bluuebunny/crossref_metadata_2025 huggingface dataset:
Studies on space charge neutralization and emittance measurement of beam from microwave ion source
Authors: Misra Anuraag , Goswami A. , Sing Babu P. , Srivastava S. , Pandit V. S.
Published: November 2015

A 2.45 GHz microwave ion source together with a beam transport system has been developed at VECC to study the problems related with the injection of high current beam into a compact cyclotron. This paper presents the results of beam profile measurement of high current proton beam at different degrees of space charge neutralisation with the introduction of neon gas in the beam line using a fine leak valve. The beam profiles have been measured at different pressures in the beam line by capturing the residual gas fluorescence using a CCD camera. It has been found that with space charge compensation at the present current level (∼5 mA at 75 keV), it is possible to reduce the beam spot size by ∼34%. We have measured the variation of beam profile as a function of the current in the solenoid magnet under the neutralised condition and used these data to estimate the rms emittance of the beam. Simulations performed using equivalent Kapchinsky-Vladimirsky beam envelope equations with space charge neutralization factor are also presented to interpret the experimental results.
Composite electrolyte with proton conductivity for low-temperature solid oxide fuel cell
Authors: Raza Rizwan , Ahmed Akhlaq , Akram Nadeem , Saleem Muhammad , Niaz Akhtar Majid , Sherazi Tauqir A. , Ajmal Khan M. , Abbas Ghazanfar , Shakir Imran , Mohsin Munazza , Alvi Farah , Javed Muhammad Sufyan , Yasir Rafique M. , Zhu Bin
Published: November 2015

In the present work, cost-effective nanocomposite electrolyte (Ba-SDC) oxide is developed for efficient low-temperature solid oxide fuel cells (LTSOFCs). Analysis has shown that dual phase conduction of O−2 (oxygen ions) and H+ (protons) plays a significant role in the development of advanced LTSOFCs. Comparatively high proton ion conductivity (0.19 s/cm) for LTSOFCs was achieved at low temperature (460 °C). In this article, the ionic conduction behaviour of LTSOFCs is explained by carrying out electrochemical impedance spectroscopy measurements. Further, the phase and structure analysis are investigated by X-ray diffraction and scanning electron microscopy techniques. Finally, we achieved an ionic transport number of the composite electrolyte for LTSOFCs as high as 0.95 and energy and power density of 90% and 550 mW/cm2, respectively, after sintering the composite electrolyte at 800 °C for 4 h, which is promising. Our current effort toward the development of an efficient, green, low-temperature solid oxide fuel cell with the incorporation of high proton conductivity composite electrolyte may open frontiers in the fields of energy and fuel cell technology.
Effects of surface wettability on fast liquid transfer
Authors: Chen H. , Tang T. , Amirfazli A.
Published: November 2015

A systematic experimental study was performed to understand the role of surface contact angles in affecting the process of fast liquid transfer. Surfaces with different wettabilities were used, and the transfer ratio (α, the amount of liquid transferred to the acceptor surface over the total amount of liquid) was measured for each pair of surfaces. A numerical model based on the volume of fluid method was developed to help understand the experimental results. The surface wettability was shown to significantly affect the boundaries between three regimes based on stretching speeds: quasi-static (surface force dominated), transition (surface/viscous/inertia forces all important) and dynamic (viscous/inertia forces dominated). Specifically, the values of the boundary speeds were found to increase with |α0 − 0.5|, where α0 is the transfer ratio in the quasi-static regime, and α0 is governed by the surface receding contact angles. Based on our results, an empirical equation to describe the transfer ratio as function of stretching speed was proposed. This equation can also be used as a prediction tool for the value of α for a fast transfer system.
An X-band high-impedance relativistic klystron amplifier with an annular explosive cathode
Authors: Zhu Danni , Zhang Jun , Zhong Huihuang , Qi Zumin
Published: November 2015

The feasibility of employing an annular beam instead of a solid one in the X-band high-impedance relativistic klystron amplifier (RKA) is investigated in theory and simulation. Small-signal theory analysis indicates that the optimum bunching distance, fundamental current modulation depth, beam-coupling coefficient, and beam-loaded quality factor of annular beams are all larger than the corresponding parameters of solid beams at the same beam voltage and current. An annular beam RKA and a solid beam RKA with almost the same geometric parameters are compared in particle-in-cell simulation. Output microwave power of 100 MW, gain of 50 dB, and power conversion efficiency of 42% are obtained in an annular beam RKA. The annular beam needs a 15% lower uniform guiding magnetic field than the solid beam. Our investigations demonstrate that we are able to use a simple annular explosive cathode immersed in a lower uniform magnetic field instead of a solid thermionic cathode in a complicated partially shielding magnetic field for designing high-impedance RKA, which avoids high temperature requirement, complicated electron-optical system, large area convergence, high current density, and emission uniformity for the solid beam. An equivalent method for the annular beam and the solid beam on bunching features is proposed and agrees with the simulation. The annular beam has the primary advantages over the solid beam that it can employ the immersing uniform magnetic field avoiding the complicated shielding magnetic field system and needs a lower optimum guiding field due to the smaller space charge effect.
Probing Co/Pd interfacial alloying by the extraordinary Hall effect
Authors: Winer G. , Segal A. , Karpovski M. , Shelukhin V. , Gerber A.
Published: November 2015

