bluuebunny/crossref_metadata_2025 huggingface dataset:
Neoliberal accumulation and class: a tribute to Gavin Williams
Authors: Cliffe Lionel
Published: July 2012

The articles in this collection emerged as presentations made at a conference in July 2010 which marked the retirement from Oxford of Gavin Williams, one of the founding editors of the Review of African Political Economy (ROAPE) and today a member of its International Advisory Board. Conference papers celebrated his several contributions, covering themes that resonated with his best known work, and in several cases that had been inspired by him – as some of the published articles here make explicit. The countries they focus on are South Africa and Nigeria, which are recognised as the geographical centres of gravity of his work, but extend, characteristically, to broader issues of political economy, such as privatisation (Pitcher) and overall development trajectories in Africa as compared with East Asia (Meagher). To set the scene for these five articles and to provide an overview of the conference as a whole and to the broad sweep of Gavin's lifetime contribution, not least to this journal, the following paragraphs are based on remarks I made to launch the conference.
Measurement of the temporal evolution of electron density in a nanosecond pulsed argon microplasma: using both Stark broadening and an OES line-ratio method
Authors: Zhu Xi-Ming , Walsh James L , Chen Wen-Cong , Pu Yi-Kang
Published: July 2012

The temporal evolution of electron density in a nanosecond pulsed argon microplasma is measured using a combination of Stark broadening and the optical emission line-ratio method. In the initial discharge period (0–100 ns), the electron density can reach as high as ∼1018 cm−3. It decreases to ∼1017–1016 cm−3 in the early afterglow period (100 ns–1 µs after the ignition) and ∼1016–1013 cm−3 in the late afterglow period (1–20 µs). It is demonstrated that the optical emission spectroscopy (OES) line-ratio method can obtain the electron density in the range 1013–1016 cm−3, while in the range 1016–1018 cm−3, the Stark broadening technique with argon 2p–1s lines (in Paschen's notation) is a better choice. These results are in good agreement with those from the Stark broadening technique with hydrogen Balmer lines. Finally, a possible mechanism for such a density evolution is briefly discussed.
Synthesis and characterization of titanium-containing graphite-like carbon films with low internal stress and superior tribological properties
Authors: Wang Yongjun , Li Hongxuan , Ji Li , Liu Xiaohong , Wu Yanxia , Lv Yanhong , Fu Yingying , Zhou Huidi , Chen Jianmin
Published: July 2012

Titanium-containing graphite-like carbon films were deposited on silicon substrates by an unbalanced magnetron sputtering system. The effect of titanium concentration on the film microstructure and properties was subsequently investigated by means of different characterization techniques. It is found that the current carbon films have a graphite-like structure with some fine titanium carbide particles dispersed in an amorphous carbon matrix. With increasing titanium concentration from 0 at% to ∼9.6 at%, the sp2 concentration in the film shows a slight increase, while the hardness of the carbon films decreases evidently when a small quantity of titanium (∼2.9 at%) is introduced into the film structure, but it does not suffer an obvious change with further increase in titanium concentration until the titanium concentration is up to ∼9.6 at%. The increased hardness of the film with a titanium concentration of about 9.6 at% is probably due to the formation of specified dimension titanium carbide crystals in the amorphous carbon matrix. All the current carbon films have low internal stress and rough surface, and the doping of titanium has little influence on their internal stress and root mean square roughness. The friction coefficient of the films decreases distinctly as the titanium concentration increases from 0 at% to ∼9.6 at%, but the wear rate does not increase evidently until the titanium concentration exceeds over ∼6.2 at% in air tests. The titanium-containing graphite-like carbon films show a stable friction coefficient and extremely low wear under oil lubricated conditions. The unique graphite-like structure, the high hardness and elastic modulus ratio (H/E) and the easy formation of a transfer film are mainly responsible for the superior tribological properties of the resulting titanium-containing graphite-like carbon films.
Measuring thermal conductivity of thin films and coatings with the ultra-fast transient hot-strip technique
Authors: Belkerk B E , Soussou M A , Carette M , Djouadi M A , Scudeller Y
Published: July 2012

This paper reports the ultra-fast transient hot-strip (THS) technique for determining the thermal conductivity of thin films and coatings of materials on substrates. The film thicknesses can vary between 10 nm and more than 10 µm. Precise measurement of thermal conductivity was performed with an experimental device generating ultra-short electrical pulses, and subsequent temperature increases were electrically measured on nanosecond and microsecond time scales. The electrical pulses were applied within metallized micro-strips patterned on the sample films and the temperature increases were analysed within time periods selected in the window [100 ns–10 µs]. The thermal conductivity of the films was extracted from the time-dependent thermal impedance of the samples derived from a three-dimensional heat diffusion model. The technique is described and its performance demonstrated on different materials covering a large thermal conductivity range. Experiments were carried out on bulk Si and thin films of amorphous SiO2 and crystallized aluminum nitride (AlN). The present approach can assess film thermal resistances as low as 10−8 K m2 W−1 with a precision of about 10%. This has never been attained before with the THS technique.
Genetic Loci Controlling Lethal Cell Death in Tomato Caused by Viral Satellite RNA Infection
Authors: Xu Ping , Wang Hua , Coker Frank , Ma Jun-ying , Tang Yuhong , Taylor Mark , Roossinck Marilyn J.
Published: July 2012

