bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphorus-31 MRI of hard and soft solids using quadratic echo line-narrowing
Authors: Frey Merideth A. , Michaud Michael , VanHouten Joshua N. , Insogna Karl L. , Madri Joseph A. , Barrett Sean E.
Published: March 2012

Magnetic resonance imaging (MRI) of solids is rarely attempted. One of the main reasons is that the broader MR linewidths, compared to the narrow resonance of the hydrogen (
1
H) in free water, limit both the attainable spatial resolution and the signal-to-noise ratio. Basic physics research, stimulated by the quest to build a quantum computer, gave rise to a unique MR pulse sequence that offers a solution to this long-standing problem. The “quadratic echo” significantly narrows the broad MR spectrum of solids. Applying field gradients in sync with this line-narrowing sequence offers a fresh approach to carry out MRI of hard and soft solids with high spatial resolution and with a wide range of potential uses. Here we demonstrate that this method can be used to carry out three-dimensional MRI of the phosphorus (
31
P) in ex vivo bone and soft tissue samples.
Pantropic retroviruses as a transduction tool for sea urchin embryos
Authors: Core Amanda B. , Reyna Arlene E. , Conaway Evan A. , Bradham Cynthia A.
Published: March 2012

Sea urchins are an important model for experiments at the intersection of development and systems biology, and technical innovations that enhance the utility of this model are of great value. This study explores pantropic retroviruses as a transduction tool for sea urchin embryos, and demonstrates that pantropic retroviruses infect sea urchin embryos with high efficiency and genomically integrate at a copy number of one per cell. We successfully used a self-inactivation strategy to both insert a sea urchin-specific enhancer and disrupt the endogenous viral enhancer. The resulting self-inactivating viruses drive global and persistent gene expression, consistent with genomic integration during the first cell cycle. Together, these data provide substantial proof of principle for transduction technology in sea urchin embryos.
Dissecting the substrate recognition of 3-
O
-sulfotransferase for the biosynthesis of anticoagulant heparin
Authors: Moon Andrea F. , Xu Yongmei , Woody Susan M. , Krahn Joseph M. , Linhardt Robert J. , Liu Jian , Pedersen Lars C.
Published: March 2012

Heparin is a polysaccharide-based natural product that is used clinically as an anticoagulant drug. Heparan sulfate 3-
O
-sulfotransferase (3-OST) is an enzyme that transfers a sulfo group to the 3-OH position of a glucosamine unit. 3-OST is present in multiple isoforms, and the polysaccharides modified by these different isoforms perform distinct biological functions. 3-OST isoform 1 (3-OST-1) is the key enzyme for the biosynthesis of anticoagulant heparin. Here, we report the crystal structure of the ternary complex of 3-OST-1, 3′-phosphoadenosine 5′-phosphate, and a heptasaccharide substrate. Comparisons to previously determined structures of 3-OST-3 reveal unique binding modes used by the different isoforms of 3-OST for distinguishing the fine structures of saccharide substrates. Our data demonstrate that the saccharide substrates display distinct conformations when interacting with the different 3-OST isoforms. Site-directed mutagenesis data suggest that several key amino residues, including Lys259, Thr256, and Trp283 in 3-OST-3 and Arg268 in 3-OST-1, play important roles in substrate binding and specificity between isoforms. These results deepen our understanding of the biosynthetic mechanism of heparan sulfate and provide structural information for engineering enzymes for an enhanced biosynthetic approach to heparin production.
Crystal structure of a complete ternary complex of T-cell receptor, peptide–MHC, and CD4
Authors: Yin Yiyuan , Wang Xin Xiang , Mariuzza Roy A.
Published: March 2012

Adaptive immunity depends on specific recognition by a T-cell receptor (TCR) of an antigenic peptide bound to a major histocompatibility complex (pMHC) molecule on an antigen-presenting cell (APC). In addition, T-cell activation generally requires binding of this same pMHC to a CD4 or CD8 coreceptor. Here, we report the structure of a complete TCR–pMHC–CD4 ternary complex involving a human autoimmune TCR, a myelin-derived self-peptide bound to HLA-DR4, and CD4. The complex resembles a pointed arch in which TCR and CD4 are each tilted ∼65° relative to the T-cell membrane. By precluding direct contacts between TCR and CD4, the structure explains how TCR and CD4 on the T cell can simultaneously, yet independently, engage the same pMHC on the APC. The structure, in conjunction with previous mutagenesis data, places TCR-associated CD3εγ and CD3εδ subunits, which transmit activation signals to the T cell, inside the TCR–pMHC–CD4 arch, facing CD4. By establishing anchor points for TCR and CD4 on the T-cell membrane, the complex provides a basis for understanding how the CD4 coreceptor focuses TCR on MHC to guide TCR docking on pMHC during thymic T-cell selection.
Control of cell division in
Streptococcus pneumoniae
by the conserved Ser/Thr protein kinase StkP
Authors: Beilharz Katrin , Nováková Linda , Fadda Daniela , Branny Pavel , Massidda Orietta , Veening Jan-Willem
Published: March 2012

