bluuebunny/crossref_metadata_2025 huggingface dataset:
CYP1B1 and MYOC Mutations in Vietnamese Primary Congenital Glaucoma Patients
Authors: Do Tan , Shei William , Chau Pham Thi Minh , Trang Doan Le , Yong Victor H.K. , Ng Xiao Yu , Chen Yue Ming , Aung Tin , Vithana Eranga N.
Published: November 2015

Purpose:

Primary congenital glaucoma (PCG, OMIM 231300), the most common glaucoma in infancy, is caused by developmental defects in the anterior chamber angle. The 3 implicated genes are cytochrome P450 family I subfamily B polypeptide 1 (CYP1B1), latent transforming growth factor β-binding protein 2 (LTBP2), and myocilin (MYOC). In this study, we sought to determine CYP1B1 and MYOC sequence variations in a Vietnamese cohort of index cases with PCG and their families.

Methods:

Thirty Vietnamese subjects with PCG and 120 normal Vietnamese subjects were recruited. PCG was defined by the presence of at least 2 of the following clinical manifestations: increased corneal diameter (>10 mm at birth), corneal edema, Haab’s striae, optic disc changes, and absence of other ocular or systemic diseases associated with childhood glaucoma. The coding exons, intron and exon boundaries, and untranslated regions of CYP1B1 and MYOC genes were PCR amplified and subjected to bidirectional sequencing in all subjects.

Results:

We identified 2 homozygous and 3 heterozygous CYP1B1 sequence alterations in our study subjects. Among the 5 mutations identified, 2 (p.H279L and p.L283F) were novel mutations, whereas 3 (p.A121_S122insDRPAFA, p.L107V, and p.V320L) had been previously reported in PCG cases. None of these mutations was observed in any of the 120 controls. Haplotypes generated with 6 non–disease-causing intragenic single nucleotide polymorphisms detected in CYP1B1 indicated that the most common haplotype in Vietnamese population is similar to that found in Chinese and Japanese. The genotype-phenotype correlation showed no significant difference between mutation and no-mutation groups for quantitative clinical features (presenting intraocular pressure, corneal diameter, number of surgeries performed, the cup-to-disc ratio) as well as for qualitative factors (bilateral cases, phenotype severity, and the prognosis) (P>0.05).

Conclusions:

Five out of 30 families with PCG (16.7%) had disease attributable to CYP1B1 alterations suggesting that CYP1B1 is not the major gene causing PCG in Vietnamese unlike in the case of Arab or Romany patients. This percentage is similar to that detected in studies of Japanese and Chinese patients with sporadic PCG. PCG has proven to be an ocular disease of genetic heterogeneity, calling for further studies to identify novel genes causing this disease.
Dynamic stem cell states: naïve to primed pluripotency in rodents and humans
Authors: Weinberger Leehee , Ayyash Muneef , Novershtern Noa , Hanna Jacob H.
Published: November 2015

Preface

The molecular mechanisms and signalling pathways that regulate thein vitropreservation of distinct pluripotent stem cell configurations, and their induction in somatic cells via direct reprogramming approaches, continue to constitute a highly exciting area of research. In this review, we provide an integrative synthesis on recent discoveries related to isolating unique naïve and primed pluripotent stem cell states with altered functional and molecular characteristics, and from different species. We overview pathways underlying pluripotent state transitions and interconversionin vitroandin vivo.We conclude by highlighting unresolved key questions, future directions and potential novel applications of such dynamic pluripotent cell states.
Fitness costs of herbicide resistance across natural populations of the common morning glory,Ipomoea purpurea
Authors: van Etten Megan L. , Kuester Adam , Chang Shu-Mei , Baucom Regina S
Published: November 2015

Although fitness costs associated with plant defensive traits are widely expected, they are not universally detected, calling into question their generality. Here we examine the potential for life history trade-offs associated with herbicide resistance by examining seed germination, root growth, and above-ground growth across 43 naturally occurring populations ofIpomoea purpureathat vary in their resistance to RoundUp®, the most commonly used herbicide worldwide. We find evidence for life history trade-offs associated with all three traits; highly resistant populations had lower germination rates, shorter roots and smaller above-ground size. A visual exploration of the data indicated that the type of trade-off may differ among populations. Our results demonstrate that costs of adaptation may be present at stages other than simply the production of progeny in this agricultural weed. Additionally, the cumulative effect of costs at multiple life cycle stages can result in severe consequences to fitness when adapting to novel environments.
Adaptation to an invasive host is collapsing a native ecotype
Authors: Cenzer M L
Published: November 2015

Locally adapted populations are often used as model systems for the early stages of ecological speciation, but most of these young divergent lineages will never become complete species. While the collapse of incipient species is theoretically common, very few examples have been documented in nature. Here I show that soapberry bugs (Jadera haematoloma) have lost adaptations to their native host plant (Cardiospermum corindum) and are regionally specializing on an invasive host plant (Koelreuteria elegans), collapsing a classic and well-documented example of local adaptation. All populations that were adapted to the native host - including those still found on that host today - are now better adapted to the invasive in multiple phenotypes. Weak differentiation remains in two traits, suggesting that homogenization across the region is incomplete. This study highlights the potential for adaptation to invasive species to disrupt native communities by swamping adaptation to native conditions through maladaptive gene flow.
A pan-cancer analysis of prognostic genes
Authors: Anaya Jordan , Reon Brian J. , Chen Wei-Min , Bekiranov Stefan , Dutta Anindya
Published: November 2015

