bluuebunny/crossref_metadata_2025 huggingface dataset:
Melting anomaly and occurrence of a liquid–liquid phase transition
Authors: Fuchizaki Kazuhiro , Hamaya Nozomu
Published: November 2015

A liquid–liquid phase transition is discussed in view of singularity in a melting line. Possible existence of a liquid–liquid phase transition has been discussed thus far in relation to existence of a maximum in a melting curve [1]. We claim that it is the existence of a breakpoint, rather than a maximum, that can potentially influence the occurrence of a liquid-to-liquid transition. Our in situ synchrotron x-ray diffraction measurements revealed that the molecular crystal tin tetraiodide has an unusual melting curve. It rapidly increases with a pressure up to about 1.5 GPa, at which it abruptly breaks. The melting curve becomes almost flat on the high-pressure side of the breakpoint (with a slight maximum at about 3 GPa). Kechin proposed the differential equation [2], which can be handled with an aid of Padé approximation, to capture the overall aspect of such a melting curve. We could show that the melting curve obtained as the solution to the differential equation became closer to the actual melting curve with the improvement of the degree of the Padé approximation. Kevin's proposal thus seems to be appropriate to handle the differential equation provided the slope of the melting line is everywhere continuous. We believe that this is not the case for the melting curve in question at the breakpoint, as inferred from the nature of breakdown of the Kraut–Kennedy and the Magalinskiii–Zubov relationships [3]. We propose that the breakdown of these relationships is rather a manifestation of such a qualitative change in the intermolecular interaction as electronic (bonding) transformation in the liquid state. The breakpoint may then be a triple point among the crystalline phase and two liquid phases, whose existence has been confirmed.
Dynamics of nanoparticles in elongated rubber investigated with heterodyne XPCS
Authors: Yamamoto Naoko , Shinohara Yuya , Kishimoto Hiroyuki , Matsumoto Norihiro , Amemiya Yoshiyuki
Published: November 2015

Addition of nanoparticles into rubber is indispensable process for production of rubbery materials, as it improves the viscoelastic and mechanical properties of rubber (reinforcement effect). However, the understanding of reinforcement effect is far from satisfactory in spite of many studies. Further microscopic-scale investigation is required for controlling and improving the properties of rubbery materials. Aiming to construct a microscopic model of filled rubber under elongation, we have investigated nanoparticle dynamics in uniaxially stretched rubber using heterodyne X-ray photon correlation spectroscopy (heterodyne XPCS)[1] at BL03XU, SPring-8, Japan. In heterodyne XPCS, information on the fluctuating and dissipative dynamics of nanoparticles and that on their advective motion are separately extracted from the time correlation of X-ray scattering intensity. The results of heterodyne XPCS experiments showed that the direction of nanoparticles' advective motion corresponds to the macroscopic deformation of the sample in stress relaxation process. Furthermore, we found that chemical bond between nanoparticle and rubber polymer influences the dynamics of nanoparticles. In this presentation, we will show detailed analysis of the heterodyne XPCS results and discuss a microscopic description of filled rubber under elongation. This study was conducted under the approval of the SPring-8 Proposal Advisory Committee (2013A7210, 2013B7259).
SUNBIM a package for X-ray imaging of materials with SWAXS & GISWAXS techniques
Authors: Siliqi Dritan , De Caro Liberato , Ladisa Massimo , Mazzone Annamaria , Altamura Davide , Sibillano Teresa , Jiang Licai , Pennartz Paul , Giannini Cinzia
Published: November 2015

SUNBIM (Supramolecular & SUbmolecular Nano & Bio Materials X-ray IMaging Project) is a suite of integrated programs developed, in collaboration with Rigaku Innovative Technologies, to treat Small and Wide Angle X-ray Scattering data, collected either in transmission geometry (SAXS/WAXS) or in reflection geometry (GISAXS/GIWAXS). In addition, a specific routine to collect and analyze data in SAXS scanning transmission microscopy has been developed as additional tool to investigate tissues or material science samples through a focused X-ray beam which is used to raster scan a specimen while acquiring SAXS scattering patterns with a 2D detector. Indeed, a first-generation-synchrotron-class FrE+ SuperBright Rigaku microsource, coupled to a three pinhole S-MAX3000 camera, was recently installed at the X-ray MicroImaging Laboratory (XMI-L@b) and used with success in SAXS/WAXS/GISAXS/GIWAXS experiments (De Caro et al, 2012; 2013)and for SAXS scanning microscopy (Altamura et al, 2012; Giannini et al, 2013). The SUNBIM package was developed and interfaced to the XMI-L@b to perform: i) q-scale calibration and 2D->1D folding on SAXS/GISAXS/WAXS data, including also possible eccentricity corrections studied in the case of WAXS/GIWAXS data (Cervellino et al., 2006; 2008); ii) background evaluation and subtraction, denoising and primary beam angular divergence deconvolution on SAXS/GISAXS profiles (De Caro et al, 2012; 2013); iii) indexing of 2D GISAXS frames (Tate et al., 2006) and extraction of 1D GISAXS profiles along specific cuts; iv) scanning SAXS microscopy: collection of SAXS data in a mesh across mm2 area, composite of the as-collected 2D SAXS frames into a single image, analysis of the composed data to derive the transmitted intensity microscopy as well as the distribution and orientation of nano-scale structures over the analyzed area (Bunk et al., 2009).
Particle sizing and counting with accurate SAXS measurements
Authors: Rodrigues Sergio , Desvergne-Bleneau Sandra , Bossan Frédéric , Fernandez-Martinez Manuel , Lantz Blandine , Mahé Ronan , Panine Pierre , Hoghoj Peter
Published: November 2015

