bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of ABCG-type ABC transporters in phytohormone transport
Authors: Borghi Lorenzo , Kang Joohyun , Ko Donghwi , Lee Youngsook , Martinoia Enrico
Published: October 2015

Plant hormones (phytohormones) integrate endogenous and exogenous signals thus synchronizing plant growth with environmental and developmental changes. Similar to animals, phytohormones have distinct source and target tissues, hence controlled transport and focused targeting are required for their functions. Many evidences accumulated in the last years about the regulation of long-distance and directional transport of phytohormones. ATP-binding cassette (ABC) transporters turned out to play major roles in routing phytohormones not only in the plant body but also towards the outer environment. The ABCG-type proteins ABCG25 and ABCG40 are high affinity abscisic acid (ABA) transporters. ABCG14 is highly co-expressed with cytokinin biosynthesis and is the major root-to-shoot cytokinin transporter. Pleiotropic drug resistance1 (PDR1) from Petunia hybrida transports strigolactones (SLs) from the root tip to the plant shoot but also outside to the rhizosphere, where SLs are the main attractants to mycorrhizal fungi. Last but not least, ABCG36 and ABCG37 possibly play a dual role in coumarine and IBA transport.
Role of family D ATP-binding cassette transporters (ABCD) in cancer
Authors: Hlaváč Viktor , Souček Pavel
Published: October 2015

ATP-binding cassette (ABC) transporters, belonging to the family D, are expressed in peroxisomes, endoplasmic reticulum or lysosomes. ABCD transporters play a role in transport of lipids, bile acids and vitamin B12 and associate with peroxisomal disorders. ABCD1 performs transport of coenzyme A esters of very-long-chain fatty acids (VLCFA) in peroxisomes and a number of mutations in ABCD1 gene were linked to an X-linked adrenoleucodystrophy (X-ALD). The role of ABCD transporters in tumour growth has not been studied in detail, but there is some evidence that ABCDs levels differ between undifferentiated stem or tumour cells and differentiated cells suggesting a possible link to tumorigenesis. In this mini-review, we discuss the available information about the role of ABCD transporters in cancer.
Signalling to eIF4E in cancer
Authors: Siddiqui Nadeem , Sonenberg Nahum
Published: October 2015

Translational control plays a critical role in the regulation of gene expression in eukaryotes and affects many essential cellular processes, including proliferation, apoptosis and differentiation. Under most circumstances, translational control occurs at the initiation step at which the ribosome is recruited to the mRNA. The eukaryotic translation initiation factor 4E (eIF4E), as part of the eIF4F complex, interacts first with the mRNA and facilitates the recruitment of the 40S ribosomal subunit. The activity of eIF4E is regulated at many levels, most profoundly by two major signalling pathways: PI3K (phosphoinositide 3-kinase)/Akt (also known and Protein Kinase B, PKB)/mTOR (mechanistic/mammalian target of rapamycin) and Ras (rat sarcoma)/MAPK (mitogen-activated protein kinase)/Mnk (MAPK-interacting kinases). mTOR directly phosphorylates the 4E-BPs (eIF4E-binding proteins), which are inhibitors of eIF4E, to relieve translational suppression, whereas Mnk phosphorylates eIF4E to stimulate translation. Hyperactivation of these pathways occurs in the majority of cancers, which results in increased eIF4E activity. Thus, translational control via eIF4E acts as a convergence point for hyperactive signalling pathways to promote tumorigenesis. Consequently, recent works have aimed to target these pathways and ultimately the translational machinery for cancer therapy.
Providing a molecular mechanism for P-glycoprotein; why would I bother?
Authors: Callaghan Richard
Published: October 2015

It is almost 40 years since the drug efflux pump P-glycoprotein (permeability glycoprotein or P-gp) was shown to confer multi-drug resistance in cancer cells. This protein has been one of the most extensively investigated transport proteins due to its intriguing mechanism and its affect in oncology. P-gp is known to interact with over 300 compounds and the ability to achieve this has not yet been revealed. Following the binding of substrate and nucleotide, a complex series of conformational changes in the membrane and cytosolic domains translocates substrate across the membrane. Despite over 30 years of biochemical investigation, the availability of structural data and a plethora of chemical tools to modulate its function, the molecular mechanism remains a mystery. In addition, overcoming its activity in resistant cancer cells has not been achieved in the clinic, thereby garnering some degree of pessimism in the field. This review highlights the progress that has been achieved in understanding this complex protein and the value of undertaking molecular studies.
Lipid flopping in the liver
Authors: Linton Kenneth J.
Published: October 2015