Numerous studies have identified prognostic genes in individual cancers, but a thorough pan-cancer analysis has not been performed. In addition, previous studies have mostly used microarray data instead of RNA-SEQ, and have not published comprehensive lists of associations with survival. Using recently available RNA-SEQ and clinical data from the The Cancer Genome Atlas for 6,495 patients, we have investigated every annotated and expressed gene’s association with survival across 16 cancer types. The most statistically significant harmful and protective genes were not shared across cancers, but were enriched in distinct gene sets which were shared across certain groups of cancers. These groups of cancers were independently reconstructed by unsupervised clustering of Cox coefficients (a measure of association with survival) for individual genes or for gene programs. This analysis has revealed unappreciated commonalities among cancers which may provide insights into cancer pathogenesis and rationales for co-opting treatments between cancers.
Assisted reproduction causes intrauterus growth restriction by disrupting placental lipid metabolism
Authors: Wei Yubao , Chen Shuqiang , Huang Xiuying , Lam Sin Man , Shui Guanghou , Sun Fangzhen
Published: November 2015

IVF related intrauterus growth restriction or low birth weight (LBW) is very common in ART clinic. This study is focus on the aberrant lipid metabolism induced by in vitro fertilization and its mechanism. Firstly, we investigated the effect of IVF on fetal weight and placenta efficiency at E18.5 (at birth) and E14.5 (middle gestation). Data shows that IVF caused LBW and low placenta efficiency. Then we studied the lipidomics of E18.5 placenta and E14.5 placenta. The IVF group has an eccentric lipid content compared toin vivogroup. All the 15 lipid classes are largely accumulated in E18.5 IVF placenta and are deficient in E14.5 IVF placenta. In detail, most of the 287 lipid species is accumulated at E18.5 and went short at E14.5. Using qRT-PCR we detected the expression level of genes related to lipid uptake, transport and metabolism. Most of these genes are down-regulated which indicated the metabolism function of placenta is disrupted seriously. To the imprinted genes for lipid metabolism regulation asGNASandGrb10, IVF not only disrupt their imprinting status (methylation level) but also disrupt their gene expression. The expression ofDNMTsandTetsare also disrupted in the placenta. These data demonstrate that IVF impaired the regulation network of lipid metabolism. These results prove the hypothesis: imperfect IVF condition of fertilization jeopardize the expressionDNMTs,Tetsand imprinting status of imprinted genes for lipid metabolism regulation. Then it causes to abnormal expression of genes for lipid metabolism and regulation. This leads to the significant differences in lipid species quantification and lipid metabolism. So it contributed to low lipid transport efficiency, restricted fetal growth and LBW. This study provides a renewed knowledge of lipid metabolism in placenta and its relation to imprinted genes and gave some clinical aware for optimizing the ART practice.

Funding

This work was supported by grants from the National Basic Research Program of China (973 Program) and National Natural Science Foundation of China.

Competing Interests

The authors have declared that no competing interests exist.

Abbreviations

ART

artificial reproductive technology

IVF

in vitro fertilization

LBW

low birth weight

GNAS

Guanine Nucleotide Binding Protein Alpha

Grb10

Growth factor receptor-bound protein 10
Determination of deviatoric elastic strain and lattice orientation by applying digital image correlation to Laue microdiffraction images: the enhanced Laue-DIC method
Authors: Zhang F. G. , Castelnau O. , Bornert M. , Petit J. , Marijon J. B. , Plancher E.
Published: November 2015

A new method of determining the deviatoric elastic strain and lattice orientation from Laue microdiffraction images is presented. Standard data treatment methods can suffer from the difficulty of precisely pinpointing the positions of diffraction peaks on two-dimensional Laue images. In a previous article, digital image correlation (DIC) was introduced for the treatment of Laue images, leading to the so-called Laue-DIC method. This performed better than the standard method in terms of the deviatoric elastic strain increment and relative rotation from one lattice to another, particularly when the shape of the Laue spots departs from regular ellipsoids. The present work intends to push forward the Laue-DIC method, aiming to determine the deviatoric elastic strain and lattice orientation, as well as the calibration parameters. The performance of this new method, named enhanced Laue-DIC, is assessed by modeling the spot displacements and accounting for random fluctuations relevant for typical experimental conditions. When the enhanced Laue-DIC method is applied to the case of anin situdeformed Si crystal, the obtained standard deviation of local stress is of the order of 1–2 MPa, while the calibration parameters are optimized to high accuracy.
Compositional and architectural variation in urinary calculi from nucleus to periphery: an integrated IR spectroscopy, scanning electron microscopy and powder X-ray diffraction approach
Authors: Chatterjee Paramita , Pramanik Samiran , Mukherjee Alok Kumar
Published: November 2015