We report on the study of the extraordinary Hall effect (EHE) in Co-Pd alloys, bi-layers, and multilayers. Polarity of the effect and its changes with aging and post-deposition annealing are attributed to a gradual intermixing and formation of interfacial Co-Pd alloys. In multilayers with sub-monoatomic layers of Co, the intermixing is mostly accomplished during the fabrication itself. In bi-layers and multilayers with thicker Co, the process of spontaneous interfacial alloying continues after the deposition with an effective room temperature alloying period of 100 days. As far as the EHE is concerned, the stabilized Co/Pd multilayers behave as alloys with effective concentration corresponding to the thickness ratio between the Co and Pd layers.
Experimental study of an X-band phase-locked relativistic backward wave oscillator
Authors: Wu Y. , Li Z. H. , Xu Z.
Published: November 2015

To achieve high power microwave combined with high frequency band, an X-band phase-locked relativistic backward wave oscillator (RBWO) is proposed and investigated theoretically and experimentally using a modulated electron beam. In the device, an overmoded input cavity and a buncher cavity are employed to premodulate the electron beam. Particle-in-cell simulation shows that an input power of 90 kW is sufficient to lock the frequency and phase of 1.5 GW output microwave with the locking bandwidth of 60 MHz. Moreover, phase and frequency locking of an RBWO has been accomplished experimentally with an output power of 1.5 GW. The fluctuation of the relative phase difference between output microwave and input RF signal is less than ±20° with the locking duration of about 50 ns. The input RF power required to lock the oscillator is only 90 kW.
Instability of plasma plume of micro-hollow cathode discharge
Authors: Levko D. , Bliokh Y. P. , Gurovich V. Tz. , Krasik Ya. E.
Published: November 2015

The micro-hollow cathode gas discharge driven by thermionic emission is studied using the two-dimensional particle-in-cell Monte Carlo collisions simulation. The electron current is extracted from the plasma plume penetrating into the keeper–anode space through a small keeper orifice from the cathode-keeper space. The results of simulations and a simplified analytical model showed that the plasma density and extracted current can exhibit deep modulation in the range of frequencies of tens of MHz. This modulation appears when the space-charge limited current between the plume boundary and the anode exceeds the plasma thermal electron current through the orifice.
Damage imaging in a laminated composite plate using an air-coupled time reversal mirror
Authors: Le Bas P.-Y. , Remillieux M. C. , Pieczonka L. , Ten Cate J. A. , Anderson B. E. , Ulrich T. J.
Published: November 2015

We demonstrate the possibility of selectively imaging the features of a barely visible impact damage in a laminated composite plate by using an air-coupled time reversal mirror. The mirror consists of a number of piezoelectric transducers affixed to wedges of power law profiles, which act as unconventional matching layers. The transducers are enclosed in a hollow reverberant cavity with an opening to allow progressive emission of the ultrasonic wave field towards the composite plate. The principle of time reversal is used to focus elastic waves at each point of a scanning grid spanning the surface of the plate, thus allowing localized inspection at each of these points. The proposed device and signal processing removes the need to be in direct contact with the plate and reveals the same features as vibrothermography and more features than a C-scan. More importantly, this device can decouple the features of the defect according to their orientation, by selectively focusing vector components of motion into the object, through air. For instance, a delamination can be imaged in one experiment using out-of-plane focusing, whereas a crack can be imaged in a separate experiment using in-plane focusing. This capability, inherited from the principle of time reversal, cannot be found in conventional air-coupled transducers.
Manipulation of orbital occupancy by ferroelectric polarization in LaNiO3/BaTiO3−δ heterostructures
Authors: Peng J. J. , Song C. , Cui B. , Li F. , Mao H. J. , Wang G. Y. , Pan F.
Published: November 2015

We investigate the control of orbital occupancy by ferroelectric polarization in LaNiO3/BaTiO3−δ heterostructures. It is achieved by the ferroelectric displacement of Ti ions polarized downward (upward) to form (break) Ni–O–Ti covalent bonding at the interface, accompanied by charge transfer between them and the modulation of the conductivity of ultrathin LaNiO3. This electrically switchable and bi-direction control of orbital polarization in LaNiO3 is up to 25%, different from the manipulation by epitaxial strain or quantum confinement. Our finding opens a window for electrical control of orbital polarization at an oxide interface.
Impact of electric-field dependent dielectric constants on two-dimensional electron gases in complex oxides
Authors: Peelaers H. , Krishnaswamy K. , Gordon L. , Steiauf D. , Sarwe A. , Janotti A. , Van de Walle C. G.
Published: November 2015