Cucumber mosaic virus (CMV) associated with D satellite RNA (satRNA) causes lethal systemic necrosis (LSN) in tomato (Solanum lycopersicum), which involves programmed cell death. No resistance to this disease has been found in tomato. We obtained a line of wild tomato, S. habrochaitis, with a homogeneous non-lethal response (NLR) to the infection. This line of S. habrochaitis was crossed with tomato to generate F1 plants that survived the infection with NLR, indicating that NLR is a dominant trait. The NLR trait was successfully passed on to the next generation. The phenotype and genotype segregation was analyzed in the first backcross population. The analyses indicate that the NLR trait is determined by quantitative trait loci (QTL). Major QTL associated with the NLR trait were mapped to chromosomes 5 and 12. Results from Northern blot and in situ hybridization analyses revealed that the F1 and S. habrochaitis plants accumulated minus-strand satRNA more slowly than tomato, and fewer vascular cells were infected. In addition, D satRNA-induced LSN in tomato is correlated with higher accumulation of the minus-strand satRNA compared with the accumulation of the minus strand of a non-necrogenic mutant D satRNA.
XagR, a LuxR Homolog, Contributes to the Virulence of Xanthomonas axonopodis pv. glycines to Soybean
Authors: Chatnaparat Tiyakhon , Prathuangwong Sutruedee , Ionescu Michael , Lindow Steven E.
Published: July 2012

A novel luxR homolog, termed XagR, in Xanthomonas axonopodis pv. glycines, the cause of soybean pustule, controls expression of pip, yapH, and at least 77 other genes. Although XagR and Pip are required for full virulence of X. axonopodis pv. glycines to soybean, constitutive overproduction of XagR suppresses infection. The xagR-dependent induction of pip occurs in planta only 2 days or more after inoculation. Although the transcription of xagR appears constitutive, XagR accumulates only in cells that have colonized soybean plants for more than 2 days suggesting that some components produced during the infection process mediate post-transcriptional control, likely by protecting XagR from proteolytic degradation. XagR modulates the adhesiveness of the pathogen during the infection process by suppressing the adhesin YapH. Although yapH mutants incite more infections of soybean leaves than the wild-type strain when topically applied under dry conditions, the mutant causes fewer infections when leaves are subject to simulated rain events after inoculation. Likewise, yapH mutants and cells in which XagR was overexpressed exhibited much more egress from infected leaves than the wild-type strain. Thus, XagR differentially modulates expression of a variety of genes during the infection process in response to feedback from plant molecules elaborated during infection to coordinate processes such as invasion, infection, and cell egress needed to complete the disease cycle.
Remodeling of Cytokinin Metabolism at Infection Sites of Colletotrichum graminicola on Maize Leaves
Authors: Behr Michael , Motyka Václav , Weihmann Fabian , Malbeck Jiří , Deising Holger B. , Wirsel Stefan G. R.
Published: July 2012

When inoculated onto maize leaves at the onset of senescence, the hemibiotroph Colletotrichum graminicola causes green islands that are surrounded by senescing tissue. Taking advantage of green islands as indicators of sites of the establishment of successful infection and of advanced high-performance liquid chromatography tandem mass spectrometry methodology, we analyzed changes in the patterns and levels of cytokinins (CK) at high spatial and analytical resolution. Twenty individual CK were detected in green islands. Levels of cis-zeatin-9-riboside and cis-zeatin-9-riboside-5′-monophosphate increased drastically, whereas that of the most prominent CK, cis-zeatin-O-glucoside, decreased. The fungus likely performed these conversions because corresponding activities were also detected in in vitro cultures amended with CK. We found no evidence that C. graminicola is able to synthesize CK entirely de novo in minimal medium but, after adding dimethylallyl diphosphate, a precursor of CK biosynthesis occurring in plants, a series of trans-zeatin isoforms (i.e., trans-zeatin-9-riboside-5′-monophosphate, trans-zeatin-9-riboside, and trans-zeatin) was formed. After applying CK onto uninfected leaves, transcripts of marker genes for senescence, photosynthesis, and assimilate distribution were measured by quantitative reverse-transcribed polymerase chain reaction; furthermore, pulse-amplitude modulation chlorophyll fluorometry and single-photon avalanche diode analyses were conducted. These experiments suggested that modulation of CK metabolism at the infection site affects host physiology.
Multifunctional Roles for the N-Terminal Basic Motif of Alfalfa mosaic virus Coat Protein: Nucleolar/Cytoplasmic Shuttling, Modulation of RNA-Binding Activity, and Virion Formation
Authors: Herranz Mari Carmen , Pallas Vicente , Aparicio Frederic
Published: July 2012

In addition to virion formation, the coat protein (CP) of Alfalfa mosaic virus (AMV) is involved in the regulation of replication and translation of viral RNAs, and in cell-to-cell and systemic movement of the virus. An intriguing feature of the AMV CP is its nuclear and nucleolar accumulation. Here, we identify an N-terminal lysine-rich nucleolar localization signal (NoLS) in the AMV CP required to both enter the nucleus and accumulate in the nucleolus of infected cells, and a C-terminal leucine-rich domain which might function as a nuclear export signal. Moreover, we demonstrate that AMV CP interacts with importin-α, a component of the classical nuclear import pathway. A mutant AMV RNA 3 unable to target the nucleolus exhibited reduced plus-strand RNA synthesis and cell-to-cell spread. Moreover, virion formation and systemic movement were completely abolished in plants infected with this mutant. In vitro analysis demonstrated that specific lysine residues within the NoLS are also involved in modulating CP-RNA binding and CP dimerization, suggesting that the NoLS represents a multifunctional domain within the AMV CP. The observation that nuclear and nucleolar import signals mask RNA-binding properties of AMV CP, essential for viral replication and translation, supports a model in which viral expression is carefully modulated by a cytoplasmic/nuclear balance of CP accumulation.
Peak shape analysis of diagonal and off-diagonal features in the two-dimensional electronic spectra of the Fenna–Matthews–Olson complex
Authors: Hayes Dugan , Engel Gregory S.
Published: July 2012

