bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis, crystal structure, and properties of a perovskite-related bismuth phase, (NH4)3Bi2I9
Authors: Sun Shijing , Tominaka Satoshi , Lee Jung-Hoon , Xie Fei , Bristowe Paul D. , Cheetham Anthony K.
Published: March 2016

Organic-inorganic halide perovskites, especially methylammonium lead halide, have recently led to remarkable advances in photovoltaic devices. However, due to environmental and stability concerns around the use of lead, research into lead-free perovskite structures has been attracting increasing attention. In this study, a layered perovskite-like architecture, (NH4)3Bi2I9, is prepared from solution and the structure solved by single crystal X-ray diffraction. The band gap, which is estimated to be 2.04 eV using UV-visible spectroscopy, is lower than that of CH3NH3PbBr3. The energy-minimized structure obtained from first principles calculations is in excellent agreement with the X-ray results and establishes the locations of the hydrogen atoms. The calculations also point to a significant lone pair effect on the bismuth ion. Single crystal and powder conductivity measurements are performed to examine the potential application of (NH4)3Bi2I9 as an alternative to the lead containing perovskites.
Contact induced spin relaxation in graphene spin valves with Al2O3 and MgO tunnel barriers
Authors: Amamou Walid , Lin Zhisheng , van Baren Jeremiah , Turkyilmaz Serol , Shi Jing , Kawakami Roland K.
Published: March 2016

We investigate spin relaxation in graphene by systematically comparing the roles of spin absorption, other contact-induced effects (e.g., fringe fields), and bulk spin relaxation for graphene spin valves with MgO barriers, Al2O3 barriers, and transparent contacts. We obtain effective spin lifetimes by fitting the Hanle spin precession data with two models that include or exclude the effect of spin absorption. Results indicate that additional contact-induced spin relaxation other than spin absorption dominates the contact effect. For tunneling contacts, we find reasonable agreement between the two models with median discrepancy of ∼20% for MgO and ∼10% for Al2O3.
On the mechanisms of cation injection in conducting bridge memories: The case of HfO2 in contact with noble metal anodes (Au, Cu, Ag)
Authors: Saadi M. , Gonon P. , Vallée C. , Mannequin C. , Grampeix H. , Jalaguier E. , Jomni F. , Bsiesy A.
Published: March 2016

Resistance switching is studied in HfO2 as a function of the anode metal (Au, Cu, and Ag) in view of its application to resistive memories (resistive random access memories, RRAM). Current-voltage (I-V) and current-time (I-t) characteristics are presented. For Au anodes, resistance transition is controlled by oxygen vacancies (oxygen-based resistive random access memory, OxRRAM). For Ag anodes, resistance switching is governed by cation injection (Conducting Bridge random access memory, CBRAM). Cu anodes lead to an intermediate case. I-t experiments are shown to be a valuable tool to distinguish between OxRRAM and CBRAM behaviors. A model is proposed to explain the high-to-low resistance transition in CBRAMs. The model is based on the theory of low-temperature oxidation of metals (Cabrera-Mott theory). Upon electron injection, oxygen vacancies and oxygen ions are generated in the oxide. Oxygen ions are drifted to the anode, and an interfacial oxide is formed at the HfO2/anode interface. If oxygen ion mobility is low in the interfacial oxide, a negative space charge builds-up at the HfO2/oxide interface. This negative space charge is the source of a strong electric field across the interfacial oxide thickness, which pulls out cations from the anode (CBRAM case). Inversely, if oxygen ions migration through the interfacial oxide is important (or if the anode does not oxidize such as Au), bulk oxygen vacancies govern resistance transition (OxRRAM case).
Landau damping of electrostatic waves in arbitrarily degenerate quantum plasmas
Authors: Rightley Shane , Uzdensky Dmitri
Published: March 2016

We carry out a systematic study of the dispersion relation for linear electrostatic waves in an arbitrarily degenerate quantum electron plasma. We solve for the complex frequency spectrum for arbitrary values of wavenumber k and level of degeneracy μ. Our finding is that for large k and high μ the real part of the frequency ωr grows linearly with k and scales with μ, only because of the scaling of the Fermi energy. In this regime, the relative Landau damping rate γ/ωr becomes independent of k and varies inversely with μ. Thus, damping is weak but finite at moderate levels of degeneracy for short wavelengths.
Ultraviolet-assisted microfluidic generation of ferroelectric composite particles
Authors: Zhang Cancan , Yu Xiaolei , You Sujian , Cai Bo , Liu Huiqin , Zhang Lingling , Rao Lang , Liu Wei , Guo Shi-Shang , Zhao Xing-Zhong
Published: March 2016

