bluuebunny/crossref_metadata_2025 huggingface dataset:
On the evolution and relative merits of hard X-ray phase-contrast imaging methods
Authors: Wilkins S. W. , Nesterets Ya. I. , Gureyev T. E. , Mayo S. C. , Pogany A. , Stevenson A. W.
Published: January 2014

This review provides a brief overview, albeit from a somewhat personal perspective, of the evolution and key features of various hard X-ray phase-contrast imaging (PCI) methods of current interest in connection with translation to a wide range of imaging applications. Although such methods have already found wide-ranging applications using synchrotron sources, application to dynamic studies in a laboratory/clinical context, for example for
in vivo
imaging, has been slow due to the current limitations in the brilliance of compact laboratory sources and the availability of suitable high-performance X-ray detectors. On the theoretical side, promising new PCI methods are evolving which can record both components of the phase gradient in a single exposure and which can accept a relatively large spectral bandpass. In order to help to identify the most promising paths forward, we make some suggestions as to how the various PCI methods might be compared for performance with a particular view to identifying those which are the most efficient, given the fact that source performance is currently a key limiting factor on the improved performance and applicability of PCI systems, especially in the context of dynamic sample studies. The rapid ongoing development of both suitable improved sources and detectors gives strong encouragement to the view that hard X-ray PCI methods are poised for improved performance and an even wider range of applications in the near future.
The determinants of alpine butterfly richness and composition vary according to the ecological traits of species
Authors: Sonnay Vincent , Pellissier Loïc , Pradervand Jean-Nicolas , Maiorano Luigi , Dubuis Anne , Wisz Mary S. , Guisan Antoine
Published: January 2014

Predicting spatial patterns of species diversity and composition using suitable environmental predictors is an essential element in conservation planning. Although species have distinct relationships to environmental conditions, some similarities may exist among species that share functional characteristics or traits. We investigated the relationship between species richness, composition and abiotic and biotic environment in different groups of butterflies that share ecological characteristics. We inventoried butterfly species richness in 192 sites and classified all inventoried species in three traits categories: the caterpillars diet breadth, the habitat requirements and the dispersal ability of the adults. We studied how environment, including influence butterfly species richness and composition within each trait category. Across four modelling approaches, the relative influence of environmental variables on butterfly species richness differed for specialists and generalists. Climatic variables were the main determinants of butterfly species richness and composition for generalists, whereas habitat diversity, and plant richness were also important for specialists. Prediction accuracy was lower for specialists than for generalists. Although climate variables represent the strongest drivers affecting butterfly species richness and composition for generalists, plant richness and habitat diversity are at least as important for specialist butterfly species. As specialist butterflies are among those species particularly threatened by global changes, devising accurate predictors to model specialist species richness is extremely important. However, our results indicate that this task will be challenging because more complex predictors are required.
Structure of the full-length yeast Arp7–Arp9 heterodimer
Authors: Lobsiger Joel , Hunziker Yvonne , Richmond Timothy J.
Published: January 2014

The nuclear actin-related proteins Arp7 and Arp9 are components of the yeast SWI/SNF and RSC chromatin-remodelling complexes. The 3.1 Å resolution crystal structure reported here shows that the full-length Arp7 and Arp9 proteins exist as a dimer without a requirement for additional polypeptides. Of the 11 actin-related proteins, Arp7 and Arp9 are the only two directly demonstrated to form a dimer within this family. The Arp7–Arp9 heterodimer is unlikely to form an actin-like filament based on modelling using the structure. The Arp7–Arp9 structure reveals that its dimerization interface is not altered when bound in a complex with the SWI/SNF Snf2 HSA domain and the regulatory protein Rtt102.
Stealth carriers for low-resolution structure determination of membrane proteins in solution
Authors: Maric Selma , Skar-Gislinge Nicholas , Midtgaard Søren , Thygesen Mikkel B. , Schiller Jürgen , Frielinghaus Henrich , Moulin Martine , Haertlein Michael , Forsyth V. Trevor , Pomorski Thomas Günther , Arleth Lise
Published: January 2014

Structural studies of membrane proteins remain a great experimental challenge. Functional reconstitution into artificial nanoscale bilayer disc carriers that mimic the native bilayer environment allows the handling of membrane proteins in solution. This enables the use of small-angle scattering techniques for fast and reliable structural analysis. The difficulty with this approach is that the carrier discs contribute to the measured scattering intensity in a highly nontrivial fashion, making subsequent data analysis challenging. Here, an elegant solution to circumvent the intrinsic complexity brought about by the presence of the carrier disc is presented. In combination with small-angle neutron scattering (SANS) and the D2O/H2O-based solvent contrast-variation method, it is demonstrated that it is possible to prepare specifically deuterated carriers that become invisible to neutrons in 100% D2O at the length scales relevant to SANS. These `stealth' carrier discs may be used as a general platform for low-resolution structural studies of membrane proteins using well established data-analysis tools originally developed for soluble proteins.
Structural analysis of the endogenous glycoallergen Hev b 2 (endo-β-1,3-glucanase) fromHevea brasiliensisand its recognition by human basophils
Authors: Rodríguez-Romero Adela , Hernández-Santoyo Alejandra , Fuentes-Silva Deyanira , Palomares Laura A. , Muñoz-Cruz Samira , Yépez-Mulia Lilian , Orozco-Martínez Socorro
Published: January 2014

