bluuebunny/crossref_metadata_2025 huggingface dataset:
Increased expression with differential subcellular location of cytidine deaminase APOBEC3G in human CD4+ T‐cell activation and dendritic cell maturation
Authors: Oliva Harold , Pacheco Rodrigo , Martinez‐Navio José M , Rodríguez‐García Marta , Naranjo‐Gómez Mar , Climent Núria , Prado Carolina , Gil Cristina , Plana Montserrat , García Felipe , Miró José M , Franco Rafael , Borras Francesc E , Navaratnam Naveenan , Gatell José M , Gallart Teresa
Published: March 2016

APOBEC3G (apolipoprotein B mRNA editing enzyme catalytic polypeptide‐like 3G; A3G) is an innate defense protein showing activity against retroviruses and retrotransposons. Activated CD4+ T cells are highly permissive for HIV‐1 replication, whereas resting CD4+ T cells are refractory. Dendritic cells (DCs), especially mature DCs, are also refractory. We investigated whether these differences could be related to a differential A3G expression and/or subcellular distribution. We found that A3G mRNA and protein expression is very low in resting CD4+ T cells and immature DCs, but increases strongly following T‐cell activation and DC maturation. The Apo‐7 anti‐A3G monoclonal antibody (mAb), which was specifically developed, confirmed these differences at the protein level and disclosed that A3G is mainly cytoplasmic in resting CD4+ T cells and immature DCs. Nevertheless, A3G translocates to the nucleus in activated‐proliferating CD4+ T cells, yet remaining cytoplasmic in matured DCs, a finding confirmed by immunoblotting analysis of cytoplasmic and nuclear fractions. Apo‐7 mAb was able to immunoprecipitate endogenous A3G allowing to detect complexes with numerous proteins in activated‐proliferating but not in resting CD4+ T cells. The results show for the first time the nuclear translocation of A3G in activated‐proliferating CD4+ T cells.
A conserved motif in JNK/p38-specific MAPK phosphatases as a determinant for JNK1 recognition and inactivation
Authors: Liu Xin , Zhang Chen-Song , Lu Chang , Lin Sheng-Cai , Wu Jia-Wei , Wang Zhi-Xin
Published: March 2016

Mitogen-activated protein kinases (MAPKs), important in a large array of signalling pathways, are tightly controlled by a cascade of protein kinases and by MAPK phosphatases (MKPs). MAPK signalling efficiency and specificity is modulated by protein–protein interactions between individual MAPKs and the docking motifs in cognate binding partners. Two types of docking interactions have been identified: D-motif-mediated interaction and FXF-docking interaction. Here we report the crystal structure of JNK1 bound to the catalytic domain of MKP7 at 2.4-Å resolution, providing high-resolution structural insight into the FXF-docking interaction. The 285FNFL288 segment in MKP7 directly binds to a hydrophobic site on JNK1 that is near the MAPK insertion and helix αG. Biochemical studies further reveal that this highly conserved structural motif is present in all members of the MKP family, and the interaction mode is universal and critical for the MKP-MAPK recognition and biological function.
Regulation at a distance of biomolecular interactions using a DNA origami nanoactuator
Authors: Ke Yonggang , Meyer Travis , Shih William M. , Bellot Gaetan
Published: March 2016

The creation of nanometre-sized structures that exhibit controllable motions and functions is a critical step towards building nanomachines. Recent developments in the field of DNA nanotechnology have begun to address these goals, demonstrating complex static or dynamic nanostructures made of DNA. Here we have designed and constructed a rhombus-shaped DNA origami ‘nanoactuator’ that uses mechanical linkages to copy distance changes induced on one half (‘the driver’) to be propagated to the other half (‘the mirror’). By combining this nanoactuator with split enhanced green fluorescent protein (eGFP), we have constructed a DNA–protein hybrid nanostructure that demonstrates tunable fluorescent behaviours via long-range allosteric regulation. In addition, the nanoactuator can be used as a sensor that responds to specific stimuli, including changes in buffer composition and the presence of restriction enzymes or specific nucleic acids.
Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus
Authors: Ji Quanjiang , Chen Peter J. , Qin Guangrong , Deng Xin , Hao Ziyang , Wawrzak Zdzislaw , Yeo Won-Sik , Quang Jenny Winjing , Cho Hoonsik , Luo Guan-Zheng , Weng Xiaocheng , You Qiancheng , Luan Chi-Hao , Yang Xiaojing , Bae Taeok , Yu Kunqian , Jiang Hualiang , He Chuan
Published: March 2016

Most low GC Gram-positive bacteria possess an essential walKR two-component system (TCS) for signal transduction involved in regulating cell wall homoeostasis. Despite the well-established intracellular regulatory mechanism, the role of this TCS in extracellular signal recognition and factors that modulate the activity of this TCS remain largely unknown. Here we identify the extracellular receptor of the kinase ‘WalK’ (erWalK) as a key hub for bridging extracellular signal input and intracellular kinase activity modulation in Staphylococcus aureus. Characterization of the crystal structure of erWalK revealed a canonical Per-Arnt-Sim (PAS) domain for signal sensing. Single amino-acid mutation of potential signal-transduction residues resulted in severely impaired function of WalKR. A small molecule derived from structure-based virtual screening against erWalK is capable of selectively activating the walKR TCS. The molecular level characterization of erWalK will not only facilitate exploration of natural signal(s) but also provide a template for rational design of erWalK inhibitors.
A CEP215–HSET complex links centrosomes with spindle poles and drives centrosome clustering in cancer
Authors: Chavali Pavithra L. , Chandrasekaran Gayathri , Barr Alexis R. , Tátrai Péter , Taylor Chris , Papachristou Evaggelia K. , Woods C. Geoffrey , Chavali Sreenivas , Gergely Fanni
Published: March 2016

