bluuebunny/crossref_metadata_2025 huggingface dataset:
Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria
Authors: Haft Rembrandt J. F. , Keating David H. , Schwaegler Tyler , Schwalbach Michael S. , Vinokur Jeffrey , Tremaine Mary , Peters Jason M. , Kotlajich Matthew V. , Pohlmann Edward L. , Ong Irene M. , Grass Jeffrey A. , Kiley Patricia J. , Landick Robert
Published: June 2014

Significance

Microbially produced aliphatic alcohols are important biocommodities but exert toxic effects on cells. Understanding the mechanisms by which these alcohols inhibit microbial growth and generate resistant microbes will provide insight into microbial physiology and improve prospects for microbial biotechnology and biofuel production. We find that
Escherichia coli
ribosomes and RNA polymerase are mechanistically affected by ethanol, identifying the ribosome decoding center as a likely target of ethanol-mediated conformational disruption and showing that ethanol inhibits transcript elongation via direct effects on RNA polymerase. Our findings provide conceptual frameworks for the study of ethanol toxicity in microbes and for the engineering of ethanol tolerance that may be extensible to other microbes and to other short-chain alcohols.
Self-assembly of amphiphilic Janus dendrimers into uniform onion-like dendrimersomes with predictable size and number of bilayers
Authors: Zhang Shaodong , Sun Hao-Jan , Hughes Andrew D. , Moussodia Ralph-Olivier , Bertin Annabelle , Chen Yingchao , Pochan Darrin J. , Heiney Paul A. , Klein Michael L. , Percec Virgil
Published: June 2014

Significance

Simple injection of a solution of amphiphilic Janus dendrimer with specific primary structure into water or buffer has been shown to yield uniform submicrometer-size onion-like vesicles denoted dendrimersomes. The size and number of alternating internally confined bilayers is predicted by the final concentration of the Janus dendrimer. Onion-like dendrimersomes provide mimics of various biological membranes and can be elaborated to provide time-dependent delivery of drugs. Their ease of preparation contrasts with conventional methods used to make onion-like vesicles that are both complicated and time-consuming.
Social identification moderates the effect of crowd density on safety at the Hajj
Authors: Alnabulsi Hani , Drury John
Published: June 2014

Significance

A large-scale survey of pilgrims on the Hajj to Mecca (also called Makkah) showed that where there is identification with the crowd the negative effect of crowd density on safety is diminished or even reversed: a new finding. The reason that identification with the crowd moderates the effect of density on safety is because crowd identification increases the perception that others will be supportive. This process also helps to explain national differences among pilgrims in feelings of safety during the event. In contrast both to engineering approaches, which neglect crowd psychology, and traditional crowd psychology, which assumes that the crowd is inherently a “problem,” this study shows how the crowd can be part of the solution in crowd safety management.
Marker for type VI secretion system effectors
Authors: Salomon Dor , Kinch Lisa N. , Trudgian David C. , Guo Xiaofeng , Klimko John A. , Grishin Nick V. , Mirzaei Hamid , Orth Kim
Published: June 2014

Significance

The recently discovered type VI secretion system (T6SS) is used by Gram-negative bacteria to deliver effector proteins into both eukaryotic and prokaryotic neighboring cells to mediate virulence and competition, respectively. Even though several T6SS effector families have been described, many T6SSs are not associated with known effectors. In this work, we report the discovery of a conserved motif named MIX (marker for type six effectors) that is often located near the T6SS genome neighborhood and is found in numerous proteins from diverse Proteobacteria, among them several T6SS effectors. We show that the MIX motif can be used as a marker to identify new T6SS effectors, thereby significantly enlarging the list of known T6SS effector families.
Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Δ32 mutation confers resistance to HIV infection
Authors: Ye Lin , Wang Jiaming , Beyer Ashley I. , Teque Fernando , Cradick Thomas J. , Qi Zhongxia , Chang Judy C. , Bao Gang , Muench Marcus O. , Yu Jingwei , Levy Jay A. , Kan Yuet Wai
Published: June 2014

Significance

Patients homozygous for the C-C chemokine receptor type 5 (CCR5) gene with 32-bp deletions (Δ32) are resistant to HIV infection. Using the piggyBac technology plus transcription activator-like effector nucleases or clustered regularly interspaced short palindromic repeats-Cas9, the authors report, to our knowledge, for the first time in induced pluripotent stem cells (iPSCs) the efficient and seamless derivation of a homozygous CCR5Δ32 mutation, exactly mimicking the natural mutation. Monocytes and macrophages differentiated from these mutated iPSCs in vitro are resistant to HIV infection. This approach can be applied in the future toward the functional cure of HIV infection. The findings are also of great interest to researchers in many fields who wish to correct or introduce mutations in specific genes.
Compositional landscape for glass formation in metal alloys
Authors: Na Jong Hyun , Demetriou Marios D. , Floyd Michael , Hoff Andrew , Garrett Glenn R. , Johnson William L.
Published: June 2014

