bluuebunny/crossref_metadata_2025_split huggingface dataset:
Myogenic differentiation triggers PML nuclear body loss and DAXX relocalization to chromocentres
Authors: Salsman Jayme , Rapkin Lindsy M , Margam Nandini N , Duncan Roy , Bazett-Jones David P , Dellaire Graham 
Published: March 2017

AbstractThe promyelocytic leukemia protein (PML) is expressed in most normal human tissues and forms nuclear bodies (NBs) that have roles in gene regulation and cellular processes such as DNA repair, cell cycle control, and cell fate decisions. Using murine C2C12 myoblasts, we demonstrate that activation of skeletal muscle differentiation results in loss of PML and PML NBs prior to myotube fusion. Myotube formation was associated with marked chromatin reorganization and the relocalization of DAXX from PML NBs to chromocentres. MyoD expression was sufficient to cause PML NB loss, and silencing of PML induced DAXX relocalization. Fusion of C2C12 cells using the reptilian reovirus p14 fusogenic protein failed to disrupt PML NBs yet still promoted DAXX redistribution and loss; whereas ectopic expression of PML in differentiated cells only partially restored PML NB formation and DAXX localization at NBs. Finally, we determined that the C-terminal SUMO-interacting motif of DAXX is required for its colocalization with ATRX in heterochromatin domains during myotube formation. These data support a model in which activation of myogenic differentiation results in PML NB loss, chromatin reorganization and DAXX relocalization, and provides a paradigm for understanding the consequence of PML loss in other cellular contexts, such as during cancer development and progression.
Allosteric cross-talk in chromatin can mediate drug-drug synergy
Authors: Adhireksan Zenita , Palermo Giulia , Riedel Tina , Ma Zhujun , Muhammad Reyhan , Rothlisberger Ursula , Dyson Paul J. , Davey Curt A. 
Published: March 2017

AbstractExploitation of drug–drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug–drug synergy mediated by allosteric cross-talk in chromatin, whereby the binding of one drug alters the activity of the second. We found two unrelated drugs, RAPTA-T and auranofin, that yield a synergistic activity in killing cancer cells, which coincides with a substantially greater number of chromatin adducts formed by one of the compounds when adducts from the other agent are also present. We show that this occurs through an allosteric mechanism within the nucleosome, whereby defined histone adducts of one drug promote reaction of the other drug at a distant, specific histone site. This opens up possibilities for epigenetic targeting and suggests that allosteric modulation in nucleosomes may have biological relevance and potential for therapeutic interventions.
The Par3 polarity protein is an exocyst receptor essential for mammary cell survival
Authors: Ahmed Syed Mukhtar , Macara Ian G. 
Published: March 2017

AbstractThe exocyst is an essential component of the secretory pathway required for delivery of basolateral proteins to the plasma membranes of epithelial cells. Delivery occurs adjacent to tight junctions (TJ), suggesting that it recognizes a receptor at this location. However, no such receptor has been identified. The Par3 polarity protein associates with TJs but has no known function in membrane traffic. We now show that, unexpectedly, Par3 is essential for mammary cell survival. Par3 silencing causes apoptosis, triggered by phosphoinositide trisphosphate depletion and decreased Akt phosphorylation, resulting from failure of the exocyst to deliver basolateral proteins to the cortex. A small region of PAR3 binds directly to Exo70 and is sufficient for exocyst docking, membrane-protein delivery and cell survival. PAR3 lacking this domain can associate with the cortex but cannot support exocyst function. We conclude that Par3 is the long-sought exocyst receptor required for targeted membrane-protein delivery.
Cholesterol-mediated allosteric regulation of the mitochondrial translocator protein structure
Authors: Jaipuria Garima , Leonov Andrei , Giller Karin , Vasa Suresh Kumar , Jaremko Łukasz , Jaremko Mariusz , Linser Rasmus , Becker Stefan , Zweckstetter Markus 
Published: March 2017