A combination of IR spectroscopy, scanning electron microscopy (SEM) and powder X-ray diffraction has been used to analyze the compositional and architectural variation across the different parts (core, middle and outer layers) of five human urinary calculi (KS1–KS5) from eastern India. Rietveld quantitative phase analysis using X-ray powder diffraction revealed that the composition of the core regions in KS1–KS3 and KS5 is exclusively whewellite, whereas in KS4 it is a mixture of whewellite (84.5 wt%) and carbonated hydroxyapatite (15.5 wt%). While one of the renal stones, KS1, is composed of only whewellite in all three regions, a distinct variation in phase composition from the core towards the periphery has been observed in KS2–KS5. A drastic change in phase composition has been noted in KS5, with the major constituent phases in the core, middle and outer layers as whewellite (100.0 wt%), anhydrous uric acid (60.7 wt%) and carbonated hydroxyapatite (69.6 wt%), respectively. The crystallite size of whewellite in different parts of the kidney stones varies between 91 (1) and 167 (1) nm, while the corresponding sizes of the anhydrous uric acid in KS5 and carbonated hydroxyapatite in KS3 are 107 (1) and 18 (1)–20 (1) nm, respectively. SEM images of the kidney stones showed different levels of organization, resulting from an agglomeration of crystallites with diverse shapes and sizes.
Spinel materials for Li-ion batteries: new insights obtained byoperandoneutron and synchrotron X-ray diffraction
Authors: Bianchini Matteo , Fauth François , Suard Emmanuelle , Leriche Jean-Bernard , Masquelier Christian , Croguennec Laurence
Published: November 2015

In the last few decades Li-ion batteries changed the way we store energy, becoming a key element of our everyday life. Their continuous improvement is tightly bound to the understanding of lithium (de)intercalation phenomena in electrode materials. Here we address the use ofoperandodiffraction techniques to understand these mechanisms. We focus on powerful probes such as neutrons and synchrotron X-ray radiation, which have become increasingly familiar to the electrochemical community. After discussing the general benefits (and drawbacks) of these characterization techniques and the work of customization required to adapt standard electrochemical cells to anoperandodiffraction experiment, we highlight several very recent results. We concentrate on important electrode materials such as the spinels Li1 + xMn2 − xO4(0 ≤x≤ 0.10) and LiNi0.4Mn1.6O4. Thorough investigations led byoperandoneutron powder diffraction demonstrated that neutrons are highly sensitive to structural parameters that cannot be captured by other means (for example, atomic Debye–Waller factors and lithium site occupancy). Synchrotron radiation X-ray powder diffraction reveals how LiMn2O4is subject to irreversibility upon the first electrochemical cycle, resulting in severe Bragg peak broadening. Even more interestingly, we show for the first time an ordering scheme of the elusive composition Li0.5Mn2O4, through the coexistence of Mn3+:Mn4+1:3 cation ordering and lithium/vacancy ordering. More accurately written as Li0.5Mn3+0.5Mn4+1.5O4, this intermediate phase loses the Fd\overline 3m symmetry, to be correctly described in theP213 space group.
Synthesis, structural characterization and biological properties of copper complexes with ligands containing phosphonium substituent
Authors: Kong Mun Lo , Shin Thung Chew , Kong Wai Tan
Published: November 2015

A series of copper(II) complexes containing phosphonium substituted hydrazone, (L) with the formulations [CuL]Cl and [Cu(L')L]Cl, where L = doubly deprotonated hydrazone; L' = 1,10'-phenanthroline, 2,2'-bipyridine, 4,4-bipyridine and 5,5'-dimethyl-2,2'-bipyridine has been synthesized. The compounds were characterized by elemental analysis, IR and NMR spectroscopic methods and in the case of crystalline products by X-ray crystallography. The crystal structure of [CuL]Cl and the extent of distortion from ideal square pyramidal geometry for CuL')(l)]Cl will be discussed. The cytotoxicity and topoisomerase I (topo I) inhibition activities of these compounds were also studied. It is noteworthy that the addition of N,N-ligands to the copper(II) complex lead to the enhancement in the cytotoxicity of the compounds, especially against human prostate adenocarcinoma cell line (PC-3). The complexes can also inhibit topo I through the binding to DNA and the enzyme.
Structural studies on oxalate decarboxylase from Photorhabdus luminescens
Authors: Mathivanan Subashini , Chellappan Sreeja , Thippeswamy R. , Nagesh M. , Savithri H.S , Murthy M.R.N
Published: November 2015