Small Angle X-Ray Scattering (SAXS)[1] is a technique well suited for investigating the structure of materials in the range from 1 to beyond 100 nm. The technique gives information on sample structure parameters such as shape or size, size distribution, orientation and anisotropy, surface to volume ratio. X-ray radiation enables to penetrate sample and typically probes a sample volume from 0.1-1 mm3. The information on structure is therefore obtained from inside the sample and is statistically representative of the sample volume probed. Furthermore, little sample preparation is needed and the technique is non-destructive. Developments in instrumentation (sources and detection) enable to observe fast changes in the sample as a function of parameters such as (but not limited to) temperature. The capability of laboratory based solutions for characterization at the nano-scale is recognized in the ISO standard currently being drafted [2] on measurement of particle size. We will show different examples of particle sizing and size-distribution measurements with SAXS, including particle/matrix with low electronic contrast and poly-dispersity studies. Comparisons will be done with alternative methods such as light scattering techniques. Stable and accurate measurement of incident and scattering intensity offers capability for particle sizing, further it allows for counting or surface to volume ratio determination providing valuable information in industrial applications such as nanoparticle sizes quantification in complex matrix (automotive) or nano porous material structure characterization for catalysts as few examples.
Instrumentation of SAXS for the Analysis of Heterogeneous Structure in Polymer
Authors: Masunaga Hiroyasu , Ogawa Hiroki , Fujiwara Akihiko , Takata Masaki , Takahara Atsushi , Takeda Toshiro
Published: November 2015

Polymer materials have hierarchal structure in the very wide range of scale. It is well known that the property is dependent on the hierarchical structure. In order to improve the performance of the materials, clarifying the hierarchical structure in a wide range and the feed back to the manufacturing process are important. However, it is difficult to clarify the hierarchical heterogeneous structure of polymer materials using only single method. Therefore the combination of microbeam small- and wide- angle X-ray scattering (SAXS/WAXS) is useful for evaluation of the hierarchical heterogeneous structural of polymer materials. The BL03XU, in alias, FSBL, in SPring-8 was constructed by consortium of industrial and academic groups and has been used from 20101),2). Structure characterization of advanced materials in the industrial field has been carried out using microbeam SAXS/WAXS method. In addition to the description of the SAXS/WAXS measurement system at BL03XU, we will report on the local structural evaluation of carbon fiber (CF). A hierarchal heterogeneous structure of CFs was visualized in the space resolution of 1 μm using a microbeam and an X-ray imaging technique. The image contrasts were identified by the difference in peak positions corresponding to the void size, the peak width corresponding to the crystallite size, and intensities corresponding to the amount of crystallites and voids. The X-ray scattering images of high-modulus CF are shown in a figure. Nanometer-size voids estimated by SAXS are abundant in the center of a fiber, on the other hand, the crystallite is abundant in the vicinity of a surface was revealed. It is suggested that the voids were generated near the center of the fiber to relax the strain during the crystallization process from the surface during the graphitization of fibers. We succeeded in visualizing the distribution of voids and crystallite of a few nanometers, which cannot be observed by an X-ray transmission imaging method.
Nutrient and Wind Effects on Dragline Properties: Perspectives from WAXS & SAXS
Authors: Sheu Hwo-Shuenn , Chang Chung-Kai , Chuang Yu-Chun , Chuang Wei-Tsung , Chen Chun-Yu , Blamires Sean , Liao Chen-Pan , Tso I-Min
Published: November 2015

Spider dragline silk is one of the strongest nature fibers and some of their features are even better than those of the best synthetic fibers. Understanding the mechanisms inducing silk variability may have implications for biomimetics and the synthesis of environmentally responsive materials. Dragline silk contains both elasticity (amorphous) and crystalline regions. Our previous studies had demonstrated that spiders might vary the protein composition and thus physical properties of silks when experiencing food with different nutrient level. In this study we fed Nephila pilipes with high, low and no protein foods and collected their dragline silks for synchrotron Radiation (SR) wide-angle X-ray scattering (WAXS) and small-angle X-ray scattering (SAXS) examinations. The WAXS data showed a significant difference in crystalline fractions of dragline silks produced by N. pilipes experiencing different food treatments. In addition, the orientation of crystallines also varied considerably among silks produced by spiders in three treatment groups. The SAXS data, obtained with the beam incident along and perpendicular to the fiber axis revealed a mesostructure comprising nano crystallites (beta sheets) stack spirally along the spider fibril axis. Such results indicate that spiders experiencing different nutrient stress level might produce dragline silks of different physical properties due to variations in crystalline density, orientation and the meso-phase structures in nano scale. Furthermore, varying environmental wind strength leads to changes in tensile mechanics of spider dragline silk hence produced. Exposing the spider Cyclosa mulmeinensis to controlled stress from constant airflow, we found correlated changes in (i) amino acid composition, (ii) tensile mechanics and (iii) crystallinity, of the dragline silk; which results suggest that protein variation and/or post secretion crystalline variations are associated with the mechanical properties of the spider silks.
IYCr2014: Special Events Organized in Brazil - ABCr
Authors: Torriani Iris , Speziali Nivaldo , Sabino José
Published: November 2015

