bluuebunny/crossref_metadata_2025 huggingface dataset:
Whose land is it? Land reform, minorities, and the titular “nation” in Kazakhstan, Kyrgyzstan, and Tajikistan
Authors: Hierman Brent , Nekbakhtshoev Navruz
Published: March 2014

Each of the post-Soviet Central Asian states inherited both inefficient collectivized agricultural systems and an understanding of the nation rooted in categories defined by Soviet nationality policy. Despite the importance placed on territorial homelands in many contemporary understandings of nationalism, the divergent formal responses to these dual Soviet legacies have generally been studied in isolation from one another. However, there are conceptual reasons to expect more overlap in these responses than generally assumed; in this paper, we engage in a focused comparison of three post-Soviet Central Asian states (Kazakhstan, Kyrgyzstan, and Tajikistan) in order to investigate how nationalizing policies and discourse, land distribution, and ethnic tensions interact with each other over time. We reveal that the nationalizing discourses of the three states – despite promoting the titular groups vis-à-vis other groups – have had limited influence on the actual processes of land distribution. Furthermore, the Kyrgyzstani case challenges the assumption that the effect flows unidirectionally from nationalizing policies and discourse to land reform implementation; in this case, there is evidence that the disruption caused by farm reorganization generated grievances which werethenarticulated by some nationalistic political elites.
From local to global: transformations of Bukharan Jewish community organization in the twentieth century
Authors: Levin Zeev
Published: March 2014

This article is a review of the development of the Bukharan Jewish community organization. It describes the transformations it has undergone in the twentieth century and examines the changes that Bukharan Jews underwent from demographic, social, and organizational perspectives, and the far-reaching processes that have occurred later in community organizations, particularly in light of the establishment of the World Congress of Bukharan Jewry in 2000. Traditionally, when dealing with Jewish communities the term “diaspora” refers to different Jewish communities scattered away from the “promised land” (Diatlov 1999). Thus, the terminology of: “Jewish immigration” traditionally is considered as their return. In this article, which focuses on Bukharan Jews, I use “diaspora” to describe different Bukharan communities created due to immigration to the land of Israel and to other destinations from the cradle of Central Asia.
Stoichiometry of altered hERG1 channel gating by small molecule activators
Authors: Wu Wei , Sachse Frank B. , Gardner Alison , Sanguinetti Michael C.
Published: March 2014

Voltage-gated K+ channels are tetramers formed by coassembly of four identical or highly related subunits. All four subunits contribute to formation of the selectivity filter, the narrowest region of the channel pore which determines K+ selective conductance. In some K+ channels, the selectivity filter can undergo a conformational change to reduce K+ flux by a mechanism called C-type inactivation. In human ether-a-go-go–related gene 1 (hERG1) K+ channels, C-type inactivation is allosterically inhibited by ICA-105574, a substituted benzamide. PD-118057, a 2-(phenylamino) benzoic acid, alters selectivity filter gating to enhance open probability of channels. Both compounds bind to a hydrophobic pocket located between adjacent hERG1 subunits. Accordingly, a homotetrameric channel contains four identical activator binding sites. Here we determine the number of binding sites required for maximal drug effect and determine the role of subunit interactions in the modulation of hERG1 gating by these compounds. Concatenated tetramers were constructed to contain a variable number (zero to four) of wild-type and mutant hERG1 subunits, either L646E to inhibit PD-118057 binding or F557L to inhibit ICA-105574 binding. Enhancement of hERG1 channel current magnitude by PD-118057 and attenuated inactivation by ICA-105574 were mediated by cooperative subunit interactions. Maximal effects of the both compounds required the presence of all four binding sites. Understanding how hERG1 agonists allosterically modify channel gating may facilitate mechanism-based drug design of novel agents for treatment of long QT syndrome.
Mechanotransduction and hyperpolarization-activated currents contribute to spontaneous activity in mouse vestibular ganglion neurons
Authors: Horwitz Geoffrey C. , Risner-Janiczek Jessica R. , Holt Jeffrey R.
Published: March 2014

The hyperpolarization-activated, cyclic nucleotide–sensitive current, Ih, is present in vestibular hair cells and vestibular ganglion neurons, and is required for normal balance function. We sought to identify the molecular correlates and functional relevance of Ih in vestibular ganglion neurons. Ih is carried by channels consisting of homo- or heteromeric assemblies of four protein subunits from the Hcn gene family. The relative expression of Hcn1–4 mRNA was examined using a quantitative reverse transcription PCR (RT-PCR) screen. Hcn2 was the most highly expressed subunit in vestibular neuron cell bodies. Immunolocalization of HCN2 revealed robust expression in cell bodies of all vestibular ganglion neurons. To characterize Ih in vestibular neuron cell bodies and at hair cell–afferent synapses, we developed an intact, ex vivo preparation. We found robust physiological expression of Ih in 89% of cell bodies and 100% of calyx terminals. Ih was significantly larger in calyx terminals than in cell bodies; however, other biophysical characteristics were similar. Ih was absent in calyces lacking Hcn1 and Hcn2, but small Ih was still present in cell bodies, which suggests expression of an additional subunit, perhaps Hcn4. To determine the contributions of hair cell mechanotransduction and Ih to the firing patterns of calyx terminals, we recorded action potentials in current-clamp mode. Mechanotransduction currents were modulated by hair bundle defection and application of calcium chelators to disrupt tip links. Ih activity was modulated using ZD7288 and cAMP. We found that both hair cell transduction and Ih contribute to the rate and regularity of spontaneous action potentials in the vestibular afferent neurons. We propose that modulation of Ih in vestibular ganglion neurons may provide a mechanism for modulation of spontaneous activity in the vestibular periphery.
Prenatal Programming of Pulmonary Hypertension Induced by Chronic Hypoxia or Ductal Ligation in Sheep
Authors: Papamatheakis Demosthenes G. , Chundu Madalitso , Blood Arlin B. , Wilson Sean M.
Published: March 2014

