bluuebunny/crossref_metadata_2025 huggingface dataset:
Coarse-graining Calcium Dynamics on Stochastic Reaction-diffusion Lattice Model
Authors: Shen Chuan-sheng , Chen Han-shuang
Published: May 2013

We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and deriving CG reaction rates using local mean field approximation, we perform CG kinetic Monte Carlo (kMC) simulations and find the results of CG-kMC simulations are in excellent agreement with that of the microscopic ones. Strikingly, there is an appropriate range of coarse proportion m, corresponding to the minimal deviation of the phase transition point compared to the microscopic one. For fixed m, the critical point increases monotonously as the system size increases, especially, there exists scaling law between the deviations of the phase transition point and the system size. Moreover, the CG approach provides significantly faster Monte Carlo simulations which are easy to implement and are directly related to the microscopics, so that one can study the system size effects at the cost of reasonable computational time.
Effect of Gate Electric Field on Single Organic Molecular Devices
Authors: Li Zong-liang , Fu Xiao-xiao , Zhang Guang-ping , Wang Chuan-kui
Published: May 2013

Based on the first-principles computational method and elastic scattering Green's function theory, we have investigated the effect of gate electric field on electronic transport properties of a series of single organic molecular junctions theoretically. The numerical results show that the molecular junctions that have redox centers and relatively large dipole moments parallel gate direction can respond to the gate electric field remarkably. The current-voltage properties of 2,5-dimethyl-thiophene-dithiol present N-channel-metal-oxide-semiconductor-like characteristics. Its distinct current-voltage properties can be understood from the evolution of eigenvalues, coupling energies, and atomic charges with gate electric field.
Dynamics of Micelle Formation from Mixed Lipid Droplets
Authors: Xu Rui , Wang Zi-lu , Li Hua-ping , He Xue-hao
Published: May 2013

Amphiphilic lipid molecules can form various micelles depending on not only their molecular composition but also their self-assembly pathway. In this work, coarse-grained molecular dynamics simulations have been applied to study the micellization behaviors of mixed dipalmitoylphosphatidylcholine (DPPC)/hexadecylphosphocholine (HPC) droplets. By varying DPPC/HPC composition and the size of lipid droplets, various micelles such as spherical and nonspherical (oblate or prolate) vesicles, disk-like micelles, double or single ring-like and worm-like micelles were observed. It is found that the lipid droplet as an initial state favors forming vesicles and ring-like micelles due to in situ micellization. Our simulation results demonstrate that using special initial conditions combined with various molecular compositions is an effective way to tune lipid micellar structure.
High Performance Ultraviolet Photodetector Fabricated with ZnO Nanoparticles-graphene Hybrid Structures
Authors: Liu Jin-yang , Yu Xin-xin , Zhang Guang-hui , Wu Yu-kun , Zhang Kun , Pan Nan , Wang Xiao-ping
Published: May 2013

Ultraviolet (UV) photodetector constructed by ZnO material has attracted intense research and commercial interest. However, its photoresistivity and photoresonse are still unsatisfied. Herein, we report a novel method to assemble ZnO nanoparticles (NPs) onto the reduced graphite oxide (RGO) sheet by simple hydrothermal process without any surfactant. It is found that the high-quality crystallized ZnO NPs with the average diameter of 5 nm are well dispersed on the RGO surface, and the density of ZnO NPs can be readily controlled by the concentration of the precursor. The photodetector fabricated with this ZnO NPs-RGO hybrid structure demonstrates an excellent photoresponse for the UV irradiation. The results make this hybrid especially suitable as a novel material for the design and fabrication of high performance UV photodector.
Electronic Response of Nano-sized Cages of ZnO and MgO to Presence of Nitric Oxide
Authors: Peyghan Ali Ahmadi , Noei Maziar
Published: May 2013

We have performed a comparative theoretical study on the adsorption of nitric oxide (NO) on Zn12O12 and Mg12O12 nanocages in terms of their energetic, geometric, and electronic properties. It has been found that NO adsorption on the MgO nanocage is energetically more favorable than that on the ZnO one. In contrast to the ZnO nanocage, HOMO-LUMO energy gap (Eg) of MgO one is dramatically decreased in the presence of NO molecule so that it is transformed from an intrinsic semiconductor (Eg≈5.00 eV) to a p-type one (Eg≈1.93 eV). We have predicted that electronic and conductance properties of the Mg12O12 nanocage are sensitive toward NO molecule, thus it may be potential candidate in detection of NO molecules.
Production of Low-carbon Light Olefins from Catalytic Cracking of Crude Bio-oil
Authors: Yuan Yan-ni , Wang Tie-jun , Li Quan-xin
Published: May 2013