Bile is synthesized in the liver and is essential for the emulsification of dietary lipids and lipid-soluble vitamins. It is a complex mixture of amphiphilic bile acids (BAs; which act as detergent molecules), the membrane phospholipid phosphatidylcholine (PC), cholesterol and a variety of endogenous metabolites and waste products. Over the last 20 years, the combined effort of clinicians, geneticists, physiologists and biochemists has shown that each of these bile components is transported across the canalicular membrane of the hepatocyte by its own specific ATP-binding cassette (ABC) transporter. The bile salt export pump (BSEP) ABCB11 transports the BAs and drives bile flow from the liver, but it is now clear that two lipid transporters, ABCB4 (which flops PC into the bile) and the P-type ATPase ATP8B1/CDC50 (which flips a different phospholipid in the opposite direction) play equally critical roles that protect the biliary tree from the detergent activity of the bile acids. Understanding the interdependency of these lipid floppases and flippases has allowed the development of an assay to measure ABCB4 function. ABCB4 harbours numerous mis-sense mutations which probably reflects the spectrum of liver disease rooted in ABCB4 aetiology. Characterization of the effect of these mutations at the protein level opens the possibility for the development of personalized prognosis and treatment.
Amplitude‐adaptive spread‐spectrum data embedding
Authors: Li Ming , Liu Qian , Guo Yanqing , Wang Bo , Kong Xiangwei
Published: October 2015

In this study, the authors consider additive spread‐spectrum (SS) data embedding in transform‐domain host data. Conventional additive SS embedding schemes use an equal‐amplitude modulated carrier to deposit one information symbol across a group of host data coefficients which act as interference to SS signal of interest. If there is a flexibility of assigning different amplitudes across symbol bits, the probability of error can be further reduced by adaptively allocating amplitude to each symbol bit based on its own host/interference. In this study, they present a novel amplitude‐adaptive SS embedding scheme. Particularly, symbol‐by‐symbol adaptive amplitude allocation algorithms are developed to compensate for the impact from the known interference. They aim at designing the SS embedding amplitude for each symbol adaptively in order to minimise the receiver bit‐error‐rate (BER) at any given distortion level. Then, optimised amplitude allocation for multi‐carrier/multi‐message embedding in the same host data is studied as well. Finally, they consider the problem of amplitude optimisation for an ideal scenario where no external noise is introduced during embedding and transmission. Extensive experimental results illustrate that the proposed amplitude‐adaptive SS embedding scheme can provide order‐of‐magnitude performance improvement over several other state‐of‐the‐art SS embedding schemes.
Extrinsic parameters and focal length calibration using rotation‐symmetric patterns
Authors: Liu Ruizhi , Zhang Hongran , Lu Jian , Sun Yi
Published: October 2015

The authors present a camera calibration method for estimating the extrinsic parameters and focal length of a camera using only a single image of a planar rotation‐symmetric pattern. The frontal parallel image of the pattern can preserve the rotation‐symmetric pattern, causing the corresponding frieze‐expansion (FE) pattern to be expressed as a low‐rank matrix, which does not exist when the image is captured from an oblique view. The proposed method derives the forward formulation between the FE of the image observed from an oblique view and the low‐rank, FE pattern of the frontal parallel image. An optimisation problem arises when rank minimisation techniques are introduced; by solving this problem, one can obtain the camera parameters relative to the front view. Simultaneously, the rotation‐symmetric texture is recovered as a by‐product. This new method takes advantage of the raw intensity values of the observed image itself, bypassing the need to extract any low‐level features and simplifying human intervention. Experimental results demonstrate the validity of the proposed method.
Reduced switch multilevel inverter for performance enhancement of induction motor drive with intelligent rotor resistance estimator
Authors: Chitra A. , Himavathi S.
Published: October 2015

Multilevel inverters (MLI) are suitable for renewable energy sources as they operate at lower switching frequency and voltage. The sinusoidal PWM (SPWM) techniques are popularly employed in MLIs to improve the drive performance. However as the number of switches increase it leads to more switching losses, higher price and size of the inverter. In this study, a modified reduced switch MLI (RSMLI) with five switches is proposed. Various multilevel inverter topologies with different multicarrier SPWM techniques such as phase disposition, phase opposition disposition, and alternative phase opposition disposition (APOD) are derived, analysed and presented for the proposed RSMLI. All the inverter topologies are simulated and the scheme with lowest THD is identified. The hardware setup is built for the proposed RSMLI using F28335 digital signal processor (DSP) for pulse generation and the results are validated. The vector control scheme of industrial standard requires an accurate and fast Rr estimator for stable performance. Neural based Rr estimator proposed by the authors is implemented on FPGA. The proposed RSMLI fed induction motor drive is examined with and without the neural based Rr estimator. Encouraging results obtained using the proposed RSMLI are reported.
Far-UV phase dependence and surface characteristics of comet
67P/Churyumov-Gerasimenko as observed with Rosetta Alice
Authors: Feaga L. M. , Protopapa S. , Schindhelm R. , Stern S. A. , A’Hearn M. F. , Bertaux J.-L. , Feldman P. D. , Parker J. Wm. , Steffl A. J. , Weaver H. A.
Published: October 2015

Aims. The Alice far-ultraviolet (FUV) spectrograph onboard Rosetta has,
for the first time, imaged the surface of a comet, 67P/Churyumov-Gerasimenko (67P), in the
FUV. With spatially resolved data, the nucleus properties are characterized in the FUV,
including phase dependence, albedo, and spectral slope. Regional measurements across the
nucleus are compared to discern any compositional variations.

Methods. Hapke theory was utilized to model the phase dependence of the
material on the surface of 67P. The phase dependence of 67P was derived from a subset of
data acquired at various phase angles in November 2014, within 50 km of the comet such
that the nucleus was spatially resolved. The derived photometric correction was then
applied to a different subset of spatially resolved data sampling several distinct
geographical regions on the nucleus acquired in August−November 2014 under similar viewing
geometries.

