bluuebunny/crossref_metadata_2025 huggingface dataset:
Intense predation of non-colonial, ground-nesting bird eggs by corvid and mammalian predators
Authors: Ekanayake Kasun B. , Whisson Desley A. , Tan Laura X. L. , Weston Michael A.
Published: November 2015

Context Loss of eggs to predators is a major cause of reproductive failure among birds. It is especially pronounced among ground-nesting birds because their eggs are accessible to a wide range of predators. Few studies document the main causes of clutch fate of ground-nesting birds. Aims The main objective of the present study was to identify the major egg predator of red-capped plovers (Charadrius ruficapillus). We also investigated the effectiveness of the following two primary strategies available to the plovers to avoid egg predation: (1) the placement of clutches under vegetative cover and (2) avoiding predators by nesting outside the peak season of predator occurrence. Methods Remote-sensing cameras were deployed on plover nests to identify egg predators and nests were monitored over four breeding seasons to document reproductive success and fate. An experiment using false clutches with model eggs investigated the influence of nest cover on the risk of egg predation throughout the year. Line-transect surveys were conducted to estimate the abundance of egg predators in and around the wetlands. Key results The little raven (Corvus mellori) was the major egg predator identified in 78.6% of red-capped plover clutches and in 92.4% of false clutches that were camera-monitored. The hatching success of plover eggs was not influenced by nest cover (P = 0.36), but model egg survival in false clutches improved significantly with the presence of nest cover (P = 0.02). The abundance of little ravens increased during the plover breeding season and was highly negatively correlated with false clutch survival (rpearson = –0.768, P = 0.005). Conclusions Little ravens were the major predator of red-capped plover eggs and their abundance increased significantly during the plover breeding season. Any influence of nest cover on hatching success of eggs may have been masked by the extremely high rate of egg loss associated with the increased little raven abundance during the plover breeding season. Implications The high rate of egg predation is likely to have negative consequences on the local red-capped plover population, suggesting management is warranted. Little raven populations have expanded and, thus, their impact as egg predators needs to be investigated especially on threatened species.
SUMO enters the ring
Authors: Short Ben
Published: November 2015

In 1996, Matunis et al. were one of several groups to identify a novel, ubiquitin-like protein modification.
Anne Brunet: Gracefully studying how we age
Authors: Sedwick Caitlin
Published: November 2015

Brunet studies longevity, aging, and epigenetics in established and novel model systems.
Effects of Milling and Cooking Conditions of Rice on In Vitro Starch Digestibility and Blood Glucose Response
Authors: Sasaki Tomoko , Okunishi Tomoya , Sotome Itaru , Okadome Hiroshi
Published: November 2015

The objective of this study was to investigate the effects of milling and cooking conditions of cooked rice prepared from cultivar Koshihikari on in vitro starch digestibility and in vivo glucose response in humans. In addition, compression and adhesiveness tests were conducted for texture analysis of the cooked rice. Brown rice (BR) and surface‐abraded BR (SABR, ≥99.5% of the original weight) were digested more slowly than white rice (91% of the original weight) when cooked rice grain was used for the in vitro test, but they were digested more rapidly in the initial stage of the reaction when cooked rice ground by a meat grinder was used. The increase in water added for cooking significantly increased the extent of starch digestion with BR and SABR. The changes in blood glucose levels after the ingestion of cooked rice were dependent on the sample type. The cooking conditions dramatically influenced the glucose response after the ingestion of BR. A significant correlation was found between blood glucose levels at 45 min and the extent of starch digestion with ground samples, whereas no relationship was found with cooked rice grain samples for in vitro digestibility.
Satellite RNAs and Satellite Viruses
Authors: Palukaitis Peter
Published: November 2015

Satellite RNAs and satellite viruses are extraviral components that can affect either the pathogenicity, the accumulation, or both of their associated viruses while themselves being dependent on the associated viruses as helper viruses for their infection. Most of these satellite RNAs are noncoding RNAs, and in many cases, have been shown to alter the interaction of their helper viruses with their hosts. In only a few cases have the functions of these satellite RNAs in such interactions been studied in detail. In particular, work on the satellite RNAs of Cucumber mosaic virus and Turnip crinkle virus have provided novel insights into RNAs functioning as noncoding RNAs. These effects are described and potential roles for satellite RNAs in the processes involved in symptom intensification or attenuation are discussed. In most cases, models describing these roles involve some aspect of RNA silencing or its suppression, either directly or indirectly involving the particular satellite RNA.
Cryptosphaeria Dieback of Fremont Cottonwood Caused by Cryptosphaeria pullmanensis and C. multicontinentalis in California
Authors: Trouillas F. P. , Gubler W. D.
Published: November 2015