Low-carbon light olefins are the basic feedstocks for the petrochemical industry. Catalytic cracking of crude bio-oil and its model compounds (including methanol, ethanol, acetic acid, acetone, and phenol) to light olefins were performed by using the La/HZSM-5 catalyst. The highest olefins yield from crude bio-oil reached 0.19 kg/(kg crude bio-oil). The reaction conditions including temperature, weight hourly space velocity, and addition of La into the HZSM-5 zeolite can be used to control both olefins yield and selectivity. Moderate adjusting the acidity with a suitable ratio between the strong acid and weak acid sites through adding La to the zeolite effectively enhanced the olefins selectivity and improved the catalyst stability. The production of light olefins from crude bio-oil is closely associated with the chemical composition and hydrogen to carbon effective ratios of feedstock. The comparison between the catalytic cracking and pyrolysis of bio-oil was studied. The mechanism of the bio-oil conversion to light olefins was also discussed.
Are soluble carbohydrates ecologically relevant for salt tolerance in halophytes?
Authors: Gil Ricardo , Boscaiu Monica , Lull Cristina , Bautista Inmaculada , Lidón Antonio , Vicente Oscar
Published: May 2013

A general response of plants to high soil salinity relies on the cellular accumulation of osmolytes, which help the plant to maintain osmotic balance under salt stress condition and/or act as ‘osmoprotectants’ with chaperon or reactive oxygen species (ROS) scavenging activities. Yet the ecological relevance of this response for the salt tolerance mechanisms of halophytes in their natural habitats remains largely unknown. In this review, we describe and discuss published data supporting the participation of compatible solutes in those mechanisms, with especial focus on soluble carbohydrates. Evidence for a functional role of carbohydrates in salt tolerance include: (i) relatively high levels of specific sugars and polyols have been detected in many halophytic taxa; (ii) an increase in salt tolerance has often been observed in parallel with increased intracellular levels of particular soluble carbohydrates, in transgenic plants overexpressing the corresponding biosynthetic enzymes; (iii) there are several examples of genes involved in carbohydrate metabolism which are induced under salt stress conditions; (iv) specific sugars or polyols have been shown to accumulate in different halophytes upon controlled salt treatments; and (v) although very few field studies on environmentally induced carbohydrate changes in halophytes exist, in general they also support the involvement of this type of osmolytes in salt stress tolerance mechanisms. We also highlight the complexities of unequivocally attributing carbohydrates a biological role in salt tolerance mechanisms of a given tolerant species. It is proposed that research on halophytes in their natural ecosystems should be intensified, correlating seasonal changes in carbohydrate contents with the degree of environmental stress affecting the plants. This could be an important complement to experiments made under more controlled (but artificial) conditions, such as laboratory set-ups.
Zoonosis emergence linked to agricultural intensification and environmental change
Authors: Jones Bryony A. , Grace Delia , Kock Richard , Alonso Silvia , Rushton Jonathan , Said Mohammed Y. , McKeever Declan , Mutua Florence , Young Jarrah , McDermott John , Pfeiffer Dirk Udo
Published: May 2013

A systematic review was conducted by a multidisciplinary team to analyze qualitatively best available scientific evidence on the effect of agricultural intensification and environmental changes on the risk of zoonoses for which there are epidemiological interactions between wildlife and livestock. The study found several examples in which agricultural intensification and/or environmental change were associated with an increased risk of zoonotic disease emergence, driven by the impact of an expanding human population and changing human behavior on the environment. We conclude that the rate of future zoonotic disease emergence or reemergence will be closely linked to the evolution of the agriculture–environment nexus. However, available research inadequately addresses the complexity and interrelatedness of environmental, biological, economic, and social dimensions of zoonotic pathogen emergence, which significantly limits our ability to predict, prevent, and respond to zoonotic disease emergence.
Innovations in capture fisheries are an imperative for nutrition security in the developing world
Authors: Hall Stephen J. , Hilborn Ray , Andrew Neil L. , Allison Edward H.
Published: May 2013

This article examines two strands of discourse on wild capture fisheries; one that focuses on resource sustainability and environmental impacts, another related to food and nutrition security and human well-being. Available data and research show that, for countries most dependent on fish to meet the nutritional requirements of their population, wild capture fisheries remain the dominant supplier. Although, contrary to popular narratives, the sustainability of these fisheries is not always and everywhere in crisis, securing their sustainability is essential and requires considerable effort across a broad spectrum of fishery systems. An impediment to achieving this is that the current research and policy discourses on environmental sustainability of fisheries and food security remain only loosely and superficially linked. Overcoming this requires adoption of a broader sustainability science paradigm to help harness synergies and negotiate tradeoffs between food security, resource conservation, and macroeconomic development goals. The way society chooses to govern fisheries is, however, an ethical choice, not just a technical one, and we recommend adding an ethical dimension to sustainability science as applied to fisheries.
Interactive effects among ecosystem services and management practices on crop production: Pollination in coffee agroforestry systems
Authors: Boreux Virginie , Kushalappa Cheppudira G. , Vaast Philippe , Ghazoul Jaboury
Published: May 2013

Crop productivity is improved by ecosystem services, including pollination, but this should be set in the context of trade-offs among multiple management practices. We investigated the impact of pollination services on coffee production, considering variation in fertilization, irrigation, shade cover, and environmental variables such as rainfall (which stimulates coffee flowering across all plantations), soil pH, and nitrogen availability. After accounting for management interventions, bee abundance improved coffee production (number of berries harvested). Some management interventions, such as irrigation, used once to trigger asynchronous flowering, dramatically increased bee abundance at coffee trees. Others, such as the extent and type of tree cover, revealed interacting effects on pollination and, ultimately, crop production. The effects of management interventions, notably irrigation and addition of lime, had, however, far more substantial positive effects on coffee production than tree cover. These results suggest that pollination services matter, but managing the asynchrony of flowering was a more effective tool for securing good pollination than maintaining high shade tree densities as pollinator habitat. Complex interactions across farm and landscape scales, including both management practices and environmental conditions, shape pollination outcomes. Effective production systems therefore require the integrated consideration of management practices in the context of the surrounding habitat structure. This paper points toward a more strategic use of ecosystem services in agricultural systems, where ecosystem services are shaped by the coupling of management interventions and environmental variables.
Coevolution of farming and private property during the early Holocene
Authors: Bowles Samuel , Choi Jung-Kyoo
Published: May 2013