Results. In the FUV, the surface of 67P is dark, blue sloped, has an
average geometric albedo of 0.054±0.008 at 1475 Å near the center of the Alice bandpass, and is mostly
uniform from region to region, with the exception of the Hatmehit region, which is
slightly more reflective. These results are consistent with the suggestion made by the
Rosetta OSIRIS and VIRTIS teams that the surface of 67P is covered with a homogeneous
layer of material and that surface ice is not ubiquitous in large abundances. The modeled
Hapke parameters, specifically the single scattering albedo (w) and the asymmetry factor
(ζ), are
determined to be 0.031 ± 0.003
and −0.530 ± 0.025 near the
center of the Alice bandpass at 1475 Å. These parameters are consistent with measurements
of other comet nuclei that have been observed by flyby missions in the visible and the
near-infrared regimes.
Helical plasma thruster
Authors: Beklemishev A. D.
Published: October 2015

A new scheme of plasma thruster is proposed. It is based on axial acceleration of rotating magnetized plasmas in magnetic field with helical corrugation. The idea is that the propellant ionization zone can be placed into the local magnetic well, so that initially the ions are trapped. The E × B rotation is provided by an applied radial electric field that makes the setup similar to a magnetron discharge. Then, from the rotating plasma viewpoint, the magnetic wells of the helically corrugated field look like axially moving mirror traps. Specific shaping of the corrugation can allow continuous acceleration of trapped plasma ions along the magnetic field by diamagnetic forces. The accelerated propellant is expelled through the expanding field of magnetic nozzle. By features of the acceleration principle, the helical plasma thruster may operate at high energy densities but requires a rather high axial magnetic field, which places it in the same class as the VASIMR® rocket engine.
Role of many-body effects in the coherent dynamics of excitons in low-temperature-grown GaAs
Authors: Webber D. , Hacquebard L. , Liu X. , Dobrowolska M. , Furdyna J. K. , Hall K. C.
Published: October 2015

Femtosecond four-wave mixing experiments on low-temperature-grown (LT-) GaAs indicate a polarization-dependent nonlinear optical response at the exciton, which we attribute to Coulomb-mediated coupling between excitons and electron-hole pairs simultaneously excited by the broad-bandwidth laser pulses. Strong suppression of the exciton response through screening by carriers injected by a third pump pulse was observed, an effect that is transient due to rapid carrier trapping. Our findings highlight the need to account for the complex interplay of disorder and many-body effects in the design of ultrafast optoelectronic devices using this material.
The local semicircle law for random matrices with a fourfold symmetry
Authors: Alt Johannes
Published: October 2015

We consider real symmetric and complex Hermitian random matrices with the additional symmetry hxy = hN−y,N−x. The matrix elements are independent (up to the fourfold symmetry) and not necessarily identically distributed. This ensemble naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. It also occurs as the flip matrix model — an approximation of the two-dimensional Anderson model at small disorder. We show that the density of states converges to the Wigner semicircle law despite the new symmetry type. We also prove the local version of the semicircle law on the optimal scale.
Substrate effects and diffusion dominated roughening in Cu2O electrodeposition
Authors: Brandt I. S. , Zoldan V. C. , Stenger V. , Plá Cid C. C. , Pasa A. A. , Oliveira T. J. , Aarão Reis F. D. A.
Published: October 2015

Cuprous oxide (Cu2O) films from 25 nm to 1500 nm were electrodeposited on n-Si(100) and Ni/n-Si(100) substrates from aqueous solution at room temperature. X-ray diffraction and transmission electron microscopy imaging show that the Cu2O structure and morphology are strongly affected by the substrate choice, with V shape and U shape columnar growth on n-Si(100) and Ni/n-Si(100), respectively. Atomic force microscopy reveals the presence of rounded grains at the surface in both cases. Anomalous and normal roughening are observed in films grown on n-Si and Ni, respectively, but estimates of scaling exponents are not conclusive. On the other hand, the distributions of local heights, roughness, and extremal heights show good agreement with those of the fourth order linear stochastic equation of Mullins and Herring (MH). Thus, surface dynamics in both systems is dominated by diffusion of adsorbed molecules, with no large scale effect of possible inhomogeneities in mass flux from the solution or in reaction and adsorption rates. In growth on n-Si substrates, the noise amplitude of the MH equation increases in time as t0.8, while the coefficient of the curvature-related term is time-independent. Step edge energy barriers restrict the mass flux across grain boundaries, thus a broad size distribution of initial grains leads to coarsening of the larger ones. This explains their V shape in the thickest films and establishes a connection with the anomalous roughening. These effects are reduced in films grown on Ni/n-Si, which initially have much larger grains with narrower size distributions and, consequently, smaller fluctuations in coarse grained growth rates. Thus, despite the relevance of electrochemical conditions for Cu2O films to grow and their influence on crystallographic orientation, large scale surface features are determined by physical properties of the material and its interactions with the substrate, with a universal microscopic dynamics similar to vapor deposition.
Harmonium: A pulse preserving source of monochromatic extreme ultraviolet (30–110 eV) radiation for ultrafast photoelectron spectroscopy of liquids
Authors: Ojeda J. , Arrell C. A. , Grilj J. , Frassetto F. , Mewes L. , Zhang H. , van Mourik F. , Poletto L. , Chergui M.
Published: October 2015

