bluuebunny/crossref_metadata_2025 huggingface dataset:
The All Sky Young Association (ASYA): a New Young Association
Authors: Torres C. A. O. , Quast G. R. , Montes D.
Published: January 2016

To analyze the SACY (Search for Associations Containing Young stars) survey we developed a method to find young associations and to define their high probability members. These bona fide members enable to obtain the kinematical and the physical properties of each association in a proper way. Recently we noted a concentration in the UV plane and we found a new association we are calling ASYA (All Sky Young Association) for its overall distribution in the sky with a total of 38 bonafide members and an estimated age of 110 Myr, the oldest young association found in the SACY survey. We present here its kinematical, space and Li distributions and its HR diagram.
Kinematics of M dwarfs in the CARMENES Input Catalogue: Membership in Young Moving Groups
Authors: Montes D. , Caballero J. A. , Gallardo I. , Cortés-Contreras M. , Alonso-Floriano F. J.
Published: January 2016

We present a detailed study of the kinematics of M dwarfs in the CARMENES (Calar Alto high-Resolution search for M dwarfs with Exoearths with Near-infrared and optical Échelle Spectrographs) input catalog. We have selected all M dwarfs with known parallactic distance or a good photometric distance estimation, precise proper motion in the literature or as determined by us, and radial velocity measurements. Using these parameters, we computed the M dwarfs galactic space motions (U, V, W). For the stars with U and V velocity components inside or near the boundaries that determine the young disk population, we have analyzed the possible membership in the classical moving groups and nearby loose associations with ages between 10 and 600 Myr. For the candidate members, we have compiled information available in the literature in order to constrain their membership by applying other age-dating methods.
Cloud Driven Variability on Young Brown Dwarfs and Giant Exoplanets
Authors: Biller Beth
Published: January 2016

Variability has now been robustly observed in a range of L and T type field brown dwarfs, primarily at near-IR and mid-IR wavelengths. The probable cause of this variability is surface inhomogeneities in the clouds of these objects, causing a semi-periodic variability signal when combined with the rotational modulation from the 3-12 hour period expected for these objects. Variability at similar or even higher amplitudes may be expected for young brown dwarfs and giant exoplanets, which share similar Teff as field brown dwarfs, but have considerably lower surface gravities. Variability studies of these objects relative to old field objects is then a direct probe of the effects of surface gravity on atmospheric structure. Here I discuss ongoing efforts to detect variability from these young objects, both for free-floating objects and companions to stars, including preliminary results from an ongoing survey of young, low surface gravity objects with NTT SOFI.
Lithium Depletion Boundary Ages of Young Stars: Inconsistencies in Pre-Main Sequence Models
Authors: Song Inseok
Published: January 2016

For proper interpretations of various phenomena in young stars and planetary systems, knowledge of accurate stellar ages is very important. Among a handful of age dating methods commonly used for young (≲500 Myr) stars, lithium depletion boundary (LDB) ages have recently become the most cited and accepted age estimates. However, because of inconsistencies in theoretical evolutionary models, especially for lithium depletion calculations, one has to be cautious in using LDB ages. For a given luminosity, the lithium depletion process is too slow, causing LDB ages to appear older. Various stellar processes affect the surface lithium abundance, and these effects include star spots, accretion history, and magnetic fields. Until we have a self-consistent theoretical evolutionary model for young stars including all relevant stellar effects, caution should be taken when LDB ages are used.
Generation of coherent spin-wave modes in yttrium iron garnet microdiscs by spin–orbit torque
Authors: Collet M. , de Milly X. , d’Allivy Kelly O. , Naletov V. V. , Bernard R. , Bortolotti P. , Ben Youssef J. , Demidov V. E. , Demokritov S. O. , Prieto J. L. , Muñoz M. , Cros V. , Anane A. , de Loubens G. , Klein O.
Published: January 2016

In recent years, spin–orbit effects have been widely used to produce and detect spin currents in spintronic devices. The peculiar symmetry of the spin Hall effect allows creation of a spin accumulation at the interface between a metal with strong spin–orbit interaction and a magnetic insulator, which can lead to a net pure spin current flowing from the metal into the insulator. This spin current applies a torque on the magnetization, which can eventually be driven into steady motion. Tailoring this experiment on extended films has proven to be elusive, probably due to mode competition. This requires the reduction of both the thickness and lateral size to reach full damping compensation. Here we show clear evidence of coherent spin–orbit torque-induced auto-oscillation in micron-sized yttrium iron garnet discs of thickness 20 nm. Our results emphasize the key role of quasi-degenerate spin-wave modes, which increase the threshold current.
Polaronic metal state at the LaAlO3/SrTiO3 interface
Authors: Cancellieri C. , Mishchenko A. S. , Aschauer U. , Filippetti A. , Faber C. , Barišić O. S. , Rogalev V. A. , Schmitt T. , Nagaosa N. , Strocov V. N.
Published: January 2016

