisticated bioinformatics tools has become an increasingly stringent fixture of today’s molecular biology research.

The Mathematical and Statistical Aspects in Molecular Biology (MASAMB) meeting has brought together every year since 1989 a relatively small number of researchers (usually around 100) from the fields of mathematics, statistics, computer science, bioinformatics, and biology to discuss and exchange ideas on methodological and applied research in an “intimate” workshop setting. This year’s MASAMB will take place on April 11^th and 12^th at Imperial College London, with the main topics of discussion being statistical bioinformatics, computational cell biology, next-generation sequencing, systems biology, and evolution.

Since their birth in 2006, both Nature Protocols and the Protocol Exchange (which was originally called the Protocols Network) have published a steady flow of protocols that can be categorized under the general term “computational biology”. Unsurprisingly, some of these protocols have proven very popular with our readership, with a number of these articles ranking among the journals’ most cited papers.

As we anticipate the number of published protocols in this field to increase further — as well as the interest in them from our readers — for the first time this year, we have decided to attend as a journal MASAMB, sending along one of our associate editors, well, sending along myself, Baldo Lucchese. I will be covering the workshop for Nature Protocols attending as many talks as possible and speaking to as many researchers and, hopefully, readers as humanly feasible. The objective will of course be to gain the wherewithal to make Nature Protocols a more helpful source for researchers in bioinformatics and statistical genetics and for readers with an interest in these fields. It will also be an excellent opportunity for me to meet in person a few of our authors. I certainly look forward to that too.

If you too are going to be at the conference, please do come by to say hi.

Stay tuned for the next blog post on this issue after I come back from MASAMB XXIII.