bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-sufficient redox biotransformation of lignin-related benzoic acids with Aspergillus flavus
Authors: Palazzolo Martín A , Mascotti María L , Lewkowicz Elizabeth S , Kurina-Sanz Marcela
Published: October 2015

Aromatic carboxylic acids are readily obtained from lignin in biomass processing facilities. However, efficient technologies for lignin valorization are missing. In this work, a microbial screening was conducted to find versatile biocatalysts capable of transforming several benzoic acids structurally related to lignin, employing vanillic acid as model substrate. The wild-type Aspergillus flavus growing cells exhibited exquisite selectivity towards the oxidative decarboxylation product, 2-methoxybenzene-1,4-diol. Interestingly, when assaying a set of structurally related substrates, the biocatalyst displayed the oxidative removal of the carboxyl moiety or its reduction to the primary alcohol whether electron withdrawing or donating groups were present in the aromatic ring, respectively. Additionally, A. flavus proved to be highly tolerant to vanillic acid increasing concentrations (up to 8 g/L), demonstrating its potential application in chemical synthesis. A. flavus growing cells were found to be efficient biotechnological tools to perform self-sufficient, structure-dependent redox reactions. To the best of our knowledge, this is the first report of a biocatalyst exhibiting opposite redox transformations of the carboxylic acid moiety in benzoic acid derivatives, namely oxidative decarboxylation and carboxyl reduction, in a structure-dependent fashion.
The 2015 IUIS Phenotypic Classification for Primary Immunodeficiencies
Authors: Bousfiha Aziz , Jeddane Leïla , Al-Herz Waleed , Ailal Fatima , Casanova Jean‐Laurent , Chatila Talal , Conley Mary Ellen , Cunningham‐Rundles Charlotte , Etzioni Amos , Franco Jose Luis , Gaspar H. Bobby , Holland Steven M. , Klein Christoph , Nonoyama Shigeaki , Ochs Hans D. , Oksenhendler Eric , Picard Capucine , Puck Jennifer M. , Sullivan Kathleen E. , Tang Mimi L. K.
Published: October 2015

There are now nearly 300 single-gene inborn errors of immunity underlying phenotypes as diverse as infection, malignancy, allergy, auto-immunity, and auto-inflammation. For each of these five categories, a growing variety of phenotypes are ascribed to Primary Immunodeficiency Diseases (PID), making PIDs a rapidly expanding field of medicine. The International Union of Immunological Societies (IUIS) PID expert committee (EC) has published every other year a classification of these disorders into tables, defined by shared pathogenesis and/or clinical consequences. In 2013, the IUIS committee also proposed a more user-friendly, phenotypic classification, based on the selection of key phenotypes at the bedside. We herein propose the revised figures, based on the accompanying 2015 IUIS PID EC classification.
Stochastic Galerkin Formulations for $$\hbox {CO}_2$$ Transport in Aquifers: Numerical Solutions with Uncertain Material Properties
Authors: Pettersson Per
Published: October 2015

A stochastic Galerkin formulation for the transport of

$$\hbox {CO}_2$$

CO
2

in a tilted aquifer with uncertain heterogeneous properties is presented. We consider a simplified physics model assuming capillary pressure to be negligible compared to hydrostatic and viscous pressure. The flow is dominated by buoyancy and capillary trapping. We assume a stochastic permeability field and a stochastic model for the uncertain relative permeabilities. We prove that the proposed stochastic Galerkin formulation results in a hyperbolic system of equations, and we devise a numerical method that captures the expected solution discontinuities. The shock-capturing solver for the flux function is combined with an adaptive quadrature method for discontinuous isosurfaces that is used to compute the discontinuous stochastic accumulation coefficient. The stochastic solver is validated against Monte Carlo sampling of an analytical solution for the deterministic problem. The sharp features of the statistics of the solution are accurately captured by the numerical solver. The polynomial chaos framework admits low-cost post-processing of the output to obtain statistics of interest. By construction of an accurate polynomial chaos surrogate model of the output, fast sampling admits calculation of risk for leakage and failure probabilities.
Direct control of the small-scale energy balance in two-dimensional fluid dynamics
Authors: Frank Jason , Leimkuhler Benedict , Myerscough Keith W.
Published: October 2015

We explore the direct modification of the pseudo-spectral truncation of two-dimensional, incompressible fluid dynamics to maintain a prescribed kinetic energy spectrum. The method provides a means of simulating fluid states with defined spectral properties, for the purpose of matching simulation statistics to given information, arising from observations, theoretical prediction or high-fidelity simulation. In the scheme outlined here, Nosé–Hoover thermostats, commonly used in molecular dynamics, are introduced as feedback controls applied to energy shells of the Fourier-discretized Navier–Stokes equations. As we demonstrate in numerical experiments, the dynamical properties (quantified using autocorrelation functions) are only modestly perturbed by our device, while ensemble dispersion is significantly enhanced compared with simulations of a corresponding truncation incorporating hyperviscosity.
Optical Modulation in the X-Ray Binary 4U 1543–624 Revisited
Authors: Wang Z. , Tziamtzis A. , Kaplan D. L. , Chakrabarty D.
Published: October 2015