IYCr2014 activities of the Brazilian Crystallographic Association started last year, with its members actively participating in the First Latin American Congress of Crystallography (Oct.29-Nov.2, 2013) in Córdoba, Argentina. This meeting was a milestone to integrate the Latin American Crystallographic community, originating the Founding Act of the Latin American Crystallographic Association. After this event, groups from different parts of Brazil started planning activities for the celebration of IYCr2014. Some of the main events are: The EMBL sponsored the Structural and Biophysical Methods for Macromolecules in Solution course (Jan.19-26), that took place at the Univ. of Sao Paulo, within the Global Exchange Lecture Course Program. At IFSC-USP, a Macromolecular Crystallography School "from data processing to structure refinement and beyond" will be held on April 8-16, organized by CCCP4 and local researchers. At the annual meeting of the Braz. Chem. Soc. the symposium Past, Present and Future of Protein Crystallography in Brazil (26-29 May) is being organized. A Latin American Summit Meeting on Biological Crystallography and Complementary Methods will take place at the Brazilian Synchrotron Laboratory (22-24 Sept), with the presence of Nobel Prize laureate Ada Yonath. In the state of Minas Gerais, a Symposium on Evolution of Crystallography and a two month exhibition entitled Symmetry and diffraction: from the art to crystal structure in our daily lives will take place in October. Other exhibitions are also being planned with panels from the "100 Years of Crystallography" Grenoble team. An International Symposium on Crystallography will take place in Fortaleza/CE (UFC, 12-15 Oct.). Workshops and Lecture Courses on Appl. Crystallography (UFES, Vitoria- 23-25 May) and Rietveld methods (USP-SP, 1-5 Sep.) are also being announced. Two Open Lab activities are being planned with commercial sponsorship: Bruker-Axs (in Goiás–Oct.), Rigaku and Panalytical (SP, Aug. 20-21).
Bordeaux celebrates the International Year of Crystallography
Authors: Rosa Patrick , Dautant Alain , Guionneau Philippe
Published: November 2015

The Association Bordelaise de Cristallographie (ABC) is a local crystallographic society founded in the tradition of the Laboratoire de Cristallographie of Bordeaux which organized the IUCr 15th Congress in 1990. Since 2006, researchers from laboratories all over the campus of the Bordeaux area collaborate and meet annually to exchange on their results and studies using single crystal and powder X-ray diffraction, SAXS/WAXS, etc... covering all disciplinary fields including Chemistry, Biology, Physics, Pharmacy, Archeometry and Geology. In collaboration with CNRS, Université de Bordeaux, the Association Française de Cristallographie (AFC), and CEA, the Muséum d'Histoire Naturelle of Bordeaux and the ABC organizes a series of events to celebrate the UNESCO International Year on Crystallography. This poster will present the events taking place in the Bordeaux region along 2014.
Now I know Dorothy!
Authors: Rajesh Mudivedu Shroff , Padmaja Nandikotkur
Published: November 2015

"Our message is – dare I say – crystal clear," observed UNESCO Director-General Irina Bokova in her opening remarks at UNESCO headquarters in Paris on 20 January 2014. At exactly the same time some 6480.2 miles away in a school at Hyderabad, India echoed a message "Now I know Dorothy" this was an excited exclamation from hundreds of high school children. The occasion was an IYCr2014 outreach programme motivated and supported by the President of the International Union of Crystallography (IUCr) Professor Gautam R. Desiraju. The occasion was an IYCr2014 outreach programme that matched IYCr2014 goals and objectives. The project next moved to smaller places. To make IYCr2014 relevant specifically to young students in villages and small towns, it was thought that the student audience must be comprised from non-English medium schools. This prompted translating "Crystallography Matters!" from English to a widely spoken (60 million) South Indian language called Telugu. the next step was to prepare power point presentations in Telugu, prepare crystallography related simple multiple choice questions, quiz papers, buy chocolates to represent crystallization process in making chocolates, sugar candy (Kalkand) to show them real crystals so that students connect to the subject with ease. Then travel to schools and start with an introduction to what and why is IYCr, demonstrate uses of crystals with examples, tell them why we cannot use microscope to "see" the inside of crystals, lecture, demo interactive sessions and so on .The presentation involved introducing science behind crystallography, explaining how to grow crystals, relevance to everyday life with references to NaCl and other medical uses. Sessions end with taking questions, ask mass questions like who is Dorothy, poster readings, who is Bragg, valuations of quiz papers and distribution of prizes, chocolates and sugar candy. Finally Crystallography Matters! books are given to the students and copies to school libraries.
Auguste Bravais: a major human contribution
Authors: Luneau Dominique , Jeanneau Erwann , Jal Jean-François , San Miguel Alfonso , Gueguen-Chaignon Virginie , Haser Richard , Perillat Jean-Philippe , Bonneviot Laurent , Oehler Daniele , Guy Bernard , Pilet Guillaume , Pischedda Vittoria , Daniel Isabelle
Published: November 2015