Significance

This paper reports and explains the exponential dependence of crystal nucleation rates on alloy composition for an undercooled liquid. It is shown that maxima in alloy glass-forming ability (GFA) take the form of exponential hypercusps in composition space. The approach is illustrated by optimizing the composition of a five-component nickel–chromium-base metallic glass to achieve order-of-magnitude improvements in GFA over prior work. Variations in GFA are shown to arise from the interplay between alloy-melting behavior and the liquid rheology.
L’hypothèse de Firth
Authors: Godart-Wendling Béatrice
Published: June 2014

Le but de cet article est d’évaluer l’hypothèse de John Rupert Firth (1890–1960) énonçant que l’article de l’anthropologue Bronislaw Malinowski (1884–1942), “The Problem of Meaning in Primitive Languages” (1923), constituerait une des sources d’inspiration ayant conduit Ludwig Wittgenstein (1889–1951) à élaborer une nouvelle conception de la signification en termes d’‘usage’. S’appuyant sur certains passages des Philosophical Investigations (1953), Firth établit ainsi une filiation entre les deux grandes idées phares de Malinowski, à savoir l’importance de la notion de ‘contexte de situation’ et l’idée que le langage serait un ‘mode d’action’ et les principales thèses (la signification comme usage, l’acquisition du langage, le langage comme un ensemble de jeux) que développera Wittgenstein. L’examen du bien fondé de cette hypothèse conduira à préciser la synergie des idées qui eut lieu en matière de pragmatique dans l’Angleterre de la première moitié du XXe siècle.
L’étrange destin d’un livre
Authors: Larcher Pierre
Published: June 2014

Les arabisants “classicisants” continuent de se référer à A Grammar of the Arabic Language de William Wright (1830–1889), qu’ils citent généralement sans plus de précision. Ce faisant, ils dissimulent la longue histoire de cet ouvrage. Au premier chef, il est la traduction, parue en 2 volumes (1859 et 1862), de la 2e édition, en langue allemande, de la Grammatik der arabischen Sprache (1859) de Carl Paul Caspari (1814–1892). Mais cet ouvrage a lui-même une longue histoire. Une première édition en était parue, en latin, en 1848, sous le titre de Grammatica arabica. La première partie (Doctrina de elementis et formis) avait même été imprimée, une première fois, en 1844. Dans la préface à l’édition latine de 1848, Caspari cite ses deux principales sources: la Grammaire arabe (11810, 21831) d’Antoine-Isaac Silvestre de Sacy (1758–1838) et la Grammatica critica linguae arabicae, en deux volumes (1831 et 1833), de Heinrich Ewald (1803–1875). La version allemande de la Grammaire arabe de Caspari fut rééditée en 1866. Une nouvelle édition en parut en 1876, révisée par August Müller (1848–1892). Cette 4e édition fut traduite en français (deux tirages en 1880 et 1881) par une personnalité étonnante, le Colombien Ezequiel Uricoechea (1834–1880). Elle fut également rééditée (5e et dernière édition) en 1887. Quant à la Grammaire arabe de Wright, une seconde édition, “révisée et grandement augmentée”, en parut, en 2 volumes, en 1874 et 1875, et une troisième édition, révisée par William Robertson Smith (1846–1894) et Michael Jan de Goeje (1836–1909), également en 2 volumes, en 1896 et 1898. Cette troisième édition, avec quelques modifications dues à Anthony Ashley Bevan (1859–1933), fut réimprimée en 1933: c’est à elle, constamment réimprimée, que se réfèrent généralement les arabisants. La Grammaire arabe de Wright apparaît ainsi comme le travail collectif de l’orientalisme européen du XIXe et de la première moitié du XXe siècle, en venant rappeler au passage qu’il est impossible d’en faire l’histoire sans la connaissance de deux de ses grandes langues académiques: le latin et l’allemand.
Design of a gaze behavior at a small mistake moment for a robot
Authors: Shiomi Masahiro , Nakagawa Kayako , Hagita Norihiro
Published: June 2014

A change of gaze behavior at a small mistake moment is a natural response that reveals our own mistakes and suggests an apology to others with whom we are working or interacting. In this paper we investigate how robot gaze behaviors at small mistake moments change the impressions of others. To prepare gaze behaviors for a robot, first, we identified by questionnaires how human gaze behaviors change in such situations and extracted three kinds: looking at the other, looking down, and looking away. We prepared each gaze behavior, added a no-gaze behavior, and investigated how a robot’s gaze behavior at a small mistake moment changes the impressions of the interacting people in a simple cooperative task. Experiment results show that the ‘looking at the other’ gaze behavior outperforms the other gaze behaviors and indicates the degrees of perceived apologeticness and friendliness. Keywords: Communication robots; gaze; mistake; mitigation
Interactions between a quiz robot and multiple participants
Authors: Yamazaki Akiko , Yamazaki Keiichi , Ikeda Keiko , Burdelski Matthew , Fukushima Mihoko , Suzuki Tomoyuki , Kurihara Miyuki , Kuno Yoshinori , Kobayashi Yoshinori
Published: June 2014