A tuneable repetition rate extreme ultraviolet source (Harmonium) for time resolved photoelectron spectroscopy of liquids is presented. High harmonic generation produces 30–110 eV photons, with fluxes ranging from ∼2 × 1011 photons/s at 36 eV to ∼2 × 108 photons/s at 100 eV. Four different gratings in a time-preserving grating monochromator provide either high energy resolution (0.2 eV) or high temporal resolution (40 fs) between 30 and 110 eV. Laser assisted photoemission was used to measure the temporal response of the system. Vibrational progressions in gas phase water were measured demonstrating the ∼0.2 eV energy resolution.
Communication: Fully coherent quantum state hopping
Authors: Martens Craig C.
Published: October 2015

In this paper, we describe a new and fully coherent stochastic surface hopping method for simulating mixed quantum-classical systems. We illustrate the approach on the simple but unforgiving problem of quantum evolution of a two-state quantum system in the limit of unperturbed pure state dynamics and for dissipative evolution in the presence of both stationary and nonstationary random environments. We formulate our approach in the Liouville representation and describe the density matrix elements by ensembles of trajectories. Population dynamics are represented by stochastic surface hops for trajectories representing diagonal density matrix elements. These are combined with an unconventional coherent stochastic hopping algorithm for trajectories representing off-diagonal quantum coherences. The latter generalizes the binary (0,1) “probability” of a trajectory to be associated with a given state to allow integers that can be negative or greater than unity in magnitude. Unlike existing surface hopping methods, the dynamics of the ensembles are fully entangled, correctly capturing the coherent and nonlocal structure of quantum mechanics.
Three dimensional numerical study of different parameters effect on the external magnetic field applied to center the arc of the horizontal mercury discharge lamp
Authors: Ben Hamida Mohamed Bechir , Charrada Kamel
Published: October 2015

The aim of this paper is to evaluate the magnitude of the external magnetic field to be applied to a horizontal mercury discharge lamp such that the Lorentz forces counterbalance buoyancy forces and the hot region of the arc remains centered inside the lamp with the variation of six parameters of the lamp such as the external temperature of the lamp, envelope thickness, convective loss, Interelectrodeslength, pressure and current supply pointing to the influence of the parameters to the compensating magnetic field value. To achieve this objective, a commercial numerical software “Comsol Multiphysics” is used to implement the model that solves the equations of mass, energy and momentum for laminar compressible flow combined with the Laplace equation for the plasma in a three dimensional.
Season and reproductive status rather than genetic factors influence change in ewe weight and fat over time. 4. Genetic relationships of ewe weight and fat score with fleece, reproduction and milk traits
Authors: Walkom S. F. , Brien F. D. , Hebart M. L. , Fogarty N. M. , Hatcher S. , Pitchford W. S.
Published: October 2015

The profitability of a sheep enterprise is greatly influenced by the ability of the ewe to produce a lamb annually. This paper examines the between- and within-breed association between the liveweight and fat score of the adult ewe and key fleece, reproduction and milk production traits. The study analysed the performance of 2846 first-cross Merino and Corriedale ewes from the maternal central progeny test (MCPT) over their first three production cycles. Breed (9 sire breeds) and within-breed (91 sires) correlations were calculated from bivariate correlations of adult liveweight and fat score with fleece, reproduction and milk production traits. The mean liveweight and fatness of the breeds were low to moderately negatively correlated with greasy fleece weight (–0.55 and –0.25, respectively) and moderate to strongly positively correlated with fibre diameter (0.88 and 0.41, respectively). However, the within-breed correlations were generally low to negligible. The genetic relationships between ewe fat score and reproductive traits at the breed and within-breed level was generally low to negligible and, in some cases, negative under production conditions where the ewes were well managed and averaged a fat score of 3.5 pre-joining and became too fat across the production cycle. Strong breed correlations between ewe fat score and milk fat concentration (0.88) suggest that selection of fatter sire breeds will lead to increased fat in their progenies’ milk, which was associated with larger lambs. The potential advantages of selecting for more fat to improve the maternal performance of the ewe seem to be limited in enterprises where the production system can easily be adjusted to restrict the influence of temporary and long-term feed deficiencies, as was achieved within the MCPT research flocks.
Antimicrobial Properties of Mono- and Di-fac-rhenium Tricarbonyl 2-Pyridyl-1,2,3-triazole Complexes
Authors: Kumar Sreedhar V. , Lo Warrick K. C. , Brooks Heather J. L. , Hanton Lyall R. , Crowley James D.
Published: October 2015

