bluuebunny/crossref_metadata_2025 huggingface dataset:
First Report of Fusarium Wilt of Strawberry Caused by Fusarium oxysporum in Serbia
Authors: Stanković I. , Ristić D. , Vučurović A. , Milojević K. , Nikolić D. , Krstić B. , Bulajić A.
Published: July 2014

Strawberry (Fragaria × ananassa Duch.) is the third most important berry crop in Serbia with average production ranging from 30,000 to 35,000 t on approximately 5,000 ha (2). In June 2013, symptoms of wilt and whole plant collapse were observed on approximately 25% plants growing in commercial strawberry crop of cv. Alba in the locality of Zablaće (Moravica district). Initial symptoms included leaf chlorosis and wilt, followed by withering and necrosis of older leaves and reduced fruit production, eventually leading to plant collapse and desiccations. Internal vascular tissues of the crown showed distinct brown reddish discoloration. Three small pieces of infected roots, petioles, or crown vascular tissues were surface disinfested with 2% NaOCl and placed on five potato dextrose agars (PDA) per sample. After 7 days incubation at 23°C under 12 h of fluorescent light, nine monoconidial isolates were obtained (1) forming colonies with light purple mycelia. Colonies produced numerous hyaline, oval to ellipsoid microconidia (5 to 15 × 2.5 to 4.5 μm, average 8.45 × 2.25 μm), 3 to 5 septate fusoid macroconidia with pedicellate bases (20 to 50 × 2.70 to 6 μm, average 32.35 × 3.25 μm from 100 measured) and chlamydospores. Morphological and growth features were similar to the descriptions of Fusarium oxysporum Schlechtend emend. Snyder & Hansen (1). Pathogenicity of one selected isolate (97-13) was tested by dipping for 15 min the roots of five plants of each cultivar: Alba, Arosa, Clery, and Roxana into a conidial suspension (1 × 106 conidia/ml) harvested from a 7-day-old culture on PDA. Control plants were dipped in sterile distilled water. The inoculated plants were transplanted into pots containing sterilized peat and maintained in the greenhouse at 25°C. Thirty to thirty-five days post-inoculation, all plants developed wilt symptoms and vascular discoloration of crown tissues from which F. oxysporum was successfully re-isolated using the same method as for isolation. No symptoms were observed on any of the control plants. Morphological identification was confirmed by amplification and sequencing of a portion of the translation elongation factor-1 alpha (EF-1α) gene. Total DNA was extracted directly from fungal mycelium with a DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) and PCR amplification performed with primers EF-1/EF-2 (4). Sequence analysis of EF-1α region revealed that Serbian isolate 97-13 (GenBank Accession No. KJ647280) shared 99 to 100% identity with the F. oxysporum sequences in GenBank. To our knowledge, this is the first report of Fusarium wilt on strawberry in Serbia. The presence of a new and potentially harmful disease may represent a serious constraint for strawberry production in Serbia.

References: (1) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual, Blackwell Publishing, London, UK, 2006. (2) M. Nikolić et al. Acta Hort. 842:615, 2009. (3) K. O'Donnell et al. Proc. Natl. Acad. Sci. USA 95:2044, 1998.
First Report of the Root-Knot Nematode Meloidogyne enterolobii Infecting Jujube in China
Authors: Long H. B. , Bai C. , Peng J. , Zeng F. Y.
Published: July 2014

Jujube (Ziziphus jujuba Mill.) is an economically-important fruit crop grown in Europe, Australia, and southern/eastern Asia. In China, it is often called red date and the fruit is used in traditional Chinese herbal medicine and wine. In February 2014, jujube plants growing in a sandy soil in Sanya, Hainan Province, China, were observed exhibiting symptoms of decline, including stunting, wilting, and no flowering or fruit set. Roots systems of sick plants (n = 20) had many galls, the typical symptoms of root-knot nematode infection, and the incidence of infection was 100%. These galls were formed in the primary, secondary, and tertiary roots. Meloidogyne spp. females and egg masses were dissected from the symptomatic roots. Each root contained about 72 females on average (n = 20). The perineal patterns of females (n = 10) were oval shaped with moderate to high dorsal arches and mostly lacking obvious lateral lines. Second-stage juveniles (n = 20) had large and triangular lateral lips and broad, bluntly rounded tail tips. These morphological characteristics are the same as those for Meloidogyne enterolobii Yang & Eisenback 1983 (5). Identification was further confirmed after DNA extraction from 12 nematodes. Part of the rDNA spanning the internal transcribed spacer (ITS) 1, 5.8S gene, and ITS2 was amplified with primers V5367/26S (TTGATTACGTCCCTGCCCTTT/TTTCACTCGCCGTTACTAAGG) (4). A 764-bp fragment was amplified, which was 100% identical to sequences of M. enterolobii (GenBank Accession Nos. KJ146863, KF418369, JQ082448, and JX024149) in GenBank. Species identification was confirmed by using PCR to amplify mitochondrial (mt) DNA and rDNA intergenic spacers (IGS) 2 with primers C2F3/1108 (GGTCAATGTTCAGAAATTTGTGG/TACCTTTGACCAATCACGCT) (3) and M. enterolobii specific primers Me-F/Me-R (AACTTTTGTGAAAGTGCCGCTG/TCAGTTCAGGCAGGATCAACC), respectively (2). The PCR products were approximately 700 bp for mtDNA and 200 bp for rDNA-IGS2, which were also identical to those previously reported for M. enterolobii (2,3). M. enterolobii is considered as one of the most damaging root-knot nematode species due to its wide host range, high reproduction rate, and ability to overcome the resistance genes (Mi-1, Mh, Mir1, N, Tabasco, and Rk) in several crops (1). It is reported that over 20 plant species from eight families (Annonaceae, Apiaceae, Cucurbitaceae, Convolvulaceae, Fabaceae, Marantaceae, Myrtaceae, and Solanaceae) in China are hosts for M. enterolobii. To our knowledge, this is the first report of jujube as a host of M. enterolobii and the first record of M. enterolobii as a parasite of a plant in the family Rhamnaceae in China.

