X'Press 2/2016

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X'Press 2/2016

Our periodical X'Press, the customers' voice, contains news items, reports of trips and conferences and customer stories.

'How to solve?' is the central theme of this second issue of X’Press in 2016. This is indeed an important question in a world with ever-increasing competition where it is essential to be noticed in order to be selected. And how else can you be noticed than by being better than others or excelling.

A tailor-made solution for Yara

Yara’s Siilinjärvi mine has been in continuous operation since 1979. The carbonatite deposit is mined in two large open pits and is subsequently processed on-site to extract apatite from the host rock with tailings stored in a tailings pond. Yara is continuously investing in guaranteeing that their operations are safe, reliable and profitable at the same time. When they noticed that production recovery and quality of the apatite concentrate were sometimes below their target values, they consulted PANalytical for a possible solution of these problems.

Yara’s mine in Siilinjärvi (Finland) is the only apatite mine in Western Europe and ca. 3 km long, 1 km wide and with a deepest point of 240 m.

The desired solution should cover a few aspects at the same time. The mine is not very homogeneous and therefore it is important to receive accurate feedback on the mined material. In this way inefficient mining of less useful rock can be avoided. Additionally Yara wants to precisely control their beneficiation process of apatite to achieve an increased recovery rate and enhance their product quality. This can be realized by frequent analyses of the concentrates and tailings, delivering fast results. The methods of choice are X-ray diffraction (XRD) and X-ray fluorescence (XRF), which can be automated and deliver quantitative elemental and qualitative mineralogical information in a relatively short time.

Together with Yara, PANalytical developed a unique automated installation, which is now taking care of Yara’s demands. Incoming samples from 5 control points in the production process are split into several portions for XRD, XRF, LOI (loss on ignition) and combustion analyses. Robots take care of the sample transport between various sample preparation stations (such as a mill, press and bead maker)and the analytical instruments. In this way laboratory technicians can concentrate on other tasks as well.

With this customized automation, feedback time is now approximately half of that in the past. This allows us to make informed decisions about our mining and production processes much faster, resulting in a more efficient process control. Pauli Moilanen, Chemist, Project Manager XR-automation at Yara’s Siilinjärvi site

Samples are mostly delivered in continuous batches and processed automatically 24 hours per day excluding 2-3 hours maintenance break. If necessary, however, highpriority samples can always be inserted manually and are analyzed as soon as a station has been freed. The analysis time is one hour and 15 minutes excluding LOI; with LOI the typical analysis time is one hour and 50 minutes, including the sample taking. In this completely automated solution the analyses are performed by PANalytical’s HighScore (XRD) and SuperQ (XRF) software packages; SamTracs takes care of the automated process and seamlessly communicates all results to Yara’s LIMS (laboratory information management system).

Fertilizers

are natural or synthetic materials applied to plants in order to enhance their growth. They contain precisely formulated targeted nutrition to suit each specific situation. Besides a number of micronutrients such as copper, iron or manganese they typically contain the three macronutrients nitrogen, phosphorus and potassium in varying proportions (NPK-fertilizers).

85% of the world phosphate utilization goes into the production of fertilizers. With the continuous growth of the world population the demand for nutrients and subsequently for phosphates is still increasing. The main source for phosphates is apatite, a group of phosphate minerals.

Yara

Yara is the world’s largest producer of ammonia, nitrates and fertilizers with 12,000 employees working in 51 countries worldwide. Their fertilizers, crop nutrition programs and technologies increase yields, improve product quality and reduce the environmental impact of agricultural practices.

The Siilinjärvi site in Finland employs 400 people and produces mainly fertilizers and phosphoric acid, but also other industrial chemicals. It consists of a mine, two sulfuric acid plants, one phosphoric acid plant, one nitric acid plant and one NPK-fertilizer plant. The mine is the only apatite mine in Western Europe, and it’s main product is apatite concentrate.



Together towards the optimal solution

Mark A. Pals, manager Priority Lane group at PANalytical


We try to be a real sparring partner for the customer, to get the most out of a project. Simon Milner, product marketing manager X-ray fluorescence

Download X'Press 2/2016 -at the bottom of this page- to read the full article.