The advent of farming around 12 millennia ago was a cultural as well as technological revolution, requiring a new system of property rights. Among mobile hunter–gatherers during the late Pleistocene, food was almost certainly widely shared as it was acquired. If a harvested crop or the meat of a domesticated animal were to have been distributed to other group members, a late Pleistocene would-be farmer would have had little incentive to engage in the required investments in clearing, cultivation, animal tending, and storage. However, the new property rights that farming required—secure individual claims to the products of one’s labor—were infeasible because most of the mobile and dispersed resources of a forager economy could not cost-effectively be delimited and defended. The resulting chicken-and-egg puzzle might be resolved if farming had been much more productive than foraging, but initially it was not. Our model and simulations explain how, despite being an unlikely event, farming and a new system of farming-friendly property rights nonetheless jointly emerged when they did. This Holocene revolution was not sparked by a superior technology. It occurred because possession of the wealth of farmers—crops, dwellings, and animals—could be unambiguously demarcated and defended. This facilitated the spread of new property rights that were advantageous to the groups adopting them. Our results thus challenge unicausal models of historical dynamics driven by advances in technology, population pressure, or other exogenous changes. Our approach may be applied to other technological and institutional revolutions such as the 18th- and 19th-century industrial revolution and the information revolution today.
High regional climate sensitivity over continental China constrained by glacial-recent changes in temperature and the hydrological cycle
Authors: Eagle Robert A. , Risi Camille , Mitchell Jonathan L. , Eiler John M. , Seibt Ulrike , Neelin J. David , Li Gaojun , Tripati Aradhna K.
Published: May 2013

The East Asian monsoon is one of Earth’s most significant climatic phenomena, and numerous paleoclimate archives have revealed that it exhibits variations on orbital and suborbital time scales. Quantitative constraints on the climate changes associated with these past variations are limited, yet are needed to constrain sensitivity of the region to changes in greenhouse gas levels. Here, we show central China is a region that experienced a much larger temperature change since the Last Glacial Maximum than typically simulated by climate models. We applied clumped isotope thermometry to carbonates from the central Chinese Loess Plateau to reconstruct temperature and water isotope shifts from the Last Glacial Maximum to present. We find a summertime temperature change of 6–7 °C that is reproduced by climate model simulations presented here. Proxy data reveal evidence for a shift to lighter isotopic composition of meteoric waters in glacial times, which is also captured by our model. Analysis of model outputs suggests that glacial cooling over continental China is significantly amplified by the influence of stationary waves, which, in turn, are enhanced by continental ice sheets. These results not only support high regional climate sensitivity in Central China but highlight the fundamental role of planetary-scale atmospheric dynamics in the sensitivity of regional climates to continental glaciation, changing greenhouse gas levels, and insolation.
Dependence of hydropower energy generation on forests in the Amazon Basin at local and regional scales
Authors: Stickler Claudia M. , Coe Michael T. , Costa Marcos H. , Nepstad Daniel C. , McGrath David G. , Dias Livia C. P. , Rodrigues Hermann O. , Soares-Filho Britaldo S.
Published: May 2013

Tropical rainforest regions have large hydropower generation potential that figures prominently in many nations’ energy growth strategies. Feasibility studies of hydropower plants typically ignore the effect of future deforestation or assume that deforestation will have a positive effect on river discharge and energy generation resulting from declines in evapotranspiration (ET) associated with forest conversion. Forest loss can also reduce river discharge, however, by inhibiting rainfall. We used land use, hydrological, and climate models to examine the local “direct” effects (through changes in ET within the watershed) and the potential regional “indirect” effects (through changes in rainfall) of deforestation on river discharge and energy generation potential for the Belo Monte energy complex, one of the world’s largest hydropower plants that is currently under construction on the Xingu River in the eastern Amazon. In the absence of indirect effects of deforestation, simulated deforestation of 20% and 40% within the Xingu River basin increased discharge by 4–8% and 10–12%, with similar increases in energy generation. When indirect effects were considered, deforestation of the Amazon region inhibited rainfall within the Xingu Basin, counterbalancing declines in ET and decreasing discharge by 6–36%. Under business-as-usual projections of forest loss for 2050 (40%), simulated power generation declined to only 25% of maximum plant output and 60% of the industry’s own projections. Like other energy sources, hydropower plants present large social and environmental costs. Their reliability as energy sources, however, must take into account their dependence on forests.
Cross-talk between
Akkermansia muciniphila
and intestinal epithelium controls diet-induced obesity
Authors: Everard Amandine , Belzer Clara , Geurts Lucie , Ouwerkerk Janneke P. , Druart Céline , Bindels Laure B. , Guiot Yves , Derrien Muriel , Muccioli Giulio G. , Delzenne Nathalie M. , de Vos Willem M. , Cani Patrice D.
Published: May 2013