Numerical centrosome aberrations underlie certain developmental abnormalities and may promote cancer. A cell maintains normal centrosome numbers by coupling centrosome duplication with segregation, which is achieved through sustained association of each centrosome with a mitotic spindle pole. Although the microcephaly- and primordial dwarfism-linked centrosomal protein CEP215 has been implicated in this process, the molecular mechanism responsible remains unclear. Here, using proteomic profiling, we identify the minus end-directed microtubule motor protein HSET as a direct binding partner of CEP215. Targeted deletion of the HSET-binding domain of CEP215 in vertebrate cells causes centrosome detachment and results in HSET depletion at centrosomes, a phenotype also observed in CEP215-deficient patient-derived cells. Moreover, in cancer cells with centrosome amplification, the CEP215–HSET complex promotes the clustering of extra centrosomes into pseudo-bipolar spindles, thereby ensuring viable cell division. Therefore, stabilization of the centrosome–spindle pole interface by the CEP215–HSET complex could promote survival of cancer cells containing supernumerary centrosomes.
Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance
Authors: Kabe Yasuaki , Nakane Takanori , Koike Ikko , Yamamoto Tatsuya , Sugiura Yuki , Harada Erisa , Sugase Kenji , Shimamura Tatsuro , Ohmura Mitsuyo , Muraoka Kazumi , Yamamoto Ayumi , Uchida Takeshi , Iwata So , Yamaguchi Yuki , Krayukhina Elena , Noda Masanori , Handa Hiroshi , Ishimori Koichiro , Uchiyama Susumu , Kobayashi Takuya , Suematsu Makoto
Published: March 2016

Progesterone-receptor membrane component 1 (PGRMC1/Sigma-2 receptor) is a haem-containing protein that interacts with epidermal growth factor receptor (EGFR) and cytochromes P450 to regulate cancer proliferation and chemoresistance; its structural basis remains unknown. Here crystallographic analyses of the PGRMC1 cytosolic domain at 1.95 Å resolution reveal that it forms a stable dimer through stacking interactions of two protruding haem molecules. The haem iron is five-coordinated by Tyr113, and the open surface of the haem mediates dimerization. Carbon monoxide (CO) interferes with PGRMC1 dimerization by binding to the sixth coordination site of the haem. Haem-mediated PGRMC1 dimerization is required for interactions with EGFR and cytochromes P450, cancer proliferation and chemoresistance against anti-cancer drugs; these events are attenuated by either CO or haem deprivation in cancer cells. This study demonstrates protein dimerization via haem–haem stacking, which has not been seen in eukaryotes, and provides insights into its functional significance in cancer.
Versatile protein tagging in cells with split fluorescent protein
Authors: Kamiyama Daichi , Sekine Sayaka , Barsi-Rhyne Benjamin , Hu Jeffrey , Chen Baohui , Gilbert Luke A. , Ishikawa Hiroaki , Leonetti Manuel D. , Marshall Wallace F. , Weissman Jonathan S. , Huang Bo
Published: March 2016

In addition to the popular method of fluorescent protein fusion, live cell protein imaging has now seen more and more application of epitope tags. The small size of these tags may reduce functional perturbation and enable signal amplification. To address their background issue, we adapt self-complementing split fluorescent proteins as epitope tags for live cell protein labelling. The two tags, GFP11 and sfCherry11 are derived from the eleventh β-strand of super-folder GFP and sfCherry, respectively. The small size of FP11-tags enables a cost-effective and scalable way to insert them into endogenous genomic loci via CRISPR-mediated homology-directed repair. Tandem arrangement FP11-tags allows proportional enhancement of fluorescence signal in tracking intraflagellar transport particles, or reduction of photobleaching for live microtubule imaging. Finally, we show the utility of tandem GFP11-tag in scaffolding protein oligomerization. These experiments illustrate the versatility of FP11-tag as a labelling tool as well as a multimerization-control tool for both imaging and non-imaging applications.
The fertilization-induced zinc spark is a novel biomarker of mouse embryo quality and early development
Authors: Zhang Nan , Duncan Francesca E. , Que Emily L. , O’Halloran Thomas V. , Woodruff Teresa K.
Published: March 2016

Upon activation, mammalian eggs release billions of zinc ions in an exocytotic event termed the “zinc spark.” The zinc spark is dependent on and occurs coordinately with intracellular calcium transients, which are tightly associated with embryonic development. Thus, we hypothesized that the zinc spark represents an early extracellular physicochemical marker of the developmental potential of the zygote. To test this hypothesis, we monitored zinc exocytosis in individual mouse eggs following parthenogenetic activation or in vitro fertilization (IVF) and tracked their development. Retrospective analysis of zinc spark profiles revealed that parthenotes and zygotes that developed into blastocysts released more zinc than those that failed to develop. Prospective selection of embryos based on their zinc spark profile significantly improved developmental outcomes and more than doubled the percentage of embryos that reached the blastocyst stage. Moreover, the zinc spark profile was also associated with embryo quality as the total cell number in the resulting morulae and blastocysts positively correlated with the zinc spark amplitude (R = 0.9209). Zinc sparks can thus serve as an early biomarker of zygote quality in mouse model.
Nanoscale precipitates strengthened lanthanum-bearing Mg-3Sn-1Mn alloys through continuous rheo-rolling
Authors: Guan R. G. , Shen Y. F. , Zhao Z. Y. , Misra R. D. K.
Published: March 2016