AbstractCholesterol is an important regulator of membrane protein function. However, the exact mechanisms involved in this process are still not fully understood. Here we study how the tertiary and quaternary structure of the mitochondrial translocator protein TSPO, which binds cholesterol with nanomolar affinity, is affected by this sterol. Residue-specific analysis of TSPO by solid-state NMR spectroscopy reveals a dynamic monomer–dimer equilibrium of TSPO in the membrane. Binding of cholesterol to TSPO’s cholesterol-recognition motif leads to structural changes across the protein that shifts the dynamic equilibrium towards the translocator monomer. Consistent with an allosteric mechanism, a mutation within the oligomerization interface perturbs transmembrane regions located up to 35 Å away from the interface, reaching TSPO’s cholesterol-binding motif. The lower structural stability of the intervening transmembrane regions provides a mechanistic basis for signal transmission. Our study thus reveals an allosteric signal pathway that connects membrane protein tertiary and quaternary structure with cholesterol binding.
Structure and vacancy distribution in copper telluride nanoparticles influence plasmonic activity in the near-infrared
Authors: Willhammar Tom , Sentosun Kadir , Mourdikoudis Stefanos , Goris Bart , Kurttepeli Mert , Bercx Marnik , Lamoen Dirk , Partoens Bart , Pastoriza-Santos Isabel , Pérez-Juste Jorge , Liz-Marzán Luis M. , Bals Sara , Van Tendeloo Gustaaf 
Published: March 2017

AbstractCopper chalcogenides find applications in different domains including photonics, photothermal therapy and photovoltaics. CuTe nanocrystals have been proposed as an alternative to noble metal particles for plasmonics. Although it is known that deviations from stoichiometry are a prerequisite for plasmonic activity in the near-infrared, an accurate description of the material and its (optical) properties is hindered by an insufficient understanding of the atomic structure and the influence of defects, especially for materials in their nanocrystalline form. We demonstrate that the structure of Cu1.5±xTe nanocrystals can be determined using electron diffraction tomography. Real-space high-resolution electron tomography directly reveals the three-dimensional distribution of vacancies in the structure. Through first-principles density functional theory, we furthermore demonstrate that the influence of these vacancies on the optical properties of the nanocrystals is determined. Since our methodology is applicable to a variety of crystalline nanostructured materials, it is expected to provide unique insights concerning structure–property correlations.
Hydrolysis of nicosulfuron under acidic environment caused by oxalate secretion of a novel Penicillium oxalicum strain YC-WM1
Authors: Feng Weimin , Wei Zheng , Song Jinlong , Qin Qiao , Yu Kaimin , Li Guochao , Zhang Jiayu , Wu Wei , Yan Yanchun 
Published: March 2017

AbstractA novel Penicillium oxalicum strain YC-WM1, isolated from activated sludge, was found to be capable of completely degrading 100 mg/L of nicosulfuron within six days when incubated in GSM at 33 °C. Nicosulfuron degradation rates were affected by GSM initial pH, nicosulfuron initial concentration, glucose initial concentration, and carbon source. After inoculation, the medium pH was decreased from 7.0 to 4.5 within one day and remained at around 3.5 during the next few days, in which nicosulfuron degraded quickly. Besides, 100 mg/L of nicosulfuron were completely degraded in GSM medium at pH of 3.5 without incubation after 4 days. So, nicosulfuron degradation by YC-WM1 may be acidolysis. Based on HPLC analysis, GSM medium acidification was due to oxalate accumulation instead of lactic acid and oxalate, which was influenced by different carbon sources and had no relationship to nicosulfuron initial concentration. Furthermore, nicosulfuron broke into aminopyrimidine and pyridylsulfonamide as final products and could not be used as nitrogen source and mycelium didn’t increase in GSM medium. Metabolomics results further showed that nicosulfuron degradation was not detected in intracellular. Therefore, oxalate secretion in GSM medium by strain YC-WM1 led to nicosulfuron acidolysis.
20S immunoproteasomes remove formaldehyde-damaged cytoplasmic proteins suppressing caspase-independent cell death
Authors: Ortega-Atienza Sara , Krawic Casey , Watts Lauren , McCarthy Caitlin , Luczak Michal W. , Zhitkovich Anatoly 
Published: March 2017