Auguste Bravais by his fundamental work on lattice has pioneered modern crystallography. He was born in 1811 in Annonay (France) at a short distance from Lyon and Saint-Etienne. He was then educated at the College Stanislas in Paris and entered the École Polytechnique in Paris in 1829. In 1832, he joined the French Navy as an officer and took part at scientific explorations to the Algerian Coast and Northern Europe. In 1837 he defended a PhD in Astronomy at the Faculty of Sciences in Lyon where he became Professor in 1841 to teach mathematics in astronomy. Then, in 1845, he moved at Ecole Polytechnique in Paris to take the chair of Physics, which he held till 1856. He published his first studies dealing with crystal lattice in 1849 in a short paper [1] and later wrote a book where he developed his theory fully based on geometrical theorems [2]. He died prematurely in 1863 exhausted by the loss of his only son. Like many scientists of that time Auguste Bravais was universalist and has been successively astronomer, geologist, mathematician, physicist, mineralogist, and crystallographer as well as an explorer from Lapland to the top of Mont Blanc [3]. In this communication, the steering committee Lyon-Saint-Etienne will recall the contribution of Auguste Bravais to crystallography and will show some aspect of his life that may be less known in our community.
The 100 Years History of Crystallography in Japan
Authors: Fujiwara Akihiko , Sugawara Yoko , Nakagawa Atsushi , Takata Masaki
Published: November 2015

A century ago, crystallogtaphy ushered in the era of modern science & technology in Japan. The beginning of modern crystallography in Japan dates back to 1913. Torahiko Terada (Tokyo Imperial University) demonstrated X-ray diffraction[1] and Shoji Nishikawa (Tokyo Imperial University) reported on X-ray patterns of fibrous, lamellar and granular substances[2]. In 1936, Ukichiro Nakaya (Hokkaido University) successfully classified natural snow crystals and made the first artificial snow crystals. In the last half-century, developments in crystallography helped form thriving manufacturing sectors such as the semiconductor industry, the iron and steel industries, the pharmaceutical industry, the electronics industry, the textile industry, and the polymer industry, as well as a wide array of academic research.
Argentinean crystal growing competition for high school students
Authors: Baggio Ricardo , Di Salvo Florencia , Foi Ana , Klinke Sebastián , Narda Griselda , Polla Griselda , Serquis Adriana , Suárez Sebastián , Vega Daniel , Lamas Diego
Published: November 2015

To celebrate the International Year of Crystallography 2014, the Argentinian Crystallography Association ("Asociación Argentina de Cristalografía", AACr) [1] has launched the Crystal Growing Competition to be held June-October 2014 among Argentinean high school students. This activity is sponsored by the IUCr, CONICET (Argentinean Science Council) and MinCyT (Argentinean Ministry of Science, Innovation and Technology). Based on IUCr suggestion [2] and successful previous experiences in other countries [3], we planned the program of the activity. Before the contest, a five hours course including the basic concepts of crystal growing and crystallization experiences demonstrations will be offer for the teachers of the interested schools. They will take place at different regions of the country during April. The information of the contest together with the instructions on how to grow crystals and guidelines for the teachers will be provided on the web. After the students sign up, they will growth their crystals and create a slideshow presentation or a video to show their work to the evaluation committee before the end of August 2014. Winners will be announced on September 15th, they will be invited to show their work at the X Annual Meeting of the Argentinean Crystallographic Association, Mar del Plata, Argentine, 28-31 October 2014. A special session will be held as a satellite activity of the meeting on October 27th and the awards ceremony of the Crystal Growing Competition will be during the opening ceremony. Besides this, everyone participating of the Argentinean contest has a chance to compete in the International Crystal Growing Competition. Trough this exciting, funny and hands-on scientific experience, crystallography and other related scientific fields will be promoted along the high school community across the country being also, a way to encourage youth to continue exploring science and developing their scientific skills.
Stimulating the development of Crystallography in Africa, a southern perspective
Authors: Billing David
Published: November 2015

During the last two to three decades the author has been aware of a number of initiatives aimed at stimulating and/or assisting the development of crystallography in various parts of Africa. This includes the CCDC initiatives of the 90's that let to them making the database available to African researchers. As well as a number of attempts to get basic diffraction equipment up and running in a number of locations. During the same time period I have been directly involved in the installation and commissioning of at least seven systems at Wits University. Also during this same period I organised at least three international meetings, in which African delegates were encouraged to attend via the provision of targeted financial assistance. This I believe has provided me with a rather unique perspective on the challenges faced by initiatives to stimulate the development of crystallography in Africa. In this presentation I hope to present an overview of some of the successes to date as well as some of the unique challenges we have encountered.
Bruker proudly contributes to IYCR
Authors: Adam Martin , Hovestreydt Eric , Ruf Michael
Published: November 2015