Endogenous glycosylated Hev b 2 (endo-β-1,3-glucanase) fromHevea brasiliensisis an important latex allergen that is recognized by IgE antibodies from patients who suffer from latex allergy. The carbohydrate moieties of Hev b 2 constitute a potentially important IgE-binding epitope that could be responsible for its cross-reactivity. Here, the structure of the endogenous isoform II of Hev b 2 that exhibits three post-translational modifications, including an N-terminal pyroglutamate and two glycosylation sites at Asn27 and at Asn314, is reported from two crystal polymorphs. These modifications form a patch on the surface of the molecule that is proposed to be one of the binding sites for IgE. A structure is also proposed for the most importantN-glycan present in this protein as determined by digestion with specific enzymes. To analyze the role of the carbohydrate moieties in IgE antibody binding and in human basophil activation, the glycoallergen was enzymatically deglycosylated and evaluated. Time-lapse automated video microscopy of basophils stimulated with glycosylated Hev b 2 revealed basophil activation and degranulation. Immunological studies suggested that carbohydrates on Hev b 2 represent an allergenic IgE epitope. In addition, a dimer was found in each asymmetric unit that may reflect a regulatory mechanism of this plant defence protein.
Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography
Authors: Bhardwaj Anshul , Casjens Sherwood R. , Cingolani Gino
Published: January 2014

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.
Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides
Authors: Abdur Rob , Gerlits Oksana O. , Gan Jianhua , Jiang Jiansheng , Salon Jozef , Kovalevsky Andrey Y. , Chumanevich Alexander A. , Weber Irene T. , Huang Zhen
Published: January 2014

The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteinsviaMAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.
A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex
Authors: Russo Krauss Irene , Parkinson Gary Nigel , Merlino Antonello , Mattia Carlo Andrea , Randazzo Antonio , Novellino Ettore , Mazzarella Lelio , Sica Filomena
Published: January 2014

Locked nucleic acids (LNAs) are formed by bicyclic ribonucleotides where the O2′ and C4′ atoms are linked through a methylene bridge and the sugar is blocked in a 3′-endoconformation. They represent a promising tool for therapeutic and diagnostic applications and are characterized by higher thermal stability and nuclease resistance with respect to their natural counterparts. However, structural descriptions of LNA-containing quadruplexes are rather limited, since few NMR models have been reported in the literature. Here, the first crystallographically derived model of an all-LNA-substituted quadruplex-forming sequence 5′-TGGGT-3′ is presented refined at 1.7 Å resolution. This high-resolution crystallographic analysis reveals a regular parallel G-quadruplex arrangement terminating in a well defined thymine tetrad at the 3′-end. The detailed picture of the hydration pattern reveals LNA-specific features in the solvent distribution. Interestingly, two closely packed quadruplexes are present in the asymmetric unit. They face one another with their 3′-ends giving rise to a compact higher-order structure. This new assembly suggests a possible way in which sequential quadruplexes can be disposed in the crowded cell environment. Furthermore, as the formation of ordered structures by molecular self-assembly is an effective strategy to obtain nanostructures, this study could open the way to the design of a new class of LNA-based building blocks for nanotechnology.
Small-angle scattering gives direct structural information about a membrane protein inside a lipid environment
Authors: Kynde Søren A. R. , Skar-Gislinge Nicholas , Pedersen Martin Cramer , Midtgaard Søren Roi , Simonsen Jens Baek , Schweins Ralf , Mortensen Kell , Arleth Lise
Published: January 2014

Monomeric bacteriorhodopsin (bR) reconstituted into POPC/POPG-containing nanodiscs was investigated by combined small-angle neutron and X-ray scattering. A novel hybrid approach to small-angle scattering data analysis was developed. In combination, these provided direct structural insight into membrane-protein localization in the nanodisc and into the protein–lipid interactions. It was found that bR is laterally decentred in the plane of the disc and is slightly tilted in the phospholipid bilayer. The thickness of the bilayer is reduced in response to the incorporation of bR. The observed tilt of bR is in good accordance with previously performed theoretical predictions and computer simulations based on the bR crystal structure. The result is a significant and essential step on the way to developing a general small-angle scattering-based method for determining the low-resolution structures of membrane proteins in physiologically relevant environments.
Structural and enzymatic characterization of a host-specificity determinant fromSalmonella
Authors: Kohler Amanda C. , Spanò Stefania , Galán Jorge E. , Stebbins C. Erec
Published: January 2014