High-density two-dimensional electron gas (2DEG) can be formed at complex oxide interfaces such as SrTiO3/GdTiO3 and SrTiO3/LaAlO3. The electric field in the vicinity of the interface depends on the dielectric properties of the material as well as on the electron distribution. However, it is known that electric fields can strongly modify the dielectric constant of SrTiO3 as well as other complex oxides. Solving the electrostatic problem thus requires a self-consistent approach in which the dielectric constant varies according to the local magnitude of the field. We have implemented the field dependence of the dielectric constant in a Schrödinger-Poisson solver in order to study its effect on the electron distribution in a 2DEG. Using the SrTiO3/GdTiO3 interface as an example, we demonstrate that including the field dependence results in the 2DEG being confined closer to the interface compared to assuming a single field-independent value for the dielectric constant. Our conclusions also apply to SrTiO3/LaAlO3 as well as other similar interfaces.
Ab initio calculations of the optical properties of crystalline and liquid InSb
Authors: Sano Haruyuki , Mizutani Goro
Published: November 2015

Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.
Low temperature fabrication and doping concentration analysis of Au/Sb ohmic contacts to n-type Si
Authors: Liu J. Q. , Wang C. , Zhu T. , Wu W. J. , Fan J. , Tu L. C.
Published: November 2015

This paper investigates low temperature ohmic contact formation of Au/Sb to n-type Si substrates through AuSb/NiCr/Au metal stacks. Liquid epitaxy growth is utilized to incorporate Sb dopants into Si substrate in AuSi melt. The best specific contact resistivity achieved is 0.003 Ω ⋅ cm2 at 425 oC. Scanning electron microscopy (SEM) reveals inverted pyramidal crater regions at the metal/semiconductor interface, indicating that AuSi alloying efficiently occurs at such sites. Secondary ion mass spectroscopy (SIMS) shows that Sb atoms are successfully incorporated into Si as doping impurities during the anneal process, and the Sb doping concentration at the contact interface is found to be higher than the solid solubility limit in a Si crystal. This ohmic contacts formation method is suitable for semiconductor fabrication processes with limited thermal budget, such as post CMOS integration of MEMS.
Chronic wounds should be one of Australia’s National Health Priority Areas
Authors: Kapp Suzanne , Santamaria Nick
Published: November 2015

Chronic wounds are a poorly recognised chronic disease that cause pain and suffering and cost the Australian healthcare system A$2.85 billion dollars per annum. Unlike the highly profiled and relatively well-funded chronic diseases that comprise the Australian National Health Priority Areas, chronic wounds remain a largely hidden and poorly supported problem in the Australian community. This perspective article proposes that one approach to generate action to reduce the burden of chronic wounds is to better articulate the relationship between chronic wounds and the Australian National Health Priority Areas, and to establish a profile of chronic wounds as a chronic disease of national significance in its own right. This approach has the potential to raise awareness of the significance of chronic wounds and garner support from the public, healthcare sector, research funders and policy makers to improve the outcomes for people who are living with or at risk of developing this condition and to potentially reduce expenditure in this area.
Seasonal variability in turbidity currents in Lake Ohau, New Zealand, and their influence on sedimentation
Authors: Cossu R. , Forrest A. L. , Roop H. A. , Dunbar G. B. , Vandergoes M. J. , Levy R. H. , Stumpner P. , Schladow S. G.
Published: November 2015

Layers of sediment that are deposited on the floor of Lake Ohau, New Zealand, offer a means to reconstruct past climate conditions in the Southern Hemisphere at subdecadal and annual resolution. A robust understanding of the modern physical processes that control the influx and dispersal of sediment in the lake is required to reconstruct climate from these sedimentary archives. In this study, water temperature and velocity measurements collected during 2012–13 were analysed to determine the primary physical processes that influence sediment transport in the lake. Sediment input from river inflow occurs throughout the year but exhibits strong seasonal variation. Large inflow events (Q>500m3s–1) that follow strong summer rainstorms trigger high-concentration turbidity currents, which are the main agents for sediment delivery and deposition. During winter, smaller turbidity currents also occur after rain events and contribute to annual sediment accumulation. In addition, large internal waves were observed during the summer and may influence sedimentation. In conclusion, several processes including river inflow, internal waves and convectively driven flows control sediment deposition and accumulation in the Lake Ohau system. We utilise these observations to establish a conceptual model to explain the observed infill stratigraphy in Lake Ohau and guide interpretation of the longer sedimentary record.
Path selection in the growth of rivers
Authors: Cohen Yossi , Devauchelle Olivier , Seybold Hansjörg F. , Yi Robert S. , Szymczak Piotr , Rothman Daniel H.
Published: November 2015

Significance

The complex patterns of river networks evolve from interactions between growing streams. Here we show that the principle of local symmetry, a concept originating in fracture mechanics, explains the path followed by growing streams fed by groundwater. Although path selection does not by itself imply a rate of growth, we additionally show how local symmetry may be used to infer how rates of growth scale with water flux. Our methods are applicable to other problems of unstable pattern formation, such as the growth of hierarchical crack patterns and geologic fault networks, where dynamics remain poorly understood.
Telomeric repeat-containing RNA (TERRA) constitutes a nucleoprotein component of extracellular inflammatory exosomes
Authors: Wang Zhuo , Deng Zhong , Dahmane Nadia , Tsai Kevin , Wang Pu , Williams Dewight R. , Kossenkov Andrew V. , Showe Louise C. , Zhang Rugang , Huang Qihong , Conejo-Garcia José R. , Lieberman Paul M.
Published: November 2015