Obesity and type 2 diabetes are characterized by altered gut microbiota, inflammation, and gut barrier disruption. Microbial composition and the mechanisms of interaction with the host that affect gut barrier function during obesity and type 2 diabetes have not been elucidated. We recently isolated
Akkermansia muciniphila
, which is a mucin-degrading bacterium that resides in the mucus layer. The presence of this bacterium inversely correlates with body weight in rodents and humans. However, the precise physiological roles played by this bacterium during obesity and metabolic disorders are unknown. This study demonstrated that the abundance of
A. muciniphila
decreased in obese and type 2 diabetic mice. We also observed that prebiotic feeding normalized
A. muciniphila
abundance, which correlated with an improved metabolic profile. In addition, we demonstrated that
A. muciniphila
treatment reversed high-fat diet-induced metabolic disorders, including fat-mass gain, metabolic endotoxemia, adipose tissue inflammation, and insulin resistance.
A. muciniphila
administration increased the intestinal levels of endocannabinoids that control inflammation, the gut barrier, and gut peptide secretion. Finally, we demonstrated that all these effects required viable
A. muciniphila
because treatment with heat-killed cells did not improve the metabolic profile or the mucus layer thickness. In summary, this study provides substantial insight into the intricate mechanisms of bacterial (i.e.,
A. muciniphila
) regulation of the cross-talk between the host and gut microbiota. These results also provide a rationale for the development of a treatment that uses this human mucus colonizer for the prevention or treatment of obesity and its associated metabolic disorders.
Visualization of pinholin lesions in vivo
Authors: Pang Ting , Fleming Tinya C. , Pogliano Kit , Young Ry
Published: May 2013

Significance

How a virus schedules the termination of its infection cycle is a mystery. Here, we show that a small-membrane protein called a pinholin controls the infection cycle of a bacterial virus. By tagging the pinholin with a fluorescent marker, we show that, while the virus is replicating, the pinholin accumulates harmlessly and uniformly in the membrane until suddenly aggregating into foci (rafts), causing a fatal deenergization of the bacterial membrane and the onset of lysis. The entire temporal program of the virus may, thus, depend on achieving a critical concentration of a single protein.
Nuclease activity of
Saccharomyces cerevisiae
Dna2 inhibits its potent DNA helicase activity
Authors: Levikova Maryna , Klaue Daniel , Seidel Ralf , Cejka Petr
Published: May 2013

Significance

The integrity of DNA must be preserved to pass genetic information onto the next generation and to prevent genomic instability. One of the key enzymes involved in DNA metabolism is the nuclease-helicase Dna2, which is required for both DNA replication and the repair of broken DNA. Our work revealed that Dna2 from
Saccharomyces cerevisiae
possesses a potent but cryptic helicase capacity, which is controlled by the nuclease activity of the same polypeptide. Regulating the interplay between both enzymatic activities might explain how Dna2 can take on its distinct cellular roles.
Functional ecology of an Antarctic Dry Valley
Authors: Chan Yuki , Van Nostrand Joy D. , Zhou Jizhong , Pointing Stephen B. , Farrell Roberta L.
Published: May 2013

The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution.
Role of the ubiquitin ligase E6AP/UBE3A in controlling levels of the synaptic protein Arc
Authors: Kühnle Simone , Mothes Benedikt , Matentzoglu Konstantin , Scheffner Martin
Published: May 2013

Inactivation of the ubiquitin ligase E6 associated protein (E6AP) encoded by theUBE3Agene has been associated with development of the Angelman syndrome. Recently, it was reported that in mice, loss of E6AP expression results in increased levels of the synaptic protein Arc and a concomitant impaired synaptic function, providing an explanation for some phenotypic features of Angelman syndrome patients. Accordingly, E6AP has been shown to negatively regulate activity-regulated cytoskeleton-associated protein (Arc) and it has been suggested that E6AP targets Arc for ubiquitination and degradation. In our study, we provide evidence that Arc is not a direct substrate for E6AP and binds only weakly to E6AP, if at all. Furthermore, we show that down-regulation of E6AP expression stimulates estradiol-induced transcription of theArcgene. Thus, we propose that Arc protein levels are controlled by E6AP at the transcriptional rather than at the posttranslational level.
Graphene field effect transistor without an energy gap
Authors: Jang Min Seok , Kim Hyungjun , Son Young-Woo , Atwater Harry A. , Goddard William A.
Published: May 2013