References: (1) P. Castagnone-Sereno. Nematology 14:133, 2002. (2) H. Long et al. Acta Phytopathol. Sinica 36:109, 2006. (3) T. O. Powers and T. S. Harris. J. Nematol. 25:1, 1993. (4) T. C. Vrain et al. Fundam. Appl. Nematol. 15:565, 1992. (5) B. Yang and J. D. Eisenback. J. Nematol. 15:381, 1983.
Grafting Using Rootstocks with Resistance to Ralstonia solanacearum Against Meloidogyne incognita in Tomato Production
Authors: Kunwar Sanju , Paret Mathews L. , Olson Stephen M. , Ritchie Laura , Rich Jimmy R. , Freeman Josh , McAvoy Theodore
Published: July 2014

Root-knot nematodes (RKNs; Meloidogyne spp.) and Ralstonia solanacearum, the causal agent of bacterial wilt, are major soilborne pathogens in U.S. tomato production. Methyl bromide has been used for decades to effectively manage RKN but its phase-out and the high cost of other effective fumigants such as 1,3-dichloropropene has resulted in a need to develop sustainable alternatives. Many of the commercially popular varieties used by the tomato industry do not have resistance to RKNs and R. solanacearum. Recent studies worldwide have shown the potential for grafting using resistant rootstocks as a sustainable and ecofriendly practice for R. solanacearum management. However, the effectiveness of R. solanacearum-resistant rootstocks on RKN management is not known. In this study, three commercially available R. solanacearum-resistant tomato rootstocks (‘RST-04-106-T’, ‘BHN 998’, and ‘BHN 1054’) were evaluated for resistance to Meloidogyne incognita in field tomato production in four field trials conducted for two consecutive years in two geographical locations: Florida and Virginia. Grafting rootstocks onto ‘BHN 602’ a tomato scion susceptible to bacterial wilt and RKNs, significantly reduced root galling caused by RKNs in all four field trials and increased yield in two of the trials compared with the nongrafted treatment. This study demonstrates the potential of grafting for managing multiple soilborne pathogens using the same rootstocks.
Leaf Gas Exchange and ChlorophyllaFluorescence in Maize Leaves Infected withStenocarpella macrospora
Authors: Bermúdez-Cardona Maria Bianney , Filho João Américo Wordell , Rodrigues Fabrício Ávila
Published: July 2014

This study investigated the effect of macrospora leaf spot (MLS), caused by Stenocarpella macrospora, on photosynthetic gas exchange parameters and chlorophyll a fluorescence parameters determined in leaves of plants from two maize cultivars (‘ECVSCS155’ and ‘HIB 32R48H’) susceptible and highly susceptible, respectively, to S. macrospora. MLS severity was significantly lower in the leaves of plants from ECVSCS155 relative to the leaves of plants from HIB 32R48H. In both cultivars, net CO2assimilation rate, stomatal conductance, and transpiration rate significantly decreased, while the internal to ambient CO2concentration ratio increased in inoculated plants relative to noninoculated plants. The initial fluorescence and nonphotochemical quenching significantly increased in inoculated plants of ECVSCS155 and HIB 32R48H, respectively, relative to noninoculated plants. The maximum fluorescence, maximum PSII quantum efficiency, coefficient for photochemical quenching, and electron transport rate significantly decreased in inoculated plants relative to noninoculated plants. For both cultivars, concentrations of total chlorophyll (Chl) (a + b) and carotenoids and the Chl a/b ratio significantly decreased in inoculated plants relative to noninoculated plants. In conclusion, the results from the present study demonstrate, for the first time, that photosynthesis in the leaves of maize plants is dramatically affected during the infection process of S. macrospora, and impacts are primarily associated with limitations of a diffusive and biochemical nature.
Clinical Assessment of Auto-positive End-expiratory Pressure by Diaphragmatic Electrical Activity during Pressure Support and Neurally Adjusted Ventilatory Assist
Authors: Bellani Giacomo , Coppadoro Andrea , Patroniti Nicolò , Turella Marta , Arrigoni Marocco Stefano , Grasselli Giacomo , Mauri Tommaso , Pesenti Antonio
Published: July 2014

Background:

Auto-positive end-expiratory pressure (auto-PEEP) may substantially increase the inspiratory effort during assisted mechanical ventilation. Purpose of this study was to assess whether the electrical activity of the diaphragm (EAdi) signal can be reliably used to estimate auto-PEEP in patients undergoing pressure support ventilation and neurally adjusted ventilatory assist (NAVA) and whether NAVA was beneficial in comparison with pressure support ventilation in patients affected by auto-PEEP.

Methods:

In 10 patients with a clinical suspicion of auto-PEEP, the authors simultaneously recorded EAdi, airway, esophageal pressure, and flow during pressure support and NAVA, whereas external PEEP was increased from 2 to 14 cm H2O. Tracings were analyzed to measure apparent “dynamic” auto-PEEP (decrease in esophageal pressure to generate inspiratory flow), auto-EAdi (EAdi value at the onset of inspiratory flow), and IDEAdi (inspiratory delay between the onset of EAdi and the inspiratory flow).

Results:

The pressure necessary to overcome auto-PEEP, auto-EAdi, and IDEAdi was significantly lower in NAVA as compared with pressure support ventilation, decreased with increase in external PEEP, although the effect of external PEEP was less pronounced in NAVA. Both auto-EAdi and IDEAdi were tightly correlated with auto-PEEP (r
2 = 0.94 and r
2 = 0.75, respectively). In the presence of auto-PEEP at lower external PEEP levels, NAVA was characterized by a characteristic shape of the airway pressure.

