bluuebunny/crossref_metadata_2025 huggingface dataset:
Microscopic observation of carrier-transport dynamics in quantum-structure solar cells using a time-of-flight technique
Authors: Toprasertpong Kasidit , Kasamatsu Naofumi , Fujii Hiromasa , Kada Tomoyuki , Asahi Shigeo , Wang Yunpeng , Watanabe Kentaroh , Sugiyama Masakazu , Kita Takashi , Nakano Yoshiaki
Published: July 2015

In this study, we propose a carrier time-of-flight technique to evaluate the carrier transport time across a quantum structure in an active region of solar cells. By observing the time-resolved photoluminescence signal with a quantum-well probe inserted under the quantum structure at forward bias, the carrier transport time can be efficiently determined at room temperature. The averaged drift velocity shows linear dependence on the internal field, allowing us to estimate the quantum structure as a quasi-bulk material with low effective mobility containing the information of carrier dynamics. We show that this direct and real-time observation is more sensitive to carrier transport than other conventional techniques, providing better insights into microscopic carrier transport dynamics to overcome a device design difficulty.
Abnormal variation of band gap in Zn doped Bi0.9La0.1FeO3 nanoparticles: Role of Fe-O-Fe bond angle and Fe-O bond anisotropy
Authors: Xu Xunling , Liu Weifang , Wu Ping , Zhang Hong , Guo Minchen , Han Yuling , Zhang Chuang , Gao Ju , Rao Guanghui , Wang Shouyu
Published: July 2015

Bi0.9La0.1FeO3 (BLFO) and Bi0.9La0.1Fe0.99Zn0.01O3 (BLFZO) nanoparticles were prepared via a sol-gel method. The oxygen vacancies and holes increase with Zn doping analyzed through X-ray photoelectron spectroscopy, which could contribute to the increase of leakage current density. However, with the increase of the defects (oxygen vacancies and holes), the band gap of BLFZO also is increased. To explain the abnormal phenomenon, the bandwidth of occupied and unoccupied bands was analyzed based on the structural symmetry driven by the Fe-O-Fe bond angle and Fe-O bond anisotropy.
Tunneling electron induced molecular electroluminescence from individual porphyrin J-aggregates
Authors: Meng Qiushi , Zhang Chao , Zhang Yang , Zhang Yao , Liao Yuan , Dong Zhenchao
Published: July 2015

We investigate molecular electroluminescence from individual tubular porphyrin J-aggregates on Au(111) by tunneling electron excitations in an ultrahigh-vacuum scanning tunneling microscope (STM). High-resolution STM images suggest a spiral tubular structure for the porphyrin J-aggregate with highly ordered “brickwork”-like arrangements. Such aggregated nanotube is found to behave like a self-decoupled molecular architecture and shows red-shifted electroluminescence characteristics of J-aggregates originated from the delocalized excitons. The positions of the emission peaks are found to shift slightly depending on the excitation sites, which, together with the changes in the observed spectral profiles with vibronic progressions, suggest a limited exciton coherence number within several molecules. The J-aggregate electroluminescence is also found unipolar, occurring only at negative sample voltages, which is presumably related to the junction asymmetry in the context of molecular excitations via the carrier injection mechanism.
Proximity effect on hydrodynamic interaction between a sphere and a plane measured by force feedback microscopy at different frequencies
Authors: Carpentier Simon , S. Rodrigues Mario , Charlaix Elisabeth , Chevrier Joël
Published: July 2015

In this article, we measure the viscous damping G″, and the associated stiffness G′, of a liquid flow in sphere-plane geometry over a large frequency range. In this regime, the lubrication approximation is expected to dominate. We first measure the static force applied to the tip. This is made possible thanks to a force feedback method. Adding a sub-nanometer oscillation of the tip, we obtain the dynamic part of the interaction with solely the knowledge of the lever properties in the experimental context using a linear transformation of the amplitude and phase change. Using a Force Feedback Microscope (FFM), we are then able to measure simultaneously the static force, the stiffness, and the dissipative part of the interaction in a broad frequency range using a single AFM probe. Similar measurements have been performed by the Surface Force Apparatus (SFA) with a probe radius hundred times bigger. In this context, the FFM can be called nano-SFA.
Longer than 1.9 μm photoluminescence emission from InAs quantum structure on GaAs (001) substrate
Authors: Liu Ke , Ma Wenquan , Huang Jianliang , Zhang Yanhua , Cao Yulian , Huang Wenjun , Luo Shuai , Yang Tao
Published: July 2015

We report on photoluminescence (PL) emission with long wavelength for quantum structure by the sub-monolayer (SML) growth technique on GaAs (001) substrate. It is found that the PL emission wavelength can be controlled by controlling the SML InAs deposition amount. At 12 K, the PL peak position of the grown samples changes from about 1.66 to 1.78 μm. At 120 K, the PL emission of a sample reaches 1.91 μm. The physical mechanism responsible for the measured long wavelength PL emission may be related to strong In segregation and intermixing effects occurred in the structure grown by SML growth technique.
Uncovering high thermoelectric figure of merit in (Hf,Zr)NiSn half-Heusler alloys
Authors: Chen L. , Gao S. , Zeng X. , Mehdizadeh Dehkordi A. , Tritt T. M. , Poon S. J.
Published: July 2015