We report on the feasible fabrication of microfluidic devices for ferroelectric polymers' synthesis in a rapid and stable fashion. Utilizing micro-mixing and flow-focusing in microchannels, poly(vinylidene fluoride-trifluoroethylene) and copper phthalocyanine are uniformly dispersed in one hydrogel particle, which are then demonstrated to immediate and complete on-chip steady polymerization by moderate ultraviolet treatment. The advantage of our droplet-based microfluidic devices is generating versatile particles from simple spheres to disks or rods, and the lengths of particles can be precisely tuned from 30 to 400 μm through adjusting the flow rates of both disperse and oil phases. In addition, this mixed technique allows for the continuous production of dielectric microparticles with controlled dielectric properties between 10 and 160. Such a microfluidic device offers a flexible platform for multiferroic applications.
Fabrication of universal serial bus flash disk type microfluidic chip electrophoresis and application for protein analysis under ultra low voltage
Authors: Cong Hailin , Xu Xiaodan , Yu Bing , Liu Huwei , Yuan Hua
Published: March 2016

A simple and effective universal serial bus (USB) flash disk type microfluidic chip electrophoresis (MCE) was developed by using poly(dimethylsiloxane) based soft lithography and dry film based printed circuit board etching techniques in this paper. The MCE had a microchannel diameter of 375 μm and an effective length of 25 mm. Equipped with a conventional online electrochemical detector, the device enabled effectively separation of bovine serum albumin, lysozyme, and cytochrome c in 80 s under the ultra low voltage from a computer USB interface. Compared with traditional capillary electrophoresis, the USB flash disk type MCE is not only portable and inexpensive but also fast with high separation efficiency.
Droplet impact behavior on heated micro-patterned surfaces
Authors: Zhang Wenbin , Yu Tongxu , Fan Jing , Sun Weijie , Cao Zexian
Published: March 2016

Impact behavior of droplets on a surface is an intriguing research topic, and its control should be very useful in diverse industrial applications. We investigated the impact behavior of water droplets on the textured and chemically treated surface of silicon and obtained the impact mode map on the parameter plane subtended by the Weber number (up to 85) and temperature (up to 320 °C). The patterns comprise of micropillars (14 μm in height) in square lattice with a lattice constant of 10 and 20 μm, and the surface was further made superhydrophobic by coating with graphene nanosheets. Six distinct impact modes are identified. It was found that the impact mode map can be dramatically altered by modifying the texture and chemistry of the surface, and the observations are well explained with regard to heat transfer, vapor/bubble generation and vapor flow beneath the droplet. Instability in the droplet arising from the mismatch between vapor generation rate and exhaust conditions is the dominant factor in determining the impact mode. Our results revealed more facts and features of the droplet impact phenomenon and can be very useful for target-oriented surface design towards precise control of droplet impact behavior on heated substrates.
Characterization of LiMn2O4 cathodes by electrochemical strain microscopy
Authors: Alikin D. O. , Ievlev A. V. , Luchkin S. Yu. , Turygin A. P. , Shur V. Ya. , Kalinin S. V. , Kholkin A. L.
Published: March 2016

Electrochemical strain microscopy (ESM) is a scanning probe microscopy (SPM) method in which the local electrodiffusion is probed via application of AC voltage to the SPM tip and registration of resulting electrochemical strain. Here, we implemented ESM to measure local strain in bulk LiMn2O4 cathodes of a commercial Li-battery in different states of charge to investigate distribution of Li-ion mobility and concentration. Ramped AC ESM imaging and voltage spectroscopy were used to find the most reliable regime of measurements allowing separating and diminishing different contributions to ESM. This is not a trivial task due to complex geometry of the sample and various obstacles resulting in less predictable contributions of different origins into ESM response: electrostatic tip–surface interactions, charge injection, electrostriction, and flexoelectricity. Understanding and control of these contributions is an important step towards quantitative interpretation of ESM data.
Quasi-particle electronic band structure and alignment of the V-VI-VII semiconductors SbSI, SbSBr, and SbSeI for solar cells
Authors: Butler Keith T. , McKechnie Scott , Azarhoosh Pooya , van Schilfgaarde Mark , Scanlon David O. , Walsh Aron
Published: March 2016

The ternary V-VI-VII chalcohalides consist of one cation and two anions. Trivalent antimony—with a distinctive 5s2 electronic configuration—can be combined with a chalcogen (e.g., S or Se) and halide (e.g., Br or I) to produce photoactive ferroelectric semiconductors with similarities to the Pb halide perovskites. We report—from relativistic quasi-particle self-consistent GW theory—that these materials have a multi-valley electronic structure with several electron and hole basins close to the band extrema. We predict ionisation potentials of 5.3–5.8 eV from first-principles for the three materials, and assess electrical contacts that will be suitable for achieving photovoltaic action from these unconventional compounds.
Active control of near-field coupling in conductively coupled microelectromechanical system metamaterial devices
Authors: Pitchappa Prakash , Manjappa Manukumara , Ho Chong Pei , Qian You , Singh Ranjan , Singh Navab , Lee Chengkuo
Published: March 2016