As a part of exploration of novel bacterial genes coding for insecticidal proteins, we have initiated structural and functional studies on oxalate decarboxylase from Photorhabdus luminescens, a symbiotic bacteria inhabiting guts of nematodes that parasitize insects. Oxalate decarboxylases (OXDC) are enzymes that catalyze the conversion of oxalate to formate and carbondioxide (CO2) in the presence of manganese and dioxygen. Structures of OXDC in complex with ethylene glycol (EDO), EDO/formate (FMT) and FMT/CO2 were determined at resolutions of 1.97Å, 2.36Å and 2.5Å, respectively. The asymmetric unit of these crystals contained a trimeric molecule. A protomer of the enzyme consists of two β-barrel domains belonging to the cupin family of proteins. All the three ligand bound structures of OXDC resemble the closed form of OXDC from B. subtilis reported earlier. Comparison of these structures with the open and closed forms of B. subtilis OXDC indicated that the conformation of Glu166 (corresponding to Glu162 of B. subtilis) in cupin domain I but not in domain II is in a conformation suitable to function as the catalytic base/acid and hence only domain I may be catalytically active. It is observed that the hydrogen bonding interaction between Arg95 and Thr169 of cupin domain I is essential for the positioning of Glu166 for catalysis. A corresponding threonine residue is absent in cupin domain II. An analysis of the similarities and differences between OXDC structures from P. luminescens and other reported bacterial OXDC structures and oxalate oxidase from Hordeum vulgare has been carried out with the view of understanding substrate and functional specificities of these enzymes. The structure provides the molecular framework required to investigate the mode of action of the enzyme, which may be a suitable candidate for developing P. luminescens as a bio-insecticide against plant pests.
The State of the Union
Authors: Sicard Taylor , Ngo Maria , Jocius Jordan , Brown Ryan , Suits Michael
Published: November 2015

With 2014 marking the International Year of Crystallography (IYRc) one can't help but look back in awe with respect to how far the science has come. At the same time, we are always looking forward to new techniques, technologies and transformational methods that push our science even further. So what is the state of the union, what are the major areas for growth, and what will crystallography look like in 5, 10, 25 and 100 years? In seeking to answer these questions, we are providing conference attendees an opportunity to peer into their crystal balls and answer these questions.
HP/HT synthesis and characterization of novel multiferroic Bi-based perovskites
Authors: Delmonte Davide , Mezzadri Francesco , Pernechele Chiara , Solzi Massimo , Calestani Gianluca , Bolzoni Fulvio , Cabassi Riccardo , Gilioli Edmondo
Published: November 2015

Bi-based perovskites (BiM1-xM'xO3, where M e M' are 3d and 4d metal ions) are considered very promising candidates to show multiferroic magnetoelectric character. A multiferroic magnetoelectric is a material in which ferromagnetism and ferroelectricity are not only coexistent but also coupled. Such properties, very rare in natural materials, are suitable for electronics, data storage and spintronics applications. Therefore, the interest in this class of compound showed an increasing trend of scientific publications in the last ten years. Unfortunately most members of this family cannot be synthesized with conventional techniques, due to their highly unstable and distorted crystallographic structure. High isostatic pressures and high temperatures can be exploited to overcome this fundamental drawback. The strategy is to induce ferroelectricity (e.g. polar symmetry) achieving the stereochemical effect of Bi3+ 6s2 lone pair, that polarizes the bonds with the neighboring oxygen anions, and independently to bring magnetism through the introduction of magnetic ions of the third or the fourth period on the octahedral coordinated B-site of the perovskite structure. We have synthesized simple and complex (quadruple [1,2] and double [3]) Bi-based perovskites in wide ranges of pressure (from 3 to 9 GPa) and temperature (from 9000C to 16500C) by means of solid state reactions in a multi-anvil Walker-type Press. We present an accurate study of the structural, magnetic and electric properties. Furthermore, unconventional home-made set-ups are also presented as the tools to probe the coupling between the electric and the magnetic properties through crossed magnetic characterizations (magnetic susceptibility dependence on an applied electric field) and reversely crossed electric characterizations (polarization as a function of an external magnetic field).
Structural characterization of a potent humanized anti-CD38 antibody in phase I
Authors: Vallée Francois , Pouzieux Stephanie , Rak Alexey , Michoux François , Wetzel Marie-Cécile , Deckert Jutta , Kannt Aimo , Blanc Veronique , Mikol Vincent
Published: November 2015

CD38 is a type II transmembrane glycoprotein with both ADP-rybosyl cyclase and glycohydrolase activities. CD38 is highly expressed at the surface of malignant plasma cells of multiple myeloma. SAR650984 is a humanized IgG1 antibody targeting CD38 in early clinical developement that is acting through several potential mechanisms including ADCC, CDC and pro-apoptotic activity. Here we report further preclinical characterization of SAR650984 with a high resolution structure of Fab-SAR650984 in complex with CD38 allowing an epitope mapping. The crystal structure of SAR650984-Fab/huCD38 complex shows that SAR650984 neither blocks the access nor alters the configuration of the ADPRC catalytic site of CD38 although in vitro assays have demonstrated that SAR650984 behaves as a strong inhibitor of the ADPRC activity of CD38. These results suggest that SAR650984 is likely an allosteric antagonist of CD38 that alters the dynamics of enzyme upon binding.
Structural Characterization of Albendazole with the Use of X-Ray Diffraction
Authors: Lixandrão Kelly , Ferreira Fabio
Published: November 2015