The X-ray binary 4U 1543–624 has been provisionally identified as an ultra-compact system with an orbital period of ≃ 18 min. We have carried out time-resolved optical imaging of the binary to verify the ultra-short orbital period. Using 140 min of high-cadence r′-band photometry, we recover the previously-seen sinusoidal modulation and determine a period P = 18.20 ± 0.09 min. In addition, we also see a 7.0 × 10−4 mag min−1 linear decay, likely related to variations in the source's accretion activity. Assuming that the sinusoidal modulation arises from X-ray heating of the inner face of the companion star, we estimate a distance of 6.0–6.7 kpc and an inclination angle of 34°–61° (90% confidence) for the binary. Given the stability of the modulation, we can confirm that the modulation is orbital in origin and 4U 1543–624 is an ultra-compact X-ray binary.
Diversity and patterns of interaction of an anuran–parasite network in a neotropical wetland
Authors: CAMPIÃO K. M. , RIBAS A. , TAVARES L. E. R.
Published: October 2015

We describe the diversity and structure of a host–parasite network of 11 anuran species and their helminth parasites in the Pantanal wetland, Brazil. Specifically, we investigate how the heterogeneous use of space by hosts changes parasite community diversity, and how the local pool of parasites exploits sympatric host species of different habits. We examined 229 anuran specimens, interacting with 32 helminth parasite taxa. Mixed effect models indicated the influence of anuran body size, but not habit, as a determinant of parasite species richness. Variation in parasite taxonomic diversity, however, was not significantly correlated with host size or habit. Parasite community composition was not correlated with host phylogeny, indicating no strong effect of the evolutionary relationships among anurans on the similarities in their parasite communities. Host–parasite network showed a nested and non-modular pattern of interaction, which is probably a result of the low host specificity observed for most helminths in this study. Overall, we found host body size was important in determining parasite community richness, whereas low parasite specificity was important to network structure.
Convolution estimates for singular measures and some global nonlinear Brascamp—Lieb inequalities
Authors: Koch Herbert , Steinerberger Stefan
Published: October 2015

We give an L2 x L2 → L2 convolution estimate for singular measures supported on transversal hypersurfaces in ℝn, which improves earlier results of Bejenaru et al. as well as Bejenaru and Herr. The quantities arising are relevant to the study of the validity of bilinear estimates for dispersive partial differential equations. We also prove a class of global, nonlinear Brascamp–Lieb inequalities with explicit constants in the same spirit.
Influence of provider mix and regulation on primary care services supplied to US patients
Authors: Richards Michael R. , Polsky Daniel
Published: October 2015

Access to medical care and how it differs for various patients remain key policy issues. While existing work has examined clinic structure’s influence on productivity, less research has explored the link between provider mix and access for different patient types – which also correspond to different service prices. We exploit experimental data from a large field study spanning 10 US states where trained audit callers were randomly assigned an insurance status and then contacted primary care physician practices seeking new patient appointments. We find clinics with more non-physician clinicians are associated with better access for Medicaid patients and lower prices for office visits; however, these relationships are only found in states granting full practice autonomy to these providers. Substituting more non-physician labor in primary care settings may facilitate greater appointment availability for Medicaid patients, but this likely rests on a favorable policy environment. Relaxing regulations for non-physicians may be an important initiative as US health reforms continue and also relevant to other countries coping with greater demands for medical care and related financial strain.
Phase shift combiner for multi-channel VHF communication
Authors: Holdengreber E. , Mizrahi M. , Glassner E. , Koral Y. , Schacham S.E. , Farber E.
Published: October 2015

The growing demand for communication systems requires multi-channel solutions. However, the number of antennas in communication systems is dictated by the number of channels in each system which is limited by the available space on a broadcasting platform and by the limited available resources. We have developed a Multi-Channel Phase Control coupler in the VHF frequency range enabling a reduction in the number of antennas to a third of the original setup. The system is based on a phase shifter in a meander stripline geometry connected to each channel individually. The channels are then phase matched simultaneously to a single antenna through a computer-controlled capacitor bank connected to each phase shifter. The system performance shows a low insertion loss of 0.5 dB and a low return loss of −15 dB for the multi-channel setup.
Increasing Relationship Between Negative Emotionality and Conduct Problems During Childhood: A Cross-Sectional Behavioral Genetic Analysis
Authors: Hur Yoon-Mi , Hwang Sunyung , Chung Un-Sun
Published: October 2015

Age difference in the etiology of the relationship between childhood negative emotionality (NE) and conduct problems (CP) has not been previously investigated. Mothers of 662 pairs of twins completed questions on the emotionality (NE) scale of the EAS temperament survey and the CP scale of the Strengths and Difficulties Questionnaires (SDQ) via a telephone interview. Twin data were analyzed separately in younger (ages 3 to 7 years; mostly pre-schoolers) and older children (ages 8 to 13 years; mostly elementary school children). The phenotypic correlation between NE and CP increased from 0.33 among younger twins to 0.43 among older twins. Bivariate model-fitting analysis was performed to determine age difference in the etiology of the relationship between NE and CP. Among younger twins, the correlation between NE and CP was entirely explained by additive genetic factors common to NE and CP. Among older children, however, a small but significant amount of unique environmental correlation emerged to account for about 47% of the phenotypic correlation between NE and CP. The remaining 53% of the phenotypic correlation was due to shared additive genetic factors. We speculate that environmental factors associated with school adjustment may exert influences on the relationship between NE and CP among elementary school children.
Magnetized Collisionless Shock Waves Measured in the Lab
Authors: Minnehan Catherine
Published: October 2015