Fremont cottonwood is a large and tall tree native to riparian areas in the southwestern United States. It grows along streams, rivers, and wetlands and serves many ecological and socioeconomic functions. In recent years, we observed a severe decline of Fremont cottonwood trees in California. Trees showed branches dying back, with dark-brown internal discoloration and decay of the wood of twigs, branches, or trunks. Eventually, the cambium and the bark were killed, causing a canker. The fungus Cryptosphaeria pullmanensis was isolated consistently from the necrotic wood of branches and twigs. On rare occasion, C. multicontinentalis was also isolated from symptomatic wood. Therefore, we investigated the pathogenicity in Fremont cottonwood of C. pullmanensis and C. multicontinentalis. Koch’s postulates were completed in saplings and both species appeared highly virulent, producing internal necrosis and staining of the wood. This study is the first to report Cryptosphaeria dieback of Populus fremontii caused by C. pullmanensis and C. multicontinentalis. Symptoms and signs of this new disease are described and illustrated.
Localization of ‘Candidatus Liberibacter solanacearum’ and Evidence for Surface Appendages in the Potato Psyllid Vector
Authors: Cicero J. M. , Fisher T. W. , Brown J. K.
Published: November 2015

The potato psyllid Bactericera cockerelli is implicated as the vector of the causal agent of zebra chip of potato and vein-greening of tomato diseases. Until now, visual identification of bacteria in the genus ‘Candidatus Liberibacter’ has relied on direct imaging by light and electron microscopy without labeling, or with whole-organ fluorescence labeling only. In this study, aldehyde fixative followed by a coagulant fixative, was used to process adult psyllids for transmission electron microscopy (TEM) colloidal gold in situ hybridization experiments. Results indicated that ‘Ca. Liberibacter solanacearum’ (CLso)-specific DNA probes annealed to a bacterium that formed extensive, monocultural biofilms on gut, salivary gland, and oral region tissues, confirming that it is one morphotype of potentially others, that is rod-shaped, approximately 2.5 µm in diameter and of variable length, and has a rough, granular cytosol. In addition, CLso, prepared from shredded midguts, and negatively stained for TEM, possessed pili- and flagella-like surface appendages. Genes implicating coding capacity for both types of surface structures are encoded in the CLso genome sequence. Neither type was seen for CLso associated with biofilms within or on digestive organs, suggesting that their production is stimulated only in certain environments, putatively, in the gut during adhesion leading to multiplication, and in hemolymph to afford systemic invasion.
Metalaxyl Resistance in Phytophthora infestans: Assessing Role of RPA190 Gene and Diversity Within Clonal Lineages
Authors: Matson Michael E. H. , Small Ian M. , Fry William E. , Judelson Howard S.
Published: November 2015

Prior work has shown that the inheritance of resistance to metalaxyl, an oomycete-specific fungicide, is complex and may involve multiple genes. Recent research indicated that a single nucleotide polymorphism (SNP) in the gene encoding RPA190, the largest subunit of RNA polymerase I, confers resistance to metalaxyl (or mefenoxam) in some isolates of the potato late blight pathogen Phytophthora infestans. Using both DNA sequencing and high resolution melt assays for distinguishing RPA190 alleles, we show here that the SNP is absent from certain resistant isolates of P. infestans from North America, Europe, and Mexico. The SNP is present in some members of the US-23 and US-24 clonal lineages, but these tend to be fairly sensitive to the fungicide based on artificial media and field test data. Diversity in the level of sensitivity, RPA190 genotype, and RPA190 copy number was observed in these lineages but were uncorrelated. Controlled laboratory crosses demonstrated that RPA190 did not cosegregate with metalaxyl resistance from a Mexican and British isolate. We conclude that while metalaxyl may be used to control many contemporary strains of P. infestans, an assay based on RPA190 will not be sufficient to diagnose the sensitivity levels of isolates.
Host Transcriptional Profiling at Early and Later Stages of the Compatible Interaction BetweenPhaseolus vulgarisandMeloidogyne incognita
Authors: Santini Luciane , Munhoz Carla de Freitas , Bonfim Mauro Ferreira , Brandão Marcelo Mendes , Inomoto Mário Massayuki , Vieira Maria Lucia Carneiro
Published: November 2015

The root-knot nematode (Meloidogyne incognita) is one of most devastating pathogens that attack the common bean crop. Although there is evidence that some cultivars have race-specific resistance against M. incognita, these resistance sources have not proved effective, and nematodes are able to circumvent the host’s defense system. We constructed RNA-seq based libraries and used a high-throughput sequencing platform to analyze the plant responses to M. incognita. Assessments were performed at 4 and 10 days after inoculation corresponding to the stages of nematode penetration and giant cell development, respectively. Large-scale transcript mapping to the common bean reference genome (G19833) resulted in the identification of 27,195 unigenes. Of these, 797 host genes were found to be differentially expressed. The functional annotation results confirm the complex interplay between abiotic and biotic stress signaling pathways. High expression levels of the wounding-responsive genes were observed over the interaction. At early response, an overexpression of the N gene, a TIR-NBS-LRR resistance gene, was understood as a host attempt to overcome the pathogen attack. However, the repression of heat shock proteins resulted in a lack of reactive oxygen species accumulation and absence of a hypersensitive response. Furthermore, the host basal response was broken by the repression of the ethylene/jasmonate pathway later in the response, resulting in a continuous compatible process with consequent plant susceptibility.
An Approximate Markov Model for the Wright-Fisher Diffusion
Authors: Ferrer-Admetlla Anna , Leuenberger Christoph , Jensen Jeffrey D. , Wegmann Daniel
Published: November 2015