This paper reports on a quiz robot experiment in which we explore similarities and differences in human participant speech, gaze, and bodily conduct in responding to a robot’s speech, gaze, and bodily conduct across two languages. Our experiment involved three-person groups of Japanese and English-speaking participants who stood facing the robot and a projection screen that displayed pictures related to the robot’s questions. The robot was programmed so that its speech was coordinated with its gaze, body position, and gestures in relation to transition relevance places (TRPs), key words, and deictic words and expressions (e.g. this, this picture) in both languages. Contrary to findings on human interaction, we found that the frequency of English speakers’ head nodding was higher than that of Japanese speakers in human-robot interaction (HRI). Our findings suggest that the coordination of the robot’s verbal and non-verbal actions surrounding TRPs, key words, and deictic words and expressions is important for facilitating HRI irrespective of participants’ native language. Keywords: coordination of verbal and non-verbal actions; robot gaze comparison between English and Japanese; human-robot interaction (HRI); transition relevance place (TRP); conversation analysis
Learning where to look
Authors: Mohammad Yasser F.O. , Nishida Toyoaki
Published: June 2014

Autonomous development of gaze behavior for natural human-robot interaction
Designing robot eyes for communicating gaze
Authors: Onuki Tomomi , Ishinoda Takafumi , Tsuburaya Emi , Miyata Yuki , Kobayashi Yoshinori , Kuno Yoshinori
Published: June 2014

Abstract—Human eyes not only serve the function of enabling us “to see” something, but also perform the vital role of allowing us “to show” our gaze for non-verbal communication, such as through establishing eye contact and joint attention. The eyes of service robots should therefore also perform both of these functions. Moreover, they should be friendly in appearance so that humans may feel comfortable with the robots. Therefore we maintain that it is important to consider gaze communication capability and friendliness in designing the appearance of robot eyes. In this paper, we propose a new robot face with rear-projected eyes for changing their appearance while simultaneously realizing the showing of gaze by incorporating stereo cameras. Additionally, we examine which shape of robot eyes is most suitable for gaze reading and gives the friendliest impression, through experiments where we altered the shape and iris size of robot eyes. Keywords: Gaze reading; facial design; projector camera system
Tutoring in adult-child interaction
Authors: Pitsch Karola , Vollmer Anna-Lisa , Rohlfing Katharina J. , Fritsch Jannik , Wrede Britta
Published: June 2014

Research of tutoring in parent-infant interaction has shown that tutors – when presenting some action – modify both their verbal and manual performance for the learner (‘motherese’, ‘motionese’). Investigating the sources and effects of the tutors’ action modifications, we suggest an interactional account of ‘motionese’. Using video-data from a semi-experimental study in which parents taught their 8- to 11-month old infants how to nest a set of differently sized cups, we found that the tutors’ action modifications (in particular: high arches) functioned as an orienting device to guide the infant’s visual attention (gaze). Action modification and the recipient’s gaze can be seen to have a reciprocal sequential relationship and to constitute a constant loop of mutual adjustments. Implications are discussed for developmental research and for robotic ‘Social Learning’. We argue that a robot system could use on-line feedback strategies (e.g. gaze) to pro-actively shape a tutor’s action presentation as it emerges.
“The language of Europe is translation”
Authors: Wolf Michaela
Published: June 2014

Umberto Eco’s statement “the language of Europe is translation” suggests that translation is one of the main assets of daily communication in Europe. While such a statement undoubtedly is a stand against national—or, in many instances, nationalistic—language cultures, it also raises a series of questions which can be discussed within a re-formulation of EST’s aims and scope: Which ‘Europe’ is meant here? What sort of translation concept underpins this statement? In which way do migration movements shape today’s translation landscapes? What are the control mechanisms behind the phenomenon of translation understood in Eco’s sense? This paper discusses the limits of Europeanness and its potentially transgressive nature against the backdrop of EST’s founding moment in Vienna and the city’s central shaping force in pluricultural issues in the Habsburg Monarchy. It argues that translation has the task of breaking the deadlock of identitarian differences and the political practices based on them. So, what is the impact of these reflections for future activities in EST?
EST 2012—A vision fulfilled?
Authors: Snell-Hornby Mary
Published: June 2014

The essay traces the position of the EST within the discipline of Translation Studies since the Society was established in 1992. The main emphasis is on the original objectives (as laid down in the Constitution) along with the changes naturally brought about by technological and sociological developments over the last twenty years. These involve the character of EST, the role of International English and the significance of Translation Studies, for which tentative prognoses are sketched in conclusion.
The coming of age of a learned society in Translation Studies
Authors: Gile Daniel
Published: June 2014

The author reviews ideas, projects and actions generated and implemented within and with EST over the past twenty years. He concludes in his analysis that predictors of success or failure for EST operations are individual motivation, organization with specific duties and institutional weight. He considers that EST is doing rather well, suggests that there is potential for development in service provision in the form of short courses provided by experts from within the Society, but that one should not be overambitious in terms of institutional influence.
De quelques effets de l’internationalisation et de la technologisation
Authors: Gambier Yves
Published: June 2014

