bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeting Nucleic Acids using Dynamic Combinatorial Chemistry
Authors: Durai Chandramathi R. Sherman , Harding Margaret M.
Published: February 2014

Dynamic combinatorial chemistry (DCC) is a powerful method for the identification of novel ligands for the molecular recognition of receptor molecules. The method relies on self-assembly processes to generate libraries of compounds under reversible conditions, allowing a receptor molecule to select the optimal binding ligand from the mixture. However, while DCC is now an established field of chemistry, there are limited examples of the application of DCC to nucleic acids. The requirement to conduct experiments under physiologically relevant conditions, and avoid reaction with, or denaturation of, the target nucleic acid secondary structure, limits the choice of the reversible chemistry, and presents restrictions on the building block design. This review will summarize recent examples of applications of DCC to the recognition of nucleic acids. Studies with duplex DNA, quadruplex DNA, and RNA have utilized mainly thiol disulfide libraries, although applications of imine libraries, in combination with metal coordination, have been reported. The use of thiol disulfide libraries produces lead compounds with limited biostability, and hence design of stable analogues or mimics is required for many applications.
Quantifying causal mechanisms to determine how protected areas affect poverty through changes in ecosystem services and infrastructure
Authors: Ferraro Paul J. , Hanauer Merlin M.
Published: February 2014

Significance

Scholars are accumulating evidence about the effects of environmental programs on social outcomes. Quantifying these effects is important, but to design better programs we need to understand how these effects arise. Little is known about the mechanisms through which ecosystem conservation programs affect human welfare. Our study demonstrates that, with existing data and appropriate empirical designs, scientists and policymakers can elucidate these previously unidentified mechanisms. We estimate how Costa Rica’s protected area system reduced poverty in neighboring communities. Nearly two-thirds of the impact is causally attributable to opportunities afforded by tourism. The rest is attributable to unobserved mechanisms. Changes in infrastructure or land cover contributed little, on average, to poverty reduction.
Task context impacts visual object processing differentially across the cortex
Authors: Harel Assaf , Kravitz Dwight J. , Baker Chris I.
Published: February 2014

Significance

Visual recognition is often thought to depend on neural representations that primarily reflect the physical properties of the environment. However, in this study we demonstrate that the intent of the observer fundamentally perturbs cortical representations of visual objects. Using functional MRI we measured the patterns of response to identical objects under six different tasks. In any given task, these patterns could be used to distinguish which object was being viewed. However, this ability was disrupted when the task changed, indicating that object representations reflect not only the physical properties of the stimulus, but also the internal state of the observer.
Obstacles to integrated pest management adoption in developing countries
Authors: Parsa Soroush , Morse Stephen , Bonifacio Alejandro , Chancellor Timothy C. B. , Condori Bruno , Crespo-Pérez Verónica , Hobbs Shaun L. A. , Kroschel Jürgen , Ba Malick N. , Rebaudo François , Sherwood Stephen G. , Vanek Steven J. , Faye Emile , Herrera Mario A. , Dangles Olivier
Published: February 2014

Significance

Integrated pest management (IPM) has been the dominant crop protection paradigm promoted globally since the 1960s. However, its adoption by developing country farmers is surprisingly low. This article reports 51 potential reasons why, identified and prioritized by hundreds of IPM professionals and practitioners around the world. Stakeholders from developing countries prioritized different adoption obstacles than those from high-income countries. Surprisingly, a few of the obstacles prioritized in developing countries appear to be overlooked by the literature. We suggest that a more vigorous analysis and discussion of the factors discouraging IPM adoption in developing countries may accelerate the progress needed to bring about its full potential.
Agreeing to disagree on climate policy
Authors: Heal Geoffrey M. , Millner Antony
Published: February 2014

Significance

The social cost of carbon—the cost to society of an additional ton of CO2emissions—is a crucial measure of the desirable intensity of climate policy. The models economists use to calculate it, however, are highly sensitive to the choice of discount rate, which measures our concern for the well-being of future generations. Different economists favor different values, and this leads to radically different policy prescriptions. We present a method for combining a diverse set of discount rates into a single “representative” rate and apply it to the analysis of the social cost of carbon performed by the US government. This approach may help resolve ethical conflicts and, hence, lead to consensus policy recommendations.
Oral glycotoxins are a modifiable cause of dementia and the metabolic syndrome in mice and humans
Authors: Cai Weijing , Uribarri Jaime , Zhu Li , Chen Xue , Swamy Shobha , Zhao Zhengshan , Grosjean Fabrizio , Simonaro Calogera , Kuchel George A. , Schnaider-Beeri Michal , Woodward Mark , Striker Gary E. , Vlassara Helen
Published: February 2014

Significance

Suppression of NAD
+
-dependent sirtuin 1 (SIRT1) is linked to dementia or Alzheimer’s disease (AD) and the metabolic syndrome (MS). Because advanced glycation end products (AGEs) promote MS and neurotoxicity, we conducted studies of C57BL6 mice fed isocaloric diets containing defined AGEs [methyl-glyoxal derivatives (MG)] to determine whether food AGEs promote AD and MS. MG
+
-fed, but not MG
−
-fed, mice developed brain SIRT1 deficiency, amyloid-β deposits, cognitive and motor deficits, and MS. These findings were validated in older healthy humans with high baseline circulating MG levels by a time-dependent decline in cognition and insulin sensitivity. The data suggest that food-derived AGEs, an environmental factor, contribute to both AD and MS by causing chronic SIRT1 suppression. Importantly, reduction of food-derived AGEs is feasible and may provide an effective treatment strategy for both these epidemics.
Using thermal boundary conditions to engineer the quantum state of a bulk magnet
Authors: Schmidt M. A. , Silevitch D. M. , Aeppli G. , Rosenbaum T. F.
Published: February 2014