Interplay of spin, charge, orbital and lattice degrees of freedom in oxide heterostructures results in a plethora of fascinating properties, which can be exploited in new generations of electronic devices with enhanced functionalities. The paradigm example is the interface between the two band insulators LaAlO3 and SrTiO3 that hosts a two-dimensional electron system. Apart from the mobile charge carriers, this system exhibits a range of intriguing properties such as field effect, superconductivity and ferromagnetism, whose fundamental origins are still debated. Here we use soft-X-ray angle-resolved photoelectron spectroscopy to penetrate through the LaAlO3 overlayer and access charge carriers at the buried interface. The experimental spectral function directly identifies the interface charge carriers as large polarons, emerging from coupling of charge and lattice degrees of freedom, and involving two phonons of different energy and thermal activity. This phenomenon fundamentally limits the carrier mobility and explains its puzzling drop at high temperatures.
Wavelength-tunable entangled photons from silicon-integrated III–V quantum dots
Authors: Chen Yan , Zhang Jiaxiang , Zopf Michael , Jung Kyubong , Zhang Yang , Keil Robert , Ding Fei , Schmidt Oliver G.
Published: January 2016

Many of the quantum information applications rely on indistinguishable sources of polarization-entangled photons. Semiconductor quantum dots are among the leading candidates for a deterministic entangled photon source; however, due to their random growth nature, it is impossible to find different quantum dots emitting entangled photons with identical wavelengths. The wavelength tunability has therefore become a fundamental requirement for a number of envisioned applications, for example, nesting different dots via the entanglement swapping and interfacing dots with cavities/atoms. Here we report the generation of wavelength-tunable entangled photons from on-chip integrated InAs/GaAs quantum dots. With a novel anisotropic strain engineering technique based on PMN-PT/silicon micro-electromechanical system, we can recover the quantum dot electronic symmetry at different exciton emission wavelengths. Together with a footprint of several hundred microns, our device facilitates the scalable integration of indistinguishable entangled photon sources on-chip, and therefore removes a major stumbling block to the quantum-dot-based solid-state quantum information platforms.
Harnessing spin precession with dissipation
Authors: Crisan A. D. , Datta S. , Viennot J. J. , Delbecq M. R. , Cottet A. , Kontos T.
Published: January 2016

Non-collinear spin transport is at the heart of spin or magnetization control in spintronics devices. The use of nanoscale conductors exhibiting quantum effects in transport could provide new paths for that purpose. Here we study non-collinear spin transport in a quantum dot. We use a device made out of a single-wall carbon nanotube connected to orthogonal ferromagnetic electrodes. In the spin transport signals, we observe signatures of out of equilibrium spin precession that are electrically tunable through dissipation. This could provide a new path to harness spin precession in nanoscale conductors.
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
Authors: Eloe-Fadrosh Emiley A. , Paez-Espino David , Jarett Jessica , Dunfield Peter F. , Hedlund Brian P. , Dekas Anne E. , Grasby Stephen E. , Brady Allyson L. , Dong Hailiang , Briggs Brandon R. , Li Wen-Jun , Goudeau Danielle , Malmstrom Rex , Pati Amrita , Pett-Ridge Jennifer , Rubin Edward M. , Woyke Tanja , Kyrpides Nikos C. , Ivanova Natalia N.
Published: January 2016

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.
High-contrast and fast electrochromic switching enabled by plasmonics
Authors: Xu Ting , Walter Erich C. , Agrawal Amit , Bohn Christopher , Velmurugan Jeyavel , Zhu Wenqi , Lezec Henri J. , Talin A. Alec
Published: January 2016

With vibrant colours and simple, room-temperature processing methods, electrochromic polymers have attracted attention as active materials for flexible, low-power-consuming devices. However, slow switching speeds in devices realized to date, as well as the complexity of having to combine several distinct polymers to achieve a full-colour gamut, have limited electrochromic materials to niche applications. Here we achieve fast, high-contrast electrochromic switching by significantly enhancing the interaction of light—propagating as deep-subwavelength-confined surface plasmon polaritons through arrays of metallic nanoslits, with an electrochromic polymer—present as an ultra-thin coating on the slit sidewalls. The switchable configuration retains the short temporal charge-diffusion characteristics of thin electrochromic films, while maintaining the high optical contrast associated with thicker electrochromic coatings. We further demonstrate that by controlling the pitch of the nanoslit arrays, it is possible to achieve a full-colour response with high contrast and fast switching speeds, while relying on just one electrochromic polymer.
Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types
Authors: Wang Cheng , Gu Yayun , Zhang Kai , Xie Kaipeng , Zhu Meng , Dai Ningbin , Jiang Yue , Guo Xuejiang , Liu Mingxi , Dai Juncheng , Wu Linxiang , Jin Guangfu , Ma Hongxia , Jiang Tao , Yin Rong , Xia Yankai , Liu Li , Wang Shouyu , Shen Bin , Huo Ran , Wang Qianghu , Xu Lin , Yang Liuqing , Huang Xingxu , Shen Hongbing , Sha Jiahao , Hu Zhibin
Published: January 2016