We experimentally report a structurally reconfigurable metamaterial for active switching of near-field coupling in conductively coupled, orthogonally twisted split ring resonators (SRRs) operating in the terahertz spectral region. Out-of-plane reconfigurable microcantilevers integrated into the dark SRR geometry are used to provide active frequency tuning of dark SRR resonance. The geometrical parameters of individual SRRs are designed to have identical inductive-capacitive resonant frequency. This allows for the excitation of classical analogue of electromagnetically induced transparency (EIT) due to the strong conductive coupling between the SRRs. When the microcantilevers are curved up, the resonant frequency of dark SRR blue-shifts and the EIT peak is completely modulated while the SRRs are still conductively connected. EIT modulation contrast of ∼50% is experimentally achieved with actively switchable group delay of ∼2.5 ps. Electrical control, miniaturized size, and readily integrable fabrication process of the proposed structurally reconfigurable metamaterial make it an ideal candidate for the realization of various terahertz communication devices such as electrically controllable terahertz delay lines, buffers, and tunable data-rate channels.
Temperature-dependent spin injection dynamics in InGaAs/GaAs quantum well-dot tunnel-coupled nanostructures
Authors: Chen S. L. , Kiba T. , Yang X. J. , Takayama J. , Murayama A.
Published: March 2016

Time-resolved optical spin orientation spectroscopy was employed to investigate the temperature-dependent electron spin injection in In0.1Ga0.9As quantum well (QW) and In0.5Ga0.5As quantum dots (QDs) tunnel-coupled nanostructures with 4, 6, and 8 nm-thick GaAs barriers. The fast picosecond-ranged spin injection from QW to QD excited states (ES) was observed to speed up with temperature, as induced by pronounced longitudinal-optical (LO)-phonon-involved multiple scattering process, which contributes to a thermally stable and almost fully spin-conserving injection within 5–180 K. The LO-phonon coupling was also found to cause accelerated electron spin relaxation of QD ES at elevated temperature, mainly via hyperfine interaction with random nuclear field.
Critical rolling angle of microparticles
Authors: Farzi Bahman , Vallabh Chaitanya K. P. , Stephens James D. , Cetinkaya Cetin
Published: March 2016

At the micrometer-scale and below, particle adhesion becomes particularly relevant as van der Waals force often dominates volume and surface proportional forces. The rolling resistance of microparticles and their critical rolling angles prior to the initiation of free-rolling and/or complete detachment are critical in numerous industrial processes and natural phenomenon involving particle adhesion and granular dynamics. The current work describes a non-contact measurement approach for determining the critical rolling angle of a single microparticle under the influence of a contact-point base-excitation generated by a transient displacement field of a prescribed surface acoustic wave pulse and reports the critical rolling angle data for a set of polystyrene latex microparticles.
Communication: Enhanced chemical reactivity of graphene on a Ni(111) substrate
Authors: Ambrosetti Alberto , Silvestrelli Pier Luigi
Published: March 2016

Due to the unique combination of structural, mechanical, and transport properties, graphene has emerged as an exceptional candidate for catalysis applications. The low chemical reactivity caused by sp2 hybridization and strongly delocalized π electrons, however, represents a main challenge for straightforward use of graphene in its pristine, free-standing form. Following recent experimental indications, we show that due to charge hybridization, a Ni(111) substrate can enhance the chemical reactivity of graphene, as exemplified by the interaction with the CO molecule. While CO only physisorbs on free-standing graphene, chemisorption of CO involving formation of ethylene dione complexes is predicted in Ni(111)-graphene. Higher chemical reactivity is also suggested in the case of oxidized graphene, opening the way to a simple and efficient control of graphene chemical properties, devoid of complex defect patterning or active metallic structures deposition.
Low rates of nitrogen fixation in eastern tropical South Pacific surface waters
Authors: Knapp Angela N. , Casciotti Karen L. , Berelson William M. , Prokopenko Maria G. , Capone Douglas G.
Published: March 2016

Significance

We present direct, field-based measurements of low nitrogen fixation rates in the eastern tropical South Pacific (ETSP) Ocean demonstrating that N
2
fixation plays a minor role supporting export production regionally. These results are in contrast to indirect estimates that the highest global rates of N
2
fixation occur in the ETSP. The low N
2
-fixation rates occur in a region with relatively high surface ocean phosphate concentrations (and low nitrate concentrations) but where atmospheric iron deposition rates are diminishingly low. Consequently, these results indicate that the ETSP hosts a minor fraction of global N
2
-fixation fluxes and that low nitrate to phosphate concentration ratios alone are insufficient to support high N
2
-fixation fluxes.
Impacts of classifying New York City students as overweight
Authors: Almond Douglas , Lee Ajin , Schwartz Amy Ellen
Published: March 2016