Pulmonary hypertension of the newborn is caused by a spectrum of functional and structural abnormalities of the cardiopulmonary circuit. The existence of multiple etiologies and an incomplete understanding of the mechanisms of disease progression have hindered the development of effective therapies. Animal models offer a means of gaining a better understanding of the fundamental basis of the disease. To that effect, a number of experimental animal models are being used to generate pulmonary hypertension in the fetus and newborn. In this review, we compare the mechanisms associated with pulmonary hypertension caused by two such models: in utero ligation of the ductus arteriosus and chronic perinatal hypoxia in sheep fetuses and newborns. In this manner, we make direct comparisons between ductal ligation and chronic hypoxia with respect to the associated mechanisms of disease, since multiple studies have been performed with both models in a single species. We present evidence that the mechanisms associated with pulmonary hypertension are dependent on the type of stress to which the fetus is subjected. Such an analysis allows for a more thorough evaluation of the disease etiology, which can help focus clinical treatments. The final part of the review provides a clinical appraisal of current treatment strategies and lays the foundation for developing individualized therapies that depend on the causative factors.
Rescue Balloon Pulmonary Angioplasty in a Rapidly Deteriorating Chronic Thromboembolic Pulmonary Hypertension Patient with Liver Failure and Refractory Infection
Authors: Tsuji Akihiro , Ogo Takeshi , Demachi Jun , Ono Yusuke , Sanda Yoshihiro , Morita Yoshihiro , Fukuda Tetsuya , Nakanishi Norifumi
Published: March 2014

Pulmonary endarterectomy (PEA) is the standard therapy for chronic thromboembolic pulmonary hypertension (CTEPH). Balloon pulmonary angioplasty (BPA) is an alternative therapy for such patients. Here we report the case of a 60‐year‐old woman who presented with severe CTEPH resulting in low cardiac output and liver failure. Her clinical status rapidly deteriorated after she developed a respiratory infection that was refractory to antibiotic treatment. PEA was risky because of her unstable hemodynamics, uncontrolled infection, and liver failure with jaundice. We thus performed rescue BPA. After 3 BPA procedures, her cardiac symptoms improved from World Health Organization functional class IV to II, and her jaundice resolved. The day after her final BPA procedure, her hemodynamics dramatically improved, and she continued to show improvement 3 months later. We thus suggest that BPA is a good treatment option in CTEPH patients with rapidly deteriorating heart failure and uncontrolled comorbidities.
The History of ICSID
Authors: Parra Antonio R.
Published: March 2014

This book details the history and development of the International Centre for Settlement of Investment Disputes (ICSID) and its constituent treaty, the Convention on the Settlement of Investment Disputes between States and Nationals of Other States, covering the years from 1955 to 2010. The book traces the immediate origins of the Convention, in the years 1955 to 1962, and gives a stage-by-stage narrative of the drafting of the Convention between 1962 and 1965. It recounts details of bringing the Convention into force in 1966 and the elaboration of the initial versions of the Regulations and Rules of ICSID adopted at the first meetings of its Administrative Council in 1967. The three periods 1968 to 1988, 1989 to 1999, and 2000 to June 30, 2010, are covered in separate chapters which examine the expansion of the Centre's activities and changes made to the Regulations and Rules over the years. There are also overviews of the conciliation and arbitration cases submitted to ICSID in the respective periods, followed by in-depth discussions of selected cases and key issues within them. A concluding chapter discusses some of the broad themes and findings of the book, and includes several suggestions for further changes at ICSID to help ensure its continued success.
Perceptual awareness and its neural basis: bridging experimental and theoretical paradigms
Authors: Raffone Antonino , Srinivasan Narayanan , van Leeuwen Cees
Published: March 2014