Scientists create collisionless shock waves to better understand the phenomenon in nature.
Erratum: Nanometre-scale probing of spin waves using single electron spins
Authors: van der Sar Toeno , Casola Francesco , Walsworth Ronald , Yacoby Amir
Published: October 2015

Nature Communications 6: Article number: 7886 (2015); Published: 7 August 2015; Updated: 7 October 2015 The original version of this Article contained an error in the phrase ‘single electron spins’ in the title. This has now been corrected in both the PDF and HTML versions of the Article.
Cardiovascular and pharmacological implications of haem-deficient NO-unresponsive soluble guanylate cyclase knock-in mice
Authors: Thoonen Robrecht , Cauwels Anje , Decaluwe Kelly , Geschka Sandra , Tainsh Robert E. , Delanghe Joris , Hochepied Tino , De Cauwer Lode , Rogge Elke , Voet Sofie , Sips Patrick , Karas Richard H. , Bloch Kenneth D. , Vuylsteke Marnik , Stasch Johannes-Peter , Van de Voorde Johan , Buys Emmanuel S. , Brouckaert Peter
Published: October 2015

Oxidative stress, a central mediator of cardiovascular disease, results in loss of the prosthetic haem group of soluble guanylate cyclase (sGC), preventing its activation by nitric oxide (NO). Here we introduce Apo-sGC mice expressing haem-free sGC. Apo-sGC mice are viable and develop hypertension. The haemodynamic effects of NO are abolished, but those of the sGC activator cinaciguat are enhanced in apo-sGC mice, suggesting that the effects of NO on smooth muscle relaxation, blood pressure regulation and inhibition of platelet aggregation require sGC activation by NO. Tumour necrosis factor (TNF)-induced hypotension and mortality are preserved in apo-sGC mice, indicating that pathways other than sGC signalling mediate the cardiovascular collapse in shock. Apo-sGC mice allow for differentiation between sGC-dependent and -independent NO effects and between haem-dependent and -independent sGC effects. Apo-sGC mice represent a unique experimental platform to study thein vivoconsequences of sGC oxidation and the therapeutic potential of sGC activators.
Energetics of proton release on the first oxidation step in the water-oxidizing enzyme
Authors: Saito Keisuke , William Rutherford A. , Ishikita Hiroshi
Published: October 2015

In photosystem II (PSII), the Mn4CaO5 cluster catalyses the water splitting reaction. The crystal structure of PSII shows the presence of a hydrogen-bonded water molecule directly linked to O4. Here we show the detailed properties of the H-bonds associated with the Mn4CaO5 cluster using a quantum mechanical/molecular mechanical approach. When O4 is taken as a μ-hydroxo bridge acting as a hydrogen-bond donor to water539 (W539), the S0 redox state best describes the unusually short O4–OW539 distance (2.5 Å) seen in the crystal structure. We find that in S1, O4 easily releases the proton into a chain of eight strongly hydrogen-bonded water molecules. The corresponding hydrogen-bond network is absent for O5 in S1. The present study suggests that the O4-water chain could facilitate the initial deprotonation event in PSII. This unexpected insight is likely to be of real relevance to mechanistic models for water oxidation.
Detoxification of hostplant’s chemical defence rather than its anti-predator co-option drives β-glucosidase-mediated lepidopteran counteradaptation
Authors: Poreddy Spoorthi , Mitra Sirsha , Schöttner Matthias , Chandran Jima , Schneider Bernd , Baldwin Ian T. , Kumar Pavan , Pandit Sagar S.
Published: October 2015

The evolutionary plant–herbivore arms race sometimes gives rise to remarkably unique adaptation strategies. Here we report one such strategy in the lepidopteran herbivore Manduca sexta against its hostplant Nicotiana attenuata’s major phytotoxins, 17-hydroxygeranyllinalool diterpene glycoside, lyciumoside IV and its malonylated forms. We show that alkalinity of larval regurgitant non-enzymatically demalonylates the malonylated forms to lyciumoside IV. Lyciumoside IV is then detoxified in the midgut by β-glucosidase 1-catalysed deglycosylation, which is unusual, as typically the deglycosylation of glycosylated phytochemicals by insects results in the opposite: toxin activation. Suppression of deglucosylation by silencing larval β-glucosidase 1 by plant-mediated RNAi causes moulting impairments and mortality. In the native habitat of N. attenuata, β-glucosidase 1 silencing also increases larval unpalatability to native predatory spiders, suggesting that the defensive co-option of lyciumoside IV may be ecologically advantageous. We infer that M. sexta detoxifies this allelochemical to avoid its deleterious effects, rather than co-opting it against predators.
Fermi states and anisotropy of Brillouin zone scattering in the decagonal Al–Ni–Co quasicrystal
Authors: Rogalev V. A. , Gröning O. , Widmer R. , Dil J. H. , Bisti F. , Lev L. L. , Schmitt T. , Strocov V. N.
Published: October 2015

