Biochem Blogs

Biochemistry blog, science writing

Launching 2014 in Paris: The international year of crystallography

Dr. Sue Fetics

Dr. Sue Fetics
I'm on ScienceSeeker-Microscope

 

 

Guest Blogger Dr. Susan K. Fetics is the International Vice President, Iota Nu Chapter of Graduate Women in Science.

She is a post-doctoral fellow in the Laboratoire d’Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France.

 

 

The United Nations and United Nations Educational, Scientific and Cultural Organization (UNESCO) has declared 2014 the International Year of Crystallography. As a scientist, more specifically, a protein crystallographer, this is an exciting time. This year marks the 100th anniversary of the discovery of X-ray diffraction of crystals. And interestingly, 25 Nobel Prizes in the past 100 years have been awarded for research involving X-ray crystallography. The opening ceremony took place on January 20 & 21 at the UNESCO building in Paris, in the 7th Arrondissement under the shadow of the Eiffel Tower. There were many inspiring talks: we heard welcoming remarks from Irina Bokova, the Director-General of UNESCO and Gautam R. Desiraju, the President of the International Union of Crystallography. Many exciting research presentations were also given, namely: Prof Brian Kobika from Stanford University USA, 2012 Nobel Prize winner in Chemistry, who discussed his work on G-protein coupled receptors, which is the largest class of proteins used as pharmaceutical targets; Prof David Bish from Indiana University USA, presented the first  X-ray diffraction data results from another planet, Mars. He explained that the soil on Mars is similar to the soil found on the dunes of Mauna Loa, Hawaii, USA. As a scientist starting her career in crystallography, it was comforting to hear that powerful results take decades of hard work with a singular focus on one research project. As a woman in science, it was uplifting to hear that crystallography has historically been an area where women, such as Dorothy Hodgkin, Kathleen Lonsdale and Rosalind Franklin, have made a significant impact – this is rare for a scientific field. Juliette Pardon from the Cambridge Crystallography Data Center, England, discussed how her organization is using X-ray crystallography to explore the natural ores and minerals in the Democratic Republic of Congo (DRC), Africa, in collaboration with professors and graduate students at the University of Kinshasa, DRC. These crystals are used in our everyday electronics. The use of these minerals has raised ethical and environmental concerns for the DRC.

From attending the opening ceremony, one can understand that crystallography is a field of science which reaches across many boundaries such as gender, politics, scientific disciplines, countries, continents, and now planets. Crystallography is used to make cement, it is found in lithium ion batteries, it is the reason windows on airplanes are circular and it aids in pharmaceutical drug design. Despite the fact that the technique is 100 years old, crystallography remains at the cutting edge of science.

Many events are occurring this year all over the world to celebrate crystallography. For example, on January 17 & 18 at the School of Medicine in Paris, the “Festival de la Cristallographie” allowed crystallographers to explain the concepts and applications of crystallography to children and adults of the general public. Throughout the year, many countries, such as France, Greece, Tunisia and USA, have organized national crystal growth competitions for high school students. Workshops, exhibitions and lectures for the public are taking place all over the globe. For more information on events near you, you can visit www.iycr2014.org

 

Dr. Susan Fetics explaining protein crystallography to the general public at “Festival de la Cristallographie” in Paris, 18 January, 2014

Dr. Susan Fetics explaining protein crystallography to the general public at “Festival de la Cristallographie” in Paris, 18 January, 2014

 

 

 

 

 

 

 

 

 

PhD student Elise Azar (right) and Prof. Marianne Imperor (2nd right) of University Paris-Sud, Orsay, France, demonstrating crystallography concepts to the general public at “Festival de la Cristallographie” in Paris

PhD student Elise Azar (right) and Prof. Marianne Imperor (2nd right) of University Paris-Sud, Orsay, France, demonstrating crystallography concepts to the general public at “Festival de la Cristallographie” in Paris

 

 

 

 

 

 

 

 