How the human pathogen
Streptococcus pneumoniae
coordinates cell-wall synthesis during growth and division to achieve its characteristic oval shape is poorly understood. The conserved eukaryotic-type Ser/Thr kinase of
S. pneumoniae
, StkP, previously was reported to phosphorylate the cell-division protein DivIVA. Consistent with a role in cell division, GFP-StkP and its cognate phosphatase, GFP-PhpP, both localize to the division site. StkP localization depends on its penicillin-binding protein and Ser/Thr-associated domains that likely sense uncross-linked peptidoglycan, because StkP and PhpP delocalize in the presence of antibiotics that target the latest stages of cell-wall biosynthesis and in cells that have stopped dividing. Time-lapse microscopy shows that StkP displays an intermediate timing of recruitment to midcell: StkP arrives shortly after FtsA but before DivIVA. Furthermore, StkP remains at midcell longer than FtsA, until division is complete. Cells mutated for
stkP
are perturbed in cell-wall synthesis and display elongated morphologies with multiple, often unconstricted, FtsA and DivIVA rings. The data show that StkP plays an important role in regulating cell-wall synthesis and controls correct septum progression and closure. Overall, our results indicate that StkP signals information about the cell-wall status to key cell-division proteins and in this way acts as a regulator of cell division.
X-ray crystallographic and computational studies of the O
2
-tolerant [NiFe]-hydrogenase 1 from
Escherichia coli
Authors: Volbeda Anne , Amara Patricia , Darnault Claudine , Mouesca Jean-Marie , Parkin Alison , Roessler Maxie M. , Armstrong Fraser A. , Fontecilla-Camps Juan C.
Published: March 2012

The crystal structure of the membrane-bound O
2
-tolerant [NiFe]-hydrogenase 1 from
Escherichia coli
(
Ec
Hyd-1) has been solved in three different states: as-isolated, H
2
-reduced, and chemically oxidized. As very recently reported for similar enzymes from
Ralstonia eutropha
and
Hydrogenovibrio marinus
, two supernumerary Cys residues coordinate the proximal [FeS] cluster in
Ec
Hyd-1, which lacks one of the inorganic sulfide ligands. We find that the as-isolated, aerobically purified species contains a mixture of at least two conformations for one of the cluster iron ions and Glu76. In one of them, Glu76 and the iron occupy positions that are similar to those found in O
2
-sensitive [NiFe]-hydrogenases. In the other conformation, this iron binds, besides three sulfur ligands, the amide N from Cys20 and one Oϵ of Glu76. Our calculations show that oxidation of this unique iron generates the high-potential form of the proximal cluster. The structural rearrangement caused by oxidation is confirmed by our H
2
-reduced and oxidized
Ec
Hyd-1 structures. Thus, thanks to the peculiar coordination of the unique iron, the proximal cluster can contribute two successive electrons to secure complete reduction of O
2
to H
2
O at the active site. The two observed conformations of Glu76 are consistent with this residue playing the role of a base to deprotonate the amide moiety of Cys20 upon iron binding and transfer the resulting proton away, thus allowing the second oxidation to be electroneutral. The comparison of our structures also shows the existence of a dynamic chain of water molecules, resulting from O
2
reduction, located near the active site.
Structure of components of an intercellular channel complex in sporulating
Bacillus subtilis
Authors: Levdikov Vladimir M. , Blagova Elena V. , McFeat Amanda , Fogg Mark J. , Wilson Keith S. , Wilkinson Anthony J.
Published: March 2012

Following asymmetric cell division during spore formation in
Bacillus subtilis
, a forespore expressed membrane protein SpoIIQ, interacts across an intercellular space with a mother cell-expressed membrane protein, SpoIIIAH. Their interaction can serve as a molecular “ratchet” contributing to the migration of the mother cell membrane around that of the forespore in a phagocytosis-like process termed engulfment. Upon completion of engulfment, SpoIIQ and SpoIIIAH are integral components of a recently proposed intercellular channel allowing passage from the mother cell into the forespore of factors required for late gene expression in this compartment. Here we show that the extracellular domains of SpoIIQ and SpoIIIAH form a heterodimeric complex in solution. The crystal structure of this complex reveals that SpoIIQ has a LytM-like zinc-metalloprotease fold but with an incomplete zinc coordination sphere and no metal. SpoIIIAH has an α-helical subdomain and a protruding β-sheet subdomain, which mediates interactions with SpoIIQ. SpoIIIAH has sequence and structural homology to EscJ, a type III secretion system protein that forms a 24-fold symmetric ring. Superposition of the structures of SpoIIIAH and EscJ reveals that the SpoIIIAH protomer overlaps with two adjacent protomers of EscJ, allowing us to generate a dodecameric SpoIIIAH ring by using structural homology. Following this superposition, the SpoIIQ chains also form a closed dodecameric ring abutting the SpoIIIAH ring, producing an assembly surrounding a 60 Å channel. The dimensions and organization of the proposed complex suggest it is a plausible model for the extracellular component of a gap junction-like intercellular channel.
Structure of the basal components of a bacterial transporter
Authors: Meisner Jeffrey , Maehigashi Tatsuya , André Ingemar , Dunham Christine M. , Moran Charles P.
Published: March 2012

Proteins SpoIIQ and SpoIIIAH interact through two membranes to connect the forespore and the mother cell during endospore development in the bacterium
Bacillus subtilis
. SpoIIIAH consists of a transmembrane segment and an extracellular domain with similarity to YscJ proteins. YscJ proteins form large multimeric rings that are the structural scaffolds for the assembly of type III secretion systems in Gram-negative bacteria. The predicted ring-forming motif of SpoIIIAH and other evidence led to the model that SpoIIQ and SpoIIIAH form the core components of a channel or transporter through which the mother cell nurtures forespore development. Therefore, to understand the roles of SpoIIIAH and SpoIIQ in channel formation, it is critical to determine whether SpoIIIAH adopts a ring-forming structural motif, and whether interaction of SpoIIIAH with SpoIIQ would preclude ring formation. We report a 2.8-Å resolution structure of a complex of SpoIIQ and SpoIIIAH. SpoIIIAH folds into the ring-building structural motif, and modeling shows that the structure of the SpoIIQ–SpoIIIAH complex is compatible with forming a symmetrical oligomer that is similar to those in type III systems. The inner diameters of the two most likely ring models are large enough to accommodate several copies of other integral membrane proteins. SpoIIQ contains a LytM domain, which is found in metalloendopeptidases, but lacks residues important for metalloprotease activity. Other LytM domains appear to be involved in protein–protein interactions. We found that the LytM domain of SpoIIQ contains an accessory region that interacts with SpoIIIAH.
Whole-brain, time-locked activation with simple tasks revealed using massive averaging and model-free analysis
Authors: Gonzalez-Castillo Javier , Saad Ziad S. , Handwerker Daniel A. , Inati Souheil J. , Brenowitz Noah , Bandettini Peter A.
Published: March 2012