We have recorded a series of two-dimensional electronic spectra of the Fenna–Matthews–Olson (FMO) complex from
Prosthecochloris aestuarii
, with several crosspeaks sufficiently resolved to permit a quantitative analysis of both the amplitude and the two-dimensional peak shape. The exponential growth and/or decay of peaks on and off the main diagonal provides information on population transfer rates between pairs of excitons. Quantum beats observed in the amplitudes and shapes of these peaks persist throughout the relaxation process, indicating that energy transfer in FMO involves both incoherent and coherent dynamics. By comparing the oscillations in the amplitude and shape of crosspeaks, we confirm theoretical predictions regarding their correlation and identify previously indistinguishable combinations of nonlinear response pathways that contribute to the signal at particular positions in the spectra. Such analysis is crucial to understanding the enormous amount of information contained in two-dimensional electronic spectra and offers a new route to uncovering a complete description of the energy transfer kinetics in photosynthetic antennae.
A critical view on transport and entanglement in models of photosynthesis
Authors: Tiersch Markus , Popescu Sandu , Briegel Hans J.
Published: July 2012

We revisit critically the recent claims, inspired by quantum optics and quantum information, that there is entanglement in the biological pigment–protein complexes, and that it is responsible for the high transport efficiency. While unexpectedly long coherence times were experimentally demonstrated, the existence of entanglement is, at the moment, a purely theoretical conjecture; it is this conjecture that we analyse. As demonstrated by a toy model, a similar transport phenomenology can be obtained without generating entanglement. Furthermore, we also argue that, even if entanglement does exist, it is purely incidental and seems to play no essential role for the transport efficiency. We emphasize that our paper is
not
a proof that entanglement does not exist in light-harvesting complexes—this would require a knowledge of the system and its parameters well beyond the state of the art. Rather, we present a counter-example to the recent claims of entanglement, showing that the arguments, as they stand at the moment, are not sufficiently justified and hence cannot be taken as a proof for the existence of entanglement, let alone of its essential role, in the excitation transport.
Theoretical description of quantum effects in multi-chromophoric aggregates
Authors: Zimanyi Eric N. , Silbey Robert J.
Published: July 2012

Recent experiments on light-harvesting complexes have shown clear indication of coherent transport of excitations in these aggregates. We discuss the theoretical models that have been used to study energy transfer in molecular aggregates, beginning with the early models of Förster and Davydov and ending with the theoretical models of the present day.
Excitation energy migration processes in various multi-porphyrin assemblies
Authors: Yang Jaesung , Kim Dongho
Published: July 2012

The electronic interactions and excitation energy transfer (EET) processes of a variety of multi-porphyrin arrays with linear, cyclic and box architectures have been explored. Directly
meso
–
meso
linked linear arrays (
Z

N

) exhibit strong excitonic coupling with an exciton coherence length of approximately 6 porphyrin units, while fused linear arrays (
T

N

) exhibit extensive
π
-conjugation over the whole array. The excitonic coherence length in directly linked cyclic porphyrin rings (
CZ

N

) was determined to be approximately 2.7 porphyrin units by simultaneous analysis of fluorescence intensities and lifetimes at the single-molecule level. By performing transient absorption (TA) and TA anisotropy decay measurements, the EET rates in
m
-phenylene linked cyclic porphyrin wheels
C12ZA
and
C24ZB
were determined to be 4 and 36 ps
−1
, respectively. With increasing the size of
C

N

ZA
, the EET efficiencies decrease owing to the structural distortions that produce considerable non-radiative decay pathways. Finally, the EET rates of self-assembled porphyrin boxes consisting of directly linked diporphyrins,
B1A
,
B2A
and
B3A
, are 48, 98 and 361 ps
−1
, respectively. The EET rates of porphyrin boxes consisting of alkynylene-bridged diporphyrins,
B2B
and
B4B
, depend on the conformation of building blocks (planar or orthogonal) rather than the length of alkynylene linkers.
Microscopic quantum coherence in a photosynthetic-light-harvesting antenna
Authors: Dawlaty Jahan M. , Ishizaki Akihito , De Arijit K. , Fleming Graham R.
Published: July 2012