Significance

Loss of telomere repeats leads to cellular senescence and the secretion of inflammatory cytokines. How telomere dysfunction is linked to this inflammatory phenotype and its role in aging and cancer is not yet understood. We show here that noncoding telomere RNA transcripts [telomeric repeat-containing RNA (TERRA)] are secreted into the extracellular environment in exosome vesicle fractions. This cell-free TERRA (cfTERRA) is shorter and more stable than intracellular TERRA, is associated with histone proteins, and can induce inflammatory cytokines in responsive cells. These findings suggest that TERRA can have a cell extrinsic function and provide a mechanism through which telomere dysfunction can lead to the activation of inflammatory cytokine signals in the tissue microenvironment through the signaling capacity of cfTERRA.
PML IV/ARF interaction enhances p53 SUMO-1 conjugation, activation, and senescence
Authors: Ivanschitz Lisa , Takahashi Yuki , Jollivet Florence , Ayrault Olivier , Le Bras Morgane , de Thé Hugues
Published: November 2015

Significance

Promyelocytic leukemia protein (PML) nuclear bodies (NBs) are subnuclear domains proposed to facilitate posttranslational modifications. Among NB partners, proteins are p53 and are most of the regulators. Overexpression of a single PML splice variant, PML IV, triggers p53-driven senescence. We demonstrate an interaction between PML IV C terminus and the ARF tumor suppressor. This interaction is required to promote p53 SUMOylation and subsequent stabilization. These results unexpectedly bridge three key tumor suppressors and stress the key role of PML NBs as SUMOylation factories and regulators of senescence.
Development and aging of cortical thickness correspond to genetic organization patterns
Authors: Fjell Anders M. , Grydeland Håkon , Krogsrud Stine K. , Amlien Inge , Rohani Darius A. , Ferschmann Lia , Storsve Andreas B. , Tamnes Christian K. , Sala-Llonch Roser , Due-Tønnessen Paulina , Bjørnerud Atle , Sølsnes Anne Elisabeth , Håberg Asta K. , Skranes Jon , Bartsch Hauke , Chen Chi-Hua , Thompson Wesley K. , Panizzon Matthew S. , Kremen William S. , Dale Anders M. , Walhovd Kristine B.
Published: November 2015

Significance

Here we show that developmental and adult aging-related changes in cortical thickness follow closely the genetic organization of the cerebral cortex. A total of 1,633 MRI scans from 974 participants from 4.1 to 88.5 y of age were used to measure longitudinal changes in cortical thickness, and the topographic pattern of change was compared with the genetic relationship between cortical subdivisions of maximal shared genetic influence, obtained from an independent sample of 406 middle-aged twins. Cortical changes due to maturation and adult age changes adhered to the genetic organization of the cortex, indicating that individual differences in cortical architecture in middle-aged adults have a neurodevelopmental origin and that genetic factors affect cortical changes through life.
Amino-terminal p53 mutations lead to expression of apoptosis proficient p47 and prognosticate better survival, but predispose to tumorigenesis
Authors: Phang Beng Hooi , Othman Rashidah , Bougeard Gaelle , Chia Ren Hui , Frebourg Thierry , Tang Choong Leong , Cheah Peh Yean , Sabapathy Kanaga
Published: November 2015

Significance

Mutations in the amino-terminal transactivation domain of the tumor-suppressor
p53
are mostly insertions or deletions, and result in loss of full-length p53 expression. However, these changes concomitantly result in the expression of a truncated p47 isoform, which retains the ability to selectively transactivate some apoptotic target genes. The selectivity appears to be due to a default feature, stemming from the lack of acetylation on K382 at the carboxyl terminus, which requires the amino terminus. Consistently, expression of p47 could prognosticate better survival in sporadic cancer patients, corroborating with its ability to induce apoptosis. However, apoptosis proficiency appears to be insufficient for tumor suppression, because these amino-terminal mutations are found in the germ line, leading to the Li–Fraumeni syndrome.
Host target modification as a strategy to counter pathogen hijacking of the jasmonate hormone receptor
Authors: Zhang Li , Yao Jian , Withers John , Xin Xiu-Fang , Banerjee Rahul , Fariduddin Qazi , Nakamura Yoko , Nomura Kinya , Howe Gregg A. , Boland Wilhelm , Yan Honggao , He Sheng Yang
Published: November 2015

Significance

Pathogen infections can cause significant crop losses worldwide and major disturbances in natural ecosystems. Understanding the molecular basis of plant disease susceptibility is important for the development of new strategies to prevent disease outbreaks. Recent studies have identified the plant jasmonate (JA) hormone receptor as one of the common targets of pathogen virulence factors. In this study, we modified the JA receptor and showed that transgenicArabidopsisplants with the modified JA receptor gained resistance to bacterial pathogens that secrete a potent JA-mimicking toxin to promote infection. Our results suggest that host target modification may be developed as a new strategy to protect the disease-vulnerable components of the susceptible plant against highly evolved pathogens.
Kinetics methods for clinical epidemiology problems
Authors: Corlan Alexandru Dan , Ross John
Published: November 2015