Conclusions:

In patients with auto-PEEP, NAVA, compared with pressure support ventilation, led to a decrease in the pressure necessary to overcome auto-PEEP, which could be reliably monitored by the electrical activity of the diaphragm before inspiratory flow onset (auto-EAdi).
Effect of Hydroxyethyl Starch on Postoperative Kidney Function in Patients Having Noncardiac Surgery
Authors: Kashy Babak Kateby , Podolyak Attila , Makarova Natalya , Dalton Jarrod E. , Sessler Daniel I. , Kurz Andrea
Published: July 2014

Background:

Whether intraoperative use of hydroxyethyl starch impairs kidney function remains unknown. The authors thus tested the primary hypothesis that Hextend promotes renal injury in surgical patients. Secondarily, the authors evaluated the dose–outcome relationship, in-hospital and 90-day mortality, and whether the relationship between colloid use and acute kidney injury (AKI) depends on baseline risk for AKI.

Methods:

The authors evaluated the data of 44,176 adults without preexisting kidney failure who had inpatient noncardiac surgery from 2005 to 2012. Patients given a combination of colloid and crystalloid were propensity matched on morphometric, and baseline characteristics to patients given only crystalloid. The primary analysis was a proportional odds logistic regression with AKI as an ordinal outcome based on the Acute Kidney Injury Network classification.

Results:

The authors matched 14,680 patients receiving colloids with 14,680 patients receiving noncolloids for a total of 29,360 patients. After controlling for potential confounding variables, the odds of developing a more serious level of AKI with Hextend was 21% (6 to 38%) greater than with crystalloid only (P = 0.001). AKI risk increased as a function of colloid volume (P < 0.001). In contrast, the relationship between colloid use and AKI did not differ on baseline AKI risk (P = 0.84). There was no association between colloid use and risk of in-hospital (P = 0.81) or 90-day (P = 0.02) mortality.

Conclusion:

Dose-dependent renal toxicity associated with Hextend in patients having noncardiac surgery is consistent with randomized trials in critical care patients.
Lessons from yeast: the spindle pole body and the centrosome
Authors: Kilmartin John V.
Published: July 2014

The yeast spindle pole body (SPB) is the functional equivalent of the centrosome. Most SPB components have been identified and their functions partly established. This involved a large variety of techniques which are described here, and the potential use of some of these in the centrosome field is highlighted. In particular, very useful structural information on the SPB was obtained from a reconstituted complex, the γ-tubulin complex, and also from a sub-particle, SPB cores, prepared by extraction of an enriched SPB preparation. The labelling of SPB proteins with GFP at the N or C termini, using GFP tags inserted into the genome, gave informative electron microscopy localization and fluorescence resonance energy transfer data. Examples are given of more precise functional data obtained by removing domains from one SPB protein, Spc110p, without affecting its essential function. Finally, a structural model for SPB duplication is described and the differences between SPB and centrosome duplication discussed.
Centriole structure
Authors: Winey Mark , O'Toole Eileen
Published: July 2014

Centrioles are among the largest protein-based structures found in most cell types, measuring approximately 250 nm in diameter and approximately 500 nm long in vertebrate cells. Here, we briefly review ultrastructural observations about centrioles and associated structures. At the core of most centrioles is a microtubule scaffold formed from a radial array of nine triplet microtubules. Beyond the microtubule triplets of the centriole, we discuss the critically important cartwheel structure and the more enigmatic luminal density, both found on the inside of the centriole. Finally, we discuss the connectors between centrioles, and the distal and subdistal appendages outside of the microtubule scaffold that reflect centriole age and impart special functions to the centriole. Most of the work we review has been done with electron microscopy or electron tomography of resin-embedded samples, but we also highlight recent work performed with cryoelectron microscopy, cryotomography and subvolume averaging. Significant opportunities remain in the description of centriolar structure, both in mapping of component proteins within the structure and in determining the effect of mutations on components that contribute to the structure and function of the centriole.
Cartwheel assembly
Authors: Hirono Masafumi
Published: July 2014

The cartwheel is a subcentriolar structure consisting of a central hub and nine radially arranged spokes, located at the proximal end of the centriole. It appears at the initial stage of the centriole assembly process as the first ninefold symmetrical structure. The cartwheel was first described more than 50 years ago, but it is only recently that its pivotal role in establishing the ninefold symmetry of the centriole was demonstrated. Significant progress has since been made in understanding its fine structure and assembly mechanism. Most importantly, the central part of the cartwheel, from which the ninefold symmetry originates, is shown to form by self-association of nine dimers of the protein SAS-6. This finding, together with emerging data on other components of the cartwheel, has opened new avenues in centrosome biology.
Separate to operate: control of centrosome positioning and separation
Authors: Agircan Fikret G. , Schiebel Elmar , Mardin Balca R.
Published: July 2014

The centrosome is the main microtubule (MT)-organizing centre of animal cells. It consists of two centrioles and a multi-layered proteinaceous structure that surrounds the centrioles, the so-called pericentriolar material. Centrosomes promote de novo assembly of MTs and thus play important roles in Golgi organization, cell polarity, cell motility and the organization of the mitotic spindle. To execute these functions, centrosomes have to adopt particular cellular positions. Actin and MT networks and the association of the centrosomes to the nuclear envelope define the correct positioning of the centrosomes. Another important feature of centrosomes is the centrosomal linker that connects the two centrosomes. The centrosome linker assembles in late mitosis/G1 simultaneously with centriole disengagement and is dissolved before or at the beginning of mitosis. Linker dissolution is important for mitotic spindle formation, and its cell cycle timing has profound influences on the execution of mitosis and proficiency of chromosome segregation. In this review, we will focus on the mechanisms of centrosome positioning and separation, and describe their functions and mechanisms in the light of recent findings.
Communication, the centrosome and the immunological synapse
Authors: Stinchcombe Jane C. , Griffiths Gillian M.
Published: July 2014