We briefly review the coherent quantum beats observed in recent two-dimensional electronic spectroscopy experiments in a photosynthetic-light-harvesting antenna. We emphasize that the decay of the quantum beats in these experiments is limited by ensemble averaging. The
in vivo
dynamics of energy transport depends upon the local fluctuations of a single photosynthetic complex during the energy transfer time (a few picoseconds). Recent analyses suggest that it remains possible that the quantum-coherent motion may be robust under individual realizations of the environment-induced fluctuations contrary to intuition obtained from condensed phase spectroscopic measurements and reduced density matrices. This result indicates that the decay of the observed quantum coherence can be understood as ensemble dephasing. We propose a fluorescence-detected single-molecule experiment with phase-locked excitation pulses to investigate the coherent dynamics at the level of a single molecule without hindrance by ensemble averaging. We discuss the advantages and limitations of this method. We report our initial results on bulk fluorescence-detected coherent spectroscopy of the Fenna–Mathews–Olson complex.
Exciton diffusion length in complex quantum systems: the effects of disorder and environmental fluctuations on symmetry-enhanced supertransfer
Authors: Abasto D. F. , Mohseni M. , Lloyd S. , Zanardi P.
Published: July 2012

Symmetric couplings among aggregates of
n
chromophores increase the transfer rate of excitons by a factor
n
2
, a quantum-mechanical phenomenon called ‘supertransfer’. In this work, we demonstrate how supertransfer effects induced by geometrical symmetries can enhance the exciton diffusion length by a factor
n
along cylindrically symmetric structures, consisting of arrays of rings of chromophores, and along spiral arrays. We analyse both closed-system dynamics and open quantum dynamics, modelled by combining a random bosonic bath with static disorder. In the closed-system case, we use the symmetries of the system within a short-time approximation to obtain a closed analytical expression for the diffusion length that explicitly reveals the supertransfer contribution. When subject to disorder, we show that supertransfer can enhance excitonic diffusion lengths for small disorders and characterize the crossover from coherent to incoherent motion. Owing to the quasi-one-dimensional nature of the model, disorder ultimately localizes the excitons, diminishing but not destroying the effects of supertransfer. When dephasing effects are included, we study the scaling of diffusion with both time and number of chromophores and observe that the transition from a coherent, ballistic regime to an incoherent, random-walk regime occurs at the same point as the change from supertransfer to classical scaling.
Coherent nonlinear optical studies of elementary processes in biological complexes: diagrammatic techniques based on the wave function versus the density matrix
Authors: Biggs Jason D. , Voll Judith A. , Mukamel Shaul
Published: July 2012

Two types of diagrammatic approaches for the design and simulation of nonlinear optical experiments (closed-time path loops based on the wave function and double-sided Feynman diagrams for the density matrix) are presented and compared. We give guidelines for the assignment of relevant pathways and provide rules for the interpretation of existing nonlinear experiments in carotenoids.
Learning from photosynthesis: how to use solar energy to make fuels
Authors: Cogdell Richard J. , Gardiner Alastair T. , Cronin Leroy
Published: July 2012

This short review describes how the basic reactions of photosynthesis can be broken down into four distinct steps. The current understanding of the molecular mechanisms of these steps, within light-harvesting complexes and reaction centres, in this process is discussed as a framework for the construction of artificial systems capable of using solar energy to make fuels.
A shared molecular mechanism underlies the human rasopathies Legius syndrome and Neurofibromatosis-1
Authors: Stowe Irma B. , Mercado Ellen L. , Stowe Timothy R. , Bell Erika L. , Oses-Prieto Juan A. , Hernández Hilda , Burlingame Alma L. , McCormick Frank
Published: July 2012

The Ras/mitogen-activated protein kinase (MAPK) pathway plays a critical role in transducing mitogenic signals from receptor tyrosine kinases. Loss-of-function mutations in one feedback regulator of Ras/MAPK signaling, SPRED1 (Sprouty-related protein with an EVH1 domain), cause Legius syndrome, an autosomal dominant human disorder that resembles Neurofibromatosis-1 (NF1). Spred1 functions as a negative regulator of the Ras/MAPK pathway; however, the underlying molecular mechanism is poorly understood. Here we show that neurofibromin, the NF1 gene product, is a Spred1-interacting protein that is necessary for Spred1's inhibitory function. We show that Spred1 binding induces the plasma membrane localization of NF1, which subsequently down-regulates Ras-GTP levels. This novel mechanism for the regulation of neurofibromin provides a molecular bridge for understanding the overlapping pathophysiology of NF1 and Legius syndrome.
Regulation of DNA cross-link repair by the Fanconi anemia/BRCA pathway
Authors: Kim Hyungjin , D'Andrea Alan D.
Published: July 2012

The maintenance of genome stability is critical for survival, and its failure is often associated with tumorigenesis. The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand cross-links (ICLs), and a germline defect in the pathway results in FA, a cancer predisposition syndrome driven by genome instability. Central to this pathway is the monoubiquitination of FANCD2, which coordinates multiple DNA repair activities required for the resolution of ICLs. Recent studies have demonstrated how the FA pathway coordinates three critical DNA repair processes, including nucleolytic incision, translesion DNA synthesis (TLS), and homologous recombination (HR). Here, we review recent advances in our understanding of the downstream ICL repair steps initiated by ubiquitin-mediated FA pathway activation.
Rabbit Ear Chambers
Authors: Jain Rakesh K. , Munn Lance L. , Fukumura Dai
Published: July 2012

This protocol describes a procedure to surgically implant transparent chambers in the ears of male New Zealand white rabbits. Such chambers allow continuous, noninvasive, long-term monitoring of angiogenesis during wound healing, as well as the study of tumor angiogenesis. A method for tumor implantation is also provided.
Forward-Filling of Dextran-Conjugated Indicators for Calcium Imaging at the Drosophila Larval Neuromuscular Junction
Authors: Macleod Gregory T.
Published: July 2012