AbstractImmunoproteasomes are known for their involvement in antigen presentation. However, their broad tissue presence and other evidence are indicative of nonimmune functions. We examined a role for immunoproteasomes in cellular responses to the endogenous and environmental carcinogen formaldehyde (FA) that binds to cytosolic and nuclear proteins producing proteotoxic stress and genotoxic DNA-histone crosslinks. We found that immunoproteasomes were important for suppression of a caspase-independent cell death and the long-term survival of FA-treated cells. All major genotoxic responses to FA, including replication inhibition and activation of the transcription factor p53 and the apical ATM and ATR kinases, were unaffected by immunoproteasome inactivity. Immunoproteasome inhibition enhanced activation of the cytosolic protein damage sensor HSF1, elevated levels of K48-polyubiquitinated cytoplasmic proteins and increased depletion of unconjugated ubiquitin. We further found that FA induced the disassembly of 26S immunoproteasomes, but not standard 26S proteasomes, releasing the 20S catalytic immunoproteasome. FA-treated cells also had higher amounts of small activators PA28αβ and PA28γ bound to 20S particles. Our findings highlight the significance of nonnuclear damage in FA injury and reveal a major role for immunoproteasomes in elimination of FA-damaged cytoplasmic proteins through ubiquitin-independent proteolysis.
Acid-Sensing Ion Channel 1a in the amygdala is involved in pain and anxiety-related behaviours associated with arthritis
Authors: Aissouni Youssef , El Guerrab Abderrahim , Hamieh Al Mahdy , Ferrier Jérémy , Chalus Maryse , Lemaire Diane , Grégoire Stéphanie , Etienne Monique , Eschalier Alain , Ardid Denis , Lingueglia Eric , Marchand Fabien 
Published: March 2017

AbstractChronic pain is associated with anxiety and depression episodes. The amygdala plays a key role in the relationship between emotional responses and chronic pain. Here, we investigated the role of Acid-Sensing Ion Channels 1a within the basolateral amygdala (BLA), in pain and associated anxiety in a rat model of monoarthritis (MoAr). Administration within the BLA of PcTx1 or mambalgin-1, two specific inhibitors of ASIC1a-containing channels significantly inhibited pain and anxiety-related behaviours in MoAr rats. The effect of PcTx1 was correlated with a reduction of c-Fos expression in the BLA. We examined the expression profile of ASICs and other genes in the amygdala in MoAr and sham animals, and found no variation of the expression of ASIC1a, which was confirmed at the protein level. However, an increase in the BLA of MoAr rats of both PI3Kinase mRNA and the phosphorylated form of Akt, along with Bdnf mRNA, suggest that the BDNF/PI3-kinase/Akt pathway might regulate ASIC1a in BLA neurons as demonstrated in spinal sensitisation phenomenon. We also observed changes in several kinase mRNAs expression (PICK1, Sgk1) that are potentially involved in ASIC1a regulation. These results show a crucial role of ASIC1a channels in the BLA in pain and anxiety-related behaviours during arthritis.
Serine protease SP105 activates prophenoloxidase in Asian corn borer melanization, and is regulated by serpin-3
Authors: Chu Yuan , Hong Fang , Liu Qizhi , An Chunju 
Published: March 2017

AbstractMelanization reaction, resulting from the activation of prophenoloxidase, is a vital immune response in insects for encapsulating and killing the invasive organisms. Prophenoloxidase needs to be proteolytically activated by its upstream prophenoloxidase-activating protease (PAP) in melanization. Identification and characterization of PAPs facilitates the understanding of the molecular mechanisms involved in insect immunity. We here cloned a full-length cDNA for a serine protease, named as SP105, from Asian corn borer, Ostrinia furnacalis (Guenée). The open reading frame of SP105 encodes 424-amino acid residue protein with a 19-residue signal peptide. Sequence comparison indicates that SP105 is most similar to Manduca sexta PAP3, a defined prophenoloxidase-activating protease. qRT-PCR analysis showed that SP105 mRNA levels increased significantly after a bacterial injection. Recombinant SP105 directly cleaved and activated Asian corn borer prophenoloxidase and therefore acted as the prophenoloxidase-activating protease. Additionally, SP105 formed SDS-stable complexes with a serine protease inhibitor, serpin-3, and its activity in activating prophenoloxidase was efficiently inhibited by serpin-3. Our work thus illustrated a prophenoloxidase-activating protease and revealed its regulation by serpin-3. The results would allow further advances in the understanding of the melanization in Asian corn borer and other insects.
Altered (neo-) lacto series glycolipid biosynthesis impairs α2-6 sialylation on N-glycoproteins in ovarian cancer cells
Authors: Alam Shahidul , Anugraham Merrina , Huang Yen-Lin , Kohler Reto S. , Hettich Timm , Winkelbach Katharina , Grether Yasmin , López Mónica Núñez , Khasbiullina Nailia , Bovin Nicolai V. , Schlotterbeck Götz , Jacob Francis 
Published: March 2017