Drugs may present polycrystalline polymorphism (property of a substance to crystallize in more than one form or crystal structure). These variations can cause changes in physical-chemical properties and differences between the polymorphs as shape, solubility, density, melting range, among other consequences, leading to formulations that are not effective, although the chemical formula is the same [1]. Drugs such as albendazole (C12H15N3O2S, which is one of the most effective anthelmintics, [2] showing activity against nematodes, trematodes and cestodes, reasons that added to its safety and low cost have made it a drug widely used in human medicine and veterinary), has more than two different crystal structures, and only two of them are known. The X-ray powder diffraction is a powerful technique used in the structural characterization of drugs, and coupled with the Rietveld method [4], the quantification of the active phases, through the knowledge of their crystal structures, becomes possible. In this paper we discuss results on the differences between the polymorphs of albendazole, with data obtained by means of X-ray diffraction, thermal analysis (differential scanning calorimetry and thermogravimetric analysis), Fourier transform infrared spectroscopy and scanning electron microscopy.
PDF calculations from STOE STADI P Ag Kα1 low- and high-temperature data
Authors: Fink Lothar , Rademacher Nicole , Hartmann Thomas
Published: November 2015

An impressive comparison of G(r) calculated with PDFgetX2(1) from data of Naphthalen taken at room temperature with a Stoe Stadi P powder diffractometer in Transmission mode equipped with a Ag-tube, a Ge(111)-monochromator for pure Ag-Kα1-radiation (0.5594 Å) as well as the Dectris MYTHEN 1K with1mm chip size and from synchrotron data, beamline X17A, NSLS Brookhaven with a wavelength of 0.1839 Å, yields amazingly similar peak widths for both experiment sites. To observe the temperature dependence of this resolution, the same laboratory setup with an additional Oxford Cryosystems Cobra or a Stoe furnace has been chosen to compare the signal width as a function of T. Low temperature data for these PDF calculation experiments has been taken from LaB6 as a crystalline standard and Naphthalene as well known organic phase. In addition high temperature G(r)-data from Ammonium Nitride will be demonstrated.
Modelling the release of biological molecules from ordered mesoporous silica
Authors: Mariano-Neto Francisco , Oliveira Cristiano , Fantini Márcia , Cavalcanti Leide , Sant'Anna Osvaldo
Published: November 2015

This work reports preliminary results of the application of a theoretical model [1] in the study of incorporation and release of biological molecules from the porous structure of the SBA-15 [2] ordered mesoporous silica. A theoretical model taking into account the shape and spatial coordination of the pores in the amorphous silica structure is fitted through a non-linear least-squares method and the behavior of the parameters obtained from curves acquired in-situ during incorporation and release experiments are interpreted in the context of different media. Preliminary studies included experiments regarding the coating of the SBA-15 silica with the Eudragit® polymer and the stability of SBA-15 in experimental media (water and PBS solution) and in simulated body fluids. Small angle X-ray scattering experiments were performed mainly with bovine serum albumin (BSA) and insulin, and showed the silica's capacity of sheltering those molecules inside its structure, as well as the influence of Eudragit® on their release dynamics. In-situ experiments made during the incorporation and release of insulin helped elucidate the dynamics of those phenomena, through the reinterpretation of the theoretical model, which was originally designed to study the synthesis process of SBA-15. In this model, fit parameters were monitored during the experiment and, from their behaviors, some conclusions are drawn, such as the delay in BSA release for the SBA-15 plus Eudragit® in gastric fluid. The in-situ studies of insulin loading showed that this molecule's uptake takes place in the course of a few minutes and that it remains inside the pores. Also the in-situ studies of insulin release showed that this molecule is protected inside the silica walls, and the use of Eudragit® is, in a way, optional.
A novel facile route to stabilize highly reactive organotellurenyl(II) chlorides
Authors: Khrustalev Victor , Matsulevich Zhanna , Aysin Rinat , Peregudov Alexander , Leites Larissa , Borisov Alexander
Published: November 2015

Recently we reported a new possibility for stabilizing highly reactive organoselenenyl(II) chlorides by N-functionalization of an organyl substituent and the subsequent addition of a hydrochloric acid molecule [Ref.]. It is well-known that organotellurenyl(II) chlorides are even less stable than the related organoselenenyl(II) chlorides. This fact prompted us to apply the same approach to organotellurenyl(II) chlorides containing an N-functionalized aryl substituent. In the present work, a novel facile route for stabilizing highly reactive Ar*TeCl species (Ar* = nitrogen-containing aryl) by hydrochloric acid addition has been demonstrated, exemplified by two new T-shaped tellurenyl chloride adducts, viz. 1H-pyridine-2-tellurenyl-dichloride (Fig.) and 4,6-dimethyl-1H-pyrimidine-2-tellurenyl-dichloride. Their quasi-planar zwitterionic structures with strong intramolecular N–H...Cl hydrogen bonds have been evidenced by experimental (single-crystal X-ray diffraction, multi-nuclear NMR, vibrational spectroscopy) and theoretical (DFT and QTAIM) methods. Due to this structure, the studied heteroaryl tellurenyl dichlorides react with alkenes in a similar manner to the corresponding monomeric tellurenyl chlorides affording the same cycloaddition products. The described approach to difficult-to-obtain, extremely unstable organotellurenyl(II) chlorides opens alluring prospects in the synthesis and study of low-valent chalcogen compounds.
An in silico structural insights into Plasmodium LytB protein and its inhibition
Authors: Bhunya Rajabrata , Nandy Suman , Seal Alpana
Published: November 2015