Half-Heusler alloys (MgAgSb structure) are promising thermoelectric materials. RNiSn half-Heusler phases (R = Hf, Zr, and Ti) are the most studied in view of thermal stability. The highest dimensionless figure of merit (ZT) obtained is ∼1 in the temperature range ∼450–900 °C, primarily achieved in nanostructured alloys. Through proper annealing, ZT ∼ 1.2 has been obtained in a previous ZT ∼ 1 n-type (Hf,Zr)NiSn phase without the nanostructure. There is an appreciable increase in power factor, decrease in charge carrier density, and increase in carrier mobility. The findings are attributed to improved structural order. Present approach may be applied to optimize the functional properties of Heusler-type alloys.
Passivating boron silicate glasses for co-diffused high-efficiency n-type silicon solar cell application
Authors: Engelhardt Josh , Frey Alexander , Gloger Sebastian , Hahn Giso , Terheiden Barbara
Published: July 2015

Doping layers commonly have but one function: supplying the dopants to form a doped region within a substrate. This work presents B doping layers/stacks, which at the same time supply dopant atoms, passivate the B-doped crystalline Si surface sufficiently well (j0E < 50 fA/cm2), and show optical properties suitable for anti-reflective coating. Furthermore, these boron silicate glasses can act as a barrier against parasitic P in-diffusion during a co-diffusion step. The boron emitters diffused from the inductively coupled plasma plasma-enhanced chemical vapor-deposited B containing SiOx layers are investigated and optimized concerning passivation quality and contact properties for high-efficiency n-type solar Si cell designs. It is shown that even 10 nm thin SiOx:B films already allow for suitable emitter sheet resistance for screen-printed contacts. Furthermore, SiOx:B layers presented here allow for iVOC values of 675 mV and contact resistivity of 1 mΩcm2 for commercial Ag instead of Ag/Al pastes on the diffused boron emitter passivated with the SiOx:B layer supporting the contact formation. All of these properties can be achieved within one single B doping layer/stack.
Indicating pressure and environmental effects by means of the spectral shift with rhodamine B and fluorescein
Authors: Johann R. M.
Published: July 2015

Fluorescence absorption and emission wavelengths can be influenced by environmental conditions, such as pressure, temperature and concentration. Here those effects are explored with an emphasis on determining the potential of rhodamine B and fluorescein as high-pressure indicators. The red shift of the emission peak maxima of rhodamine B and fluorescein are investigated in dependence of pressure up to 200 MPa using as the solvents water, ethanol and poly(dimethylsiloxane) (PDMS) with rhodamine B and water, polystyrene beads and melamine resin beads with fluorescein. Emission spectra recording and peak fitting is done automatically at time intervals of down to a second and with 0.3 nm wavelength resolution. The wavenumber-pressure relation for rhodamine B reveals increasing divergence from linear behavior in the sequence of the solvents water, ethanol and silicone rubber. Graphical correlation of the data diverging only slightly from linearity with a selection of polarity functions is enabled using the concept of ‘deviation from linearity (DL)’ plots. Using the example of rhodamine B dissolved in PDMS elastomer it is shown that there is a temperature induced irreversible molecular reordering, when scanning between 3 and ∼50°C, and a polarity change in the proximity of the embedded dye molecule. Swelling studies are performed with PDMS containing rhodamine B, where the elastomer is first put in water, then in ethanol and again in water. There a complex solvent exchange process is revealed in the elastomer demonstrating the feasibility of fluorescence spectroscopy, when observing variations in wavelength, to indicate and enlighten molecular rearrangements and swelling dynamics in the polymer, and polarity changes and solvent exchange processes in the dye solvation shell.
Double-functionalised magnetic nanoparticles for efficient extraction of bisphenol A from river water
Authors: Sheng Yipei , Guan Huaqin , Zhang Yanfang , Zhang Xuemei , Zhou Qingqing , Lin Zhenkun
Published: July 2015

Environmental context Conventional pre-treatment methods are usually ineffective for the extraction of bisphenol A (BPA) from environmental water samples. We report that a novel magnetic nanoparticle with double-functionalisation is an excellent solid-phase adsorbent for extracting BPA from river water samples. This study provides a simple but efficient approach for extraction of low-concentration pollutants from water samples. Abstract In this study, double functionalised magnetic nanoparticles (DFMNPs) for extraction of bisphenol A (BPA) in an aqueous phase were designed and prepared. In the preparation of DFMNPs, amide and pyridine groups were simultaneously introduced into the surface of magnetic nanoparticles. A new dispersed solid-phase extraction (DSPE) method adopting DFMNPs as the adsorbents was developed for separating and enriching BPA from river water samples. This DSPE method showed fast magnetic response, high binding efficiency to target BPA, and short experimental time. The recovery of BPA in spiked river water was 94.4% with the DSPE method, which was much higher than those with traditional solid-phase extraction (SPE) methods. The high performance of DFMNPs on extraction of BPA from river water was attributed to the synergistic function of the amide and pyridine groups. The hydrophilic amide groups caused DFMNPs to disperse well in water, whereas the alkaline pyridine groups bound BPA effectively by ionic bonds. Our DSPE was particularly superior to conventional SPE in the pre-treatment of large-volume water samples as the time taken could be remarkably reduced.
Effects of myo-inositol hexakisphosphate and orthophosphate adsorption on aggregation of CeO2 nanoparticles: roles of pH and surface coverage
Authors: Wan Biao , Yan Yupeng , Liu Fan , Tan Wenfeng , He Jiajie , Feng Xionghan
Published: July 2015

Environmental context
To understand the behaviour and fate of nanoparticles (NPs) in the natural environment requires knowledge of their aggregation state under environmentally relevant conditions. This work investigates the influence of myo-inositol hexakisphosphate and orthophosphate on the colloidal stability of CeO2 NPs, and shows that adsorption of organic and inorganic phosphorus plays an important role on the interaction between the nanoparticles. Surface phosphorus coverage should be considered when predicting the fate of CeO2 NPs and other similar NPs in the environment.