AbstractThe (neo-) lacto series glycosphingolipids (nsGSLs) comprise of glycan epitopes that are present as blood group antigens, act as primary receptors for human pathogens and are also increasingly associated with malignant diseases. Beta-1, 3-N-acetyl-glucosaminyl-transferase 5 (B3GNT5) is suggested as the key glycosyltransferase for the biosynthesis of nsGSLs. In this study, we investigated the impact of CRISPR-Cas9 -mediated gene disruption of B3GNT5 (∆B3GNT5) on the expression of glycosphingolipids and N-glycoproteins by utilizing immunostaining and glycomics-based PGC-UHPLC-ESI-QTOF-MS/MS profiling. ∆B3GNT5 cells lost nsGSL expression coinciding with reduction of α2-6 sialylation on N-glycoproteins. In contrast, disruption of B4GALNT1, a glycosyltransferase for ganglio series GSLs did not affect α2-6 sialylation on N-glycoproteins. We further profiled all known α2-6 sialyltransferase-encoding genes and showed that the loss of α2-6 sialylation is due to silencing of ST6GAL1 expression in ∆B3GNT5 cells. These results demonstrate that nsGSLs are part of a complex network affecting N-glycosylation in ovarian cancer cells.
Combined effects of temperature and the herbicide diuron on Photosystem II activity of the tropical seagrass Halophila ovalis
Authors: Wilkinson Adam D. , Collier Catherine J. , Flores Florita , Langlois Lucas , Ralph Peter J. , Negri Andrew P. 
Published: March 2017

AbstractTropical seagrasses are at their highest risk of exposure to photosystem II (PSII) herbicides when elevated rainfall and runoff from farms transports these toxicants into coastal habitats during summer, coinciding with periods of elevated temperature. PSII herbicides, such as diuron, can increase the sensitivity of corals to thermal stress, but little is known of the potential for herbicides to impact the thermal optima of tropical seagrass. Here we employed a well-plate approach to experimentally assess the effects of diuron on the photosynthetic performance of Halophila ovalis leaves across a 25 °C temperature range (36 combinations of these stressors across 15–40 °C). The thermal optimum for photosynthetic efficiency (▵"Equation missing") in H. ovalis was 31 °C while lower and higher temperatures reduced ▵"Equation missing" as did all elevated concentrations of diuron. There were significant interactions between the effects of temperature and diuron, with a majority of the combined stresses causing sub-additive (antagonistic) effects. However, both stressors caused negative responses and the sum of the responses was greater than that caused by temperature or diuron alone. These results indicate that improving water quality (reducing herbicide in runoff) is likely to maximise seagrass health during extreme temperature events that will become more common as the climate changes.
Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi
Authors: Li Juan , Gu Fei , Wu Runian , Yang JinKui , Zhang Ke-Qin 
Published: March 2017

AbstractSubtilases belong to a superfamily of serine proteases which are ubiquitous in fungi and are suspected to have developed distinct functional properties to help fungi adapt to different ecological niches. In this study, we conducted a large-scale phylogenomic survey of subtilase protease genes in 83 whole genome sequenced fungal species in order to identify the evolutionary patterns and subsequent functional divergences of different subtilase families among the main lineages of the fungal kingdom. Our comparative genomic analyses of the subtilase superfamily indicated that extensive gene duplications, losses and functional diversifications have occurred in fungi, and that the four families of subtilase enzymes in fungi, including proteinase K-like, Pyrolisin, kexin and S53, have distinct evolutionary histories which may have facilitated the adaptation of fungi to a broad array of life strategies. Our study provides new insights into the evolution of the subtilase superfamily in fungi and expands our understanding of the evolution of fungi with different lifestyles.
Single crystalline superstructured stable single domain magnetite nanoparticles
Authors: Reichel Victoria , Kovács András , Kumari Monika , Bereczk-Tompa Éva , Schneck Emanuel , Diehle Patrick , Pósfai Mihály , Hirt Ann M. , Duchamp Martial , Dunin-Borkowski Rafal E. , Faivre Damien 
Published: March 2017

AbstractMagnetite nanoparticles exhibit magnetic properties that are size and organization dependent and, for applications that rely on their magnetic state, they usually have to be monodisperse. Forming such particles, however, has remained a challenge. Here, we synthesize 40 nm particles of magnetite in the presence of polyarginine and show that they are composed of 10 nm building blocks, yet diffract like single crystals. We use both bulk magnetic measurements and magnetic induction maps recorded from individual particles using off-axis electron holography to show that each 40 nm particle typically contains a single magnetic domain. The magnetic state is therefore determined primarily by the size of the superstructure and not by the sizes of the constituent sub-units. Our results fundamentally demonstrate the structure – property relationship in a magnetic mesoparticle.
Three dimensional characterization of GaN-based light emitting diode grown on patterned sapphire substrate by confocal Raman and photoluminescence spectromicroscopy
Authors: Li Heng , Cheng Hui-Yu , Chen Wei-Liang , Huang Yi-Hsin , Li Chi-Kang , Chang Chiao-Yun , Wu Yuh-Renn , Lu Tien-Chang , Chang Yu-Ming 
Published: March 2017