Le 20ème anniversaire d’une association n’est jamais anodin, à la fois pour la discipline représentée et pour ses agents. En outre, pendant ces 20 ans, la traductologie a tracé un extraordinaire parcours. Nous nous proposons non pas d’articuler les efforts de l’EST et les développements de cette traductologie mais de poser quelques jalons pour mieux envisager le futur.
A National Intervention to Prevent the Spread of Carbapenem-Resistant Enterobacteriaceae in Israeli Post-Acute Care Hospitals
Authors: Ben-David Debby , Masarwa Samira , Adler Amos , Mishali Hagit , Carmeli Yehuda , Schwaber Mitchell J. ,   the Post-Acute Care Hospital Carbapenem-Resistant Enterobacteriaceae Working Group
Published: June 2014

Objective

Patients hospitalized in post-acute care hospitals (PACHs) constitute an important reservoir of antimicrobial-resistant bacteria. High carriage prevalence of carbapenem-resistant Enterobacteriaceae (CRE) has been observed among patients hospitalized in PACHs. The objective of the study is to describe the impact of a national infection control intervention on the prevalence of CRE in PACHs.

Design

A prospective cohort interventional study.

Setting

Thirteen PACHs in Israel.

Intervention

A multifaceted intervention was initiated between 2008 and 2011 as part of a national program involving all Israeli healthcare facilities. The intervention has included (1) periodic on-site assessments of infection control policies and resources, using a score comprised of 16 elements; (2) assessment of risk factors for CRE colonization; (3) development of national guidelines for CRE control in PACHs involving active surveillance and contact isolation of carriers; and (4) 3 cross-sectional surveys of rectal carriage of CRE that were conducted in representative wards.

Results

The infection control score increased from 6.8 to 14.0 (P< .001) over the course of the study period. A total of 3,516 patients were screened in the 3 surveys. Prevalence of carriage among those not known to be carriers decreased from 12.1% to 7.9% (P= .008). Overall carrier prevalence decreased from 16.8% to 12.5% (P= .013). Availability of alcohol-based hand rub, appropriate use of gloves, and a policy of CRE surveillance at admission to the hospital were independently associated with lower new carrier prevalence.

Conclusion

A nationwide infection control intervention was associated with enhanced infection control measures and a reduction in the prevalence of CRE in PACHs.
A model approach to identify the spawning grounds and describing the early life history of Northeast Arctic haddock (Melanogrammus aeglefinus)
Authors: Castaño-Primo Rocío , Vikebø Frode Bendiksen , Sundby Svein
Published: June 2014

The time-series of recruitment of Northeast Arctic (NEA) haddock (Melanogrammus aeglefinus) reveals larger interannual fluctuations than other gadoid species of the region. The position of spawning sites and the subsequent drift pattern of the offspring may contribute to the large transport variability, and hence, to the large variation in recruitment. A mechanistic individual-based biophysical model covering the egg stage to presettling juveniles, together with observations of 0-group distribution in the Barents Sea and time-series of abundance estimates are used to analyse these factors. The model indicates that spawning north of 67°N is favourable for offspring transport into the nursery grounds in the Barents Sea. The effect of latitude is stronger than across-shelf position for both growth and transport to the nursery grounds. The model predicts 0-group haddock outside the standard sampling area of the annual 0-group survey in the Barents Sea, which could partially explain the occasional occurrence of increase in cohort abundance from the 0-group to 1-year stage.
Recombinants of Bean common mosaic virus (BCMV) and Genetic Determinants of BCMV Involved in Overcoming Resistance in Common Bean
Authors: Feng Xue , Poplawsky Alan R. , Nikolaeva Olga V. , Myers James R. , Karasev Alexander V.
Published: June 2014

Bean common mosaic virus (BCMV) exists as a complex of strains classified by reactions to resistance genes found in common bean (Phaseolus vulgaris); seven BCMV pathotypes have been distinguished thus far, numbered I to VII. Virus genetic determinants involved in pathogenicity interactions with resistance genes have not yet been identified. Here, we describe the characterization of two novel field isolates of BCMV that helped to narrow down these genetic determinants interacting with specific P. vulgaris resistance factors. Based on a biological characterization on common bean differentials, both isolates were classified as belonging to pathotype VII, similar to control isolate US10, and both isolates exhibited the B serotype. The whole genome was sequenced for both isolates and found to be 98 to 99% identical to the BCMV isolate RU1 (pathotype VI), and a single name was retained: BCMV RU1-OR. To identify a genetic determinant of BCMV linked to the BCMV pathotype VII, the whole genome was also sequenced for two control isolates, US10 and RU1-P. Inspection of the nucleotide sequences for BCMV RU1-OR and US10 (both pathotype VII) and three closely related sequences of BCMV (RU1-P, RU1-D, and RU1-W, all pathotype VI) revealed that RU1-OR originated through a series of recombination events between US10 and an as-yet-unidentified BCMV parental genome, resulting in changes in virus pathology. The data obtained suggest that a fragment of the RU1-OR genome between positions 723 and 1,961 nucleotides that is common to US10 and RU1-OR in the P1-HC-Pro region of the BCMV genome may be responsible for the ability to overcome resistance in bean conferred by the bc-22 gene. This is the first report of a virus genetic determinant responsible for overcoming a specific BCMV resistance gene in common bean.
Synergism Between Southern rice black-streaked dwarf virus and Rice ragged stunt virus Enhances Their Insect Vector Acquisition
Authors: Li Shu , Wang Han , Zhou Guohui
Published: June 2014