The brain is the body's largest energy consumer, even in the absence of demanding tasks. Electrophysiologists report on-going neuronal firing during stimulation or task in regions beyond those of primary relationship to the perturbation. Although the biological origin of consciousness remains elusive, it is argued that it emerges from complex, continuous whole-brain neuronal collaboration. Despite converging evidence suggesting the whole brain is continuously working and adapting to anticipate and actuate in response to the environment, over the last 20 y, task-based functional MRI (fMRI) have emphasized a localizationist view of brain function, with fMRI showing only a handful of activated regions in response to task/stimulation. Here, we challenge that view with evidence that under optimal noise conditions, fMRI activations extend well beyond areas of primary relationship to the task; and blood-oxygen level-dependent signal changes correlated with task-timing appear in over 95% of the brain for a simple visual stimulation plus attention control task. Moreover, we show that response shape varies substantially across regions, and that whole-brain parcellations based on those differences produce distributed clusters that are anatomically and functionally meaningful, symmetrical across hemispheres, and reproducible across subjects. These findings highlight the exquisite detail lying in fMRI signals beyond what is normally examined, and emphasize both the pervasiveness of false negatives, and how the sparseness of fMRI maps is not a result of localized brain function, but a consequence of high noise and overly strict predictive response models.
Persistence and uncertainty in the academic career
Authors: Petersen Alexander M. , Riccaboni Massimo , Stanley H. Eugene , Pammolli Fabio
Published: March 2012

Understanding how institutional changes within academia may affect the overall potential of science requires a better quantitative representation of how careers evolve over time. Because knowledge spillovers, cumulative advantage, competition, and collaboration are distinctive features of the academic profession, both the employment relationship and the procedures for assigning recognition and allocating funding should be designed to account for these factors. We study the annual production
n

i

(
t
) of a given scientist
i
by analyzing longitudinal career data for 200 leading scientists and 100 assistant professors from the physics community. Our empirical analysis of individual productivity dynamics shows that (
i
) there are increasing returns for the top individuals within the competitive cohort, and that (
ii
) the distribution of production growth is a leptokurtic “tent-shaped” distribution that is remarkably symmetric. Our methodology is general, and we speculate that similar features appear in other disciplines where academic publication is essential and collaboration is a key feature. We introduce a model of proportional growth which reproduces these two observations, and additionally accounts for the significantly right-skewed distributions of career longevity and achievement in science. Using this theoretical model, we show that short-term contracts can amplify the effects of competition and uncertainty making careers more vulnerable to early termination, not necessarily due to lack of individual talent and persistence, but because of random negative production shocks. We show that fluctuations in scientific production are quantitatively related to a scientist’s collaboration radius and team efficiency.
TWIK1, a unique background channel with variable ion selectivity
Authors: Chatelain Franck C. , Bichet Delphine , Douguet Dominique , Feliciangeli Sylvain , Bendahhou Saïd , Reichold Markus , Warth Richard , Barhanin Jacques , Lesage Florian
Published: March 2012

TWIK1 belongs to the family of background K
+
channels with two pore domains. In native and transfected cells, TWIK1 is detected mainly in recycling endosomes. In principal cells in the kidney, TWIK1 gene inactivation leads to the loss of a nonselective cationic conductance, an unexpected effect that was attributed to adaptive regulation of other channels. Here, we show that TWIK1 ion selectivity is modulated by extracellular pH. Although TWIK1 is K
+
selective at neutral pH, it becomes permeable to Na
+
at the acidic pH found in endosomes. Selectivity recovery is slow after restoration of a neutral pH. Such hysteresis makes plausible a role of TWIK1 as a background channel in which selectivity and resulting inhibitory or excitatory influences on cell excitability rely on its recycling rate between internal acidic stores and the plasma membrane. TWIK1
−/−
pancreatic β cells are more polarized than control cells, confirming a depolarizing role of TWIK1 in kidney and pancreatic cells.
Plasmodium falciparum
merozoite surface protein 1 blocks the proinflammatory protein S100P
Authors: Waisberg Michael , Cerqueira Gustavo C. , Yager Stephanie B. , Francischetti Ivo M. B. , Lu Jinghua , Gera Nidhi , Srinivasan Prakash , Miura Kazutoyo , Rada Balazs , Lukszo Jan , Barbian Kent D. , Leto Thomas L. , Porcella Stephen F. , Narum David L. , El-Sayed Najib , Miller Louis H. , Pierce Susan K.
Published: March 2012