Understanding consciousness is a major scientific challenge of our times, and perceptual awareness is an integral part of that challenge. This Theme Issue aims to provide a timely focus on crucial insights from leading scientists on perceptual awareness and its neural basis. The issue refers to key research questions and findings in perceptual awareness research and aims to be a catalyst for further research, by bringing together the state-of-the-art. It shows how bridges are being built between empirical and theoretical research and proposes new directions for the study of multisensory awareness and the role of the states of the body therein. In this introduction, we highlight crucial problems that have characterized the development of the study of perceptual awareness. We then provide an overview of major experimental and theoretical paradigms related to perceptual awareness and its neural basis. Finally, we present an overview of the Theme Issue, with reference to the contributed articles and their relationships.
The neural subjective frame: from bodily signals to perceptual consciousness
Authors: Park Hyeong-Dong , Tallon-Baudry Catherine
Published: March 2014

The report ‘I saw the stimulus’ operationally defines visual consciousness, but where does the ‘I’ come from? To account for the subjective dimension of perceptual experience, we introduce the concept of the neural subjective frame. The neural subjective frame would be based on the constantly updated neural maps of the internal state of the body and constitute a neural referential from which first person experience can be created. We propose to root the neural subjective frame in the neural representation of visceral information which is transmitted through multiple anatomical pathways to a number of target sites, including posterior insula, ventral anterior cingulate cortex, amygdala and somatosensory cortex. We review existing experimental evidence showing that the processing of external stimuli can interact with visceral function. The neural subjective frame is a low-level building block of subjective experience which is not explicitly experienced by itself which is necessary but not sufficient for perceptual experience. It could also underlie other types of subjective experiences such as self-consciousness and emotional feelings. Because the neural subjective frame is tightly linked to homeostatic regulations involved in vigilance, it could also make a link between state and content consciousness.
Visual perception from the perspective of a representational, non-reductionistic, level-dependent account of perception and conscious awareness
Authors: Overgaard Morten , Mogensen Jesper
Published: March 2014

This article proposes a new model to interpret seemingly conflicting evidence concerning the correlation of consciousness and neural processes. Based on an analysis of research of blindsight and subliminal perception, the reorganization of elementary functions and consciousness framework suggests that mental representations consist of functions at several different levels of analysis, including truly localized perceptual elementary functions and perceptual algorithmic modules, which are interconnections of the elementary functions. We suggest that conscious content relates to the ‘top level’ of analysis in a ‘situational algorithmic strategy’ that reflects the general state of an individual. We argue that conscious experience is intrinsically related to representations that are available to guide behaviour. From this perspective, we find that blindsight and subliminal perception can be explained partly by too coarse-grained methodology, and partly by top-down enhancing of representations that normally would not be relevant to action.
The graded and dichotomous nature of visual awareness
Authors: Windey Bert , Vermeiren Astrid , Atas Anne , Cleeremans Axel
Published: March 2014

Is our visual experience of the world graded or dichotomous? Opposite pre-theoretical intuitions apply in different cases. For instance, when looking at a scene, one has a distinct sense that our experience has a graded character: one cannot say that there is no experience of contents that fall outside the focus of attention, but one cannot say that there is full awareness of such contents either. By contrast, when performing a visual detection task, our sense of having perceived the stimulus or not exhibits a more dichotomous character. Such issues have recently been the object of intense debate because different theoretical frameworks make different predictions about the graded versus dichotomous character of consciousness. Here, we review both relevant empirical findings as well as the associated theories (i.e. local recurrent processing versus global neural workspace theory). Next, we attempt to reconcile such contradictory theories by suggesting that level of processing is an often-ignored but highly relevant dimension through which we can cast a novel look at existing empirical findings. Thus, using a range of different stimuli, tasks and subjective scales, we show that processing low-level, non-semantic content results in graded visual experience, whereas processing high-level semantic content is experienced in a more dichotomous manner. We close by comparing our perspective with existing proposals, focusing in particular on the partial awareness hypothesis.
Subjective visual perception: from local processing to emergent phenomena of brain activity
Authors: Panagiotaropoulos Theofanis I. , Kapoor Vishal , Logothetis Nikos K.
Published: March 2014

The combination of electrophysiological recordings with ambiguous visual stimulation made possible the detection of neurons that represent the content of subjective visual perception and perceptual suppression in multiple cortical and subcortical brain regions. These neuronal populations, commonly referred to as the
neural correlates of consciousness
, are more likely to be found in the temporal and prefrontal cortices as well as the pulvinar, indicating that the content of perceptual awareness is represented with higher fidelity in higher-order association areas of the cortical and thalamic hierarchy, reflecting the outcome of competitive interactions between conflicting sensory information resolved in earlier stages. However, despite the significant insights into conscious perception gained through monitoring the activities of single neurons and small, local populations, the immense functional complexity of the brain arising from correlations in the activity of its constituent parts suggests that local, microscopic activity could only partially reveal the mechanisms involved in perceptual awareness. Rather, the dynamics of functional connectivity patterns on a mesoscopic and macroscopic level could be critical for conscious perception. Understanding these emergent spatio-temporal patterns could be informative not only for the stability of subjective perception but also for spontaneous perceptual transitions suggested to depend either on the dynamics of antagonistic ensembles or on global intrinsic activity fluctuations that may act upon explicit neural representations of sensory stimuli and induce perceptual reorganization. Here, we review the most recent results from local activity recordings and discuss the potential role of effective, correlated interactions during perceptual awareness.
Hydrogen peroxide thermochemical oscillator as driver for primordial RNA replication
Authors: Ball Rowena , Brindley John
Published: March 2014