Southern rice black-streaked dwarf virus (SRBSDV), a tentative species in the genus Fijivirus, family Reoviridae, is a novel rice virus transmitted by the white-backed planthopper (Sogatella furcifera). Since its discovery in 2001, SRBSDV has spread rapidly throughout eastern and southeastern Asia and caused large rice losses in China and Vietnam. Rice ragged stunt virus (RRSV) (genus Oryzavirus, family Reoviridae) is a common rice virus vectored by the brown planthopper (Nilaparvata lugens). RRSV is also widely distributed in eastern and southeastern Asia but has not previously caused serious problems in China owing to its low incidence. With SRBSDV's spread, however, RRSV has become increasingly common in China, and is frequently found in co-infection with SRBSDV. In this study, we show that SRBSDV and RRSV interact synergistically, the first example of synergism between plant viruses in the family Reoviridae. Rice plants co-infected with both viruses displayed enhanced stunting, earlier symptoms, and higher virus titers compared with singly infected plants. Furthermore, white-backed and brown planthoppers acquired SRBSDV and RRSV, respectively, from co-infected plants at higher rates. We propose that increased RRSV incidence in Chinese fields is partly due to synergism between SRBSDV and RRSV.
Microcrystallization techniques for serial femtosecond crystallography using photosystem II from
Thermosynechococcus elongatus
as a model system
Authors: Kupitz Christopher , Grotjohann Ingo , Conrad Chelsie E. , Roy-Chowdhury Shatabdi , Fromme Raimund , Fromme Petra
Published: June 2014

Serial femtosecond crystallography (SFX) is a new emerging method, where X-ray diffraction data are collected from a fully hydrated stream of nano- or microcrystals of biomolecules in their mother liquor using high-energy, X-ray free-electron lasers. The success of SFX experiments strongly depends on the ability to grow large amounts of well-ordered nano/microcrystals of homogeneous size distribution. While methods to grow large single crystals have been extensively explored in the past, method developments to grow nano/microcrystals in sufficient amounts for SFX experiments are still in their infancy. Here, we describe and compare three methods (batch, free interface diffusion (FID) and FID centrifugation) for growth of nano/microcrystals for time-resolved SFX experiments using the large membrane protein complex photosystem II as a model system.
The correlation of single-particle diffraction patterns as a continuous function of particle orientation
Authors: Martin Andrew V.
Published: June 2014

A statistical model for X-ray scattering of a non-periodic sample to high angles is introduced. It is used to calculate analytically the correlation of distinct diffraction measurements of a particle as a continuous function of particle orientation. Diffraction measurements with shot-noise are also considered. This theory provides a general framework for a deeper understanding of single particle imaging techniques used at X-ray free-electron lasers. Many of these techniques use correlations as a measure of diffraction-pattern similarity in order to determine properties of the sample, such as particle orientation.
Phasing coherently illuminated nanocrystals bounded by partial unit cells
Authors: Kirian Richard A. , Bean Richard J. , Beyerlein Kenneth R. , Yefanov Oleksandr M. , White Thomas A. , Barty Anton , Chapman Henry N.
Published: June 2014

With the use of highly coherent femtosecond X-ray pulses from a free-electron laser, it is possible to record protein nanocrystal diffraction patterns with far more information than is present in conventional crystallographic diffraction data. It has been suggested that diffraction phases may be retrieved from such data via iterative algorithms, without the use of
a priori
information and without restrictions on resolution. Here, we investigate the extension of this approach to nanocrystals with edge terminations that produce partial unit cells, and hence cannot be described by a common repeating unit cell. In this situation, the phase problem described in previous work must be reformulated. We demonstrate an approximate solution to this phase problem for crystals with random edge terminations.
Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography
Authors: Yefanov Oleksandr , Gati Cornelius , Bourenkov Gleb , Kirian Richard A. , White Thomas A. , Spence John C. H. , Chapman Henry N. , Barty Anton
Published: June 2014

Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 µm in size. This manuscript describes an alternative way of handling diffraction data recorded by serial femtosecond crystallography, by mapping the diffracted intensities into three-dimensional reciprocal space rather than integrating each image in two dimensions as in the classical approach. We call this procedure ‘three-dimensional merging’. This procedure retains information about asymmetry in Bragg peaks and diffracted intensities between Bragg spots. This intensity distribution can be used to extract reflection intensities for structure determination and opens up novel avenues for post-refinement, while observed intensity between Bragg peaks and peak asymmetry are of potential use in novel direct phasing strategies.
Two-dimensional imaging detectors for structural biology with X-ray lasers
Authors: Denes Peter
Published: June 2014