We elucidate the effect of lanthanum (La) on the microstructure and mechanical properties of Mg-3Sn-1Mn-xLa (wt.%) alloy plates processed through continuous rheo-rolling for the first time. At x = 0.2 wt.%, La dissolved completely in the α-Mg matrix. As the La content was increased to 0.6 wt.%, a new plate-shaped three-phase compound composed of La5Sn3, Mg2Sn and Mg17La2 phases was formed with an average length of 380 ± 10 nm and an average width of 110 ± 5 nm. This compound had a pinning effect on the α-Mg grain boundary and on dislocations. With further increase in La-content to 1.0 wt.%, the length of the plate-shaped compound increased to an average length of 560 ± 10 nm, while the width was reduced to 90 ± 5 nm. The particle size of Mg2Sn decreased from 100 nm to 50 nm with increase in La-content from 0.2 to 1.4 wt.%. At La content of 1.0 wt.%, the tensile strength and elongation of the alloy was maximum, with 29% and 32% increase, respectively, compared to the Mg-3Sn-1Mn (wt.%) alloy, and 37% and 89% increase, in comparison to the Mg-3Sn-1Mn-0.87 Ce (wt.%) alloy.
Functional Genome Screening to Elucidate the Colistin Resistance Mechanism
Authors: Kumar Mohit , Gupta Ashutosh , Sahoo Rajesh Kumar , Jena Jayanti , Debata Nagen Kumar , Subudhi Enketeswara
Published: March 2016

Antibiogram profile of 1590 clinical bacterial isolates based on thirteen different antimicrobial compounds showed that 1.6% of the bacterial isolates are multidrug resistant. Distribution pattern based on 16S rRNA sequence analysis showed that Pseudomonas aeruginosa constituted the largest group (83.6%) followed by Burkholderia pseudomallei sp. A191 (5.17%), Staphylococcus sp. A261 (3.45%). Among the various antibiotics used, colistin appeared to be the most effective against the Gram negative bacteria. Burkholderia pseudomallei sp. A191 and Pseudomonas aeruginosa sp. A111 showed resistance to 1500 μg/ml and 750 μg/ml of colistin respectively which constitutes 7.7% of the bacterial population. A functional genomics strategy was employed to discover the molecular support for colistin resistance in Burkholderia pseudomallei sp. A191. A pUC plasmid-based genomic expression library was constructed with an estimated library size of 2.1 × 107bp. Five colistin resistant clones were obtained after functional screening of the library. Analysis of DNA sequence of five colistin resistant clones showed homology to two component regularity systems (TCRS) encoding for a histidine kinase (mrgS) and its regulatory component (mrgR). Cross complementation assay showed that mutations in mrgS were sufficient enough to confer colistin resistant phenotype in a sensitive strain.
Proteome analysis of the macroscopically affected colonic mucosa of Crohn’s disease and intestinal tuberculosis
Authors: Rukmangadachar Lokesh A. , Makharia Govind K. , Mishra Asha , Das Prasenjit , Hariprasad Gururao , Srinivasan Alagiri , Gupta Siddhartha Datta , Ahuja Vineet , Acharya Subrat K.
Published: March 2016

Differentiation between intestinal tuberculosis (ITB) and Crohn’s disease (CD) is challenging in geographical regions where both these diseases are prevalent. There is a need of biomarkers for differentiation between these two disorders. Colonic biopsies from inflamed mucosa of treatment-naive patients with ITB, CD and controls were used for analysis. Protein extracted from biopsies was digested with trypsin and resulting peptides were labeled with iTRAQ reagents. The peptides were subsequently analyzed using LC-MS/MS for identification and quantification. Gene ontology annotation for proteins was analyzed in PANTHER. Validation experiments were done for six differentially expressed proteins using immunohistochemistry. 533 proteins were identified and 241 proteins were quantified from 5 sets of iTRAQ experiments. While 63 were differentially expressed in colonic mucosa of patients with CD and ITB in at least one set of iTRAQ experiment, 11 proteins were differentially expressed in more than one set of experiments. Six proteins used for validation using immunohistochemistry in a larger cohort of patients; none of them however was differentially expressed in patients with ITB and CD. There are differentially expressed proteins in tissue proteome of CD and ITB. Further experiments are required using a larger cohort of homogeneous tissue samples.
Spatiotemporal transcriptome provides insights into early fruit development of tomato (Solanum lycopersicum)
Authors: Zhang Shuaibin , Xu Meng , Qiu Zhengkun , Wang Ketao , Du Yongchen , Gu Lianfeng , Cui Xia
Published: March 2016

Early fruit development is crucial for crop production in tomato. After fertilization, the ovary undergoes cell division and cell expansion before maturation. Although the roles of regulatory signals such as hormone and carbohydrate during early fruit development have been studied, the spatial distribution and the sequential initiation of these regulatory signals still need to be explored. Using the tomato cultivar ‘Moneymaker’, we analyzed the transcriptome of the ovule and the ovary wall/pericarp dissected from four different stages of the early developing fruits by stereoscope. These datasets give us the whole picture about the spatial and temporal signal distribution in early development of ovule and pericarp. Our results indicate that the hormone signal was initiated in both ovule and pericarp after fertilization. After that, different signals were activated in ovule and pericarp due to their distinct developmental processes. Our study provides spatiotemporal regulatory landscape of gene expression with sequential information which was not studied by previous work and further strengthens the comprehension of the regulatory and metabolic events controlling early fruit development.
Spines slow down dendritic chloride diffusion and affect short-term ionic plasticity of GABAergic inhibition
Authors: Mohapatra Namrata , Tønnesen Jan , Vlachos Andreas , Kuner Thomas , Deller Thomas , Nägerl U. Valentin , Santamaria Fidel , Jedlicka Peter
Published: March 2016