Cancer-testis (CT) genes represent the similarity between the processes of spermatogenesis and tumorigenesis. It is possible that their selective expression pattern can help identify driver genes in cancer. In this study, we integrate transcriptomics data from multiple databases and systematically identify 876 new CT genes in 19 cancer types. We explore their relationship with testis-specific regulatory elements. We propose that extremely highly expressed CT genes (EECTGs) are potential drivers activated through epigenetic mechanisms. We find mutually exclusive associations between EECTGs and somatic mutations in mutated genes, such as PIK3CA in breast cancer. We also provide evidence that promoter demethylation and close non-coding RNAs (namely, CT-ncRNAs) may be two mechanisms to reactivate EECTG gene expression. We show that the meiosis-related EECTG (MEIOB) and its nearby CT-ncRNA have a role in tumorigenesis in lung adenocarcinoma. Our findings provide methods for identifying epigenetic-driver genes of cancer, which could serve as targets of future cancer therapies.
Direct growth of single-crystalline III–V semiconductors on amorphous substrates
Authors: Chen Kevin , Kapadia Rehan , Harker Audrey , Desai Sujay , Seuk Kang Jeong , Chuang Steven , Tosun Mahmut , Sutter-Fella Carolin M. , Tsang Michael , Zeng Yuping , Kiriya Daisuke , Hazra Jubin , Madhvapathy Surabhi Rao , Hettick Mark , Chen Yu-Ze , Mastandrea James , Amani Matin , Cabrini Stefano , Chueh Yu-Lun , Ager III Joel W. , Chrzan Daryl C. , Javey Ali
Published: January 2016

The III–V compound semiconductors exhibit superb electronic and optoelectronic properties. Traditionally, closely lattice-matched epitaxial substrates have been required for the growth of high-quality single-crystal III–V thin films and patterned microstructures. To remove this materials constraint, here we introduce a growth mode that enables direct writing of single-crystalline III–V’s on amorphous substrates, thus further expanding their utility for various applications. The process utilizes templated liquid-phase crystal growth that results in user-tunable, patterned micro and nanostructures of single-crystalline III–V’s of up to tens of micrometres in lateral dimensions. InP is chosen as a model material system owing to its technological importance. The patterned InP single crystals are configured as high-performance transistors and photodetectors directly on amorphous SiO2 growth substrates, with performance matching state-of-the-art epitaxially grown devices. The work presents an important advance towards universal integration of III–V’s on application-specific substrates by direct growth.
Human IgG1 antibodies suppress angiogenesis in a target-independent manner
Authors: Bogdanovich Sasha , Kim Younghee , Mizutani Takeshi , Yasuma Reo , Tudisco Laura , Cicatiello Valeria , Bastos-Carvalho Ana , Kerur Nagaraj , Hirano Yoshio , Baffi Judit Z , Tarallo Valeria , Li Shengjian , Yasuma Tetsuhiro , Arpitha Parthasarathy , Fowler Benjamin J , Wright Charles B , Apicella Ivana , Greco Adelaide , Brunetti Arturo , Ruvo Menotti , Sandomenico Annamaria , Nozaki Miho , Ijima Ryo , Kaneko Hiroki , Ogura Yuichiro , Terasaki Hiroko , Ambati Balamurali K , Leusen Jeanette HW , Langdon Wallace Y , Clark Michael R , Armour Kathryn L , Bruhns Pierre , Verbeek J Sjef , Gelfand Bradley D , De Falco Sandro , Ambati Jayakrishna
Published: January 2016

Aberrant angiogenesis is implicated in diseases affecting nearly 10% of the world’s population. The most widely used anti-angiogenic drug is bevacizumab, a humanized IgG1 monoclonal antibody that targets human VEGFA. Although bevacizumab does not recognize mouse Vegfa, it inhibits angiogenesis in mice. Here we show bevacizumab suppressed angiogenesis in three mouse models not via Vegfa blockade but rather Fc-mediated signaling through FcγRI (CD64) and c-Cbl, impairing macrophage migration. Other approved humanized or human IgG1 antibodies without mouse targets (adalimumab, alemtuzumab, ofatumumab, omalizumab, palivizumab and tocilizumab), mouse IgG2a, and overexpression of human IgG1-Fc or mouse IgG2a-Fc, also inhibited angiogenesis in wild-type and FcγR humanized mice. This anti-angiogenic effect was abolished by Fcgr1 ablation or knockdown, Fc cleavage, IgG-Fc inhibition, disruption of Fc-FcγR interaction, or elimination of FcRγ-initated signaling. Furthermore, bevacizumab’s Fc region potentiated its anti-angiogenic activity in humanized VEGFA mice. Finally, mice deficient in FcγRI exhibited increased developmental and pathological angiogenesis. These findings reveal an unexpected anti-angiogenic function for FcγRI and a potentially concerning off-target effect of hIgG1 therapies.
The role of MicroRNAs in human cancer
Authors: Peng Yong , Croce Carlo M
Published: January 2016

MicroRNAs (miRNAs) are endogenous, small non-coding RNAs that function in regulation of gene expression. Compelling evidences have demonstrated that miRNA expression is dysregulated in human cancer through various mechanisms, including amplification or deletion of miRNA genes, abnormal transcriptional control of miRNAs, dysregulated epigenetic changes and defects in the miRNA biogenesis machinery. MiRNAs may function as either oncogenes or tumor suppressors under certain conditions. The dysregulated miRNAs have been shown to affect the hallmarks of cancer, including sustaining proliferative signaling, evading growth suppressors, resisting cell death, activating invasion and metastasis, and inducing angiogenesis. An increasing number of studies have identified miRNAs as potential biomarkers for human cancer diagnosis, prognosis and therapeutic targets or tools, which needs further investigation and validation. In this review, we focus on how miRNAs regulate the development of human tumors by acting as tumor suppressors or oncogenes.
Controlled Phase and Tunable Magnetism in Ordered Iron Oxide Nanotube Arrays Prepared by Atomic Layer Deposition
Authors: Zhang Yijun , Liu Ming , Peng Bin , Zhou Ziyao , Chen Xing , Yang Shu-Ming , Jiang Zhuang-De , Zhang Jie , Ren Wei , Ye Zuo-Guang
Published: January 2016