Calcium imaging is a technique in which Ca2+-binding molecules are loaded into live cells and as they bind Ca2+ they “indicate” the concentration of free calcium through a change in either the intensity or the wavelength of light emitted (fluorescence or bioluminescence). There are several possible methods for loading synthetic Ca2+ indicators into subcellular compartments, including topical application of membrane-permeant Ca2+ indicators, forward-filling of dextran conjugates, and direct injection. Calcium imaging is a highly informative technique in neurobiology because Ca2+ is involved in many neuronal signaling pathways and serves as the trigger for neurotransmitter release. This article describes the forward-filling of dextran-conjugated indicators at the Drosophila larval neuromuscular junction (NMJ). This technique is particularly well suited for imaging changes in cytosolic Ca2+ as dextran conjugation prevents compartmentalization of the Ca2+ indicator. The major drawback is that the nerves must be severed at the start of the loading process, several hours before nerve terminals are ready to examine.
Determination of Alphaviral Titers: Figure 1.
Authors: Lundstrom Kenneth
Published: July 2012

The alphaviruses Semliki Forest virus and Sindbis virus have been used frequently as expression vectors in vitro and in vivo. Usually, these systems consist of replication-deficient vectors that require a helper vector for packaging of recombinant particles. Replication-proficient vectors have also been engineered. Alphaviral vectors can be used as nucleic-acid-based vectors (DNA and RNA) or infectious particles. The broad host range of alphaviruses facilitates studies in mammalian and nonmammalian cell lines, primary cells in culture, and in vivo. The strong preference for expression in neuronal cells has made alphaviruses particularly useful in neurobiological studies. Unfortunately, their strong cytotoxic effect on host cells, relatively short-term transient expression patterns, and the reasonably high cost of viral production remain drawbacks. However, novel mutant alphaviruses have showed reduced cytotoxicity and prolonged expression. Alphaviruses have also been applied in vaccine development and gene therapy. Before use in vitro or in vivo, it is essential to determine the titer of the generated alphaviral particles. Because defective alphaviruses do not produce plaques, their titers cannot be determined by conventional methods. However, viral titers can be determined readily in cases where the recombinant viruses express reporter genes such as green fluorescent protein or β-galactosidase, as well as indirectly by immunofluorescence methods. The potency of viral stocks can also be evaluated by light microscopic analysis. Alphavirus-infected cells show a dramatic decrease in growth and can be easily distinguished from noninfected control cells through their rounded morphology.
Confirming the Functional Importance of a Protein–DNA Interaction
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T.
Published: July 2012

Identifying DNA-binding proteins that interact with a control region of interest has become quite straightforward. However, the functional relevance of a given protein–DNA interaction is difficult to establish. The hypothesis that an interaction is relevant can be tested by several different experiments, 12 of which are outlined in this article. It must be remembered that none of these experiments by itself is conclusive. The information gained from each approach is described and explanations are given for why each yields useful but inconclusive results. The approaches vary widely with respect to the amount of effort required and the quality of information obtained.
Development of the mandibular, hyoid arch and gill arch skeleton in the Chinese barb Puntius semifasciolatus: comparisons of ossification sequences among Cypriniformes
Authors: Block A. J. , Mabee P. M.
Published: July 2012

The morphogenesis and sequence of ossification and chondrification of skeletal elements of the jaws, and hyoid arch and gill arches of Puntius semifasciolatus are described. These data provide a baseline for further studies and enable comparisons with other described cypriniforms. Some general patterns of ossification in the hyoid arch and branchial arches in cypriniforms were notable. First, the overall development is from anterior to posterior, with the exception of the fifth ceratobranchial bone, which ossifies first. Second, where ossification of iterated elements is sequential, it tends to proceed from posterior to anterior, even when more posterior chondrifications are the smallest in the series. Ossification of the ceratobranchial, epibranchial and pharyngobranchial bones tends to proceed from ventral to dorsal. The comparisons revealed small sets of skeletal elements whose ossification sequence appears to be relatively conserved across cyprinid cypriniforms. Several potentially key timing changes in the ossification sequence of the jaws, hyoid arch and gill arches were identified, such as the accelerated timing of ossification of the fifth ceratobranchial bone, which may be unique to cypriniforms.
The gene expression response of the catadromous perciform barramundi Lates calcarifer to an acute heat stress
Authors: Newton J. R. , De Santis C. , Jerry D. R.
Published: July 2012