This paper presents and tests a previously unrecognised mechanism for driving a replicating molecular system on the prebiotic earth. It is proposed that cell-free RNA replication in the primordial soup may have been driven by self-sustained oscillatory thermochemical reactions. To test this hypothesis a well-characterised hydrogen peroxide oscillator was chosen as the driver and complementary RNA strands with known association and melting kinetics were used as the substrate. An open flow system model for the self-consistent, coupled evolution of the temperature and concentrations in a simple autocatalytic scheme is solved numerically, and it is shown that thermochemical cycling drives replication of the RNA strands. For the (justifiably realistic) values of parameters chosen for the simulated example system, the mean amount of replicant produced at steady state is 6.56 times the input amount, given a constant supply of substrate species. The spontaneous onset of sustained thermochemical oscillations via slowly drifting parameters is demonstrated, and a scheme is given for prebiotic production of complementary RNA strands on rock surfaces.
Metabolic free energy and biological codes: a ‘Data Rate Theorem’ aging model
Authors: Wallace Rodrick
Published: March 2014

The living state is cognitive at every scale and level of organization. Since it is possible to associate a broad class of cognitive processes with ‘dual’ information sources, many pathologies can be addressed using statistical models based on the Shannon Coding, the Shannon-McMillan Source Coding, the Rate Distortion, and the Data Rate Theorems, as these impose powerful necessary condition constraints on information generation and exchange, and on system control. Deterministic-but-for-error biological codes do not directly invoke cognition, although they may be essential subcomponents within larger cognitive processes. A formal argument, however, places such codes within a similar framework, with metabolic free energy serving as a ‘control signal’ stabilizing biochemical code-and-translator dynamics in the presence of noise. Demand beyond available energy supply then expresses itself in punctuated destabilization of the coding channel, affecting a spectrum of essential biological functions. Aging, normal or prematurely driven by psychosocial or environmental stressors, must eventually interfere with the routine operation of such mechanisms, triggering chronic diseases associated with senescence. Amyloid fibril formation, intrinsically disordered protein logic gates, and cell surface glycan/lectin ‘kelp bed’ logic gates are reviewed from this perspective. The results, however, generalize beyond coding machineries having easily recognizable symmetry modes, and strip a full layer of mathematical complication from the study of phase transitions in nonequilibrium biological systems.
Genetic variation in COMT activity impacts learning and dopamine release capacity in the striatum
Authors: Simpson Eleanor H. , Morud Julia , Winiger Vanessa , Biezonski Dominik , Zhu Judy P. , Bach Mary Elizabeth , Malleret Gael , Polan H. Jonathan , Ng-Evans Scott , Phillips Paul E.M. , Kellendonk Christoph , Kandel Eric R.
Published: March 2014

A common genetic polymorphism that results in increased activity of the dopamine regulating enzyme COMT (theCOMT Val158allele) has been found to associate with poorer cognitive performance and increased susceptibility to develop psychiatric disorders. It is generally assumed that this increase in COMT activity influences cognitive function and psychiatric disease risk by increasing dopamine turnover in cortical synapses, though this cannot be directly measured in humans. Here we explore a novel transgenic mouse model of increased COMT activity, equivalent to the relative increase in activity observed with the humanCOMT Val158allele. By performing an extensive battery of behavioral tests, we found that COMT overexpressing mice (COMT-OE mice) exhibit cognitive deficits selectively in the domains that are affected by theCOMT Val158allele, stimulus–response learning and working memory, functionally validating our model of increased COMT activity. Although we detected no changes in the level of markers for dopamine synthesis and dopamine transport, we found that COMT-OE mice display an increase in dopamine release capacity in the striatum. This result suggests that increased COMT activity may not only affect dopamine signaling by enhancing synaptic clearance in the cortex, but may also cause changes in presynaptic dopamine function in the striatum. These changes may underlie the behavioral deficits observed in the mice and might also play a role in the cognitive deficits and increased psychiatric disease risk associated with genetic variation in COMT activity in humans.
Activity-dependent inhibitory gating in molecular signaling cascades induces a novel form of intermediate-term synaptic facilitation in Aplysia californica
Authors: Fischbach Soren , Kopec Ashley M. , Carew Thomas J.
Published: March 2014