Significance

Medical predictions rely on probabilistic models that link the risk of future events to diagnostic and therapeutic variables. These models result from epidemiologic studies based on direct observation of events and variables in population samples. They work well for acute diseases in otherwise healthy individuals. For chronic, multiple conditions and diseases, more complex predictive models are needed. Such models have been developed for chemical kinetics problems that are analogous to epidemiologic problems if we view molecules as individuals and macroscopic systems as populations: Deterministic kinetics with one reaction are like most direct epidemiologic studies; the Arrhenius model is analogous to survival analysis. Stochastic systems with time-dependent reaction coefficients are worth exploring for deriving new epidemiologic methods.
Temperature compensation and temperature sensation in the circadian clock
Authors: Kidd Philip B. , Young Michael W. , Siggia Eric D.
Published: November 2015

Significance

Circadian clocks in animals, plants, and fungi possess the remarkable property of temperature compensation: the clock has a temperature-insensitive period, while retaining the ability to synchronize to temperature cycles. The conservation of temperature compensation across clades means it is likely critical to the function of circadian clocks. Temperature compensation also places the circadian clock in contrast to other biological pathways, which generally have temperature-sensitive time scales. However, the mechanism of temperature compensation remains unknown. We present a general scheme by which a circadian oscillator can be temperature-compensated while still synchronizing to environmental temperature cycles. In particular, we give experimental evidence that the circadian clock consists of a temperature-insensitive core oscillator coupled to a specific adaptive temperature signaling pathway.
Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth
Authors: Basenko Evelina Y. , Sasaki Takahiko , Ji Lexiang , Prybol Cameron J. , Burckhardt Rachel M. , Schmitz Robert J. , Lewis Zachary A.
Published: November 2015

Significance

Regulators of chromatin structure play critical roles in DNA-based processes. Lysine (K) Methyltransferase 1 (KMT1) homologs perform methylation of H3 lysine-9 and are best known for their essential role in heterochromatin formation and transcriptional silencing. Heterochromatin formation is also important for maintenance of genome stability, although the mechanisms are not well understood. We report that altered activity of Polycomb repressive complex-2 (PRC2), a histone lysine-27 methyltransferase complex, is responsible for genotoxic stress, poor growth, and defective development in KMT1-deficient mutants of
Neurospora crassa
. Mammalian KMT1 and PRC2 are required for development and are frequently mutated in cancer. This work provides information about the cellular consequences of KMT1 and PRC2 deficiency and provides insights into the regulatory and functional relationships of these conserved enzymes.
Fate of MgSiO
3
melts at core–mantle boundary conditions
Authors: Petitgirard Sylvain , Malfait Wim J. , Sinmyo Ryosuke , Kupenko Ilya , Hennet Louis , Harries Dennis , Dane Thomas , Burghammer Manfred , Rubie Dave C.
Published: November 2015

Significance

A new technique has been developed to measure in situ the density of amorphous material composed of light elements under extreme conditions of pressure using the X-ray absorption method. At core–mantle boundary (CMB) pressure, the densities of MgSiO
3
glass and melts are similar to the one of the crystalline bridgmanite, within uncertainty. Due to the affinity of iron oxide for silicate liquids, melting in the MgSiO
3
–FeSiO
3
system will produce dense melts that could accumulate above the CMB, leading to the formation of a dense basal magma ocean in the early Earth's mantle.
Collapse of the West Antarctic Ice Sheet after local destabilization of the Amundsen Basin
Authors: Feldmann Johannes , Levermann Anders
Published: November 2015

Significance

The Antarctic Ice Sheet is losing mass at an accelerating rate, and playing a more important role in terms of global sea-level rise. The Amundsen Sea sector of West Antarctica has most likely been destabilized. Although previous numerical modeling studies examined the short-term future evolution of this region, here we take the next step and simulate the long-term evolution of the whole West Antarctic Ice Sheet. Our results show that if the Amundsen Sea sector is destabilized, then the entire marine ice sheet will discharge into the ocean, causing a global sea-level rise of about 3 m. We thus might be witnessing the beginning of a period of self-sustained ice discharge from West Antarctica that requires long-term global adaptation of coastal protection.
Gating mechanisms of a natural anion channelrhodopsin
Authors: Sineshchekov Oleg A. , Govorunova Elena G. , Li Hai , Spudich John L.
Published: November 2015

Significance

The recently discovered natural anion channelrhodopsins (ACRs) have exceptional properties for use as membrane-hyperpolarizing tools for neural silencing, but our knowledge about them is only rudimentary. We have gained, to our knowledge, first insights into the molecular mechanisms of their unique light-gated anion conductance by photocurrent measurements and mutant analysis. We identified a mutant constitutively open in the dark—to our knowledge, the first such mutant of any light-gated channel, invaluable for probing the structure of the channel open state—and a “step function” ACR mutant useful in some optogenetics protocols. Our results will help decipher the mechanism of channelrhodopsin ion conductance and facilitate rational design of inhibitory tools tailored to the needs of optogenetic studies and potential clinical applications.
The bioenergetic costs of a gene
Authors: Lynch Michael , Marinov Georgi K.
Published: November 2015