Cl−plays a crucial role in neuronal function and synaptic inhibition. However, the impact of neuronal morphology on the diffusion and redistribution of intracellular Cl−is not well understood. The role of spines in Cl−diffusion along dendritic trees has not been addressed so far. Because measuring fast and spatially restricted Cl−changes within dendrites is not yet technically possible, we used computational approaches to predict the effects of spines on Cl−dynamics in morphologically complex dendrites. In all morphologies tested, including dendrites imaged by super-resolution STED microscopy in live brain tissue, spines slowed down longitudinal Cl−diffusion along dendrites. This effect was robust and could be observed in both deterministic as well as stochastic simulations. Cl−extrusion altered Cl−diffusion to a much lesser extent than the presence of spines. The spine-dependent slowing of Cl−diffusion affected the amount and spatial spread of changes in the GABA reversal potential thereby altering homosynaptic as well as heterosynaptic short-term ionic plasticity at GABAergic synapses in dendrites. Altogether, our results suggest a fundamental role of dendritic spines in shaping Cl−diffusion, which could be of relevance in the context of pathological conditions where spine densities and neural excitability are perturbed.
Abnormal proplatelet formation and emperipolesis in cultured human megakaryocytes from gray platelet syndrome patients
Authors: Di Buduo Christian A. , Alberelli Maria Adele , Glembotsky Ana C. , Podda Gianmarco , Lev Paola R. , Cattaneo Marco , Landolfi Raffaele , Heller Paula G. , Balduini Alessandra , De Candia Erica
Published: March 2016

The Gray Platelet Syndrome (GPS) is a rare inherited bleeding disorder characterized by deficiency of platelet α-granules, macrothrombocytopenia and marrow fibrosis. The autosomal recessive form of GPS is linked to loss of function mutations in NBEAL2, which is predicted to regulate granule trafficking in megakaryocytes, the platelet progenitors. We report the first analysis of cultured megakaryocytes from GPS patients with NBEAL2 mutations. Megakaryocytes cultured from peripheral blood or bone marrow hematopoietic progenitor cells from four patients were used to investigate megakaryopoiesis, megakaryocyte morphology and platelet formation. In vitro differentiation of megakaryocytes was normal, whereas we observed deficiency of megakaryocyte α-granule proteins and emperipolesis. Importantly, we first demonstrated that platelet formation by GPS megakaryocytes was severely affected, a defect which might be the major cause of thrombocytopenia in patients. These results demonstrate that cultured megakaryocytes from GPS patients provide a valuable model to understand the pathogenesis of GPS in humans.
Glycoprotein nonmetastatic melanoma protein B extracellular fragment shows neuroprotective effects and activates the PI3K/Akt and MEK/ERK pathways via the Na+/K+-ATPase
Authors: Ono Yoko , Tsuruma Kazuhiro , Takata Masafumi , Shimazawa Masamitsu , Hara Hideaki
Published: March 2016

Glycoprotein nonmetastatic melanoma protein B (GPNMB) plays important roles in various types of cancer and amyotrophic lateral sclerosis (ALS). The details of GPNMB function and its interacting protein have not been clarified. Therefore, to identify GPNMB binding partners on the cell membrane, we used membrane protein library/BLOTCHIP-MS technology, which enables us to analyze all cell membrane proteins as binding partners of the GPNMB extracellular fragment. As a result of a comprehensive search, we identified the alpha subunits of Na+/K+-ATPase (NKA) as a possible binding partner. We confirmed the interaction between the GPNMB extracellular fragment and NKA by immunoprecipitation and immunostaining in NSC-34 cells. Indeed, endogenous GPNMB extracellular fragment bound to and colocalized with NKA alpha subunits. Furthermore, exogenous GPNMB extracellular fragment, i.e., human recombinant GPNMB, also bound to and colocalized with NKA alpha subunits. Additionally, we found that the GPNMB extracellular fragment had neuroprotective effects and activated the phosphoinositide 3-kinase (PI3K)/Akt and mitogen-activated protein kinase (MAPK)-extracellular signal-regulated kinase (ERK) kinase (MEK)/ERK pathways via NKA. These findings indicated that NKA may act as a novel “receptor” for the GPNMB extracellular fragment, offering additional molecular targets for the treatment of GPNMB-related diseases, including various types of cancer and ALS.
Preferred Barefoot Step Frequency is Influenced by Factors Beyond Minimizing Metabolic Rate
Authors: Yandell Matthew B. , Zelik Karl E.
Published: March 2016

Humans tend to increase their step frequency in barefoot walking, as compared to shod walking at the same speed. Based on prior studies and the energy minimization hypothesis we predicted that people make this adjustment to minimize metabolic cost. We performed an experiment quantifying barefoot walking metabolic rate at different step frequencies, specifically comparing preferred barefoot to preferred shod step frequency. We found that subjects increased their preferred frequency when walking barefoot at 1.4 m/s (~123 vs. ~117 steps/min shod, P = 2e-5). However, average barefoot walking metabolic rates at the preferred barefoot and shod step frequencies were not significantly different (P = 0.40). Instead, we observed subject-specific trends: five subjects consistently reduced (−8% average) and three subjects consistently increased (+10% average) their metabolic rate at preferred barefoot vs. preferred shod frequency. Thus, it does not appear that people ubiquitously select a barefoot step frequency that minimizes metabolic rate. We concluded that preferred barefoot step frequency is influenced by factors beyond minimizing metabolic rate, such as shoe properties and/or perceived comfort. Our results highlight the subject-specific nature of locomotor adaptations and how averaging data across subjects may obscure meaningful trends. Alternative experimental designs may be needed to better understand individual adaptations.
Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC
Authors: Pucci Fabrizio , Bourgeas Raphaël , Rooman Marianne
Published: March 2016