Our ability to harness the advances in microelectronics over the past decade(s) for X-ray detection has resulted in significant improvements in the state of the art. Biology with X-ray free-electron lasers present daunting detector challenges: all of the photons arrive at the same time, and individual high peak power pulses must be read out shot-by-shot. Direct X-ray detection in silicon pixel detectors—monolithic or hybrid—are the standard for XFELs today. For structural biology, improvements are needed for today's 10–100 Hz XFELs, and further improvements are required for tomorrow's 10+ kHz XFELs. This article will discuss detector challenges, why they arise and ways to overcome them, along with the current state of the art.
Singular value decomposition as a tool for background corrections in time-resolved XFEL scattering data
Authors: Haldrup Kristoffer
Published: June 2014

The development of new X-ray light sources, XFELs, with unprecedented time and brilliance characteristics has led to the availability of very large datasets with high time resolution and superior signal strength. The chaotic nature of the emission processes in such sources as well as entirely novel detector demands has also led to significant challenges in terms of data analysis. This paper describes a heuristic approach to datasets where spurious background contributions of a magnitude similar to (or larger) than the signal of interest prevents conventional analysis approaches. The method relies on singular-value decomposition of no-signal subsets of acquired datasets in combination with model inputs and appears generally applicable to time-resolved X-ray diffuse scattering experiments.
Aspects of direct phasing in femtosecond nanocrystallography
Authors: Millane Rick P. , Chen Joe P. J.
Published: June 2014

X-ray free-electron laser diffraction patterns from protein nanocrystals provide information on the diffracted amplitudes between the Bragg reflections, offering the possibility of direct phase retrieval without the use of ancillary experimental data. Proposals for implementing direct phase retrieval are reviewed. These approaches are limited by the signal-to-noise levels in the data and the presence of different and incomplete unit cells in the nanocrystals. The effects of low signal to noise can be ameliorated by appropriate selection of the intensity data samples that are used. The effects of incomplete unit cells may be small in some cases, and a unique solution is likely if there are four or fewer molecular orientations in the unit cell.
7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source
Authors: Pedrini Bill , Tsai Ching-Ju , Capitani Guido , Padeste Celestino , Hunter Mark S. , Zatsepin Nadia A. , Barty Anton , Benner W. Henry , Boutet Sébastien , Feld Geoffrey K. , Hau-Riege Stefan P. , Kirian Richard A. , Kupitz Christopher , Messerschmitt Marc , Ogren John I. , Pardini Tommaso , Segelke Brent , Williams Garth J. , Spence John C. H. , Abela Rafael , Coleman Matthew , Evans James E. , Schertler Gebhard F. X. , Frank Matthias , Li Xiao-Dan
Published: June 2014

Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump–probe experiments at subpicosecond time resolution.
Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers
Authors: Kern Jan , Hattne Johan , Tran Rosalie , Alonso-Mori Roberto , Laksmono Hartawan , Gul Sheraz , Sierra Raymond G. , Rehanek Jens , Erko Alexei , Mitzner Rolf , Wernet Phillip , Bergmann Uwe , Sauter Nicholas K. , Yachandra Vittal , Yano Junko
Published: June 2014

X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite,
cctbx.xfel
. This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL.
MicroRNA expression in mice infected with seasonal H1N1, swine H1N1 or highly pathogenic H5N1
Authors: Vela Eric M. , Kasoji Manjula D. , Wendling Morgan Q. , Price Jennifer A. , Knostman Katherine A. B. , Bresler Herbert S. , Long James P.
Published: June 2014

Influenza virus infections in humans remain a healthcare concern, and the need for vaccines, therapeutics and prophylactics remains a high priority. Understanding the molecular events associated with influenza-virus-induced pathology may lead to the identification of clinical disease biomarkers and novel antiviral targets. MicroRNAs (miRNAs) are well-conserved endogenous non-coding RNAs known to regulate post-transcriptional gene expression as well as play a major role in many biological processes and pathways. Animal studies have demonstrated that miRNAs are involved in viral disease and controlling inflammation. In this study, we examined the differences in the miRNA expression profiles associated with the lung in mice infected with influenza viruses that varied in virulence and pathogenicity. A statistical model was employed that utilized changes in miRNA expression to identify the virus that was used to infect the mice. This study identified a unique fingerprint of viral pathogenicity associated with seasonal H1N1, swine H1N1 and highly pathogenic H5N1 in the mouse model, and may lead to the identification of novel therapeutic and prophylactic targets.
Characterization of recombinant influenza A virus as a vector expressing respiratory syncytial virus fusion protein epitopes
Authors: Zhang Peirui , Gu Hongjing , Bian Chengrong , Liu Na , Li Zhiwei , Duan Yueqiang , Zhang Shaogeng , Wang Xiliang , Yang Penghui
Published: June 2014