Recent findings on the behaviour of the centrosome at the immunological synapse suggest a critical role for centrosome polarization in controlling the communication between immune cells required to generate an effective immune response. The features observed at the immunological synapse show parallels to centrosome (basal body) polarization seen in cilia and flagella, and the cellular communication that is now known to occur at all of these sites.
Centrosomes as signalling centres
Authors: Arquint Christian , Gabryjonczyk Anna-Maria , Nigg Erich A.
Published: July 2014

Centrosomes—as well as the related spindle pole bodies (SPBs) of yeast—have been extensively studied from the perspective of their microtubule-organizing roles. Moreover, the biogenesis and duplication of these organelles have been the subject of much attention, and the importance of centrosomes and the centriole–ciliary apparatus for human disease is well recognized. Much less developed is our understanding of another facet of centrosomes and SPBs, namely their possible role as signalling centres. Yet, many signalling components, including kinases and phosphatases, have been associated with centrosomes and spindle poles, giving rise to the hypothesis that these organelles might serve as hubs for the integration and coordination of signalling pathways. In this review, we discuss a number of selected studies that bear on this notion. We cover different processes (cell cycle control, development, DNA damage response) and organisms (yeast, invertebrates and vertebrates), but have made no attempt to be comprehensive. This field is still young and although the concept of centrosomes and SPBs as signalling centres is attractive, it remains primarily a concept—in need of further scrutiny. We hope that this review will stimulate thought and experimentation.
Psychroflexus salarius sp. nov., isolated from Gomso salt pan
Authors: Chun Jeesun , Kang Ji Young , Jahng Kwang Yeop
Published: July 2014

A taxonomic study was carried out on a novel bacterial strain, designated MIC1008T, which was isolated from the Gomso salt pan, located in Buan County, Korea. Cells were Gram-stain-negative, aerobic, non-motile and moderately halophilic rods, 0.2–0.4 µm wide and 0.7–1.2 µm long. The optimum temperature and pH for growth were 25 °C and pH 6.5–8.5, respectively. Catalase and oxidase activities were positive. Carotenoid pigments were produced. Comparison of 16S rRNA gene sequences indicated that the isolate belonged to the genus

Psychroflexus

, with

Psychroflexus halocasei

WCC 4520T as its closest relative, with a 16S rRNA gene sequence similarity of 95.4 %. The isolate contained iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, anteiso-C15 : 0 and iso-C15 : 0 3-OH as the major fatty acids and menaquinone MK-6 as the isoprenoid quinone. The major polar lipid profile of strain MIC1008T revealed the presence of phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. The DNA G+C content of the isolate was 32.9 mol%. On the basis of the evidences presented, it is concluded that strain MIC1008T represents a novel species of the genus

Psychroflexus

within the family

Flavobacteriaceae

, for which the name Psychroflexus
http://dx.doi.org/10.1601/nm.8182
salarius sp. nov. is proposed. The type strain is MIC1008T ( = KACC 17063T = DSM 25661T).
Selection of chromosomal DNA libraries using a multiplex CRISPR system inSaccharomyces cerevisiae
Authors: Ryan Owen W. , Skerker Jeffrey M. , Maurer Matthew J. , Li Xin , Tsai Jordan C. , Poddar Snigdha , Lee Michael E. , DeLoache Will , Dueber John E. , Arkin Adam P. , Cate Jamie H. D.
Published: July 2014

The directed evolution of biomolecules to improve or change their activity is central to many engineering and synthetic biology efforts. However, selecting improved variants from gene libraries in living cells requires plasmid expression systems that suffer from variable copy number effects, or the use of complex marker-dependent chromosomal integration strategies. We developed quantitative gene assembly and DNA library insertion into theSaccharomyces cerevisiaegenome by optimizing an efficient single-step and marker-free genome editing system using CRISPR-Cas9. With this Multiplex CRISPR (CRISPRm) system, we selected an improved cellobiose utilization pathway in diploid yeast in a single round of mutagenesis and selection, which increased cellobiose fermentation rates by over ten-fold. Mutations recovered in the best cellodextrin transporters reveal synergy between substrate binding and transporter dynamics, and demonstrate the power of CRISPRm to accelerate selection experiments and discoveries of the molecular determinants that enhance biomolecule function.
Efficient site-specific editing of theC. elegansgenome
Authors: Zhang Donglei , Glotzer Michael
Published: July 2014

In just two years, genome editing with the CRISPR-associated endonuclease Cas9 has transformed genetic analysis in conventional and emerging model organisms. The efficiency of this method varies among systems and continues to be optimized. Numerous strategies have been reported for editing theC. elegansgenome. To date, these strategies do not provide a simple, rapid and inexpensive means to introduce and isolate arbitrary point mutants. Here, we report a strategy with all three of these desirable properties. It utilizes oligonucleotides as donor templates for homology-dependent repair and visible markers that are edited in parallel that markedly reduce the number of animals that must be molecularly screened in order to isolate mutants that lack visible phenotypes.
ASCORBATE PEROXIDASE6 Protects Arabidopsis Desiccating and Germinating Seeds from Stress and Mediates Cross Talk between Reactive Oxygen Species, Abscisic Acid, and Auxin
Authors: Chen Changming , Letnik Ilya , Hacham Yael , Dobrev Petre , Ben-Daniel Bat-Hen , Vanková Radomíra , Amir Rachel , Miller Gad
Published: July 2014