The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature ΔTm upon point mutations, given the protein structure and, when available, the melting temperature Tm of the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured ΔTm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental ΔTm values of 4.2 °C that reduces to 2.9 °C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use at soft.dezyme.com.
Nighttime warming enhances drought resistance of plant communities in a temperate steppe
Authors: Yang Zhongling , Jiang Lin , Su Fanglong , Zhang Qian , Xia Jianyang , Wan Shiqiang
Published: March 2016

Drought events could have profound influence on plant community structure and ecosystem function, and have subsequent impacts on community stability, but we know little about how different climate warming scenarios affect community resistance and resilience to drought. Combining a daytime and nighttime warming experiment in the temperate steppe of north China with a natural drought event during the study period, we tested how daytime and nighttime warming influences drought resistance and resilience. Our results showed that the semi-arid steppe in north China was resistant to both daytime and nighttime warming, but vulnerable to drought. Nighttime warming, but not daytime warming, enhanced community resistance to drought via stimulating carbon sequestration, whereas neither daytime nor nighttime warming affected community resilience to drought. Large decline in plant community cover, primarily caused by the reduction in the cover of dominant and rare species rather than subordinate species during drought, did not preclude rapid ecosystem recovery. These findings suggest that nighttime warming may facilitate ecosystem sustainability and highlight the need to assess the effects of climate extremes on ecosystem functions at finer temporal resolutions than based on diurnal mean temperature.
Sox2 in the differentiation of cochlear progenitor cells
Authors: Kempfle Judith S. , Turban Jack L. , Edge Albert S. B.
Published: March 2016

HMG domain transcription factor, Sox2, is a critical gene for the development of cochlear hair cells, the receptor cells for hearing, but this has been ascribed to expansion of the progenitors that become hair cells. Here, we show that Sox2 activated Atoh1, a transcription factor important for hair cell differentiation, through an interaction with the 3′ enhancer of Atoh1. Binding to consensus sequences in the Atoh1 enhancer was dependent on the level of Sox2 and the extent of enhancer binding correlated to the extent of activation. Atoh1 activation by Sox2 was required for embryonic hair cell development: deletion of Sox2 in an inducible mutant, even after progenitor cells were fully established, halted development of hair cells and silencing also inhibited postnatal differentiation of hair cells induced by inhibition of γ-secretase. Sox2 is thus required in the cochlea to both expand the progenitor cells and initiate their differentiation to hair cells.
Demonstration of single crystal growth via solid-solid transformation of a glass
Authors: Savytskii Dmytro , Knorr Brian , Dierolf Volkmar , Jain Himanshu
Published: March 2016

Many advanced technologies have relied on the availability of single crystals of appropriate material such as silicon for microelectronics or superalloys for turbine blades. Similarly, many promising materials could unleash their full potential if they were available in a single crystal form. However, the current methods are unsuitable for growing single crystals of these oftentimes incongruently melting, unstable or metastable materials. Here we demonstrate a strategy to overcome this hurdle by avoiding the gaseous or liquid phase and directly converting glass into a single crystal. Specifically, Sb2S3 single crystals are grown in Sb-S-I glasses as an example of this approach. In this first unambiguous demonstration of an all-solid-state glass → crystal transformation, extraneous nucleation is avoided relative to crystal growth via spatially localized laser heating and inclusion of a suitable glass former in the composition. The ability to fabricate patterned single-crystal architecture on a glass surface is demonstrated, providing a new class of micro-structured substrate for low cost epitaxial growth, active planar devices, etc.
More for less: Improving the biomass yield of a pear cell suspension culture by design of experiments
Authors: Rasche Stefan , Herwartz Denise , Schuster Flora , Jablonka Natalia , Weber Andrea , Fischer Rainer , Schillberg Stefan
Published: March 2016

Plant cell suspension cultures are widely used for the production of recombinant proteins and secondary metabolites. One of the most important steps during process development is the optimization of yields by testing different cultivation parameters, including the components of the growth medium. However, we have shown that the biomass yield of a cell suspension culture derived from the pear cultivar Pyrus communis cv. Champagner Bratbirne can be significantly improved solely by varying the temperature, inoculum density, illumination and incubation time. In contrast to medium optimization, these simple physical factors are easily controlled and varied, thereby reducing the effort required. Using an experimental design approach, we improved the biomass yield from 146 g fresh weight (FW)/L to 407 g FW/L in only 5 weeks, simultaneously reducing the costs of goods sold per kg biomass from €125 to €45. Our simple approach therefore offers a rapid, efficient and economical process for the optimization of plant cell suspension cultures.
NMR Observation of Mobile Protons in Proton-Implanted ZnO Nanorods
Authors: Park Jun Kue , Kwon Hyeok-Jung , Lee Cheol Eui
Published: March 2016

The diffusion properties of H+ in ZnO nanorods are investigated before and after 20 MeV proton beam irradiation by using 1H nuclear magnetic resonance (NMR) spectroscopy. Herein, we unambiguously observe that the implanted protons occupy thermally unstable site of ZnO, giving rise to a narrow NMR line at 4.1 ppm. The activation barrier of the implanted protons was found to be 0.46 eV by means of the rotating-frame spin-lattice relaxation measurements, apparently being interstitial hydrogens. High-energy beam irradiation also leads to correlated jump diffusion of the surface hydroxyl group of multiple lines at ~1 ppm, implying the presence of structural disorder at the ZnO surface.
Pathobiological Characterization of a Novel Reassortant Highly Pathogenic H5N1 Virus Isolated in British Columbia, Canada, 2015
Authors: Berhane Yohannes , Kobasa Darwyn , Embury-Hyatt Carissa , Pickering Brad , Babiuk Shawn , Joseph Tomy , Bowes Victoria , Suderman Mathew , Leung Anders , Cottam-Birt Colleen , Hisanaga Tamiko , Pasick John
Published: March 2016