The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional information for disentangling these effects may be obtained by observing changes in allele frequencies over multiple time points. Such data is common in experimental evolution studies, as well as in the comparison of ancient and contemporary samples. Leveraging this information, however, has been computationally challenging, particularly when considering multi-locus data sets. To overcome these issues, we introduce a novel, discrete approximation for diffusion processes, termedmean transition time approximation, which preserves the long-term behavior of the underlying continuous diffusion process. We then derive this approximation for the particular case of inferring selection and demography from time series data under the classic Wright-Fisher model and demonstrate that our approximation is well suited to describe allele trajectories through time, even when only a few states are used. We then develop a Bayesian inference approach to jointly infer the population size and locus-specific selection coefficients with high accuracy, and further extend this model to also infer the rates of sequencing errors and mutations. We finally apply our approach to recent experimental data on the evolution of drug resistance in Influenza virus, identifying likely targets of selection and finding evidence for much larger viral population sizes than previously reported.
Structure refinement using precession electron diffraction tomography and dynamical diffraction: tests on experimental data
Authors: Palatinus Lukáš , Corrêa Cinthia Antunes , Steciuk Gwladys , Jacob Damien , Roussel Pascal , Boullay Philippe , Klementová Mariana , Gemmi Mauro , Kopeček Jaromír , Domeneghetti M. Chiara , Cámara Fernando , Petříček Václav
Published: November 2015

The recently published method for the structure refinement from three-dimensional precession electron diffraction data using dynamical diffraction theory [Palatinuset al.(2015).Acta Cryst.A71, 235–244] has been applied to a set of experimental data sets from five different samples – Ni2Si, PrVO3, kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable reference structure was available. A large series of tests revealed that the method provides structure models with an average error in atomic positions typically between 0.01 and 0.02 Å. The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approximation for the calculation of model intensities. The method also allows a reliable determination of site occupancies and determination of absolute structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.
Lipid-directed cytoskeletal protein oligomerization at sites of cell adhesion
Authors: Chinthalapudi Krishna , Rangarajan Erumbi , Patil Dipak , Izard Tina
Published: November 2015

Vertebrate cell growth, division, migration, morphogenesis, and development, rely on the dynamic interactions of cells with components the extracellular matrix (ECM) via cell surface complexes. These focal adhesions (FAs) are comprised of integrin receptors, associated signaling molecules, and talin, which is required for "inside-out" signaling that stabilizes contacts of integrin receptors with the ECM by linking FAs to the actin cytoskeleton by binding to vinculin. The highly dynamic interactions with the actin cytoskeleton are also essential for the formation of membrane protrusions (lamellopodia and filopodia). Second messengers are found at the plasma cell membrane and include signaling lipids such as phosphoinositides, which play essential roles in signal transduction pathways and in directing the oligomerization of cytoskeletal proteins that function as essential links of FAs to the actin cytoskeleton. Notably, the most abundant phosphoinositide, phosphatidyl (4,5) bisphosphate (PIP2), directly binds to key cytoskeletal proteins, where it triggers homotypic and heterotypic interactions that amplify binding to the actin network. Binding of the inositol head group and the hydrophobic acyl chain pose difficulties in generating protein/PIP2 complex crystals and here we present the only second non-membrane protein structure of such a complex. Our crystal structure and biochemical approaches define the roles of PIP2 in controlling the oligomerization of cytoskeletal proteins and their binding to adhesion receptors and to the actin cytoskeleton. Importantly, we also determined the contribution of PIP2-directed oligomerization of cytoskeletal proteins to the formation and stabilization of adhesion complexes. These studies provide important new insights into how dynamic interactions of cytoskeletal proteins with the lipid membrane, adhesion complexes, and the actin network direct the mechanical behaviors of cells.
Assembly of Sesbania mosaic virus: Role of the coat protein N-terminal R domain
Authors: Gulati Ashutosh , Savithri H.S. , Murthy M.R.N
Published: November 2015

Coat proteins of several isometric viruses consist of two domains, a disordered N-terminal R-domain consisting of several positively charged residues and a shell (S) domain characterized by a jelly roll β-barrel structure. The three-dimensional structure of Sesbania mosaic virus (SeMV), a T=3 plant virus, has been determined at 3 Å resolution. The full length coat protein, when expressed in E. coli, assembles into T=3 icosahedral shells (VLPs) resembling native virus particles. In the present investigations, the role of N-terminal R domain in the assembly of VLPs was explored by replacing the R domain with a presumably globular domain (SeMV-P10) and other intrinsically disordered (SeMV-P8, and SeMV-VPg) SeMV encoded domains. The R domain was also replaced with the non-viral globular B-domain of Staphyloccocus aureus protein A. These domains were of nearly the same size as that of the R-domain. Most of the chimeric coat proteins, when expressed in E.coli, formed VLPs, which could be purified by ultra-centrifugation. The purified VLPs were examined by transmission electron microscopy (TEM), which suggested that a fraction of the expressed proteins could assemble into T=3 VLPs, although often, the particles were heterogeneous. Interestingly, the SeMV NΔ65B CP could also be purified by Ni-NTA chromatography as a dimer which assembled into T=1 VLPs under crystallization conditions. The structure of NΔ65B-CP VLPs revealed that the assembled particles were devoid of divalent metal ions at the canonical site and there was no density corresponding to the B domain. However, the S domain could be superimposed on that of SeMV NΔ65VLPs determined earlier. The other VLPs- SeMVNΔ65P10 CP, SeMVNΔ65P8 CP and SeMVNΔ65VPg could not be crystallized because of their heterogeneity. These studies suggest a subtle interplay between the length, sequence and structure of the R-domain polypeptide and the assembly of particles.
Synthon robustness by C-F groups in halogen substituted N-benzylideneanilines
Authors: Kaur Gurpreet , Roy Choudhury Angshuman
Published: November 2015