Highly-ordered and conformal iron oxide nanotube arrays on an atomic scale are successfully prepared by atomic layer deposition (ALD) with controlled oxidization states and tunable magnetic properties between superparamagnetism and ferrimagnetism. Non-magnetic α-Fe2O3 and superparamagnetic Fe3O4 with a blocking temperature of 120 K are in-situ obtained by finely controlling the oxidation reaction. Both of them exhibit a very small grain size of only several nanometers due to the nature of atom-by-atom growth of the ALD technique. Post-annealing α-Fe2O3 in a reducing atmosphere leads to the formation of the spinel Fe3O4 phase which displays a distinct ferrimagnetic anisotropy and the Verwey metal-insulator transition that usually takes place only in single crystal magnetite or thick epitaxial films at low temperatures. The ALD deposition of iron oxide with well-controlled phase and tunable magnetism demonstrated in this work provides a promising opportunity for the fabrication of 3D nano-devices to be used in catalysis, spintronics, microelectronics, data storages and bio-applications.
The Hydrophobic Effect in Solute Partitioning and Interfacial Tension
Authors: Jackson Meyer B.
Published: January 2016

Studies of the partitioning of hydrophobic solutes between water and nonpolar solvents provide estimates for the energy cost of creating hydrophobic-water contacts. This energy is a factor of three lower than the work of adhesion derived from interfacial tension measurements. This discrepancy noted by Tanford in 1979 is widely viewed as a serious challenge to our understanding of hydrophobic interactions. However, the interfacial energy of a water-alkane interface depends on chain length. A simple analysis of published data shows that the loss of rotational freedom of an alkane chain at an interface accounts quantitatively for the length-dependent contribution to interfacial tension, leaving a length-independent contribution very close to the free energy of transfer per unit of solvent accessible surface area. This analysis thus clarifies the discrepancy between the thermodynamic and interfacial tension measurements of hydrophobic interaction energy. Alkanes do not loose rotational freedom when transferred between two different liquid phases but they do at an interface. This reconciles the difference between microscopic and macroscopic measurements. Like the partitioning free energy, the work of adhesion also has a large entropy and small enthalpy at 20 oC.
Historical photographs revisited: A case study for dating and characterizing recent loss of coral cover on the inshore Great Barrier Reef
Authors: Clark Tara R. , Leonard Nicole D. , Zhao Jian-xin , Brodie Jon , McCook Laurence J. , Wachenfeld David R. , Duc Nguyen Ai , Markham Hannah L. , Pandolfi John M.
Published: January 2016

Long-term data with high-precision chronology are essential to elucidate past ecological changes on coral reefs beyond the period of modern-day monitoring programs. In 2012 we revisited two inshore reefs within the central Great Barrier Reef, where a series of historical photographs document a loss of hard coral cover between c.1890–1994 AD. Here we use an integrated approach that includes high-precision U-Th dating specifically tailored for determining the age of extremely young corals to provide a robust, objective characterisation of ecological transition. The timing of mortality for most of the dead in situ corals sampled from the historical photograph locations was found to coincide with major flood events in 1990–1991 at Bramston Reef and 1970 and 2008 at Stone Island. Evidence of some recovery was found at Bramston Reef with living coral genera similar to what was described in c.1890 present in 2012. In contrast, very little sign of coral re-establishment was found at Stone Island suggesting delayed recovery. These results provide a valuable reference point for managers to continue monitoring the recovery (or lack thereof) of coral communities at these reefs.
Activating mutations in CTNNB1 in aldosterone producing adenomas
Authors: Åkerström Tobias , Maharjan Rajani , Sven Willenberg Holger , Cupisti Kenko , Ip Julian , Moser Ana , Stålberg Peter , Robinson Bruce , Alexander Iwen K. , Dralle Henning , Walz Martin K. , Lehnert Hendrik , Sidhu Stan , Gomez-Sanchez Celso , Hellman Per , Björklund Peyman
Published: January 2016

Primary aldosteronism (PA) is the most common cause of secondary hypertension with a prevalence of 5–10% in unreferred hypertensive patients. Aldosterone producing adenomas (APAs) constitute a large proportion of PA cases and represent a surgically correctable form of the disease. The WNT signaling pathway is activated in APAs. In other tumors, a frequent cause of aberrant WNT signaling is mutation in theCTNNB1gene coding for β-catenin. Our objective was to screen forCTNNB1mutations in a well-characterized cohort of 198 APAs. SomaticCTNNB1mutations were detected in 5.1% of the tumors, occurring mutually exclusive from mutations inKCNJ5, ATP1A1, ATP2B3andCACNA1D. All of the observed mutations altered serine/threonine residues in the GSK3β binding domain in exon 3. The mutations were associated with stabilized β-catenin and increased AXIN2 expression, suggesting activation of WNT signaling. By CYP11B2 mRNA expression, CYP11B2 protein expression and direct measurement of aldosterone in tumor tissue, we confirmed the ability for aldosterone production. This report provides compelling evidence that aberrant WNT signaling caused by mutations inCTNNB1occur in APAs. This also suggests that other mechanisms that constitutively activate the WNT pathway may be important in APA formation.
Short range smectic order driving long range nematic order: example of cuprates
Authors: Markiewicz R. S. , Lorenzana J. , Seibold G. , Bansil A.
Published: January 2016