In the current study, we describe the pathobiologic characteristics of a novel reassortant virus - A/chicken/BC/FAV-002/2015 (H5N1) belonging to clade 2.3.4.4 that was isolated from backyard chickens in British Columbia, Canada. Sequence analyses demonstrate PB1, PA, NA and NS gene segments were of North American lineage while PB2, HA, NP and M were derived from a Eurasian lineage H5N8 virus. This novel virus had a 19 amino acid deletion in the neuraminidase stalk. We evaluated the pathogenic potential of this isolate in various animal models. The virus was highly pathogenic to mice with a LD50 of 10 plaque forming units (PFU), but had limited tissue tropism. It caused only subclinical infection in pigs which did result in seroconversion. This virus was highly pathogenic to chickens, turkeys, juvenile Muscovy ducks (Cairnia moschata foma domestica) and adult Chinese geese (Anser cynoides domesticus) causing a systemic infection in all species. The virus was also efficiently transmitted and resulted in mortality in naïve contact ducks, geese and chickens. Our findings indicate that this novel H5N1 virus has a wide host range and enhanced surveillance of migratory waterfowl may be necessary in order to determine its potential to establish itself in the wild bird reservoir.
The effect of positioning cations on acidity and stability of the framework structure of Y zeolite
Authors: Deng Changshun , Zhang Junji , Dong Lihui , Huang Meina , Bin Li  , Jin Guangzhou , Gao Junbin , Zhang Feiyue , Fan Minguang , Zhang Luoming , Gong Yanjun
Published: March 2016

The investigation on the modification of NaY zeolite on LaHY and AEHY (AE refers Ca and Sr and the molar ratio of Ca and Sr is 1:1) zeolites was proformed by XRD, N2-physisorption (BET), XRF, XPS, NH3-TPD, Py-IR, hydrothermal stability, and catalytic cracking test. These results indicate that HY zeolite with ultra low content Na can be obtained from NaY zeolite through four exchange four calcination method. The positioning capability of La3+ in sodalite cage is much better than that of AE2+ and about 12 La3+ can be well coordinated in sodalite cages of one unit cell of Y zeolite. Appropriate acid amount and strength favor the formation of propylene and La3+ is more suitable for the catalytic cracking of cyclohexane than that of AE2+. Our results not only elaborate the variation of the strong and weak acid sites as well as the Brönsted and Lewis acid sites with the change of exchanged ion content but also explore the influence of hydrothermal aging of LaHY and AEHY zeolites and find the optimum ion exchange content for the most reserved acid sites. At last, the coordination state and stabilization of ion exchanged Y zeolites were discussed in detail.
A rapid method to authenticate vegetable oils through surface-enhanced Raman scattering
Authors: Lv Ming Yang , Zhang Xin , Ren Hai Rui , Liu Luo , Zhao Yong Mei , Wang Zheng , Wu Zheng Long , Liu Li Min , Xu Hai Jun
Published: March 2016

Vegetable oils are essential in our daily diet. Among various vegetable oils, the major difference lies in the composition of fatty acids, including unsaturated fatty acids (USFA) and saturated fatty acids (SFA). USFA include oleic acid (OA), linoleic acid (LA), and α-linolenic acid (ALA), while SFA are mainly palmitic acid (PA). In this study, the most typical and abundant USFA present with PA in vegetable oils were quantified. More importantly, certain proportional relationships between the integrated intensities of peaks centered at 1656 cm−1 (S1656) in the surface-enhanced Raman scattering spectra of different USFA were confirmed. Therefore, the LA or ALA content could be converted into an equivalent virtual OA content enabling the characterization of the USFA content in vegetable oils using the equivalent total OA content. In combination with the S1656 of pure OA and using peanut, sesame, and soybean oils as examples, the ranges of S1656 corresponding to the National Standards of China were established to allow the rapid authentication of vegetable oils. Gas chromatograph-mass spectrometer analyses verified the accuracy of the method, with relative errors of less than 5%. Moreover, this method can be extended to other detection fields, such as diseases.
AHNAK deficiency promotes browning and lipolysis in mice via increased responsiveness to β-adrenergic signalling
Authors: Shin Jae Hoon , Lee Seo Hyun , Kim Yo Na , Kim Il Yong , Kim Youn Ju , Kyeong Dong Soo , Lim Hee Jung , Cho Soo Young , Choi Junhee , Wi Young Jin , Choi Jae-Hoon , Yoon Yeo Sung , Bae Yun Soo , Seong Je Kyung
Published: March 2016

In adipose tissue, agonists of the β3-adrenergic receptor (ADRB3) regulate lipolysis, lipid oxidation, and thermogenesis. The deficiency in the thermogenesis induced by neuroblast differentiation-associated protein AHNAK in white adipose tissue (WAT) of mice fed a high-fat diet suggests that AHNAK may stimulate energy expenditure via development of beige fat. Here, we report that AHNAK deficiency promoted browning and thermogenic gene expression in WAT but not in brown adipose tissue of mice stimulated with the ADRB3 agonist CL-316243. Consistent with the increased thermogenesis, Ahnak−/− mice exhibited an increase in energy expenditure, accompanied by elevated mitochondrial biogenesis in WAT depots in response to CL-316243. Additionally, AHNAK-deficient WAT contained more eosinophils and higher levels of type 2 cytokines (IL-4/IL-13) to promote browning of WAT in response to CL-316243. This was associated with enhanced sympathetic tone in the WAT via upregulation of adrb3 and tyrosine hydroxylase (TH) in response to β-adrenergic activation. CL-316243 activated PKA signalling and enhanced lipolysis, as evidenced by increased phosphorylation of hormone-sensitive lipase and release of free glycerol in Ahnak−/− mice compared to wild-type mice. Overall, these findings suggest an important role of AHNAK in the regulation of thermogenesis and lipolysis in WAT via β-adrenergic signalling.
PI3K in the ventromedial hypothalamic nucleus mediates estrogenic actions on energy expenditure in female mice
Authors: Saito Kenji , He Yanlin , Yang Yongjie , Zhu Liangru , Wang Chunmei , Xu Pingwen , Hinton Antentor Othrell , Yan Xiaofeng , Zhao Jean , Fukuda Makoto , Tong Qingchun , Clegg Deborah J. , Xu Yong
Published: March 2016