GtgE is an effector protein fromSalmonellaTyphimurium that modulates trafficking of theSalmonella-containing vacuole. It exerts its function by cleaving the Rab-family GTPases Rab29, Rab32 and Rab38, thereby preventing the delivery of antimicrobial factors to the bacteria-containing vacuole. Here, the crystal structure of GtgE at 1.65 Å resolution is presented, and structure-based mutagenesis andin vivoinfection assays are used to identify its catalytic triad. A panel of cysteine protease inhibitors were examined and it was determined thatN-ethylmaleimide, antipain and chymostatin inhibit GtgE activityin vitro. These findings provide the basis for the development of novel therapeutic strategies to combatSalmonellainfections.
Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002
Authors: Parker Lorien J. , Taruya Shigenao , Tsuganezawa Keiko , Ogawa Naoko , Mikuni Junko , Honda Keiko , Tomabechi Yuri , Handa Noriko , Shirouzu Mikako , Yokoyama Shigeyuki , Tanaka Akiko
Published: January 2014

The small kinase inhibitor SKF86002 lacks intrinsic fluorescence but becomes fluorescent upon binding to the ATP-binding sites of p38 mitogen-activated protein kinase (p38α). It was found that co-crystals of this compound with various kinases were distinguishable by their strong fluorescence. The co-crystals of SKF86002 with p38α, Pim1, ASK1, HCK and AMPK were fluorescent. Addition of SKF86002, which binds to the ATP site, to the co-crystallization solution of HCK promoted protein stability and thus facilitated the production of crystals that otherwise would not grow in the apo form. It was further demonstrated that the fluorescence of SKF86002 co-crystals can be applied to screen for candidate kinase inhibitors. When a compound binds competitively to the ATP-binding site of a kinase crystallized with SKF86002, it displaces the fluorescent SKF86002 and the crystal loses its fluorescence. Lower fluorescent signals were reported after soaking SKF86002–Pim1 and SKF86002–HCK co-crystals with the inhibitors quercetin, a quinazoline derivative and A-419259. Determination of the SKF86002–Pim1 and SKF86002–HCK co-crystal structures confirmed that SKF86002 interacts with the ATP-binding sites of Pim1 and HCK. The structures of Pim1–SKF86002 crystals soaked with the inhibitors quercetin and a quinazoline derivative and of HCK–SKF86002 crystals soaked with A-419259 were determined. These structures were virtually identical to the deposited crystal structures of the same complexes. A KINOMEscanassay revealed that SKF86002 binds a wide variety of kinases. Thus, for a broad range of kinases, SKF86002 is useful as a crystal marker, a crystal stabilizer and a marker to identify ligand co-crystals for structural analysis.
Factors correlating with significant differences between X-ray structures of myoglobin
Authors: Rashin Alexander A. , Domagalski Marcin J. , Zimmermann Michael T. , Minor Wladek , Chruszcz Maksymilian , Jernigan Robert L.
Published: January 2014

Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horse and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are very similar to the cluster of horse structures, which all have a similar GH-loop distortion apparently owing to intermolecular crystal lattice hydrogen bonds to the GH loop from residues near the distal histidine His64. The variations of the GH-loop coordinates in the whale structures are likely to be owing to the observed alternative intermolecular crystal lattice bond, with the change to the GH loop distorting bonds correlated with the binding of specific `unusual' ligands. Such an alternative intermolecular bond is not observed in horse myoglobins, obliterating any correlation with the ligands. Intermolecular bonds do not usually cause significant coordinate differences and cannot be validated as their universal cause. Most of the native-like whale myoglobin structure outliers can be correlated with a few specific factors. However, these factors do not always lead to coordinate differences beyond the previously determined uncertainty thresholds. The binding of unusual ligands by myoglobin, leading to crystal-induced distortions, suggests that some of the conformational differences between the apo and holo structures might not be `functionally important' but rather artifacts caused by the binding of `unusual' substrate analogs. The causes ofP6 symmetry in myoglobin crystals and the relationship between crystal and solution structures are also discussed.
Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant
Authors: Munshi Parthapratim , Snell Edward H. , van der Woerd Mark J. , Judge Russell A. , Myles Dean A. A. , Ren Zhong , Meilleur Flora
Published: January 2014

Ketol-isomerases catalyze the reversible isomerization between aldoses and ketoses. D-Xylose isomerase carries out the first reaction in the catabolism of D-xylose, but is also able to convert D-glucose to D-fructose. The first step of the reaction is an enzyme-catalyzed ring opening of the cyclic substrate. The active-site amino-acid acid/base pair involved in ring opening has long been investigated and several models have been proposed. Here, the structure of the xylose isomerase E186Q mutant with cyclic glucose bound at the active site, refined against joint X-ray and neutron diffraction data, is reported. Detailed analysis of the hydrogen-bond networks at the active site of the enzyme suggests that His54, which is doubly protonated, is poised to protonate the glucose O5 position, while Lys289, which is neutral, promotes deprotonation of the glucose O1H hydroxyl groupviaan activated water molecule. The structure also reveals an extended hydrogen-bonding network that connects the conserved residues Lys289 and Lys183 through three structurally conserved water molecules and residue 186, which is a glutamic acid to glutamine mutation.
Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors
Authors: Pachl Petr , Fábry Milan , Rosenberg Ivan , Šimák Ondřej , Řezáčová Pavlína , Brynda Jiří
Published: January 2014