Welcoming remarks at the opening ceremony of the International Year of Crystallography, UNESCO building, Paris, 20 January, 2014

Welcoming remarks at the opening ceremony of the International Year of Crystallography, UNESCO building, Paris, 20 January, 2014

 

 

The traveling biochemist: Enzymes, pathways, proteases, and homeostasis

@biochemprof

Clay Clark – @biochemprofI'm on ScienceSeeker-Microscope

As I’ve written before in this blog, one of the advantages of working in an academic institution is the opportunity of international travel. Science is a world-wide endeavor, and one should take opportunities to visit international colleagues whenever possible. I was invited recently to two international conferences to give seminars on caspases and allostery. The first conference was in Playa Del Carmen – Xcaret, Mexico (Enzymes, Coenzymes and Metabolic Pathways), and the second conference was in Navi Mumbai, India, at ACTREC (Advanced Center for Treatment, Research, and Education in Cancer), part of the TATA Memorial Cancer Center in India.

The enzymes conference in Xcaret was organized by Beatrice Golinelli-Pimpaneau and Elizabeth Komives and focused on enzyme function and regulation, coenzymes, metabolism, and methods for examining enzyme structure and function. There were many good talks on protein conformational changes, protein dynamics, kinases, and morpheeins. (If you are not sure what a morpheein is or how it relates to enzyme allostery, then see the review below by Eileen Jaffee (1)). The schedule of speakers is provided here. The five-day conference was held in the beautiful Occidental Grand Xcaret resort, an all-inclusive environment with great food, drinks, pools, and a private bay for swimming and snorkeling (a couple of pictures are below along with a video of flamingos out for a walk). The weather was ~85 ºF all week, compared to mid-50s in Raleigh, so it was good to be in the Caribbean for a few days. Overall, the environment was terrific, and the seminars were outstanding.

IMG_2366

Playa Del Carmen – Xcaret

Macaws

Macaw at Xcaret Hotel

 

 

 

 

 

Continue Reading >>

The traveling biochemist: Science in the far east

Clay Clark

Clay Clark – @biochemprof I'm on ScienceSeeker-Microscope

When I’m lucky enough to be invited to a conference outside the United States, I jump at the chance to visit faculty and students at other institutes. Recently, I was invited by the Biochemical Journal to attend the yearly editorial meeting in Beijing, China. I’ve been a member of the editorial board for several years, and the editors usually meet in London each spring to discuss issues pertaining to the journal. Two years ago BJ opened an office in Beijing in anticipation of the tremendous growth in scientific research occurring in Asian countries. In order to highlight research of the editorial board members, BJ held a one-day research symposium (Cellular Processes: the Life and Death Decisions of a Cell) at Tsinghua University prior to the board meeting. The talks focused on new imaging techniques, nanotubes and intercellular communications, membrane dynamics and tumor suppression, and molecular switches between apoptosis, autophagy, and programmed necrosis.

I traveled to Beijing several days before the meeting in order to visit tourist sites around Beijing as well as to visit Dr. Yigong Shi and his students at Tsinghua University. I’ve crossed paths with Yigong on several occasions since we are both interested in cell death mechanisms and we both served on NIH study section, so he invited me to give a seminar on my research. The room was packed with faculty and students who were quite engaging. Yigong then treated me to a lunch of Peking Duck and other delicious dishes before he returned to his duties as a delegate to the National People’s Congress, which was in session at the time.

Continue Reading >>

The traveling biochemist: Biochemistry in Dar es Salaam

Trino Ascencio-Ibanez

Trino Ascencio-Ibanez

Part 1: The multinational project

It sounds exotic, and it certainly is. Dar es Salaam is the biggest city in Tanzania, but is not the capital (Dodoma). It is a port with 2.5 million people in 2002 (last official census) and is also the richest city in the country. This is my second visit since I spent two weeks here in May 2012 training people in the use of the low pressure DNA acceleration device, qPCR for gene expression, cloning and Agrobacterium transformation. This time the purpose of my visit was quite different. In our research, Dr. Linda Hanley-Bowdoin and I have been collaborating with Dr. Joseph Ndunguru, director of the Mikocheni Agricultural Research Institute (MARI) in Dar es Salaam. He just received a Phase II grant from the Bill and Melinda Gates Foundation (BMGF) for 9.4 million US$. It is an international, multinational effort including sub-grantees from Tanzania, Kenya, Uganda, Rwanda, Malawi, Mozambique, Zambia, Rutgers University and North Carolina State University (Go Pack !!).