Significance

One third of US children are overweight. Childhood obesity is strongly associated with academic performance, predicts obesity in adulthood, and may be easier to modify than adult weight. Parents who are unaware their children are overweight may impede healthier weight ranges. We consider an informational intervention of New York City’s obesity report cards using a regression discontinuity design framework. To a surprising degree, discontinuous assignment rules are commonplace in allocating program services and shaping clinical care decisions by health care providers. Regression discontinuity designs offer a relatively untapped methodological approach for isolating causal effects, particularly as they relate to health.
Small genome of the fungus
Escovopsis weberi
, a specialized disease agent of ant agriculture
Authors: de Man Tom J. B. , Stajich Jason E. , Kubicek Christian P. , Teiling Clotilde , Chenthamara Komal , Atanasova Lea , Druzhinina Irina S. , Levenkova Natasha , Birnbaum Stephanie S. L. , Barribeau Seth M. , Bozick Brooke A. , Suen Garret , Currie Cameron R. , Gerardo Nicole M.
Published: March 2016

Significance

Many organisms are specialists living within a narrow range of conditions. Pathogens are often adapted to efficiently exploit only a few hosts species, or sometimes, only some genotypes within a species. The genomes of such parasites are predicted to maintain genes critical for host utilization and to lose genes no longer necessary outside their constrained lifestyle. We demonstrate that the genomic content of a fungal pathogen specialized to attack and consume fungus cultivated by ants meets these predictions. Despite a reduced genome size and gene content in comparison with less specialized relatives, the genome of this agricultural pathogen retains genes necessary for production of toxins, a step critical to host attack, and for breaking down nutrients abundant in its host.
Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor
Authors: Song Min-Suk , Kumar Gyanendra , Shadrick William R. , Zhou Wei , Jeevan Trushar , Li Zhenmei , Slavish P. Jake , Fabrizio Thomas P. , Yoon Sun-Woo , Webb Thomas R. , Webby Richard J. , White Stephen W.
Published: March 2016

Significance

The endonuclease domain within the influenza virus heterotrimeric replication machinery is essential and represents an attractive drug target. It is important to understand the structural basis of potential inhibitor resistance, to design appropriate inhibitors and to prioritize drug candidates that are unlikely to cause the rapid development of clinically-relevant resistance mutations. Using a prototypical endonuclease inhibitor (L-742,001), we used mutagenesis to select for replication competent resistant mutants and studied the structural and functional basis for the observed resistance. These studies confirm that the endonuclease domain is an excellent drug target for treating influenza. They also provide reagents (mutant viruses and constructs) and crucial pharmacophore knowledge that will aid in the development of new drug candidates for urgently needed influenza therapies.
Autocratic strategies for iterated games with arbitrary action spaces
Authors: McAvoy Alex , Hauert Christoph
Published: March 2016

Significance

Games with two actions (“cooperate” and “defect”) have been extremely useful in modeling biological interactions. Despite their utility, however, there are many naturally occurring encounters that these games cannot fully capture. For example, the effort expended in animal grooming or the rate of siderophore production by microbes can take on a continuous range of values. Such interactions are better modeled by games with more general (continuous) action spaces. In this setting, we prove the existence of autocratic strategies that unilaterally enforce linear relationships on the payoffs for repeated games. In particular, we show that a player can often enforce such a relationship by playing only two actions throughout the repeated game.
Acetyl-CoA carboxylase inhibition by ND-630 reduces hepatic steatosis, improves insulin sensitivity, and modulates dyslipidemia in rats
Authors: Harriman Geraldine , Greenwood Jeremy , Bhat Sathesh , Huang Xinyi , Wang Ruiying , Paul Debamita , Tong Liang , Saha Asish K. , Westlin William F. , Kapeller Rosana , Harwood H. James
Published: March 2016

Significance

Using structure-based drug design, we have identified a series of potent allosteric protein–protein interaction acetyl-CoA carboxylase inhibitors, exemplified by ND-630, that interact within the acetyl-CoA carboxylase subunit phosphopeptide acceptor and dimerization site to prevent dimerization and inhibit enzymatic activity. ND-630 reduces fatty acid synthesis and stimulates fatty acid oxidation in cultured cells and experimental animals, reduces hepatic steatosis, improves insulin sensitivity, reduces weight gain without affecting food intake, and favorably affects dyslipidemia in diet-induced obese rats and reduces hepatic steatosis, improves glucose-stimulated insulin secretion, and reduces hemoglobin A1c in Zucker diabetic fatty rats. These data suggest that ND-630 may be useful in treating a variety of metabolic disorders, including metabolic syndrome, type 2 diabetes, and fatty liver disease.
Discovery of fairy circles in Australia supports self-organization theory
Authors: Getzin Stephan , Yizhaq Hezi , Bell Bronwyn , Erickson Todd E. , Postle Anthony C. , Katra Itzhak , Tzuk Omer , Zelnik Yuval R. , Wiegand Kerstin , Wiegand Thorsten , Meron Ehud
Published: March 2016