The arrangement of the molecules in their crystal structure is controlled by the non-covalent intermolecular interactions other than the effectual space filling. The role of strong hydrogen bonds in guiding the crystal packing is well-known in the literature. But, how significant are the weak interactions in the field of crystal engineering, has yet not been fully understood. Our aim is to comprehend the nature and strength of the weak interactions involving fluorine in guiding the packing of small organic molecules in their respective crystal structure. The reason being the controversies, which are involved regarding the interactions offered by "organic fluorine"[1] and also due to the importance of these interactions in the pharmaceutical industry. Some of the research groups indicate the incapability of interactions offered by fluorine in the formation of supramolecular motifs, whereas other groups have indicated that substantial role is being played by fluorine in constructing the lattice through C-H···F, C-F···F and C-F···π interactions in the presence and absence of strong hydrogen bond donor and acceptor groups. To understand more about these interactions, we have chosen a model system of halogen substituted N-benzylideneanilines[2]. In this system, we have analysed the impact of fluorine mediated interactions on the crystal packing by having fluorine as a substituent on both the phenyl rings. Then the robustness of the synthons offered by organic fluorine has been anticipated in the same system, but with one of the substituent as chlorine or bromine in either of the phenyl ring. It has been observed that the replacement of the non-interacting fluorine by its heavier analogue has not altered the supramolecular motif, which was formed by the other fluorine. But the crystal packing has been found to be completely altered in the molecules where the interacting fluorine was replaced by its heavier analogue. Salient features of our computational studies, which include the calculation of the stabilization energies of the studied dimers using MP2 method and their topological analysis using AIM2000, to support the experimental observations will also be presented to highlight the sturdiness of the synthons formed by so called "organic fluorine".
Complexes of Fabs with a mimetic of the HIV-1 gp41 trimeric coiled-coil.
Authors: Li Mi , Gustchina Elena , Gustchina Alla , Clore Marius , Wlodawer Alexander
Published: November 2015

A series of mini-antibodies (monovalent and bivalent Fabs) targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 has been previously constructed and reported. Crystal structures of two closely related monovalent Fabs, one (Fab 8066) broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses, and the other (Fab 8062) non-neutralizing, representing the extremes of this series, were previously solved as complexes with 5-Helix, a gp41 pre-hairpin intermediate mimetic. Binding of these Fabs to covalently stabilized chimeric trimers of N-peptides of HIV-1 gp41 (named (CCIZN36)3 or 3-H) has now been investigated using X-ray crystallography, cryo-electron microscopy, and a variety of biophysical methods. Crystal structures of the complexes between 3-H and Fab 8066 and Fab 8062 were determined at 2.8 and 3.0 Å resolution, respectively. Although the structures of the complexes with the neutralizing Fab 8066 and its non-neutralizing counterpart Fab 8062 were generally similar, small differences between them could be correlated with the biological properties of these antibodies. The conformations of the corresponding CDRs of each antibody in the complexes with 3-H and 5-Helix are very similar. The adaptation to a different target upon complex formation is predominantly achieved by changes in the structure of the trimer of N-HR helices, as well as by adjustment of the orientation of the Fab molecule relative to the N-HR in the complex, via rigid-body movement. The structural data presented here indicate that binding of three Fabs 8062 with high affinity requires more significant changes in the structure of the N-HR trimer compared to binding of Fab 8066. A comparative analysis of the structures of Fabs complexed to different gp41 intermediate mimetics allows further evaluation of biological relevance for generation of neutralizing antibodies, as well as provides novel structural insights into immunogen design.
Crystal structure of the complex of GLPO with an anti-thyroid drug PTU
Authors: Bhushan Asha , SINGH Rashmi , Singh Avinash , Sinha Mau , Kaur Punit , Sharma Sujata , Singh T.P.
Published: November 2015