Significance

The interactions of a material with its environment can determine its behavior and induce changes of state. We show that, at temperatures near absolute zero, a magnetic material can be made more quantum mechanical by isolating it from the environment. Local clusters of spins within the material stay liquid and refuse to freeze. An oscillating magnetic field serves as an effective tool to address and manipulate these “protected” spin clusters, while a DC magnetic field can enhance the spin-tunneling rate and lead to quantum speedup. When the material is more strongly connected to a heat bath, the local magnetic clusters behave more classically and freeze en masse into a glassy state.
The ecology in the hematopoietic stem cell niche determines the clinical outcome in chronic myeloid leukemia
Authors: MacLean Adam L. , Filippi Sarah , Stumpf Michael P. H.
Published: February 2014

Significance

Three contrasting models of the ecological interactions in the hematopoietic stem cell niche explain clinical progression of chronic myeloid leukemia equally well, but do so in different ways. We identify key differences between models and find that we can conclusively rule out those that fail to take competition between healthy and leukemic lineages explicitly into account. Detailed analysis of population dynamics within the bone marrow niche allows us to ascribe mechanisms to distinct disease outcomes and suggests experiments to distinguish between these mechanisms.
Self-assembly of the general membrane-remodeling protein PVAP into sevenfold virus-associated pyramids
Authors: Daum Bertram , Quax Tessa E. F. , Sachse Martin , Mills Deryck J. , Reimann Julia , Yildiz Özkan , Häder Sabine , Saveanu Cosmin , Forterre Patrick , Albers Sonja-Verena , Kühlbrandt Werner , Prangishvili David
Published: February 2014

Significance

The
Sulfolobus islandicus
rod-shaped virus 2 (SIRV2) has developed unique mechanisms to penetrate the plasma membrane and S-layer of its host
Sulfolobus islandicus
in order to leave the cell after replication. SIRV2 encodes the 10-kDa protein PVAP, which assembles into sevenfold symmetric virus-associated pyramids (VAPs) in the host cell plasma membrane. Toward the end of the viral replication cycle, these VAPs open to form pores through the plasma membrane and S-layer, allowing viral egress. Here we show that PVAP inserts spontaneously and forms VAPs in any kind of biological membrane. By electron cryotomography we have obtained a 3D map of the VAP and present a model describing the assembly of PVAP into VAPs. Our findings open new avenues for a large variety of biotechnological applications.
Loss of mTOR complex 1 induces developmental blockage in early T-lymphopoiesis and eradicates T-cell acute lymphoblastic leukemia cells
Authors: Hoshii Takayuki , Kasada Atsuo , Hatakeyama Tomoki , Ohtani Masashi , Tadokoro Yuko , Naka Kazuhito , Ikenoue Tsuneo , Ikawa Tomokatsu , Kawamoto Hiroshi , Fehling Hans Joerg , Araki Kimi , Yamamura Ken-ichi , Matsuda Satoshi , Hirao Atsushi
Published: February 2014

Significance

mTOR, a kinase that senses and responds to nutrients, plays critical roles in organogenesis and tumorigenesis. Although mTOR inhibitors have been developed as immunosuppressants and anticancer drugs, it has remained controversial whether such medications contribute to cancer eradication. In addition, mTOR inhibition by chemical inhibitors is complicated because it may not produce predictable inhibition of the mTOR complexes mTORC1 and mTORC2. By using a genetic approach, our study clearly demonstrates that mTORC1, but not mTORC2, is essential for cell cycling of early T-cell progenitors. More importantly, we reveal that loss of mTORC1 efficiently eradicates T-cell acute lymphoblastic leukemia cells, but not myeloid leukemia. Thus, understanding the cell-context–dependent role of mTOR illustrates the potential importance of mTOR signals as therapeutic targets.
Chemical defenses and resource trade-offs structure sponge communities on Caribbean coral reefs
Authors: Loh Tse-Lynn , Pawlik Joseph R.
Published: February 2014

Significance

Chemical defenses are known to protect some species from consumers, but it is often difficult to detect this advantage at the community or ecosystem levels because of the complexity of abiotic and biotic factors that influence species abundances. We surveyed the community of sponges and sponge predators (angelfishes and parrotfishes) on coral reefs across the Caribbean ranging from heavily overfished sites to protected marine reserves. High predator abundance correlated with high abundance of chemically defended sponge species, but reefs with few predators were dominated by undefended sponge species, which grow or reproduce faster than defended species. Overfishing may enhance competition between palatable sponge species and reef-building stony corals, further impeding the recovery of Caribbean coral reefs.
Niemann–Pick type C2 protein mediating chemical communication in the worker ant
Authors: Ishida Yuko , Tsuchiya Wataru , Fujii Takeshi , Fujimoto Zui , Miyazawa Mitsuhiro , Ishibashi Jun , Matsuyama Shigeru , Ishikawa Yukio , Yamazaki Toshimasa
Published: February 2014

Significance

Worker ants are responsible for various tasks for their colony. In their chemical communication, odorant-binding proteins and chemosensory proteins, which accumulate in the sensillum lymph in the antennae, play roles in transporting semiochemicals to chemosensory receptors. However, the number of these proteins is not sufficient to interact with a large number of semiochemicals. Niemann–Pick type C2 protein was identified from the antenna of the worker Japanese carpenter ant,
Camponotus japonicus
(CjapNPC2). CjapNPC2 accumulated in the sensillum cavity in the basiconic sensillum. The ligand-binding pocket was composed of a flexible β-structure, which allowed binding to various potential semiochemicals, some of which elicited antennal electrophysiological responses. CjapNPC2 might play crucial roles in chemical communication required to perform worker ant tasks.
Communication modes
Authors: Zbenovich Claudia
Published: February 2014

The article discusses linguistic forms and pragmatic features of the verbal interaction that occurred in interviews with Russian politicians in the last decade of the 20th century. The genre of political interview emerged in Russia after the fall of the Soviet Union; it was exposed to different trends in verbal communication, gradually shaping its own discourse norms and structure. The study investigates the ways of expression by communicants their intentions and offers a comparative analysis of the ‘talk’ and ‘attack’ interview styles. These two counter types of political discourse dramatically illustrate the inherent features of the Russian culture of communication as a whole.
What statements do not state
Authors: Pozhidaev Dmitry D.
Published: February 2014

Building on the ideas of Michel Foucault and Jacque Derrida, the paper examines a statement issued by the Serb Orthodox Church in Kosovo as an example of particular political discourse. The paper draws on the concept of problematization to reveal explicit and implicit aspects of this discourse. Combining the analytical framework used for Critical Discourse Analysis with that designed for analysis of conflict situations, the paper contends that the analyzed discourse contains explicit as well as implicit topics, sometimes complementary and sometimes mutually contradictory. The paper analyzes the practical consequences of the statement’s implicit problematization, arguing that this problematization leads to further confrontation and leaves no option for the Serb community in Kosovo. An analysis of the emotional aspect of the implicit problematization, which the text contains, shows that it represents a discourse of fear and rejection, not that of understanding and reconciliation. In conclusion, the paper introduces some “what if’s” pointing out several topics in the statement’s discourse which can and should be questioned and revised to open up prospects for survival of the Serb community in Kosovo.
Presuppositions and strategic functions in Bush’s 20/9/2001 speech
Authors: Mazid Bahaa-eddin M.
Published: February 2014

This paper provides a critical discourse analysis of presuppositions and strategic functions, in addition to brief comments on the use of propaganda devices in the speech delivered by George W. Bush nine days after the attacks on the World Trade Center and the Pentagon and some other US targets, September 11, 2001. This approach makes it possible to explore the tension between idealism and pragmatism, the conflict between ‘us’ and ‘them’, and the other aspects of ideologies and power relationships found in the speech.
What does ‘we’ mean?
Authors: Petersoo Pille
Published: February 2014

The contextual nature of deictic expressions, including the personal pronoun ‘we’, is a given to linguists, but has only recently caught the interest of social scientists. The following article, firmly grounded in sociology, attempts to introduce some linguistic concepts while looking at the role of the personal pronoun ‘we’ in the discursive construction of national identities in the media. Focusing on Scotland, and looking at media language in the context of constitutional change in the United Kingdom, the article shows how different category relations are created through the ambiguous and under-specified use of deictic expressions. Scotland provides an interesting case study for such analysis, as references to the ‘nation’ during the 20th century have been ambiguous, sometimes referring to Scotland, sometimes to Britain. Consequently, the media/nation relationship has been contested, and this is reflected in media language. The paper introduces the concept of a wandering ‘we’ to describe the shifting reference point of the deictic expressions and situates this phenomenon in the wider nationalism literature. By doing this, the article revisits some of the notions introduced by Billig in his Banal Nationalism.
Senescence-inducing stress promotes proteolysis of phosphoglycerate mutase via ubiquitin ligase Mdm2
Authors: Mikawa Takumi , Maruyama Takeshi , Okamoto Koji , Nakagama Hitoshi , Lleonart Matilde E. , Tsusaka Takeshi , Hori Kousuke , Murakami Itsuo , Izumi Taisuke , Takaori-Kondo Akifumi , Yokode Masayuki , Peters Gordon , Beach David , Kondoh Hiroshi
Published: February 2014

Despite the well-documented clinical significance of the Warburg effect, it remains unclear how the aggressive glycolytic rates of tumor cells might contribute to other hallmarks of cancer, such as bypass of senescence. Here, we report that, during oncogene- or DNA damage–induced senescence, Pak1-mediated phosphorylation of phosphoglycerate mutase (PGAM) predisposes the glycolytic enzyme to ubiquitin-mediated degradation. We identify Mdm2 as a direct binding partner and ubiquitin ligase for PGAM in cultured cells and in vitro. Mutations in PGAM and Mdm2 that abrogate ubiquitination of PGAM restored the proliferative potential of primary cells under stress conditions and promoted neoplastic transformation. We propose that Mdm2, a downstream effector of p53, attenuates the Warburg effect via ubiquitination and degradation of PGAM.
Nuclear lamin stiffness is a barrier to 3D migration, but softness can limit survival
Authors: Harada Takamasa , Swift Joe , Irianto Jerome , Shin Jae-Won , Spinler Kyle R. , Athirasala Avathamsa , Diegmiller Rocky , Dingal P.C. Dave P. , Ivanovska Irena L. , Discher Dennis E.
Published: February 2014

Cell migration through solid tissue often involves large contortions of the nucleus, but biological significance is largely unclear. The nucleoskeletal protein lamin-A varies both within and between cell types and was shown here to contribute to cell sorting and survival in migration through constraining micropores. Lamin-A proved rate-limiting in 3D migration of diverse human cells that ranged from glioma and adenocarcinoma lines to primary mesenchymal stem cells (MSCs). Stoichiometry of A- to B-type lamins established an activation barrier, with high lamin-A:B producing extruded nuclear shapes after migration. Because the juxtaposed A and B polymer assemblies respectively conferred viscous and elastic stiffness to the nucleus, subpopulations with different A:B levels sorted in 3D migration. However, net migration was also biphasic in lamin-A, as wild-type lamin-A levels protected against stress-induced death, whereas deep knockdown caused broad defects in stress resistance. In vivo xenografts proved consistent with A:B-based cell sorting, and intermediate A:B-enhanced tumor growth. Lamins thus impede 3D migration but also promote survival against migration-induced stresses.
Co-targeting of convergent nucleotide biosynthetic pathways for leukemia eradication
Authors: Nathanson David A. , Armijo Amanda L. , Tom Michelle , Li Zheng , Dimitrova Elizabeth , Austin Wayne R. , Nomme Julian , Campbell Dean O. , Ta Lisa , Le Thuc M. , Lee Jason T. , Darvish Ryan , Gordin Ari , Wei Liu , Liao Hsiang-I , Wilks Moses , Martin Colette , Sadeghi Saman , Murphy Jennifer M. , Boulos Nidal , Phelps Michael E. , Faull Kym F. , Herschman Harvey R. , Jung Michael E. , Czernin Johannes , Lavie Arnon , Radu Caius G.
Published: February 2014

Pharmacological targeting of metabolic processes in cancer must overcome redundancy in biosynthetic pathways. Deoxycytidine (dC) triphosphate (dCTP) can be produced both by the de novo pathway (DNP) and by the nucleoside salvage pathway (NSP). However, the role of the NSP in dCTP production and DNA synthesis in cancer cells is currently not well understood. We show that acute lymphoblastic leukemia (ALL) cells avoid lethal replication stress after thymidine (dT)-induced inhibition of DNP dCTP synthesis by switching to NSP-mediated dCTP production. The metabolic switch in dCTP production triggered by DNP inhibition is accompanied by NSP up-regulation and can be prevented using DI-39, a new high-affinity small-molecule inhibitor of the NSP rate-limiting enzyme dC kinase (dCK). Positron emission tomography (PET) imaging was useful for following both the duration and degree of dCK inhibition by DI-39 treatment in vivo, thus providing a companion pharmacodynamic biomarker. Pharmacological co-targeting of the DNP with dT and the NSP with DI-39 was efficacious against ALL models in mice, without detectable host toxicity. These findings advance our understanding of nucleotide metabolism in leukemic cells, and identify dCTP biosynthesis as a potential new therapeutic target for metabolic interventions in ALL and possibly other hematological malignancies.
Theorizing the Constitutional Revolution
Authors: Jacobsohn Gary Jeffrey
Published: February 2014

The concept of the constitutional revolution has become ubiquitous, but it is applied to all manner of things that are unlike each other in notable ways. It has been generously applied to events in such far-flung places as South Africa, Eastern Europe, Great Britain, India, Canada, Iran, Israel, and the United States. Despite its oxymoronic character, it has the potential to illuminate a much-vexed subject of scholarly inquiry. This article seeks to sharpen conceptual clarity in the way we depict constitutional change, specifically that species of change that entails significant breaks or departures in the workings of the constitutional order.
How Judicial Qualification Ratings May Disadvantage Minority and Female Candidates
Authors: Sen Maya
Published: February 2014

This article uses two newly collected data sets to investigate the reliance by political actors on the external vetting of judicial candidates, in particular vetting conducted by the nation’s largest legal organization, the American Bar Association (ABA). Using these data, I show that minority and female nominees are more likely than whites and males to receive lower ratings, even after controlling for education, experience, and partisanship via matching. These discrepancies are important for two reasons. First, as I show, receiving poor ABA ratings is correlated with confirmation failure. Second, I demonstrate that ABA ratings do not actually predict whether judges will be “better” in terms of reversal rates. Taken together, these findings complicate the ABA’s influential role in judicial nominations, both in terms of setting up possible barriers against minority and female candidates and also in terms of its actual utility in predicting judicial performance.
Plasmonics with two-dimensional conductors
Authors: Yoon Hosang , Yeung Kitty Y. M. , Kim Philip , Ham Donhee
Published: February 2014

A wealth of effort in photonics has been dedicated to the study and engineering of surface plasmonic waves in the skin of three-dimensional bulk metals, owing largely to their trait of subwavelength confinement. Plasmonic waves in two-dimensional conductors, such as semiconductor heterojunction and graphene, contrast the surface plasmonic waves on bulk metals, as the former emerge at gigahertz to terahertz and infrared frequencies well below the photonics regime and can exhibit far stronger subwavelength confinement. This review elucidates the machinery behind the unique behaviours of the two-dimensional plasmonic waves and discusses how they can be engineered to create ultra-subwavelength plasmonic circuits and metamaterials for infrared and gigahertz to terahertz integrated electronics.
Beyond CMOS: heterogeneous integration of III–V devices, RF MEMS and other dissimilar materials/devices with Si CMOS to create intelligent microsystems
Authors: Kazior Thomas E.
Published: February 2014

Advances in silicon technology continue to revolutionize micro-/nano-electronics. However, Si cannot do everything, and devices/components based on other materials systems are required. What is the best way to integrate these dissimilar materials and to enhance the capabilities of Si, thereby continuing the micro-/nano-electronics revolution? In this paper, I review different approaches to heterogeneously integrate dissimilar materials with Si complementary metal oxide semiconductor (CMOS) technology. In particular, I summarize results on the successful integration of III–V electronic devices (InP heterojunction bipolar transistors (HBTs) and GaN high-electron-mobility transistors (HEMTs)) with Si CMOS on a common silicon-based wafer using an integration/fabrication process similar to a SiGe BiCMOS process (BiCMOS integrates bipolar junction and CMOS transistors). Our III–V BiCMOS process has been scaled to 200 mm diameter wafers for integration with scaled CMOS and used to fabricate radio-frequency (RF) and mixed signals circuits with on-chip digital control/calibration. I also show that RF microelectromechanical systems (MEMS) can be integrated onto this platform to create tunable or reconfigurable circuits. Thus, heterogeneous integration of III–V devices, MEMS and other dissimilar materials with Si CMOS enables a new class of high-performance integrated circuits that enhance the capabilities of existing systems, enable new circuit architectures and facilitate the continued proliferation of low-cost micro-/nano-electronics for a wide range of applications.
High-throughput impedance spectroscopy biosensor array chip
Authors: Liu Xiaowen , Li Lin , Mason Andrew J.
Published: February 2014

Impedance spectroscopy is a powerful tool for characterizing materials that exhibit a frequency dependent behaviour to an applied electric field. This paper introduces a fully integrated multi-channel impedance extraction circuit that can both generate AC stimulus signals over a broad frequency range and also measure and digitize the real and imaginary components of the impedance response. The circuit was fabricated in a 0.5 μm complementary metal-oxide semiconductor. Tailored for cellular membrane interface characterization, the signal generator produces sinusoidal waves from 10 mHz to 10 kHz. To suit a variety of applications, the impedance extraction circuit provides a programmable current measurement range from 100 pA to 100 nA with a measured resolution of approximately 100 fA. Occupying only 0.045 mm
2
per measurement channel, the circuit is compact enough to include nearly 200 channels in a 3×3 mm
2
die area.
Starmerella aceti f.a., sp. nov., an ascomycetous yeast species isolated from fungus garden of the leafcutter ant Acromyrmex balzani
Authors: Melo Weilan G. P. , Arcuri Silvio L. , Rodrigues Andre , Morais Paula B. , Meirelles Lucas A. , Pagnocca Fernando C.
Published: February 2014

A novel yeast species was recovered from the fungus garden of the leaf-cutting antAcromyrmex balzani(Hymenoptera: Formicidae). The growth of the novel yeast species is limited by its ability to metabolize only a few carbon and nitrogenous compounds. A remarkable characteristic of this strain is the vigorous growth in 1 % acetic acid. Sequence analysis of the D1/D2 domains of the LSU rRNA gene showed that the novel species belongs to theStarmerellaclade and is phenotypically and genetically divergent from currently recognized species in this clade. Described here asStarmerella acetif.a., sp. nov., it differs by 37 nucleotide substitutions in the D1/D2 region fromStarmerella jinningensisCBS 11864T, the most closely related species. The type strain ofStarmerella acetisp. nov. is TO 125T( = CBMAI 1594T = CBS 13086T).
Efficient synergistic single-cell genome assembly
Authors: Movahedi Narjes S. , Taghavi Zeinab , Embree Mallory , Nagarajan Harish , Zengler Karsten , Chitsaz Hamidreza
Published: February 2014

As the vast majority of all microbes are unculturable, single-cell sequencing has become a significant method to gain insight into microbial physiology. Single-cell sequencing methods, currently powered by multiple displacement genome amplification (MDA), have passed important milestones such as finishing and closing the genome of a prokaryote. However, the quality and reliability of genome assemblies from single cells are still unsatisfactory due to uneven coverage depth and the absence of scattered chunks of the genome in the final collection of reads caused by MDA bias. In this work, our new algorithm HybridDe novoAssembler (HyDA) demonstrates the power of co-assembly of multiple single-cell genomic data sets through significant improvement of the assembly quality in terms of predicted functional elements and length statistics. Co-assemblies contain significantly more base pairs and protein coding genes, cover more subsystems, and consist of longer contigs compared to individual assemblies by the same algorithm as well as state-of-the-art single-cell assemblers SPAdes and IDBA-UD. HybridDe novoAssembler (HyDA) is also able to avoid chimeric assemblies by detecting and separating shared and exclusive pieces of sequence for input data sets. By replacing one deep single-cell sequencing experiment with a few single-cell sequencing experiments of lower depth, the co-assembly method can hedge against the risk of failure and loss of the sample, without significantly increasing sequencing cost. Application of the single-cell coassembler HyDA to the study of three uncultured members of an alkane-degrading methanogenic community validated the usefulness of the co-assembly concept.
Tempo and mode of regulatory evolution in Drosophila
Authors: Coolon Joseph D. , McManus C. Joel , Stevenson Kraig R. , Graveley Brenton R. , Wittkopp Patricia J.
Published: February 2014

Genetic changes affecting gene expression contribute to phenotypic divergence; thus, understanding how regulatory networks controlling gene expression change over time is critical for understanding evolution. Prior studies of expression differences within and between species have identified properties of regulatory divergence, but technical and biological differences among these studies make it difficult to assess the generality of these properties or to understand how regulatory changes accumulate with divergence time. Here, we address these issues by comparing gene expression among strains and species of Drosophila with a range of divergence times and use F1 hybrids to examine inheritance patterns and disentangle cis- and trans-regulatory changes. We find that the fixation of compensatory changes has caused the regulation of gene expression to diverge more rapidly than gene expression itself. Specifically, we observed that the proportion of genes with evidence of cis-regulatory divergence has increased more rapidly with divergence time than the proportion of genes with evidence of expression differences. Surprisingly, the amount of expression divergence explained by cis-regulatory changes did not increase steadily with divergence time, as was previously proposed. Rather, one species (Drosophila sechellia) showed an excess of cis-regulatory divergence that we argue most likely resulted from positive selection in this lineage. Taken together, this work reveals not only the rate at which gene expression evolves, but also the molecular and evolutionary mechanisms responsible for this evolution.
The Solanum lycopersicum Zinc Finger2 Cysteine-2/Histidine-2 Repressor-Like Transcription Factor Regulates Development and Tolerance to Salinity in Tomato and Arabidopsis
Authors: Hichri Imène , Muhovski Yordan , Žižková Eva , Dobrev Petre I. , Franco-Zorrilla Jose Manuel , Solano Roberto , Lopez-Vidriero Irene , Motyka Vaclav , Lutts Stanley
Published: February 2014

The zinc finger superfamily includes transcription factors that regulate multiple aspects of plant development and were recently shown to regulate abiotic stress tolerance. Cultivated tomato (Solanum lycopersicum Zinc Finger2 [SIZF2]) is a cysteine-2/histidine-2-type zinc finger transcription factor bearing an ERF-associated amphiphilic repression domain and binding to the ACGTCAGTG sequence containing two AGT core motifs. SlZF2 is ubiquitously expressed during plant development, and is rapidly induced by sodium chloride, drought, and potassium chloride treatments. Its ectopic expression in Arabidopsis (Arabidopsis thaliana) and tomato impaired development and influenced leaf and flower shape, while causing a general stress visible by anthocyanin and malonyldialdehyde accumulation. SlZF2 enhanced salt sensitivity in Arabidopsis, whereas SlZF2 delayed senescence and improved tomato salt tolerance, particularly by maintaining photosynthesis and increasing polyamine biosynthesis, in salt-treated hydroponic cultures (125 mm sodium chloride, 20 d). SlZF2 may be involved in abscisic acid (ABA) biosynthesis/signaling, because SlZF2 is rapidly induced by ABA treatment and 35S::SlZF2 tomatoes accumulate more ABA than wild-type plants. Transcriptome analysis of 35S::SlZF2 revealed that SlZF2 both increased and reduced expression of a comparable number of genes involved in various physiological processes such as photosynthesis, polyamine biosynthesis, and hormone (notably ABA) biosynthesis/signaling. Involvement of these different metabolic pathways in salt stress tolerance is discussed.
Origin of β-Carotene-Rich Plastoglobuli in Dunaliella bardawil
Authors: Davidi Lital , Shimoni Eyal , Khozin-Goldberg Inna , Zamir Ada , Pick Uri
Published: February 2014

The halotolerant microalgae Dunaliella bardawil accumulates under nitrogen deprivation two types of lipid droplets: plastoglobuli rich in β-carotene (βC-plastoglobuli) and cytoplasmatic lipid droplets (CLDs). We describe the isolation, composition, and origin of these lipid droplets. Plastoglobuli contain β-carotene, phytoene, and galactolipids missing in CLDs. The two preparations contain different lipid-associated proteins: major lipid droplet protein in CLD and the Prorich carotene globule protein in βC-plastoglobuli. The compositions of triglyceride (TAG) molecular species, total fatty acids, and sn-1+3 and sn-2 positions in the two lipid pools are similar, except for a small increase in palmitic acid in plastoglobuli, suggesting a common origin. The formation of CLD TAG precedes that of βC-plastoglobuli, reaching a maximum after 48 h of nitrogen deprivation and then decreasing. Palmitic acid incorporation kinetics indicated that, at early stages of nitrogen deprivation, CLD TAG is synthesized mostly from newly formed fatty acids, whereas in βC-plastoglobuli, a large part of TAG is produced from fatty acids of preformed membrane lipids. Electron microscopic analyses revealed that CLDs adhere to chloroplast envelope membranes concomitant with appearance of small βC-plastoglobuli within the chloroplast. Based on these results, we propose that CLDs in D. bardawil are produced in the endoplasmatic reticulum, whereas βC-plastoglobuli are made, in part, from hydrolysis of chloroplast membrane lipids and in part, by a continual transfer of TAG or fatty acids derived from CLD.
Arabidopsis VASCULAR-RELATED UNKNOWN PROTEIN1 Regulates Xylem Development and Growth by a Conserved Mechanism That Modulates Hormone Signaling
Authors: Grienenberger Etienne , Douglas Carl J.
Published: February 2014

Despite a strict conservation of the vascular tissues in vascular plants (tracheophytes), our understanding of the genetic basis underlying the differentiation of secondary cell wall-containing cells in the xylem of tracheophytes is still far from complete. Using coexpression analysis and phylogenetic conservation across sequenced tracheophyte genomes, we identified a number of Arabidopsis (Arabidopsis thaliana) genes of unknown function whose expression is correlated with secondary cell wall deposition. Among these, the Arabidopsis VASCULAR-RELATED UNKNOWN PROTEIN1 (VUP1) gene encodes a predicted protein of 24 kD with no annotated functional domains but containing domains that are highly conserved in tracheophytes. Here, we show that the VUP1 expression pattern, determined by promoter-β-glucuronidase reporter gene expression, is associated with vascular tissues, while vup1 loss-of-function mutants exhibit collapsed morphology of xylem vessel cells. Constitutive overexpression of VUP1 caused dramatic and pleiotropic developmental defects, including severe dwarfism, dark green leaves, reduced apical dominance, and altered photomorphogenesis, resembling brassinosteroid-deficient mutants. Constitutive overexpression of VUP homologs from multiple tracheophyte species induced similar defects. Whole-genome transcriptome analysis revealed that overexpression of VUP1 represses the expression of many brassinosteroid- and auxin-responsive genes. Additionally, deletion constructs and site-directed mutagenesis were used to identify critical domains and amino acids required for VUP1 function. Altogether, our data suggest a conserved role for VUP1 in regulating secondary wall formation during vascular development by tissue- or cell-specific modulation of hormone signaling pathways.
(E)-1-Ferrocenyl-3-(2-methoxyphenyl)prop-2-en-1-one
Authors: Otaño Vega Myrna R. , Rivero Kennett I. , Montes González Ingrid
Published: February 2014

The structure of the title compound, [Fe(C5H5)(C15H13O2)], consists of a ferrocenyl moiety and a 2-methoxyphenyl group linked through a prop-2-en-1-one spacer in anEconformation. In the ferrocene unit, the substituted cyclopentadienyl (Cps) ring and the unsubstituted cyclopentadienyl ring (Cp) are almost parallel to one another [dihedral angle = 1.78 (14)°], and the Cp and Cps rings are in agaucheconformation. The benzene ring is twisted by 10.02 (14) and 11.38 (11)° with respect to the Cp and Cps rings, respectively. In the crystal, molecules are linked by weak C—H...O hydrogen bonds into supramolecular chains running along theb-axis direction.
N′-[(E)-(Furan-2-yl)methylidene]-2-[4-(2-methylpropyl)phenyl]propanohydrazide
Authors: Akkurt Mehmet , Mohamed Shaaban K. , Mague Joel T. , Albayati Mustafa R. , Younes Sabry H. H.
Published: February 2014

In the title molecule, C18H22N2O2, the furan and benzene rings form a dihedral angle of 70.17 (14)°. In the crystal, strong N—H...O and weak C—H...O hydrogen bonds link the molecules into chains running parallel to [010].
1-(Prop-2-ynyl)indoline-2,3-dione
Authors: Qachchachi Fatima-Zahrae , Ouazzani Chahdi Fouad , Misbahi Houria , Bodensteiner Michael , El Ammari Lahcen
Published: February 2014

The structure of the title compound, C11H7NO2, is isotypic to that of its homologue, 1-octylindoline-2,3-dione [Qachchachiet al.(2013).Acta Cryst.E69, o1801]. The indoline ring and the two carbonyl O atoms are approximately coplanar, the largest deviation from the mean plane being 0.021 (1) Å for one of the O atoms. The mean plane through the fused ring system is nearly perpendicular to the propynyl group, as indicated by the N—C—C—C torsion angle of 77.9 (1)°. In the crystal, molecules are linked by C—H...O hydrogen bonds and π–π interactions between benzene rings [intercentroid distance = 3.5630 (10) Å], forming a three-dimensional structure.
College students and HR professionals: conflicting views on information available on Facebook
Authors: Curran Michael J. , Draus Peter , Schrager Michael , Zappala Steve
Published: February 2014

Increasingly employers are using social media as a mechanism to screen potential job candidates. This study examined college students' perceptions of the amount and degree of information available to potential employers who use social media. The study employed a survey of college students to determine how much information they felt someone could learn about them through their Facebook page. Results indicated that participants did not perceive much information about key job categories could be derived from their pages and they planned very few changes even though many believed it highly likely an employer would review their page. A subgroup also had their pages reviewed by HR professionals. A comparison analysis revealed that in several key job‐related areas, such as potential unethical behaviours and communication skills, HR personnel felt that they were able to learn significantly more about the participants than the participants believed themselves.
New Material of Zhenyuanopterus (Pterosauria) from the Early Cretaceous Yixian Formation of Western Liaoning
Authors: TENG Fangfang , LÜ Junchang , WEI Xuefang , HSIAO Yufu , PITTMAN Michael
Published: February 2014

A new partial specimen of Zhenyuanopterus from the Lower Cretaceous Yixian Formation of Beipiao city, Liaoning Province is described. This specimen is slightly larger than half the size of the holotype. Although it is not complete, it provides new information on Zhenyuanopterus both in taxonomy and ontogeny: the total number of the caudal vertebrae is 15; the forelimb is more robust than the hindlimb; the growth rate of the humerus and femur is constant, and their ratio is about 1. Compared with the holotype, the scapula and coracoid grow faster than the humerus and the femur. The scapula and coracoid may slow their growth rate after a certain ontogenetic stage. The pectoral girdle, robust forelimb and weak hindlimb of the new material (XHPM1088) together with data from the holotype of Zhenyuanopterus indicate that this taxon spent less time on land than in the sky or other ecological niches such as forests and cliffs.
A Megatheropod Tooth from the Early Cretaceous of Fusui, Guangxi, Southern China
Authors: MO Jinyou , HUANG Chaolin , XIE Shaowen , ERIC Buffetaut
Published: February 2014

A nearly complete right maxillary or left dentary tooth (NHMG 10858) from the Lower Cretaceous Xinlong Formation of the Napai Basin, Fusui County, Guangxi, southern China, is described. The tooth is large in size, with a CBL of 37 mm. Given the geological age and its crown morphology, including the size, it is most likely that the tooth belongs to a carcharodontosaurid. The recovered specimen represents one of the largest theropod teeth hitherto reported from the Early Cretaceous of Asia.
A New Fossil Hangingfly (Mecoptera: Cimbrophlebiidae) from the Early Cretaceous of China
Authors: WANG Chen , SHIH Chungkun , REN Dong
Published: February 2014

A new species, Cimbrophlebia rara sp. nov., in the family Cimbrophlebiidae (Mecoptera) is described and illustrated. This specimen was collected from the Early Cretaceous Yixian Formation at Liutiaogou in Inner Mongolia, China. This is the first record of a cimbrophlebiid from the Jehol biota. A key to all species of Cimbrophlebia is given. A preliminary review of published taxa data indicates that from the Middle Jurassic to the Early Cretaceous, Mecoptera became less diverse and less abundant in northeastern China at familiar level (from 11 to 6), generic level (from 32 to 8) and specific level (from 44 to 14).
Zircon Geochronology and Trace Element Geochemistry from the Xiaozhen Copper Deposit, North Daba Mountain: Constraints on Albitites Petrogenesis
Authors: WANG Gang , WANG Zongqi , ZHANG Yingli , WANG Kunming
Published: February 2014

Albitite often accompanies with various metal and gem mineral deposits and a large number of occurrences have been reported globally, including the South Qinling orogen, China. The Xiaozhen copper deposit is a typical deposit in the North Daba Mountain area of the South Qinling orogen whose distribution is controlled by albitite veins and fractures. As there are few studies on the petrogenesis of albitite in Xiaozhen copper deposit, this paper focuses on the petrogenesis of albitite and its mineralization age. Detailed fieldwork and mineral microscopic observations initially suggest that albitite from the Xiaozhen copper deposit is igneous in origin. Further zircon trace element geochemistry studies indicate that these zircons have high Th/U ratios (>0.5), low La content, high (Sm/La)N and Ce/Ce* values, and a strong negative Eu anomaly, which are commonly seen in magmatic zircons. The chondrite–normalized rare earth element (REE) patterns are consistent with magmatic zircons from throughout the world, and they fall within or near the field of magmatic zircons on discriminant diagrams. The calculated average apparent Ti–in–zircon temperature for young zircons is 780°C, consistent with magmatic zircon crystallization temperatures. Therefore, zircon geochemistry indicates that the albitite origin is magmatic. SIMS U–Pb dating on nine magmatic zircons yielded a concordia age of 154.8±2.2 Ma, which represents the formation of albitite and the metallogenic age. More importantly, it is consistent with the ages of Yanshanian magmatism and metallogenesis in the South Qinling orogen, so formation of the Xiaozhen copper deposit may be a closely related geological event.
Microtexture and Distribution of Minerals in Hydrothermal Barite‐Silica Chimney from the Franklin Seamount, SW Pacific: Constraints on Mode of Formation
Authors: Durbar RAY , KOTA Dalayya , DAS Pranab , L. Surya Prakash , V.D. KHEDEKAR , Anil L. PAROPKARI , Abhay V. MUDHOLKAR
Published: February 2014

An extinct hydrothermal barite‐silica chimney from the Franklin Seamount of the Woodlark Basin, in the southwestern Pacific Ocean, was investigated for mineral distribution and geochemical composition. Six layers on either side of the orifice of a chimney show significant disparity in color, mineral assemblage and major element composition. Electron microscope (SEM) images reveal that the peripheral wall of the chimney is composed of colloform silica, suggesting that incipient precipitation of silica‐saturated hydrothermal fluid initiated the development of the chimney wall. Intermediate layers, between the exterior wall and the inner fluid‐orifice, dominate with barite and sulfides. Low Sr‐to‐Ba ratios (SrO/BaO = 0.015–0.017) indicate restricted fluid‐seawater mixing, which causes relatively high‐temperature formation of the intermediate layers. Whereas the innermost layer bordering the chimney orifice is characterized by more silica and a higher Sr‐to‐Ba ratio (SrO/BaO = 0.023), could have formed due to a paragenetic shift from a high‐temperature active phase to a cooler waning stage of formation. A paragenetic shift is also probably responsible for the change in mineral formation mechanism that resulted in the textural variation of barite and colloform silica developed during different growth phases of this barite‐silica chimney.