Significance

Pattern-formation theory predicts that vegetation gap patterns, such as the fairy circles of Namibia, emerge through the action of pattern-forming biomass–water feedbacks and that such patterns should be found elsewhere in water-limited systems around the world. We report here the exciting discovery of fairy-circle patterns in the remote outback of Australia. Using fieldwork, remote sensing, spatial pattern analysis, mathematical modeling, and pattern-formation theory we show that the Australian gap patterns share with their Namibian counterparts the same characteristics but are driven by a different biomass–water feedback. These observations are in line with a central universality principle of pattern-formation theory and support the applicability of this theory to wider contexts of spatial self-organization in ecology.
Open complex scrunching before nucleotide addition accounts for the unusual transcription start site of
E. coli
ribosomal RNA promoters
Authors: Winkelman Jared T. , Chandrangsu Pete , Ross Wilma , Gourse Richard L.
Published: March 2016

Significance

Although it has long been appreciated that there are multiple RNA polymerase recognition elements in promoters, the determinants of transcription start site (TSS) selection are poorly understood. We find here that the absence of strong interactions between σ and the –10 element region of
Escherichia coli
rRNA promoters results in expansion of the transcription bubble prior to nucleotide addition, a phenomenon referred to as scrunching. Open complex scrunching accounts for the unusually long distance between the –10 element and the TSS and appears to contribute to the extraordinary activity of these promoters by minimizing abortive product formation, thereby increasing transcriptional output. These data provide insights into the determinants of TSS selection, promoter function, and promoter evolution.
Reevaluation of whether a soma–to–germ-line transformation extends lifespan in
Caenorhabditis elegans
Authors: Knutson Andrew Kekūpa'a , Rechtsteiner Andreas , Strome Susan
Published: March 2016

Significance

Understanding the genetic mechanisms that control lifespan is essential for the development of regenerative therapies that seek to reverse the aging process. In the nematode
Caenorhabditis elegans
, long-lived mutants that are defective in insulin signaling up-regulate a number of stress response genes to promote survival. A study published in 2009 reported that these long-lived mutants also express in their somatic cells factors that are normally restricted to germ cells and that these mutants rely on germ-line factors for some of their lifespan extension. Our studies call these findings into question and instead suggest that expression of certain germ-line factors in the somatic cells of worms is detrimental to the health of worms and reduces lifespan.
Aurone synthase is a catechol oxidase with hydroxylase activity and provides insights into the mechanism of plant polyphenol oxidases
Authors: Molitor Christian , Mauracher Stephan Gerhard , Rompel Annette
Published: March 2016

Significance

Catechol oxidases and tyrosinases belong to the family of polyphenol oxidases (PPOs). In contrast to tyrosinases, catechol oxidases were so far defined to lack hydroxylase activity toward monophenols. Aurone synthase (AUS1) is a plant catechol oxidase that specializes in the conversion of chalcones to aurones (flower pigments). We evidence for the first time, to our knowledge, hydroxylase activity for a catechol oxidase (AUS1) toward its natural monophenolic substrate (chalcone). The presented first crystal structure of a plant pro-PPO provides insights into its activation mechanisms, and based on biochemical and structural studies of AUS1, we propose a novel catalytic reaction mechanism for plant PPOs. The proven hydroxylase functionality of AUS1 suggests that other catechol oxidases might also be involved in the plant’s secondary metabolism.
Carnosic acid biosynthesis elucidated by a synthetic biology platform
Authors: Ignea Codruta , Athanasakoglou Anastasia , Ioannou Efstathia , Georgantea Panagiota , Trikka Fotini A. , Loupassaki Sofia , Roussis Vassilios , Makris Antonios M. , Kampranis Sotirios C.
Published: March 2016

Significance

Here we report on the development of a modular terpene production platform as a screening tool for the functional characterization of next-generation sequencing information and on the application of this system in the characterization of the biosynthetic pathway leading to the potent antioxidant carnosic acid in
Lamiaceae
. In addition to revealing an important plant natural product biosynthetic pathway, this work highlights the usefulness of synthetic biology approaches in the elucidation of plant natural product biosynthetic pathways and develops yeast as a tool to exploit the wealth of next-generation sequencing data that are constantly being produced through transcriptomic, genomic, or metagenomic studies. The approach described here will be useful to numerous researchers studying terpene biosynthesis in plants and microorganisms.
Truncated mu opioid GPCR variant involvement in opioid-dependent and opioid-independent pain modulatory systems within the CNS
Authors: Marrone Gina F. , Grinnell Steven G. , Lu Zhigang , Rossi Grace C. , Le Rouzic Valerie , Xu Jin , Majumdar Susruta , Pan Ying-Xian , Pasternak Gavril W.
Published: March 2016