Lactoperoxidase is a member of mammalian heme peroxidase superfamily that consists of lactoperoxidase (LPO), myloperoxidase (MPO), thyroid peroxidase (TPO), eosinophil peroxidase (EPO). So far crystal structures of only two mammalian peroxidases LPO and MPO have been determined. The structures of LPO have been determined from the samples obtained from bovine, buffalo, goat and sheep. Their complexes have also been determined with inhibitors and substrate analogues. However, the structures of EPO and TPO have not been obtained so far. Due to significant sequence identity between LPO and TPO, the structures of these proteins are expected to be similar. Similarly their substrates will also have similarity as well as the substrate and enzyme interactions will be similar. Therefore, a complex of LPO was prepared with propylthiouracil (PTU), a compound used as a drug in thyroid ailments. The complex was crystallized using co-crystallization. The crystals of native LPO were also soaked in the solution containing PTU. The crystals belonged to monoclinic space group with cell dimensions a = 80.2 Å, b = 82.5, c = 95.0, β = 73.7° There were four molecules of LPO in the asymmetric unit. The structure determination of the complex revealed that PTU binds to the LPO at the distal heme site. It is held at this site through several hydrogen bonds and van der Waals contacts. The mode of binding and number of interactions suggest that a similar mode of binding may occur with TPO. Based on the information of interactions and the missing potential interactions, the modifications in the structure of PTU are suggested so that the improved design of the TPO inhibitor is obtained.
Breaking the structure complexity limits for powder based structure solution
Authors: Hušák Michal
Published: November 2015

There exist theoretical predictions trying to determine how much complex crystal structure can be solved from perfect powder diffraction data [1]. The theoretical limit for perfect synchrotron data is about 300 DOF (degree of freedom) while one of the current record solves only 42 DOF problem simplified by heavy atom presence [2]. We have tried to determine a realistic DOF limit based on perfect simulated powder diffraction data. For the simulation we have chosen structures from CSD with 1 single peptide molecule in asymmetric unit cell, 2-8 amino acids, 10-39 DOF. The parameters of the simulated powder diffractogram used were close to typical perfect measurement on ID31 of ESRF - wavelength 0.5 Å, range 0.5°-15°, step 0.002°, FWHM 0.01°. The structure solution tests were done by SA (simulated annealing) in DASH 3.2 software [3]. To speed up the computation we have used parallel processing obtained by MDASH extension. Influence of Mogul CSD based torsion angles bias on the calculation effectiveness was investigated as well. The results demonstrate the required number of SA steps depends exponentially on the problems DOF. This requires for problems close to 30 DOF about 10E+10 SA steps and years of single CPU computational time. The Mogul based bias can significantly help for compounds like peptides - e.g. for simulation based on compound CSD code AHAREH (4 peptides, DOF 24) the Mogul based calculation gives 50 times more often correct result than non-restricted SA run. We believe the 40 DOF structures can be solved routinely on 16-32 CPU clusters from perfect data not influenced by preferred orientation when the Mogul CSD torsion angles bias will be used. Without developing a more efficient algorithm than SA solution we do not see a way how to get really close to the 300 DOF theoretical limit. Acknowledgement: This work was supported by the Grant Agency of Czech Republic, Grant No. 106/14/03636S. Fig. caption: Dependence of required simulated annealing steps required to get one solution on DOF and the use of Mogul based bias.
Single Crystal X-ray Analysis of Trace Compounds Using Porous Network Crystals
Authors: Inokuma Yasuhide , Fujita Makoto
Published: November 2015

Crystallization of compounds has been one of the major drawbacks of single crystal X-ray analysis. The situation becomes more difficult when we deal with volatile, oily, and trace amount of samples. We have developed a new method to prepare a single crystal sample for X-ray measurement from non-crystalline compounds on nanogram-to-microgram scale using porous coordination network crystals. Here porous crystals are used as crystalline sponges that can accommodate and three-dimensionally align the compounds in a single-crystal to single-crystal fashion. In this method, a crystalline sponge is soaked in a solution containing ~5 µg of target samples. Upon slow evaporation of solvent, target compounds are accommodated and concentrated in crystal so that they are oriented along the pores with high occupancies. Thus, the structures of target compounds are analysed along with the coordination framework without crystallization of the samples. Moreover, since single crystal samples can be prepared using one tiny crystal, molecular structure of 50 ng of non-crystalline compound has been successfully determined by this method. In this presentation, we will show a variety of structures determined by using this new method, so-called crystalline sponge method.
Structural Studies on Human Calpain-3 Protease Core
Authors: Ye Qilu , Campbell Robert , Davies Peter
Published: November 2015