Mechanistically distinct forms of long-lasting plasticity and memory can be induced by a variety of different training patterns. Although several studies have identified distinct molecular pathways that are engaged during these different training patterns, relatively little work has explored potential interactions between pathways when they are simultaneously engaged in the same neurons and circuits during memory formation. Aplysia californica exhibits two forms of intermediate-term synaptic facilitation (ITF) in response to two different training patterns: (1) repeated trial (RT) ITF (induced by repeated tail nerve shocks [TNSs] or repeated serotonin [5HT] application) and (2) activity-dependent (AD) ITF (induced by sensory neuron activation paired with a single TNS or 5HT pulse). RT-ITF requires PKA activation and de novo protein synthesis, while AD-ITF requires PKC activation and has no requirement for protein synthesis. Here, we explored how these distinct molecular pathways underlying ITF interact when both training patterns occur in temporal register (an “Interactive” training pattern). We found that (1) RT, AD, and Interactive training all induce ITF; (2) Interactive ITF requires PKC activity but not de novo protein synthesis; and (3), surprisingly, Interactive training blocks persistent PKA activity 1 h after training, and this block is PKC-independent. These data support the hypothesis that sensory neuron activity coincident with the last RT training trial is sufficient to convert the molecular signaling already established by RT training into an AD-like molecular phenotype.
Behavioral flexibility is increased by optogenetic inhibition of neurons in the nucleus accumbens shell during specific time segments
Authors: Aquili Luca , Liu Andrew W. , Shindou Mayumi , Shindou Tomomi , Wickens Jeffery R.
Published: March 2014

Behavioral flexibility is vital for survival in an environment of changing contingencies. The nucleus accumbens may play an important role in behavioral flexibility, representing learned stimulus–reward associations in neural activity during response selection and learning from results. To investigate the role of nucleus accumbens neural activity in behavioral flexibility, we used light-activated halorhodopsin to inhibit nucleus accumbens shell neurons during specific time segments of a bar-pressing task requiring a win–stay/lose–shift strategy. We found that optogenetic inhibition during action selection in the time segment preceding a lever press had no effect on performance. However, inhibition occurring in the time segment during feedback of results—whether rewards or nonrewards—reduced the errors that occurred after a change in contingency. Our results demonstrate critical time segments during which nucleus accumbens shell neurons integrate feedback into subsequent responses. Inhibiting nucleus accumbens shell neurons in these time segments, during reinforced performance or after a change in contingencies, increases lose–shift behavior. We propose that the activity of nucleus shell accumbens shell neurons in these time segments plays a key role in integrating knowledge of results into subsequent behavior, as well as in modulating lose–shift behavior when contingencies change.
Structural and biochemical characterization of MdaB from cariogenicStreptococcus mutansreveals an NADPH-specific quinone oxidoreductase
Authors: Wang Zixi , Li Lanfen , Dong Yu-Hui , Su Xiao-Dong
Published: March 2014

Thesmu.1420 gene from the cariogenic pathogenStreptococcus mutansencodes a putative protein which has sequence homology to NQO [NAD(P)H:quinone oxidoreductase] family members, including mammalian NQO and bacterial MdaB (modulator of drug activity B). NQO can detoxify quinones by converting them to hydroquinones and prevent the generation of reactive oxygen species. Thus, comprehensive studies on Smu.1420 will be important for uncovering the antioxidation and antidrug mechanisms ofS. mutans. Here, the catalytic properties of Smu.1420 have been characterized, and its structure was determined in complexes with NADP+and menadione, respectively. Smu.1420 binds menadione directly and exhibits a pronounced preference for NADPH over NADH as a substrate, demonstrating that it is an NADPH-specific quinone oxidoreductase. The structure of Smu.1420 shows a compact homodimer with two substrate pockets located in the cleft of the dimer interface. The nicotinamide moiety of NADP+is bound on top of the isoalloxazine moiety of the FAD cofactor and overlaps with the binding site of menadione, suggesting a hydride-transfer process from NADPH to FAD and then to menadione. Two strongly basic patches near the substrate pocket are expected to confer the preference for NADPH over NADH. These studies shed light on future drug development against the cariogenic pathogenS. mutans.
Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase fromMethanococcus jannaschii
Authors: Lee Eun Hye , Lee Kitaik , Hwang Kwang Yeon
Published: March 2014

The aconitase family of proteins includes three classes of hydro-lyase enzymes: aconitases, homoaconitases and isopropylmalate (IPM) isomerases. They have a common Fe–S cluster-binding site and catalyze the isomerization of specific substrates by sequential dehydration and hydration. The archaeonMethanococcus jannaschiicontains two aconitase family proteins, IPM isomerase and homoaconitase, which have 50% sequence identity. These two enzymes are heterodimeric proteins composed of large and small subunits encoded by separate genes. Although structures have been reported for the small subunits of the two enzymes, the first structures of oxidized and reduced forms of the large subunit of IPM isomerase (ox-MJ0499 and red-MJ0499, respectively) fromM. jannaschiiare reported here at 1.8 and 2.7 Å resolution, respectively, together with the structure of the large subunit of homoaconitase (MJ1003) at 2.5 Å resolution. The structures of both proteins have unbound Fe–S clusters and contain a fourth cysteine in the active site. The active site of MJ1003 is homologous to that of aconitase, whereas MJ0499 has significant structural distortion at the active site compared with aconitase. In addition, significant large conformational changes were observed in the active site of red-MJ0499 when compared with ox-MJ0499. The active sites of the two proteins adopt two different states before changing to the Fe–S cluster-bound `activated' state observed in aconitase. MJ1003 has an `open' active site, which forms an active pocket for the cluster, while ox-MJ0499 has a `closed' active site, with four cysteines in disulfide bonds. These data will be helpful in understanding the biochemical mechanism of clustering of the Fe–S protein family.
Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting
Authors: Chen Lei , Liu Tian , Zhou Yong , Chen Qi , Shen Xu , Yang Qing
Published: March 2014