The human 5′(3′)-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08 Å) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4 Å) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.
Flupentixol tartrate
Authors: Yamuna Thammarse S. , Kaur Manpreet , Anderson Brian J. , Jasinski Jerry P. , Yathirajan H.S.
Published: January 2014

In the title salt, C23H26F3N2OS+·C4H5O6−[systematic name: 1-(2-hydroxyethyl)-4-[3-(2-(trifluoromethyl)thioxanthen-9-ylidene)propyl]piperazin-1-ium 3-carboxy-2,3-dihydroxypropionate], the monoprotonated piperazine ring in the cation adopts a chair conformation, while the thiopyran ring of the thioxanthene group has a boat conformation. The dihedral angle between the mean planes of the two outer aromatic rings of the thioxanthene groups is 31.6 (2)°. In the crystal, the cations and anions are linkedviaO—H...O, N—H...O, O—H...N and C—H...O hydrogen bonds, forming chains propagating along [100]. In addition,R22(7),R22(11),R22(10) andR22(12) graph-set ring motifs involving the anions, andR22(9) graph-set ring motifs involving both the cations and anions are observed. The three F atoms of the trifluoromethyl group are disordered over two sets of sites and the individual atoms were refined with occupancy ratios of 0.54 (6):0.46 (6), 0.72 (2):0.28 (2) and 0.67 (3):0.33 (3).
Ethyl (4-{[(diethylcarbamothioyl)sulfanyl]methyl}-2-oxo-2H-chromen-7-yl)carbamate
Authors: Roopashree K. R. , Kumar K. Mahesh , Anitha B. R. , Ravi A. J. , Devarajegowda H. C.
Published: January 2014

In the title compound, C18H22N2O4S2, the 2H-chromene ring system is essentially planar (r.m.s. deviation = 0.012 Å). The molecular conformation is stabilized by a C—H...O hydrogen bond. In the crystal, N—H...S and C—H...O hydrogen bonds occur, the former enclosing anR22(22) ring motif, and lead to the formation of a two-dimensional slab-like network lying parallel to (10-1). π–π interactions are observed between inversion-related aromatic rings [shortest centroid–centroid distance = 3.6300 (11) Å].
N-Ethyl-2,2-dimethyl-N-(3-methylphenyl)propanamide
Authors: Palakshamurthy B. S. , Suchetan P. A. , Sreenivasa S , Lokanath N. K. , Madhu Chakrapani Rao T
Published: January 2014

In the title compound, C14H21NO, the conformation across the N—C(O) bond issyn-periplanar, the C—N—C—C torsion being −5.9 (5)°. The atoms of the ethyl group attached to the N atom are disordered over two sets of sites with occupancy ratios of 0.65 (2):0.35 (2) (CH2) and 0.689 (14):0.311 (14) (CH3)are linked by very weak C—H...O interactions formingC(8) chains along [001]. C—H...π interactions link the molecules along thec-axis direction.
GSTA1*‐69C/T and GSTO2*N142D as asthma‐ and allergy‐related risk factors in Italian adult patients
Authors: Piacentini Sara , Polimanti Renato , Iorio Andrea , Cortesi Maurizio , Papa Fabrizio , Rongioletti Mauro , Liumbruno Giancarlo M. , Manfellotto Dario , Fuciarelli Maria
Published: January 2014

Asthma and allergies are characterized by variable and subjective symptoms influenced by many genes, molecular mechanisms and environmental factors. The presence of inflammation and oxidative stress in the airways are important biochemical features of asthma and respiratory allergies. Glutathione S‐transferase (GSTs) enzymes play an important role in cellular protection against inflammation, and functional genetic polymorphisms in GST genes show a significant association with asthma and allergy risk. Specifically, our previous study on asthmatic children highlighted GSTA1 and GSTO2 as novel susceptibility loci for asthma.

In the present study we focused our attention on GSTA1*‐69C/T (rs3957357) and GSTO2*N142D (rs156697) polymorphisms to confirm our previous results in an independent adult study population and to clarify whether GSTA1 and GSTO2 gene polymorphisms are involved in a non‐discriminative pathway towards asthma and respiratory allergy.

To accomplish this, we recruited 103 patients with respiratory allergies, 199 patients with asthma and 200 healthy controls. Genomic DNA extracted from buccal cells was screened for GSTA1*‐69C/T and GSTO2*N142D single nucleotide polymorphisms.

The GSTA1*‐69T and GSTO2*D142 variants are both associated with a significantly increased risk of asthma, whereas only GSTA1*‐69C/T is significantly associated with allergies. These outcomes confirm the involvement of GSTO2 loci in asthma and suggest that GSTA1 is a common risk factor for asthma and allergies.
Association of inflammation, myocardial fibrosis and cardiac remodelling in patients with mild aortic stenosis as assessed by biomarkers and echocardiography
Authors: Park Ji Young , Ryu Sung Kee , Choi Jae Woong , Kim Min Ho , Jun Jin Hyun , Rha Seung‐Woon , Park Seong‐Mi , Kim Hyo Jeong , Choi Byoung Geol , Noh Yung‐Kyun , Kim Seunghwan
Published: January 2014

The aim of the present study was to investigate the relationships of inflammation, myocardial fibrosis and cardiac remodelling in patients with mild aortic stenosis (AS), as assessed by biomarkers and echocardiography.