A seed’s ability to properly germinate largely depends on its oxidative poise. The level of reactive oxygen species (ROS) in Arabidopsis (Arabidopsis thaliana) is controlled by a large gene network, which includes the gene coding for the hydrogen peroxide-scavenging enzyme, cytosolic ASCORBATE PEROXIDASE6 (APX6), yet its specific function has remained unknown. In this study, we show that seeds lacking APX6 accumulate higher levels of ROS, exhibit increased oxidative damage, and display reduced germination on soil under control conditions and that these effects are further exacerbated under osmotic, salt, or heat stress. In addition, ripening APX6-deficient seeds exposed to heat stress displayed reduced germination vigor. This, together with the increased abundance of APX6 during late stages of maturation, indicates that APX6 activity is critical for the maturation-drying phase. Metabolic profiling revealed an altered activity of the tricarboxylic acid cycle, changes in amino acid levels, and elevated metabolism of abscisic acid (ABA) and auxin in drying apx6 mutant seeds. Further germination assays showed an impaired response of the apx6 mutants to ABA and to indole-3-acetic acid. Relative suppression of abscisic acid insensitive3 (ABI3) and ABI5 expression, two of the major ABA signaling downstream components controlling dormancy, suggested that an alternative signaling route inhibiting germination was activated. Thus, our study uncovered a new role for APX6, in protecting mature desiccating and germinating seeds from excessive oxidative damage, and suggested that APX6 modulate the ROS signal cross talk with hormone signals to properly execute the germination program in Arabidopsis.
Bis(isoquinolin-2-ium) tetrachloridozincate dihydrate
Authors: Govindan Elumalai , Thirumurugan Subramani , Rajkumar Kanniah , Anbalagan Krishnamoorthy , SubbiahPandi Arunachalam
Published: July 2014

In the title compound, (C9H8N)2[ZnCl4]·2H2O, the tetrachloridozincate ion is located on a twofold rotation axis with the Zn atom on a special position. The crystal packing is stabilized by N—H...O and O—H...Cl interactions.
(3-Methylbenzonitrile-1κN)-cis-tetrakis(μ-N-phenylacetamidato)-1:2κ4N:O;1:2κ4O:N-dirhodium(II)(Rh—Rh)
Authors: Eagle Cassandra T. , Quarshie Fredricka , Cook Kevin M.
Published: July 2014

The complex molecule of the title compound, [Rh2{N(C6H5)COCH3}4(NCC7H7)], has crystallographically-imposed mirror symmetry. The four acetamide ligands bridging the dirhodium core are arranged in a 2,2-cismanner with two N atoms and two O atoms coordinating to the unique RhIIatomcisto one another. The Neq—Rh—Rh—Oeqtorsion angles on the acetamide bridge are 0.75 (7) and 1.99 (9)°. The axial nitrile ligand completes the distorted octahedral coordination sphere of one RhIIatom and shows a nonlinear coordination, with an Rh—N—C bond angle of 162.8 (5)°; the N—C bond length is 1.154 (7) Å.
Bis(methylsulfonyl)methane
Authors: Awad Riad , Mallah Eyad , Abu Dayyih Wael , Sweidan Kamal , Steimann Manfred
Published: July 2014

In the title compound, C3H8O4S2, the two central S—C(H2) bond lengths are almost identical [1.781 (2) and 1.789 (2) Å]. In the crystal, each molecule utilizes CH2and CH3bonds to form weak C—H...O hydrogen bonds to six other molecules, thus linking molecules into a three-dimensional network.
Crystal structure of a two-dimensional grid-type iron(II) coordination polymer: poly[[diaquatetra-μ-cyanido-diargentate(I)iron(II)]trans-1,2-bis(pyridin-2-yl)ethylene disolvate]
Authors: Othong Jintana , Wannarit Nanthawat , Pakawatchai Chaveng , Youngme Sujittra
Published: July 2014

In the title compound, {[Ag2Fe(CN)4(H2O)2]·2C12H10N2}n, the asymmetric unit contains one FeIIcation, two water molecules, two dicyanidoargentate(I) anions and two uncoordinating 1,2-bis(pyridin-2-yl)ethylene (2,2′-bpe) molecules. Each FeIIatom is six-coordinated in a nearly regular octahedral geometry by four N atoms from dicyanidoargentate(I) bridges and two coordinating water molecules. The FeIIatoms are bridged by dicyanidoargentate(I) units to give a two-dimensional layer with square-grid spaces. The intergrid spaces with interlayer distance of 6.550 (2) Å are occupied by 2,2′-bpe guest molecules which form O—H...N hydrogen bonds to the host layers. This leads to an extended three-dimensional supramolecular architecture. The structure of the title compound is compared with some related compounds containing dicyanidoargentate(I) ligands and N-donor organic co-ligands.
4-(2-Fluorophenyl)-2-methoxy-5,6,7,8,9,10-hexahydrocycloocta[b]pyridine-3-carbonitrile
Authors: Vishnupriya R. , Suresh J. , Maharani S. , Kumar R. Ranjith , Lakshman P. L. Nilantha
Published: July 2014

In the title compound, C19H19FN2O, the cyclooctene ring adopts a twisted boat–chair conformation. The dihedral angle between the plane of the fluorophenyl substituent and that of the pyridine ring is 76.39 (8)°. The F andortho-H atoms of the fluorobenzene ring are disordered, with occupancy factors of 0.226 (5) and 0.774 (5). In the crystal, no significant interactions are observed between the molecules beyond van der Waals contacts.
3,10,14,21-Tetrakis(4-methoxyphenyl)pentacyclo[11.8.0.02,11.04,9.015,20]henicosa-1(21),2,4(9),5,7,10,13,15(20),16,18-decaen-12-one chloroform monosolvate
Authors: Gopinath S. , Narayanan P. , Sethusankar K. , Nandakumar Meganathan , Mohanakrishnan Arasambattu K.
Published: July 2014