Quasicrystals (QCs) are intermetallic alloys that have excellent long-range order but lack translational symmetry in at least one dimension. The valence band electronic structure near the Fermi energy EF in such materials is of special interest since it has a direct relation to their unusual physical properties. However, the Fermi surface (FS) topology as well as the mechanism of QC structure stabilization are still under debate. Here we report the first observation of the three-dimensional FS and valence band dispersions near EF in decagonal Al70Ni20Co10 (d-AlNiCo) QCs using soft X-ray angle-resolved photoemission spectroscopy. We show that the FS, formed by dispersive Al sp-states, has a multicomponent character due to a large contribution from high-order bands. Moreover, we discover that the magnitude of the gap at the FS related to the interaction with Brillouin zone boundary (Hume–Rothery gap) critically differs for the periodic and quasiperiodic directions.
Comparison between thulium laser resection of prostate and transurethral plasmakinetic resection of prostate or transurethral resection of prostate
Authors: DeCao Hong , Wang Jia , Huang Yu , LiangLiu Ren , JunLei Hao , Gao Liang , Tang Zhuang , YingHu Chun , Li Xiang , JiuYuan Hong , Dong Qiang , Wei Qiang
Published: October 2015

Benign prostatic hyperplasia (BPH) is one of the most common diseases in middle-aged and elderly men. In the present study, we aimed to compare the efficacy and safety of thulium laser resection of the prostate (TMLRP) with either transurethral plasmakinetic resection of the prostate (TUPKP) or transurethral resection of the prostate (TURP). A literature search was performed, eventually, 14 studies involving 1587 patients were included. Forest plots were produced by using Revman 5.2.0 software. Our meta-analysis showed that operation time, decrease in hemoglobin level, length of hospital stay, catheterization time and development of urethral stricture significantly differed, whereas the transitory urge incontinence rate, urinary tract infection rate and recatheterization rate did not significantly differ between TMLRP and either TURP or TUPKP. The blood transfusion rate was significantly different between TMLRP and TURP, but not between TMLRP and TUPKP. In addition, the retrograde ejaculation rate between TMLRP and TURP did not significantly differ. At 1, 3, 6 and 12 months of postoperative follow-up, the maximum flow rate, post-void residual, quality of life and International Prostate Symptom Score did not significantly differ among the procedures. Thus, the findings of this study indicate that TMLRP may be a safe and feasible alternative.
Comparative analyses of fecal microbiota in Tibetan and Chinese Han living at low or high altitude by barcoded 454 pyrosequencing
Authors: Li Long , Zhao Xin
Published: October 2015

Knowledge about the impact of altitude and ethnicity on human gut microbiota is currently limited. In this study, fecal microbiota from 12 Tibetans (T group), 11 Chinese Han living in Tibet (HH group) and 12 Chinese Han living in Shaanxi province (LH group) were profiled by 454 pyrosequencing. Analysis of UniFrac principal coordinates showed significant structural changes in fecal microbiota among the three groups. There were significant differences in the composition of fecal microbiota among the three groups at phylum and genus levels. At the phylum level, the fecal samples of HH and T groups had higher relative abundances of Firmicutes, whereas the LH group had a higher relative abundance of Bacteroidetes. These changes at the phylum level reflected different dominant genus compositions. Compared with the LH group, changes of Firmicutes and Bacteroidetes were mainly due to a significant decrease of Prevotella in the HH group and were primarily attributable to significant decreases of Bacteroides and Prevotella as well as a significant increase of Catenibacterium in the T group. In conclusion, our results suggest that high altitude may contribute to shaping human gut microbiota. Genetic and dietary factors may also explain the different microbiota compositions between Tibetan and Chinese Han.
A strategy to discover decoy chemokine ligands with an anti-inflammatory activity
Authors: Abboud Dayana , Daubeuf François , Do Quoc Tuan , Utard Valérie , Villa Pascal , Haiech Jacques , Bonnet Dominique , Hibert Marcel , Bernard Philippe , Galzi Jean-Luc , Frossard Nelly
Published: October 2015

Excessive signaling by chemokines has been associated with chronic inflammation or cancer, thus attracting substantial attention as promising therapeutic targets. Inspired by chemokine-clearing molecules shaped by pathogens to escape the immune system, we designed a generic screening assay to discover chemokine neutralizing molecules (neutraligands) and unambiguously distinguish them from molecules that block the receptor (receptor antagonists). This assay, called TRIC-r, combines time-resolved intracellular calcium recordings with pre-incubation of bioactive compounds either with the chemokine or the receptor-expressing cells. We describe here the identification of high affinity neutraligands of CCL17 and CCL22, two chemokines involved in the Th2-type of lung inflammation. The decoy molecules inhibit in vitro CCL17- or CCL22-induced intracellular calcium responses, CCR4 endocytosis and human T cell migration. In vivo, they inhibit inflammation in a murine model of asthma, in particular the recruitment of eosinophils, dendritic cells and CD4+T cells. Altogether, we developed a successful strategy to discover as new class of pharmacological tools to potently control cell chemotaxis in vitro and in vivo.
HDAC inhibitor misprocesses bantam oncomiRNA, but stimulates hid induced apoptotic pathway
Authors: Bhadra Utpal , Mondal Tanmoy , Bag Indira , Mukhopadhyay Debasmita , Das Paromita , Parida Bibhuti B. , Mainkar Prathama S. , Reddy Chada Raji , Bhadra Manika Pal
Published: October 2015