Bruker congratulates the IUCR to the proclamation of the International Year of Crystallography (IYCR). As one of the world's leading analytical instrumentation companies, Bruker enthusiastically supports the IYCr activities to increase public awareness of the science of crystallography with a variety of activity. In addition to a direct donation to the IUCR our customers participate in the IYCR's Openlab initiative with state-of-the-art instrument in Pakistan, South Africa, United Arab Emirates and Vietnam. During the entire year Bruker supports meetings and conferences and organizes workshops and user meetings to inspire new blood as well as old hands. In countries with a small base of installed instruments Bruker contributes to the OpenLab initiative loaning a complete for the entire year 2014. Education and research at sites in Ivory Coast, South Africa, Morocco, Indonesia & Brazil benefit from this single crystal X-ray diffraction solution. The system is covered by a free-of-charge service contract and warranty. Personnel from each site receive training prior to the arrival of the instrument and get unlimited support by Bruker's service desk. Bruker is happy to contribute with knowledge, instrumentation and sponsorship to the success of the IYCr all over the planet. We are convinced that the combined efforts of the global crystallographic community demonstrate the importance of crystallography in most technological developments and increase interest in this interdisciplinary method. The talk will provide an summary on the events held, the impact achieved and provide an outlook on activities planned for the remaining IYCR.
Crystallography and the IYCr2014 in Uruguay and Latin America
Authors: Suescun Leopoldo
Published: November 2015

X-ray Crystallography has been present in Uruguay since the 50's. A project funded by UNESCO brought Prof. S. Furberg to Montevideo and introduced equipment in a laboratory of Universidad de la República, Facultad de Ingeniería where Prof. Stephenson Caticha Ellis worked.[1] During the period 1968-1995 the political and economic situation of the country reduced research in general and crystallography in particular, re-emerging in the late 90's with the acquisition of an automatic single-crystal diffractometer by Facultad de Química. After the opening of the Brazilian Synchrotron Light Laboratory in 1997 several projects in crystallography have also developed with the successful realization of half a dozen postgraduate projects. Currently there are chemical, biological and physical crystallography labs in the country, with a reduced but sufficient pool of research equipment. The main institutions where Crystallography is developed are Universidad de la República (3 groups) and the Institut Pasteur de Montevideo. There has been an explosive growth of crystallography in the country in recent years. From the 4-people group found at F. de Química in 2000 to over 50 people of the Red Uruguaya de Cristalografía recently founded.[2] This development wouldn't have happened without the strong influence of Latin American crystallographers, mainly but not only from Argentina and Brazil, and also collaboration from extra-regional colleagues from USA, the UK, France and Switzerland. Very recently additional impulse has come from Latin America with the formation of the Latin American Cryst. Assoc. LACA[3]. Uruguayan crystallographers are currently involved in dissemination and academic projects for IYCr2014 such as an open-sky photo-gallery in Montevideo, a national crystal growth competition, a protein crystallography school and two UNESCO/IUCr OpenLab Type 1 sponsored by Bruker. A description of on-going projects in Uruguay and the region will be outlined in the presentation
The International Year of Crystallography
Authors: Lecomte Claude , Desiraju Gautam
Published: November 2015

IYCr2014 aims at improving public awareness of the field, boost access to instrumentation and high-level research, nurture "home-grown" crystallographers in developing nations, and increase international collaborations for the benefit of future generations. The IUCr-UNESCO OpenLab is a network of operational crystallographic laboratories based mainly in Africa, Asia and South America, and implemented in partnership with industry. The OpenLabs will enable students in far-flung lands to have hands-on training in modern techniques and expose them to cutting-edge research in the field. Such project was started based on the strong experience gained through the IUCr Initiative in Africa . The Summit meetings are intended to bring together scientists from countries in three widely separated parts of the world. Karachi (Pakistan), Campinas (Brazil) and Bloemfontein (South Africa). These meetings, attended by scientists from academia and industry and by science administrators, will focus on high-level science, and also highlight the difficulties and problems of conducting competitive scientific research in different parts of the developing world. Moreover, a worldwide crystal-growing competition aims at attracting and inspiring youngsters.
Microtubule chemical complexity: mechanism of tubulin modification enzymes
Authors: Roll-Mecak Antonina , Szyk Agnieszka , Kormendi Vasilisa
Published: November 2015

Tubulin is subject to an abundant and diverse set of post-translational modifications that include phosphorylation, acetylation, poly-glutamylation, poly-glycylation and tyrosination. The highest density and variety of post-translational modifications are found in especially complex microtubule arrays like those of neurons or cilia. Not surprisingly, tubulin modification enzymes have been linked to human diseases including cancers and neurodegenerative disorders. I will present recent data from my lab on the mechanism of action of two tubulin modification enzymes that illustrate two divergent paradigms of tubulin recognition. Tubulin tyrosine ligase (TTL) adds a C-terminal Tyr to the exposed C-terminus of alpha-tubulin as part of a tyrosination/detyrosination cycle present in most eukaryotic cells. We solved the first crystal structure of tubulin tyrosine ligase that revealed how the TTL scaffold supported the expansion of the repertory of tubulin post-translational modification enzymes of the TTL like family that recognize either alpha- or beta-tubulin C-terminal tails. In addition to modifying tubulin, TTL also prevents tubulin from incorporating into microtubules by recognizing a tubulin dimer interface that would otherwise be involved in microtubule lattice interactions. I will also present recent work from my group on the structure and mechanism of action of tubulin acetyltransferase (TAT). TAT acetylates Lys-40 on alpha-tubulin in the microtubule lumen. We solved the 2.7Å structure of TAT bound to its ac-coA substrate as well as the 2.45Å structure of a catalytic inactive TAT mutant that reveals a domain swapped dimer in which the functionally essential N-terminus shows evidence of unprecedented structural plasticity. Implications for catalysis and microtubule stimulation of TAT activity will be discussed.
Structural, Functional and Dynamic Studies of F Plasmid T4SS Proteins
Authors: Audette Gerald
Published: November 2015