We consecutively evaluated 32 patients with mild AS, as well as 30 age‐ and gender‐matched healthy individuals with normal aortic valves as control subjects.

Baseline echocardiography showed that the left ventricular (LV) mass index (111.3 ± 26.9 vs 94.5 ± 18.2 g/m2; P = 0.006) and left atrial (LA) volume index (LAVI 27.5 ± 9.0 vs 21.9 ± 5.2 mm3/mm2; P = 0.005) were significantly higher in patients with mild AS.

Furthermore, LA enlargement (LAVI > 33 mm3/mm2; 32.4% vs 3.3%;P = 0.003) and elevated LV filling pressure (E/e′ > 15; 50.0% vs 23.3%; P = 0.036) were higher in patients with mild AS.

In patients with mild AS, stepwise, multivariate linear regression analysis revealed that the LV end‐diastolic volume index was independently associated with matrix metalloproteinase (MMP)‐1 (β = 0.371; P = 0.015), that the aortic valve mean pressure gradient was independently associated with MMP‐2 (β = 0.19; P = 0.019), that MMP‐2 was independently associated with transforming growth factor‐β (β = 0.95; P < 0.001) and interleukin (IL)‐1 (β = 0.17; P = 0.019) and that IL‐1 was independently associated with tissue inhibitor of matrix metalloproteinase‐1 (β = 0.68; P = 0.001).

Myocardial fibrosis in mild AS is independently associated with three factors: LV volume overload, aortic valve pressure overload and inflammation.
Enalapril attenuates ischaemic brain oedema and protects the blood–brain barrier in rats via an anti‐oxidant action
Authors: Panahpour Hamdollah , Dehghani Gholam Abbas , Bohlooli Shahab
Published: January 2014

In the present study, we investigated the effects of postischaemic angiotensin‐converting enzyme (ACE) inhibition with enalapril on vasogenic oedema formation and blood–brain barrier (BBB) integrity following transient focal cerebral ischaemia in rats.

Cerebral ischaemia was induced by 60 min occlusion of the right middle cerebral artery, followed by 24 h reperfusion. Vehicle and a non‐hypotensive dose of enalapril (0.03 mg/kg) were administered at the beginning of the reperfusion period. A neurological deficit score (NDS) was determined for all rats at the end of the reperfusion period. Then, brain oedema formation was investigated using the wet–dry weight method and BBB permeability was evaluated on the basis of extravasation of Evans blue (EB) dye. In addition, oxidative stress was assessed by measuring reduced glutathione (GSH) and malondialdehyde (MDA) in brain homogenates.

Inhibition of ACE by enalapril significantly reduced NDS and decreased brain oedema formation (P < 0.05 for both). Disruption of the BBB following ischaemia resulted in considerable leakage of EB dye into the brain parenchyma of the ipsilateral hemispheres of vehicle‐treated rats. Enalapril significantly (P < 0.05) decreased EB extravasation into the lesioned hemisphere. Enalapril also augmented anti‐oxidant activity in ischaemic brain tissue by increasing GSH concentrations and significantly (P < 0.05) attenuating the increased MDA levels in response to ischaemia.

In conclusion, inhibition of ACE with a non‐hypotensive dose of enalapril may protect BBB function and attenuate oedema formation via anti‐oxidant actions.
Degradation of oxalic acid by the mycoparasite Coniothyrium minitans plays an important role in interacting with Sclerotinia sclerotiorum
Authors: Zeng Li‐Mei , Zhang Jing , Han Yong‐Chao , Yang Long , Wu Ming‐de , Jiang Dao‐Hong , Chen Weidong , Li Guo‐Qing
Published: January 2014

Coniothyrium minitans (Cm) is a mycoparasite of the phytopathogenic fungus Sclerotinia sclerotiorum (Ss). Ss produces a virulence factor oxalic acid (OA) which is toxic to plants and also to Cm, and Cm detoxifies OA by degradation. In this study, two oxalate decarboxylase genes, Cmoxdc1 and Cmoxdc2, were cloned from Cm strain Chy‐1. OA and low pH induced expression of Cmoxdc1, but not Cmoxdc2. Cmoxdc1 was partially responsible for OA degradation, whereas Cmoxdc2 had no effect on OA degradation. Disruption of Cmoxdc1 in Cm reduced its ability to infect Ss in dual cultures where OA accumulated. Compared with Chy‐1, the Cmoxdc1‐disrupted mutants had reduced expression levels of two mycoparasitism‐related genes chitinase (Cmch1) and β‐1,3‐glucanase (Cmg1), and had no detectable activity of extracellular proteases in the presence of OA. On the other hand, the cultural filtrates of the Cmoxdc1‐disrupted mutants in OA‐amended media showed enhanced antifungal activity, possibly because of increased production of antifungal substances under acidic pH condition resulted from reduced Cmoxdc1‐mediated OA degradation. This study provides direct genetic evidence of OA degradation regulating mycoparasitism and antibiosis of Cm against Ss, and sheds light on the sophisticated strategies of Cm in interacting with metabolically active mycelia and dormant sclerotia of Ss.
Microbial consumption of zero‐valence sulfur in marine benthic habitats
Authors: Pjevac Petra , Kamyshny Alexey , Dyksma Stefan , Mußmann Marc
Published: January 2014