A family of mono- and di-fac-rhenium tricarbonyl 2-pyridyl-1,2,3-triazole complexes with different aliphatic and aromatic substituents was synthesized in good-to-excellent yields (46–99 %). The complexes were characterized by 1H and 13C NMR spectroscopy, infrared spectroscopy, electronic (UV-visible) spectroscopy, high-resolution electrospray mass spectrometry, and elemental analyses. In four examples, the solid-state structures of the rhenium(i) complexes were confirmed by X-ray crystallography. The family of the mono- and di-rhenium(i) complexes and the corresponding 2-pyridyl-1,2,3-triazole was tested for antimicrobial activity in vitro against both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) microorganisms. Agar-based disk diffusion assays indicated that most of the rhenium(i) complexes were active against Staphylococcus aureus and that the cationic rhenium(i) complexes were more active than the related neutral systems. However, in all cases, the minimum inhibitory concentrations for all the complexes were modest (i.e. 16–1024 µg mL–1).
Determiner Sharing from a Crosslinguistic Perspective
Authors: Citko Barbara
Published: October 2015

This paper examines determiner sharing from a crosslinguistic perspective. After reviewing the restrictions on English determiner sharing, it prevents new data, coming mostly from Polish, showing that these restrictions are not universal. The properties of Polish determiner sharing are further shown to be problematic for the currently most popular analysis of this construction, the so-called small conjunct analysis of Johnson (2000) and Lin (2000). The alternative suggested in the paper, based on Citko’s (2005) multi-dominance analysis of ATB wh-movement, derives the properties of determiner sharing from a structure in which the determiner is literally shared between the two conjuncts.
Bare Infinitives in Alemannic and the Categorial Status of Infinitival Complements
Authors: Brandner Ellen
Published: October 2015

This article deals mainly with the distribution and function of the infinitival marker in Standard German and in Alemannic, a dialect spoken in Southern Germany.* At first sight both form and distribution differ in these two variants to a great extent. The most important difference is that Alemannic generally lacks the infinitival marker zu (to in English, te in Dutch) in the environments where it occurs in SG. Instead, bare infinitives are used to a much greater extent than in SG.

A detailed comparison shows how these Alemannic data can shed some new light on SG infinitival constructions — which are notoriously hard to analyze, especially the use of zu. It will turn out that zu plays hardly any syntactic role in restructuring contexts and is thus best accounted for in the word formation component rather than in the syntax. Another important issue to be discussed is extraposition. As will be shown below, extraposition is a much more widely used option in Alemannic than in SG — nevertheless, the Alemannic constructions show mono-clausal, i.e. coherent properties. I will argue that extraposition should not be taken as an indication for a bi-clausal structure — as it is done traditionally — but rather that the preferred intraposed order in SG should be analyzed in terms of a PF “flip-operation”. The attested variation between SG and Alemannic will thus turn out to be merely variation on the surface. But there are constructions where both variants differ more profoundly, namely in the context of propositional verbs. These differences will be traced back to the existence of a second kind of zu — existing only in SG — that can indeed license a full CP.
Influence of buffer layers on Ni thin film structure and graphene growth by CVD
Authors: Ozceri Elif , Selamet Yusuf
Published: October 2015

Buffer and/or adhesive layers were used to decrease the dewetting of Ni thin film at graphene growth temperatures of around 900 °C. Depositing a thin buffer (Al2O3) layer onto SiO2/Si substrate significantly reduced the dewetting effect and surface roughness of Ni catalyst film. Thin adhesive (Cr) layers with or without Al2O3 buffer layers increased the texturing in (1 1 1) orientation, which was promoted by growing at an elevated temperature (450 °C). The effects of pretreatment and growth temperature on crystal orientation, grain size and surface roughness of Ni film were analyzed. Our results indicated a large positive correlation coefficient between the film thickness and surface roughness for thinner and non-buffered films, and a negative correlation coefficient between the thickness and 900 °C -annealed film roughness for thicker and buffered films. The graphene coverage was greatly improved over the films grown with Al2O3 and/or Cr layers. In summary, we suggest that growing high quality, large area, 1- or 2-layer graphene on polycrystalline Ni transition metal thin film is optimized by using Al2O3 and/or Cr layers to reduce Ni dewetting, surface roughness, and groove depth while controlling grain size and texturing in (1 1 1) orientation by annealing at 900 °C.
Identification of a Novel Mycoplasma Species in a Patient With Septic Arthritis of the Hip and Seal Finger
Authors: Westley Benjamin P. , Horazdovsky Ryan D. , Michaels Dina L. , Brown Daniel R.
Published: October 2015

An Alaska Native hunter developed fever, swollen finger, and septic hips after harvesting seals. Evaluation of hip tissue by 16S rRNA gene polymerase chain reaction and sequencing revealed a putative novel mycoplasma species. We report the identification of this organism and describe the first known case of disseminated seal finger mycoplasmosis.
Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case
Authors: Pullan Steven T. , Pearson Talima R. , Latham Jennie , Mason Joanne , Atkinson Barry , Silman Nigel J. , Marston Chung K. , Sahl Jason W. , Birdsell Dawn , Hoffmaster Alex R. , Keim Paul , Vipond Richard
Published: October 2015

