bluuebunny/crossref_metadata_2025 huggingface dataset:
Germanium fin light-emitting diode
Authors: Saito S. , Oda K. , Takahama T. , Tani K. , Mine T.
Published: December 2011

We propose a germanium fin light-emitting diode for a monolithic light source on a Si photonics chip. The germanium fins were fabricated by the oxidation condensation of silicon-germanium sidewalls epitaxially grown on silicon fins. We found that a tensile stress is applied to the pure germanium fins by the difference of the thermal expansion coefficient with that of the surrounding oxide. The electroluminescence spectra were consistent with those expected from direct recombination in germanium with a tensile stress. The strong immunity of germanium fins against high current densities would be favourable to achieve population inversions by electrical pumping.
Lack of genetic differentiation observed in Pacific bluefin tuna (Thunnus orientalis) from Taiwanese and New Zealand waters using mitochondrial and nuclear DNA markers
Authors: Tseng Mei-Chen , Smith Peter J.
Published: December 2011

The Pacific bluefin tuna, Thunnus orientalis, is distributed mainly in the north Pacific Ocean, but a few individuals are also found in the south Pacific Ocean. We tested the ‘one-stock’ hypothesis that genetic differentiation is absent between populations from the north and south Pacific Oceans. Three molecular markers, cytochrome (Cyt) b, control region (CR) and microsatellites, were applied to identify species, investigate the population genetic structure and infer the population demographics of T. orientalis in Taiwanese and New Zealand waters. Tissue samples of T. orientalis were collected from Taiwanese (n = 53) and New Zealand (n = 70) waters. A neighbour-joining (NJ) tree of the Cyt b gene revealed a monophyletic topology. An NJ tree of the CR showed insignificant geographical grouping. Nei’s genetic identity (0.971), FST (0.003, P = 0.243) and RST (0.019, P = 0.099) between the two sets of samples were estimated from seven microsatellite loci. A factorial correspondence analysis and assignment test showed that these two sample sets lacked genetic differentiation. All these results support the one-stock hypothesis in these two samples from Taiwanese and New Zealand waters implying that they should compose the single management unit.
Self-assembly of soft-matter quasicrystals and their approximants
Authors: Iacovella Christopher R. , Keys Aaron S. , Glotzer Sharon C.
Published: December 2011

The surprising recent discoveries of quasicrystals and their approximants in soft-matter systems poses the intriguing possibility that these structures can be realized in a broad range of nanoscale and microscale assemblies. It has been theorized that soft-matter quasicrystals and approximants are largely entropically stabilized, but the thermodynamic mechanism underlying their formation remains elusive. Here, we use computer simulation and free-energy calculations to demonstrate a simple design heuristic for assembling quasicrystals and approximants in soft-matter systems. Our study builds on previous simulation studies of the self-assembly of dodecagonal quasicrystals and approximants in minimal systems of spherical particles with complex, highly specific interaction potentials. We demonstrate an alternative entropy-based approach for assembling dodecagonal quasicrystals and approximants based solely on particle functionalization and shape, thereby recasting the interaction-potential-based assembly strategy in terms of simpler-to-achieve bonded and excluded-volume interactions. Here, spherical building blocks are functionalized with mobile surface entities to encourage the formation of structures with low surface contact area, including non-close-packed and polytetrahedral structures. The building blocks also possess shape polydispersity, where a subset of the building blocks deviate from the ideal spherical shape, discouraging the formation of close-packed crystals. We show that three different model systems with both of these features—mobile surface entities and shape polydispersity—consistently assemble quasicrystals and/or approximants. We argue that this design strategy can be widely exploited to assemble quasicrystals and approximants on the nanoscale and microscale. In addition, our results further elucidate the formation of soft-matter quasicrystals in experiment.
Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution
Authors: Rego E. Hesper , Shao Lin , Macklin John J. , Winoto Lukman , Johansson Göran A. , Kamps-Hughes Nicholas , Davidson Michael W. , Gustafsson Mats G. L.
Published: December 2011