The transfer of genetic material within a bacterial population through the process of conjugation distributes novel genetic elements for survival in unique environments. Bacterial conjugation is important to public health as the spread antibiotic resistance genes among bacteria results in multi-drug resistance. Indeed, approximately 70% of bacteria that cause hospital-acquired infections are resistant to at least one antibiotic. Conjugative systems, such as the F plasmid of Escherichia coli, consist of proteins that share similarities to type IV secretion systems (T4SS). T4SS proteins of the F plasmid form a membrane spanning protein complex and surface exposed pilus. The periplasmic T4SS proteins TraF, TraW and TrbC play important roles during the F pilus assembly and DNA transfer. Functional analysis of a series of TraF mutants has shown that modification to TraF abolishes pilus synthesis and in turn F plasmid conjugation. In addition, dynamic analysis of TraF using time-resolved hydrogen-deuterium exchange mass spectrometry has revealed a well structured C-terminal thioredoxin-like domain and a more dynamic N-terminal domain that is predicted to interact with companion T4SS protein TraH. In addition, interaction analysis of the putative pore forming proteins TraW and TrbC indicate that the C-terminal domain of TrbC is not required for interaction with TraW, unlike previous models of F T4SS assembly. Rather the C-terminal domain of TraW preferentially interacts with the N-terminal domain of TrbC. These studies are providing a clearer picture of the structures and interactions that occur within the F T4SS assembly during the conjugative process.
A novel architecture of 600 kDa bacterial citrate lyase complex
Authors: Forouhar Farhad , Lew Scott , Seetharaman Jayaraman , Xiao Rong , Acton Thomas , Montelione Gaetano , Hunt John
Published: November 2015

Citrate lyase activity exists in eukaryotes, bacteria, and archaea and plays a central role in cellular energy metabolism. There are two types of citrate lyases, ATP-dependent and ATP-independent. The latter, which exists only in bacteria, converts citrate to acetate and oxaloacetate using a two-step reaction catalyzed by a stable heterotrimeric protein complex comprising alpha-beta-gamma subunits. We selected three bacterial genomes in which the alpha-beta-gamma subunits of citrate lyase are all encoded on the chromosome in a continuous, co-cistronic geometry. The genes encoding the entire complex were subsequently amplified together using a single PCR reaction on genomic DNA. This approach enabled the entire citrate lyase complex from three organisms to be purified to homogeneity using a single step of Ni-NTA chromatography followed by gel-filtration chromatography. One of the three citrate lyase complexes purified yielded crystals diffracting to 4 Å. Six-fold non-crystallographic symmetry averaging enabled a high quality structure to be determined for the 18-subunit alpha-beta-gamma citrate lyase complex. This structure provides insight into the multistep catalytic mechanism employed by this enzyme.
Functional CBS modules make IMPDHs octameric
Authors: Labesse Gilles , Alexandre Thomas , Vaupré Laurène , Salard-Arnaud Isabelle , Lai Kee Him Joséphine , Haouz Ahmed , Raynal Bertrand , Bron Patrick , Munier-Lehmann Hélène
Published: November 2015

Inosine-5'-monophosphate dehydrogenase (1, 2) (IMPDH) is a major target for antiviral, antiparasitic, antileukemic and immunosuppressive therapies. It is an ubiquitous and essential enzyme for the biosynthesis of guanosine nucleotides. Up to now, IMPDHs have been reported as tetrameric enzymes harbouring a catalytic domain and a tandem of cystathionine-ß-synthase (CBS) modules. The latter had no precise function assigned despite their nearly absolute conservation among IMPDHs and consistent indication of their importance in vivo. The aim of our study was to provide evidence for the role of the CBS modules on the quaternary structure and on the regulation of IMPDHs. A multidisciplinary approach involving enzymology, site-directed mutagenesis, analytical ultracentrifugation, X-ray crystallography, SAXS, cryo-electron microscopy and molecular modelling allowed us to demonstrate that the Pseudomonas aeruginosa IMPDH is functionally active as an octamer and allosterically regulated by MgATP via each CBS module. Revisiting deposited structural data, we found this newly discovered octameric organization conserved in other IMPDH structures. Meanwhile, we demonstrated that the human IMPDH1 formed two distinct octamers that can pile up into isolated fibres in the presence of MgATP while its pathogenic mutant D226N, localised into the CBS domains, appeared to form massively aggregating fibres. The dramatic impact of this mutation could explain the severe retinopathy adRP10. Our data (3) revealed for the first time that IMPDH has an octameric architecture modulated by MgATP binding to the CBS modules, inducing large structural rearrangements. Thus, the regulatory CBS modules in IMPDHs are functional and they can either modulate catalysis or/and macromolecular assembly. Targeting the conserved effector binding pockets identified within the CBS modules might be promising to develop antibacterial compounds or drugs to counter retinopathy onset.
Substrate recruitment and inhibition of the PAR polarity complex
Authors: McDonald Neil
Published: November 2015