The asymmetric unit of the title compound, C49H36O6·CHCl3, contains half an organic molecule, the complete molecule being generated by the operation of a crystallographic twofold rotation axis, and half a highly disordered chloroform molecule. The contribution to the diffraction pattern of the latter was removed using the program SQUEEZE inPLATON[Spek (2009).Acta Cryst. D65, 148–155]; the unit-cell characteristics take into account the presence of CHCl3. The dihedral angles between the planes of the naphthalene ring system and the methoxybenzene rings are 71.05 (7) (synto the central C=O group) and 57.27 (6)° (antito the central C=O group). In the crystal, molecules are linked by C—H...O interactions, generatingC(12) chains running parallel to thebaxis.
Crystal structure of bis{2-[(E)-(4-methoxylbenzyl)iminomethyl]phenolato-κ2N,O1}nickel(II)
Authors: Bahron Hadariah , Tajuddin Amalina Mohd , Ibrahim Wan Nazihah Wan , Fun Hoong-Kun , Chantrapromma Suchada
Published: July 2014

The asymmetric unit of the title compound, [Ni(C15H14NO2)2], comprises an NiIIcation, lying on an inversion centre, and a Schiff base anion that acts as a bidentate ligand. The NiIIcation is in a square-planar coordination environment binding to the imine N and phenolate O atoms of the two Schiff base ligands. The N- and O-donor atoms of the two ligands are mutuallytrans, with Ni—N and Ni—O bond lengths of 1.9191 (11) and 1.8407 (9) Å, respectively. The plane of the methoxybenzene ring makes a dihedral angle of 84.92 (6)° with that of the phenolate ring. In the crystal, molecules are linked into screw chains by weak C—H...O hydrogen bonds. Additional C—H...O hydrogen bonds, together with C—H...π contacts, arrange the molecules into sheets parallel to theacplane.
The structure of α-haemoglobin in complex with a haemoglobin-binding domain fromStaphylococcus aureusreveals the elusive α-haemoglobin dimerization interface
Authors: Krishna Kumar Kaavya , Jacques David A. , Guss J. Mitchell , Gell David A.
Published: July 2014

Adult haemoglobin (Hb) is made up of two α and two β subunits. Mutations that reduce expression of the α- or β-globin genes lead to the conditions α- or β-thalassaemia, respectively. Whilst both conditions are characterized by anaemia of variable severity, other details of their pathophysiology are different, in part owing to the greater stability of the β chains that is conferred through β self-association. In contrast, α subunits interact weakly, and in the absence of stabilizing quaternary interactions the α chain (α) is prone to haem loss and denaturation. The molecular contacts that confer weak self-association of α have not been determined previously. Here, the first structure of an α2homodimer is reported in complex with one domain of the Hb receptor fromStaphylococcus aureus. The α2dimer interface has a highly unusual, approximately linear, arrangement of four His side chains within hydrogen-bonding distance of each other. Some interactions present in the α1β1 dimer interface of native Hb are preserved in the α2dimer. However, a marked asymmetry is observed in the α2interface, suggesting that steric factors limit the number of stabilizing interactions that can form simultaneously across the interface.
Expression, purification and crystallization of pecan (Carya illinoinensis) vicilin
Authors: Lee BoRam , Zhang Renhao , Du Wen-Xian , Grauke Larry J. , McHugh Tara H. , Zhang Yu-Zhu
Published: July 2014

Tree nuts are responsible for many cases of severe food allergies. The 7S seed storage protein vicilin has been identified as a food allergen in many kinds of tree nuts. The vicilin protein consists of an N-terminal low-complexity region with antimicrobial activity and a C-terminal domain that forms a trimeric structure that belongs to the cupin superfamily. In this study, vicilin from pecan (Carya illinoinensis) was isolated and was expressed in bacteria for the first time. The cupin structural core of the protein, residues 369–792, was purified by metal-affinity and gel-filtration chromatography to high purity. Vicilin crystals were obtained and the best crystal diffracted to 2.65 Å resolution in space groupP212121.
Preliminary X-ray crystallographic studies of the TIR domain of human Toll-like receptor 6
Authors: Jang Tae-ho , Park Hyun Ho
Published: July 2014

Toll-like receptor (TLR) proteins have been identified and shown to play a role in the innate immune response. TLR6 associated with TLR2 can recognize diacylated lipoprotein. In this study, the human TLR6 TIR domain corresponding to amino acids 640–796 was overexpressed inEscherichia coliusing engineered C-terminal His tags. The TLR6 TIR domain was then purified to homogeneity and crystallized at 20°C. Finally, X-ray diffraction data were collected to a resolution of 2.2 Å from a crystal belonging to space groupC2, with unit-cell parametersa= 127.60,b= 44.20,c= 75.72 Å, β = 118.89°
Cloning, expression, purification, crystallization and X-ray crystallographic analysis ofD-lactate dehydrogenase fromLactobacillus jensenii
Authors: Kim Sangwoo , Kim Yong Hwan , Kim Kyung-Jin
Published: July 2014

The thermostable D-lactate dehydrogenase fromLactobacillus jensenii(LjD-LDH) is a key enzyme for the production of the D-form of lactic acid from pyruvate concomitant with the oxidation of NADH to NAD+. The polymers of lactic acid are used as biodegradable bioplastics. TheLjD-LDH protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 28%(w/v) polyethylene glycol 400, 100 mMTris–HCl pH 9, 200 mMmagnesium sulfate at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.1 Å. The crystal belonged to space groupP3121, with unit-cell parametersa=b= 90.5,c= 157.8 Å. With two molecules per asymmetric unit, the crystal volume per unit protein weight (VM) is 2.58 Å3 Da−1, which corresponds to a solvent content of approximately 52.3%. The structure was solved by single-wavelength anomalous dispersion using a selenomethionine derivative.
Overexpression, crystallization and preliminary X-ray characterization ofRuminococcus flavefaciensscaffoldin C cohesin in complex with a dockerin from an uncharacterized CBM-containing protein
Authors: Bule Pedro , Ruimy-Israeli Vered , Cardoso Vânia , Bayer Edward A. , Fontes Carlos M. G. A. , Najmudin Shabir
Published: July 2014