Abstract
The effects of myo-inositol hexakisphosphate (IHP) and orthophosphate (Pi) adsorption on aggregation and dispersion of CeO2 nanoparticles (NPs) in suspension and the underlying mechanism were investigated. The results show that IHP and Pi play a significant role in the colloidal chemistry behaviour of CeO2 NPs through inner-sphere complex formation on adsorption as indicated by concurrent hydroxyl release, zeta (ζ) potential measurements and in situ attenuated total reflectance Fourier-transform infrared spectroscopy. The ratio of IHP/Pi adsorption density suggests that IHP may complex on the CeO2 surface through four of its six phosphate groups with the other two free and dissociated. Sedimentation and aggregation of CeO2 NPs in suspension are mainly dependent on their surface potentials, which are greatly regulated by pH and surface phosphorous coverage. At pH 3.0, IHP led to aggregation of CeO2 NPs at a loading lower than 0.15μmolL–1, whereas a higher IHP loading made them disperse again. However, Pi adsorption merely caused an increase of the aggregate size of CeO2 NPs. At pH 7.0, both IHP and Pi can apparently stabilise the suspension of CeO2 NPs from aggregation by alteration of the zeta potential from near zero down to –38mV. The effect of IHP on the aggregation and dispersion of CeO2 NPs is much greater than that of Pi, which agrees well with calculations from Derjaguin–Landau–Verwey–Overbeek (DLVO) theory.
Flexible brain network reconfiguration supporting inhibitory control
Authors: Spielberg Jeffrey M. , Miller Gregory A. , Heller Wendy , Banich Marie T.
Published: July 2015

Significance

The ability to inhibit distracting stimuli from interfering with goal-directed behavior is crucial for success in most spheres of life and is disrupted across a variety of disorders. Here we show via network analysis that global brain connectivity patterns change when inhibitory demands increase, including greater communication efficiency and robustness against disruption. In addition, the connectivity pattern of regions previously identified as crucial for inhibitory control (right inferior frontal gyrus and anterior insula) become more central network hubs, whereas dorsal anterior cingulate becomes more interconnected within its local network. Findings provide a framework to elucidate and differentiate difficulties in inhibitory control in clinical groups by examining connectivity of specific global network metrics and/or critical hubs known to influence inhibitory control.
Splicing inhibition of U2AF
65
leads to alternative exon skipping
Authors: Cho Sunghee , Moon Heegyum , Loh Tiing Jen , Jang Ha Na , Liu Yongchao , Zhou Jianhua , Ohn Takbum , Zheng Xuexiu , Shen Haihong
Published: July 2015

Significance

Transcription is a biological procedure in which DNA is transcribed to an RNA molecule. However, only fragments of this RNA are needed for protein synthesis. These fragments are exons that are interrupted by introns. Introns are removed by so-called RNA splicing process. Some exons could be alternatively included or excluded from the final RNA molecule. In this study, we have found that U2 snRNP auxiliary factor 65 kDa (U2AF
65
), a general splicing regulator, can significantly promote the exclusion of alternative exons. Strikingly, U2AF
65
suppresses flanking intron splicing of alternative exons, and even constitutive intron splicing. We deduce that the stimulatory effects of U2AF
65
on alternative exon exclusion are induced by the splicing inhibitory effects of U2AF
65
.
Metabolite profiling stratifies pancreatic ductal adenocarcinomas into subtypes with distinct sensitivities to metabolic inhibitors
Authors: Daemen Anneleen , Peterson David , Sahu Nisebita , McCord Ron , Du Xiangnan , Liu Bonnie , Kowanetz Katarzyna , Hong Rebecca , Moffat John , Gao Min , Boudreau Aaron , Mroue Rana , Corson Laura , O’Brien Thomas , Qing Jing , Sampath Deepak , Merchant Mark , Yauch Robert , Manning Gerard , Settleman Jeffrey , Hatzivassiliou Georgia , Evangelista Marie
Published: July 2015

Significance

Targeting cancer metabolism requires personalized diagnostics for clinical success. Pancreatic ductal adenocarcinoma (PDAC) is characterized by metabolism addiction. To identify metabolic dependencies within PDAC, we conducted broad metabolite profiling and identified three subtypes that showed distinct metabolite profiles associated with glycolysis, lipogenesis, and redox pathways. Importantly, these profiles significantly correlated with enriched sensitivity to a variety of metabolic inhibitors including inhibitors targeting glycolysis, glutaminolysis, lipogenesis, and redox balance. In primary PDAC tumor samples, the lipid subtype was strongly associated with an epithelial phenotype, whereas the glycolytic subtype was strongly associated with a mesenchymal phenotype, suggesting functional relevance in disease progression. Our findings will provide valuable predictive utility for a number of metabolic inhibitors currently undergoing phase I testing.
Divergent evolution of an atypical
S
-adenosyl-
l
-methionine–dependent monooxygenase involved in anthracycline biosynthesis
Authors: Grocholski Thadée , Dinis Pedro , Niiranen Laila , Niemi Jarmo , Metsä-Ketelä Mikko
Published: July 2015