Graphene is a room temperature ballistic electron conductor and also a very good thermal conductor. Thus, it has been regarded as an ideal material for postsilicon electronic applications. A major complication is that the relativistic massless electrons in pristine graphene exhibit unimpeded Klein tunneling penetration through gate potential barriers. Thus, previous efforts to realize a field effect transistor for logic applications have assumed that introduction of a band gap in graphene is a prerequisite. Unfortunately, extrinsic treatments designed to open a band gap seriously degrade device quality, yielding very low mobility and uncontrolled on/off current ratios. To solve this dilemma, we propose a gating mechanism that leads to a hundredfold enhancement in on/off transmittance ratio for normally incident electrons without any band gap engineering. Thus, our saw-shaped geometry gate potential (in place of the conventional bar-shaped geometry) leads to switching to an off state while retaining the ultrahigh electron mobility in the on state. In particular, we report that an on/off transmittance ratio of 130 is achievable for a sawtooth gate with a gate length of 80 nm. Our switching mechanism demonstrates that intrinsic graphene can be used in designing logic devices without serious alteration of the conventional field effect transistor architecture. This suggests a new variable for the optimization of the graphene-based device—geometry of the gate electrode.
Circadian patterns of gene expression in the human brain and disruption in major depressive disorder
Authors: Li Jun Z. , Bunney Blynn G. , Meng Fan , Hagenauer Megan H. , Walsh David M. , Vawter Marquis P. , Evans Simon J. , Choudary Prabhakara V. , Cartagena Preston , Barchas Jack D. , Schatzberg Alan F. , Jones Edward G. , Myers Richard M. , Watson Stanley J. , Akil Huda , Bunney William E.
Published: May 2013

A cardinal symptom of major depressive disorder (MDD) is the disruption of circadian patterns. However, to date, there is no direct evidence of circadian clock dysregulation in the brains of patients who have MDD. Circadian rhythmicity of gene expression has been observed in animals and peripheral human tissues, but its presence and variability in the human brain were difficult to characterize. Here, we applied time-of-death analysis to gene expression data from high-quality postmortem brains, examining 24-h cyclic patterns in six cortical and limbic regions of 55 subjects with no history of psychiatric or neurological illnesses (“controls”) and 34 patients with MDD. Our dataset covered ∼12,000 transcripts in the dorsolateral prefrontal cortex, anterior cingulate cortex, hippocampus, amygdala, nucleus accumbens, and cerebellum. Several hundred transcripts in each region showed 24-h cyclic patterns in controls, and >100 transcripts exhibited consistent rhythmicity and phase synchrony across regions. Among the top-ranked rhythmic genes were the canonical clock genes
BMAL1(ARNTL), PER1-2-3, NR1D1(REV-ERBa), DBP, BHLHE40 (DEC1)
, and
BHLHE41(DEC2)
. The phasing of known circadian genes was consistent with data derived from other diurnal mammals. Cyclic patterns were much weaker in the brains of patients with MDD due to shifted peak timing and potentially disrupted phase relationships between individual circadian genes. This transcriptome-wide analysis of the human brain demonstrates a rhythmic rise and fall of gene expression in regions outside of the suprachiasmatic nucleus in control subjects. The description of its breakdown in MDD suggests potentially important molecular targets for treatment of mood disorders.
Distinct preplay of multiple novel spatial experiences in the rat
Authors: Dragoi George , Tonegawa Susumu
Published: May 2013

The activity of ensembles of hippocampal place cells represents a hallmark of an animal’s spatial experience. The neuronal mechanisms that enable the rapid expression of novel place cell sequences are not entirely understood. Here we report that during sleep or rest, distinct sets of hippocampal temporal sequences in the rat preplay multiple corresponding novel spatial experiences with high specificity. These findings suggest that the place cell sequence of a novel spatial experience is determined, in part, by an online selection of a subset of cellular firing sequences from a larger repertoire of preexisting temporal firing sequences in the hippocampal cellular assembly network that become rapidly bound to the novel experience. We estimate that for the given context, the recorded hippocampal network activity has the capacity to preplay an extended repertoire of at least 15 future spatial experiences of similar distinctiveness and complexity.
Trp replacements for tightly interacting Gly–Gly pairs in LacY stabilize an outward-facing conformation
Authors: Smirnova Irina , Kasho Vladimir , Sugihara Junichi , Kaback H. Ronald
Published: May 2013

Trp replacements for conserved Gly–Gly pairs between the N- and C-terminal six-helix bundles on the periplasmic side of lactose permease (LacY) cause complete loss of transport activity with little or no effect on sugar binding. Moreover, the detergent-solubilized mutants exhibit much greater thermal stability than WT LacY. A Cys replacement for Asn245, which is inaccessible/unreactive in WT LacY, alkylates readily in the Gly→Trp mutants, indicating that the periplasmic cavity is patent. Stopped-flow kinetic measurements of sugar binding with the Gly→Trp mutants in detergent reveal linear dependence of binding rates on sugar concentration, as observed with WT or the C154G mutant of LacY, and are compatible with free access to the sugar-binding site in the middle of the molecule. Remarkably, after reconstitution of the Gly→Trp mutants into proteoliposomes, the concentration dependence of sugar-binding rates increases sharply with even faster rates than measured in detergent. Such behavior is strikingly different from that observed for reconstituted WT LacY, in which sugar-binding rates are independent of sugar concentration because opening of the periplasmic cavity is limiting for sugar binding. The observations clearly indicate that Gly→Trp replacements, which introduce bulky residues into tight Gly–Gly interdomain interactions on the periplasmic side of LacY, prevent closure of the periplasmic cavity and, as a result, shift the distribution of LacY toward an outward-open conformation.
The Iranian Diaspora in Sydney: Migration Experience of Recent Iranian Immigrants
Authors: Tenty Tiffany Amber , Houston Christopher
Published: May 2013