AbstractWe performed depth-resolved PL and Raman spectral mappings of a GaN-based LED structure grown on a patterned sapphire substrate (PSS). Our results showed that the Raman mapping in the PSS-GaN heterointerface and the PL mapping in the InxGa1−xN/GaN MQWs active layer are spatially correlated. Based on the 3D construction of E2(high) Raman peak intensity and frequency shift, V-shaped pits in the MQWs can be traced down to the dislocations originated in the cone tip area of PSS. Detail analysis of the PL peak distribution further revealed that the indium composition in the MQWs is related to the residual strain propagating from the PSS-GaN heterointerface toward the LED surface. Numerical simulation based on the indium composition distribution also led to a radiative recombination rate distribution that shows agreement with the experimental PL intensity distribution in the InxGa1−xN/GaN MQWs active layer.
Thermochromic Luminescent Materials and Multi-Emission Bands in d10 Clusters
Authors: Gautier Romain , Latouche Camille , Paris Michael , Massuyeau Florian 
Published: March 2017

AbstractThermochromic luminescent compounds with d10 metal ions are interesting materials for applications such as sensors or display devices. However, these properties are difficult to predict prior to their synthesis. In this communication, we investigated materials with structural assemblies known to be responsible of distinct luminescence mechanisms and show that they can be interesting potential thermometers. Thus, we compared the synthesis of a zinc halide and a copper halide based compounds which only differ in their ability to create clusters with metallophilic interactions. The compounds synthesized by hydrothermal method have been structurally characterized by Single-crystal X-ray diffraction, Solid-State NMR, FTIR, UV-Visible spectroscopy, thermal analysis and EPR. The photoluminescence properties of the two materials have been characterized at different temperatures. The copper bromide compound shows luminescence thermochromism in a wide spectrum of colors owing to the formation of clusters generating multi-emission bands while the zinc bromide exhibits a single emission band and no thermochromism.
Rheotaxis in the Ediacaran epibenthic organism Parvancorina from South Australia
Authors: Paterson John R. , Gehling James G. , Droser Mary L. , Bicknell Russell D. C. 
Published: March 2017

AbstractDiverse interpretations of Ediacaran organisms arise not only from their enigmatic body plans, but also from confusion surrounding the sedimentary environments they inhabited and the processes responsible for their preservation. Excavation of Ediacaran bedding surfaces of the Rawnsley Quartzite in South Australia has provided the opportunity to study the community structure of the Ediacara biota, as well as the autecology of individual organisms. Analysis of two bedding surfaces preserving large numbers of Parvancorina illustrates that individuals display a preferred, unidirectional orientation aligned with current, as indicated by the identified current proxies: tool marks, overfolded edges of Dickinsonia, felled fronds and drag structures generated by uprooted frond holdfasts. Taphonomic and morphological evidence suggests that the preferred orientations of Parvancorina individuals are not the result of passive current alignment, but represent a rheotactic response at some stage during their life cycle. These results illustrate a previously unrecognized life mode for an Ediacaran organism and arguably the oldest known example of rheotaxis in the fossil record. The morphology and previously suggested phylogenetic affinities of Parvancorina are also re-evaluated. Apart from possessing a bilaterally symmetrical body, there are no unequivocal morphological characters to support placement of Parvancorina within the Euarthropoda or even the Bilateria.
Irreversibility transition of colloidal polycrystals under cyclic deformation
Authors: Jana Pritam Kumar , Alava Mikko J. , Zapperi Stefano 
Published: March 2017

AbstractCyclically loaded disordered particle systems, such as granular packings and amorphous media, display a non-equilibrium phase transition towards irreversibility. Here, we investigate numerically the cyclic deformation of a colloidal polycrystal with impurities and reveal a transition to irreversible behavior driven by the displacement of dislocations. At the phase transition we observe enhanced particle diffusion, system size effects and broadly distributed strain bursts. In addition to provide an analogy between the deformation of amorphous and polycrystalline materials, our results allow to reinterpret Zener pinning of grain boundaries as a way to prevent the onset of irreversible crystal ordering.