Significance

Natural products produced by
Streptomyces
are widely used in the treatment of various medical conditions. Over the years, thousands of metabolites with complex chemical structures have been isolated from cultures of these soil bacteria. An evolutionary pressure that promotes chemical diversity appears to be critical for generation of this rich source of biologically active compounds. This is reflected in the biosynthetic enzymes, where functions of similar proteins may greatly differ. Here, we have clarified the molecular basis of how a classical methyltransferase has evolved into an unusual hydroxylase on the biosynthetic pathways of two anthracycline anticancer agents. Detailed understanding of enzymes involved in antibiotic biosynthesis will facilitate future protein engineering efforts for generation of improved bioactive natural products.
The isolation of an RNA aptamer targeting to p53 protein with single amino acid mutation
Authors: Chen Liang , Rashid Farooq , Shah Abdullah , Awan Hassaan M. , Wu Mingming , Liu An , Wang Jun , Zhu Tao , Luo Zhaofeng , Shan Ge
Published: July 2015

Significance

We have developed a contrast screening strategy of systematic evolution of ligand exponential enrichment to isolate an RNA aptamer targeting specifically to p53R175H. This RNA aptamer partially rescued p53R175H in both cell cultures and tumor xenografts. p53 mutations are found in more than half of human cancers, and it is of biomedical significance to be able to isolate an RNA aptamer against a p53 mutation. This may also be the first report about an RNA aptamer specific to a mutant protein with a single amino acid change, and a plethora of human diseases are actually caused by single amino acid mutation. Thus, we present here a proof-of-concept study in isolating a specific and physiologically functional RNA aptamer against mutant protein with single amino acid substitution.
Indirect nitrous oxide emissions from streams within the US Corn Belt scale with stream order
Authors: Turner Peter A. , Griffis Timothy J. , Lee Xuhui , Baker John M. , Venterea Rodney T. , Wood Jeffrey D.
Published: July 2015

Significance

N
2
O emissions from riverine systems are poorly constrained, giving rise to highly uncertain indirect emission factors that are used in bottom-up inventories. Using a non–steady-state flow-through chamber system, N
2
O fluxes were measured across a stream order gradient within the US Corn Belt. The results show that N
2
O emissions scale with the Strahler stream order. This information was used to estimate riverine emissions at the local and regional scales and demonstrates that previous bottom-up inventories based on the Intergovernmental Panel on Climate Change default values have significantly underestimated these indirect emissions.
Socially mediated induction and suppression of antibiosis during bacterial coexistence
Authors: Abrudan Monica I. , Smakman Fokko , Grimbergen Ard Jan , Westhoff Sanne , Miller Eric L. , van Wezel Gilles P. , Rozen Daniel E.
Published: July 2015

Significance

Antibiotics have profoundly changed human medicine, yet we know surprisingly little about the role of antibiotics in nature for the bacteria that produce them. Here we examine antibiotic use in the prolific antibiotic-producing genus
Streptomyces
across divergent social and competitive growth conditions. Our results provide clear experimental evidence that antibiotics are weapons whose use is strongly modified by intermicrobial social interactions. Simultaneously, using experiments and computer simulations, we show that social and competitive dynamics between bacteria have a crucial and previously unrecognized influence on the maintenance of microbial diversity in soil environments. These insights have implications for both bacterial coexistence and diversity and also for drug discovery.
Coexistence of Y, W, and Z sex chromosomes in
Xenopus tropicalis
Authors: Roco Álvaro S. , Olmstead Allen W. , Degitz Sigmund J. , Amano Tosikazu , Zimmerman Lyle B. , Bullejos Mónica
Published: July 2015

Significance

As in most amphibians, sex chromosomes of the model species
Xenopus tropicalis
are homomorphic, complicating identification of the heterogametic sex. Using genetic approaches, we have proved the existence of three types of sex chromosomes (Y, W, and Z), defining three kinds of males (YZ, YW, and ZZ) and two kinds of females (ZW and WW). The existence of both male and female heterogametic individuals in one species is an extremely rare situation in nature, because some sex chromosome combinations produce offspring with sex ratios different from 1:1. Thus, parental sex chromosomes must be taken into account when
X
.
tropicalis
is used in multigeneration genetic studies or in ecotoxicological assays of endocrine disruptors with gender effects.
Baculovirus protein PK2 subverts eIF2α kinase function by mimicry of its kinase domain C-lobe
Authors: Li John J. , Cao Chune , Fixsen Sarah M. , Young Janet M. , Ono Chikako , Bando Hisanori , Elde Nels C. , Katsuma Susumu , Dever Thomas E. , Sicheri Frank
Published: July 2015

Significance

Many pathogens use molecular mimicry to subvert key cellular processes of the host. RNA-dependent protein kinase (PKR), a member of the eukaryotic translation initiation factor 2α (eIF2α) kinase family, is an important component of innate immunity in vertebrates and has often been subjected to inhibition by viral mimicry. In this study we show that the paradigm of host–virus mimicry extends to invertebrates where there is no discernable PKR homologue. We characterize an eIF2α kinase-mimic protein called “PK2,” encoded by baculoviruses, that inhibits a heme-regulated inhibitor kinase (HRI)-like eIF2α kinase, possibly through a lobe-swap mechanism. The inhibition of the HRI-like kinase confers a growth advantage to the baculovirus during infection of its insect host. These experiments suggest the independent emergence of eIF2α kinase antiviral defense mechanisms in vertebrates and invertebrates.
Role of ubiquitin and the HPV E6 oncoprotein in E6AP-mediated ubiquitination
Authors: Mortensen Franziska , Schneider Daniel , Barbic Tanja , Sladewska-Marquardt Anna , Kühnle Simone , Marx Andreas , Scheffner Martin
Published: July 2015