The acute heat‐shock response of the tropical estuarine fish species barramundi Lates calcarifer as indicated by the expression of genes within stress (hsp 90AA, hsp 90AB, hsp 70 and hsc 70), metabolic (cisy, cco II and ldh) and growth (igf1 and mstn 1) related pathways was examined following an increase in water temperature from 28 to 36° C over 30 min. Lates calcarifer were maintained at the acute stress temperature of 36° C for 1 h before being returned to 28° C and allowed to recover at this temperature for a further 2 weeks. Muscle tissue sampling over the experimental period allowed for the expression quantification of stress, metabolic and growth‐related genes via quantitative real‐time polymerase chain reaction (qrt‐PCR) where a robust and reliable normalization approach identified both α‐tub and Rpl8 as appropriate genes for the analysis of gene expression in response to an acute heat stress. hsp90AA and hsp70 of the inducible heat‐shock response pathway showed a massive up‐regulation of gene expression in response to heat stress, whilst the constitutive heat‐shock genes hsp90AB and hsp70 showed no change over the course of the experiment and a small increase after 2 weeks of recovery, respectively. Of the three genes representing the metabolic pathway (cisy, cco II and ldh) only cco II changed significantly showing a decrease in gene expression, which may suggest a small suppression of aerobic metabolism. igf1 of the growth pathway showed no significant differences in response to an acute heat stress, whilst mstn1 increased at the beginning of the heat stress but returned to basal levels soon after. Overall, the results demonstrate that an acute heat stress in L. calcarifer caused a significant increase in the expression of genes from the stress response pathway and a possible decrease in aerobic metabolism with only relatively minor changes to the growth pathway highlighting the hardy nature of L. calcarifer and its resilience in coping with sudden temperature changes routinely encountered within its natural environment.
Temperature‐dependent prey capture efficiency and foraging modes of brown trout Salmo trutta
Authors: Watz J. , Piccolo J. J. , Greenberg L. , Bergman E.
Published: July 2012

Prey capture success and foraging mode were studied in brown trout Salmo trutta at temperatures ranging from 5·7 to 14·0° C. At low temperatures, there was a positive correlation between prey capture success and the proportion of time that the fish spent holding feeding stations. This correlation was not found at temperatures >10° C.
Relationship between roving behaviour and the diet and client composition of the cleaner fish Labroides bicolor
Authors: Oates J. , Manica A. , Bshary R. , Grutter A. S.
Published: July 2012

Diet analyses and observations of cleaning behaviour of two cleaner fishes revealed that Labroides bicolor fed more on client mucus, but Labroides dimidiatus fed more on ectoparasites, and that L. bicolor interacted with fewer species (36 species) compared with L. dimidiatus (44 species). The client species which contributed most to the dissimilarity between cleaner species were the dusky farmerfish Stegastes nigricans and bicolor chromis Chromis margaritifer damselfishes, which L. dimidiatus interacted with more often than L. bicolor, and the striated Ctenochaetus striatus and brown Acanthurus nigrofuscus surgeonfishes, which L. bicolor interacted with more; L. bicolor interacted with all parrotfishes (Scaridae) more. These results confirm the importance of repeated interactions and partner choice in determining the nature of interactions in mutualisms.
Cytokeratin 7: a re‐evaluation of the ‘tried and true’ in triple‐negative breast cancers
Authors: Davion Simone M , Siziopikou Kalliopi P , Sullivan Megan E
Published: July 2012

Davion S M, Siziopikou K P & Sullivan M E  (2012) Histopathology 61, 660–666

Cytokeratin 7: a re‐evaluation of the ‘tried and true’ in triple‐negative breast cancers

Aims:  Triple‐negative breast cancers (TNBCs) are often poorly differentiated tumours that can present clinically as metastases of an unknown primary. Immunohistochemical panels are frequently used to determine the likelihood of a breast primary, but in this tumour subset cytokeratin (CK)7 may be the only positive finding. In this study we aimed to evaluate a commonly employed immunohistochemical panel using a large group of TNBCs (both basal‐like and unclassified), and to analyse the CK7 staining patterns.

Methods and results:  Tissue microarrays containing 138 TNBCs were stained with antibodies against CK7, CK20, gross cystic disease fluid protein 15 (GCDFP‐15), and mammaglobin. CK5/6 staining was used to identify basal‐like tumours. CK7 staining was notably heterogeneous, with 14.5% of all cases demonstrating ≤20% tumour cell staining. A greater proportion of basal‐like TNBCs than of unclassified TNBCs showed focal staining. GCDFP‐15 and mammaglobin were not expressed in the majority of TNBCs, and were less frequently positive in basal‐like than in unclassified TNBCs.

Conclusions:  TNBCs are commonly negative for most immunomarkers indicative of breast origin, with the exception of CK7. As about one in five TNBCs showed only focal CK7 positivity, use of this marker must be interpreted with caution, especially in small samples, so that the possibility of a breast primary is not overlooked.
The effectiveness of phytosanitary controls in preventing the entry of Colletotrichum acutatum in the UK strawberry sector
Authors: Calleja E. J. , Ilbery B. , Spence N. J. , Mills P. R.
Published: July 2012

Phytosanitary legislation is widely thought to be the most effective means of limiting the entry of alien pathogens without hindering trade. However, there is increasing evidence of limitations and weaknesses in phytosanitary systems worldwide. One such case is the entry and establishment of Colletotrichum acutatum in the UK in the 1980s. To investigate this further, data sets of disease incidence gathered by the authorities responsible for plant health between 1984 and 2008 were analysed to determine how and why the pathogen entered the UK and became established on strawberries. Results suggest that the disease entered the UK in 1982 on plants originating from the USA, a year earlier than the first UK record of the disease was reported. At least 54 further cases of infested plant material breached phytosanitary procedures and entered the UK, 75% of which originated from EU countries. Moreover, internal trade transmission was found to be highly influential in the successful spread of the disease. The effectiveness of phytosanitary procedures is limited when the sector is importing large numbers of plants from nurseries that have a track record of selling infested plant material, even if they are accompanied by a plant passport. By taking greater responsibility in limiting the spread of quarantine diseases, nurseries throughout the EU have an important role to play in limiting the entry of alien pathogens.
Relationship between Spongospora subterranea f. sp. subterranea soil inoculum level, host resistance and powdery scab on potato tubers in the field
Authors: Brierley J. L. , Sullivan L. , Wale S. J. , Hilton A. J. , Kiezebrink D. T. , Lees A. K.
Published: July 2012