Significance

Many classes of G protein-coupled receptors (GPCRs) produce truncated variants. Truncated forms of the mu opioid receptor gene
Oprm1
containing only six transmembrane domains (6TM) can mediate a potent analgesia without producing many classical opioid side effects. We now show that 6TM
Oprm1
splice variants are essential in the analgesic actions of delta and kappa opioids as well as α
2
adrenergic drugs, but not neurotensin, cannabinoids, or muscarinic drugs. The role of the 6TM variants seems limited to analgesia because they are not involved with kappa aversion, delta-induced seizure activity, or α
2
adrenergic hypolocomotion. These findings emphasize the importance of 6TM
Oprm1
variants in opioid and nonopioid sensory processing and illustrate the potential importance of the vast array of other classes of truncated GPCR variants.
New inducible genetic method reveals critical roles of GABA in the control of feeding and metabolism
Authors: Meng Fantao , Han Yong , Srisai Dollada , Belakhov Valery , Farias Monica , Xu Yong , Palmiter Richard D. , Baasov Timor , Wu Qi
Published: March 2016

Significance

We established a new genetic method for rapidly activating Cre recombinase that is based on suppression of a nonsense codon within Cre by a new generation of aminoglycosides. We applied this strategy to successfully silence both enzymes responsible for GABA biosynthesis in hypothalamic agouti-related peptide (AgRP) neurons that control appetite and other behaviors. Inactivation of GABA signaling in AgRP neurons of young adult mice resulted in severe loss of body weight and abnormal glucose metabolism, whereas older mice only manifested transient appetite deficiency. This genetic system adds another robust tool that can be used to understand complex neurological processes.
Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives
Authors: Sjuts Hanno , Vargiu Attilio V. , Kwasny Steven M. , Nguyen Son T. , Kim Hong-Suk , Ding Xiaoyuan , Ornik Alina R. , Ruggerone Paolo , Bowlin Terry L. , Nikaido Hiroshi , Pos Klaas M. , Opperman Timothy J.
Published: March 2016

Significance

AcrB is one of the major multidrug resistance-conferring antibiotic efflux pumps from pathogenic bacteria. We have designed and produced the periplasmic, substrate binding domain of AcrB and solved its crystal structure in complex with multiple novel pyranopyridine inhibitors, as well as with drugs transported by AcrB. The structural data are corroborated by various cellular assays and molecular dynamics (MD) simulations, and allow us to propose a mechanism for AcrB efflux inhibition. Furthermore, the results provide a molecular platform for the development of combinational therapies against pathogenic Enterobacteriaceae.
Recognition of the disordered p53 transactivation domain by the transcriptional adapter zinc finger domains of CREB-binding protein
Authors: Krois Alexander S. , Ferreon Josephine C. , Martinez-Yamout Maria A. , Dyson H. Jane , Wright Peter E.
Published: March 2016

Significance

The tumor suppressor p53 regulates the cellular response to genomic damage by recruiting the transcriptional coactivator cyclic-AMP response element-binding protein (CREB)-binding protein (CBP) and its paralog p300 to activate stress response genes. We report NMR structures of the complexes formed between the full-length, intrinsically disordered N-terminal transactivation domain of p53 and the transcriptional adapter zinc finger domains (TAZ1 and TAZ2) of CBP. Exchange broadening of NMR spectra of the complexes was ameliorated by using fusion proteins and segmental isotope labeling. The structures show how the p53 transactivation domain uses bipartite binding motifs to recognize diverse partners, reveal the critical interactions required for high affinity binding, and provide insights into the mechanism by which phosphorylation enhances the ability of p53 to recruit CBP and p300.
Re-evaluation of the roles of
DROSHA
,
Exportin 5
, and
DICER
in microRNA biogenesis
Authors: Kim Young-Kook , Kim Boseon , Kim V. Narry
Published: March 2016

Significance

MicroRNAs (miRNAs) are noncoding RNAs with diverse roles in development and pathogenesis. Biogenesis of canonical miRNA requires nuclear processing by DROSHA, nuclear export by Exportin 5, and cytoplasmic processing by DICER. To gain a deeper understanding of the maturation processes, we here ablated the
DROSHA
,
Exportin 5
, and
DICER
genes using the same human cell line. Canonical miRNA production was abolished in
DROSHA
-deleted cells, revealing an irreplaceable role of DROSHA. Interestingly, however, some canonical miRNAs were still produced without DICER albeit at markedly reduced levels, and many were detected in
Exportin 5
-deleted cells at only modestly decreased levels. Our study allows us to understand differential contributions of key biogenesis factors, and provides valuable resources for miRNA research.
Transient contractions of urinary bladder smooth muscle are drivers of afferent nerve activity during filling
Authors: Heppner Thomas J. , Tykocki Nathan R. , Hill-Eubanks David , Nelson Mark T.
Published: March 2016