Zero‐valence sulfur (S0) is a central intermediate in the marine sulfur cycle and forms conspicuous accumulations at sediment surfaces, hydrothermal vents and in oxygen minimum zones. Diverse microorganisms can utilize S0, but those consuming S0 in the environment are largely unknown. We identified possible key players in S0 turnover on native or introduced S0 in benthic coastal and deep‐sea habitats using the 16S ribosomal RNA approach, (in situ) growth experiments and activity measurements. In all habitats, the epsilonproteobacterial Sulfurimonas/Sulfurovum group accounted for a substantial fraction of the microbial community. Deltaproteobacterial Desulfobulbaceae and Desulfuromonadales were also frequently detected, indicating S0 disproportionation and S0 respiration under anoxic conditions. Sulfate production from S0 particles colonized in situ with Sulfurimonas/Sulfurovum suggested that this group oxidized S0. We also show that the type strain Sulfurimonas denitrificans is able to access cyclooctasulfur (S8), a metabolic feature not yet demonstrated for sulfur oxidizers. The ability to oxidize S0, in particular S8, likely facilitates niche partitioning among sulfur oxidizers in habitats with intense microbial sulfur cycling such as sulfidic sediment surfaces. Our results underscore the previously overlooked but central role of Sulfurimonas/Sulfurovum group for conversion of free S0 at the seafloor surface.
Systems‐level analysis of the metabolic responses of the diatom Phaeodactylum tricornutum to phosphorus stress
Authors: Yang Zhi‐Kai , Zheng Jian‐Wei , Niu Ying‐Fang , Yang Wei‐Dong , Liu Jie‐Sheng , Li Hong‐Ye
Published: January 2014

Phosphorus is an important macronutrient. To understand the molecular and cellular responses to phosphorus stress better, transcriptome profiling in combination with biochemical investigations was conducted in the model diatom Phaeodactylum tricornutum. Out of 10 402 predicted genes, 2491 and 405 genes were significantly upregulated or downregulated respectively. Unsurprisingly, genes associated with phosphate uptake were upregulated, such as the phosphate transporters and alkaline phosphatases. Genes encoding stress‐shock proteins were accordingly upregulated, including genes associated with stress‐responsive proteins, signal transduction and secondary metabolism. Additionally, genes related to protein translation, carbon fixation, glycolysis and the citric acid cycle were also upregulated. Genes associated with gene transcription were downregulated, thereby resulting in the upregulation of translation to compensate for the limited supply of messenger RNA. The downregulation of genes related to β‐oxidation could contribute to the accumulation of fatty acids. Accordingly, triacylglycerols, which are important for energy storage, were determined to increase by 1.65‐fold. Intracellular membranes, other than chloroplast membranes, tended to be dispersed; this finding was in accordance with the increased transcription of a total of 11 genes encoding putative phospholipases. Taken together, this work revealed the coordination of multiple metabolic pathways and certain key genes in the adaptation of P. tricornutum to phosphorus stress.
Finding a middle ground: Conservation challenges among stakeholders in coastal Tanzania (Respond to this article at http://www.therai.org.uk/at/debate)
Authors: Naar Nicole , Mahenge Jairos
Published: January 2014

Recently, evictions associated with climate change mitigation in the Rufiji Delta of Tanzania sparked intense debate about the ethics of coastal conservation between academics, NGOs (non‐governmental organizations) and government officials working in the region. Some actors argue that environmental change is a myth used to wrest control of natural resources from local communities, while others point to the urgency of environmental protection and action on climate change. Insights gleaned from interviews with multiple government officials, NGO employees, academics, and coastal village residents in Pangani, however, reveal a more complex and perhaps less contentious situation in coastal Tanzania. Although they often proffered different solutions, different stakeholder groups articulated the same key challenges in nuanced ways that shed a more hopeful light on currently heated conservation and development issues.
The Research–Teaching Nexus in Politics and International Relations in the UK: A Survey of Practices and Attitudes
Authors: Lightfoot Simon , Piotukh Volha
Published: January 2014

This article discusses the results of a small-N survey of established academic staff within the discipline of politics and international relations and how they view research–teaching links. It reveals that even among this small group there are very different views as to the relationship between teaching and research. The article argues that more work is needed to produce a fuller understanding of the nexus across the discipline and that research needs to be integrated at all levels of undergraduate study. Fundamentally, we need to make the link explicit to both students and other stakeholders to ensure that the nexus remains viable in the future.
Political Party Supporters' Attitudes towards and Involvement with Green Issues in Britain
Authors: Clements Ben
Published: January 2014