Significance

Deregulation of components of the ubiquitin–proteasome system contributes to the development of various diseases. A prominent example is the ubiquitin ligase E6AP/UBE3A, which is associated with three disorders: in complex with the E6 oncoprotein of human papillomaviruses, it contributes to cervical carcinogenesis; loss of E6AP expression results in the development of Angelman syndrome; and increased E6AP expression has been associated with autism spectrum disorders. This indicates that E6AP has to be tightly controlled; however, only little is known about how this is achieved. By analyzing the role of ubiquitin and the E6 oncoprotein in E6AP-mediated ubiquitination, we provide evidence that E6AP exists in an active state and a latent state and that its activity is controlled by allosteric effectors.
Sequence, structure, and cooperativity in folding of elementary protein structural motifs
Authors: Lai Jason K. , Kubelka Ginka S. , Kubelka Jan
Published: July 2015

Significance

Although novel experimental approaches open exciting opportunities for understanding the elusive protein-folding pathways, interpreting experiments in terms of microscopic folding mechanisms often poses a serious challenge. Here, we demonstrate that extensive sets of global and site-specific unfolding data for two small proteins can be quantitatively explained by a simple statistical–mechanical model derived from known native protein structures. Remarkably, differences in folding between two proteins with similar structures are captured without need to consider sequence-specific interresidue interactions. This finding is significant because it implies that knowledge of the native structure—which implicitly includes sequence information—is sufficient for predicting detailed, site-specific folding mechanisms.
MIR retrotransposon sequences provide insulators to the human genome
Authors: Wang Jianrong , Vicente-García Cristina , Seruggia Davide , Moltó Eduardo , Fernandez-Miñán Ana , Neto Ana , Lee Elbert , Gómez-Skarmeta José Luis , Montoliu Lluís , Lunyak Victoria V. , Jordan I. King
Published: July 2015

Significance

Insulators are genome sequence elements that help to organize eukaryotic genomes into coherent regulatory domains. Insulators can encode both enhancer-blocking activity, which prevents the interaction between enhancers and promoters located in distinct regulatory domains, and/or chromatin barrier activity that helps to delineate active and repressive chromatin domains. The origins and functional characteristics of insulator sequence elements are important, open questions in molecular biology and genomics. This report provides insight into these questions by demonstrating the origins of a number of human insulator sequences from a family of transposable-element–derived repetitive sequence elements: mammalian-wide interspersed repeats (MIRs). Human MIR-derived insulators are characterized by distinct sequence, expression, and chromatin features that provide clues as to their potential mechanisms of action.
Structural basis for inhibition of the histone chaperone activity of SET/TAF-Iβ by cytochromec
Authors: González-Arzola Katiuska , Díaz-Moreno Irene , Cano-González Ana , Díaz-Quintana Antonio , Velázquez-Campoy Adrián , Moreno-Beltrán Blas , López-Rivas Abelardo , De la Rosa Miguel A.
Published: July 2015

Significance

Histone chaperones are key regulators of transcriptional activity in damaged chromatin regions in the DNA damage response. Here we show that cytochromec(Cc) targets the histone chaperone SET/template-activating factor (TAF)-Iβ (SET/TAF-Iβ) in the cell nucleus upon DNA damage, resulting in the blocking of the SET/TAF-Iβ function. Ccis actually translocated into the nuclei of cells treated with specific DNA damage inducers and not upon death-receptor pathway or stress-induced stimuli. Cclocks the domains engaged in histone binding of SET/TAF-Iβ, inhibiting its nucleosome assembly activity. Structural characterization of the complex between Ccand SET/TAF-Iβ provides a valuable template for designing drugs aimed at silencing the oncogenic effect of SET/TAF-Iβ.
Sinuous flow in metals
Authors: Yeung Ho , Viswanathan Koushik , Compton Walter Dale , Chandrasekar Srinivasan
Published: July 2015

Significance

It is counterintuitive, yet well known, that cutting a soft metal, vis-à-vis a hardened one, involves significantly larger forces, with the formation of a thick chip. Using in situ imaging we show that this phenomenon results from a hitherto unidentified flow mode in metals, called sinuous flow due to its repeatedly folded nature, that resembles irreversible flows in geological rocks and some complex fluids. We also demonstrate how sinuous flow can be suppressed, by simply applying common marking ink remote from the cutting interface—the forces are reduced significantly and the thick chip is eliminated. Besides explaining some important decades-old phenomena in metal cutting, our work has broad implications for many natural and industrial cutting processes.
Single-cell measurement of red blood cell oxygen affinity
Authors: Di Caprio Giuseppe , Stokes Chris , Higgins John M. , Schonbrun Ethan
Published: July 2015