Activation of afferent nerves during urinary bladder (UB) filling conveys the sensation of UB fullness to the central nervous system (CNS). Although this sensory outflow is presumed to reflect graded increases in pressure associated with filling, UBs also exhibit nonvoiding, transient contractions (TCs) that cause small, rapid increases in intravesical pressure. Here, using an ex vivo mouse bladder preparation, we explored the relative contributions of filling pressure and TC-induced pressure transients to sensory nerve stimulation. Continuous UB filling caused an increase in afferent nerve activity composed of a graded increase in baseline activity and activity associated with increases in intravesical pressure produced by TCs. For each ∼4-mmHg pressure increase, filling pressure increased baseline afferent activity by ∼60 action potentials per second. In contrast, a similar pressure elevation induced by a TC evoked an ∼10-fold greater increase in afferent activity. Filling pressure did not affect TC frequency but did increase the TC rate of rise, reflecting a change in the length-tension relationship of detrusor smooth muscle. The frequency of afferent bursts depended on the TC rate of rise and peaked before maximum pressure. Inhibition of small- and large-conductance Ca2+-activated K+ (SK and BK) channels increased TC amplitude and afferent nerve activity. After inhibiting detrusor muscle contractility, simulating the waveform of a TC by gently compressing the bladder evoked similar increases in afferent activity. Notably, afferent activity elicited by simulated TCs was augmented by SK channel inhibition. Our results show that afferent nerve activity evoked by TCs represents the majority of afferent outflow conveyed to the CNS during UB filling and suggest that the maximum TC rate of rise corresponds to an optimal length-tension relationship for efficient UB contraction. Furthermore, our findings implicate SK channels in controlling the gain of sensory outflow independent of UB contractility.
Droughts may increase susceptibility of prairie dogs to fleas: incongruity with hypothesized mechanisms of plague cycles in rodents
Authors: Eads David A. , Biggins Dean E. , Long Dustin H. , Gage Kenneth L. , Antolin Michael F.
Published: March 2016

Plague is a reemerging, rodent-associated zoonosis caused by the flea-borne bacterium Yersinia pestis. As a vector-borne disease, rates of plague transmission may increase when fleas are abundant. Fleas are highly susceptible to desiccation under hot-dry conditions; we posited that their densities decline during droughts. We evaluated this hypothesis with black-tailed prairie dogs (Cynomys ludovicianus) in New Mexico, June–August 2010–2012. Precipitation was relatively plentiful during 2010 and 2012 but scarce during 2011, the driest spring–summer on record for the northeastern grasslands of New Mexico. Unexpectedly, fleas were 200% more abundant in 2011 than in 2010 and 2012. Prairie dogs were in 27% better condition during 2010 and 2012, and they devoted 287% more time to grooming in 2012 than in 2011. During 2012, prairie dogs provided with supplemental food and water were in 23% better condition and carried 40% fewer fleas. Collectively, these results suggest that during dry years, prairie dogs are limited by food and water, and they exhibit weakened defenses against fleas. Long-term data are needed to evaluate the generality of whether droughts increase flea densities and how changes in flea abundance during sequences of dry and wet years might affect plague cycles in mammalian hosts.
Effects of Kernel Vitreousness and Protein Level on Protein Molecular Weight Distribution, Milling Quality, and Breadmaking Quality in Hard Red Spring Wheat
Authors: Baasandorj Tsogtbayar , Ohm Jae‐Bom , Simsek Senay
Published: March 2016

Dark, hard, and vitreous kernel content is an important grading characteristic for hard red spring (HRS) wheat in the United States. This research investigated the associations of kernel vitreousness (KV) and protein content (PC) levels with protein molecular weight distribution (MWD), milling quality, and breadmaking quality characteristics of HRS wheat. The U.S. regional crop quality survey samples from three consecutive growing years were combined into three composite samples with different levels of wheat PC and then further segregated into separate samples with three different levels of KV. Analysis of variance showed that KV level had significant (P < 0.001) effect on variation in test weight, break flour yield, and damaged starch content. Among protein MWD parameters analyzed by size‐exclusion HPLC, the high‐molecular‐weight polymeric proteins in the SDS‐unextractable fraction had significant (P < 0.01) association with KV. Regression analysis indicated that addition of KV to the PC level improved the model for both farinograph and baking water absorption values in all three growing years. This information could help the flour milling and baking industries to further segregate HRS wheat based on KV levels in addition to PC levels for their intended end‐use applications.
Blueberry necrotic ring blotch virus in Southern Highbush Blueberry: Insights into In Planta and In-Field Movement
Authors: Robinson Tanisha S. , Scherm Harald , Brannen Phillip M. , Allen Renee , Deom C. Michael
Published: March 2016