In most of the pathogenic organisms including Plasmodium falciparum, isoprenoids are synthesized via MEP (MethylErythritol 4-Phosphate) pathway. LytB is the last enzyme of this pathway which catalyzes the conversion of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Since the MEP pathway is not used by humans, it represents an attractive target for the development of new antimalarial compounds or inhibitors. Here a systematic in-silico study has been conducted to get an insight into the structure of Plasmodium lytB as well as its affinities towards different inhibitors. We used comparative modeling technique to predict the three dimensional (3D) structure of Plasmodium LytB taking E. Coli LytB protein (PDB ID: 3KE8) as template and the model was subsequently refined through molecular dynamics (MD) simulation. A large ligand dataset containing diphospate group was subjected for virtual screening against the target using GOLD 5.2 program. Considering the mode of binding and affinities, 17 leads were selected on basis of binding energies in comparison to its substrate HMBPP (Gold.Chemscore.DG: -20.9734 kcal/mol). Among them, 5 were discarded because of their inhibitory activity towards other human enzymes. The rest 12 potential leads carry all the properties of any "drug like" molecule and the knowledge of Plasmodium LytB inhibitory mechanism which can provide valuable support for the antimalarial inhibitor design in future.
Study of hydrogen storage of the TiFe alloy by neutron powderdiffraction
Authors: Gosselin Catherine , Huot Jacques , Flacau Roxana
Published: November 2015

Metal hydrides are interesting materials from a fundamental as well as practical point of view. Hydrogen storage applications have been the main driving force of research on these materials but lately, uses such as thermal storage are considered. In this presentation, we will review the use of neutron diffraction for the development of new metal hydrides. A good candidate for hydrogen storage applications is the low cost intermetallic compound TiFe which operates near room temperature (RT) under mild pressure conditions. However, the biggest disadvantage of TiFe alloy synthesized by conventional metallurgical method is it poor activation characteristics [1]. The alloy reacts with hydrogen only after complicated activation procedure involving exposure to high temperature (~4000C) and high pressure for several days. In the '90, some researches showed that the change in the nanocristallinity can modify the sorption property of the TiFe[2]. Other research works found that palladium increase the contaminant resistance. However, addition of palladium is too expansive for practical applications [3]. Recently, we found that, when doping TiFe with Zr and Zr7Ni10, the activation could be easily done at room temperature. We present here a neutron diffraction study of these compounds that shows the structural difference between the activated compound and the one cycled under hydrogen.
Fast, reliable automation of protein crystallisation drop set-up
Authors: Schenker Ben , Jenkins Joby , Smith David
Published: November 2015

The automation of protein crystallography screening has contributed significantly to the rapid progress of crystallography-based structural biology. Automation offers increased throughput and repeatability. It also offers the ability to accurately dispense smaller volumes of both protein and screen solutions, which saves valuable protein and reduces reagent costs. Automation of protein crystallisation screening trials requires accurate placement of nanoliter volumes of protein and screen drops, in addition to the reproducible and accurate dispensing of solutions of varying viscosities. This is particularly important for the set-up of the highly viscous lipid mesophases in the Lipidic Cubic Phase (LCP) crystallisation technique for membrane protein crystallisation trials. This poster describes the features of TTP Labtech's mosquito® Crystal and mosquito® LCP, showing their ability to address the issues inherent in the automated set-up of protein crystallisation screen trials. An instrument capable of automating both microbatch and vapour diffusion methods of protein crystallography (sitting drop, hanging drop) as well as crystallisation of membrane proteins using the bicelle and LCP methods, without instrument configuration changes, offers significant flexibility for the crystallography laboratory mosquito Crystal and mosquito LCP offer fast throughput, high precision, unrivalled reproducibility and low volume accuracy.
Chemical Crystallography at the Australian Synchrotron MX Beamlines
Authors: Price Jason , Aragao David , Cowieson Nathan , Panjikar Santosh , Riboldi-Tunnicliffe Alan , Williamson Rachel , Caradoc-Davies Tom
Published: November 2015

The Macromolecular Crystallography (MX) Beamlines at the Australian Synchrotron collect data on protein samples (PX) and chemical samples (CX). This broad range of sample types requires us to consider a number of experimental and data processing considerations. Protein samples have very large unit cells but diffract weakly, the chemical samples on the other hand have very small unit cell and diffract comparatively strongly. From an experimental point of view, this requires substantially different geometrical considerations which can be handled by changing the energy of the monochromated X-rays and detector distance. Another consideration is detector type, the detectors at the MX beamlines are from the Area Detector Systems Corporation (ADSC) and they have generally been used for PX data collections. This has lead to investigation regarding high incidence angle phosphor thickness corrections. As the detectors have mainly been used for PX work, the software for sample handling has also been developed with PX considerations rather than CX. For example, the software for space group determinations is set my default to assumes that your space group is only ever one of the 65 space groups that don't contain mirror, inversion or glide operations. Another area of interest is the way data scaling is handled. The data is often scaled with PX data for a number of reasons, with the most common scaling of data is due t the prevalence of radiation damage to the samples. By contrast the most common form of scaling for CX data is for sample anisotropy in strong absorbers. A discussion of the challenges faced for the chemical crystallography experiments at the Australian Synchrotron will be presented.
Depolarized Dynamic Light Scattering a method to analyse Particle Shape and Size
Authors: Meyer Arne , Dierks Karsten , Betzel Christian
Published: November 2015