There have been two anthrax cases affecting people that played and/or made animal-skin drums in the UK during the last 10 years, with single fatal occurrences in Scotland in 2006 and London in 2008. Investigations by the Health Protection Agency (now Public Health England) employing multi-locus-variable number tandem repeat analysis had previously linked the clinical cases to spores associated with animal skins and drums the patients had been in contact with. In this study, whole-genome sequencing of 23 Bacillus anthracis isolates harvested during the investigations was performed. High-quality draft assemblies of these genomes provided greater characterization of the B. anthracis strains present and placed them all upon a new branch of the global phylogeny. Although closely related, the clinical isolates from the two events, and another isolated from a drum-skin-associated case in New York in 2006, were distinct from each other. Multiple distinct genotypes were found during both investigations, implying either multiple contamination events or a single heterogeneous contamination. One environmental isolate from the Scottish incident was more closely related to London isolates than to the other Scottish isolates. As B. anthracis of this subgroup was present at both geographically and temporally distinct events, it may be more widespread at the source of contamination. All isolates were distinct from currently characterized West African strains, despite this being the likely origin of the drums and hides, therefore adding to our knowledge of B. anthracis diversity in the region.
Social context modulates idiosyncrasy of behaviour in the gregarious cockroach Blaberus discoidalis
Authors: Crall James , Souffrant Andre , Akandwanaho Dominic , Hescock Sawyer , Callan Sarah , Coronado W Melissa , Baldwin Maude , de Bivort Benjamin
Published: October 2015

Individuals are different, but they can work together to perform adaptive collective behaviours. Despite emerging evidence that individual variation strongly affects group performance, it is less clear to what extent individual variation is modulated by participation in collective behaviour. We examined light avoidance (negative phototaxis) in the gregarious cockroach Blaberus discoidalis, in both solitary and group contexts. Cockroaches in groups exhibit idiosyncratic light-avoidance performance that persists across days, with some individual cockroaches avoiding a light stimulus 75% of the time, and others avoiding the light just above chance (i.e. ~50% of the time). These individual differences are robust to group composition. Surprisingly, these differences do not persist when individuals are tested in isolation, but return when testing is once again done with groups. During the solo testing phase cockroaches exhibited individually consistent light-avoidance tendencies, but these differences were uncorrelated with performance in any group context. Therefore, we have observed not only that individual variation affects group-level performance, but also that whether or not a task is performed collectively can have a significant, predictable effect on how an individual behaves. That individual behavioural variation is modulated by whether a task is performed collectively has major implications for understanding variation in behaviours that are facultatively social, and it is essential that ethologists consider social context when evaluating individual behavioural differences.
Insights into the phenology of migration and survival of a long migrant land bird
Authors: Madon Bénédicte , Le Nuz Eric , Ferlat Cédric , Hingrat Yves
Published: October 2015

Lay summary

For polygamous long-migrant birds, the choice of migration strategy depends on social pressure and experience and influences the chance of survival. If you are a male, you’d better leave early in the spring to secure the best site to show off. In fall, juveniles have a hard time surviving to migration as they leave before the adults and lack experience on where to go and where to stop to rest.

The process of migration stems from an adaptation of climatic seasonality and animals have developed various strategies to complete the journey between a wintering and breeding ground. Understanding the migratory behavior and determining when and where mortality occurs during the annual cycle is fundamental to understand population dynamics and implement appropriate conservation measures. Based on a big data set and advanced statistical methods, we inspected the phenology of migration of a polygynous land bird, the Macqueen’s bustard,Chlamydotis macqueenii.We explored its migration strategies between sex, age, season and geographical origin. We show that departure for migration depended on age in the fall with juveniles being the first to leave and on age and sex in the spring with juveniles departing later and males induced to arrive early in spring to secure high-quality territories. Birds breeding at higher latitudes were the first to leave in the fall and more likely to perform longer stopovers. Bustards exhibited different strategies for spring and fall migrations: spring migration was significantly longer than fall migration with more but shorter stopovers. Survival was lower for juveniles experiencing their first migration and for all birds during fall migration and on their wintering ground. Experience linked to social hierarchical pressures and environmental conditions might be the key drivers of migration strategies and survival in long-distance polygynous migrants.
Single molecule sequencing of THCA synthase reveals copy number variation in modern drug-type Cannabis sativa L.
Authors: McKernan Kevin J , Helbert Yvonne , Tadigotla Vasisht , McLaughlin Stephen , Spangler Jessica , Zhang Lei , Smith Douglas
Published: October 2015

Cannabinoid expression is an important genetically determined feature of cannabis that presents clinical and legal implications for patients seeking cannabinoid specific therapies like Cannabidiol (CBD). Cannabinoid, terpenoid, and flavonoid marker assisted selection can accelerate breeding efforts by offering genetic tools to select for desired traits at an early stage in growth. To this end, multiple models for chemotype inheritance have been described suggesting a complex picture for chemical phenotype determination. Here we explore the potential role of copy number variation of THCA Synthase using phased single molecule sequencing and demonstrate that copy number and sequence variation of this gene is common and suggests a more nuanced view of chemotype prediction.
Within and among-population variation in vital rates and population dynamics in a variable environment
Authors: Vincenzi Simone , Mangel Marc , Jesensek Dusan , Garza John Carlos , Crivelli Alain J
Published: October 2015

Understanding the causes of within-and among-population differences in vital rates, life histories, and population dynamics is a central topic in ecology. To understand how within-and among-population variation emerges, we need long-term studies that include episodic events and contrasting environmental conditions, data to characterize individual and shared variation, and statistical models that can tease apart population-, shared-, and individual contribution to the observed variation.