We present a model for describing the combined presence of nematic and ‘smectic’ or stripe-like orders seen in recent scanning tunneling microscopy (STM) experiments on cuprates. The smectic order is treated as an electronic charge density wave with an associated Peierls distortion or a ‘Pomeranchuk wave’. This primary order is restricted to nanoscale domains by disorder effects, while the secondary coupling to strain generates the nematic order with a considerably longer range. A variety of experimental results are shown to be consistent with our theoretical predictions.
Correlating confocal microscopy and atomic force indentation reveals metastatic cancer cells stiffen during invasion into collagen I matrices
Authors: Staunton Jack R. , Doss Bryant L. , Lindsay Stuart , Ros Robert
Published: January 2016

Mechanical interactions between cells and their microenvironment dictate cell phenotype and behavior, calling for cell mechanics measurements in three-dimensional (3D) extracellular matrices (ECM). Here we describe a novel technique for quantitative mechanical characterization of soft, heterogeneous samples in 3D. The technique is based on the integration of atomic force microscopy (AFM) based deep indentation, confocal fluorescence microscopy, finite element (FE) simulations and analytical modeling. With this method, the force response of a cell embedded in 3D ECM can be decoupled from that of its surroundings, enabling quantitative determination of the elastic properties of both the cell and the matrix. We applied the technique to the quantification of the elastic properties of metastatic breast adenocarcinoma cells invading into collagen hydrogels. We found that actively invading and fully embedded cells are significantly stiffer than cells remaining on top of the collagen, a clear example of phenotypical change in response to the 3D environment. Treatment with Rho-associated protein kinase (ROCK) inhibitor significantly reduces this stiffening, indicating that actomyosin contractility plays a major role in the initial steps of metastatic invasion.
Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite
Authors: Cobbold Simon A. , Santos Joana M. , Ochoa Alejandro , Perlman David H. , Llinás Manuel
Published: January 2016

Lysine acetylation is a ubiquitous post-translational modification in many organisms including the malaria parasite Plasmodium falciparum, yet the full extent of acetylation across the parasite proteome remains unresolved. Moreover, the functional significance of acetylation or how specific acetyl-lysine sites are regulated is largely unknown. Here we report a seven-fold expansion of the known parasite ‘acetylome’, characterizing 2,876 acetylation sites on 1,146 proteins. We observe that lysine acetylation targets a diverse range of protein complexes and is particularly enriched within the Apicomplexan AP2 (ApiAP2) DNA-binding protein family. Using quantitative proteomics we determined that artificial perturbation of the acetate/acetyl-CoA balance alters the acetyl-lysine occupancy of several ApiAP2 DNA-binding proteins and related transcriptional proteins. This metabolic signaling could mediate significant downstream transcriptional responses, as we show that acetylation of an ApiAP2 DNA-binding domain ablates its DNA-binding propensity. Lastly, we investigated the acetyl-lysine targets of each class of lysine deacetylase in order to begin to explore how each class of enzyme contributes to regulating the P. falciparum acetylome.
A cotton miRNA is involved in regulation of plant response to salt stress
Authors: Gao Shuai , Yang Lu , Zeng Hou Qing , Zhou Zhao Sheng , Yang Zhi Min , Li Hua , Sun Di , Xie Fuliang , Zhang Baohong
Published: January 2016

The present study functionally identified a new microRNA (microRNA ovual line 5, miRNVL5) with its target geneGhCHRfrom cotton (Gossypium hirsutum). The sequence of miRNVL5 precursor is 104 nt long, with a well developed secondary structure. GhCHR contains two DC1 and three PHD Cys/His-rich domains, suggesting thatGhCHRencodes a zinc-finger domain-containing transcription factor. miRNVL5 andGhCHRexpress at various developmental stages of cotton. Under salt stress (50–400 mM NaCl), miRNVL5 expression was repressed, with concomitant high expression ofGhCHRin cotton seedlings. Ectopic expression ofGhCHRinArabidopsisconferred salt stress tolerance by reducing Na+accumulation in plants and improving primary root growth and biomass. Interestingly,Arabidopsisconstitutively expressing miRNVL5 showed hypersensitivity to salt stress. AGhCHRorthorlous gene At2g44380 fromArabidopsisthat can be cleaved by miRNVL5 was identified by degradome sequencing, but no confidential miRNVL5 homologs inArabidopsishave been identified. Microarray analysis of miRNVL5 transgenicArabidopsisshowed six downstream genes (CBF1,CBF2,CBF3,ERF4,AT3G22920andAT3G49200), which were induced by salt stress in wild-type but repressed in miRNVL5-expressingArabidopsis. These results indicate that miRNVL5 is involved in regulation of plant response to salt stress.
Natural motion trajectory enhances the coding of speed in primate extrastriate cortex
Authors: Davies Amanda J. , Chaplin Tristan A. , Rosa Marcello G. P. , Yu Hsin-Hao
Published: January 2016

The ability to estimate the speed of an object irrespective of size or texture is a crucial function of the visual system. However, previous studies have suggested that the neuronal coding of speed in the middle temporal area (MT, a key cortical area for motion analysis in primates) is ambiguous, with most neurons changing their speed tuning depending on the spatial frequency (SF) of a visual pattern. Here we demonstrate that the ability of MT neurons to encode speed is markedly improved when stimuli follow a trajectory across the visual field, prior to entering their receptive fields. We also show that this effect is much less marked in the primary visual area. These results indicate that MT neurons build up on computations performed at earlier levels of the visual system to provide accurate coding of speed in natural situations and provide additional evidence that nonlinear pooling underlie motion processing.
Selection of suitable reference genes for qRT-PCR normalization during leaf development and hormonal stimuli in tea plant (Camellia sinensis)
Authors: Wu Zhi-Jun , Tian Chang , Jiang Qian , Li Xing-Hui , Zhuang Jing
Published: January 2016