Using ultralow light intensities that are well suited for investigating biological samples, we demonstrate whole-cell superresolution imaging by nonlinear structured-illumination microscopy. Structured-illumination microscopy can increase the spatial resolution of a wide-field light microscope by a factor of two, with greater resolution extension possible if the emission rate of the sample responds nonlinearly to the illumination intensity. Saturating the fluorophore excited state is one such nonlinear response, and a realization of this idea, saturated structured-illumination microscopy, has achieved approximately 50-nm resolution on dye-filled polystyrene beads. Unfortunately, because saturation requires extremely high light intensities that are likely to accelerate photobleaching and damage even fixed tissue, this implementation is of limited use for studying biological samples. Here, reversible photoswitching of a fluorescent protein provides the required nonlinearity at light intensities six orders of magnitude lower than those needed for saturation. We experimentally demonstrate approximately 40-nm resolution on purified microtubules labeled with the fluorescent photoswitchable protein Dronpa, and we visualize cellular structures by imaging the mammalian nuclear pore and actin cytoskeleton. As a result, nonlinear structured-illumination microscopy is now a biologically compatible superresolution imaging method.
Imaging protein synthesis in cells and tissues with an alkyne analog of puromycin
Authors: Liu Jing , Xu Yangqing , Stoleru Dan , Salic Adrian
Published: December 2011

Synthesis of many proteins is tightly controlled at the level of translation, and plays an essential role in fundamental processes such as cell growth and proliferation, signaling, differentiation, or death. Methods that allow imaging and identification of nascent proteins are critical for dissecting regulation of translation, both spatially and temporally, particularly in whole organisms. We introduce a simple and robust chemical method to image and affinity-purify nascent proteins in cells and in animals, based on an alkyne analog of puromycin, O-propargyl-puromycin (OP-puro). OP-puro forms covalent conjugates with nascent polypeptide chains, which are rapidly turned over by the proteasome and can be visualized or captured by copper(I)-catalyzed azide-alkyne cycloaddition. Unlike methionine analogs, OP-puro does not require methionine-free conditions and, uniquely, can be used to label and assay nascent proteins in whole organisms. This strategy should have broad applicability for imaging protein synthesis and for identifying proteins synthesized under various physiological and pathological conditions in vivo.
Human monocytes are severely impaired in base and DNA double-strand break repair that renders them vulnerable to oxidative stress
Authors: Bauer Martina , Goldstein Michael , Christmann Markus , Becker Huong , Heylmann Daniel , Kaina Bernd
Published: December 2011

Monocytes are key players in the immune system. Crossing the blood barrier, they infiltrate tissues and differentiate into (
i
) macrophages that fight off pathogens and (
ii
) dendritic cells (DCs) that activate the immune response. A hallmark of monocyte/macrophage activation is the generation of reactive oxygen species (ROS) as a defense against invading microorganisms. How monocytes, macrophages, and DCs in particular respond to ROS is largely unknown. Here we studied the sensitivity of primary human monocytes isolated from peripheral blood and compared them with macrophages and DCs derived from them by cytokine maturation following DNA damage induced by ROS. We show that monocytes are hypersensitive to ROS, undergoing excessive apoptosis. These cells exhibited a high yield of ROS-induced DNA single- and double-strand breaks and activation of the ATR-Chk1-ATM-Chk2-p53 pathway that led to Fas and caspase-8, -3, and -7 activation, whereas macrophages and DCs derived from them were protected. Monocytes are also hypersensitive to ionizing radiation and oxidized low-density lipoprotein. The remarkable sensitivity of monocytes to oxidative stress is caused by a lack of expression of the DNA repair proteins XRCC1, ligase IIIα, poly(ADP-ribose) polymerase-1, and catalytic subunit of DNA-dependent protein kinase (DNA-PK
cs
), causing a severe DNA repair defect that impacts base excision repair and double-strand break repair by nonhomologous end-joining. During maturation of monocytes into macrophages and DCs triggered by the cytokines GM-CSF and IL-4, these proteins become up-regulated, making macrophages and DCs repair-competent and ROS-resistant. We propose that impaired DNA repair in monocytes plays a role in the regulation of the monocyte/macrophage/DC system following ROS exposure.
Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site
Authors: Hatoum-Aslan Asma , Maniv Inbal , Marraffini Luciano A.
Published: December 2011