The malaria parasite,
Plasmodium falciparum
, and the human immune system have coevolved to ensure that the parasite is not eliminated and reinfection is not resisted. This relationship is likely mediated through a myriad of host–parasite interactions, although surprisingly few such interactions have been identified. Here we show that the 33-kDa fragment of
P. falciparum
merozoite surface protein 1 (MSP1
33
), an abundant protein that is shed during red blood cell invasion, binds to the proinflammatory protein, S100P. MSP1
33
blocks S100P-induced NFκB activation in monocytes and chemotaxis in neutrophils. Remarkably, S100P binds to both dimorphic alleles of MSP1, estimated to have diverged >27 Mya, suggesting an ancient, conserved relationship between these parasite and host proteins that may serve to attenuate potentially damaging inflammatory responses.
Globally diverse
Toxoplasma gondii
isolates comprise six major clades originating from a small number of distinct ancestral lineages
Authors: Su Chunlei , Khan Asis , Zhou Peng , Majumdar Debashree , Ajzenberg Daniel , Dardé Marie-Laure , Zhu Xing-Quan , Ajioka James W. , Rosenthal Benjamin M. , Dubey Jitender P. , Sibley L. David
Published: March 2012

Marked phenotypic variation characterizes isolates of
Toxoplasma gondii,
a ubiquitous zoonotic parasite that serves as an important experimental model for studying apicomplexan parasites. Progress in identifying the heritable basis for clinically and epidemiologically significant differences requires a robust system for describing and interpreting evolutionary subdivisions in this prevalent pathogen. To develop such a system, we have examined more than 950 isolates collected from around the world and genotyped them using three independent sets of polymorphic DNA markers, sampling 30 loci distributed across all nuclear chromosomes as well as the plastid genome. Our studies reveal a biphasic pattern consisting of regions in the Northern Hemisphere where a few, highly clonal and abundant lineages predominate; elsewhere, and especially in portions of South America are characterized by a diverse assemblage of less common genotypes that show greater evidence of recombination. Clustering methods were used to organize the marked genetic diversity of 138 unique genotypes into 15 haplogroups that collectively define six major clades. Analysis of gene flow indicates that a small number of ancestral lineages gave rise to the existing diversity through a process of limited admixture. Identification of reference strains for these major groups should facilitate future studies on comparative genomics and identification of genes that control important biological phenotypes including pathogenesis and transmission.
Prevalence of streaming in UK primary schools: evidence from the Millennium Cohort Study
Authors: Hallam Susan , Parsons Samantha
Published: March 2012

The adoption of streaming in the primary school (where children are placed in a class on the basis of measures of attainment and remain in that class all of the time) was commonplace when the 11 plus examination was used to select children for grammar school places. During the 1950s and 1960s the practice died out with most children being taught in mixed ability classes with some in‐class grouping. During the 1990s successive governments indicated that some form of ability grouping should be introduced in primary schools, setting (children placed in ability groups for some subjects and taught in mixed groups for the remainder of the time) being preferred, however, streaming was introduced in some schools despite evidence that movement between structured ability groups is infrequent and that children tend to remain in the same groups throughout their school careers limiting their educational opportunities. Recent research based on 8875 children, in the Millennium Cohort Study showed that 16.4% of children in Year 2 were in streamed classes. Logistic regression analysis showed that the best predictors of being in the top stream were whether the child was born in autumn or winter 2000, parents owning their own home, and the child's cognitive ability score. The measures predicting being in the bottom stream were being a boy, being born in the spring/summer of 2001, having a behaviour problem, being born into a lone parent family, and cognitive ability score.
Simplification of macrozoobenthic assemblages related to anthropogenic eutrophication and cyanobacterial blooms in two large shallow subtropical lakes in China
Authors: Cai Yongjiu , Jiang Jiahu , Zhang Lu , Chen Yuwei , Gong Zhijun
Published: March 2012

Eutrophication has become a serious problem in lakes in the middle and lower reaches of the Yangtze River, and is exerting profound pressures on the aquatic communities. However, little research has been conducted on the effects of eutrophication on benthic communities in these lakes. In this study, we investigated macrozoobenthic assemblages in two large shallow lakes (Lake Chaohu and Meiliang Bay in Lake Taihu), which have each experienced severe environmental deterioration and increased occurrences of cyanobacterial blooms in the past few decades. To analyze the changes in benthic community structure over the long-term, we compared the present community with communities from previous studies. Our results showed that present benthic assemblages have simplified substantially compared to communities in the past. In Meiliang Bay, Tubificidae and Chironomidae exclusively dominated the benthic community in 2007, in contrast with the relatively high diversity of benthic community in 1994, with several taxa sharing dominance of the community. Similarly, benthic assemblages in Lake Chaohu changed greatly over two decades, shifting from dominance by Bivalvia in 1980–1981 to dominance by Tubificidae and Chironomidae in 2008–2009. These observed changes in benthic assemblages are discussed relative to the ability of individual different taxa to tolerate eutrophication, algal blooms, Microcystins and associated habitat deterioration.
Upper layer circulation in the Luzon Strait
Authors: Wang Guihua , Wang Dongxiao , Zhou Tianjun
Published: March 2012

Several observations including Argos satellite-tracked drifters, Argo profilers and altimetry satellite data were analyzed to understand the upper layer circulation in the Luzon Strait. The different role of the wind and the Kuroshio on the Luzon upper layer circulation has been revealed using a reduced gravity model. The observations show that the Kuroshio has a relatively stable pattern with some of Kuroshio water entering the South China Sea in winter. Circulation in the Luzon Strait is mainly controlled by the Kuroshio and the monsoon wind, which have different roles. The Kuroshio could induce a cyclonic gyre west of the Luzon Strait in either summer or winter which is stronger and extends more westward as the Kuroshio becomes stronger. The monsoon wind could drive a cyclonic gyre in the Luzon Strait in summer. In winter, an anticyclonic gyre and a cyclonic gyre are produced southwest of Taiwan Island and northwest of Luzon Island respectively, resulting in a strong westward current in the middle of the Luzon Strait.
MYC pathway activation in triple-negative breast cancer is synthetic lethal with CDK inhibition
Authors: Horiuchi Dai , Kusdra Leonard , Huskey Noelle E. , Chandriani Sanjay , Lenburg Marc E. , Gonzalez-Angulo Ana Maria , Creasman Katelyn J. , Bazarov Alexey V. , Smyth James W. , Davis Sarah E. , Yaswen Paul , Mills Gordon B. , Esserman Laura J. , Goga Andrei
Published: March 2012