Tea plant (Camellia sinensis) leaf is an important non-alcoholic beverage resource. The application of quantitative real time polymerase chain reaction (qRT-PCR) has a profound significance for the gene expression studies of tea plant, especially when applied to tea leaf development and metabolism. In this study, nine candidate reference genes (i.e.,CsACT7,CsEF-1α,CseIF-4α, CsGAPDH,CsPP2A,CsSAND,CsTBP,CsTIP41andCsTUB) ofC. sinensiswere cloned. The quantitative expression data of these genes were investigated in five tea leaf developmental stages (i.e., 1st, 2nd, 3rd, 4th and older leaves) and normal growth tea leaves subjected to five hormonal stimuli (i.e., ABA, GA, IAA, MeJA and SA) and gene expression stability was calculated using three common statistical algorithms, namely, geNorm, NormFinder and Bestkeeper. Results indicated thatCsTBPandCsTIP41were the most stable genes in tea leaf development andCsTBPwas the best gene under hormonal stimuli; by contrast,CsGAPDHandCsTUBgenes showed the least stability. The gene expression profile ofCsNAMgene was analyzed to confirm the validity of the reference genes in this study. Our data provide basis for the selection of reference genes for future biological research in the leaf development and hormonal stimuli ofC. sinensis.
Generation of 2,000 breast cancer metabolic landscapes reveals a poor prognosis group with active serotonin production
Authors: Leoncikas Vytautas , Wu Huihai , Ward Lara T. , Kierzek Andrzej M. , Plant Nick J.
Published: January 2016

A major roadblock in the effective treatment of cancers is their heterogeneity, whereby multiple molecular landscapes are classified as a single disease. To explore the contribution of cellular metabolism to cancer heterogeneity, we analyse the Metabric dataset, a landmark genomic and transcriptomic study of 2,000 individual breast tumours, in the context of the human genome-scale metabolic network. We create personalized metabolic landscapes for each tumour by exploring sets of active reactions that satisfy constraints derived from human biochemistry and maximize congruency with the Metabric transcriptome data. Classification of the personalized landscapes derived from 997 tumour samples within the Metabric discovery dataset reveals a novel poor prognosis cluster, reproducible in the 995-sample validation dataset. We experimentally follow mechanistic hypotheses resulting from the computational study and establish that active serotonin production is a major metabolic feature of the poor prognosis group. These data support the reconsideration of concomitant serotonin-specific uptake inhibitors treatment during breast cancer chemotherapy.
Skeletal muscle Heat shock protein 60 increases after endurance training and induces peroxisome proliferator-activated receptor gamma coactivator 1 α1 expression
Authors: Barone Rosario , Macaluso Filippo , Sangiorgi Claudia , Campanella Claudia , Marino Gammazza Antonella , Moresi Viviana , Coletti Dario , Conway de Macario Everly , Macario Alberto JL , Cappello Francesco , Adamo Sergio , Farina Felicia , Zummo Giovanni , Di Felice Valentina
Published: January 2016

Heat shock protein 60 (Hsp60) is a chaperone localizing in skeletal muscle mitochondria, whose role is poorly understood. In the present study, the levels of Hsp60 in fibres of the entire posterior group of hindlimb muscles (gastrocnemius, soleus and plantaris) were evaluated in mice after completing a 6-week endurance training program. The correlation between Hsp60 levels and the expression of four isoforms of peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC1α) were investigated only in soleus. Short-term overexpression of hsp60, achieved by in vitro plasmid transfection, was then performed to determine whether this chaperone could have a role in the activation of the expression levels of PGC1α isoforms. The levels of Hsp60 protein were fibre-type specific in the posterior muscles and endurance training increased its content in type I muscle fibers. Concomitantly with the increased levels of Hsp60 released in the blood stream of trained mice, mitochondrial copy number and the expression of three isoforms of PGC1α increased. Overexpressing hsp60 in cultured myoblasts induced only the expression of PGC1 1α, suggesting a correlation between Hsp60 overexpression and PGC1 1 α activation.
A microbial carbonate response in synchrony with the end-Triassic mass extinction across the SW UK
Authors: Ibarra Yadira , Corsetti Frank A. , Greene Sarah E. , Bottjer David J.
Published: January 2016