The aPKC [atypical PKC (protein kinase C)] isoforms ι and ζ play crucial roles in the formation and maintenance of cell polarity and represent attractive anti-oncogenic drug targets in Ras-dependent tumours. Deregulation of PKCι signalling has multiple effects including aberrant cell polarity, which is a hallmark of aggressive cancers. PKCι associates with two discrete polarity complexes; one containing the polarity proteins Par3 and Par6 (the PAR complex) and the other contains Crumbs, Stardust and PatJ (the Crbs complex). Both complexes are found in vertebrates and invertebrates where they are crucial for maintaining apical-basal polarity. We are interested in how these two complexes recruit Par6-aPKC to the cell membrane and how aPKC activity is stimulated once within the PAR complex. Several substrates of the PAR complex are also able to inhibit its catalytic activity suggesting a complex regulatory mechanism. Our structural, biochemical and in vivo results from studying the PAR complex will be presented. Our data indicate a hierarchy among PAR complex substrates. In parallel, we have characterised somatic mutations found in PKCι in human cancer, indicating that perturbing a substrate-specific recruitment site selectively disrupts the polarizing activity of PKCι. Finally, a series of ATP-competitive thieno[3,2-d]pyrimidine- based PKCι inhibitors that show potent and selective inhibition of PKCι in biochemical, cellular and in vivo models will be presented.
Structure of PhnZ reveals a novel oxygenase mechanism for C-P bond cleavage
Authors: van Staalduinen Laura , McSorley Fern , Zechel David , Jia Zongchao
Published: November 2015

Inorganic phosphate is an essential component of many biological molecules and processes including cellular signaling, generation of metabolic energy, DNA and RNA, and membrane phospholipids. Organophosphonates, which contain a highly stable carbon-phosphorus bond, are widely used as herbicidal, chelation, anti-scale, and medicinal agents. PhnY and PhnZ consist of a new oxidative catabolic pathway that is employed by marine bacteria to use 2-aminoethylphosphonic acid as a source of inorganic phosphate. PhnZ is notable for catalyzing the oxidative cleavage of a carbon-phosphorus bond using Fe(II) and dioxygen (see figure), despite belonging to a large family of hydrolytic enzymes, the HD-phosphohydrolase superfamily. We have determined structures of PhnZ in complex with its substrate, (R)-2-amino-1-hydroxyethylphosphonate. The structure reveals PhnZ to have an active site containing two Fe ions bound by 4 histidines and 2 aspartates (see figure) that is strikingly similar to the carbon-carbon bond cleaving enzyme, myo-inositol-oxygenase. Site-directed mutagenesis and kinetic analysis with substrate analogues revealed the roles of key active site residues. A 5th histidine that is conserved in the PhnZ subfamily specifically interacts with the substrate 1-hydroxyl. The structure also revealed that PhnZ possesses a unique induced-fit mechanism whereby an active-site aspartate specifically recognizes the 2-amino group of the substrate and toggles the release of an aromatic residue from the active site, thereby creating space for molecular oxygen bind to the second Fe ion. Structural comparisons of PhnZ reveal an evolutionary connection between Fe(II)-dependent hydrolysis of phosphate esters and oxidative carbon-phosphorus or carbon-carbon bond cleavage, thus uniting the diverse chemistries that are found in the HD superfamily.
Delivering practical crystallography experience to undergraduate students
Authors: Mapp Lucy , Coles Simon
Published: November 2015

Teaching of laboratory-based chemistry in universities has barely evolved since its inception. Practical work is generally conducted in a highly structured, dedicated teaching laboratory environment or on a `student-as-apprentice' basis in an active research laboratory. Exposure to crystallography as an undergraduate is generally limited to theoretical lecture-based courses, with little or no practical experience, despite the fact that training in the use of expensive research-based instruments is becoming a necessity of modern science. We present a course based around the solid-state structural chemistry of a molecular polymorphic system, delivered to third year undergraduates (70 students) at the University of Southampton which contains numerous novel features: 1) Students work in pairs (maximum group size of 8). 2) It is a `hands-on' experience for every participant, involving single crystal and powder diffractometers (Rigaku XtaLab mini and MiniFlex benchtop systems) dedicated to educational activities. 3) It is a student-led activity, designed as an `advanced practical' providing a taste of the research experience. 4) Laboratory manuals are available to students via an Electronic Laboratory Notebook (ELN) system. 5) Plans, experimental enactments, observations and conclusions are recorded by students in the ELN (directly linked to the manual sections). 6) Feedback and assessment is delivered through the ELN by directly linking instructor comments to the student ELN record. The experiment comprises about 15 manual sections in the LabTrove ELN system, which has a similar design to a blog, enabling student comments and assessor feedback to be linked to these sections. This talk will outline the design of the experiment and instruments involved, the mode and logistics of delivery, and will discuss the evaluation of its impact on student learning by analysis of feedback questionnaires.
Color-Coding Point Group & Space Group Diagrams and other Mathematical Journeys
Authors: Julian Maureen
Published: November 2015

Color clarifies diagrams point group and space group diagrams. For example, consider the general position diagrams and the symbol diagrams. Symmetry operations can be represented by matrices whose determinant is either plus one or minus one. In the former case there is no change of handedness and in the latter case there is a change of handedness. The general position diagrams emphasis this information by color-coding. The symbol diagrams are a little more complicated and will be demonstrated. The second topic is a comparison of the thirty-two three-dimensional point groups with their corresponding 18 abstract mathematical groups. The corresponding trees will be explored. This discussion leads into the topic of irreducible representations.
Structure Determination in a Changing World
Authors: Puschmann Horst , Pohl Ehmke
Published: November 2015