Respiratory syncytial virus (RSV) is the most common cause of respiratory infection in infants and the elderly, and no vaccine against this virus has yet been licensed. Here, we report a recombinant PR8 influenza virus with the RSV fusion (F) protein epitopes of the subgroup A gene inserted into the influenza virus non-structural (NS) gene (rFlu/RSV/F) that was generated as an RSV vaccine candidate. The rescued viruses were assessed by microscopy and Western blotting. The proper expression of NS1, the NS gene product, and the nuclear export protein (NEP) of rFlu/RSV/F was also investigated using an immunofluorescent assay. The rescued virus replicated well in the MDCK kidney cell line, A549 lung adenocarcinoma cell line and CNE-2Z nasopharyngeal carcinoma cell line. BALB/c mice immunized intranasally with rFlu/RSV/F had specific haemagglutination inhibition antibody responses against the PR8 influenza virus and RSV neutralization test proteins. Furthermore, intranasal immunization with rFlu/RSV/F elicited T helper type 1-dominant cytokine profiles against the RSV strain A2 virus. Taken together, our findings suggested that rFlu/RSV/F was immunogenic in vivo and warrants further development as a promising candidate vaccine.
Dating the origin of the genus Flavivirus in the light of Beringian biogeography
Authors: Pettersson John H.-O. , Fiz-Palacios Omar
Published: June 2014

The genus Flavivirus includes some of the most important human viral pathogens, and its members are found in all parts of the populated world. The temporal origin of diversification of the genus has long been debated due to the inherent problems with dating deep RNA virus evolution. A generally accepted hypothesis suggests that Flavivirus emerged within the last 10 000 years. However, it has been argued that the tick-borne Powassan flavivirus was introduced into North America some time between the opening and closing of the Beringian land bridge that connected Asia and North America 15 000–11 000 years ago, indicating an even older origin for Flavivirus. To determine the temporal origin of Flavivirus, we performed Bayesian relaxed molecular clock dating on a dataset with high coverage of the presently available Flavivirus diversity by combining tip date calibrations and internal node calibration, based on the Powassan virus and Beringian land bridge biogeographical event. Our analysis suggested that Flavivirus originated ~85 000 (64 000–110 000) or 120 000 (87 000–159 000) years ago, depending on the circumscription of the genus. This is significantly older than estimated previously. In light of our results, we propose that it is likely that modern humans came in contact with several members of the genus Flavivirus much earlier than suggested previously, and that it is possible that the spread of several flaviviruses coincided with, and was facilitated by, the migration and population expansion of modern humans out of Africa.
Vaccinia virus virulence factor N1 can be ubiquitylated on multiple lysine residues
Authors: Maluquer de Motes Carlos , Schiffner Torben , Sumner Rebecca P. , Smith Geoffrey L.
Published: June 2014

Ubiquitylation is a covalent post-translational modification that regulates protein stability and is involved in many biological functions. Proteins may be modified with mono-ubiquitin or ubiquitin chains. Viruses have evolved multiple mechanisms to perturb the cell ubiquitin system and manipulate it to their own benefit. Here, we report ubiquitylation of vaccinia virus (VACV) protein N1. N1 is an inhibitor of the nuclear factor NF-κB and apoptosis that contributes to virulence, has a Bcl-2-like fold, and is highly conserved amongst orthopoxviruses. The interaction between N1 and ubiquitin occurs at endogenous protein levels during VACV infection and following ectopic expression of N1. Biochemical analysis demonstrated that N1 is covalently ubiquitylated, and heterodimers of ubiquitylated and non-ubiquitylated N1 monomers were identified, suggesting that ubiquitylation does not inhibit N1 dimerization. Studies with other VACV Bcl-2 proteins, such as C6 or B14, revealed that although these proteins also interact with ubiquitin, these interactions are non-covalent. Finally, mutagenesis of N1 showed that ubiquitylation occurs in a conventional lysine-dependent manner at multiple acceptor sites because only an N1 allele devoid of lysine residues remained unmodified. Taken together, we described a previously uncharacterized modification of the VACV protein N1 that provided a new layer of complexity to the biology of this virulence factor, and provided another example of the intricate interplay between poxviruses and the host ubiquitin system.
Evolutionary genetics of genotype H1 measles viruses in China from 1993 to 2012
Authors: Xu Songtao , Zhang Yan , Rivailler Pierre , Wang Huiling , Ji Yixin , Zhen Zhu , Mao Naiying , Li Chongshan , Bellini William J. , Xu Wenbo , Rota Paul A.
Published: June 2014

Virologic surveillance is a critical component of measles management. One of the criteria for verification of elimination of endemic measles is genetic analysis of wild-type viruses to demonstrate lack of an indigenous genotype. Measles is yet to be eliminated in China, and genotype H1 has been detected continuously since virologic surveillance was initiated in 1993. Virologic surveillance has been very active in China, providing a unique opportunity to conduct a detailed study of the evolution of a single, endemic genotype over a timespan of nearly two decades. Phylogenetic analysis performed on the 450 nt coding sequence for the C-terminal 150 amino acids of the nucleoprotein (N-450), fusion (F) gene and haemagglutinin (H) gene confirmed the continued circulation of genotype H1 viruses for 19 years. No evidence of selective pressure for the H protein was found. The substitution rates ranged from 0.75×10−3 substitutions site−1 year−1 for H to 1.65×10−3 substitutions site−1 year−1 for N-450. The time of most recent common ancestor (TMRCA) for genotype H1 was estimated as approximately 1985 (95 % highest probability density, 1979–1989). Finally, the overall diversity of measles sequences from China decreased from 2005 to 2012, coincident with a substantial decrease in measles cases. The results suggest that detailed evolutionary analyses should facilitate the documentation of eventual measles elimination in China. Moreover, the molecular approaches used in this study can be applied in other countries approaching measles elimination.
Bis(2-bromobenzyl) ether
Authors: Anuradha Venkatramu , Nagendra P. , Madan Kumar S. , Siddaraju B. P. , Lokanath N. K.
Published: June 2014