Recent developments in British politics have seen green issues become a settled part of the policy agenda, with the Conservative-Liberal Democrat coalition pledging to be the ‘greenest government ever’. Despite this party political consensus, there has been little recent analysis of attitudes towards green issues among party supporters. Are Conservative supporters less likely to be ‘green-minded’, in spite of recent efforts to improve the party's image on the environment as part of a wider modernisation strategy? This article provides a detailed assessment using a new nationally representative survey of public opinion on green issues. Based on a wide-ranging analysis of attitudes and behaviour, the findings show that Conservative supporters and those with right-wing policy preferences are less green-minded. Liberal Democrat supporters are the most consistently environmentally friendly in their beliefs and behaviour.
A Comparison of Progressive Be V‐Ing With Be In The Middle, Midst, Process or Act Of V‐Ing: The Interaction Of Lexical And Grammatical Progressive Aspect
Authors: Van Rompaey Tinne
Published: January 2014

This article presents a semantic‐pragmatic analysis and comparison of the be V‐ing construction and the emergent progressive aspect markers (PAM) be in the middle, midst, process or act of V‐ing. On the basis of data from the Corpus of Contemporary American English, I first argue that the PAMs be in the middle, midst, process or act of V‐ing show striking similarities with semi‐auxiliary be V‐ing. Both progressive constructions pattern with the same range of predicate classes, namely predominantly atelic actions and telic accomplishments. Not only is there overlap in their lexical‐collocational preferences, the emergent PAMs and be V‐ing also impose the same grammatical reading on the sentence: they represent or “actualize” the situations expressed by the following V‐ing as unbounded and durative, regardless of whether these aspectual properties are already inherent in the predicates or not. Second, I address the question in which respect the emergence of the be in NP of V‐ing aspectualizer construction causes reorganization within the paradigm of progressive aspect. The difference between be V‐ing and the PAMs lies in the expanded uses of the former and the specialization of the latter into expressions of continuousness, with the exception of be in the process of V‐ing. This particular construction seems to have developed into an aspectual marker of imminence, meaning that it refers to the preparatory phase leading up to the action. In most instances of be in the middle, midst and act of V‐ing, however, the PAMs indicate that a situation is taking place without interruption at the temporal zero point. Be V‐ing does not really display this preference for continuousness, as it takes on as often other shades of progressivity, for instance implied iterativity or habituality, and non‐aspectual functions such as prospectivity and subjective meanings. I claim that it is exactly this functional indeterminacy of the be V‐ing form that probably triggered the development of the PAM as a construction reinforcing one specific feature of progressivity, namely pure continuousness.
Extraction of Anthocyanins from Black Bean Canning Wastewater with Macroporous Resins
Authors: Wang Xiaoxi , Hansen Conly , Allen Karin
Published: January 2014

This study investigated purification of anthocyanins from black bean canning wastewater by column chromatography with 5 types of macroporous resins (Diaion Hp20, Sepabeads Sp70, Sepabeads Sp207, Sepabeads Sp700, and Sepabeads Sp710). By‐product of canned black beans was partially purified by filtration, in anticipation of higher performance during column chromatography. Equilibrium adsorption isotherms were measured and analyzed using Langmuir and Freundlich isotherm models. Both Langmuir (all R2 ≥ 0.98) and Freundlich (all R2 ≥ 0.97) models can describe the adsorption process of anthocyanins from black bean canning wastewater using the tested resins. The adsorption and desorption behaviors of anthocyanins were studied using a dynamic method on the 5 types of resins, and Sp700 presented the highest adsorption capacity (39 ± 4 mg/g; P < 0.05) as well as desorption capacity (19 ± 2%; P < 0.05), indicating that of the resins examined, Sp700 is a better candidate for purification of anthocyanins from black bean canning wastewater.
Potential for plant growth promotion by a consortium of stress‐tolerant 2,4‐dinitrotoluene‐degrading bacteria: isolation and characterization of a military soil
Authors: Thijs Sofie , Weyens Nele , Sillen Wouter , Gkorezis Panagiotis , Carleer Robert , Vangronsveld Jaco
Published: January 2014

The presence of explosives in soils and the interaction with drought stress and nutrient limitation are among the environmental factors that severely affect plant growth on military soils. In this study, we seek to isolate and identify the cultivable bacteria of a 2,4‐dinitrotoluene (DNT) contaminated soil (DS) and an adjacent grassland soil (GS) of a military training area aiming to isolate new plant growth‐promoting (PGP) and 2,4‐DNT‐degrading strains. Metabolic profiling revealed disturbances in Ecocarbon use in the bare DS; isolation of cultivable strains revealed a lower colony‐forming‐unit count and a less diverse community associated with DS in comparison with GS. New 2,4‐DNT‐tolerant strains were identified by selective enrichments, which were further characterized by auxanography for 2,4‐DNT use, resistance to drought stress, cold, nutrient starvation and PGP features. By selecting multiple beneficial PGP and abiotic stress‐resistant strains, efficient 2,4‐DNT‐degrading consortia were composed. After inoculation, consortium UHasselt Sofie 3 with seven members belonging to Burkholderia, Variovorax, Bacillus, Pseudomonas and Ralstonia species was capable to successfully enhance root length of Arabidopsis under 2,4‐DNT stress. After 9 days, doubling of main root length was observed. Our results indicate that beneficial bacteria inhabiting a disturbed environment have the potential to improve plant growth and alleviate 2,4‐DNT stress.
The potential role of angiogenic factors in rheumatoid arthritis
Authors: Azizi Gholamreza , Boghozian Roobina , Mirshafiey Abbas
Published: January 2014