We used long-term tag-recapture data and novel statistical and modeling techniques to investigate and estimate within-and among-population differences in vital rates, life histories and population dynamics of marble troutSalmo marmoratus, a endemic freshwater salmonid with a narrow range. Only ten populations of pure marble trout persist in headwaters of Alpine rivers in western Slovenia. Marble trout populations are also threatened by floods and landslides, which have caused the extinction of two populations in recent years. We estimated and determined causes of variation in growth, survival, and recruitment both within and among populations, and evaluated trade-offs between them. Specifically, we estimated the responses of these traits to variation in water temperature, density, sex, early life conditions, and the occurrence of extreme climatic events (e.g., flash floods and debris flows).

We found that the effects of population density on traits were mostly limited to the early stages of life and that individual growth trajectories were established early in life. We found no clear effects of water temperature on survival and recruitment. Population density varied over time, with flash floods and debris flows causing massive mortalities and threatening population persistence. Apart from flood events, variation in population density within streams was largely determined by variation in recruitment, with survival of older fish being relatively constant over time within populations, but substantially different among populations. Marble trout show a fast-to-slow continuum of life histories, with slow growth associated with higher survival at the population level, possibly determined by food conditions and age at maturity.

Our work provides unprecedented insight into the causes of variation in vital rates, life histories, and population dynamics in an endemic species that is teetering on the edge of extinction.
Association mapping of inflammatory bowel disease loci to single variant resolution
Authors: Huang Hailiang , Fang Ming , Jostins Luke , Mirkov Maša Umićević , Boucher Gabrielle , Anderson Carl A , Andersen Vibeke , Cleynen Isabelle , Cortes Adrian , Crins François , D’Amato Mauro , Deffontaine Valérie , Dimitrieva Julia , Docampo Elisa , Elansary Mahmoud , Farh Kyle Kai-How , Franke Andre , Gori Ann-Stephan , Goyette Philippe , Halfvarson Jonas , Haritunians Talin , Knight Jo , Lawrance Ian C , Lees Charlie W , Louis Edouard , Mariman Rob , Meuwissen Theo , Mni Myriam , Momozawa Yukihide , Parkes Miles , Spain Sarah L , Théâtre Emilie , Trynka Gosia , Satsangi Jack , van Sommeren Suzanne , Vermeire Severine , Xavier Ramnik J ,   International IBD Genetics Consortium, Weersma Rinse K , Duerr Richard H , Mathew Christopher G , Rioux John D , McGovern Dermot PB , Cho Judy H , Georges Michel , Daly Mark J , Barrett Jeffrey C
Published: October 2015

Inflammatory bowel disease (IBD) is a chronic gastrointestinal inflammatory disorder that affects millions worldwide. Genome-wide association studies (GWAS) have identified 200 IBD-associated loci, but few have been conclusively resolved to specific functional variants. Here we report fine-mapping of 94 IBD loci using high-density genotyping in 67,852 individuals. Of the 139 independent associations identified in these regions, 18 were pinpointed to a single causal variant with >95% certainty, and an additional 27 associations to a single variant with >50% certainty. These 45 variants are significantly enriched for protein-coding changes (n=13), direct disruption of transcription factor binding sites (n=3) and tissue specific epigenetic marks (n=10), with the latter category showing enrichment in specific immune cells among associations stronger in CD and gut mucosa among associations stronger in UC. The results of this study suggest that high-resolution, fine-mapping in large samples can convert many GWAS discoveries into statistically convincing causal variants, providing a powerful substrate for experimental elucidation of disease mechanisms.
Biogeographic dating of speciation times using paleogeographically informed processes
Authors: Landis Michael J.
Published: October 2015

Standard models of molecular evolution cannot estimate absolute speciation times alone, and require external calibrations to do so. Because fossil calibration methods rely on the unreliable fossil record, most nodes in the tree of life are dated with poor accuracy. However, many major paleogeographical events are dated, and since biogeographic processes depend on paleogeographical conditions, biogeographic dating may be used as an alternative or complementary method to fossil dating. I demonstrate how a time-stratified biogeographic stochastic process may be used to estimate absolute divergence times by conditioning on dated paleogeographical events. Informed by the current paleogeographical literature, I construct an empirical dispersal graph using 25 areas and 26 epochs for the past 540 Ma of Earth’s history. Simulations indicate biogeographic dating performs well so long as paleogeography imposes constraint on biogeographic character evolution. To gauge whether biogeographic dating may have any practical use, I analyze the well-studied turtle clade (Testudines) then assess how well biogeographic dating fares compared to heavily fossil-calibrated dating results as reported in the literature. Fossil-free biogeographic dating estimated the age of the most recent common ancestor of extant turtles to be approximately 201 Ma, which is consistent with fossil-based estimates. Accuracy improves further when including a root node fossil calibration. The described model, paleogeographical dispersal graph, and analysis scripts are available for use with RevBayes.
Crystal structure of tetraaqua(dimethylformamide)tetrakis(μ-N,2-dioxidobenzene-1-carboximidato)tetrakis(μ-trimethylacetato)tetramanganese(III)sodiumyttrium–dimethylformamide–water (1/8.04/0.62)
Authors: Travis Jordan R. , Zeller Matthias , Zaleski Curtis M.
Published: October 2015