Cellulosomes are massive cell-bound multienzyme complexes tethered by macromolecular scaffolds that coordinate the efforts of many anaerobic bacteria to hydrolyze plant cell-wall polysaccharides, which are a major untapped source of carbon and energy. Integration of cellulosomal components occursviahighly ordered protein–protein interactions between cohesin modules, located in the scaffold, and dockerin modules, found in the enzymes and other cellulosomal proteins. The proposed cellulosomal architecture forRuminococcus flavefaciensstrain FD-1 consists of a major scaffoldin (ScaB) that acts as the backbone to which other components attach. It has nine cohesins and a dockerin with a fused X-module that binds to the cohesin on ScaE, which in turn is covalently attached to the cell wall. The ScaA dockerin binds to ScaB cohesins allowing more carbohydrate-active modules to be assembled. ScaC acts as an adaptor that binds to both ScaA and selected ScaB cohesins, thereby increasing the repertoire of dockerin-bearing proteins that integrate into the complex. In previous studies, a screen for novel cohesin–dockerin complexes was performed which led to the identification of a total of 58 probable cohesin–dockerin pairs. Four were selected for subsequent structural and biochemical characterization based on the quality of their expression and the diversity in their specificities. One of these is C12D22, which comprises the cohesin from the adaptor ScaC protein bound to the dockerin of a CBM-containing protein. This complex has been purified and crystallized, and data were collected to resolutions of 2.5 Å (hexagonal,P65), 2.16 Å (orthorhombic,P212121) and 2.4 Å (orthorhombic,P21212) from three different crystalline forms.
Expression, high-pressure refolding, purification, crystallization and preliminary X-ray analysis of a novel single-strand-specific 3′–5′ exonuclease PhoExo I fromPyrococcus horikoshiiOT3
Authors: Miyazono Ken-ichi , Tsutsumi Kanae , Ishino Yoshizumi , Tanokura Masaru
Published: July 2014

PhoExo I is a single-strand-specific 3′–5′ exonuclease fromPyrococcus horikoshiiOT3 and is thought to be involved in a Thermococcales-specific DNA-repair pathway. The recombinant PhoExo I protein was produced as inclusion bodies inEscherichia colicells. Solubilization of the inclusion bodies was performed by the high-pressure refolding method and highly purified protein was subjected to crystallization by the sitting-drop vapour-diffusion method at 20°C. A crystal of PhoExo I was obtained in a reservoir solution consisting of 0.1 MTris–HCl pH 8.9, 27% PEG 6000 and diffracted X-rays to 1.52 Å resolution. The crystal of PhoExo I belonged to space groupH32, with unit-cell parametersa=b= 112.07,c= 202.28 Å. The crystal contained two PhoExo I molecules in the asymmetric unit.
Crystallization and preliminary crystallographic study of human coronavirus NL63 main protease in complex with an inhibitor
Authors: Wang Fenghua , Tan Yusheng , Li Huiyan , Chen Xia , Wang Jinshan , Li Shuang , Fu Sheng , Zhao Qi , Chen Cheng , Su Dan , Yang Haitao
Published: July 2014

Human coronavirus NL63 mainly infects younger children and causes cough, fever, rhinorrhoea, bronchiolitis and croup. It encodes two polyprotein precursors required for genome replication and transcription. Each polyprotein undergoes extensive proteolytic processing, resulting in functional subunits. This process is mainly mediated by its genome-encoded main protease, which is an attractive target for antiviral drug design. In this study, the main protease of human coronavirus NL63 was crystallized in complex with a Michael acceptor. The complex crystals diffracted to 2.85 Å resolution and belonged to space groupP41212, with unit-cell parametersa=b= 87.2,c= 212.1 Å. Two molecules were identified per asymmetric unit.
The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain
Authors: Chauviac Francois-Xavier , Robertson Giles , Quay Doris H. X. , Bagnéris Claire , Dumas Christian , Henderson Brian , Ward John , Keep Nicholas H. , Cohen-Gonsaud Martin
Published: July 2014

The first structure of the catalytic domain of RpfC (Rv1884), one of the resuscitation-promoting factors (RPFs) fromMycobacterium tuberculosis, is reported. The structure was solved using molecular replacement once the space group had been correctly identified as twinnedP21rather than the apparentC2221by searching for anomalous scattering sites inP1. The structure displays a very high degree of structural conservation with the previously published structures of the catalytic domains of RpfB (Rv1009) and RpfE (Rv2450). This structural conservation highlights the importance of the versatile domain composition of the RPF family.
Crystallization and preliminary X-ray crystallographic analysis of the complex between the N-D1 domain of VCP fromHomo sapiensand the N domain of OTU1 fromSaccharomyces cerevisiae
Authors: Kim Su Jin , Kim Eunice EunKyeong
Published: July 2014