Angiogenesis is an important phenomenon in the pathogenesis of some diseases, such as numerous types of tumors and autoimmunity, and also a number of soluble and cell‐bound factors may stimulate neovascularization in inflammatory reaction processes. Here, by highlighting the significance of angiogenesis reaction in rheumatoid arthritis (RA), we will mainly focus on the role of various growth factors, cytokines, enzymes, cells, hypoxic conditions and transcription factors in the angiogenic process and we will then explain some therapeutic strategies based on blockage of angiogenesis and modification of the vascular pathology in RA.
99Tc‐methylene diphosphonate improves rheumatoid arthritis disease activity by increasing the frequency of peripheral γδ T cells and CD4+CD25+Foxp3+Tregs
Authors: Su Dinglei , Shen Minning , Gu Bingjie , Wang Xiaoqin , Wang Dandan , Li Xia , Sun Lingyun
Published: January 2014

Aim

γδ T cells exhibit important functions in the pathogenesis of rheumatoid arthritis (RA). In recent years, numerous studies harnessed the γδ T cell‐activating capacity of aminobiphosphonates for the treatment of malignant tumors. As 99Tc‐methylene diphosphonate (99Tc‐MDP) has long been widely used for the treatment of RA in China with good efficacy, we are interested in whether this drug exerts its therapeutic effect on RA by modulating peripheral γδ T cells of RA patients.

Objectives

To investigate the effect of 99Tc‐MDP on the frequency of γδ T cells and CD4+CD25+Foxp3+Tregs in the peripheral blood of patients with active RA.

Methods

Nineteen patients with active RA were treated with 99Tc‐MDP intravenously at a dose of 20 μg/day consecutively for 10–14 days. Before and after treatment, the main clinical and laboratory parameters for each patient were evaluated. The frequency of CD3+γδ+T cells and CD4+CD25+Foxp3+Tregs was detected by flow cytometry. Serum levels of interferon (IFN)‐γ, tumor necrosis factor (TNF)‐α, interleukin (IL)‐6, IL‐10 and transforming growth factor (TGF)‐β were measured with enzyme‐linked immunosorbent assay.

Results

After intravenous 99Tc‐MDP therapy, the frequency of peripheral CD3+γδ+T cells and CD4+CD25+Foxp3+Tregs were significantly elevated, paralleled with decreased serum levels of TNF‐α and IL‐6 and increased level of serum TGF‐β. The elevation of peripheral CD3+γδ+T cells was positively correlated with increased serum TGF‐β and decreased disease activity.

Conclusion

99Tc‐MDP may improve the activity of RA through upregulating the frequency of peripheral γδ T cells and CD4+CD25+Foxp3+Tregs as well as affecting the serum cytokine environment by increasing TGF‐β and decreasing TNF‐α and IL‐6.
Anxiety and depression in adult patients with familial Mediterranean fever: a study comparing patients living in Germany and Turkey
Authors: Giese Arnd , Örnek Ahmet , Kilic Levent , Kurucay Mustafa , Şendur Süleyman N. , Lainka Elke , Henning Bernhard F.
Published: January 2014

Aim

To determine the prevalence of anxiety and depression among patients with familial Mediterranean fever (FMF) living in Germany or Turkey a prospective study was conducted.

Methods

Forty FMF patients living in Turkey (T), 40 FMF patients living in Germany (G) and 40 healthy controls living in Germany (C) were included. Patients and controls were of Turkish ancestry. G were compared to T and C. The Hospital Anxiety and Depression Scale (HADS) was used with a cut‐off of ≥ 8 for each subdomain score (HADS‐A, HADS‐D).

Results

Baseline characteristics of G were comparable to T and C except for age (T: 30.5 years, G: 35.2 years, C: 34.6 years; T vs. G P = 0.045), duration of disease (T: 14.4 years, G: 24; P < 0.001), C‐reactive protein (T: 0.78 mg/dL, G: 0.78 mg/dL, C: 0.35 mg/dL; G vs. C P = 0.03). Prevalence of anxiety was higher in G compared to C (T: 65%, G: 52.5%, C: 22.5%: G vs. C P < 0.05). No difference was found for the prevalence of depression (T: 30%, G: 35%, C: 20%). The association between FMF and anxiety in subjects living in Germany persisted after adjusting for age and gender in a regression analysis and was robust to an adjustment for coexisting depression. Anxiety and depression did not correlate with FMF disease severity assessed with the Pras score.

Conclusion

Anxiety, but not depression is more common among FMF patients living in Germany compared to healthy controls. No significant difference could be found between FMF patients living in Germany or Turkey concerning the prevalence of anxiety or depression.