The eruption of the Central Atlantic Magmatic Province (CAMP)—the largest igneous province known—has been linked to the end-Triassic mass extinction event, however reconciling the response of the biosphere (at local and nonlocal scales) to potential CAMP-induced geochemical excursions has remained challenging. Here we present a combined sedimentary and biological response to an ecosystem collapse in Triassic-Jurassic strata of the southwest United Kingdom (SW UK) expressed as widely distributed carbonate microbialites and associated biogeochemical facies. The microbialites (1) occur at the same stratigraphic level as the mass extinction extinction, (2) host a negative isotope excursion in δ13Corg found in other successions around the world and (3) co-occur with an acme of prasinophyte algae ‘disaster taxa’ also dominant in Triassic-Jurassic boundary strata of other European sections. Although the duration of microbialite deposition is uncertain, it is likely that they formed rapidly (perhaps fewer than ten thousand years), thus providing a high-resolution glimpse into the initial carbon isotopic perturbation coincident with the end-Triassic mass extinction. These findings indicate microbialites from the SW UK capture a nonlocal biosedimentary response to the cascading effects of massive volcanism and add to the current understanding of paleoecology in the aftermath of the end-Triassic extinction.
Regulation of human cerebro-microvascular endothelial baso-lateral adhesion and barrier function by S1P through dual involvement of S1P1 and S1P2 receptors
Authors: Wiltshire Rachael , Nelson Vicky , Kho Dan Ting , Angel Catherine E. , O’Carroll Simon J. , Graham E. Scott
Published: January 2016

Herein we show that S1P rapidly and acutely reduces the focal adhesion strength and barrier tightness of brain endothelial cells. xCELLigence biosensor technology was used to measure focal adhesion, which was reduced by S1P acutely and this response was mediated through both S1P1 and S1P2 receptors. S1P increased secretion of several pro-inflammatory mediators from brain endothelial cells. However, the magnitude of this response was small in comparison to that mediated by TNFα or IL-1β. Furthermore, S1P did not significantly increase cell-surface expression of any key cell adhesion molecules involved in leukocyte recruitment, included ICAM-1 and VCAM-1. Finally, we reveal that S1P acutely and dynamically regulates microvascular endothelial barrier tightness in a manner consistent with regulated rapid opening followed by closing and strengthening of the barrier. We hypothesise that the role of the S1P receptors in this process is not to cause barrier dysfunction, but is related to controlled opening of the endothelial junctions. This was revealed using real-time measurement of barrier integrity using ECIS ZΘ TEER technology and endothelial viability using xCELLigence technology. Finally, we show that these responses do not occur simply though the pharmacology of a single S1P receptor but involves coordinated action of S1P1 and S1P2 receptors.
Tcstv1 and Tcstv3 elongate telomeres of mouse ES cells
Authors: Zhang Qian , Dan Jiameng , Wang Hua , Guo Renpeng , Mao Jian , Fu Haifeng , Wei Xiawei , Liu Lin
Published: January 2016

Mouse embryonic stem cell (ESC) cultures exhibit a heterogeneous mixture of metastable cells sporadically entering the 2-cell (2C)-embryo-like state, critical for ESC potency. One of 2-cell genes, Zscan4, has been shown to be responsible for telomere maintenance, genomic stability and pluripotency of mouse ESCs. Functions of other 2C-genes in ESCs remain elusive. Here we show that 2C-genes Tcstv1 and Tcstv3 play a role in regulation of telomere lengths. Overexpression or knockdown Tcstv1 and Tcstv3 does not immediately affect proliferation, pluripotency and differentiation in vitro of ESCs. However, ectopic expression of Tcstv1 or Tcstv3 results in telomere elongation, whereas Tcstv1/3 knockdown shortens telomeres of ESCs. Overexpression of Tcstv1 or Tcstv3 does not alter telomere stability. Furthermore, Tcstv1 can increase Zscan4 protein levels and telomere recombination by telomere sister chromatid exchange (T-SCE). Depletion of Tcstv1/3 reduces Zscan4 protein levels. Together, Tcstv1 and Tcstv3 are involved in telomere maintenance that is required for long-term self-renewal of mouse ESCs. Our data also suggests that Tcstv1/3 may co-operate and stabilize Zscan4 protein but the molecular bases remain to be determined.
Schima superba outperforms other tree species by changing foliar chemical composition and shortening construction payback time when facilitated by shrubs
Authors: Liu Nan , Guo Qinfeng , Ren Hai , Sun Zhongyu
Published: January 2016

A 3.5-year field experiment was conducted in a subtropical degraded shrubland to assess how a nurse plant, the native shrubRhodomyrtus tomentosa, affects the growth of the target treesPinus elliottii,Schima superba,Castanopsis fissaandMichelia macclureiand to probe the intrinsic mechanisms from leaf chemical composition, construction cost (CC) and payback time aspects. We compared tree seedlings grown nearby shrub canopy (canopy subplots, CS) and in open space (open subplots, OS).S. superbain CS showed greater growth, whileP. elliottiiandM. macclureiwere lower when compared to the plants grown in the OS. The reduced levels of high-cost compounds (proteins) and increased levels of low-cost compounds (organic acids) caused reduced CC values forP. elliottiigrowing in CS. While, the levels of both low-cost minerals and high-cost proteins increased in CS such that CC values ofS. superbawere similar in OS and CS. Based on maximum photosynthetic rates,P. elliottiirequired a longer payback time to construct required carbon in canopy than in OS, but the opposite was true forS. superba. The information from this study can be used to evaluate the potential of different tree species in the reforestation of subtropical degraded shrublands.
Neuron-derived FGF10 ameliorates cerebral ischemia injury via inhibiting NF-κB-dependent neuroinflammation and activating PI3K/Akt survival signaling pathway in mice
Authors: Li Yong-Hua , Fu Hai-Long , Tian Mou-Li , Wang Yong-Qiang , Chen Wei , Cai Lin-Lin , Zhou Xu-Hui , Yuan Hong-Bin
Published: January 2016