Significance

A long-standing mystery in evolutionary genomics concerns the lineage-specific expansions of genome size in eukaryotes relative to prokaryotes. One argument is that the cellular complexity and elevated gene numbers in eukaryotes were impossible without a mitochondrion. However, the energetic burden of a gene is typically no greater, and generally becomes progressively smaller, in larger cells in both bacteria and eukaryotes, and this is true for costs measured at the DNA, RNA, and protein levels. These results eliminate the need to invoke an energetics barrier to genome complexity.
Reduced
DOCK4
expression leads to erythroid dysplasia in myelodysplastic syndromes
Authors: Sundaravel Sriram , Duggan Ryan , Bhagat Tushar , Ebenezer David L. , Liu Hui , Yu Yiting , Bartenstein Matthias , Unnikrishnan Madhu , Karmakar Subhradip , Liu Ting-Chun , Torregroza Ingrid , Quenon Thomas , Anastasi John , McGraw Kathy L. , Pellagatti Andrea , Boultwood Jacqueline , Yajnik Vijay , Artz Andrew , Le Beau Michelle M. , Steidl Ulrich , List Alan F. , Evans Todd , Verma Amit , Wickrema Amittha
Published: November 2015

Significance

Anemia is the predominant clinical manifestation of myelodysplastic syndromes (MDS). Genes that are aberrantly expressed and/or mutated that lead to the dysplastic erythroid morphology seen in −7/del(7q) MDS have not been identified. In this study, we show that reduced expression of dedicator of cytokinesis 4 (
DOCK4
) causes dysplasia by disrupting the actin cytoskeleton in developing red blood cells. In addition, our identification of the molecular pathway that leads to morphological defects in this type of MDS provides potential therapeutic targets downstream of DOCK4 that can be exploited to reverse the dysplasia in the erythroid lineage. Furthermore, we developed a novel single-cell multispectral flow cytometry assay for evaluation of disrupted F-actin filaments, which can be used for potential early detection of dysplastic cells in MDS.
Fourteen babies born after round spermatid injection into human oocytes
Authors: Tanaka Atsushi , Nagayoshi Motoi , Takemoto Youichi , Tanaka Izumi , Kusunoki Hiroshi , Watanabe Seiji , Kuroda Keiji , Takeda Satoru , Ito Masahiko , Yanagimachi Ryuzo
Published: November 2015

Significance

Men without spermatozoa or elongating spermatids in their testes have been considered sterile and are advised to consider using a sperm donor. However, these men may have round spermatids. We have been able to accurately identify these cells based on their structural and physical characteristics (verified by karyotyping and FISH). Round spermatid injection was effectively used in our clinic and resulted in the birth of 14 healthy babies. Although the current success rate of round spermatid injection is not very high compared with intracytoplasmic sperm injection, this procedure can be the last resort for men who cannot produce spermatozoa but wish to use their own genetic material to produce offspring.
Formation and evolution of molecular products in α-pinene secondary organic aerosol
Authors: Zhang Xuan , McVay Renee C. , Huang Dan D. , Dalleska Nathan F. , Aumont Bernard , Flagan Richard C. , Seinfeld John H.
Published: November 2015

Significance

Secondary organic aerosol (SOA) plays a pivotal role in climate and air quality. Characterizing the molecular makeup of SOA has been a major research goal for several decades, yet the chemical dynamics of most anthropogenic and biogenic SOA systems remain poorly resolved. We report here the time-resolved molecular characterization of SOA derived from the canonical α-pinene system, one of the most abundant biogenic emissions in the troposphere. We reveal distinct features of SOA components in terms of molecular structure, abundance, growth rates, evolution patterns, and responses to variations in temperature, relative humidity, and oxidant type. Our findings provide a comprehensive analysis of processes governing α-pinene SOA formation and aging.
Epidermal development, growth control, and homeostasis in the face of centrosome amplification
Authors: Kulukian Anita , Holland Andrew J. , Vitre Benjamin , Naik Shruti , Cleveland Don W. , Fuchs Elaine
Published: November 2015

Significance

The full extent to which centrosome amplification might directly contribute to human disease is poorly understood. We generated a mouse model for the induction of centrosome amplification in the skin, a tissue that remains proliferative even after its development. We uncover defects in stratification of the epidermis during development, which can be attributed to mitotic errors. The skin exhibits remarkable resiliency by clearing out these defective cells via a cell death program, however. Despite sustained centrosome amplification, adult animals are healthy and do not develop tumors or skin abnormalities. Our findings challenge the role for centrosome amplification in the initiation of skin tumorigenesis and demonstrate that certain tissues are better able to cope with its burden.
High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction
Authors: Thomaston Jessica L. , Alfonso-Prieto Mercedes , Woldeyes Rahel A. , Fraser James S. , Klein Michael L. , Fiorin Giacomo , DeGrado William F.
Published: November 2015