Significance

Oxygen transport is the most important function of red blood cells (RBCs). We describe a microfluidic single-cell assay that quantifies the oxygen saturation of individual RBCs in high throughput. Although single-RBC measurements of volume and mass are routinely performed in hospitals by hematology analyzers, measurements that characterize the primary function of RBCs, the delivery of oxygen, have not been made. With this system, we find measurable variation that is positively correlated with cellular hemoglobin concentration but independent of osmolarity. These results imply that the cytoplasmic environment of each cell is different and that these differences modulate the function that each cell performs.
Molecular structure of monomorphic peptide fibrils within a kinetically trapped hydrogel network
Authors: Nagy-Smith Katelyn , Moore Eric , Schneider Joel , Tycko Robert
Published: July 2015

Significance

Based on the propensity of naturally occurring peptides to assemble into polymorphic fibrils, one might assume that polymorphism and peptide self-assembly go hand-in-hand. Contrary to this expectation, we find that the designed peptide MAX1 assembles with high fidelity into monomorphic fibrils that comprise a kinetically trapped hydrogel network. Our solid-state NMR data lead to a complete molecular structural model, in which MAX1 β-hairpins form a β-sheet bilayer with specific molecular conformations and intermolecular alignments within and between layers.
Generation of MANAbodies specific to HLA-restricted epitopes encoded by somatically mutated genes
Authors: Skora Andrew D. , Douglass Jacqueline , Hwang Michael S. , Tam Ada J. , Blosser Richard L. , Gabelli Sandra B. , Cao Jianhong , Diaz Luis A. , Papadopoulos Nickolas , Kinzler Kenneth W. , Vogelstein Bert , Zhou Shibin
Published: July 2015

Significance

Mutations in oncogenes and tumor suppressor genes drive tumorigenesis and their protein products form therapeutic targets that are absent from normal cells. However, nearly all such mutant epitopes lie in the interior of the cells, either in the cytoplasm or nucleus, complicating immunotherapies directed against the mutants. We have developed an approach to identify antibodies selectively targeting complexes containing common HLA types bound to peptide products of commonly mutated oncogenes. Because these peptide-HLA complexes are expected to be exclusively present on the surface of cancer cells, antibodies targeting them could in principle be used for therapeutic purposes.
Brd4 bridges the transcriptional regulators, Aire and P-TEFb, to promote elongation of peripheral-tissue antigen transcripts in thymic stromal cells
Authors: Yoshida Hideyuki , Bansal Kushagra , Schaefer Uwe , Chapman Trevor , Rioja Inmaculada , Proekt Irina , Anderson Mark S. , Prinjha Rab K. , Tarakhovsky Alexander , Benoist Christophe , Mathis Diane
Published: July 2015

Significance

Aire is an enigmatic transcription factor that controls immunologic tolerance by inducing, specifically in the thymus, a battery of transcripts encoding proteins not usually encountered until the periphery, thereby promoting negative selection of self-reactive thymocytes and positive selection of regulatory T cells. We document a striking correspondence between those genes induced by Aire and those inhibited by a small-molecule inhibitor of the bromodomain protein Brd4. Aire and Brd4 directly interact, dependent on an orchestrated series of phosphorylation and acetylation events. Aire:Brd4 engagement draws in P-TEFb, mobilizing the transcription and splicing machineries and inducing transcription. Blocking the Aire:Brd4 interaction inhibits negative selection of self-reactive T cells in mice, and point-mutations of Aire that abrogate this association give rise to autoimmune disease.
Two transcription pause elements underlie a σ
70
-dependent pause cycle
Authors: Strobel Eric J. , Roberts Jeffrey W.
Published: July 2015

Significance

During transcription, RNA polymerase encounters DNA-encoded signals that interrupt RNA synthesis and cause the transcription elongation complex to pause. An important function of transcription pausing in gene regulation is the halting of transcription to facilitate assembly of regulatory factors into complex with RNA polymerase. An example of this function is found in the bacteriophage λ late-gene transcription, in which the initiation factor σ
70
induces a pause that mediates recruitment of the antitermination factor Q
λ
, thereby allowing the expression of genes downstream of an intrinsic terminator. In this study, we characterize the contributions of two pause signals to σ
70
-dependent pause kinetics and propose a comprehensive model for σ
70
-dependent pausing.
Synaptotagmin-7 phosphorylation mediates GLP-1–dependent potentiation of insulin secretion from β-cells
Authors: Wu Bingbing , Wei Shunhui , Petersen Natalia , Ali Yusuf , Wang Xiaorui , Bacaj Taulant , Rorsman Patrik , Hong Wanjin , Südhof Thomas C. , Han Weiping
Published: July 2015

Significance

The present study shows that glucagon-like peptide-1 (GLP-1) potentiates insulin release by inducing the PKA-mediated phosphorylation of synaptotagmin-7 in pancreatic β-cells, thereby documenting that the hormone GLP-1 acts by directly enhancing Ca
2+
-triggered insulin exocytosis. PKA phosphorylates synaptotagmin-7 at a single serine residue in the linker between the synaptotagmin-7 transmembrane region and its C-terminal C
2
domains that bind Ca
2+
; accordingly, PKA phosphorylation of synaptotagmin-7 enhances insulin secretion without changing the Ca
2+
dependence of secretion. The study documents that the efficacy of a synaptotagmin can be modulated by phosphorylation and highlights the importance of synaptotagmin-7 in mediating glucose-stimulated insulin secretion. Given the importance of enhancing β-cell function in the treatment of diabetes, the present findings may offer new pathways for developing future therapeutic strategies.
Mitochondrial calcium overload is a key determinant in heart failure
Authors: Santulli Gaetano , Xie Wenjun , Reiken Steven R. , Marks Andrew R.
Published: July 2015