Insects possess a greater number of chitinases than any other organisms. This work is the first report of unliganded and oligosaccharide-complexed crystal structures of the insect chitinaseOfChtI fromOstrinia furnacalis, which is essential to moulting. The obtained crystal structures were solved at resolutions between 1.7 and 2.2 Å. A structural comparison with other chitinases revealed thatOfChtI contains a long substrate-binding cleft similar to the bacterial chitinaseSmChiB fromSerratia marcescens. However, unlike the exo-actingSmChiB, which has a blocked and tunnel-like cleft,OfChtI possesses an open and groove-like cleft. The complexed structure of the catalytic domain ofOfChtI (OfChtI-CAD) with (GlcNAc)2/3indicates that the reducing sugar at subsite −1 is in an energetically unfavoured `boat' conformation, a state that possibly exists just before the completion of catalysis. BecauseOfChtI is known to act from nonreducing ends, (GlcNAc)3would be a hydrolysis product of (GlcNAc)6, suggesting thatOfChtI possesses an endo enzymatic activity. Furthermore, a hydrophobic plane composed of four surface-exposed aromatic residues is adjacent to the entrance to the substrate-binding cleft. Mutations of these residues greatly impair the chitin-binding activity, indicating that this hydrophobic plane endowsOfChtI-CAD with the ability to anchor chitin. This work reveals the unique structural characteristics of an insect chitinase.
Simultaneous use of solution NMR and X-ray data inREFMAC5 for joint refinement/detection of structural differences
Authors: Rinaldelli Mauro , Ravera Enrico , Calderone Vito , Parigi Giacomo , Murshudov Garib N. , Luchinat Claudio
Published: March 2014

The programREFMAC5 fromCCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints inREFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.
Characterization of the proline-utilization pathway inMycobacterium tuberculosisthrough structural and functional studies
Authors: Lagautriere Thomas , Bashiri Ghader , Paterson Neil G. , Berney Michael , Cook Gregory M. , Baker Edward N.
Published: March 2014

The proline-utilization pathway inMycobacterium tuberculosis(Mtb) has recently been identified as an important factor inMtbpersistencein vivo, suggesting that this pathway could be a valuable therapeutic target against tuberculosis (TB). InMtb, two distinct enzymes perform the conversion of proline into glutamate: the first step is the oxidation of proline into Δ1-pyrroline-5-carboxylic acid (P5C) by the flavoenzyme proline dehydrogenase (PruB), and the second reaction involves converting the tautomeric form of P5C (glutamate-γ-semialdehyde) into glutamate using the NAD+-dependent Δ1-pyrroline-5-carboxylic dehydrogenase (PruA). Here, the three-dimensional structures ofMtb-PruA, determined by X-ray crystallography, in the apo state and in complex with NAD+are described at 2.5 and 2.1 Å resolution, respectively. The structure reveals a conserved NAD+-binding mode, common to other related enzymes. Species-specific conformational differences in the active site, however, linked to changes in the dimer interface, suggest possibilities for selective inhibition ofMtb-PruA despite its reasonably high sequence identity to other PruA enzymes. Using recombinant PruA and PruB, the proline-utilization pathway inMtbhas also been reconstitutedin vitro. Functional validation using a novel NMR approach has demonstrated that the PruA and PruB enzymes are together sufficient to convert proline to glutamate, the first such demonstration for monofunctional proline-utilization enzymes.
The structures of cytosolic and plastid-located glutamine synthetases fromMedicago truncatulareveal a common and dynamic architecture
Authors: Torreira Eva , Seabra Ana Rita , Marriott Hazel , Zhou Min , Llorca Óscar , Robinson Carol V. , Carvalho Helena G. , Fernández-Tornero Carlos , Pereira Pedro José Barbosa
Published: March 2014

The first step of nitrogen assimilation in higher plants, the energy-driven incorporation of ammonia into glutamate, is catalyzed by glutamine synthetase. This central process yields the readily metabolizable glutamine, which in turn is at the basis of all subsequent biosynthesis of nitrogenous compounds. The essential role performed by glutamine synthetase makes it a prime target for herbicidal compounds, but also a suitable intervention point for the improvement of crop yields. Although the majority of crop plants are dicotyledonous, little is known about the structural organization of glutamine synthetase in these organisms and about the functional differences between the different isoforms. Here, the structural characterization of two glutamine synthetase isoforms from the model legumeMedicago truncatulais reported: the crystallographic structure of cytoplasmic GSII-1a and an electron cryomicroscopy reconstruction of plastid-located GSII-2a. Together, these structural models unveil a decameric organization of dicotyledonous glutamine synthetase, with two pentameric rings weakly connected by inter-ring loops. Moreover, rearrangement of these dynamic loops changes the relative orientation of the rings, suggesting a zipper-like mechanism for their assembly into a decameric enzyme. Finally, the atomic structure ofM. truncatulaGSII-1a provides important insights into the structural determinants of herbicide resistance in this family of enzymes, opening new avenues for the development of herbicide-resistant plants.
The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase fromThermus thermophilusHB8
Authors: Pampa Kudigana J. , Lokanath Neratur K. , Kunishima Naoki , Rai Ravishankar Vittal
Published: March 2014