Smaller crystals, faster experiments, brighter beams

Drug screening & innovation via XRPD

Knowledge of the 3D structures of proteins is a key element for understanding functions and mechanisms necessary for the conception of drugs. Drugs can be proteins, as insulin, or small molecules that interact with biological targets. To date, more than 100 proteins are approved for clinical use in the European Union and the USA. The need for a large number of experimental structural data is common in all drug-related projects and demands continuous improvement of methods for determination of protein structures.

Members of the Laboratory of Structural Biology at UPAT (left to right): Stefanos Saslis (BSc), Magda Christopoulou (MSc), Souzana Logotheti (BSc), Stavroula Fili (MSc), Fotini Karavassili (PhD), Irene Margiolaki (group leader), Eleftheria Rosmaraki (lecturer, Department of Biology, UPAT), Alexandros Valmas (PhD), Maria Spiliopoulou (BSc), Paraskevi Kontou (BSc), Nikos Nikolopoulos (BSc), Katerina Pappa (BSc)

Until now, the majority of protein structures are determined by X-ray diffraction on single crystals with typical sizes > 5-10 μm at micro-focus synchrotron beam lines. Despite significant progress there are still limitations of the research on single crystals. Difficulties in protein crystallization are the major bottleneck for single crystal diffraction. Polymorph screening – critical for drug innovation – is not possible and last but not least single crystal diffraction is not ideal for time-resolved studies (dynamics).

Already in 1999 the power of X-ray powder diffraction (XRPD) for revealing protein structures was demonstrated for hen egg white lysozyme by Bob Von Dreele. Since 2003, Irene Margiolaki and her colleagues at the ESRF and later at UPAT, have proved that protein structures can also be obtained from sub-micron crystals with typical sizes > 0.1 μm via X-ray powder diffraction using synchrotron and laboratory sourcesi,ii. This approach provides medium-resolution structural models (3-10 Å) and allows for the study of low-quality crystals; polymorph screening is a routine practice and time-resolved studies are also possibleiii,iv.

In addition, powder data reveal characteristics of the microcrystalline samples such as purity, sample homogeneity, highly accurate cell dimensions and lattice strains induced by sample preparation; critical parameters for the development of therapeutic formulations.

Our X’Pert PRO equipped with the fast PIXcel detector delivers
extremely useful powder diffraction data from proteins which are employed not only for indexing but also structure refinements.
Dr. Irene Margiolaki, head of the Structural Biology Laboratory, University of Patras (UPAT)

In 2013, the UPAT team installed a PANalytical X’Pert PRO diffractometer, which is routinely employed for structural studies of proteins. Data collection in the lab prior to synchrotron measurements is a major advance. The X’Pert PRO also allows for high throughput crystal screening and optimization, polymorph identification and delivers high statistics due to the much slower radiation damage of the biological samples in the lab.

Currently, researchers at the structural biology lab at UPAT study human insulin (HI) complexes with phenolbased ligands at different crystallization conditions. They could for example show that phenol-based molecules bind on HI and affect both HI conformation and the crystal forms adopted; they revealed very high polymorphism upon variation of crystallization pH and type of ligand and disclosed 4 novel polymorphs with enhanced characteristics as potential drug targetsv,vi,vii.

In collaboration with the R&D scientists at PANalytical, preliminary variable temperature and relative humidity studies indicated rapid phase transitions and previously unidentified polymorphs associated with distinct biological activity. Finally, combined data collected using laboratory and synchrotron instruments, allowed for the detailed structural characterization of several HI-ligand polymorphs determining not only the protein structure but also the ligand binding sites necessary for rational drug designviii.

These studies manifest that powder diffraction is moving ‘beyond demonstration experiments’ and is ready to become a strategic technique for routine characterization of microcrystalline proteins.

References:
i Margiolaki, I. & Wright J. P. (2008). Acta Cryst., A64, 169-180         v Karavassili, F. et al. (2012). Acta Cryst., D68, 1632–1641
ii Karavassili, F. & Margiolaki, I. (2016). Protein Pept. Lett., 23, 23(3):232-41   vi Valmas, A. et al. (2015). Acta Cryst., D71, 819-828
iii Margiolaki, I. et al. (2005). Acta Cryst., D61, 423-432              vii Fili, S. et al. (2015). IUCrJ., 2, 534-544 (open access)
iv Beckers, D. et al. (2015). Acta Cryst., A71 (a1), s510-s510          viii ESRFnews, Cover & article p. 18; Karavassili et al, March 2015

Laboratory data of human insulin 4-nitrophenol complex crystallized at different pHs. The data reveal a first-order phase transition at pH ~ 6 from monoclinic to hexagonal phasevi.