In the title compound, C14H12Br2O, the dihedral angle between the aromatic rings is 2.7 (3)° and the Br atoms lie on the same side of the molecule. No intermolecular interactions occur in the crystal beyond van der Waals contacts.
Corymbolone
Authors: Burrett Stacey , Taylor Dennis K. , Tiekink Edward R. T.
Published: June 2014

The title compound, C15H24O2[systematic name: (4S,4aR,6R,8aR)-4a-hydroxy-4,8a-dimethyl-6-(prop-1-en-2-yl)octahydronaphthalen-1(2H)-one], features two edge-shared six-membered rings with the hydroxyl and methyl substituents at this bridge beingtrans. One adopts a flattened chair conformation with the C atoms bearing the carbonyl and methyl substituents lying 0.5227 (16) and 0.6621 (15) Å, respectively, above and below the mean plane through the remaining four C atoms (r.m.s. deviation = 0.0145 Å). The second ring, bearing the prop-1-en-2-yl group, has a chair conformation. Supramolecular helical chains along thebaxis are found in the crystal packing, which are sustained by hydroxy–carbonyl O—H...O hydrogen bonding.
2-[4-(Trifluoromethyl)phenyl]-1H-benzimidazole
Authors: Krishnamurthy M. S. , Begum Noor Shahina
Published: June 2014

In the title compound, C14H9F3N2, the mean planes of the benzimidazole ring system and the trifluoromethyl-substituted benzene ring form a dihedral angle of 30.1 (1)°. In the crystal, molecules are linked by N—H...N hydrogen bonds into chains along [010]. Weak C—H...F hydrogen bonds and a weak C—H...π interaction connect the chains into a two-dimensional network parallel to (001).
(η6-Benzene)dichlorido(chlorodicyclohexylphosphane-κP)ruthenium(II) chloroform monosolvate
Authors: Gowrisankar Saravanan , Neumann Helfried , Spannenberg Anke , Beller Matthias
Published: June 2014

The title compound, [RuCl2(η6-C6H6)(C12H22ClP)]·CHCl3, was prepared by reaction of [RuCl2(η6-C6H6)]2with chlorodicyclohexylphosphane in CHCl3at 323 K under argon. The RuIIatom is surrounded by one arene ligand, two Cl atoms and a phosphane ligand in a piano-stool geometry. The phosphane ligand is linked by the P atom, with an Ru—P bond length of 2.3247 (4) Å. Both cyclohexyl rings at the P atom adopt a chair conformation. In the crystal, the RuIIcomplex molecule and the chloroform solvent molecule are linked by a bifurcated C—H...(Cl,Cl) hydrogen bond. Intramolecular C—H...Cl hydrogen bonds are also observed.
1-{3-(4-Chlorophenyl)-5-[4-(propan-2-yl)phenyl]-4,5-dihydro-1H-pyrazol-1-yl}butan-1-one
Authors: Narayana B. , Salian Vinutha V. , Sarojini Balladka K. , Jasinski Jerry P.
Published: June 2014

In the title compound, C22H25ClN2O, the pyrazole ring exhibits an envelope conformation with the methine C atom as the flap. The benzene rings are twisted by 3.3 (5) and 84.6 (5)° from the pyrazole mean plane, and are inclined to each other by 81.4 (4)°. In the crystal, pairs of weak C—H...O hydrogen bonds form centrosymmetric dimers with anR22(16) graph-set motif. C—H...π interactions link the dimers into columns propagating in [100].
Thortveitite-type Tm2Si2O7
Authors: Kahlenberg Volker , Aichholzer Paul
Published: June 2014

Single crystals of dithulium disilicate, Tm2Si2O7, were obtained in flux synthesis experiments in the system SiO2–Tm2O3–LiF at ambient pressure. The compound belongs to the group of sorosilicates,i.e.it is based on [Si2O7]-units and crystallizes in the thortveitite (Sc2Si2O7) structure type. The Tm3+cation (site symmetry .2.) occupies a distorted octahedral site, with Tm—O bond lengths in the range 2.217 (4)–2.289 (4) Å. Each of the octahedra shares three of its edges with adjacent [TmO6] groups, resulting in the formation of layers parallel to (001). The individual [SiO4] tetrahedra are more regular,i.e.the differences between the bond lengths between Si and the bridging and non-bridging O atoms are not very pronounced. The layers containing the octahedra and the sheets containing the [Si2O7] groups (point group symmetry 2/m) form an alternating sequence. Linkage is provided by sharing common oxygen vertices.