Estrogen, progesterone, and HER2 receptor-negative triple-negative breast cancers encompass the most clinically challenging subtype for which targeted therapeutics are lacking. We find that triple-negative tumors exhibit elevated MYC expression, as well as altered expression of MYC regulatory genes, resulting in increased activity of the MYC pathway. In primary breast tumors, MYC signaling did not predict response to neoadjuvant chemotherapy but was associated with poor prognosis. We exploit the increased MYC expression found in triple-negative breast cancers by using a synthetic-lethal approach dependent on cyclin-dependent kinase (CDK) inhibition. CDK inhibition effectively induced tumor regression in triple-negative tumor xenografts. The proapoptotic BCL-2 family member BIM is up-regulated after CDK inhibition and contributes to this synthetic-lethal mechanism. These results indicate that aggressive breast tumors with elevated MYC are uniquely sensitive to CDK inhibitors.
Notch, Id2, and RORγt sequentially orchestrate the fetal development of lymphoid tissue inducer cells
Authors: Cherrier Marie , Sawa Shinichiro , Eberl Gérard
Published: March 2012

Lymphoid tissue development is initiated during embryogenesis by the migration of lymphoid tissue inducer (LTi) cells from the fetal liver to the periphery, where they induce the formation of lymph nodes and Peyer’s patches. In the fetal liver, a subset of common lymphoid progenitors (CLPs) that expresses the integrin α4β7 gives rise to LTi cells, a process strictly dependent on the expression of the transcriptional repressor Id2 and the nuclear hormone receptor retinoic acid–related orphan receptor γ t (RORγt). In this study, we show that Id2 and RORγt are sequentially up-regulated during LTi cell development, matching two waves of differentiation with opposite requirements for Notch signaling. Both the expression of Id2 and Notch are required for the generation of α4β7+ RORγt− fetal progenitors, but Notch subsequently blocks progression to the RORγt+ stage and final maturation of LTi cells. Notch is therefore a necessary switch to engage the LTi developmental pathway, but needs to be turned off later to avoid diversion to the T cell fate.
The influence of the solid thermal conductivity on active magnetic regenerators
Authors: Nielsen K K , Engelbrecht K
Published: March 2012

The influence of the thermal conductivity of the regenerator solid on the performance of a flat plate active magnetic regenerator (AMR) is investigated using an established numerical AMR model. The cooling power at different (fixed) temperature spans is used as a measure of the performance for a range of thermal conductivities, operating frequencies, a long and short regenerator, and finally a regenerator with a low and a high number of transfer units (NTU). In this way the performance is mapped out and the impact of the thermal conductivity of the solid is probed.

Modelling shows that under certain operating conditions, the AMR cycle is sensitive to the solid conductivity. It is found that as the operating frequency is increased it is not only sufficient to have a high NTU regenerator but the regenerator performance will also benefit from increased thermal conductivity in the solid. It is also found that a longer regenerator is generally better performing than a shorter one under the otherwise exact same conditions. This suggests that the thermal conductivity of candidate magnetocaloric materials should be considered when selecting them for use in a device.
Numerical simulation on a nanosecond-pulse surface dielectric barrier discharge actuator in near space
Authors: Che Xueke , Shao Tao , Nie Wansheng , Yan Ping
Published: March 2012

Lift-enhancement–drag-reduction technology is strongly required by near-space vehicles with low Reynolds number. It is known that a flow control method by a surface dielectric barrier discharge (SDBD) plasma can play an important role in this field. In order to obtain the discharge characteristics and evaluate the flow control effect of a SDBD actuator, the nanosecond-pulse discharge and induced flow field by the SDBD plasma are simulated at various altitudes using discharge-aerodynamics models. The results show that the ignition voltage decreases with altitude and it is very easy to discharge in near space. Compared with a SDBD at ground level, the plasma is produced on both sides of the exposed electrode and distributes more uniformly in near space. Although the body force generated by the SDBD actuator is less effective in inducing a jet with nanosecond-pulse excitation than that with alternating voltage excitation, the induced jet by body force is with longer extent, thicker profile and higher velocity in near space than at ground level. The plasma bulk heating should be taken into account for nanosecond-pulse excitation. The Joule heating of electrons is the main source of plasma bulk heating which acts as a micro-explosion and mainly induces pressure perturbation. The discharge at ground level is like a ‘point explosion’, but a ‘region explosion’ in near space, which indicates a diffuse distribution of energy, should be responsible for the fact that the effect of bulk heating is reduced in near space.
Modelling of an RF plasma shower
Authors: Atanasova M , Carbone E A D , Mihailova D , Benova E , Degrez G , van der Mullen J J A M
Published: March 2012

A capacitive radiofrequency (RF) discharge at atmospheric pressure is studied by means of a time-dependent, two-dimensional fluid model. The plasma is created in a stationary argon gas flow guided through two perforated electrodes, hence resembling a shower. The inner electrode, the electrode facing the flow entrance, is powered with a frequency of 13.56 MHz, and the outer electrode is grounded. The model solves the mass balance equations for the relevant active species and the electron energy balance equation in conjunction with the Poisson equation for the field sustaining the plasma. The mass balance equations of the active species are calculated using the drift–diffusion–convection approach, thus taking the bulk velocity into account. The velocity field is calculated with the Navier–Stokes module of the Plasimo toolkit. The plasma dynamics is studied in three connected regions; the space between the electrodes, the regions before the powered electrode and the extended region behind the grounded electrode. The effect of the shower holes and the recirculation gas flow on the plasma is examined.
Towards a deeper understanding of the formation of friction-induced hillocks on monocrystalline silicon
Authors: Yu Bingjun , Li Xiaoying , Dong Hanshan , Chen Yunfei , Qian Linmao , Zhou Zhongrong
Published: March 2012