Estrogens act in the ventromedial hypothalamic nucleus (VMH) to regulate body weight homeostasis. However, the molecular mechanisms underlying these estrogenic effects are unknown. We show that activation of estrogen receptor-α (ERα) stimulates neural firing of VMH neurons expressing ERα and these effects are blocked with intracellular application of a pharmacological inhibitor of the phosphatidyl inositol 3-kinase (PI3K). Further, we demonstrated that mice with genetic inhibition of PI3K activity in VMH neurons showed a sexual dimorphic obese phenotype, with only female mutants being affected. In addition, inhibition of VMH PI3K activity blocked effects of 17β-estradiol to stimulate energy expenditure, but did not affect estrogen-induced anorexia. Collectively, our results indicate that PI3K activity in VMH neurons plays a physiologically relevant role in mediating estrogenic actions on energy expenditure in females.
Heartbeat, embryo communication and hatching synchrony in snake eggs
Authors: Aubret Fabien , Blanvillain Gaëlle , Bignon Florent , Kok Philippe J. R.
Published: March 2016

Communication is central to life at all levels of complexity, from cells to organs, through to organisms and communities. Turtle eggs were recently shown to communicate with each other in order to synchronise their development and generate beneficial hatching synchrony. Yet the mechanism underlying embryo to embryo communication remains unknown. Here we show that within a clutch, developing snake embryos use heart beats emanating from neighbouring eggs as a clue for their metabolic level, in order to synchronise development and ultimately hatching. Eggs of the water snake Natrix maura increased heart rates and hatched earlier than control eggs in response to being incubated in physical contact with more advanced eggs. The former produced shorter and slower swimming young than their control siblings. Our results suggest potential fitness consequences of embryo to embryo communication and describe a novel driver for the evolution of egg-clustering behaviour in animals.
Classification of Chinese tea leaves using laser-induced breakdown spectroscopy combined with the discriminant analysis method
Authors: Wang Jinmei , Zheng Peichao , Liu Hongdi , Fang Liang
Published: March 2016

Six types of tea leaves, including Longjing green tea, Mengding Huangya, white tea, Tie Guanyin, Wuyi black tea and Pu'er tea, were analyzed and identified using laser-induced breakdown spectroscopy (LIBS) combined with the discriminant analysis (DA) method.
Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics
Authors: Gillingham Dennis , Geigle Stefanie , Anatole von Lilienfeld O.
Published: March 2016

Selective chemistry combined with next generation sequencing is enabling the transcriptomics and epigenomics revolutions.
Electrochemical fabrication of copper-containing metal–organic framework films as amperometric detectors for bromate determination
Authors: Shi Erbin , Zou Xiaoqin , Liu Jia , Lin Huiming , Zhang Feng , Shi Shaoxuan , Liu Fenghua , Zhu Guangshan , Qu Fengyu
Published: March 2016

An electroactive metal–organic framework film (NENU-3) onto a copper electrode has been prepared by the facile electrochemical plating strategy.
Molecular basis of 5-hydroxytryptophan synthesis in Saccharomyces cerevisiae
Authors: Zhang Jiantao , Wu Chaochen , Sheng Jiayuan , Feng Xueyang
Published: March 2016

We report for the first time that 5-hydroxytryptophan can be synthesized in Saccharomyces cerevisiae by heterologously expressing prokaryotic phenylalanine 4-hydroxylase or eukaryotic tryptophan 3/5-hydroxylase, together with enhanced synthesis of MH4 or BH4 cofactors.
Small molecules targeting Mcl-1: the search for a silver bullet in cancer therapy
Authors: Nhu Duong , Lessene Guillaume , Huang David C. S. , Burns Christopher J.
Published: March 2016

Progress towards the development of potent and selective inhibitors of the pro-survival protein Mcl-1 is reviewed.
Self-supported Zn3P2 nanowire arrays grafted on carbon fabrics as an advanced integrated anode for flexible lithium ion batteries
Authors: Li Wenwu , Gan Lin , Guo Kai , Ke Linbo , Wei Yaqing , Li Huiqiao , Shen Guozhen , Zhai Tianyou
Published: March 2016

The well-aligned binary lithium-reactive metal phosphide nanowire arrays were grafted on carbon fabrics. When served as integrated electrodes, they exhibit striking high initial coulombic efficiency, large capacity, excellent rate performance.
FTIR metabolomic fingerprint reveals different modes of action exerted by active pharmaceutical ingredient based ionic liquids (API-ILs) on Salmonella typhimurium
Authors: Mester P. , Jehle A. K. , Leeb C. , Kalb R. , Grunert T. , Rossmanith P.
Published: March 2016

FTIR spectroscopic analysis of two IL species with similar high antimicrobial activity ([TC8MA]/[TMC16A]) revealed independently of their anion different modes of action against S. typhimurium through alterations in the bacterial membrane fluidity.
A new view of graphene oxide biosafety in a water environment using an eatable fish as a model
Authors: Ma Keyi , Zhang Shupeng , Ye Baoqing , Ouyang Jianyong , Yue Gen Hua
Published: March 2016