Recent research has found that discrimination against Islam and Muslims is deeply rooted in Australia. This report explores whether or how recent Iranian migrants have experienced racism, discrimination, or Islamaphobia in Sydney. These questions are explored by focusing on their experiences and issues regarding their making of new lives in Australia. This article suggests that recent Iranian migrants are experiencing far less discrimination than other Muslim diasporas in Sydney. Concluding that despite recent reports by some researchers grouping various Muslim populations together as regards Islamaphobia, there is a necessity for investigating discrimination, stereotyping, and Islamaphobia against particular diasporas to determine the needs of the Muslim population at large.
CXCR4 promotes B cell egress from Peyer’s patches
Authors: Schmidt Timothy H. , Bannard Oliver , Gray Elizabeth E. , Cyster Jason G.
Published: May 2013

Peyer’s patches (PPs) play a central role in supporting B cell responses against intestinal antigens, yet the factors controlling B cell passage through these mucosal lymphoid tissues are incompletely understood. We report that, in mixed chimeras, CXCR4-deficient B cells accumulate in PPs compared with their representation in other lymphoid tissues. CXCR4-deficient B cells egress from PPs more slowly than wild-type cells, whereas CXCR5-deficient cells egress more rapidly. The CXCR4 ligand, CXCL12, is expressed by cells adjacent to lymphatic endothelial cells in a zone that abuts but minimally overlaps with the CXCL13+ follicle. CXCR4-deficient B cells show reduced localization to these CXCL12+ perilymphatic zones, whereas CXCR5-deficient B cells preferentially localize in these regions. By photoconverting KikGR-expressing cells within surgically exposed PPs, we provide evidence that naive B cells transit PPs with an approximate residency half-life of 10 h. When CXCR4 is lacking, KikGR+ B cells show a delay in PP egress. In summary, we identify a CXCL12hi perilymphatic zone in PPs that plays a role in overcoming CXCL13-mediated retention to promote B cell egress from these gut-associated lymphoid tissues.
Channel properties of the splicing isoforms of the olfactory calcium-activated chloride channel Anoctamin 2
Authors: Ponissery Saidu Samsudeen , Stephan Aaron B. , Talaga Anna K. , Zhao Haiqing , Reisert Johannes
Published: May 2013

Anoctamin (ANO)2 (or TMEM16B) forms a cell membrane Ca2+-activated Cl− channel that is present in cilia of olfactory receptor neurons, vomeronasal microvilli, and photoreceptor synaptic terminals. Alternative splicing of Ano2 transcripts generates multiple variants with the olfactory variants skipping exon 14 and having alternative splicing of exon 4. In the present study, 5′ rapid amplification of cDNA ends analysis was conducted to characterize the 5′ end of olfactory Ano2 transcripts, which showed that the most abundant Ano2 transcripts in the olfactory epithelium contain a novel starting exon that encodes a translation initiation site, whereas transcripts of the publically available sequence variant, which has an alternative and longer 5′ end, were present in lower abundance. With two alternative starting exons and alternative splicing of exon 4, four olfactory ANO2 isoforms are thus possible. Patch-clamp experiments in transfected HEK293T cells expressing these isoforms showed that N-terminal sequences affect Ca2+ sensitivity and that the exon 4–encoded sequence is required to form functional channels. Coexpression of the two predominant isoforms, one with and one without the exon 4 sequence, as well as coexpression of the two rarer isoforms showed alterations in channel properties, indicating that different isoforms interact with each other. Furthermore, channel properties observed from the coexpression of the predominant isoforms better recapitulated the native channel properties, suggesting that the native channel may be composed of two or more splicing isoforms acting as subunits that together shape the channel properties.
Inverse problems for deformation rings
Authors: Bleher Frauke , Chinburg Ted , de Smit Bart
Published: May 2013

Let

W
W

be a complete Noetherian local commutative ring with residue field

k
k

of positive characteristic

p
p

. We study the inverse problem for the universal deformation rings

R

W

(
Γ
,
V
)

R_{W}(\Gamma ,V)

relative to

W
W

of finite dimensional representations

V
V

of a profinite group

Γ
\Gamma

over

k
k

. We show that for all

p
p

and

n
≥
1

n \ge 1

, the ring

W
[
[
t
]
]

/

(

p
n

t
,

t
2

)

W[[t]]/(p^n t,t^2)

arises as a universal deformation ring. This ring is not a complete intersection if

p
n

W
≠
{
0
}

p^nW\neq \{0\}

, so we obtain an answer to a question of M. Flach in all characteristics. We also study the ‘inverse inverse problem’ for the ring

W
[
[
t
]
]

/

(

p
n

t
,

t
2

)

W[[t]]/(p^n t,t^2)

; this is to determine all pairs

(
Γ
,
V
)

(\Gamma , V)

such that

R

W

(
Γ
,
V
)

R_{W}(\Gamma ,V)

is isomorphic to this ring.
Renin–angiotensin system blockade in heart failure patients on long‐term haemodialysis in Taiwan
Authors: Tang Chao‐Hsiun , Chen Tso‐Hsiao , Wang Chia‐Chen , Hong Chuang‐Ye , Huang Kuan‐Chih , Sue Yuh‐Mou
Published: May 2013

Aims

Heart failure is among the most frequent complications of patients on long‐term haemodialysis. The benefits of renin–angiotensin system (RAS) blockade on the outcomes of these patients have yet to be determined.