2-Keto-3-deoxygluconate (KDG) is one of the important intermediates in pectin metabolism. An enzyme involved in this pathway, 3-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (DDGDH), has been identified which converts 2,5-diketo-3-deoxygluconate to KDG. The enzyme is a member of the short-chain dehydrogenase (SDR) family. To gain insight into the function of this enzyme at the molecular level, the first crystal structure of DDGDH fromThermus thermophilusHB8 has been determined in the apo form, as well as in complexes with the cofactor and with citrate, by X-ray diffraction methods. The crystal structures reveal a tight tetrameric oligomerization. The secondary-structural elements and catalytically important residues of the enzyme were highly conserved amongst the proteins of the NAD(P)-dependent SDR family. The DDGDH protomer contains a dinucleotide-binding fold which binds the coenzyme NAD+in an intersubunit cleft; hence, the observed oligomeric state might be important for the catalytic function. This enzyme prefers NAD(H) rather than NADP(H) as the physiological cofactor. A structural comparison of DDGDH with mouse lung carbonyl reductase suggests that a significant difference in the α–loop–α region of this enzyme is associated with the coenzyme specificity. The structural data allow a detailed understanding of the functional role of the conserved catalytic triad (Ser129–Tyr144–Lys148) in cofactor and substrate recognition, thus providing substantial insights into DDGDH catalysis. From analysis of the three-dimensional structure, intersubunit hydrophobic interactions were found to be important for enzyme oligomerization and thermostability.
Structural basis for the redox sensitivity of theMycobacterium tuberculosisSigK–RskA σ–anti-σ complex
Authors: Shukla Jinal , Gupta Radhika , Thakur Krishan Gopal , Gokhale Rajesh , Gopal B.
Published: March 2014

The host–pathogen interactions inMycobacterium tuberculosisinfection are significantly influenced by redox stimuli and alterations in the levels of secreted antigens. The extracytoplasmic function (ECF) σ factor σKgoverns the transcription of the serodominant antigens MPT70 and MPT83. The cellular levels of σKare regulated by the membrane-associated anti-σK(RskA) that localizes σKin an inactive complex. The crystal structure ofM. tuberculosisσKin complex with the cytosolic domain of RskA (RskAcyto) revealed a disulfide bridge in the −35 promoter-interaction region of σK. Biochemical experiments reveal that the redox potential of the disulfide-forming cysteines in σKis consistent with its role as a sensor. The disulfide bond in σKinfluences the stability of the σK–RskAcytocomplex but does not interfere with σK–promoter DNA interactions. It is noted that these disulfide-forming cysteines are conserved across homologues, suggesting that this could be a general mechanism for redox-sensitive transcription regulation.
Benzene-1,3,5-tricarboxylic acid–pyridinium-2-olate (1/3)
Authors: Campos-Gaxiola José J. , Zamora Falcon Felipe , Corral Higuera Ramón , Höpfl Herbert , Cruz-Enríquez Adriana
Published: March 2014

The asymmetric unit of the title compound, C9H6O6·3C5H5NO, contains one benzene-1,3,5-tricarboxylic acid molecule (BTA) and three pyridin-2-ol molecules each present in the zwitterion form. In the crystal, these entities are linked through O—H...O−and N+—H...O−hydrogen bonds, forming sheets parallel to (10-1). These layers contain macrocyclic rings of composition [BTA]2[pyol]6and with graph-set notationR68(44), which are stacked alongcthrough π–π interactions [inter-centroid distances = 3.536 (2)–3.948 (3) Å]. They are interconnected by N+—H...O−hydrogen-bonded chains of pyridin-2-ol molecules running parallel toc, forming a three-dimensional network. There are also C—H...O hydrogen bonds present which reinforce the three-dimensional structure.
5-Chloro-3-ethylsulfinyl-7-methyl-2-(4-methylphenyl)-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: March 2014

In the title compound, C18H17ClO2S, the dihedral angle between the mean planes of the benzofuran ring system and the methylphenyl ring is 14.50 (4)°. The centroid–centroid distances between the benzene and the methylphenyl rings are 3.827 (2) and 3.741 (2) Å, while the centroid–centroid distance between the furan and methylphenyl rings is 3.843 (2) Å. These distances indicate π–π interactions; on the other hand, the interplanar angles between the benzene and methylphenyl rings, and between the furan and methylphenyl rings are 13.89 (4) and 15.53 (4)°, respectively. In the crystal, the molecules stack along thea-axis direction.
2,3-Bis[(3-methylbiphenyl-4-yl)imino]butane
Authors: Chen Jingjing , Yuan Jianchao , Zhao Jie , Xu Weibing , Mu Yanqiong
Published: March 2014