Skeletal muscle-specific protein calpain-3 (CAPN3/p94) is a member of the calcium-dependent cysteine protease family. CAPN3 is indispensable for the maintenance and survival of functional skeletal muscles, and defects in the CAPN3 gene that cause loss of enzyme activity lead to the development of limb-girdle muscular dystrophy type 2A. The CAPN3 protease core (domains PC1 and 2) is particularly rich in these inactivating mutations. The whole enzyme, a homodimer of CAPN3, undergoes very rapid autoproteolysis. It has two insertion sequences, IS1 and IS2 not found in other calpains, and a long N-terminal region, NS. IS1 is present in the protease core. Previous biochemistry studies from our lab have shown that IS1 contributes to the instability of CAPN3 by acting as a readily cleavable internal pro-peptide that occupies the active site of the protease core. Here we report the 2.3Å resolution crystal structure of CAPN3 (ΔNS, C129S) protease core with Ca2+ ions present. Although the architecture of this protease core is similar to those of the CAPN1 and CAPN2, with two Ca2+ bound, the crystal structure of the CAPN3 core exhibits several novel features. The N-terminal anchor is more flexible than that of CAPN1 and CAPN2 even with the N-terminal 45 residues removed. Residues in the mutation-rich region of PC1 (207 to 234) form van der Waals and H-bond interactions with residues of both IS1 and helix10. The active site is blocked by part of IS1 that forms H-bonds through the OH groups of Tyr274 and Tyr322 to Trp360 from the active site, as well as a hydrophobic interaction between Tyr274 of IS1 to His334 of the catalytic triad. This aromatic stacking will hinder substrates and inhibitors from entering the active site. The crystal structure further confirms that IS1 is a critical region governing CAPN3 activation and the binding of substrates and inhibitors. Supported by funds from CIHR and the CRC program.
In situ observation of reduction reaction of calcium ferrites by XRD and XAFS
Authors: Murao Reiko , Kimura Masao
Published: November 2015

The lime-fluxed iron ore sinter is the major iron source in the steelmaking process. Its macroscopic properties, (e.g. strength, reduction-ability and reduction-disintegration) should strongly depend on characteristics, quantity and morphology of the bonding phase. It contains several calcium ferrite phases (CFs) including solid solutions of gang materials. Most of previous studies focused on the relation of micro-texture with properties of the sinter. However, properties of individual CFs, especially, of multi-component CFs have not been clarified yet. In this study, reduction process and rates of various CFs have been investigated by in situ observation using both X-Ray Absorption Fine Structure (XAFS) and X-Ray Diffraction (XRD) methods to clarify influence of CF species on the properties of the sinter. High temperature XAFS measurements were carried out using a synchrotron radiation source at the 9A beam line in Photon Factory (KEK-PF), Japan. Powdered single phase CFs, such as CaFe2O4, Ca2(Fe,Ca)6(Fe,Al,Si)6O20 (SFCA) were diluted with BN. Fe K and Ca K-edge XAFS spectra at 9000C and 7500C in He-H2 gas atmosphere were collected repeatedly by the quick-XAFS method. Absorption variations in normalized XANES spectra were used to calculate the reduction rate constants[1]. XRD patterns of various CFs at 9000C and 7500C were corrected repeatedly at 40-second intervals in N2-H2 gas atmosphere during reduction reaction progressed. Reduction rate of CaFe2O4, determined by XANES analysis was slower than that of Fe2O3. The reduction of Fe in CaFe2O4 was a single first-order reaction, although an induction period was clearly observed at the beginning of the reduction process. In situ XRD observations showed that CaFe2O4 was reduced into Fe and CaO via Fe2+ containing CFs such as CaFe3O5 and CaFe5O7 at 9000C. These may correspond to the induction period observed in the absorption variation. Analysis results for SFCA will be discussed in the presentation.
Investigating anharmonicity and disorder in cadmium and zinc telluride
Authors: Sist Mattia , Bindzus Niels , Eikeland Espen , Iversen Bo
Published: November 2015

CdTe and ZnTe are often referred to as II-VI semiconductors. Due to the structural and photoelectric properties and low-cost manufacturability, CdTe and ZnTe based thin films are used in the photovoltaic technology and in variety of electronic devices such as infrared, X-ray and gamma ray detectors (Eisen at al., 1998). The structure of another telluride, PbTe, has recently been reviewed and the emerging atomic disorder with temperature seems to have an indissoluble liaison with the high thermoelectric figure of merit of such promising material (Bozin et al., 2010). Deviations of the cation from its position in the ideal rock-salt structure have been probed by means of Maximum Entropy Method (MEM) calculations on Synchrotron powder X-ray diffraction data (SPXRD) (Kastbjerg et al., 2013). Motivated by the peculiar structural features in lead telluride, we investigate anharmonicity and disorder of the cations in both the zincblende structures, CdTe and ZnTe. High resolution SPXRD data at 100 K have been collected for both compounds. High energy radiation and minute capillaries have been used with the aim to minimize systematic errors on the data such as absorption and anomalous scattering. Accurate Rietveld refinements have been carried out in order to extract the best dataset of structure factors. Maximum Entropy Method calculations have hence been computed, providing the least-biased information deduction from experimental data. The disorder, anharmonicity and chemical bonding within the crystalline CdTe and ZnTe have been deeply investigated through the MEM densities and comparisons with the cation displacement in the structure of lead telluride have been established.
Vitreous and Crystalline Phosphates : elaboration and electrical properties
Authors: Dardar Fatima ezzahraa , El jazouli Abdelaziz , Lachgar Abdessadek , Gross Micheal , Day Cynthia
Published: November 2015