Significance

The conduction of protons through the highly restricted paths of transmembrane proteins is an essential process of living systems and an intriguing problem in modern physical chemistry. The small size of the influenza M2 proton channel makes it an ideal system for the study of proton transport across a membrane. Additionally, the M2 channel has medical relevance as an anti-flu drug target. These high-resolution structures of the channel were obtained by crystallizing the protein in a membrane-like environment and reveal networks of hydrogen-bonded waters that change with temperature and pH. The locations of these waters, in conjunction with molecular dynamics simulations that predict their hydrogen bond orientations, provide insight into the mechanism of proton stabilization and transduction within the channel.
Chronic centrosome amplification without tumorigenesis
Authors: Vitre Benjamin , Holland Andrew J. , Kulukian Anita , Shoshani Ofer , Hirai Maretoshi , Wang Yin , Maldonado Marcus , Cho Thomas , Boubaker Jihane , Swing Deborah A. , Tessarollo Lino , Evans Sylvia M. , Fuchs Elaine , Cleveland Don W.
Published: November 2015

Significance

Centrosomes organize the microtubule cytoskeleton in interphase and mitosis. During mitosis, the centrosomes are important for the formation and positioning of the bipolar mitotic spindle on which chromosomes are segregated. The presence of more than two centrosomes can drive mitotic chromosome segregation errors and the formation of aneuploid cells. Centrosome amplification is a common feature of aneuploid cancer cells, but a long-standing question is whether this is a cause or a consequence of tumor development. To assess this question, we generated mice in which centrosome amplification can be induced widely. Despite chronic centrosome amplification, tumorigenesis was not enhanced, demonstrating that an excess of centrosomes is not sufficient to drive tumor development.
Single-molecule view of basal activity and activation mechanisms of the G protein-coupled receptor β
2
AR
Authors: Lamichhane Rajan , Liu Jeffrey J. , Pljevaljcic Goran , White Kate L. , van der Schans Edwin , Katritch Vsevolod , Stevens Raymond C. , Wüthrich Kurt , Millar David P.
Published: November 2015

Significance

Activation of G protein-coupled receptors (GPCRs) by agonists is the first step of eukaryotic cellular signal transduction. Because GPCRs are expressed in almost all human tissues and play a key role in human physiology, they are the targets for more than 30% of pharmaceutical drugs. Binding of ligands on the extracellular surface of a GPCR induces a conformational change on the cytoplasmic surface, which is recognized by G proteins or other cellular effectors. Here we show that the β
2
-adrenergic receptor, a prototypical GPCR, naturally fluctuates between inactive and active conformations, and that agonist or inverse agonist ligands modulate the conformational exchange kinetics in distinct ways, explaining their different pharmacological efficacies. These insights should assist in the design of improved GPCR-targeting drugs.
Effects of Hybridization between Nonnative Rainbow Trout and Native Westslope Cutthroat Trout on Fitness‐Related Traits
Authors: Drinan Daniel P. , Webb Molly A. H. , Naish Kerry A. , Kalinowski Steven T. , Boyer Matthew C. , Steed Amber C. , Shepard Bradley B. , Muhlfeld Clint C.
Published: November 2015

Hybridization between introduced and native fauna is a risk to native species and may threaten the long‐term persistence of numerous taxa. Rainbow TroutOncorhynchus mykisshas been one of the most widely introduced species around the globe and often hybridizes with native Cutthroat TroutO. clarkiiin the Rocky Mountains. Previous work has shown that hybridization negatively affects reproductive success, but identification of the traits contributing to that reduction has been elusive. In this study, we used a combination of field and laboratory techniques to assess how hybridization with Rainbow Trout affects seven traits during several stages of Westslope Cutthroat Trout development: embryonic survival, ova size, ova energy concentration, sperm motility, juvenile weight, juvenile survival, and burst swimming endurance. Rainbow Trout admixture was correlated with an increase in embryonic survival and ova energy concentration but with a decrease in juvenile weight and burst swimming endurance. These correlations differed from previously observed patterns of reproductive success and likely do not explain the declines in reproductive success associated with admixture. Future investigation of additional, unstudied traits and the use of different environments may shed light on the traits responsible for reproductive success in admixed Cutthroat Trout.
Trends in the Reproductive Phenology of two Great Lakes Fishes
Authors: Lyons John , Rypel Andrew L. , Rasmussen Paul W. , Burzynski Thomas E. , Eggold Bradley T. , Myers Jared T. , Paoli Tammie J. , McIntyre Peter B.
Published: November 2015

To assess potential effects of climate change on Great Lakes fish populations, we evaluated trends in the reproductive phenology of Yellow Perch Perca flavescens (spring spawner) and Lake Trout Salvelinus namaycush (autumn spawner). For Yellow Perch in Lake Michigan, the estimated reproductive midpoint date (50% of mature females ripe or spent, 50% not yet spawned) took place 6.2 d/decade earlier in the spring near Milwaukee from 1988 to 2012 and 1.8 d/decade earlier in Green Bay from 1980 to 2012. At both locations water temperatures at the spawning sites on the midpoint date showed no trends, but mean water temperatures during the spring at the spawning site and midlake increased over the study period. This suggests that Yellow Perch spawning areas were warming sooner in the spring and that Yellow Perch were spawning earlier to maintain a consistent spawning temperature. Lake Trout phenological patterns were more complex. For Lake Trout in Lake Michigan near Milwaukee, there was a marginally significant trend for spawning to take place 2.1 d/decade later in the autumn from 1983 to 2006. However, water temperatures at the spawning site at the midpoint date did not change and autumn temperatures at the site and at midlake did not show a warming trend. For Lake Trout in Lake Superior near the Apostle Islands, the midpoint date did not change from 1988 to 2012. Water temperatures at the spawning site on the midpoint date and during the autumn also showed no trends, but midlake summer and autumn water temperatures increased significantly. Overall, Yellow Perch in Lake Michigan have shifted reproductive timing in a manner consistent with a warming climate, but the relationship of climate change to reproductive phenology remains unclear for Lake Trout in Lake Michigan and Lake Superior.
Discs of mammalian rod photoreceptors form through the membrane evagination mechanism
Authors: Ding Jin-Dong , Salinas Raquel Y. , Arshavsky Vadim Y.
Published: November 2015