Apoptosis or programmed cell death is critical for embryogenesis and tissue homeostasis. Uncontrolled apoptosis leads to different human disorders including immunodeficiency, autoimmune disorder and cancer. Several small molecules that control apoptosis have been identified. Here, we have shown the functional role of triazole derivative (DCPTN-PT) that acts as a potent HDAC inhibitor and mis-express proto onco microRNA (miRNA) bantam. To further understanding the mechanism of action of the molecule in apoptotic pathway, a series of experiments were also performed in Drosophila, a well known model organism in which the nature of human apoptosis is very analogous. DCPTN-PT mis processes bantam microRNA and alters its down regulatory target hid function and cleavage of Caspase-3 which in turn influence components of the mitochondrial apoptotic pathway in Drosophila. However regulatory microRNAs in other pro-apoptotic genes are not altered. Simultaneously, treatment of same molecule also affects the mitochondrial regulatory pathway in human tumour cell lines suggesting its conservative nature between fly and human. It is reasonable to propose that triazole derivative (DCPTN-PT) controls bantam oncomiRNA and increases hid induced apoptosis and is also able to influence mitochondrial apoptotic pathway.
In-situ epitaxial growth of graphene/h-BN van der Waals heterostructures by molecular beam epitaxy
Authors: Zuo Zheng , Xu Zhongguang , Zheng Renjing , Khanaki Alireza , Zheng Jian-Guo , Liu Jianlin
Published: October 2015

Van der Waals materials have received a great deal of attention for their exceptional layered structures and exotic properties, which can open up various device applications in nanoelectronics. However, in situ epitaxial growth of dissimilar van der Waals materials remains challenging. Here we demonstrate a solution for fabricating van der Waals heterostructures. Graphene/hexagonal boron nitride (h-BN) heterostructures were synthesized on cobalt substrates by using molecular beam epitaxy. Various characterizations were carried out to evaluate the heterostructures. Wafer-scale heterostructures consisting of single-layer/bilayer graphene and multilayer h-BN were achieved. The mismatch angle between graphene and h-BN is below 1°.
Maximizing oyster-reef growth supports green infrastructure with accelerating sea-level rise
Authors: Ridge Justin T. , Rodriguez Antonio B. , Joel Fodrie F. , Lindquist Niels L. , Brodeur Michelle C. , Coleman Sara E. , Grabowski Jonathan H. , Theuerkauf Ethan J.
Published: October 2015

Within intertidal communities, aerial exposure (emergence during the tidal cycle) generates strong vertical zonation patterns with distinct growth boundaries regulated by physiological and external stressors. Forecasted accelerations in sea-level rise (SLR) will shift the position of these critical boundaries in ways we cannot yet fully predict, but landward migration will be impaired by coastal development, amplifying the importance of foundation species’ ability to maintain their position relative to rising sea levels via vertical growth. Here we show the effects of emergence on vertical oyster-reef growth by determining the conditions at which intertidal reefs thrive and the sharp boundaries where reefs fail, which shift with changes in sea level. We found that oyster reef growth is unimodal relative to emergence, with greatest growth rates occurring between 20–40% exposure and zero-growth boundaries at 10% and 55% exposures. Notably, along the lower growth boundary (10%), increased rates of SLR would outpace reef accretion, thereby reducing the depth range of substrate suitable for reef maintenance and formation and exacerbating habitat loss along developed shorelines. Our results identify where, within intertidal areas, constructed or natural oyster reefs will persist and function best as green infrastructure to enhance coastal resiliency under conditions of accelerating SLR.
Simulating photoacoustic waves produced by individual biological particles with spheroidal wave functions
Authors: Li Yong , Fang Hui , Min Changjun , Yuan Xiaocong
Published: October 2015

Under the usual approximation of treating a biological particle as a spheroidal droplet, we consider the analysis of its size and shape with the high frequency photoacoustics and develop a numerical method which can simulate its characteristic photoacoustic waves. This numerical method is based on the calculation of spheroidal wave functions and when comparing to the finite element model (FEM) calculation, can reveal more physical information and can provide results independently at each spatial points. As the demonstration, red blood cells (RBCs) and MCF7 cell nuclei are studied and their photoacoustic responses including field distribution, spectral amplitude and pulse forming are calculated. We expect that integrating this numerical method with the high frequency photoacoustic measurement will form a new modality being extra to the light scattering method, for fast assessing the morphology of a biological particle.
Stabilization of SIRT7 deacetylase by viral oncoprotein HBx leads to inhibition of growth restrictive RPS7 gene and facilitates cellular transformation
Authors: Pandey Vijaya , Kumar Vijay
Published: October 2015