Friction-induced hillocks can be produced on monocrystalline silicon by scratching under given conditions. Results show that the height of these hillocks increases with the applied normal load or number of scratching cycles, but decreases with the sliding velocity. Transmission electron microscope (TEM) and energy dispersive x-ray (EDX) analysis show that the hillock contains a thin superficial oxidation layer and a thick disturbed (amorphous and deformed) layer in the subsurface. Although the formation of the silicon hillock is the combined results of mechanical interaction and tribochemical reaction, the mechanical interaction plays a more dominant role. Further analysis indicates that the formation of hillock is mostly induced by the amorphization of crystal silicon during scratching. Low sliding speed is found to facilitate the formation of a thick amorphization layer under the same loading condition. Since the friction-induced hillock is the initial surface damage on the nanoscale, the results will shed new light on understanding and controlling the nanowear process of silicon in micro/nanoelectromechanical systems.
A key role for EZH2 and associated genes in mouse and human adult T-cell acute leukemia
Authors: Simon Camille , Chagraoui Jalila , Krosl Jana , Gendron Patrick , Wilhelm Brian , Lemieux Sébastien , Boucher Geneviève , Chagnon Pierre , Drouin Simon , Lambert Raphaëlle , Rondeau Claude , Bilodeau Annie , Lavallée Sylvie , Sauvageau Martin , Hébert Josée , Sauvageau Guy
Published: March 2012

In this study, we show the high frequency of spontaneous γδ T-cell leukemia (T-ALL) occurrence in mice with biallelic deletion of enhancer of zeste homolog 2 (Ezh2). Tumor cells show little residual H3K27 trimethylation marks compared with controls. EZH2 is a component of the PRC2 Polycomb group protein complex, which is associated with DNA methyltransferases. Using next-generation sequencing, we identify alteration in gene expression levels of EZH2 and acquired mutations in PRC2-associated genes (DNMT3A and JARID2) in human adult T-ALL. Together, these studies document that deregulation of EZH2 and associated genes leads to the development of mouse, and likely human, T-ALL.
RNAi keeps Atf1-bound stress response genes in check at nuclear pores
Authors: Woolcock Katrina J. , Stunnenberg Rieka , Gaidatzis Dimos , Hotz Hans-Rudolf , Emmerth Stephan , Barraud Pierre , Bühler Marc
Published: March 2012

RNAi pathways are prevalent throughout the eukaryotic kingdom and are well known to regulate gene expression on a post-transcriptional level in the cytoplasm. Less is known about possible functions of RNAi in the nucleus. In the fission yeast Schizosaccharomyces pombe, RNAi is crucial to establish and maintain centromeric heterochromatin and functions to repress genome activity by a chromatin silencing mechanism referred to as cotranscriptional gene silencing (CTGS). Mechanistic details and the physiological relevance of CTGS are unknown. Here we show that RNAi components interact with chromatin at nuclear pores to keep stress response genes in check. We demonstrate that RNAi-mediated CTGS represses stress-inducible genes by degrading mRNAs under noninduced conditions. Under chronic heat stress conditions, a Dicer thermoswitch deports Dicer to the cytoplasm, thereby disrupting CTGS and enabling expression of genes implicated in the acquisition of thermotolerance. Taken together, our work highlights a role for nuclear pores and the stress response transcription factor Atf1 in coordinating the interplay between the RNAi machinery and the S. pombe genome and uncovers a novel mode of RNAi regulation in response to an environmental cue.
Characterization of an Isoflavonoid-Specific Prenyltransferase from Lupinus albus
Authors: Shen Guoan , Huhman David , Lei Zhentian , Snyder John , Sumner Lloyd W. , Dixon Richard A.
Published: March 2012

Prenylated flavonoids and isoflavonoids possess antimicrobial activity against fungal pathogens of plants. However, only a few plant flavonoid and isoflavonoid prenyltransferase genes have been identified to date. In this study, an isoflavonoid prenyltransferase gene, designated as LaPT1, was identified from white lupin (Lupinus albus). The deduced protein sequence of LaPT1 shared high homologies with known flavonoid and isoflavonoid prenyltransferases. The LaPT1 gene was mainly expressed in roots, a major site for constitutive accumulation of prenylated isoflavones in white lupin. LaPT1 is predicted to be a membrane-bound protein with nine transmembrane regions and conserved functional domains similar to other flavonoid and isoflavonoid prenyltransferases; it has a predicted chloroplast transit peptide and is plastid localized. A microsomal fraction containing recombinant LaPT1 prenylated the isoflavone genistein at the B-ring 3′ position to produce isowighteone. The enzyme is also active with 2′-hydroxygenistein but has no activity with other flavonoid substrates. The apparent K  m of recombinant LaPT1 for the dimethylallyl diphosphate prenyl donor is in a similar range to that of other flavonoid prenyltransferases, but the apparent catalytic efficiency with genistein is considerably higher. Removal of the transit peptide increased the apparent overall activity but also increased the K  m. Medicago truncatula hairy roots expressing LaPT1 accumulated isowighteone, a compound that is not naturally produced in this species, indicating a strategy for metabolic engineering of novel antimicrobial compounds in legumes.
5-Amino-3-carboxy-1H-1,2,4-triazol-4-ium nitrate monohydrate
Authors: Berrah Fadila , Bouchene Rafika , Bouacida Sofiane , Roisnel Thierry
Published: March 2012