Precise RNA processing is fundamental to all small RNA-mediated interference pathways. In prokaryotes, clustered, regularly interspaced, short palindromic repeats (CRISPR) loci encode small CRISPR RNAs (crRNAs) that protect against invasive genetic elements by antisense targeting. CRISPR loci are transcribed as a long precursor that is cleaved within repeat sequences by CRISPR-associated (Cas) proteins. In many organisms, this primary processing generates crRNA intermediates that are subject to additional nucleolytic trimming to render mature crRNAs of specific lengths. The molecular mechanisms underlying this maturation event remain poorly understood. Here, we defined the genetic requirements for crRNA primary processing and maturation in
Staphylococcus epidermidis
. We show that changes in the position of the primary processing site result in extended or diminished maturation to generate mature crRNAs of constant length. These results indicate that crRNA maturation occurs by a ruler mechanism anchored at the primary processing site. We also show that maturation is mediated by specific
cas
genes distinct from those genes involved in primary processing, showing that this event is directed by CRISPR/Cas loci.
Transcranial magnetic stimulation modulates the brain's intrinsic activity in a frequency-dependent manner
Authors: Eldaief Mark C. , Halko Mark A. , Buckner Randy L. , Pascual-Leone Alvaro
Published: December 2011

Intrinsic activity in the brain is organized into networks. Although constrained by their anatomical connections, functional correlations between nodes of these networks reorganize dynamically. Dynamic organization implies that couplings between network nodes can be reconfigured to support processing demands. To explore such reconfigurations, we combined repetitive transcranial magnetic stimulation (rTMS) and functional connectivity MRI (fcMRI) to modulate cortical activity in one node of the default network, and assessed the effect of this upon functional correlations throughout the network. Two different frequencies of rTMS to the same default network node (the left posterior inferior parietal lobule, lpIPL) induced two topographically distinct changes in functional connectivity. High-frequency rTMS to lpIPL decreased functional correlations between cortical default network nodes, but not between these nodes and the hippocampal formation. In contrast, low frequency rTMS to lpIPL did not alter connectivity between cortical default network nodes, but increased functional correlations between lpIPL and the hippocampal formation. These results suggest that the default network is composed of (at least) two subsystems. More broadly, the finding that two rTMS stimulation regimens to the same default network node have distinct effects reveals that this node is embedded within a network that possesses multiple, functionally distinct relationships among its distributed partners.
Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition
Authors: Peisley Alys , Lin Cecilie , Wu Bin , Orme-Johnson McGhee , Liu Mengyuan , Walz Thomas , Hur Sun
Published: December 2011

MDA5, an RIG-I-like helicase, is a conserved cytoplasmic viral RNA sensor, which recognizes dsRNA from a wide-range of viruses in a length-dependent manner. It has been proposed that MDA5 forms higher-order structures upon viral dsRNA recognition or during antiviral signaling, however the organization and nature of this proposed oligomeric state is unknown. We report here that MDA5 cooperatively assembles into a filamentous oligomer composed of a repeating segmental arrangement of MDA5 dimers along the length of dsRNA. Binding of MDA5 to dsRNA stimulates its ATP hydrolysis activity with little coordination between neighboring molecules within a filament. Individual ATP hydrolysis in turn renders an intrinsic kinetic instability to the MDA5 filament, triggering dissociation of MDA5 from dsRNA at a rate inversely proportional to the filament length. These results suggest a previously unrecognized role of ATP hydrolysis in control of filament assembly and disassembly processes, thereby autoregulating the interaction of MDA5 with dsRNA, and provides a potential basis for dsRNA length-dependent antiviral signaling.
Hunter–gatherers and other primates as prey, predators, and competitors of snakes
Authors: Headland Thomas N. , Greene Harry W.
Published: December 2011

Relationships between primates and snakes are of widespread interest from anthropological, psychological, and evolutionary perspectives, but surprisingly, little is known about the dangers that serpents have posed to people with prehistoric lifestyles and nonhuman primates. Here, we report ethnographic observations of 120 Philippine Agta Negritos when they were still preliterate hunter–gatherers, among whom 26% of adult males had survived predation attempts by reticulated pythons. Six fatal attacks occurred between 1934 and 1973. Agta ate pythons as well as deer, wild pigs, and monkeys, which are also eaten by pythons, and therefore, the two species were reciprocally prey, predators, and potential competitors. Natural history data document snake predation on tree shrews and 26 species of nonhuman primates as well as many species of primates approaching, mobbing, killing, and sometimes eating snakes. These findings, interpreted within the context of snake and primate phylogenies, corroborate the hypothesis that complex ecological interactions have long characterized our shared evolutionary history.
Membrane protein complexes catalyze both 4- and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis
Authors: Chen Hsi-Chuan , Li Quanzi , Shuford Christopher M. , Liu Jie , Muddiman David C. , Sederoff Ronald R. , Chiang Vincent L.
Published: December 2011