The relationship between initial soil inoculum level of Spongospora subterranea f. sp. subterranea (Sss) and the incidence and severity of powdery scab on potato tubers at harvest was investigated. In all experiments soil inoculum level of Sss (sporeballs/g soil) was measured using a quantitative real‐time PCR assay. Of 113 commercial potato fields across the UK, soil inoculum was detected in 75%, ranging from 0 to 148 Sss sporeballs/g soil. When arbitrary soil inoculum threshold values of 0, <10 and >10 sporeballs/g soil were set, it was observed that the number of progeny crops developing powdery scab increased with the level of inoculum quantified in the field soil preplanting. In four field trials carried out to investigate the link between the amount of inoculum added to the soil and disease development, disease incidence and severity on progeny tubers was found to be significantly (P < 0·01) greater in plots with increasing levels of inoculum incorporated. There was a cultivar effect in all years, with disease incidence and severity scores being significantly greater in cvs Agria and Estima than in Nicola (P < 0·01).
Pathogenic variation of Mycosphaerella species infecting banana and plantain in Nigeria
Authors: Zandjanakou‐Tachin M. , Ojiambo P. S. , Vroh‐Bi I. , Tenkouano A. , Gumedzoe Y. M. , Bandyopadhyay R.
Published: July 2012

Mycosphaerella species that cause the ‘Sigatoka disease complex’ account for significant yield losses in banana and plantain worldwide. Disease surveys were conducted in the humid forest (HF) and derived savanna (DS) agroecological zones from 2004 to 2006 to determine the distribution of the disease and variation among Mycosphaerella species in Nigeria. Disease prevalence and severity were higher in the HF than in the DS zone, but significant (P < 0·001) differences between agroecological zones were only observed for disease severity. A total of 85 isolates of M. fijiensis and 11 isolates of M. eumusae were collected during the survey and used to characterize the pathogenic structure of Mycosphaerella spp. using a putative host differential cultivar set consisting of Calcutta‐4 (resistant), Valery (intermediate) and Agbagba (highly susceptible). Area under disease progress curve (AUDPC) was higher on all cultivars when inoculated with M. eumusae than with M. fijiensis, but significant (P < 0·05) differences between the two species were only observed on Valery. Based on the rank‐sum method, 8·3% of the isolates were classified as highly aggressive and 46·9% were classified as aggressive. About 11·5% of all the isolates were classified as least aggressive, and all of these were M. fijiensis. The majority of M. eumusae isolates (seven out of 11; 64%) were classified as aggressive. A total of nine pathotype clusters were identified using cluster analysis of AUDPC. At least one M. fijiensis isolate was present in all the nine pathotype clusters, while isolates of M. eumusae were present in six of the nine clusters. Isolates in pathotype clusters III and V were the most aggressive, while those in cluster VIII were the least aggressive. Shannon’s index (H) revealed a more diverse Mycosphaerella collection in the DS zone (H = 1·81) than in the HF (H = 1·50) zone, with M. fijiensis being more diverse than M. eumusae. These results describe the current pathotype structure of Mycosphaerella in Nigeria and provide a useful resource that will facilitate screening of newly developed Musa genotypes for resistance against two important leaf spot diseases of banana and plantain.
Effect of defoliation by livestock on stem canker caused by Leptosphaeria maculans in Brassica napus
Authors: Sprague S. J. , Graham J. M. , Hamblin P. J. , Kirkegaard J. A.
Published: July 2012

Brassica napus (canola, oilseed rape), an important break crop for cereals across the Australian wheat belt, is being rapidly adopted as a dual‐purpose (forage and grain) crop in mixed farming systems. Stem canker caused by the fungus Leptosphaeria maculans is the most important disease of B. napus in Australia. The primary source of inoculum is airborne ascospores released during autumn/winter which coincides with the grazing of dual‐purpose crops. Field experiments were defoliated by sheep to determine the effect of grazing on blackleg stem canker severity at plant maturity in B. napus cultivars differing in their resistance level and grazed at different times. One cultivar was sown on different dates to investigate the impact of grazing at the same time, but at different growth stages. Defoliation by mowing was compared to defoliation by livestock. Similar amounts of dry matter remained after defoliation by machinery (0·66 t ha−1) or livestock (0·52 t ha−1). However, stem canker severity was higher in the grazed (40% of crown cross‐section diseased) compared with the mown (25%) treatment, which was higher than the ungrazed control (9%). Stem canker severity generally increased with grazing, but the increase was eliminated or reduced in cultivars with good resistance. Grazing during vegetative plant growth minimized the increase in stem canker severity compared with grazing during reproductive growth. Currently, cultivars with good L. maculans resistance are recommended in high disease situations. To avoid excessive yield loss in dual‐purpose B. napus crops due to L. maculans it is recommended that such cultivars are grown even in low‐moderate disease situations.
Full‐length genome sequences of four polerovirus isolates infecting cucurbits in Taiwan determined from total RNA extracted from field samples
Authors: Knierim D. , Tsai W. S. , Deng T. C. , Green S. K. , Kenyon L.
Published: July 2012