Continue Reading >>

Visiting Poznan as a Fulbright Senior Specialist Fellow

Hanna Gracz

Hanna GraczI'm on ScienceSeeker-Microscope

The Institute of Bioorganic Chemistry Polish Academy of Sciences (IBCH PAS) was established almost 25 years ago, but its origins date back to 1969 when the Department of Stereochemistry of Natural Products was brought into being at the Institute of Organic Chemistry PAS. In 1980, the Department of Stereochemistry of Natural Products was transformed into an independent entity – Department of Bioorganic Chemistry PAS. In 1988, the latter was finally converted into the Institute of Bioorganic Chemistry Polish Academy of Sciences. Today, together with the affiliated Poznan Supercomputing and Networking Center, the IBCH PAS has more than 460 staff members, including 80 research scientists (33 Professors). In addition, about 80 Ph.D. students are currently involved in the research projects conducted at IBCH PAS.

gracz1gracz2The scientific portfolio of the Institute has many dimensions: synthesis and structure of natural products, in particular nucleic acids and their components; biochemistry, molecular and structural biology of model biological systems, genetic engineering, genomics and bioinformatics. IBCH PAS is authorized to confer the degree of doctor and habilitated doctor in chemistry and biochemistry.

The Institute is organized into 12 research departments and 10 research groups. Within the structure of the Institute, there are also other crucial units associated: the PAS Poznan Science Center, Scientific Publishers, Guest Rooms ( I like this place), and Library. In the latest years, the Institute in collaboration with the Poznan University of Technology have created a European Center for Bioinformatics and Genomics, a unique unit in Poland.

Continue Reading >>

Free energy in the woods

Clay Clark

Clay Clark – @biochemprof I'm on ScienceSeeker-Microscope

The Gibbs Conference on Biothermodynamics recently held its 26th annual meeting in Carbondale, IL. The Gibbs conference began in 1986 with a meeting to discuss the discipline of thermodynamics in biological systems. How does one apply the rigorous techniques utilized in thermodynamic studies to biological systems? How does one move away from the “garbage can thermodynamics,” as described by Gary Ackers, to learn fundamental processes in biology?

As described by Ackers and Bolen (1)

A widespread view of thermodynamics was that:

(1) Thermodynamic approaches were archaic, and, at best, ancillary to the central problems of biochemistry, as reinforced by the commonly-heard slogan ‘thermodynamics can tell us nothing about mechanisms.’

(2) The subject was usually taught poorly or not at all in departments of chemistry and biochemistry.

(3) A long-standing tradition of equating thermodynamics with only a single technique (i.e., calorimetry) had contributed to the narrow and insular perception of the field and its potential.

(4) Thermodynamics had seldom been fused with modem developments of structural analysis and computational chemistry.

The goal was to move away from simply measuring changes in Gibbs free energy to fill in tables found in textbooks and to learn how one can use the techniques to describe cellular reactions – enzymology, protein-protein and protein-ligand interactions, nucleic acid-ligand interactions, biological membranes, to name a few. In doing so, the conference has been spectacularly successful in advancing the field of biothermodynamics.

Continue Reading >>

The traveling biochemist: Cell death in Barga, Italy

Sarah MacKenzie

Sarah MacKenzie

A few weeks ago I attended my first Gordon Conference on Cell Death in Barga, Italy with my PI, Clay Clark. The conference was located in a beautiful resort nestled in the Tuscan hills off the beaten path between Florence and Pisa. It was a spectacular venue for 170 cell death aficionados to present their most current data and discuss new topics in an informal setting. We arrived in Rome the morning that the conference began, rented a car (we were in line behind Morgan Spurlock) and traversed Italy dodging Italian drivers who have no regard for lanes or speed limits. It is actually a pretty fun experience to drive in Italia! The conference began that evening with two excellent keynote addresses presented by Martin Raff and Richard Youle.