The two-dimensional crystal packing of the title compound, C3H5N4O2+·NO2−·H2O, results from the stacking of well separated layers (i.e.with nothing between the layers) parallel to the (-113) plane in which adjacent cations adopt a head-to-head arrangement such that two –COOH groups are linkedviatwo water molecules (the water O atom behaves simultaneously as donor and acceptor of hydrogen bonds) and two –NH2groups are linked through two nitrate anions. This arrangement leads to alternating hydrophilic and hydrophobic zones in which O—H...O and N—H...O hydrogen bonds, respectively, are observed.
Tetrakis(azido-κN)(di-2-pyridylamine-κ2N2,N2′)platinum(IV)
Authors: Ha Kwang
Published: March 2012

In the title complex, [Pt(N3)4(C10H9N3)], the PtIVion is six-coordinated in a slightly distorted octahedral environment by the two pyridine N atoms of the chelating di-2-pyridylamine (dpa) ligand and four N atoms from four azide anions. The dpa ligand is not planar, the dihedral angle between the pyridine rings being 20.0 (3)°. The azide ligands are slightly bent [N—N—N = 173.5 (8)–175.1 (8)°]. In the crystal, the complex molecules are connected by N—H...N hydrogen bonds, forming a chain along thebaxis. An intermolecular π–π interaction between the chains is also present, the ring centroid–centroid distance being 3.713 (4) Å.
(4R*,5R*)-Diethyl 2-(4-nitrophenyl)-1,3-dioxolane-4,5-dicarboxylate
Authors: Lv Chun-Lei , Chen Jian-Hui , Zhang Yu-Zhe , Lu Ding-Qiang , OuYang Ping-Kai
Published: March 2012

In the title compound, C15H17NO8, the nitro group is essentially coplanar with the aromatic ring [dihedral angle = 6.4 (3) Å]. The five-membered ring has a twist conformation. In the crystal, C—H...O interactions link the molecules into a helical chain propagating along [010].
TetramethylN,N′-(2,2,3,3,4,4-hexafluoro-1,5-dioxopentane-1,5-diyl)bis(phosphoramidate)
Authors: Trush Victor A. , Gubina Kateryna E. , Gumeniuk Yaroslav O. , Sliva Tetyana Yu. , Konovalova Irina S.
Published: March 2012

The molecule of the title compound, C9H14F6N2O8P2, lies on a twofold rotation axis that passes through the middle C atom of the three-atom fluoromethylene unit. The carbonyl and phosphoryl groups are in an antiperiplanar conformation. In the crystal, N—H...O=P hydrogen bonds link the molecules into polymeric chains parallel to thecaxis.
Poly[[diaquabis[μ4-5-nitroisophthalato-κ4O1:O1:O3:O3′]bis[μ3-pyridine-4-carboxylato-κ3O:O′:N]tricobalt(II)] tetrahydrate]
Authors: Yin Xia , Fan Jun , Xin Jingling , Zheng Shengrun , Zhang Weiguang
Published: March 2012

The title compound, {[Co3(C6H4NO2)2(C8H3NO6)2(H2O)2]·4H2O}n, exhibits a two-dimensional layer-like structure in which the CoIIions exhibit two kinds of coordination geometries. One nearly octahedral CoIIion with crystallographic inversion symmetry is coordinated to six carboxylate O atoms from four bridging 5-nitroisophthalate (NIPH) ligands and two isonicotinate (IN) anions, while the other type of CoIIion binds with one N atom and one carboxylate O atom from two IN anions, two carboxylate O atoms from two different NIPH anions and one ligated water molecule, displaying a distorted square-pyramidal coordination geometry. Three adjacent CoIIions are bridged by six carboxylate groups from four NIPH ligands and two IN anions to form a linear trinuclear secondary building unit (SBU). Every trinuclear SBU is linked to its nearest neighbours in theabplane, resulting in a two-dimensional layer-like structure perpendicular to thecaxis. Along thea-axis direction neighbouring molecules are connected through carboxylate and pyridyl units of the IN anions, along thebaxis through carboxylate groups of the NIPH ligands. The H atoms of one free water molecule are disordered in the crystal in a 1:1 ratio. Typical O—H...O hydrogen bonds are observed in the lattice, which include the following contacts: (a) between coordinated water molecules and carboxylate O atoms of the NIPH anions, (b) between lattice water molecules and carboxylate O atoms of the NIPH anions, and (c) between coordinated and lattice water molecules. These intermolecular hydrogen bonds connect the two-dimensional layers to form a three-dimensional supramolecular structure.
Methyl 2,2-dimethoxy-5,5-bis(methylsulfanyl)-3-oxopent-4-enedithioate
Authors: Ghorbani Mohammad Hassan
Published: March 2012

In the title molecule, C10H16O3S4, a short intramolecular S...O(=C) distance [2.726 (2) Å] indicates the presence of a nonbonding attractive interaction. In the crystal, molecules are linked into centrosymmetric dimersviaweak intermolecular C—H...O and S...S [3.405 (3) Å] interactions. These dimers are linked by further weak C—H...O interactions into columns along theaaxis.
N-(3-Bromo-2-methylphenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide
Authors: Xu Yun-Hua , Long Sihui
Published: March 2012

The title compound, C13H11BrN2O2, consists of two six-membered rings linked by an amide group and adopts a near planar conformation. The dihedral angle between the two rings is 8.38 (11)°. In the crystal structure, there are intra- and intermolecular N—H...O hydrogen bonds, the latter forming inversion dimers.
Dibromido(di-2-pyridylamine-κ2N2,N2′)platinum(II)
Authors: Ha Kwang
Published: March 2012