Surface of an insulin dimer obtained from combined laboratory and synchrotron powder diffraction, illustrating how phenol-based ligand molecules (magenta) fit within deep cavities (binding sites). Grey and green show zinc and chloride anions involved in crystallization, while blue dots represent oxygen atoms belonging to water moleculesviii.

University of Patras (UPAT)

Founded in 1964 UPAT includes 22 departments, which operate 112 labs and 14 clinics for about 25,000 students. The UPAT has a reputation for quality and innovative research and a number of its departments, laboratories and clinics have been designated as Centers of Excellence on the basis of international assessment.

The Department of Biology at UPAT was established in 1967 and was the first biology department in the Greek university system. It includes the Laboratory of Structural Biology, headed by Irene Margiolaki and is well equipped with advanced instrumentation for protein expression, purification, crystallization and X-ray diffraction studies.



Determination of postmortem interval on human cortical bone

One of the more difficult aspects of forensic anthropology is to medically and legally estimate a postmortem interval (PMI) of human skeletal remains (i.e. a determination of how long an individual has been deceased). PMI estimation becomes increasingly difficult as time of death becomes more remote, and it is therefore of immediate importance to determine whether remains are forensically significant or of non-significant origin (i.e. historical, archeological). ASD’s Goetz Instrument Support Program participant John Servello of the University of North Texas (US) has investigated whether near-infrared (NIR) spectroscopy could be useful for reliable PMI estimation.

Long-term decomposition-related changes in bone ranging over decades to millennia (due to erosion, infiltration of soil matrix and water, the addition of soil fungi and bacteria, etc.) ultimately lead to the breakdown of collagen and the replacement of normal bone content with new mineral.

It is predicted that the loss of bone organic phase over the extended PMI will manifest spectrally. John Servello, of the University of North Texas, used an ASD LabSpec® 4 benchtop analyzer to determine if NIR spectroscopy could be used to assess and assign a PMI range for human skeletal remains.

The technique of NIR analysis is appealing for examining cortical bone because the shorter wavelength light can penetrate the sample to greater depths than other vibrational techniques, allowing for interaction with the sample constituents. Additionally, NIR analysis requires minimal to no sample preparation, allows for rapid data collection, and is simple to use with minimal prior training whereas the present qualitative and quantitative tests for a determination of the PMI are timeconsuming, the methods are destructive, and they require expensive, highly specialized equipment.

Collecting spectra directly from a sectioned femoral diaphysis. Diffusion of light through the cortex is clearly visible. The PMI for this sample was short (<6 months).

Using the 1350-2100 nm band for NIR analysis of femoral bone samples, John’s research showed that historic and archaeological materials formed a welldefined and separated cluster, while forensically significant samples formed a broad and overlapping cluster with some suggested gradation with respect to time.

Ultimately, the goal of this research is the development of a robust, quantitative technique that can be used to assess and assign a PMI range for human skeletal remains.

Experimental details are described in the complete article on http://discover.asdi.com/Postmortem-Interval


A jubilant year for XRD

As already mentioned in our previous edition of X’Press, 2016 is a special year for X-ray diffraction (XRD): it was 100 years ago that Peter Debye introduced powder diffraction and it was 50 years ago that Hugo Rietveld introduced his method to refine crystal structures from these powder diffraction patterns. In order to honor these achievements of two pioneering Dutch scientists, the Dutch Crystallographic Society together with the University of Delft (the Netherlands) will organize an international scientific symposium.

The symposium titled ‘2016: Debye & Rietveld – A 100 & 50 year celebration’ will take place on Thursday 22 September at the Shell Technology Centre Amsterdam. Guest of Honor at the symposium will be Hugo Rietveld. A variety of European speakers will address the history of X-ray diffraction methods, the state-of-the-art in powder diffraction and the latest developments in the field. Scientists and students can present their work during poster sessions.

The Debye-Rietveld Scientific Symposium aims to be a worthy celebration of the anniversaries of two major events that have made X-ray diffraction a standard technique for scientists around the world.