"Dynamic Light Scattering (DLS) is already a widely used method for small particle size distribution analysis [1]. The main purpose of this method is the determination of particle sizes, respectively the hydrodynamic radius in the sub-microscopic range, i.e. 1 nm up to few µm. It is based on the Brownian motion of those particles. Light scattering methods are non-invasive and therefore a great advantage in the field of particle analysis [2a]. The next generation of Dynamic Light Scattering devices will apply depolarized dynamic light scattering (DDLS) [2b]. This technique allows to obtain beside radius distributions also information about the particle shape. However, for some time technical drawbacks made it almost unfeasible to use it for biological samples. In cooperation with the University of Hamburg we developed the first experimental set-up of a DDLS system to be used in the laboratory to analyze and characterize protein solutions as well as suspensions of nano crystals, suitable for Free-Electron-Laser applications. The fundamental difference to so far known ""standard"" DLS is that the scattered light is separated into two signal pathways, a vertically and a horizontally polarized component, applying a special designed beam splitter. DDLS allows to measure the translational diffusion and the rotational constants simultaneously. Both constants are derived from the decay times of the autocorrelation functions. With the equations of Perrin the system is capable of calculating the axis ratio of the particles, approximating the real particle shape as a rotational ellipsoid. For calibration and tests gold rod particles of 575 nm in length and 25 nm diameter were applied. The first biological sample, which was analyzed by DDLS was hemocyanin from Limulus polyphemus hemolymph [3a], which occurrs predominantly as hexamers, dodecamers and traces of higher aggregates occur at high pH. In summary, together with additional advantages like viscosity independent measurements and ten times higher resolution compared to DLS, the DDLS-technique is optimal to characterize biological samples to be used for crystallization experiments and to score solutions and suspensions of nano-crystals to be used for Free-Electron Laser applications [3b]."
Neutron diffractometer covering protein crystals with large unit cell at J-PARC
Authors: Kurihara Kazuo , Tomoyori Katsuaki , Tamada Taro , Kuroki Ryota
Published: November 2015

The structural information of hydrogen atoms and hydration waters obtained by neutron protein crystallography is expected to contribute to elucidation of protein function and its improvement. However, many proteins, especially membrane proteins and protein complexes, have larger molecular weight and then unit cells of their crystals have larger volume, which is out of range of measurable unit cell volume for conventional diffractometers. Therefore, our group had designed the diffractometer which can cover such crystals with large unit cell volume (target lattice length: 250 Å). This diffractometer is dedicated for protein single crystals and has been proposed to be installed at J-PARC (Japan Proton Accelerator Research Complex). Larger unit cell volume causes a problem to separate spots closer to each other in spatial as well as time dimension in diffraction images. Therefore, our proposed diffractometer adopts longer camera distance (L2 = 800mm) and selects decoupled hydrogen moderator as neutron source which has shorter pulse width. Under the conditions that L1 is 33.5m, beam divergence 0.40and crystal edge size 2mm, this diffractometer is estimated to be able to resolves spots diffracted from crystals with a lattice length of 220 Å in each axis at d-space of 2.0 Å. In order to cover large neutron detecting area due to long camera distance, novel large-area detector (larger than 300mm × 300mm) with a spatial resolution of better than 2.5mm is under development. More than 40 these detectors plan to be installed, providing the total solid angle coverage of larger than 33%. For neutron guide, ellipsoidal supermirror is considered to be adopted to increase neutron flux at the sample position. The final gain factor of this diffractometer is estimated to be about 20 or larger as compared with BIX-3/4 diffractometers operated in the research reactor JRR-3 at JAEA (Japan Atomic Energy Agency) [1,2].
PF BL-15A for semi-microbeam XAFS/XRF and high-brilliance SAXS/GI-SAXS
Authors: Igarashi Noriyuki , Koyama Atsushi , Mori Takeharu , Kamijo Ai , Ohta Hiromasa , Nitani Hiroaki , Niwa Yasuhiro , Abe Hitoshi , Shimizu Nobutaka
Published: November 2015

New beamline, BL-15A, was completed at the BL-15 section of the PF-ring in 2014. This new beamline has a short gap undulator which produces high brilliance X-rays ranging from 2.1 keV to 15 keV. The beamline will be dedicated to both activities, XAFS/XRF/XRD studies using semi-micro focus beams (A1 station) and SAXS experiments using collimated softer and hard X-rays (A2 station). In the XAFS/XRF studies, the semi-micro beam available in a wide range of photon energies allows analyzing the local structures of the elements and valence on inhomogeneous samples in the fields of environmental science and new energy source science. The softer X-rays up to 2.1 keV will provide access to absorption edges of phosphor and sulfur, which are very important targets for those fields. The SAXS scientific programs include structural studies of functional membranes, time-resolved X-ray scattering and large hierarchical structure analysis. All of these three programs require a high-brilliance light source. In particular, grazing incidence SAXS (GI-SAXS) using vertically small-size softer beam ranging between 2.1-3.0 keV will help to control the depth of the membrane structure analysis and reduce the roughness defects of an imperfect membrane. The combination of XAFS/XRF and SAXS experiments gives wide structural information from fine atomic structure to low and medium resolution. It can be beneficial to build these instruments as two stations on the same beamline. BL-15A is oriented toward joint advanced studies by the two techniques. Old BL-15 beamlines were scrapped and new construction work started in 2013. The construction was completed in the summer shutdown of 2013 and the first beams was delivered on Oct 17, 2013. We are pursuing the beamline commissioning and the A1 and A2 stations will be opened to users in May, 2014. Here, the beamline design and performance, and the preliminary results will be reported.
Phase I Beamlines at Taiwan Photon Source
Authors: Chung Shih-Chun , Tang Mau-Tsu , Huang Yu-Shan , Hsu Chia-Hung , Huang Di-Jing , Chang Shih-Lin
Published: November 2015