The PtIIion in the title complex, [PtBr2(C10H9N3)], is four-coordinated in an essentially square-planar environment by two N atoms from a chelating di-2-pyridylamine (dpa) ligand and two Br−anions. The dpa ligand is not planar, with the dihedral angle between the pyridine rings being 40.8 (2)°. The complex molecules are stacked in columns along [001] through π–π interactions between the pyridine rings [centroid–centroid distances = 3.437 (3) and 3.520 (3) Å]. Intermolecular N—H...Br hydrogen bonds connect the molecules into chains running along [010]. Intramolecular C—H...Br interactions are also observed.
Aquachlorido{6,6′-dimethoxy-2,2′-[ethane-1,2-diylbis(nitrilomethanylylidene)]diphenolato-κ2O1,N,N′,O1′}cobalt(III) dimethylformamide monosolvate
Authors: Wei Yun , Pang Ting , Liu Jiacheng , Li Meng , Liang Lili
Published: March 2012

In the title compound, [Co(C18H18N2O4)Cl(H2O)]·C3H7NO, the CoIIIion is six-coordinated by a tetradentate 6,6′-dimethoxy-2,2′-[ethane-1,2-diylbis(nitrilomethanylylidene)]diphenolate ligand, with a chloride ion and an aqua ligand in the apical positions. The compound crystallized as a dimethylformamide (DMF) monosolvate. In the crystal, complex molecules are linkedviaO—Hwater...O hydrogen bonds to form a dimer-like arrangement. These dimers are linkedviaa C—H...Cl interaction, and the DMF molecule is linked to the complex molecule by C—H...O interactions.
3,6-Dimethyl-1-phenyl-1H,4H-pyrano[2,3-c]pyrazol-4-one
Authors: Asiri Abdullah M. , Faidallah Hassan M. , Hameed Salem A. , Ng Seik Weng , Tiekink Edward R. T.
Published: March 2012

The title compound, C14H12N2O2, is almost planar with an r.m.s. deviation for all non-H atoms of 0.038 Å. The observed planarity is rationalized in terms of a close intramolecular C—H...O interaction. Supramolecular layers, two molecules thick and with a step topology, are formed in the crystal packingviaC—H...O contacts involving the carbonyl O atom, which accepts two such bonds, and π–π interactions between the components of the fused ring system and the phenyl ring of inversion-related molecules [centroid–centroid distances = 3.6819 (13) and 3.6759 (12) Å].
2,4-Bis(diphenylphosphanyl)-1,1,2,3,3,4-hexaphenyl-1,3-diphospha-2,4-diboracyclobutane tetrahydrofuran sesquisolvate
Authors: Peulecke Normen , Müller Bernd H. , Spannenberg Anke , Rosenthal Uwe
Published: March 2012

In the title compound, C60H50B2P4·1.5C4H8O, the diphosphadiborane molecule lies on an inversion centre, whereas the disordered tetrahydrofuran solvent molecule is in a general position with a partial occupancy of 0.75. The diphosphadiborane molecule consists of an ideal planar four-membered B2P2ring with an additional phenyl and a –PPh2group attached to each B atom.
Tetrakis(nitrato-κ2O,O′)[N,N′-1,4-phenylenebis(pyridine-4-carboxamide)-κN1](4-{[4-(pyridine-4-carboxamido-κN1)phenyl]carbamoyl}pyridin-1-ium)neodymium(III)
Authors: Zhang Yun , Hao Jiao-Jiao , Zhou Hu
Published: March 2012

In the title compound, [Nd(NO3)4(C18H15N4O2)(C18H14N4O2)], the NdIIIcentre is located on a twofold axis and exhibits a ten-coordinated distorted bicapped square-antiprismatic geometry. The pyridinium NH H atom is disordered over the two ligands. Adjacent mononuclear clusters are linked through N—H...O and N—H...N hydrogen-bonding interactions, generating layers in the (102) plane.
(2S,3R)-tert-ButylN-[4-(N-benzyl-4-fluorobenzenesulfonamido)-3-hydroxy-1-phenylbutan-2-yl]carbamate
Authors: Moreth Marcele , Souza Marcus V.N. de , Wardell James L. , Wardell Solange M. S. V. , Tiekink Edward R. T.
Published: March 2012

In the title molecule, C28H33FN2O5S, the mean plane about the tertiary amine group (sum of the angles subtended at thesp2-hybridized N atom = 359.7°) forms a dihedral angle of 16.66 (6)° with the phenyl ring adjacent to the carbamate group. The sulfonamide benzene ring and the hydroxy group lie to either side of the C2NS plane, whereas the benzylphenyl (connected to the N atom) and carbamate substituents lie to the other side. Supramolecular layers propagating in theacplane are found in the crystal, linked by hydroxy–sulfonamide O—H...O and carbamate–carbamate N—H...O hydrogen bonds along with C—H...O and C—H...π interactions.
2-(4-Sulfamoylphenyl)hydrazin-1-ium chloride
Authors: Asiri Abdullah M. , Faidallah Hassan M. , Alamry Khalid A. , Ng Seik Weng , Tiekink Edward R. T.
Published: March 2012

The hydrazinium residue in the cation of the title salt, C6H10N3O2S+·Cl−, is twisted out of the plane of the benzene ring to which it is attached [N—N—C—C torsion angle = 25.9 (2)°] and the amino group is almost perpendicular to the benzene ring [N—S—C—C torsion angle = 88.71 (16)°]. In the crystal, the cations are linked by N—H...O hydrogen bonds and π–π interactions [ring centroid distance = 3.7280 (11) Å], forming layers in thebcplane that are connected by N—H...Cl hydrogen bonds.