The synthesis and crystal structure for the title compound, [YNaMn4(C7H4NO3)4(C5H9O2)4(H2O)3.76(C3H7NO)0.24]·8.04C3H7NO·0.62H2O or [YIIINa(OTMA)4[12-MCMn(III)N(shi)-4](H2O)3.76(DMF)0.24·8.04DMF·0.62H2O, where OTMA is trimethylacetate, MC is metallacrown, shi3−is salicylhydroximate, and DMF isN,N-dimethylformamide, is reported. The macrocyclic metallacrown consists of an –[MnIII–N–O]4– ring repeat unit, and the metallacrown captures one YIIIion and one NaIion in the central cavity on opposite faces of the metallacrown. Overall the metallacrown is domed towards the side of the NaIion. Both the YIIIand NaIions are eight-coordinate, and the trimethylacetate anions bridge the central YIIIto each ring MnIIIion. The ring MnIIIions are six-coordinate with a tetragonally distorted octahedral geometry.
Crystal structure of ethyl 2-phenyl-4-(prop-2-yn-1-yloxy)-5,6,7,8-tetrahydropyrido[4′,3′:4,5]thieno[2,3-d]pyrimidine-7-carboxylate
Authors: Akkurt Mehmet , Smolenski Victoria A. , Mohamed Shaaban K. , Jasinski Jerry P. , Ahmed Essam K , Albayati Mustafa R.
Published: October 2015

In the title compound, C21H19N3O3S, the 5,6,7,8-tetrahydropyridine ring adopts a half-chair conformation. The fused-thieno[2,3-d]pyrimidine ring system is essentially planar (r.m.s. deviation = 0.001 Å) and forms a dihedral angle of 2.66 (6)° with the attached phenyl ring. The three-dimensional crystal packing is stabilized by C—H...O and C—H...N hydrogen bonds and C—H...π interactions.
Crystal structure of [μ2-3,3-dimethyl-4-(propan-2-ylidene)thietane-2,2-dithiolato-κ4S:S′:S:S′]bis[tricarbonyliron(I)](Fe—Fe)
Authors: Zhao Peihua , Bertke Jeffery A. , Rauchfuss Thomas B.
Published: October 2015

The title complex, [Fe2(C8H12S3)(CO)6] or [{Fe(CO)3}2(μ-L)] [L= 3,3-dimethyl-4-(propan-2-ylidene)thietane-2,2-bis(thiolato)], consists of two Fe(CO)3moieties double-bridged by a dithiolate ligand. Each of the two FeIatoms has a distorted anti-prismatic coordination environment consisting of three carbonyl groups, two S atoms of the dithiolate ligand and the neighboring FeIatom [Fe—Fe = 2.4921 (4) Å]. Weak C—H...O intermolecular interactions result in the formation of dimers. This is the second crystal structure reported with the 3,3-dimethyl-4-(propan-2-ylidene)thietane-2,2-bis(thiolate) ligand and the first in which it bridges two metal atoms.
Crystal structure of bis(2-{[1,1-bis(hydroxymethyl)-2-oxidoethyl]iminomethyl}-6-methoxyphenolato)manganese(IV) 0.39-hydrate
Authors: Buvaylo Elena A. , Vassilyeva Olga Yu. , Skelton Brian W.
Published: October 2015

The title compound, [Mn(C12H15NO5)2]·0.39H2O, is a 0.39 hydrate of the isostructural complex bis(2-{[1,1-bis(hydroxymethyl)-2-oxidoethyl]iminomethyl}-6-methoxyphenolato)manganese(IV) that has previously been reported by Back, Oliveira, Canabarro & Iglesias [Z. Anorg. Allg. Chem.(2015),641, 941–947], based on room-temperature data. The current structure that was determined at 100 K reveals a lengthening of theccell parameter compared with the published one due to the incorporation of the partial occupancy water molecule. The title compound crystallizes in the tetragonal chiral space groupP41212; the neutral [MnIV(C12H15NO5)2] molecule is situated on a crystallographicC2axis. The overall geometry about the central manganese ion is octahedral with an N2O4core; each ligand acts as a meridional ONO donor. The coordination environment of MnIVat 100 K displays a difference in one of the two Mn–O bond lengths, compared with the room-temperature structure. In the crystal, the neutral molecules are stacked in a helical fashion along thec-axis direction.
Crystal structure of tris(hydroxylammonium) orthophosphate
Authors: Leinemann Malte , Jess Inke , Boeckmann Jan , Näther Christian
Published: October 2015

The crystal structure of the title salt, ([H3NOH]+)3·[PO4]3−, consists of discrete hydroxylammonium cations and orthophosphate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phosphorus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by intermolecular O—H...O and N—H...O hydrogen bonds into a three-dimensional network. Altogether, one very strong O—H...O, two N—H...O hydrogen bonds of medium strength and two weaker bifurcated N—H...O interactions are observed.