Methods and results

We conducted a nationwide observational study using data from the Taiwan National Health Insurance claims database, between 1999 and 2010. We enrolled patients aged ≥35 years with new‐onset heart failure [diagnosed by International Classification of Diseases, 9th revision, clinical modification (ICD‐9‐CM) codes] under treatment with medications. New users of a RAS blocker (RASB; i.e. an ACE inhibitor or an ARB used as monotherapy or dual therapy) were selected to compare with non‐RASB users. We used Cox proportional hazards regression with and without propensity score adjustment to compare the risk of 3‐year all‐cause and cardiovascular mortality. Stratified analyses and RASB therapy duration as a time‐dependent covariate were also performed. In all, 4771 were treated with an RASB (n = 3024) or without an RASB (n = 1747). RASB users had a higher prevalence of hypertension and diabetes, and a higher number of hospitalization. Among RASB users, 1148 deaths (38.0%) occurred during 5272 person‐years of follow‐up compared with 734 deaths (42.0%) among non‐RASB users during 2683 person‐years of follow‐up. Three‐year mortality rates were 45.4% and 49.1% for patients receiving and those not receiving an RASB, respectively (log‐rank test, P < 0.001). Adjusted hazard analysis revealed that RASB therapeutic effects remained significant on all‐cause [hazard ratio (HR) 0.8; 95% confidence interval (CI) 0.72–0.89; P < 0.001] and cardiovascular mortality (HR 0.76; 95% CI 0.64–0.90; P < 0.01).

Conclusions

RASB therapy reduced all‐cause and cardiovascular mortality in heart failure patients on long‐term haemodialysis.
Arabis mosaic virus in Grapevines in New York State
Authors: Celebi-Toprak F. , Thompson J. R. , Perry K. L. , Fuchs M.
Published: May 2013

In a limited survey of commercial vineyards and a germplasm repository in Ontario County, NY, 20 vines of Vitis sp. were tested in fall and spring 2010 to 2012 for viruses using a double-antibody sandwich (DAS)-ELISA and macroarray with oligonucleotide probes for grapevine viruses ((3) and unpublished). The plants selected for analysis included those showing atypical growth including leaf deformation, yellowing, cupping or spotting, vein clearing, shortening of internodes, and reduced vigor. Arabis mosaic virus (ArMV; genus Nepovirus, family Secoviridae) was detected in leaf tissue and wood scrapings in two vines using the DAS-ELISA with antibodies from Bioreba (Reinach, Switzerland). The ArMV positive vines were from Vitis hybrid cultivars Noah and Geisenheim 26. ArMV was also detected in these two vines using the macroarray, with hybridization observed to 24 of 32 oligonucleotide probes specific to this virus. To confirm the identification of the virus, total RNAs were extracted from leaf tissues, hybridized with random hexamers, and reverse-transcribed using MMLV reverse transcriptase (Life Technologies, Grand Island, NY). Complementary DNAs were amplified by PCR using an IQ supermix (BioRad, Hercules, CA), and two sets of generic primers for nepoviruses (1,4). Thermocycler conditions were 94°C 5 min (1×); 94°C 30 s, 50°C 30 s, and 69°C 2 min (35×), and 72°C for 5 min. The PCR products were sequenced directly. Sequences from the 340-bp products obtained from cultivars Geisenheim 26 (GenBank Accession No. HE984333) and Noah (HE984334) using the Wei et al. primers (4) had 76 to 84% sequence identity to ArMV RNA1 GenBank accessions GQ369528 and AY303786. Sequences from the 301-bp products obtained from cultivars Geisenheim 26 (HE984335) and Noah (HE984336) using the Digiaro et al. primers (1) had 87 to 91% sequence identity to ArMV RNA2 GenBank accessions AY017339 and X81814. ArMV was mechanically transmitted from Geisenheim 26 to Nicotiana tabacum cultivar Xanthi NN. Inoculation gave rise to necrotic local lesions on the inoculated leaves of five plants in each of two experiments (10 of 10 plants total). The presence of ArMV in tobacco was confirmed by DAS-ELISA. Thus, the presence of ArMV in New York grapevines has been confirmed by the detection of the coat protein antigen, virus specific oligonucleotide probes, and the sequencing of portions of both genomic RNAs. There are limited reports of ArMV in North America and in grapevine in particular (2), but with a wide host range and seed and nematode transmissibility, ArMV has the ability to become more widespread among grapevine and other crops.

References: (1) M. Digiaro, et al. J. Virol. Methods 141:34, 2007. (2) B. N. Milkus et al. Am. J. Enol. Vitic. 50:56, 1999. (3) J. Thompson et al. J. Virol. Methods 183:161, 2012. (4) T. Wei et al. J. Virol. Methods 153:16, 2008.
Oxytocin Pretreatment Attenuates Oxytocin-induced Contractions in Human Myometrium In Vitro
Authors: Balki Mrinalini , Erik-Soussi Magda , Kingdom John , Carvalho Jose C. A.
Published: May 2013

Background:

Oxytocin receptor desensitization has been shown to occur in humans at biomolecular level and in isolated rat myometrium; however, its effect on human myometrial contractility has not been demonstrated. The objective of this in vitro study was to investigate the contractile response of human pregnant myometrium to oxytocin after pretreatment with different concentrations of oxytocin for variable durations.