Blueberry necrotic ring blotch virus (BNRBV) causes an emerging disease of southern highbush blueberry (SHB) in the southeastern United States. Disease incidence and severity vary considerably from year to year within the same planting. Experiments were conducted to determine how the virus spreads in the field. Leaf tissue from symptomatic field plants tested positive for BNRBV in 2011, whereas the same plants were asymptomatic in 2012 and tested negative for the virus. Symptomatic and asymptomatic leaves from individual shoots were tested for the presence of the virus, and symptomatic leaves tested positive (100%), whereas 65.4% of the asymptomatic leaves from the same shoots tested negative. Leaves were selected in which half the leaf blade was symptomatic and the other half was not; symptomatic leaf halves tested positive (100%), whereas 76.0% of the asymptomatic halves from the same leaf tested negative for the virus. When virus-free, potted trap plants were interspersed in the field among established plants that had shown disease symptoms the previous year, disease onset in trap plants was observed 2 to 3 weeks after disease onset in field plants. In a separate experiment, asymptomatic softwood cuttings were collected from mother plants symptomatic for BNRBV, rooted, and monitored for symptom development for a period of 12 to 27 months. No BNRBV symptoms were observed in the progeny, whereas disease incidence was high for cuttings taken at the same time from plants infected with Blueberry red ringspot virus used as a control. Collectively, these studies suggest that BNRBV does not infect SHB plants systemically and is not transmitted through vegetative propagation, and that the virus likely does not persist in plants after natural defoliation in the fall.
How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model
Authors: Starrfelt Jostein , Liow Lee Hsiang
Published: March 2016

The fossil record is a rich source of information about biological diversity in the past. However, the fossil record is not only incomplete but has also inherent biases due to geological, physical, chemical and biological factors. Our knowledge of past life is also biased because of differences in academic and amateur interests and sampling efforts. As a result, not all individuals or species that lived in the past are equally likely to be discovered at any point in time or space. To reconstruct temporal dynamics of diversity using the fossil record, biased sampling must be explicitly taken into account. Here, we introduce an approach that uses the variation in the number of times each species is observed in the fossil record to estimate both sampling bias and true richness. We term our technique TRiPS (
T
rue
Ri
chness estimated using a
P
oisson
S
ampling model) and explore its robustness to violation of its assumptions via simulations. We then venture to estimate sampling bias and absolute species richness of dinosaurs in the geological stages of the Mesozoic. Using TRiPS, we estimate that 1936 (1543–2468) species of dinosaurs roamed the Earth during the Mesozoic. We also present improved estimates of species richness trajectories of the three major dinosaur clades: the sauropodomorphs, ornithischians and theropods, casting doubt on the Jurassic–Cretaceous extinction event and demonstrating that all dinosaur groups are subject to considerable sampling bias throughout the Mesozoic.
Quantifying the effects of the break up of Pangaea on global terrestrial diversification with neutral theory
Authors: Jordan Sean M. R. , Barraclough Timothy G. , Rosindell James
Published: March 2016

The historic richness of most taxonomic groups increases substantially over geological time. Explanations for this fall broadly into two categories: bias in the fossil record and elevated net rates of diversification in recent periods. For example, the break up of Pangaea and isolation between continents might have increased net diversification rates. In this study, we investigate the effect on terrestrial diversification rates of the increased isolation between land masses brought about by continental drift. We use ecological neutral theory as a means to study geologically complex scenarios tractably. Our models show the effects of simulated geological events that affect all species equally, without the added complexity of further ecological processes. We find that continental drift leads to an increase in diversity only where isolation between continents leads to additional speciation through vicariance, and where higher taxa with very low global diversity are considered. We conclude that continental drift by itself is not sufficient to account for the increase in terrestrial species richness observed in the fossil record.
The impact of Cenozoic cooling on assemblage diversity in planktonic foraminifera
Authors: Fenton Isabel S. , Pearson Paul N. , Dunkley Jones Tom , Farnsworth Alexander , Lunt Daniel J. , Markwick Paul , Purvis Andy
Published: March 2016

The Cenozoic planktonic foraminifera (PF) (calcareous zooplankton) have arguably the most detailed fossil record of any group. The quality of this record allows models of environmental controls on macroecology, developed for Recent assemblages, to be tested on intervals with profoundly different climatic conditions. These analyses shed light on the role of long-term global cooling in establishing the modern latitudinal diversity gradient (LDG)—one of the most powerful generalizations in biogeography and macroecology. Here, we test the transferability of environment-diversity models developed for modern PF assemblages to the Eocene epoch (approx. 56–34 Ma), a time of pronounced global warmth. Environmental variables from global climate models are combined with Recent environment–diversity models to predict Eocene richness gradients, which are then compared with observed patterns. The results indicate the modern LDG—lower richness towards the poles—developed through the Eocene. Three possible causes are suggested for the mismatch between statistical model predictions and data in the Early Eocene: the environmental estimates are inaccurate, the statistical model misses a relevant variable, or the intercorrelations among facets of diversity—e.g. richness, evenness, functional diversity—have changed over geological time. By the Late Eocene, environment–diversity relationships were much more similar to those found today.
Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data
Authors: Silvestro Daniele , Zizka Alexander , Bacon Christine D. , Cascales-Miñana Borja , Salamin Nicolas , Antonelli Alexandre
Published: March 2016

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.
A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology
Authors: Price S. A. , Schmitz L.
Published: March 2016

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart.