bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced thermoelectric figure of merit in vertical graphene junctions
Authors: Hung Nguyen V. , Nguyen M. Chung , Nguyen Huy-Viet , Saint-Martin J. , Dollfus P.
Published: October 2014

In this work, we investigate thermoelectric properties of junctions consisting of two partially overlapped graphene sheets coupled to each other in the cross-plane direction. It is shown that because of the weak van-der Waals interactions between graphene layers, the phonon conductance in these junctions is strongly reduced, compared to that of single graphene layer structures, while their electrical performance is weakly affected. By exploiting this effect, we demonstrate that the thermoelectric figure of merit, ZT, can reach values higher than 1 at room temperature in junctions made of gapped graphene materials, for instance, graphene nanoribbons and graphene nanomeshes. The dependence of thermoelectric properties on the junction length is also discussed. This theoretical study hence suggests an efficient way to enhance thermoelectric efficiency of graphene devices.
Temperature-dependent field emission of flexible n-type silicon carbide nanoneedle emitters
Authors: Chen Shanliang , Ying Pengzhan , Wang Lin , Wei Guodong , Yang Weiyou
Published: October 2014

In this work, we reported the temperature-dependent field emission (FE) of flexible n-type SiC nanoneedles grown on the carbon fabric substrates via pyrolysis of polymeric precursor. The obtained n-type SiC nanoneedles with clear and sharp tips were incorporated by N dopants with a uniform spatial distribution. The FE behaviors of n-type SiC nanoneedles exhibit a strong dependence on the temperatures. Their turn-on fields and threshold fields decrease from 1.37 to 0.67 V/μm and 1.87 to 0.96 V/μm with the temperature raised from room temperature (RT) to 400 °C, respectively. The measured current emission stabilities of the n-type SiC nanoneedles under RT and 200 °C are ∼7.7% and 14.1%, respectively. The temperature-dependent FE characteristics could be attributed to the reduction of the work function of n-type SiC nanoneedles induced by the raise of temperatures and the incorporated N dopants.
Engineering 180° ferroelectric domains in epitaxial PbTiO3 thin films by varying the thickness of the underlying (La,Sr)MnO3 layer
Authors: Jin L. , Jia C. L. , Vrejoiu I.
Published: October 2014

Epitaxial ferroelectric thin films of PbTiO3 (PTO) grown on top of nominally La0.7Sr0.3MnO3 (LSMO) submicron hillocks on Nb-doped SrTiO3 (100) substrate were investigated by means of scanning transmission electron microscopy. 180° ferroelectric domains were observed in the c-axis oriented PTO films. The formation and configuration of ferroelectric domains and domain walls were found to exhibit strong correlation with the thickness of the underlying LSMO hillocks. The domain walls start at the locations of the hillocks where the LSMO layer has a thickness of about 3 nm. Our results demonstrate that controlling the thickness variation (shape) of the LSMO hillocks can manipulate the position and density of the ferroelectric domain walls, which are considered to be the active elements for future nanoelectronics.
Musical pitch perception starts early
Authors: Miller Johanna L.
Published: October 2014

Tasked with extracting the fundamental frequency from a complex of high harmonics, three-month-old infants outperformed many adults.
DARPA looks beyond GPS for positioning, navigating, and timing
Authors: Kramer David
Published: October 2014

Cold-atom interferometry, microelectromechanical systems, signals of opportunity, and atomic clocks are some of the technologies the defense agency is pursuing to provide precise navigation when GPS is unavailable.
How to deal with climate change
Authors: Higgins Paul A. T.
Published: October 2014

Climate change is a complex and contentious public issue, but the risk-management options available to us are straightforward and have well-characterized strengths and weaknesses.
Emergent aerodynamics in wind farms
Authors: Dabiri John O.
Published: October 2014

New designs for inexpensively harvesting wind energy were inspired by the fluid mechanics of fish schools.
Associative effects of poor-quality forages combined with food industry byproducts determined in vitro with an automated gas-production system
Authors: Tagliapietra Franco , Cattani Mirko , Guadagnin Matteo , Haddi Mohamed L. , Sulas Leonardo , Muresu Rosella , Squartini Andrea , Schiavon Stefano , Bailoni Lucia
Published: October 2014

This experiment aimed to investigate the associative effects among two low-quality forages (crown daisy, milk thistle) and three agro-industrial byproducts (apple pomace, citrus pulp, tomato peel), by means of an automated gas production (GP) system. All feeds were incubated alone or as 50 : 50 mixtures of each forage with each byproduct. Samples (0.500 ± 0.0010 g) of single feeds or mixtures were incubated for 96 h, in three replicates in individual bottles (310 mL), with 75 mL of buffered rumen fluid. Bottles were vented by an open-close valve when the internal pressure reached 3.4 kPa. The metabolisable energy content of single feeds and mixtures was computed from GP at 24 h and feed chemical composition. Feed substrates were ranked for GP in the following way: byproducts, mixtures, and forages. The two forages did not differ for GP and metabolisable energy content, although differences were observed among byproducts and among mixtures. Both forages interacted positively with apple pomace from 6 h (P < 0.001) to 24 h (P = 0.029) of incubation and with citrus pulp at 12 h (P = 0.005) and 24 h (P = 0.012), whereas no associative effects were detected when forages were incubated with tomato peels. Results suggest that in vitro fermentability of low-quality forages could be efficiently improved by combining these two forages with apple pomace or citrus pulp. These findings are relevant, because the use of low-quality forages and byproducts in ruminant feeding is considered important for improving the environmental and economic sustainability of forage systems in arid and semi-arid areas.
Native Australian shrub legume species may provide an alternative feed source for livestock
Authors: O'Keeffe P. A. , Orchard D. J. , Orchard B. A. , Piltz J. W. , Clayton E. H.
Published: October 2014

The feed quality of a variety of native shrub and herbaceous legume species from the Riverina area of southern New South Wales was determined to provide an indication of their potential use in livestock grazing systems. Fifteen species were sampled from each of two locations (chiefly low fertility roadsides or travelling stock reserves) at four times within a 12-month period viz. August, November, February and May according to the most likely plant parts to be consumed by grazing animals for each species. Digestibility was estimated using an in vitro rumen fluid digestion assay and crude protein was estimated from nitrogen analysed using the Dumas combustion method. Digestible organic matter in the dry matter (DOMD) was greater than 550 g/kg dry matter (DM) for seven of the native legume species and was highest for Daviesia spp. (D. latifolia 696.2 ± 15.0, D. leptophylla × latifolia 642.5 ± 15.1 and D. leptophylla 622.7 ± 15.4), Glycine spp. (G. clandestina 628.2 ± 18.1, G. tabacina 621.9 ± 28.0 and G. canescens 580.4 ± 25.4) and Indigofera australis (617.8 ± 15.3). Crude protein content was greater than 80 g/kg DM for all species analysed, suggesting that these plants are able to fix nitrogen under low phosphorus fertility conditions. Studies examining grazing management as well as nitrogen fixation and nitrogen transfer to companion grasses are required in order to optimise the management of these plants in grazing systems.
Benthic algal biomass and assemblage changes following environmental flow releases and unregulated tributary flows downstream of a major storage
Authors: Davie Alec W. , Mitrovic Simon M.
Published: October 2014

A large dam reducing the magnitude of flows regulates the Severn River, Australia. Environmental flows (EFs) are designed to increase the magnitude of flow and improve ecological outcomes such as reducing filamentous algal biomass and re-setting algal succession. The effectiveness of EF releases to alter benthic algal assemblages is poorly understood. We examined benthic algal biomass and assemblage structure at two cobble-dominated riffle sites downstream of Pindari Dam, before and after two EFs. Both EFs had discharges of ~11.6 m3 s–1 (velocity of ~0.9 m s–1). Neither EF reduced benthic algal biomass, and sometimes led to increases, with density of some filamentous algae increasing (Stigeoclonium and Leptolyngbya). An unregulated flow from a tributary between the two sites increased discharge to 25.2 m3 s–1 (velocity of ~1.2 m s–1), decreasing biomass and density of filamentous algae. The similarity in flow velocities between scouring and non-scouring events suggests that thresholds may exist and/or suspended sediments carried from unregulated tributaries may contribute to reduce algal biomass. Identifying velocities needed to reduce algal biomass are useful. Accordingly, EFs with flow velocities ~1.2 m s–1 may achieve this in river cobble-dominated riffle sections dominated by filamentous algae. Lower flow velocities of <0.9 m s–1 may result in no change or an increase in filamentous algae.
Variation in occurrence of the fish-parasitic cymothoid isopod, Anilocra haemuli, infecting French grunt (Haemulon flavolineatum) in the north-eastern Caribbean
Authors: Welicky Rachel L. , Sikkel Paul C.
Published: October 2014

Parasites constitute the majority of coral reef animal diversity and are believed to contribute significantly to host, community and trophic dynamics. Anilocra spp. are large conspicuous ectoparasitic isopods, making them ideal models for host–parasite studies. In the tropical western Atlantic and Caribbean, Anilocra haemuli infects the ecologically important French grunt (Haemulon flavolineatum). French grunt are trophic connectors between reef and seagrass environments, and how A. haemuli infection influences connectivity is unknown. As a first step in understanding the French grunt–A. haemuli association, we conducted reef surveys during three consecutive years to quantify the abundance and prevalence of infected fish on reef sites in the north-eastern Caribbean. We examined their correlations with fish population and aggregation size, and social affiliation. Annual infected fish abundance and prevalence per site ranged from 0–24 fish and 0–66%. Prevalence: (1) appeared autocorrelated within bays among years; (2) was inversely correlated with population and aggregation size, although the statistical significance varied; and (3) was greater for solitary than aggregating fish. Our study provides the most comprehensive dataset for prevalence of any Anilocra spp., and the necessary baseline data for future studies on Anilocra–host dynamics, and the effect of parasites on trophic and habitat connectivity.
Trajectory river modelling – a decision-support tool to help manage multiple risks associated with planning around variable water resources
Authors: Gilfedder Mat , Podger Geoff , Rassam David W. , Pagendam Dan , Robinson Catherine J.
Published: October 2014

The application of river-system models to inform water-resource planning and management is a growing global phenomenon. This requires models to be applied so that they are useful to water decision makers charged with setting targets that provide adequate water flows to sustain landholders and communities. This article examines why and how the innovative application of river-system models can facilitate interactions between water science and water management in Australia’s Murray–Darling Basin (the Basin). A trajectory river-modelling method was applied to run multiple short historical climate sequences through a river-system model to provide historical probabilities. These can allow better assessment of the risks and impacts associated with stream flow and water availability. This method allows known historical variability to be presented, and produces relevant results for a 10–15-year water-sharing plan lifetime. The benefits were demonstrated in the Basin’s Lachlan Catchment where modelled river-flow results demonstrated the increased variability between shorter 15-year sequences than for a single 114-year run. This approach highlighted the benefits of expressing modelling results as historical probabilities to inform short-term and strategic water-planning efforts.
Solid-to-fluid–like DNA transition in viruses facilitates infection
Authors: Liu Ting , Sae-Ueng Udom , Li Dong , Lander Gabriel C. , Zuo Xiaobing , Jönsson Bengt , Rau Donald , Shefer Ivetta , Evilevitch Alex
Published: October 2014

Significance

The efficiency of viral replication is limited by the ability of the virus to eject its genome into a cell. We discovered a fundamentally important mechanism for translocation of viral genomes into cells. For the first time, to our knowledge, we show that tightly packaged DNA in the viral capsid of a bacterial virus (phage λ) undergoes a solid-to-fluid–like structural transition that facilitates infection close to 37 °C. Our finding shows a remarkable physical adaptation of bacterial viruses to the environment of
Escherichia coli
cells in a human host.
Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner
Authors: Wang Zhiye , Ruan Wenyuan , Shi Jing , Zhang Li , Xiang Dan , Yang Chao , Li Changying , Wu Zhongchang , Liu Yu , Yu Yanan , Shou Huixia , Mo Xiaorong , Mao Chuanzao , Wu Ping
Published: October 2014

Significance

Phosphate (Pi) is a primary nutrient for plant growth. Because of the low availability of soil Pi, the Pi starvation signaling in plants is gaining great interest.
Arabidopsis
AtPHR1 and its rice homologue OsPHR2 are known to be central transcription factors in Pi homeostasis; however, the mechanism of how plants sense external Pi fluctuation to regulate the activity of AtPHR1/OsPHR2 has been elusive. Here, we identify rice SPX1 and SPX2 as Pi-dependent inhibitors of PHR2, implicating SPX1 and SPX2 in the Pi-sensing mechanism. We also show that the SPX domain of SPX1 and SPX2 is critical for repressing PHR2 binding to
cis
elements by protein interaction. The discovery of cellular nutrient concentration-dependent fine-tuning sheds light on a novel mechanism of plant adaption to environmental cues.
The Jespersen cycles seen from Austronesian
Authors: Vossen Frens , van der Auwera Johan
Published: October 2014

Most work on the so-called ‘Jespersen Cycle’ has been done on the languages of Europe, less on languages of Africa. In this paper the authors look at Austronesian languages, with the aim to determine to what extent Austronesian doubling is compatible with a Jespersen cycle scenario. The properties of the potential Austronesian manifestations of Jespersenian double, triple and even quadruple negation are highlighted, and the role of word order, etyma, emphasis and contact interference are investigated. However difficult it is to discuss a hypothesis about the diachrony of negation on data from 410 languages, most of which do not have a recorded history, still, it is clear that the multiple exponence of negation in Austronesian is in some cases clearly interpretable in terms of the Jespersen cycle hypothesis and in many more cases at least compatible with it, the clearest evidence concerning the partitive negative polysemy, attested in Melanesia.
Jungian screen studies – ‘Everything is Awesome…’?
Authors: Hockley Luke
Published: October 2014

Jungian film theory has reached a point where it has started to coalesce into a field. It is perhaps timely to take stock of what constitutes that field, and the extent to which a Jungian orientation to film and media is differentiated from Freudian and Lacanian approaches as well as those derived from traditional phenomenology and Deleuze.
The unconscious Indianization of ‘Western’ conservatism – is Indian conservatism a universal model?
Authors: Goldstein Björn
Published: October 2014

According to Max Horkheimer, the core dilemma of capitalist ideology is that it promotes egoism and contempt for egoism at the same time. This basic contradiction translates into belief in an organically structured society consisting of needs satisfying individuals and groups. This can be made out as a principle that prevails across all conservative schools and psychological differences. Conservative parties in the ‘West’ have started to adopt an unprecedented openness to the diversity of contemporary pluralistic societies. In doing so, they do what conservatives always did – they conform to actual social conditions. Conservatism is far from being anti-diversity, as long as the core belief remains untouched. The transformation of ‘Western’ conservatism we witness today is moulding conservatism into a form that has since long been established in India, where plurality and multiculturality have never been absent. This new development brings to the fore the key elements of a universal conservatism independent of cultural contexts.
Spectral theory of multiple intervals
Authors: Jorgensen Palle , Pedersen Steen , Tian Feng
Published: October 2014

We present a model for spectral theory of families of selfadjoint operators, and their corresponding unitary one-parameter groups (acting in Hilbert space). The models allow for a scale of complexity, indexed by the natural numbers

N

\mathbb {N}

. For each

n
∈

N

n\in \mathbb {N}

, we get families of selfadjoint operators indexed by: (i) the unitary matrix group

U
(
n
)

U(n)

, and by (ii) a prescribed set of

n
n

non-overlapping intervals. Take

Ω
\Omega

to be the complement in

R

\mathbb {R}

of

n
n

fixed closed finite and disjoint intervals, and let

L

2

(
Ω
)

L^{2}(\Omega )

be the corresponding Hilbert space. Moreover, given

B
∈
U
(
n
)

B\in U(n)

, then both the lengths of the respective intervals, and the gaps between them, show up as spectral parameters in our corresponding spectral resolutions within

L

2

(
Ω
)

L^{2}(\Omega )

. Our models have two advantages. One, they encompass realistic features from quantum theory, from acoustic wave equations and their obstacle scattering, as well as from harmonic analysis.

Secondly, each choice of the parameters in our models,

n
∈

N

n\in \mathbb {N}

,

B
∈
U
(
n
)

B\in U(n)

, and interval configuration, allows for explicit computations, and even for closed-form formulas: Computation of spectral resolutions, of generalized eigenfunctions in

L

2

(
Ω
)

L^{2}(\Omega )

for the continuous part of the spectrum, and for scattering coefficients. Our models further allow us to identify embedded point-spectrum (in the continuum), corresponding, for example, to bound-states in scattering, to trapped states, and to barriers in quantum scattering. The possibilities for the discrete atomic part of the spectrum includes both periodic and non-periodic distributions.
BioVLAB-MMIA-NGS: microRNA–mRNA integrated analysis using high-throughput sequencing data
Authors: Chae Heejoon , Rhee Sungmin , Nephew Kenneth P. , Kim Sun
Published: October 2014

Motivation: It is now well established that microRNAs (miRNAs) play a critical role in regulating gene expression in a sequence-specific manner, and genome-wide efforts are underway to predict known and novel miRNA targets. However, the integrated miRNA–mRNA analysis remains a major computational challenge, requiring powerful informatics systems and bioinformatics expertise.

Results: The objective of this study was to modify our widely recognized Web server for the integrated mRNA–miRNA analysis (MMIA) and its subsequent deployment on the Amazon cloud (BioVLAB-MMIA) to be compatible with high-throughput platforms, including next-generation sequencing (NGS) data (e.g. RNA-seq). We developed a new version called the BioVLAB-MMIA-NGS, deployed on both Amazon cloud and on a high-performance publicly available server called MAHA. By using NGS data and integrating various bioinformatics tools and databases, BioVLAB-MMIA-NGS offers several advantages. First, sequencing data is more accurate than array-based methods for determining miRNA expression levels. Second, potential novel miRNAs can be detected by using various computational methods for characterizing miRNAs. Third, because miRNA-mediated gene regulation is due to hybridization of an miRNA to its target mRNA, sequencing data can be used to identify many-to-many relationship between miRNAs and target genes with high accuracy.

Availability and implementation:  http://epigenomics.snu.ac.kr/biovlab_mmia_ngs/

Contact:  sunkim.bioinfo@snu.ac.kr , heechae@cs.indiana.edu
The Transcription Factor Con7-1 Is a Master Regulator of Morphogenesis and Virulence in Fusarium oxysporum
Authors: Ruiz-Roldán Carmen , Pareja-Jaime Yolanda , González-Reyes José Antonio , G. Roncero M. Isabel
Published: October 2014

Previous studies have demonstrated the essential role of morphogenetic regulation in Fusarium oxysporum pathogenesis, including processes such as cell-wall biogenesis, cell division, and differentiation of infection-like structures. We identified three F. oxysporum genes encoding predicted transcription factors showing significant identities to Magnaporthe oryzae Con7p, Con7-1, plus two identical copies of Con7-2. Targeted deletion of con7-1 produced nonpathogenic mutants with altered morphogenesis, including defects in cell wall structure, polar growth, hyphal branching, and conidiation. By contrast, simultaneous inactivation of both con7-2 copies caused no detectable defects in the resulting mutants. Comparative microarray-based gene expression analysis indicated that Con7-1 modulates the expression of a large number of genes involved in different biological functions, including host–pathogen interactions, morphogenesis and development, signal perception and transduction, transcriptional regulation, and primary and secondary metabolism. Taken together, our results point to Con7-1 as general regulator of morphogenesis and virulence in F. oxysporum.
Discovery of Heterodera filipjevi in Washington and Comparative Virulence with H. avenae on Wheat
Authors: Smiley Richard W. , Yan Guiping
Published: October 2014

The cereal cyst nematode Heterodera avenae suppresses wheat production in the western United States. A second species of cereal cyst nematode, H. filipjevi, was identified in eastern Oregon during 2008. This paper reports the discovery of H. filipjevi–infested fields in eastern Washington, thereby extending the known distribution of H. filipjevi in the United States. The identity of H. filipjevi was determined and confirmed by species-specific polymerase chain reaction (PCR), PCR-restriction fragment length polymorphism (RFLP), sequencing, and cyst morphology. Soils that were collected from naturally infested fields in Washington were used to compare the virulence of H. avenae and H. filipjevi on six spring wheat cultivars under controlled-environment conditions. Noninfested soils from nearby fields were used as controls. Cultivars Ouyen and WB Rockland were resistant to H. avenae and susceptible to H. filipjevi. Cultivars Sönmez and SY Steelhead were resistant to H. filipjevi and susceptible to H. avenae. Cultivars Louise and WB 936 were susceptible to both species. The resistance of SY Steelhead to ‘H. avenae’, reported in a previous paper, is corrected as resistance to H. filipjevi due to an earlier misidentification of H. filipjevi. Management guidelines that include crop rotations and resistant cultivars are presented. Discovery of additional infestations of H. filipjevi are anticipated when DNA-based tests become used routinely in commercial diagnostic laboratories.
First Report of Catharanthus mosaic virus in Mandevilla in the United States
Authors: Mollov D. , Guaragna M. A. , Lockhart B. , Rezende J. A. M. , Jordan R.
Published: October 2014

Mandevilla (Apocynaceae) is an ornamental tropical vine popular for its bright and attractive flowers. During 2012 to 2013, 12 Mandevilla sp. samples from Minnesota and Florida nurseries were submitted for analysis at the University of Minnesota Plant Disease Clinic. Plants showed mosaic symptoms, leaf deformation, premature leaf senescence, and vine dieback. Filamentous virus particles with modal lengths 700 to 900 nm were observed by transmission electron microscopy (TEM) in partially purified preparations from symptomatic leaves. Partially purified virions were obtained using 30% sucrose cushion centrifuged at 109,000 gmax for 2 h at 10°C (5). No other virus particles were observed in these samples, nor were any observed in non-symptomatic samples. One sample was submitted as potted plant (Mandevilla ‘Sunmandeho’ Sun Parasol Giant White) and was kept under greenhouse conditions for subsequent analyses. Total RNA (Qiagen) was extracted from this sample, and Potyvirus was detected using the universal primers Poty S (5′-GGN AAY AAY AGY GGN CAR CC-3′) and PV1 (5′-20(T)V-3′) (1) by reverse transcription (RT)-PCR (3). The amplified product was the expected ~1.7-kb, corresponding to the partial nuclear inclusion body gene, the coat protein (CP) gene, and the 3′ end untranslated region. The RT-PCR amplicon was cloned (NEB) and sequenced, and the 1,720-bp consensus sequence was deposited in GenBank (Accession No. KM243928). NCBI BLAST analysis at the nucleotide level revealed highest identity (83%) with an isolate of Catharanthus mosaic virus (CatMV) from Brazil (Accession No. DQ365928). Pairwise analysis of the predicted 256 amino acid CP revealed 91% identity with the CatMV Brazilian isolate (ABI94824) and 68% or less identity with other potyviruses. Two potyviruses are usually considered the same species if their CP amino acid sequences are greater than 80% identical (2). Serological analysis of the infected sample Mandevilla ‘Sunmandeho’ Sun Parasol Giant White using a CatMV specific antiserum (4) resulted in positive indirect ELISA reactions. CatMV has been previously reported in periwinkle (Catharanthus roseus) in Brazil (4). Based on the analyses by TEM, RT-PCR, nucleotide and amino acid sequence identities, and serological reactivity, we identify this virus as a U.S. Mandevilla isolate of CatMV. To our knowledge, this is the first report of Catharanthus mosaic virus both in the United States and in Mandevilla.

References: (1) J. Chen et al. Arch Virol. 146:757, 2001. (2) A. Gibbs and K. Ohshima. Ann. Rev. Phytopathol. 48:205, 2010. (3) R. L. Jordan et al. Acta Hortic. 901:159, 2011. (4) S. C. Maciell et al. Sci. Agric. Piracicaba, Brazil. 68:687, 2011. (5) D. Mollov et al. Arch Virol. 158:1917, 2013.
Importance of Toll-like Receptor 2 in Mitochondrial Dysfunction during Polymicrobial Sepsis
Authors: Gong Yu , Zou Lin , Feng Yan , Li Dan , Cai Jiayan , Chen Dunjin , Chao Wei
Published: October 2014

Background:

Toll-like receptor 2 (TLR2) contributes to sepsis pathogenesis such as deleterious systemic inflammation, cardiac dysfunction, and high mortality in animal studies. Mitochondrial dysfunction is a key molecular event that is associated with organ injury in sepsis. The role of TLR2 in sepsis-induced mitochondrial dysfunction remains unclear.

Methods:

Intracellular hydrogen peroxide (H2O2), mitochondrial superoxide (O2
-), mitochondrial membrane potential (ΔΨm), and intracellular adenosine triphosphate (ATP) were measured in peritoneal leukocytes. A mouse model of polymicrobial sepsis was generated by cecum ligation and puncture (CLP). Wild-type and TLR2-deficient (TLR2-/-) mice were subjected to sham or CLP. Mitochondrial functions including reactive oxygen species (ROS), ΔΨm, intracellular ATP, and complex III activity were measured.

Results:

TLR2/1 activation by Pam3Cys enhanced intracellular H2O2 and mitochondrial O2
- production in leukocytes, but had no effect on mitochondrial ΔΨm and ATP production. The effect was specific for TLR2/1 as TLR3 or TLR9 ligands did not induce ROS production. Polymicrobial sepsis induced mitochondrial dysfunction in leukocytes, as demonstrated by increased H2O2 and mitochondrial O2
- production (CLP vs. sham; H2O2: 3,173 ± 498, n = 5 vs. 557 ± 38, n = 4; O2
-: 707 ± 66, n = 35 vs. 485 ± 35, n = 17, mean fluorescence intensity, mean ± SEM), attenuated complex III activity (13 ± 2, n = 16 vs. 30 ± 3, n = 7, millioptical densities/min), loss of mitochondrial ΔΨm, and depletion of intracellular ATP (33 ± 6, n = 11 vs. 296 ± 29, n = 4, nmol/mg protein). In comparison, there was significant improvement in mitochondrial function in septic TLR2-/- mice as evidenced by attenuated mitochondrial ROS production, better-maintained mitochondrial ΔΨm, and higher cellular ATP production.

Conclusions:

TLR2 signaling plays a critical role in mediating mitochondrial dysfunction in peritoneal leukocytes during polymicrobial sepsis.
Alterations in gap junction connexin43/connexin45 ratio mediate a transition from quiescence to excitation in a mathematical model of the myometrium
Authors: Sheldon Rachel E. , Mashayamombe Chipo , Shi Shao-Qing , Garfield Robert E. , Shmygol Anatoly , Blanks Andrew M. , van den Berg Hugo A.
Published: October 2014

The smooth muscle cells of the uterus contract in unison during delivery. These cells achieve coordinated activity via electrical connections called gap junctions which consist of aggregated connexin proteins such as connexin43 and connexin45. The density of gap junctions governs the excitability of the myometrium (among other factors). An increase in gap junction density occurs immediately prior to parturition. We extend a mathematical model of the myometrium by incorporating the voltage-dependence of gap junctions that has been demonstrated in the experimental literature. Two functional subtypes exist, corresponding to systems with predominantly connexin43 and predominantly connexin45, respectively. Our simulation results indicate that the gap junction protein connexin45 acts as a negative modulator of uterine excitability, and hence, activity. A network with a higher proportion of connexin45 relative to connexin43 is unable to excite every cell. Connexin45 has much more rapid gating kinetics than connexin43 which we show limits the maximum duration of a local burst of activity. We propose that this effect regulates the degree of synchronous excitation attained during a contraction. Our results support the hypothesis that as labour approaches, connexin45 is downregulated to allow action potentials to spread more readily through the myometrium.
Evolution of climatic niche specialization: a phylogenetic analysis in amphibians
Authors: Bonetti Maria Fernanda , Wiens John J.
Published: October 2014

The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change.
Testing the stages model in the adaptive radiation of cichlid fishes in East African Lake Tanganyika
Authors: Muschick Moritz , Nosil Patrik , Roesti Marius , Dittmann Marie Theres , Harmon Luke , Salzburger Walter
Published: October 2014

Adaptive radiation (AR) is a key process in the origin of organismal diversity. However, the evolution of trait disparity in connection with ecological specialization is still poorly understood. Available models for vertebrate ARs predict that diversification occurs in the form of temporal stages driven by different selective forces. Here, we investigate the AR of cichlid fishes in East African Lake Tanganyika and use macroevolutionary model fitting to evaluate whether diversification happened in temporal stages. Six trait complexes, for which we also provide evidence of their adaptiveness, are analysed with comparative methods: body shape, pharyngeal jaw shape, gill raker traits, gut length, brain weight and body coloration. Overall, we do not find strong evidence for the ‘stages model’ of AR. However, our results suggest that trophic traits diversify earlier than traits implicated in macrohabitat adaptation and that sexual communication traits (i.e. coloration) diversify late in the radiation.
Evolutionary ecology of specialization: insights from phylogenetic analysis
Authors: Vamosi Jana C. , Armbruster W. Scott , Renner Susanne S.
Published: October 2014

In this Special feature, we assemble studies that illustrate phylogenetic approaches to studying salient questions regarding the effect of specialization on lineage diversification. The studies use an array of techniques involving a wide-ranging collection of biological systems (plants, butterflies, fish and amphibians are all represented). Their results reveal that macroevolutionary examination of specialization provides insight into the patterns of trade-offs in specialized systems; in particular, the genetic mechanisms of trade-offs appear to extend to very different aspects of life history in different groups. In turn, because a species may be a specialist from one perspective and a generalist in others, these trade-offs influence whether we perceive specialization to have effects on the evolutionary success of a lineage when we examine specialization only along a single axis. Finally, how geographical range influences speciation and extinction of specialist lineages remains a question offering much potential for further insight.
Actibacter haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai, and emended description of the genus Actibacter
Authors: Hyun Dong-Wook , Kim Joon Yong , Kim Min-Soo , Shin Na-Ri , Kim Hyun Sik , Lee June-Young , Bae Jin-Woo
Published: October 2014

A novel strain, designated strain W113T, was isolated from the gut of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The isolate was a Gram-staining-negative, facultatively anaerobic, non-motile, rod-shaped bacterium producing yellow-to-orange carotenoid-type pigments. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus

Actibacter

in the family

Flavobacteriaceae

and it shared the highest sequence similarity with the type strain of

Actibacter sediminis

(98.8 % similarity). Optimal growth occurred at 25 °C, at pH 7 and with 2 % (w/v) NaCl. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C15 : 1 G. Menaquinone-6 was the main respiratory quinone. The polar lipids of the isolate were phosphatidylethanolamine, three unidentified amino lipids, and three unidentified lipids. The genomic DNA G+C content was 42.6 mol% and DNA–DNA hybridization values indicated that the strain shared <18 % genomic relatedness with the most closely related species. The results of the phylogenetic, phenotypic and genotypic analyses indicated that strain W113T represents a novel species in the genus

Actibacter

, for which the name Actibacter haliotis sp. nov. is proposed. The type strain is W113T ( = KACC 17209T = JCM 18868T).
Morphology, morphogenesis and molecular phylogeny of an oxytrichid ciliate, Rubrioxytricha haematoplasma (Blatterer & Foissner, 1990) Berger, 1999 (Ciliophora, Hypotricha)
Authors: Chen Wenping , Chen Xumiao , Li Lifang , Warren Alan , Lin Xiaofeng
Published: October 2014

The morphology and morphogenesis of an oxytrichid ciliate, Rubrioxytricha haematoplasma (Blatterer & Foissner, 1990) Berger, 1999, collected from brackish and marine waters in China, were investigated using live observation and the protargol staining method. The main features of the morphogenetic process are: (i) the parental adoral zone of membranelles is retained completely in the proter and the anlage of undulating membranes originates from dedifferentiation of the old structures; (ii) three frontal, four frontoventral, one buccal, five ventral and five transverse cirri are derived from the anlagen of the undulating membranes and the five streaks of frontal-ventral-transverse anlagen in the pattern of 1 : 3 : 3 : 3 : 4 : 4 from left to right; (iii) the morphogenesis of the dorsal kineties is simpler than the Oxytricha pattern, i.e. without fragmentation of the dorsal kinety 3 anlagen; (iv) the single caudal cirrus originates from the dorsal kinety 3 anlage on the right side; (v) the two macronuclear nodules fuse into a single mass during the mid-stage of morphogenesis. These features correspond well with Rubrioxytricha indica, indicating that the morphogenetic pattern of Rubrioxytricha is stable. Phylogenetic analysis based on small-subunit rRNA gene sequence data supports the monophyly of the genus Rubrioxytricha, which is nested within the non-Stylonychinae clade.
Halovivax cerinus sp. nov., an extremely halophilic archaeon from a hypersaline lake
Authors: Amoozegar Mohammad Ali , Makhdoumi-Kakhki Ali , Mehrshad Maliheh , Rasooli Mehrnoosh , Fazeli Seyed Abolhassan Shahzadeh , Spröer Cathrin , Ventosa Antonio
Published: October 2014

An extremely halophilic archaeon, strain IC35T, was isolated from a mud sample of the Aran-Bidgol salt lake in Iran. The novel strain was cream, non-motile, rod-shaped and required at least 2.5 M NaCl, but not MgCl2, for growth. Optimal growth was achieved with 3.4 M NaCl and 0.1 M MgCl2. The optimum pH and temperature for growth were pH 7.0 (grew over a pH range of 6.5–9.0) and 40 °C (grew over a temperature range of 30–50 °C), respectively. Analysis of 16S rRNA gene sequences revealed that strain IC35T clustered with species of the genus

Halovivax

, with sequence similarities of 97.3 %, 96.6 % and 96.3 %, respectively, to

Halovivax limisalsi

IC38T,

Halovivax asiaticus

EJ-46T and

Halovivax ruber

XH-70T. The rpoB′ gene similarities between the novel strain and

Halovivax limisalsi

IBRC-M 10022T,

Halovivax ruber

JCM 13892T and

Halovivax asiaticus

JCM 14624T were 90.2 %, 90.2 % and 89.9 %, respectively. The polar lipid pattern of strain IC35T consisted of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester; six unknown glycolipids and two minor phospholipids were also observed. The only quinone present was MK-8 (II-H2). The G+C content of the genomic DNA was 63.2 mol%. DNA–DNA hybridization studies (29 % hybridization with

Halovivax limisalsi

IBRC-M 10022T), as well as biochemical and physiological characterization, allowed strain IC35T to be differentiated from other species of the genus

Halovivax

. A novel species, Halovivax
cerinus sp. nov., is therefore proposed to accommodate this strain. The type strain is IC35T ( = IBRC-M 10256T = KCTC 4050T).
Anaerobic degradation of aromatic amino acids by the hyperthermophilic archaeon Ferroglobus placidus
Authors: Aklujkar Muktak , Risso Carla , Smith Jessica , Beaulieu Derek , Dubay Ryan , Giloteaux Ludovic , DiBurro Kristin , Holmes Dawn
Published: October 2014

Ferroglobus placiduswas discovered to oxidize completely the aromatic amino acids tyrosine, phenylalanine and tryptophan when Fe(III) oxide was provided as an electron acceptor. This property had not been reported previously for a hyperthermophilic archaeon. It appeared thatF. placidusfollows a pathway for phenylalanine and tryptophan degradation similar to that of mesophilic nitrate-reducing bacteria,Thauera aromaticaandAromatoleum aromaticumEbN1. Phenylacetate, 4-hydroxyphenylacetate and indole-3-acetate were formed during anaerobic degradation of phenylalanine, tyrosine and tryptophan, respectively. Candidate genes for enzymes involved in the anaerobic oxidation of phenylalanine to phenylacetate (phenylalanine transaminase, phenylpyruvate decarboxylase and phenylacetaldehyde : ferredoxin oxidoreductase) were identified in theF. placidusgenome. In addition, transcription of candidate genes for the anaerobic phenylacetate degradation, benzoyl-CoA degradation and glutaryl-CoA degradation pathways was significantly upregulated in microarray and quantitative real-time-PCR studies comparing phenylacetate-grown cells with acetate-grown cells. These results suggested that the general strategies for anaerobic degradation of aromatic amino acids are highly conserved amongst bacteria and archaea living in both mesophilic and hyperthermophilic environments. They also provided insights into the diverse metabolism ofArchaeoglobaceaespecies living in hyperthermophilic environments.
Myelinating Cocultures of Rat Retinal Ganglion Cell Reaggregates and Optic Nerve Oligodendrocyte Precursor Cells
Authors: Watkins Trent A. , Scholze Anja R.
Published: October 2014

This protocol describes the generation of a rapidly myelinating central nervous system coculture for the study of complex neuronal-glial interactions in vitro. Postnatal rat retinal ganglion cells (RGCs) purified by immunopanning are promoted to cluster into reaggregates and then allowed to extend dense beds of radial axons for 10–14 d. Subsequently, rodent oligodendrocyte precursor cells are purified by immunopanning, transfected if desired, and seeded on top of the RGC reaggregates. Under the conditions described here, compact myelin can be observed within 6 d.
Isolation of Mitochondria from Animal Tissue
Authors: Clayton David A. , Shadel Gerald S.
Published: October 2014

Rat or mouse liver is the most frequently used tissue for mitochondrial preparations because it is readily available, easy to homogenize, and replete with mitochondria. A motor-driven Teflon and glass Potter-Elvehjem homogenizer is the best choice for homogenizing liver, but if one is not available, this tissue is soft enough that a Dounce homogenizer with a loose (A) pestle can also be used. The yield and purity of the mitochondrial preparation will be influenced by the method and speed of preparation and the age and physiological condition of the animal.
Fluorodeoxyglucose-Based Positron Emission Tomography Imaging to Monitor Drug Responses in Hematological Tumors
Authors: Newbold Andrea , Martin Ben P. , Cullinane Carleen , Bots Michael
Published: October 2014

Positron emission tomography (PET) can be used to monitor the uptake of the labeled glucose analog fluorodeoxyglucose (18F-FDG), a process that is generally believed to reflect viable tumor cell mass. The use of 18F-FDG PET can be helpful in documenting over time the reduction in tumor mass volume in response to anticancer drug therapy in vivo. In this protocol, we describe how to monitor the response of murine B-cell lymphomas to an inducer of apoptosis, the anticancer drug vorinostat (a histone deacetylase inhibitor). B-cell lymphoma cells are injected into recipient mice and, on tumor formation, the mice are treated with vorinostat. The tracer 18F-FDG is then injected into the mice at several time points, and its uptake is monitored using PET. Because the uptake of 18F-FDG is not a direct measure of apoptosis, an additional direct method proving that apoptotic cells are present should also be performed.
Tetracycline-Regulated Mouse Models of Cancer
Authors: Yeh Elizabeth S. , Vernon-Grey Ann , Martin Heather , Chodosh Lewis A.
Published: October 2014

Genetically engineered mouse models (GEMMs) have proven essential to the study of mammalian gene function in both development and disease. However, traditional constitutive transgenic mouse model systems are limited by the temporal and spatial characteristics of the experimental promoter used to drive transgene expression. To address this limitation, considerable effort has been dedicated to developing conditional and inducible mouse model systems. Although a number of approaches to generating inducible GEMMs have been pursued, several have been restricted by toxic or undesired physiological side effects of the compounds used to activate gene expression. The development of tetracycline (tet)-dependent regulatory systems has allowed for circumvention of these issues resulting in the widespread adoption of these systems as an invaluable tool for modeling the complex nature of cancer progression.
Myelinating Cocultures of Purified Oligodendrocyte Lineage Cells and Retinal Ganglion Cells
Authors: Watkins Trent A. , Scholze Anja R.
Published: October 2014

In this article, we introduce methods for generating rapidly myelinating cocultures with reaggregates of purified retinal ganglion cells and optic nerve oligodendrocyte precursor cells. This coculture system facilitates the study of complex central nervous system neuronal–glial interactions and myelination. It enables control of the extracellular environment and allows the use of transfected, virally infected, mutant, or knockout neurons and/or glial cell types. It is therefore possible to assess the role of various signaling pathways and genes in myelination and node of Ranvier formation.
Fluorescence Microscopy
Authors: Sanderson Michael J. , Smith Ian , Parker Ian , Bootman Martin D.
Published: October 2014

Fluorescence microscopy is a major tool with which to monitor cell physiology. Although the concepts of fluorescence and its optical separation using filters remain similar, microscope design varies with the aim of increasing image contrast and spatial resolution. The basics of wide-field microscopy are outlined to emphasize the selection, advantages, and correct use of laser scanning confocal microscopy, two-photon microscopy, scanning disk confocal microscopy, total internal reflection, and super-resolution microscopy. In addition, the principles of how these microscopes form images are reviewed to appreciate their capabilities, limitations, and constraints for operation.
How Vacuolar Sorting Receptor Proteins Interact with Their Cargo Proteins: Crystal Structures of Apo and Cargo-Bound Forms of the Protease-Associated Domain from an Arabidopsis Vacuolar Sorting Receptor
Authors: Luo Fang , Fong Yu Hang , Zeng Yonglun , Shen Jinbo , Jiang Liwen , Wong Kam-Bo
Published: October 2014

In plant cells, soluble proteins are directed to vacuoles because they contain vacuolar sorting determinants (VSDs) that are recognized by vacuolar sorting receptors (VSR). To understand how a VSR recognizes its cargo, we present the crystal structures of the protease-associated domain of VSR isoform 1 from Arabidopsis thaliana (VSR1PA) alone and complexed with a cognate peptide containing the barley (Hordeum vulgare) aleurain VSD sequence of 1ADSNPIRPVT10. The crystal structures show that VSR1PA binds the sequence, Ala-Asp-Ser, preceding the NPIR motif. A conserved cargo binding loop, with a consensus sequence of 95RGxCxF100, forms a cradle that accommodates the cargo-peptide. In particular, Arg-95 forms a hydrogen bond to the Ser-3 position of the VSD, and the essential role of Arg-95 and Ser-3 in receptor-cargo interaction was supported by a mutagenesis study. Cargo binding induces conformational changes that are propagated from the cargo binding loop to the C terminus via conserved residues in switch I-IV regions. The resulting 180° swivel motion of the C-terminal tail is stabilized by a hydrogen bond between Glu-24 and His-181. A mutagenesis study showed that these two residues are essential for cargo interaction and trafficking. Based on our structural and functional studies, we present a model of how VSRs recognize their cargos.