Sirtuin-7 (SIRT7) deacetylase exhibits a high selectivity for acetylated H3K18 and has been implicated in the maintenance of malignant phenotype. However, it remains unclear if SIRT7 and H3K18ac play a role in the tumorigenic program driven by oncogenic viruses. We show that ectopically expressed HBx oncoprotein of hepatitis B virus promoted intracellular stability of SIRT7 by salvaging it from ubiquitin-mediated proteasomal degradation. HBx-dependent accumulation of SIRT7 favored H3K18 deacetylation and down-regulated the small ribosomal protein gene, RPS7, involved in cell death and DNA damage response. HBx facilitated the recruitment of SIRT7 to RPS7 promoter thus impeding H3K18ac occupancy and hindering RPS7 transcription. The antagonistic relationship between SIRT7 and RPS7 was also observed in the HBx transgenic mice, where elevated levels of SIRT7 protein were coincident with low levels of H3K18ac and RPS7. Strikingly, inhibition of cellular deubiquitinase activity restored RPS7 gene transcription. Further, depletion of endogenous SIRT7 led to decreased cell viability and transformation. The biological relevance of RPS7 suppression by HBx-SIRT7 axis was evident from ectopic expression of RPS7 which attenuated clonogenicity of cells. Thus, our findings suggest that SIRT7 is a critical regulator of HBx-driven oncogenic program, through its antagonistic impact on growth restrictive ribosomal protein RPS7.
New reconstruction of the Wiwaxia scleritome, with data from Chengjiang juveniles
Authors: Zhang Zhifei , Smith Martin R. , Shu Degan
Published: October 2015

Wiwaxiids are a problematic group of scale-covered lophotrochozoans known from Cambrian Stages 3–5. Their imbricating dorsal scleritome of leaf-like scales has prompted comparison with various annelids and molluscs and has been used as a template to reconstruct the articulation pattern of isolated Small Shelly Fossils. The first articulated specimens of Wiwaxia from the Cambrian Stage 3 Chengjiang Konservat-Lagerstätte show that the Wiwaxia scleritome comprised nine equivalent transverse rows associated with outgrowths of soft tissue, but did not possess a separate zone of anterior sclerites. This serial construction is fundamentally incompatible with the circumferential disposition of sclerites in early molluscs, but does closely resemble the armature of certain annelids. A deep homology with the annelid scleritome must be reconciled with Wiwaxia’s mollusc-like mouthparts and foot; together these point to a deep phylogenetic position, close to the common ancestor of annelids and molluscs.
Uncoating Mechanism of Carnation Mottle Virus Revealed by Cryo-EM Single Particle Analysis
Authors: Wang Chun-Yan , Zhang Qin-Fen , Gao Yuan-Zhu , Xie Li , Li Hong-Mei , Hong Jian , Zhang Chuan-Xi
Published: October 2015

Genome uncoating is a prerequisite for the successful infection of plant viruses in host plants. Thus far, little is known about the genome uncoating of the Carnation mottle virus (CarMV). Here, we obtained two reconstructions of CarMV at pH7 in the presence (Ca-pH7) and absence (EDTA-pH7) of calcium ions by Cryo-EM single particle analysis, which achieved 6.4 Å and 8 Å resolutions respectively. Our results showed that chelation of the calcium ions under EDTA-pH7 resulted in reduced interaction between the subunits near the center of the asymmetric unit but not overall size change of the viral particles, which indicated that the role of the calcium ions in CarMV was not predominantly for the structural preservation. Part of the genomic RNA closest to the capsid was found to be located near the center of the asymmetric unit, which might result from the interaction between genomic RNA and Lys194 residues. Together with the electrostatic potential analysis on the inner surface of the asymmetric unit, the reduced interaction near the center of the asymmetric unit under EDTA-pH7 suggested that the genome release of CarMV might be realized through the center of the asymmetric unit.
Volcanic passive margins: another way to break up continents
Authors: Geoffroy L. , Burov E. B. , Werner P.
Published: October 2015

Two major types of passive margins are recognized, i.e. volcanic and non-volcanic, without proposing distinctive mechanisms for their formation. Volcanic passive margins are associated with the extrusion and intrusion of large volumes of magma, predominantly mafic and represent distinctive features of Larges Igneous Provinces, in which regional fissural volcanism predates localized syn-magmatic break-up of the lithosphere. In contrast with non-volcanic margins, continentward-dipping detachment faults accommodate crustal necking at both conjugate volcanic margins. These faults root on a two-layer deformed ductile crust that appears to be partly of igneous nature. This lower crust is exhumed up to the bottom of the syn-extension extrusives at the outer parts of the margin. Our numerical modelling suggests that strengthening of deep continental crust during early magmatic stages provokes a divergent flow of the ductile lithosphere away from a central continental block, which becomes thinner with time due to the flow-induced mechanical erosion acting at its base. Crustal-scale faults dipping continentward are rooted over this flowing material, thus isolating micro-continents within the future oceanic domain. Pure-shear type deformation affects the bulk lithosphere at VPMs until continental breakup and the geometry of the margin is closely related to the dynamics of an active and melting mantle.
Spillover and pandemic properties of zoonotic viruses with high host plasticity
Authors: Kreuder Johnson Christine , Hitchens Peta L. , Smiley Evans Tierra , Goldstein Tracey , Thomas Kate , Clements Andrew , Joly Damien O. , Wolfe Nathan D. , Daszak Peter , Karesh William B. , Mazet Jonna K.
Published: October 2015