Continue Reading >>

Study abroad during the 2012 UEFA European soccer championship

Euro 2012

A Study Abroad Program sponsored by NCSU College of Agriculture and Life Sciences

By Hanna Gracz

 

It was really exciting to be in Poland this year and direct four weeks of summer study abroad program from May 12 until June 10th, 2012. The atmosphere was very festive throughout the program, which was the beginning of the EURO Cup.

students in Poland

Study abroad in Poland

The program is designed for students interested in biotechnology, and students study at a University with modern biotechnology facilities. Students can earn eight credit hours by taking three courses: Dr Mark Fountain “Agriculture in the History of Poland and Central Europe”; Dr. Paul Mozdziak “Animal  Cell Culture Techniques” and  My course “Biotechnology and Society.” The courses are open to students from NC State, Life Science University and Adam Mickiewicz University in Poznan, giving them a chance to interact and learn from each other. It builds scientific and cultural bridges.

Continue Reading >>

The traveling biochemist: A trip to Mumbai, India, Vol. 10

Traveling to the joint Indo-US X-ray crystallography conference in Mumbai

Clay Clark

Clay Clark – @biochemprof

I traveled to Mumbai, India, for the first time to attend the joint Indo-US X-ray crystallography conference. This is the tenth and final blog in a series about the trip.

_______________________________________________

In this installment: Final thoughts about Mumbai

Here are some odds-n-ends topics that I jotted down during the week:

People living in poverty seem similar to me regardless of where I travel. In India, the poor areas reminded me of the rural areas of Mexico, where small run-down houses or tents were built beside piles of rubble. In India, the kids seem to know who has money based on their clothing. At one point in the trip (the Ellora caves) a teenager looked at me and I could see him sizing me up and down looking at my clothes. Even though my shirt and pants were not expensive, they were clean and not threadbare, like many of the clothes in India. I also wonder for whom these kids are hawking. At several stop lights in the city, people will walk by the cars selling toys or begging for money while showing a small, sad-looking baby. But then when the light turns green their face and demeanor changes, like they can turn off the act until the next red light. Maybe I’m cynical, but it looked to me liked they were trained.

Continue Reading >>

The traveling biochemist: A trip to Mumbai, India, Vol. 9

Traveling to the joint Indo-US X-ray crystallography conference in Mumbai

Clay Clark

Clay Clark – @biochemprof

I traveled to Mumbai, India, for the first time to attend the joint Indo-US X-ray crystallography conference. This is the ninth blog in a series about the trip.

_______________________________________________

In this installment: Research at ACTREC; Lunch with Kakoli and her students, the trip home

Showering was a bit cold this morning. There is a small hot water heater on the wall, and I think that I had the plug turned on because the water was tepid and not freezing. I showered with just the hot water faucet turned on, and I’ll describe the experience as “refreshing.” My suitcase is with Kakoli. I had hoped that she or her students would have put it in my room before I arrived, but they didn’t. You have to imagine now what I’m thinking for the trip home. I took enough clothing to Aurangabad for the two-day trip, but I planned on having my suitcase to wear clean clothes today. So now after showering I’m wearing clothes for a second day after my admittedly novice attempt as using a bidet after a long day of hiking in the sun, and my clothes still have a faint odor of mothballs. My white socks are stained brown on the bottom because we had to remove our shoes when walking through several of the caves (which are considered temples here). Overall I think it is quite funny, but whoever sits next to me on the sixteen-hour flight later tonight may be very annoyed by the time we reach the US. It’s funny how one quickly loses a sense of decorum when having to make due with what’s available.

Continue Reading >>