Significance

We demonstrate that intracellular Ca
2+
leak causes mitochondrial Ca
2+
overload and dysfunction in postischemic heart failure (HF). In particular, sarcoplasmic reticulum (SR) Ca
2+
leak via type 2 ryanodine receptor (RyR2)—but not type 2 inositol 1,4,5-trisphosphate receptor (IP3R2)—channels plays a fundamental role in the pathophysiology of mitochondrial Ca
2+
overload and dysfunction in HF. We present here a previously undisclosed molecular mechanism in HF with crucial implications in cardiac physiology. Indeed, our data establish a feedback loop between SR and mitochondria in which SR Ca
2+
leak triggers mitochondrial dysfunction and increases the production of free radicals, which in turn lead to posttranslational modifications of RyR2 and enhance intracellular Ca
2+
leak, thereby contributing to impaired cardiac function after myocardial infarction.
Identification and characterization of an injury-induced skeletal progenitor
Authors: Marecic Owen , Tevlin Ruth , McArdle Adrian , Seo Eun Young , Wearda Taylor , Duldulao Christopher , Walmsley Graham G. , Nguyen Allison , Weissman Irving L. , Chan Charles K. F. , Longaker Michael T.
Published: July 2015

Significance

Here, we characterize the injury-induced activation of a specific, highly purified population of multipotent skeletal progenitor cells. These activated progenitors show increased cell frequency, increased viability, and enhanced osteogenic potential. They also possess a unique transcriptional profile that distinguishes them from progenitors found in uninjured bone. We report that these features improve regenerative capacity, suggesting that activated progenitors play a principal role in bone healing. We hope that a better understanding of stem and progenitor activation will inspire novel therapies that restore impaired skeletal regeneration.
Roles of unphosphorylated ISGF3 in HCV infection and interferon responsiveness
Authors: Sung Pil Soo , Cheon HyeonJoo , Cho Chung Hwan , Hong Seon-Hui , Park Do Youn , Seo Hyung-Il , Park Su-Hyung , Yoon Seung Kew , Stark George R. , Shin Eui-Cheol
Published: July 2015

Significance

Hepatitis C virus (HCV) infection stimulates the production of endogenous interferons (IFNs) and the following persistent activation of interferon-stimulated genes (ISGs) in the infected liver. In the patients with chronic HCV infection, high levels of activated ISGs in the liver at baseline were proved to predict poor response to pegylated IFN-α/ribavirin therapy. In this report, we demonstrate that the level of unphosphorylated IFN-stimulated gene factor 3 (U-ISGF3), not ISGF3, is increased by endogenous IFN-λs and IFN-β in HCV-infected hepatocytes and livers, leading to persistent activation of a set of ISGs. We also demonstrate that the high level of ISG15 induced by U-ISGF3 resulted in an increased level of ubiquitin-specific protease 18 (USP18), a critical negative regulator of the response to exogenous IFN-α.
Endocytosis-dependent coordination of multiple actin regulators is required for wound healing
Authors: Matsubayashi Yutaka , Coulson-Gilmer Camilla , Millard Tom H.
Published: July 2015

The ability to heal wounds efficiently is essential for life. After wounding of an epithelium, the cells bordering the wound form dynamic actin protrusions and/or a contractile actomyosin cable, and these actin structures drive wound closure. Despite their importance in wound healing, the molecular mechanisms that regulate the assembly of these actin structures at wound edges are not well understood. In this paper, using Drosophila melanogaster embryos, we demonstrate that Diaphanous, SCAR, and WASp play distinct but overlapping roles in regulating actin assembly during wound healing. Moreover, we show that endocytosis is essential for wound edge actin assembly and wound closure. We identify adherens junctions (AJs) as a key target of endocytosis during wound healing and propose that endocytic remodeling of AJs is required to form “signaling centers” along the wound edge that control actin assembly. We conclude that coordination of actin assembly, AJ remodeling, and membrane traffic is required for the construction of a motile leading edge during wound healing.
Adhesion to fibronectin regulates Hippo signaling via the FAK–Src–PI3K pathway
Authors: Kim Nam-Gyun , Gumbiner Barry M.
Published: July 2015

The Hippo pathway is involved in the regulation of contact inhibition of proliferation and responses to various physical and chemical stimuli. Recently, several upstream negative regulators of Hippo signaling, including epidermal growth factor receptor ligands and lysophosphatidic acid, have been identified. We show that fibronectin adhesion stimulation of focal adhesion kinase (FAK)-Src signaling is another upstream negative regulator of the Hippo pathway. Inhibition of FAK or Src in MCF-10A cells plated at low cell density prevented the activation of Yes-associated protein (YAP) in a large tumor suppressor homologue (Lats)–dependent manner. Attachment of serum-starved MCF-10A cells to fibronectin, but not poly-d-lysine or laminin, induced YAP nuclear accumulation via the FAK–Src–phosphatidylinositol 4,5-bisphosphate 3-kinase (PI3K) signaling pathway. Attenuation of FAK, Src, PI3K, or PDK1 activity blocked YAP nuclear accumulation stimulated by adhesion to fibronectin. This negative regulation of the Hippo pathway by fibronectin adhesion signaling can, at least in part, explain the effects of cell spreading on YAP nuclear localization and represents a Lats-dependent component of the response to cell adhesion.
Manufacture of electrical and magnetic graded and anisotropic materials for novel manipulations of microwaves
Authors: Grant P. S. , Castles F. , Lei Q. , Wang Y. , Janurudin J. M. , Isakov D. , Speller S. , Dancer C. , Grovenor C. R. M.
Published: July 2015