Most human infectious diseases, especially recently emerging pathogens, originate from animals and ongoing disease transmission from animals to people presents a significant global health burden. Recognition of the epidemiologic circumstances involved in zoonotic spillover, amplification and spread of diseases is essential for prioritizing surveillance and predicting future disease emergence risk. We examine the animal hosts and transmission mechanisms involved in spillover of zoonotic viruses to date and discover that viruses with high host plasticity (i.e. taxonomically and ecologically diverse host range) were more likely to amplify viral spillover by secondary human-to-human transmission and have broader geographic spread. Viruses transmitted to humans during practices that facilitate mixing of diverse animal species had significantly higher host plasticity. Our findings suggest that animal-to-human spillover of new viruses that are capable of infecting diverse host species signal emerging disease events with higher pandemic potential in that these viruses are more likely to amplify by human-to-human transmission with spread on a global scale.
Rational Design of Benzylidenehydrazinyl-Substituted Thiazole Derivatives as Potent Inhibitors of Human Dihydroorotate Dehydrogenase with in Vivo Anti-arthritic Activity
Authors: Li Shiliang , Luan Guoqin , Ren Xiaoli , Song Wenlin , Xu Liuxin , Xu Minghao , Zhu Junsheng , Dong Dong , Diao Yanyan , Liu Xiaofeng , Zhu Lili , Wang Rui , Zhao Zhenjiang , Xu Yufang , Li Honglin
Published: October 2015

Human dihydroorotate dehydrogenase (hDHODH) is an attractive therapeutic target for the treatment of rheumatoid arthritis, transplant rejection and other autoimmune diseases. Based on the X-ray structure of hDHODH in complex with lead compound 7, a series of benzylidenehydrazinyl-substituted thiazole derivatives as potent inhibitors of hDHODH were designed and synthesized, of which 19 and 30 were the most potent with IC50 values in the double-digit nanomolar range. Moreover, compound 19 displayed significant anti-arthritic effects and favorable pharmacokinetic profiles in vivo. Further X-ray structure and SAR analyses revealed that the potencies of the designed inhibitors were partly attributable to additional water-mediated hydrogen bond networks formed by an unexpected buried water between hDHODH and the 2-(2-methylenehydrazinyl)thiazole scaffold. This work not only elucidates promising scaffolds targeting hDHODH for the treatment of rheumatoid arthritis, but also demonstrates that the water-mediated hydrogen bond interaction is an important factor in molecular design and optimization.
Terahertz meets sculptural and architectural art: Evaluation and conservation of stone objects with T-ray technology
Authors: Krügener K. , Schwerdtfeger M. , Busch S. F. , Soltani A. , Castro-Camus E. , Koch M. , Viöl W.
Published: October 2015

Conservation of cultural heritage is an area where novel scientific techniques are having enormous impact. Given the value and uniqueness of art pieces, non-invasive diagnostic methods are highly appreciated by conservators. Terahertz radiation has shown enormous potential as non-contact probe that can be used for the three-dimensional reconstruction of internal structure of stone-made objects. In this article we report the evaluation of the internal damage state of two art pieces, a medallion from the Castle of Celle and a window sill from the St. Peter of Trier Cathedral. We also used terahertz radiation to follow and assess the restoration process of the window sill. We found that terahertz spectroscopy is an excellent non-destructive evaluation method for stone artwork that shows enormous potential as a tool for conservation.
Observation of tunable nonlinear effects in an analogue of superconducting composite right/left hand filter
Authors: Liu Haiwen , Lei Jiuhuai , Jiang Hao , Guan Xuehui , Ji Laiyun , Ma Zhewang
Published: October 2015

Artificial structures with negative permittivity or permeability have attracted significant attention in the science community because they provide a pathway for obtaining exotic electromagnetic properties not found in natural materials. At the moment, the great challenge of these artificial structures in microwave frequency exhibits a relatively large loss. It is well-known that superconducting thin films have extremely low surface resistance. Hence, it is a good candidate to resolve this constraint. Besides, the reported artificial structures with negative permittivity or permeability are mainly focusing on linear regime of wave propagation. However, any future effort in creating tunable structures would require knowledge of nonlinear properties. In this work, a tunable superconducting filter with composite right/left-hand transmission property is proposed and fabricated. Its nonlinear effects on temperature and power are studied by theoretical analysis and experiments.
Chemiluminometric Immunosensor for High-Sensitivity Cardiac Troponin I Employing a Polymerized Enzyme Conjugate as a Tracer
Authors: Lim Guei-Sam , Seo Sung-Min , Paek Sung-Ho , Kim Seung-Wan , Jeon Jin-Woo , Kim Dong-Hyung , Cho Il-Hoon , Paek Se-Hwan
Published: October 2015

To detect high-sensitivity cardiac troponin I (hs-cTnI; <0.01 ng/mL) at points of care, we developed a rapid immunosensor by using horseradish peroxidase polymerized in 20 molecules on average (Poly-HRP) as a tracer conjugated with streptavidin (SA-Poly-HRP). As shown in the conventional system, enhanced sensitivity could be achieved by using a sequential binding scheme for the complex formation to contain the huge molecular tracer. We used a 2-dimensional chromatographic technology to carry out the sequential bindings in cross-flow directions. After the complex formation of antigen-antibody with analyte in a vertical direction, SA-Poly-HRP was horizontally supplied across the membrane strip for additional binding via a biotin-SA linkage. The HRP substrate was subsequently supplied along the same direction to produce a chemiluminometric signal, which was measured by a cooled charge-coupled device. Hs-cTnI analysis was completed in this format within 25 min and the results showed a high correlation with those of the CentaurXP® reference system (R2 > 0.99). The detection limit of the rapid immunosensor was 0.003 ± 0.001 ng/mL cTnI, corresponding to a 10-fold improvement compared to results using the plain enzyme tracer. This demonstrated the measurement of hs-cTnI in a much more cost-effective manner compared to the automated versions currently available.
Nanoscale Graphene Disk: A Natural Functionally Graded Material–How is Fourier’s Law Violated along Radius Direction of 2D Disk
Authors: Yang Nuo , Hu Shiqian , Ma Dengke , Lu Tingyu , Li Baowen
Published: October 2015