Photoreceptor discs are membrane organelles harboring components of the visual signal transduction pathway. The mechanism by which discs form remains enigmatic and is the subject of a major controversy. Classical studies suggest that discs are formed as serial plasma membrane evaginations, whereas a recent alternative postulates that discs, at least in mammalian rods, are formed through intracellular vesicular fusion. We evaluated these models in mouse rods using methods that distinguish between the intracellular vesicular structures and plasma membrane folds independently of their appearance in electron micrographs. The first differentiated membranes exposed to the extracellular space from intracellular membranes; the second interrogated the orientation of protein molecules in new discs. Both approaches revealed that new discs are plasma membrane evaginations. We further demonstrated that vesiculation and plasma membrane enclosure at the site of new disc formation are artifacts of tissue fixation. These data indicate that all vertebrate photoreceptors use the evolutionary conserved membrane evagination mechanism to build their discs.
Photoreceptor disc morphogenesis: The classical evagination model prevails
Authors: Pugh Edward N.
Published: November 2015

Vision begins in photoreceptor outer segments with light captured by opsins in continually synthesized disc membranes. The process by which rod photoreceptor discs are formed has been controversial. In this issue, Ding et al. (2015. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201508093) show conclusively that rod discs are formed by plasma membrane evagination.
Solidifying the view of RNP dynamics
Authors: Short Ben
Published: November 2015

An RNAi screen provides new insights into the regulation of RNP granules and mRNA repression.
Biochemical responses to ocean acidification contrast between tropical corals with high and low abundances at volcanic carbon dioxide seeps
Authors: Strahl J. , Francis D. S. , Doyle J. , Humphrey C. , Fabricius K. E.
Published: November 2015

At two natural volcanic seeps in Papua New Guinea, the partial pressure of carbon dioxide (pCO2) in the seawater is consistent with projections for 2100. Here, the cover of massive scleractinian corals Porites spp. is twice as high at elevated compared with ambient pCO2, while that of branching corals such as Acropora millepora is greater than twofold reduced. To assess the underlying mechanisms for such community shifts under long-term exposure to elevated pCO2, biochemical parameters related to tissue biomass, energy storage, pigmentation, cell protection, and cell damage were compared between Porites spp. and A. millepora from control (mean pHtotal = 8.1, pCO2 = 323 µatm) and CO2 seep sites (mean pHtotal = 7.8, pCO2 = 803 µatm) each at two reefs. In Porites spp., only one of the biochemical parameters investigated (the ratio of photoprotective to light-harvesting pigments) responded to pCO2, while tissue biomass, total lipids, total proteins, and some pigments differed between the two reefs, possibly reflecting differences in food availability. Furthermore, some fatty acids showed pCO2 –reef interactions. In A. millepora, most pigments investigated were reduced at elevated pCO2, while other parameters (e.g. tissue biomass, total proteins, total lipids, protein carbonyls, some fatty acids and pigments) differed between reefs or showed pCO2–reef interactions. Tissue biomass, total lipids, and cell-protective capacities were distinctly higher in Porites spp. than in A. millepora, indicating higher resistance to environmental stress in massive Porites. However, our data suggest that important biochemical measures remain relatively unaffected in these two coral species in response to elevated pCO2 up to 800 µatm, with most responses being smaller than differences between species and locations, and also when compared with responses to other environmental stressors such as ocean warming.
Hygienic tendencies correlate with low geohelminth infection in free-ranging macaques
Authors: Sarabian Cecile , MacIntosh Andrew J. J.
Published: November 2015

Parasites are ubiquitous in nature and can be costly to animal fitness, so hosts have evolved behavioural counter-strategies to mitigate infection risk. We investigated feeding-related infection-avoidance strategies in Japanese macaques via field-experimentation and observation. We first examined risk sensitivity during foraging tasks involving faecally contaminated or debris-covered food items, and then investigated individual tendencies to manipulate food items during natural foraging bouts. We concurrently monitored geohelminth infection in all subjects. We ran a principal component analysis on the observational/experimental data to generate a hygienic index across individuals and found that hygienic tendencies towards faeces avoidance and food manipulation correlated negatively with geohelminth infection. Females scored higher in hygienic tendencies than males, which might contribute to the common vertebrate pattern of male-biased infection. The behavioural tendencies observed may reflect a general form of hygiene, providing a mechanism of behavioural immunity against parasites with implications for the evolution and diversification of health maintenance strategies in humans.