Interest in mixed metals titanium phosphates, both in glass and crystalline forms, for their properties as ionic conductors or non-linear optical materials, has led to large number of studies of these materials [1-3]. Our investigation of Na2O – Li2O – CaO – TiO2 – P2O5 system led to the discovery of NaxLiyCazTit(PO4)3 solid solutions which exist in both glassy and crystalline forms. Here the preparation of NaxLiyCazTit(PO4)3 will be described. The compounds were structurally characterized by PXRD, and their chemical and physical characterization were completed using DTA, XRD, UV-visible, Raman spectroscopy and ionic conductivity measurements. NaxLiyCazTit(PO4)3 glasses have been prepared by heating stochiometric amounts of Na2CO3, Li2CO3, CaCO3, TiO2 and NH4H2PO4 in a platinum crucible at 10500C. The microcrystalline samples were obtained by crystallization of the corresponding glasses at 6400C or by standard solid state preparation at 7000C. The values of the characteristic temperatures Tg (glass transition), Tc (crystallization) and Tf (fusion) of the glasses are found in the following ranges: 400 – 5000C for Tg, 440 – 6500C for Tc and 780 – 8300C for Tf. Rietveld refinements of powder X ray diffraction data collected on crystalline samples of NaxLiyCazTit(PO4)3 shows the existence of a solid solution in the domain 0 ≤ X ≤ 0.5 and the presence of a mixture of phases in the domain 0.5 < X ≤ 1.5. The crystalline phases belong to the Nasicon family, space group R32. Their structure, determined from refinement of powder diffraction patterns , consists of a 3D network of AO6 (A = Ti, Na, Li, and Ca) octahedra and PO4 tetrahedra linked by corners. Sodium atoms fully occupy the M(1) sites and partially the M(2) sites.
The RodBot approach to automated crystal harvesting
Authors: Sargent David , Tung Hsi-Wen , Pieters Roel , Nelson Bradley
Published: November 2015

Automated crystal harvesting is the main gap in the otherwise highly automated process of structure determination by X-ray crystallography. Many approaches have been presented, but few have proceeded beyond the initial, developmental stage. We recently introduced a rod-shaped microrobot1 (the "RodBot") to assist in the harvesting process. Driven by rotating magnetic fields to roll on a substrate, RodBots induce fluid flows that can lift crystals off the surface and trap them in a cylindrical vortex that travels with the RodBot. The gentle, fluidic force acting on the crystals is in the range of a few nanoNewtons to tens of nanoNewtons, and is spread over the whole surface of the crystal. Forces of this magnitude enable the RodBot to safely manipulate crystals ranging from a few microns to sub-millimeter size. With this technique individual crystals can be selected and brought to a loop positioned in the growth droplet to accept it. Harvesting and flash-cooling is then possible using a simple mechanical linkage. In this way the whole operation of crystal selection, harvesting and flash-cooling is remotely and gently carried out without the operator jitter or application of excessive strain that lead to high late-stage failure rates in crystal harvesting. Guidance is provided by the driving magnetic field, and can involve either manual input with a joystick or fully automated algorithms with feedback control. Because of this option of remote operation, RodBots can also be used for harvesting in hostile, sensitive or inconvenient environments such as anaerobic chambers, controlled humidity environments or cold rooms. The system is compatible with existing crystallization hardware and can be integrated readily into typical laboratory setups or high-throughput platforms.
New developments and operation of the MX beamline XALOC at ALBA synchrotron
Authors: Juanhuix Jordi , Nicolás Josep , Cuní Guifré , Colldelram Carles , Rubio Alberto , Ávila Jose , González Nahikari , Enrique Alejandro , Ramos Inma , Jover Gabriel , Fullà Daniel , Gil Fernando , Benach Jordi
Published: November 2015

BL13-XALOC is a Macromolecular Crystallography beamline at the 3-GeV ALBA synchrotron near Barcelona, and is operating with users since 2012. Currently being the only MX beamline at the site, XALOC has been designed to deal not only with easily automatable x-ray diffraction experiments of medium-sized crystals, but also with more complex ones that include a variety of crystal sizes and unit-cell length dimensions, crystals with high mosaic spread, and/or poorly diffracting crystals. The aim for a reliable all-in-one beamline contrasts with the trend observed lately, i.e. MX beamlines target specific characteristics of the crystals (microcrystals, large unit cells), techniques (tunability, small or large wavelengths), or to the status of the MX projects (crystal screening). The flexibility of the beamline is achieved by providing a very stable photon beam in an enery range of 5-22 keV and by changing the beam size at the sample position without loosing flux through defocusing to accomodate the dimensions of the beam to those of the sample. The beam dimensions at the sample position range from 57×5.5 µm2 FWHM (H×V) when focused to ~300×300 µm2. The dimensions of the beam are changed without varying the beam path. The beamline optics that allows this flexibility is based on an in-vacuum undulator, a Si(111) channel-cut monochromator, and a pair of KB mirrors. The defocused beam is severely affected by the slope errors of the mirrors, which produce striations on the beam profile at the sample position, mainly in the vertical direction. To minimize these striations, we have developed a new method that corrects mirror profiles by using spring actuators. The process resulted in a 4-fold reduction of the mirror slope errors, and in striations of the beam that amount only for ~10% of the nominal defocused beam profile. We expect that this uniform, tailored beam will improve the estimation of the radiation dose onto the sample, and will help in establishing a better data collection strategy. The end station includes a high accuracy single-axis diffractometer, a removable mini-kappa stage, an automated sample mounting robot, and a Pilatus6M, photon-counting detector. A new TANGO-based beamline control system (Sardana) has also been developed. Statistics of usage of the beamline and some relevant examples will be given.
Applications with a brighter X-ray source and new detectors from Agilent
Authors: Gal Zoltan , Skarzynski Tadeusz , White Fraser , Presly Oliver , Jones Adrian , Kucharczyk Damian , Meyer Mathias
Published: November 2015