FGF10 is a member of fibroblast growth factors (FGFs). We previously showed that FGF10 protects neuron against oxygen-glucose deprivation injury in vitro; however, the effect of FGF10 in ischemic stroke in vivo is unknown. In the present study, we showed that FGF10 was mainly expressed in neurons but not astrocytes and detected FGF10 in mouse cerebrospinal fluid. The FGF10 levels in neurons culture medium and cell lysate were much higher than those in astrocytes. FGF10 expression in brain tissue and FGF10 level in CSF were increased in mouse middle cerebral artery occlusion (MCAO) model. Administration of FGF10 into lateral cerebroventricle not only decreased MCAO-induced brain infarct volume and neurological deficit, but also reduced the number of TUNEL-positive cells and activities of Caspases. Moreover, FGF10 treatment depressed the triggered inflammatory factors (TNF-α and IL-6) and NF-κB signaling pathway and increased phosphorylation of PI3K/Akt signaling pathway. Blockade of PI3K/Akt signaling pathway by wortmannin and Akt1/2-kinase inhibitor, partly compromised the neuroprotection of FGF10. However, blockade of PI3K/Akt signaling pathway did not impair the anti-inflammation action of FGF10. Collectively, our results demonstrate that neuron-derived FGF10 ameliorates cerebral ischemia injury via inhibiting NF-κB-dependent neuroinflammation and activating PI3K/Akt survival signaling pathway in mice.
The dual function of PRMT1 in modulating epithelial-mesenchymal transition and cellular senescence in breast cancer cells through regulation of ZEB1
Authors: Gao Yanyan , Zhao Yaping , Zhang Juechao , Lu Yang , Liu Xin , Geng Pengyu , Huang Baiqu , Zhang Yu , Lu Jun
Published: January 2016

Although the involvement of protein arginine methyltransferase 1 (PRMT1) in tumorigenesis has been reported, its roles in breast cancer progression and metastasis has not been elucidated. Here we identified PRMT1 as a key regulator of the epithelial-mesenchymal transition (EMT) in breast cancer. We showed that the EMT program induced by PRMT1 endowed the human mammary epithelial cells with cancer stem cell properties. Moreover, PRMT1 promoted the migratory and invasive behaviors in breast cancer cells. We also demonstrated that abrogation of PRMT1 expression in breast cancer cells abated metastasis in vivo in mouse model. In addition, knockdown of PRMT1 arrested cell growth in G1 tetraploidy and induced cellular senescence. Mechanistically, PRMT1 impacted EMT process and cellular senescence by mediating the asymmetric dimethylation of arginine 3 of histone H4 (H4R3me2as) at the ZEB1 promoter to activate its transcription, indicating the essential roles of this epigenetic control both in EMT and in senescence. Thus, we unraveled a dual function of PRMT1 in modulation of both EMT and senescence via regulating ZEB1. This finding points to the potent value of PRMT1 as a dual therapeutic target for preventing metastasis and for inhibiting cancer cell growth in malignant breast cancer patients.
Distinct cognitive effects and underlying transcriptome changes upon inhibition of individual miRNAs in hippocampal neurons
Authors: Malmevik Josephine , Petri Rebecca , Knauff Pina , Brattås Per Ludvik , Åkerblom Malin , Jakobsson Johan
Published: January 2016

MicroRNAs (miRNA) are small, non-coding RNAs mediating post-transcriptional regulation of gene expression. miRNAs have recently been implicated in hippocampus-dependent functions such as learning and memory, although the roles of individual miRNAs in these processes remain largely unknown. Here, we achieved stable inhibition using AAV-delivered miRNA sponges of individual, highly expressed and brain-enriched miRNAs; miR-124, miR-9 and miR-34, in hippocampal neurons. Molecular and cognitive studies revealed a role for miR-124 in learning and memory. Inhibition of miR-124 resulted in an enhanced spatial learning and working memory capacity, potentially through altered levels of genes linked to synaptic plasticity and neuronal transmission. In contrast, inhibition of miR-9 or miR-34 led to a decreased capacity of spatial learning and of reference memory, respectively. On a molecular level, miR-9 inhibition resulted in altered expression of genes related to cell adhesion, endocytosis and cell death, while miR-34 inhibition caused transcriptome changes linked to neuroactive ligand-receptor transduction and cell communication. In summary, this study establishes distinct roles for individual miRNAs in hippocampal function.
Climatic irregular staircases: generalized acceleration of global warming
Authors: De Saedeleer Bernard
Published: January 2016

Global warming rates mentioned in the literature are often restricted to a couple of arbitrary periods of time, or of isolated values of the starting year, lacking a global view. In this study, we perform on the contrary an exhaustive parametric analysis of the NASA GISS LOTI data and also of the HadCRUT4 data. The starting year systematically varies between 1880 and 2002 and the averaging period from 5 to 30 yr — not only decades; the ending year also varies . In this way, we uncover a whole unexplored space of values for the global warming rate and access the full picture. Additionally, stairstep averaging and linear least squares fitting to determine climatic trends have been sofar exclusive. We propose here an original hybrid method which combines both approaches in order to derive a new type of climatic trend. We find that there is an overall acceleration of the global warming whatever the value of the averaging period and that 99.9% of the 3029 Earth’s climatic irregular staircases are rising. Graphical evidence is also given that choosing an El Niño year as starting year gives lower global warming rates — except if there is a volcanic cooling in parallel. Our rates agree and generalize several results mentioned in the literature.