Poleroviruses are not mechanically transmittable by sap inoculation, which makes their isolation and multiplication in laboratory hosts for virion extraction and genome sequence analysis difficult. A reverse‐transcription polymerase chain reaction (RT‐PCR) procedure was modified to amplify the entire genomes of cucurbit‐infecting poleroviruses in three sections directly from RNA extracts from infected plant field samples. The procedure was used to determine the first full‐length genome nucleotide sequences of four polerovirus isolates from field samples collected in Taiwan. TW1 was identified as Melon aphid‐borne yellows virus (MABYV), because it had <10% variation in the deduced amino acid (aa) sequence in any of the encoded proteins when compared to MABYV‐China. C‐TW20 was most similar to Cucurbit aphid‐borne yellows virus (CABYV) from China with aa sequence identities of >90% for P3 and P3‐5 and aa identities of 78–88% for all the other proteins. TW19 represents the first full‐length sequence for the recently described Suakwa aphid‐borne yellows virus (SABYV). The deduced aa sequences for all the proteins of TW19 showed >10% variation compared to all other poleroviruses, though recombination analysis suggested MABYV as the major parent and an unidentified polerovirus as minor parent. R‐TW82 was identified as a strain of CABYV, as the deduced CP aa sequence showed >90% identity to that of other CABYV isolates, and recombination analysis suggested that MABYV was the major parent with CABYV the minor parent. Comparative details of the new full‐length sequences and their implications on criteria for distinguishing polerovirus species are discussed.
Genomics‐informed design of loop‐mediated isothermal amplification for detection of phytopathogenic Xanthomonas arboricola pv. pruni at the intraspecific level
Authors: Bühlmann A. , Pothier J. F. , Tomlinson J. A. , Frey J. E. , Boonham N. , Smits T. H. M. , Duffy B.
Published: July 2012

The objective of this study was to develop a rapid, sensitive detection assay for the quarantine pathogen Xanthomonas arboricola pv. pruni, causal agent of stone fruit bacterial spot, an economically important disease of Prunus spp. Unique targets were identified from X. arboricola pv. pruni genomes using a comparative genomics pipeline of other Xanthomonas species, subspecies and pathovars, and used to identify specific diagnostic markers. Loop‐mediated isothermal amplification (LAMP) was then applied to these markers to provide rapid, sensitive and specific detection. The method developed showed unrivalled specificity with the 79 tested strains and, in contrast to previously established techniques, distinguished between phylogenetically close subspecies such as X. arboricola pv. corylina. The sensitivity of this test is comparable to that of a previously reported TaqMan™ assay at 103 CFU mL−1, while the unrivalled speed of LAMP technology enables a positive result to be obtained in <15 min. The developed assay can be used with real‐time fluorescent detectors for quantitative results as well as with DNA‐staining dyes to function as a simplified strategy for on‐site pathogen detection.
The Pre‐B Cell Receptor; Selecting for or against Autoreactivity
Authors: Almqvist N. , Mårtensson I.‐L.
Published: July 2012

Abstract Antibodies represent a crucial component of humoral immunity as protection against invading pathogens, to which they bind and thereby trigger mechanisms that lead to the disposal of the pathogen. Antibodies are assembled from Ig heavy chains (HCs) and light chains (LCs) and are found in both a secreted and a membrane‐bound form, termed B cell receptors (BCRs), where the latter allows the ‘right’ B cell to respond upon recognition of its cognate antigen. The antibody repertoire is almost unlimited because of a process in which germ line V(D)J gene segments, encoding the variable (antigen‐binding) region of the antibody HCs and LCs, are recombined. As this process is random, it is apparent that it results in a vast variety of antibodies, those that recognize foreign but also those that recognize self‐ (auto‐) antigens. Control mechanisms are, therefore, in place to ensure that as few autoreactive B cells as possible are allowed to proceed in development. This counter‐selection takes place through various mechanisms and at several stages as the cells develop from pre‐B cells to antibody‐secreting plasma cells. At the first major checkpoint, at the pre‐BI to pre‐BII cell transition, antibody HCs assemble with the invariant surrogate LC (SLC) forming a pre‐BCR. Herein, we will discuss the role of the pre‐BCR in the selection at this stage, how a dysfunctional pre‐BCR affects selection and its effects on later stages, and whether the pre‐BCR selects for or against autoreactivity.
Sheath fold formation around slip surfaces
Authors: Reber Jacqueline E. , Dabrowski Marcin , Schmid Daniel W.
Published: July 2012

Terra Nova, 24, 417–421, 2012

Sheath folds are associated with shear zones and have been used as high strain indicators. We present results from a three‐dimensional analytical study showing that the flow perturbation around a planar weakness acting as a slip surface, in simple shear leads to the formation of sheath folds at low shear strain. Closed traces of marker layers are exhibited in cross‐sections cut perpendicular to the shear direction in the vicinity of the slip surface tip. In cross‐sections cut parallel to the shear direction and normal to the shear plane, flanking folds are observed. Our model captures the first‐order observations of natural sheath folds, such as diversity of shapes and multiple eye‐structures. Natural equivalents of the planar weaknesses that we model include fractures, veins and rheologically weak layers. Flow perturbation around these zones of weaknesses is proposed as an alternative mechanism of sheath fold formation, which emphasizes the coeval operation of brittle and ductile processes in shear zones.