Methods:

Myometrial samples were obtained from 62 women undergoing elective cesarean deliveries under regional anesthesia. The strips were pretreated with oxytocin 10−10, 10−8, 10−5
M, or physiological salt solution (control) for 2, 4, 6, or 12 h, followed by a dose–response testing with oxytocin 10−10 to 10−5
M. Amplitude and frequency of contractions, motility index, and area under the curve during the dose–response period were recorded, analyzed with linear regression models, and compared among groups.

Results:

Pretreatment with oxytocin 10−5 and 10−8
M significantly reduced motility index (estimate [standard error]: −0.771 [0.270] square root units, P = 0.005 and −0.697 [0.293], P = 0.02, respectively) and area under the curve (−3.947 [1.909], P = 0.04 and −4.241 [2.189], P = 0.05, respectively) compared with control group, whereas pretreatment with oxytocin 10−10
M did not significantly attenuate contractions. Increase in duration of oxytocin pretreatment from 2 to 12 h significantly decreased amplitude (type 3 generalized estimating equation analysis: chi-square = 14.0; df = 3; P = 0.003), motility index (chi-square = 9.3; df = 3; P = 0.03), and area under the curve (chi-square = 10.5; df = 3; P = 0.02), but not the frequency of oxytocin-induced contractions.

Conclusion:

Pretreatment with oxytocin decreases oxytocin-induced myometrial contractions in a concentration and time-dependent manner, likely as a function of the oxytocin receptor desensitization phenomenon.
Fast preparation of a desiccant array for the gradual desiccation method in protein crystallization screening
Authors: Lu Qin-Qin , Xie Xu-Zhuo , Liu Yong-Ming , Lu Hui-Meng , Chen Da , Wang Xu-Sheng , Yin Da-Chuan
Published: May 2013

The gradual desiccation method (GDM) is a modification of the vapor diffusion method for protein crystallization screening. This method can dramatically increase the chances of obtaining protein crystals and is therefore potentially useful for practical protein crystallization screening. However, it is troublesome to prepare the desiccant for the GDM because each of the 96 desiccants must be of the same mass. Repeated manual weighing of the desiccant (at least 96 times for one plate) to obtain the same amount is required, and manual distribution of the weighed desiccants to the respective reservoir wells is also necessary. These procedures require a considerable amount of labor and thus lower the efficiency of the screening process. Additionally, they reduce the applicability of this method in routine protein crystallization screening. To solve this problem, a high-throughput method is proposed, which involves dispensing an aqueous solution of salts (a combination of CoCl2and AlCl3) into a droplet array (8 × 12, corresponding to the arrangement in a standard crystallization plate) on a piece of tape, then drying this array to obtain the final desiccant array. Simply covering and sealing this desiccant array over the crystallization droplets in the crystallization plate can give a perfect vapor diffusion screen. With this method, the labor and automation requirements of the GDM will be comparable to those of the conventional vapor diffusion method; furthermore, the amount of the desiccant can be easily and accurately controlled, allowing the GDM to be applied in daily protein crystallization screening.
Chlorido[N,N′-dibenzyl-N′′-(trichloroacetyl)phosphoramidato-κ2O,O′](1,10-phenanthroline-κ2N,N′)copper(II)
Authors: Gubina Kateryna , Ovchynnikov Vladimir , Amirkhanov Vladymir , Shishkina Svetlana
Published: May 2013

In the title complex, [Cu(C16H16Cl3N3O2P)Cl(C12H8N2)], the CuIIcation presents a square-pyramidal environment, where the CuO2N2base is formed by two O atoms from carbonyl and phosphoryl groups, and by two N atoms from a 1,10-phenanthroline molecule. A coordinated Cl atom occupies the apex. N—H...Cl hydrogen bonds link the molecules into one-dimensional chains. The trichloromethyl group is rotationally disordered over two positions, with occupancies of 0.747 (7) and 0.253 (7).
catena-Poly[[[2-(2-chlorophenoxy)-N′-(2-oxidobenzylidene-κO)acetohydrazidato-κ2N′,O]copper(II)]-μ-morpholine-κ2N:O]
Authors: Wang Min , Lian Zhao-Xun
Published: May 2013

In the title compound, {[Cu(C15H11ClN2O3)(C4H9NO)]n, the CuIIcation has square-pyramidal geometry. The morpholine ligand serves as a bridge to link two symmetry-related metal atoms, resulting in an infinite chain structure along theaaxis. Adjacent chains are extended into a two-dimensional layered structureviahydrogen bonds formed between morpholine and amide N atoms [N—H...N = 2.971 (3) Å].
Modern vitiligo genetics sheds new light on an ancient disease
Authors: Spritz Richard A.
Published: May 2013

Vitiligo is a complex disorder in which autoimmune destruction of melanocytes results in white patches of skin and overlying hair. Over the past several years, extensive genetic studies have outlined a biological framework of vitiligo pathobiology that underscores its relationship to other autoimmune diseases. This biological framework offers insight into both vitiligo pathogenesis and perhaps avenues towards more effective approaches to treatment and even disease prevention.