A comprehensive evaluation on the biosafety of graphene oxide (GO) was developed by combining 16S rRNA sequencing, gene expression detection, histology and a scanning electron microscope assay on fish.
Hydrogen-bonded bent-core blue phase liquid crystal complexes containing various molar ratios of proton acceptors and donors
Authors: Han Chun-Chieh , Chou Yu-Chaing , Chen San-Yuan , Lin Hong-Cheu
Published: March 2016

The molar ratio, alkyl chain length, lateral fluoro-substitution and the chiral center of H-bonded bent-core supramolecules would affect the BP ranges of BPLC complexes. H-bonded bent-core complex PIIIC9/AIIF* (3/7 mol mol−1) displayed the widest BPI range of ΔTBPI = 12 °C.
Microstructure and corrosion behaviour of laser surface melting treated WE43 magnesium alloy
Authors: Liu Cancan , Li Qingbiao , Liang Jun , Zhou Jiansong , Wang Lingqian
Published: March 2016

An attempt has been made to improve the corrosion behavior of WE43 magnesium alloy by laser surface melting (LSM) using a 10 kW continuous-wave CO2 laser.
Calixarene-functionalized graphene oxide composites for adsorption of neodymium ions from the aqueous phase
Authors: Zhang Peng , Wang Yaling , Zhang Dongxiang , Bai Han , Tarasov Valeri V.
Published: March 2016

Calixarene-functionalized graphene oxide (GO) composites were synthesized via esterification and polymerization of calix[n]arenes (n = 4, 6, 8) onto graphene oxide surfaces for the first time.
A scaffold with a bio-mimetically designed micro/nano-fibrous structure using decellularized extracellular matrix
Authors: Lee Hyeongjin , Yang Sira , Kim Minseong , Kim GeunHyung
Published: March 2016

A new method to obtain an ECM-based fibrous scaffold consisting of a synthetic polymer (PCL) and d-ECM was proposed.
Assembly of alizarin red S/boric acid ultrathin films based on layered double hydroxide for fluorescence turn on detection of tiopronin
Authors: Wu Haiqin , Jin Lan
Published: March 2016

New facile, economical and fluorescent (ARS–H3BO3/LDH)n UTFs were developed, exhibiting response to tiopronin with high selectivity, precision and reversibility.
Chiral separation and enantioselective degradation of trichlorfon enantiomers in mariculture pond water
Authors: Jing-Nie Jing-Nie , Wang Yang-Guang , Yang Li-Ye , Wu Wei-Jian , Yu Di , OuYang Xiao-kun
Published: March 2016

Degradation of trichlorfon enantiomers (R/S = 1 : 1, rac-TF = 10 mg L−1) in seawater under native (A), sterile (B), dark (C) and dark and sterile (D) conditions at 20 °C.
New insights into water oxidation reactions from photocatalysis, electrocatalysis to chemical catalysis: an example of iron-based oxides doped with foreign elements
Authors: Huang Jingwei , Du Xiaoqiang , Feng YingYing , Zhao Yukun , Ding Yong
Published: March 2016

Our study provides the first critical evaluation of the three common driving forces. The data clearly demonstrate that water oxidation catalytic performance can differ widely and depend strongly on the driving force employed.
Time and temperature dependent multiple hierarchical NiCo2O4 for high-performance supercapacitors
Authors: Wang Shen , Sun Shumin , Li Shaodan , Gong Feilong , Li Yannan , Wu Qiong , Song Pei , Fang Shaoming , Wang Peiyuan
Published: March 2016

The time and temperature dependent multiple hierarchical NiCo2O4 constructed of nanosheets covered with nanowires shows excellent electrochemical performance.
Monitoring variations of dimethyl sulfide and dimethylsulfoniopropionate in seawater and the atmosphere based on sequential vapor generation and ion molecule reaction mass spectrometry
Authors: Iyadomi Satoshi , Ezoe Kentaro , Ohira Shin-Ichi , Toda Kei
Published: March 2016

DMS emission from seawater to atmosphere dramatically varies diurnally. This phenomenon was demonstrated by sequential vapor generation and mass spectrometry.
Correction: Sulfur isotope analysis by MC-ICP-MS and application to small medical samples
Authors: Albalat Emmanuelle , Telouk Philippe , Balter Vincent , Fujii Toshiyuki , Bondanese Victor Paky , Plissonnier Marie-Laure , Vlaeminck-Guillem Virginie , Baccheta Justine , Thiam Ndiémé , Miossec Pierre , Zoulim Fabien , Puisieux Alain , Albarède Francis
Published: March 2016

Correction for ‘Sulfur isotope analysis by MC-ICP-MS and application to small medical samples’ by Emmanuelle Albalat et al., J. Anal. At. Spectrom., 2016, DOI: 10.1039/c5ja00489f.
A fluorescent HTS assay for phosphohydrolases based on nucleoside 5′-fluorophosphates: its application in screening for inhibitors of mRNA decapping scavenger and PDE-I
Authors: Baranowski M. R. , Nowicka A. , Jemielity J. , Kowalska J.
Published: March 2016

By using a fluoride-sensitive probe, we harnessed P–F bond cleavage reaction to develop an assay to screen for nucleotide-handling phosphohydrolase inhibitors.
Well-defined (co)polypeptides bearing pendant alkyne groups
Authors: Zhao Wei , Gnanou Yves , Hadjichristidis Nikos
Published: March 2016

A novel metal-free strategy, using hydrogen-bonding catalytic ring opening polymerization of alkyne-functionalized N-carboxy anhydrites of α-amino acids, was developed for the synthesis of well-defined polypeptides bearing pendant alkyne groups.