In this Paper, we investigate numerically and analytically the thermal conductivity of nanoscale graphene disks (NGDs) and discussed the possibility to realize functionally graded material (FGM) with only one material, NGDs. Different from previous studies on divergence/non-diffusive of thermal conductivity in nano-structures with different size, we found a novel non-homogeneous (graded) thermal conductivity along the radius direction in a single nano-disk structure. We found that, instead of a constant value, the NGD has a graded thermal conductivity along the radius direction. That is, Fourier’s law of heat conduction is not valid in two dimensional graphene disk structures Moreover, we show the dependent of NGDs’ thermal conductivity on radius and temperature. Our study might inspire experimentalists to develop NGD based versatile FGMs, improve understanding of the heat removal of hot spots on chips and enhance thermoelectric energy conversion efficiency by two dimensional disk with a graded thermal conductivity.
Light attenuates lipid accumulation while enhancing cell proliferation and starch synthesis in the glucose-fed oleaginous microalga Chlorella zofingiensis
Authors: Chen Tianpeng , Liu Jin , Guo Bingbing , Ma Xiaonian , Sun Peipei , Liu Bin , Chen Feng
Published: October 2015

The objective of this study was to investigate the effect of light on lipid and starch accumulation in the oleaginous green algae Chlorella zofingiensis supplemented with glucose. C. zofingiensis, when fed with 30 g/L glucose, synthesized lipids up to 0.531 g/g dry weight; while in the presence of light, the lipid content dropped down to 0.352 g/g dry weight. Lipid yield on glucose was 0.184 g/g glucose, 14% higher than that cultured with light. The light-mediated lipid reduction was accompanied by the down-regulation of fatty acid biosynthetic genes at the transcriptional level. Furthermore, light promoted cell proliferation, starch accumulation and the starch yield based on glucose. Taken together, light may attenuate lipid accumulation, possibly through the inhibition of lipid biosynthetic pathway, leading to more carbon flux from glucose to starch. This study reveals the dual effects of light on the sugar-fed C. zofingiensis and provides valuable insights into the possible optimization of algal biomass and lipid production by manipulation of culture conditions.
Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica
Authors: Chatterjee Ankita , Kundu Sudip
Published: October 2015

Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air.
Seismological constraints on the crustal structures generated by continental rejuvenation in northeastern China
Authors: Zheng Tian-Yu , He Yu-Mei , Yang Jin-Hui , Zhao Liang
Published: October 2015

Crustal rejuvenation is a key process that has shaped the characteristics of current continental structures and components in tectonic active continental regions. Geological and geochemical observations have provided insights into crustal rejuvenation, although the crustal structural fabrics have not been well constrained. Here, we present a seismic image across the North China Craton (NCC) and Central Asian Orogenic Belt (CAOB) using a velocity structure imaging technique for receiver functions from a dense array. The crustal evolution of the eastern NCC was delineated during the Mesozoic by a dominant low seismic wave velocity with velocity inversion, a relatively shallow Moho discontinuity and a Moho offset beneath the Tanlu Fault Zone. The imaged structures and geochemical evidence, including changes in the components and ages of continental crusts and significant continental crustal growth during the Mesozoic, provide insight into the rejuvenation processes of the evolving crust in the eastern NCC caused by structural, magmatic and metamorphic processes in an extensional setting. The fossil structural fabric of the convergent boundary in the eastern CAOB indicates that the back-arc action of the Paleo-Pacific Plate subduction did not reach the hinterland of Asia.
Tolerance and reward equity predict cooperation in ravens (Corvus corax)
Authors: Massen Jorg J. M. , Ritter Caroline , Bugnyar Thomas
Published: October 2015

Cooperative decision rules have so far been shown experimentally mainly in mammal species that have variable and complex social networks. However, these traits should not necessarily be restricted to mammals. Therefore, we tested cooperative problem solving in ravens. We showed that, without training, nine ravens spontaneously cooperated in a loose-string task. Corroborating findings in several species, ravens’ cooperative success increased with increasing inter-individual tolerance levels. Importantly, we found this in both a forced dyadic setting and in a group setting where individuals had an open choice to cooperate with whomever. The ravens, moreover, also paid attention to the resulting reward distribution and ceased cooperation when being cheated upon. Nevertheless, the ravens did not seem to pay attention to the behavior of their partners while cooperating and future research should reveal whether this is task specific or a general pattern. Given their natural propensity to cooperate and the results we present here, we consider ravens as an interesting model species to study the evolution of and the mechanisms underlying cooperation.