Agilent Technologies develop and supply X-ray systems for single-crystal diffraction research, including the SuperNova; a compact, highly reliable and very low maintenance instrument providing X-ray data of the highest quality; and the PX Scanner for testing and characterization of protein crystals in their original crystallization drops (in-situ). The SuperNova and PX Scanner are constantly improving, with recent enhancements including a new range of detectors using an Intelligent Measurement System. The Eos S2, Atlas S2 and Titan S2 detector range employs a smart sensitivity control of the electronic gain and is capable of instantaneously switching its binning modes thus providing unprecedented flexibility in tuning every exposure to provide the highest data quality for a wide range of experiments. We have also developed a completely new micro-focus X-ray source based on Gradient Vacuum technology, with novel filament and target designs. This novel source is an integral part of the new Agilent GV1000 X-ray diffractometer, which has been designed for applications that require even higher brightness of the X-ray beam.
Olex2 - what is next?
Authors: Dolomanov Oleg , Puschmann Horst
Published: November 2015

Olex2 [1] is free, open source software which has been in the development at Durham University since 2004, with first public releases appearing in 2008. It is being actively developed and new versions are frequently released. Olex2 has established itself as a well-known, self-contained crystallographic package which, in additions to its own structure solution and refinement utilities, provides a unified user interface to external programs such as Sir, Superflip and the ShelX suit of programs. It provides number of tools for model building, structure and data analyses, CIF generation and reports preparation. From the beginning Olex2 was developed with visual feedback in mind and currently it provides `traffic-light' indications for data and the structure refinement and the default ADP rendering always gives an instant indication of the model quality. This presentation will focus on the aspects of the recent and future developments in Olex2.
Displacement Parameter Restraints for Dealing with Limited Data
Authors: Cooper Richard , Arnold James
Published: November 2015

Standard crystallographic structure refinements employ anisotropic displacement parameters (ADPs) to represent the probability distribution of a scattering atom. Such distributions may be due to thermal motion of the atom and / or a spatial average of multiple discrete atomic positions. An anisotropic description of an atomic distribution requires six parameters, and - in cases where data is limited or poor quality - the optimal values of these parameters may be ill-defined. Application of restraints and constraints can impose some physical and chemical reality on the set of displacement parameters. Examples include those based on the Hirshfeld Rigid Bond Test [1], and more recently SHELXL's RIGU [2]. We have implemented these and other a.d.p. restraints in CRYSTALS [3], for introducing reasonable relationships amongst common arrangements of anisotropic atoms. Use of a priori information in the form of restraints must always be justified, and we present an assessment of the applicability of the new restraints against a large data set of high quality crystal structure determinations.
X-ray Crystallography at Beamline P11 at PETRA III
Authors: Burkhardt Anja , Warmer Martin , Stuebe Nicolas , Roever Jan , Reime Bernd , Panneerselvam Saravanan , Pakendorf Tim , Meyer Jan , Fischer Pontus , Meents Alke
Published: November 2015

The bio-imaging and diffraction beamline P11 at PETRA III is dedicated to structure determination of periodic (crystalline) and aperiodic biological samples. The beamline features two experimental endstations: an X-ray microscope and a crystallography experiment. Basis of design was to provide an extremely stable and flexible setup ideally suited for micro and nano beam applications. The X-ray optics consist of a HHL double crystal monochromator, followed by two horizontal deflecting and one vertical deflecting X-ray mirrors. All mirrors are dynamically bendable and used to generate an intermediate focus at 65.5 m from the source with a size of 37 × 221 µm2FWHM (v × h). All experiments are installed on an 8 m long granite support which provides a very stable setup for micro beam experiments. The crystallography endstation is located at the end of the granite at 72.9 m from the source. The experiment is equipped with a high precision single axis goniostat with a combined sphere of confusion of less than 100 nm. X-ray energies are tunable between 5.5 and 30 keV. A second focusing bendable KB mirror system can be used for further demagnification of the secondary source. In this way the beam size can be freely adjusted between 4 × 9 µm2and 300 × 300 µm2FWHM (v × h) with 1013ph/s at 12 keV. Smaller beam sizes down to 1 × 1 µm2with more than 2 × 1011ph/s in the focus can be realized by slitting down the secondary source at the cost of flux. The crystallography endstation is equipped with a Pilatus 6M-F detector which allows fast data collection with up to 25 Hz. Due to the very small beam divergence of the X-ray beam P11 is ideally suited to measure large unit cell systems, such as viruses or large molecular complexes. In addition, the beamline is capable of high-throughput crystallography and fast crystal screening. Crystals can be mounted in less than 10 s using an automatic sample changer. The large sample dewar provides space for 368 crystals.