With rapid advances in the international scientific community as well as increasing demands for bright X-rays from users to facilitate their challenging scientific experiments, the construction of a new synchrotron facility was vital to maintaining National Synchrotron Radiation Research Center in Taiwan to be globally competitive. After conducting numerous assessments with our users, the decision to construct Taiwan Photon Source (TPS) was made at the meeting of Board of Trustee held in 2004 July. This large-scale project will establish, at the current campus of NSRRC, a new, low-emittance, synchrotron light source of circumference 518 m and with an electron beam of energy 3 GeV. TPS is designed to emphasize electron beams of small emittance and great brilliance for generating extremely bright photon beams. The superior characteristics of TPS have opened avenues for novel scientific opportunities and experimental techniques. The advanced techniques of phase-I beamlines include temporally coherent X-ray diffraction, protein microcrystollography, submicron soft X-ray spectroscopy, coherent X-ray scattering, submicron X-ray diffraction, X-ray nanoprobe, and high resolution inelastic soft X-ray scattering. Taking full advantage of the highly brilliant photon source, the seven planned beamline will aim for the forefront of science. These beamlines cover diverse research in physics, chemistry, biology, and material science, in the energy range from soft to hard X-rays for advanced research in spectroscopy, scattering and imaging.
NSLS-II MX beamlines FMX for micro-crystallography & AMX for highly automated MX
Authors: Fuchs Martin , Sweet Robert , Berman Lonny , Bhogadi Dileep , Hendrickson Wayne , Chubar Oleg , Yang Lin , McSweeney Sean , Schneider Dieter
Published: November 2015

We present the final design of the x-ray optical systems and experimental stations of the two macromolecular crystallography (MX) beamlines, FMX and AMX, at the National Synchrotron Light Source-II (NSLS-II). Along with its companion x-ray scattering beamline, LIX, this suite of Advanced Beamlines for Biological Investigations with X-rays (ABBIX, [1]) will begin user operation in 2016. The pair of MX beamlines with complementary and overlapping capabilities is located at canted undulators (IVU21) in sector 17-ID. The Frontier Microfocusing Macromolecular Crystallography beamline (FMX) will deliver a photon flux of ~5x10^12 ph/s at a wavelength of 1 Å into a spot of 1 - 50 µm size. It will cover a broad energy range from 5 - 30 keV, corresponding to wavelengths from 0.4 - 2.5 Å. The highly Automated Macromolecular Crystallography beamline (AMX) will be optimized for high throughput applications, with beam sizes from 4 - 100 µm, an energy range of 5 - 18 keV (0.7 - 2.5 Å), and a flux at 1 Å of ~10^13 ph/s. Central components of the in-house-developed experimental stations are a 100 nm sphere of confusion goniometer with a horizontal axis, piezo-slits to provide dynamic beam size changes during diffraction experiments, a dedicated secondary goniometer for crystallization plates, and sample- and plate-changing robots. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and data collection of crystals in trays, for instance to characterize membrane protein crystals and to conduct ligand-binding studies. Together with the solution scattering program at LIX, the new beamlines will offer unique opportunities for advanced diffraction experiments with micro- and mini-beams, with next generation hybrid pixel array detectors and emerging crystal delivery methods such as acoustic droplet ejection. This work is supported by the US National Institutes of Health.
Area Detector Systems: Setting Higher Standards for Data Quality
Authors: Daniels Lee , Meyer Mathias
Published: November 2015

At least four major factors affect single-crystal diffraction data quality: 1) Hardware (source, goniometer and detector), 2) the sample, 3) the data collection procedure and strategy, and 4) the integration and data reduction software. Three of these factors can be carefully designed by the instrument manufacturer, and the other (the sample) can be chosen to optimize interaction with the instrument. We can define important hardware factors to allow quantification, such as absolute detectivity, overhead, readout speed, minimizing dead time and diffractometer access. Advances in area detector technology (including the new S2 generation of area detectors) and data collection approaches will be presented. The experimental procedure includes the choice of wavelength and the geometric strategy. Details of the detector operation (gain, bin-mode) can be optimized to fit the experiment. Agilent's latest CrysAlisPro software implements the 4th generation of strategy software and includes new on-the-fly detector optimization to provide significant gains in data quality. Integration software must be flexible in order to extract consistently good intensities from excellent samples and also from those that suffer from real-life flaws. Twinned samples represent an additional challenge. Agilent's new data reduction approach for twins significantly improves the data quality of both small molecule and protein twins.