Crystal structure analysis used to be a highly complex process requiring expensive and specialised instrumentation, high-end computing and a lot of prior knowledge. In the last ten years or so, the required instrumentation has become quite affordable (to the point of being ubiquitous), what used to be high-end computing can now be found in most people's pockets and the experience level of those performing these analyses has become highly polarised: - There are those who know little about the technique and are lured into it by the undisputed high value attached to a crystal structure and the apparent ease of use of modern hardware and software. - And then there are those old hands who dream about carrying boxes of instruction cards across campus in order to pick up the same boxes a few days later - now brimming with the results - and who know what to reach for when someone asks for the 'blue book'. Has crystallographic teaching kept up with these developments? Are we preparing our students and staff adequately? This contribution will feature a number of observations and tales gleaned from various crystallographic workshops we have held all over the globe, addressing mainly mixed groups of students and highly experienced crystallographers. In my opinion, we need to turn crystallographic educations on it's head and start with teaching how to produce proper, chemically and biologically correct structures including their valid CIFs and reserve Bragg's law for the end - and those few who got infected by the crystallography bug in the process of learning about this most fascinating discipline.
Semiconductors and Aperiodic Structures in Organocyanide-Based Materials
Authors: Zhang Xuan , Zhao Hanhua , Palatinus Lukas , Gagnon Kevin , Bacsa John , Dunbar Kim
Published: November 2015

Organocyanides such as TCNQ (tetracyanoquinodimethane) and DCNQI (dicyanoquinodiimine) are excellent electron acceptors and have been extensively studied in electrically conducting/switching and magnetic materials. Supramolecular interactions such as π-stacking and hydrogen bonding in addition to coordination bonds with metal ions play an important role in the self-assembly of these functional inorganic materials. A novel semiconductor Cd2(TCNQ)3.5(H2O)2 with non-integer valences of TCNQ was synthesized and is the first example that exhibits four bridging modes of TCNQ in one structure (Figure 1). Despite the rather large stacking distance of 3.687(1) Å between the two μ3-TCNQ species, which constitute a "broken link" in the electron conducting pathway, the semiconductor exhibits a room temperature conductivity of 5.8×10-3 S·cm-1. The hydrogen bonding interactions between the coordinated water molecules and nitrogen atoms of the mu2- and mu3-TCNQ help to stabilize these coordinatively unsaturated TCNQ species. Another application of the chemistry of organocyanides in the context of this research is the study of reactions of the meta-dicyanamidobenzene dianion (DCYD2-) which was predicted by Ruiz and coworkers to facilitate ferromagnetic interactions between certain paramagnetic metal ions. The DCYD2- anion self-assembles with Mn(II) building blocks to afford a rare example of inorganic quadruple helices with an incommensurate modulated structure (Figure 2a). A supercell in the high symmetry space group P4/nnc is obtained with a c parameter five times that of the basic structure and a further 15-fold expansion in the space group of P1 along the c axis reveals that ~2% of Mn positions are disordered. The packing of these helical chains through π-stacking of pyridyl groups leads to 1D nanochannels with an estimated empty volume of 38.6% of the super cell volume (31,587Å3). However, in the presence of water, hydrogen bonding between the water molecules and the cyano-N atoms dominates and only zig-zag chains are formed (Figure 2b).
In-situ Gas Adsorption SC-XRD Study: Understanding Gas Uptake in a Sc-based MOF
Authors: Sotelo Jorge , McKellar Scott , Moggach Stephen , Mowat John , Warren Anna , Warren Mark , Wright Paul
Published: November 2015

In recent years the development of new methods of storing, trapping or separating light gases, such as CO2, CH4 and CO has become of utmost importance from an environmental and energetic point of view. Porous materials such as zeolites and porous organic polymers have long been considered good candidates for this purpose. More recently, the ample spectrum of existing metal organic frameworks (MOFs) together with their functional and mechanical properties have attracted even further interest. The porous channels found in these materials are ideal for the uptake of guests of different shapes and sizes, and with careful design they can show high selectivity. Adsorption properties of MOFs have been thoroughly studied, however obtaining in depth structural insight into the adsorption/desorption mechanism of these materials is challenging. For example, out of the hundreds of MOF structures published to date, there are less than 20 entries currently in the CSD in which the CO2 molecule can be located. Here we present our novel findings using the high-pressure gas cell at the Diamond Light Source on beamline I19, where we have studied the inclusion of CO2, CH4 and CO on the microporous scandium framework, Sc2BDC3 (BDC = benzene-1,4-dicarboxylate) and its amino-functionalised derivative, Sc2(BDC-NH2)3. Here, the different adsorption sites for CO2, CH4 and CO in both frameworks have been determined as a function of increasing gas pressure. These structures, coupled with Density Functional Theory calculations, have helped to elucidate the host-guest interactions governing the different levels of selectivity shown by both Sc2BDC3 and Sc2(BDC-NH2)3. Additionally, gas mixtures have also been studied; in particular CO2/CH4 mixtures of different compositions, explaining the selectivity of the frameworks for CO2 over other gases and showing the great potential of in situ structural experiments for investigation of the potential applications of MOFs.