VCP (valosin-containing protein; also known as p97) plays important roles in many biological processes including the ERAD (endoplasmic reticulum-associated degradation) pathway and its function is governed by binding partners. OTU1 (ovarian tumour domain-containing protein 1) is a recently discovered deubiquitinating enzyme that interacts directly with VCP in the ERAD pathway. In order to understand the interactions between the two proteins, the N-D1 domain of VCP and the UBXL domain of OTU1 were cloned, overexpressed, purified and crystallized. The crystals of the complex diffracted to 3.25 Å resolution and belonged to space groupP21, with unit-cell parametersa= 165.45,b= 176.73,c= 165.59 Å, β = 120.095°. There are two molecules of the complex in the asymmetric unit with a Matthews coefficient of 2.62 Å3 Da−1and a solvent content of 53%.
Crystallization and X-ray diffraction of virus-like particles from a piscine betanodavirus
Authors: Luo Yu-Chun , Wang Chun-Hsiung , Wu Yi-Min , Liu Wangta , Lu Ming-Wei , Lin Chan-Shing
Published: July 2014

Dragon grouper nervous necrosis virus (DGNNV), a member of the genusBetanodavirus, causes high mortality of larvae and juveniles of the grouper fishEpinephelus lanceolatus. Currently, there is no reported crystal structure of a fish nodavirus. The DGNNV virion capsid is derived from a single open reading frame that encodes a 338-amino-acid protein of approximately 37 kDa. The capsid protein of DGNNV was expressed to form virus-like particles (VLPs) inEscherichia coli. The VLP shape isT= 3 quasi-symmetric with a diameter of ∼38 nm in cryo-electron microscopy images and is highly similar to the native virion. In this report, crystals of DGNNV VLPs were grown to a size of 0.27 mm within two weeks by the hanging-drop vapour-diffusion method at 283 K and diffracted X-rays to ∼7.5 Å resolution. In-house X-ray diffraction data of the DGNNV VLP crystals showed that the crystals belonged to space groupR32, with unit-cell parametersa=b= 353.00,c= 800.40 Å, α = β = 90, γ = 120°. 23 268 unique reflections were acquired with an overallRmergeof 18.2% and a completeness of 93.2%. Self-rotation function maps confirmed the fivefold, threefold and twofold symmetries of the icosahedron of DGNNV VLPs.
Structure ofSaccharomyces cerevisiaemitochondrial Qri7 in complex with AMP
Authors: Tominaga Takumi , Kobayashi Kan , Ishii Ryohei , Ishitani Ryuichiro , Nureki Osamu
Published: July 2014

N6-Threonylcarbamoyladenosine (t6A) is a modified tRNA base required for accuracy in translation. Qri7 is localized in yeast mitochondria and is involved in t6A biosynthesis. In t6A biosynthesis, threonylcarbamoyl-adenylate (TCA) is synthesized from threonine, bicarbonate and ATP, and the threonyl-carbamoyl group is transferred to adenine 37 of tRNA by Qri7. Qri7 alone is sufficient to catalyze the second step of the reaction, whereas the Qri7 homologues YgjD (in bacteria) and Kae1 (in archaea and eukaryotes) function as parts of multi-protein complexes. In this study, the crystal structure of Qri7 complexed with AMP (a part of TCA) has been determined at 2.94 Å resolution in a new crystal form. The manner of AMP recognition is similar, with some minor variations, among the Qri7/Kae1/YgjD family proteins. The previously reported dimer formation was also observed in this new crystal form. Furthermore, a comparison with the structure of TobZ, which catalyzes a similar reaction to t6A biosynthesis, revealed the presence of a flexible loop that may be involved in tRNA binding.
Crystallization and preliminary X-ray analysis of a ribokinase fromVibrio choleraeO395
Authors: Paul Rakhi , Dandopath Patra Madhumita , Banerjee Ramanuj , Sen Udayaditya
Published: July 2014

Ribokinase (RK) is one of the principal enzymes in carbohydrate metabolism, catalyzing the reaction of D-ribose and adenosine triphosphate to produce ribose-5-phosphate and adenosine diphosphate (ADP). To provide further insight into the catalytic mechanism, therbsKgene fromVibrio choleraeO395 encoding ribokinase was cloned and the protein was overexpressed inEscherichia coliBL21 (DE3) and purified using Ni2+–NTA affinity chromatography. Crystals ofV. choleraeRK (Vc-RK) and of its complex with ribose and ADP were grown in the presence of polyethylene glycol 6000 and diffracted to 3.4 and 1.75 Å resolution, respectively. Analysis of the diffraction data showed that both crystals possess symmetry consistent with space groupP1. In the Vc-RK crystals, 16 molecules in the asymmetric unit were arranged in a spiral fashion, leaving a large empty space inside the crystal, which is consistent with its high Matthews coefficient (3.9 Å3 Da−1) and solvent content (68%). In the Vc-RK co-crystals four molecules were located in the asymmetric unit with a Matthews coefficient of 2.4 Å3 Da−1, corresponding to a solvent content of 50%.
Characterization, crystallization and preliminary X-ray crystallographic analysis of the human Uba5 C-terminus–Ufc1 complex
Authors: Xie Shutao
Published: July 2014

Human Uba5, which contains an adenylation domain and a C-terminal region, is the smallest ubiquitin-like molecule-activating enzyme. The mechanism through which the enzyme recognizes Ufc1 and catalyzes the formation of the Ufc1–Ufm1 complex remains unknown. In this study, Uba5 residues 364–404 were demonstrated to be necessary for the transthiolation of Ufm1 to Ufc1, and Uba5 381–404 was identified to be the minimal region for Ufc1 recognition. The fusion protein between Uba5 381–404 and Ufc1 was cloned, expressed and purified, and exists as a homodimer in solution. Crystallization was performed at 293 K using PEG 4000 as precipitant; the optimized crystals diffracted to 3.0 Å resolution and had unit-cell parametersa=b= 82.49,c= 62.47 Å, α = β = 90, γ = 120°. With one fusion-protein molecule in the asymmetric unit, the Matthews coefficient and solvent content were calculated to be 2.55 Å3 Da−1and 51.84%, respectively.