Spatial transformations (ST) provide a design framework to generate a required spatial distribution of electrical and magnetic properties of materials to effect manipulations of electromagnetic waves. To obtain the electromagnetic properties required by these designs, the most common materials approach has involved periodic arrays of metal-containing subwavelength elements. While aspects of ST theory have been confirmed using these structures, they are often disadvantaged by narrowband operation, high losses and difficulties in implementation. An all-dielectric approach involves weaker interactions with applied fields, but may offer more flexibility for practical implementation. This paper investigates manufacturing approaches to produce composite materials that may be conveniently arranged spatially, according to ST-based designs. A key aim is to highlight the limitations and possibilities of various manufacturing approaches, to constrain designs to those that may be achievable. The article focuses on polymer-based nano- and microcomposites in which interactions with microwaves are achieved by loading the polymers with high-permittivity and high-permeability particles, and manufacturing approaches based on spray deposition, extrusion, casting and additive manufacture.
On cosmology in the laboratory
Authors: Leonhardt Ulf
Published: July 2015

In transformation optics, ideas from general relativity have been put to practical use for engineering problems. This article asks the question how this debt can be repaid. In discussing a series of recent laboratory experiments, it shows how insights from wave phenomena shed light on the quantum physics of the event horizon.
Spatially variant periodic structures in electromagnetics
Authors: Rumpf Raymond C. , Pazos Javier J. , Digaum Jennefir L. , Kuebler Stephen M.
Published: July 2015

Spatial transforms are a popular technique for designing periodic structures that are macroscopically inhomogeneous. The structures are often required to be anisotropic, provide a magnetic response, and to have extreme values for the constitutive parameters in Maxwell's equations. Metamaterials and photonic crystals are capable of providing these, although sometimes only approximately. The problem still remains about how to generate the geometry of the final lattice when it is functionally graded, or spatially varied. This paper describes a simple numerical technique to spatially vary any periodic structure while minimizing deformations to the unit cells that would weaken or destroy the electromagnetic properties. New developments in this algorithm are disclosed that increase efficiency, improve the quality of the lattices and provide the ability to design aplanatic metasurfaces. The ability to spatially vary a lattice in this manner enables new design paradigms that are not possible using spatial transforms, three of which are discussed here. First, spatially variant self-collimating photonic crystals are shown to flow unguided waves around very tight bends using ordinary materials with low refractive index. Second, multi-mode waveguides in spatially variant band gap materials are shown to guide waves around bends without mixing power between the modes. Third, spatially variant anisotropic materials are shown to sculpt the near-field around electric components. This can be used to improve electromagnetic compatibility between components in close proximity.
Experimental model of topological defects in Minkowski space–time based on disordered ferrofluid: magnetic monopoles, cosmic strings and the space–time cloak
Authors: Smolyaninov Igor I. , Smolyaninova Vera N. , Smolyaninov Alexei I.
Published: July 2015

In the presence of an external magnetic field, cobalt nanoparticle-based ferrofluid forms a self-assembled hyperbolic metamaterial. The wave equation, which describes propagation of extraordinary light inside the ferrofluid, exhibits 2+1 dimensional Lorentz symmetry. The role of time in the corresponding effective three-dimensional Minkowski space–time is played by the spatial coordinate directed along the periodic nanoparticle chains aligned by the magnetic field. Here, we present a microscopic study of point, linear, planar and volume defects of the nanoparticle chain structure and demonstrate that they may exhibit strong similarities with such Minkowski space–time defects as magnetic monopoles, cosmic strings and the recently proposed space–time cloaks. Experimental observations of such defects are described.
Sulfurifustis variabilis gen. nov., sp. nov., a sulfur oxidizer isolated from a lake, and proposal of Acidiferrobacteraceae fam. nov. and Acidiferrobacterales ord. nov.
Authors: Kojima Hisaya , Shinohara Arisa , Fukui Manabu
Published: July 2015

A novel autotrophic bacterium, strain skN76T, was isolated from sediment of a lake in Japan. As sole electron donor to support chemolithoautotrophic growth, the strain oxidized thiosulfate, tetrathionate and elemental sulfur. For growth, the optimum temperature was 42–45 °C and the optimum pH was 6.8–8.2. The cells were Gram-stain-negative, catalase-positive and oxidase-positive. The strain exhibited changes in morphology depending on growth temperature. Cells grown at the optimum temperature were rod-shaped (0.9–3.0 μm long and 0.3–0.5 μm wide), whereas a filamentous form was observed when the strain was cultured at the lowest permissive growth temperatures. The G+C content of genomic DNA was 69 mol%. The major components in the fatty acid profile were C16 : 0, summed feature 3 (C16 : 1ω7cand/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9cand/or 10-methyl C16 : 0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the closest cultivated relative of strain skN76TwasAcidiferrobacter thiooxydansm-1T, with sequence similarity of 93 %. On the basis of its phylogenetic and phenotypic properties, strain skN76T( = DSM 100313T =  NBRC 110942T) is proposed as the type strain of a novel species of a novel genus,Sulfurifustis variabilisgen. nov., sp. nov. Novel taxa,Acidiferrobacteraceaefam. nov. andAcidiferrobacteralesord. nov., are also proposed to accommodate the generaAcidiferrobacterandSulfurifustisgen. nov.