The title compound, C30H28N2, is a product of the condensation reaction of 2-methyl-4-phenylaniline and butane-2,3-dione. The molecule lies on a crystallographic inversion centre. The C=N bond has anEconformation. The dihedral angle between the two benzene rings of the 4-phenyl-2-methylphenyl group is 29.19 (76)°. The 1,4-diazabutadiene plane makes an angle of 70.1 (10)° with the N-bonded methylphenyl ring and an angle of 81.08 (97)° with the terminal phenyl group.
On the assessment by grazing-incidence small-angle X-ray scattering of replica quality in polymer gratings fabricated by nanoimprint lithography
Authors: Soccio M. , Alayo N. , Martín-Fabiani I. , Rueda D. R. , García-Gutiérrez M. C. , Rebollar E. , Martínez-Tong D. E. , Pérez-Murano F. , Ezquerra T. A.
Published: March 2014

Grazing-incidence small-angle X-ray scattering (GISAXS) can be used to characterize the replica quality of polymer gratings prepared by thermal nanoimprint lithography (NIL). Here it is shown using GISAXS experiments that a series of NIL polymer gratings with different line quality present characteristic features that can be associated with the level of defects per line. Both stamps and NIL polymer gratings exhibit characteristic semicircle-like GISAXS patterns. However NIL polymer gratings with defective lines exhibit GISAXS patterns with an excess of diffuse scattering as compared to those of the corresponding stamps. In a first approach, this effect is attributed to a reduction of the effective length of the lines diffracting coherently as the number of defects per line increases.
Moroccan ornamental quasiperiodic patterns constructed by the multigrid method
Authors: Aboufadil Youssef , Thalal Abdelmalek , Raghni My Ahmed El Idrissi
Published: March 2014

The similarity between the structure of Islamic decorative patterns and quasicrystals has aroused the interest of several crystallographers. Many of these patterns have been analysed by different approaches, including various kinds of ornamental quasiperiodic patterns encountered in Morocco and the Alhambra (Andalusia), as well as those in the eastern Islamic world. In the present work, the interest is in the quasiperiodic patterns found in several Moroccan historical buildings constructed in the 14th century. First, thezelligepanels (fine mosaics) decorating the Madrasas (schools) Attarine and Bou Inania in Fez are described in terms of Penrose tiling, to confirm that both panels have a quasiperiodic structure. The multigrid method developed by De Bruijn [Proc. K. Ned. Akad. Wet. Ser. A Math. Sci.(1981),43, 39–66] and reformulated by Gratias [Tangente(2002),85, 34–36] to obtain a quasiperiodic paving is then used to construct known quasiperiodic patterns from periodic patterns extracted from the Madrasas Bou Inania and Ben Youssef (Marrakech). Finally, a method of construction of heptagonal, enneagonal, tetradecagonal and octadecagonal quasiperiodic patterns, not encountered in Moroccan ornamental art, is proposed. They are built from tilings (skeletons) generated by the multigrid method and decorated by motifs obtained by craftsmen.
LCDiXRay: a user-friendly program for powder diffraction indexing of columnar liquid crystals
Authors: Godbert Nicolas , Crispini Alessandra , Ghedini Mauro , Carini Manuela , Chiaravalloti Francesco , Ferrise Andrea
Published: March 2014

The formulation of a standard computerized procedure for the indexing of powder X-ray diffraction (PXRD) patterns of columnar liquid crystals, with the determination of all structural information extracted from a properly indexed PXRD spectrum and the attribution of the columnar mesophase symmetry, is presented. In particular, the proposed program notably accelerates the identification of columnar mesophases together with thein situdetermination of their structural parameters such as mesophase type, space group, cell parameters, cross-section area, intermolecular stacking distance between consecutive discoids and, in the case of ordered mesophases, the estimation of the number of molecules constituting each discoid.
Protein crystal harvesting using the RodBot: a wireless mobile microrobot
Authors: Tung Hsi-Wen , Sargent David F. , Nelson Bradley J.
Published: March 2014

A new micro-agent is proposed to assist in automated protein crystal harvesting. The microrobot, named the RodBot, is a wireless mobile device driven by rotating magnetic fields (field strength 5–10 mT). When the RodBot rolls on a substrate in a low Reynolds number liquid environment, it generates flows to lift up and trap crystals in a vortex above itself. The gentle fluidic force acting on the crystals is in the range of a few nanonewtons to tens of nanonewtons and is spread over the whole surface of the crystal. The RodBot is capable of trapping protein crystals ranging from a few micrometres to sub-millimetre size. The trapped crystal can be transported to and deposited onto a loop positioned to accept it, obviating the need for more complicated `fishing' systems dependent on particular motions of the loop, the presence of further manipulators or the use of mechanical grippers. The RodBot can be driven in 24- and 96-well plates or in a crystal soaking dish, making the system compatible with existing crystallization hardware.