The hydroxylation of 4- and 3-ring carbons of cinnamic acid derivatives during monolignol biosynthesis are key steps that determine the structure and properties of lignin. Individual enzymes have been thought to catalyze these reactions. In stem differentiating xylem (SDX) of
Populus trichocarpa
, two cinnamic acid 4-hydroxylases (PtrC4H1 and PtrC4H2) and a
p
-coumaroyl ester 3-hydroxylase (PtrC3H3) are the enzymes involved in these reactions. Here we present evidence that these hydroxylases interact, forming heterodimeric (PtrC4H1/C4H2, PtrC4H1/C3H3, and PtrC4H2/C3H3) and heterotrimeric (PtrC4H1/C4H2/C3H3) membrane protein complexes. Enzyme kinetics using yeast recombinant proteins demonstrated that the enzymatic efficiency (
V
max
/
k
m
) for any of the complexes is 70–6,500 times greater than that of the individual proteins. The highest increase in efficiency was found for the PtrC4H1/C4H2/C3H3-mediated
p
-coumaroyl ester 3-hydroxylation. Affinity purification-quantitative mass spectrometry, bimolecular fluorescence complementation, chemical cross-linking, and reciprocal coimmunoprecipitation provide further evidence for these multiprotein complexes. The activities of the recombinant and SDX plant proteins demonstrate two protein-complex–mediated 3-hydroxylation paths in monolignol biosynthesis in
P
.
trichocarpa
SDX; one converts
p
-coumaric acid to caffeic acid and the other converts
p
-coumaroyl shikimic acid to caffeoyl shikimic acid. Cinnamic acid 4-hydroxylation is also mediated by the same protein complexes. These results provide direct evidence for functional involvement of membrane protein complexes in monolignol biosynthesis.
Ultrahydrous stishovite from high-pressure hydrothermal treatment of SiO2
Authors: Spektor Kristina , Nylen Johanna , Stoyanov Emil , Navrotsky Alexandra , Hervig Richard L. , Leinenweber Kurt , Holland Gregory P. , Häussermann Ulrich
Published: December 2011

Stishovite (SiO2with the rutile structure and octahedrally coordinated silicon) is an important high-pressure mineral. It has previously been considered to be essentially anhydrous. In this study, hydrothermal treatment of silica glass and coesite at 350–550 °C near 10 GPa produces stishovite with significant amounts of H2O in its structure. A combination of methodologies (X-ray diffraction, thermal analysis, oxide melt solution calorimetry, secondary ion mass spectrometry, infrared and nuclear magnetic resonance spectroscopy) indicate the presence of 1.3 ± 0.2 wt % H2O and NMR suggests that the primary mechanism for the H2O uptake is a direct hydrogarnet-like substitution of 4H+for Si4+, with the protons clustered as hydroxyls around a silicon vacancy. This substitution is accompanied by a substantial volume decrease for the system (SiO2 + H2O), although the stishovite expands slightly, and it is only slightly unfavorable in energy. Stishovite could thus be a host for H2O at convergent plate boundaries, and in other relatively cool high-pressure environments.
High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment
Authors: Logan Aaron C. , Gao Hong , Wang Chunlin , Sahaf Bita , Jones Carol D. , Marshall Eleanor L. , Buño Ismael , Armstrong Randall , Fire Andrew Z. , Weinberg Kenneth I. , Mindrinos Michael , Zehnder James L. , Boyd Scott D. , Xiao Wenzhong , Davis Ronald W. , Miklos David B.
Published: December 2011

The primary cause of poor outcome following allogeneic hematopoietic cell transplantation (HCT) for chronic lymphocytic leukemia (CLL) is disease recurrence. Detection of increasing minimal residual disease (MRD) following HCT may permit early intervention to prevent clinical relapse; however, MRD quantification remains an uncommon diagnostic test because of logistical and financial barriers to widespread use. Here we describe a method for quantifying CLL MRD using widely available consensus primers for amplification of all Ig heavy chain (IGH) genes in a mixture of peripheral blood mononuclear cells, followed by high-throughput sequencing (HTS) for disease-specific IGH sequence quantification. To achieve accurate MRD quantification, we developed a systematic bioinformatic methodology to aggregate cancer clone sequence variants arising from systematic and random artifacts occurring during IGH-HTS. We then compared the sensitivity of IGH-HTS, flow cytometry, and allele-specific oligonucleotide PCR for MRD quantification in 28 samples collected from 6 CLL patients following allogeneic HCT. Using amplimer libraries generated with consensus primers from patient blood samples, we demonstrate the sensitivity of IGH-HTS with 454 pyrosequencing to be 10
−5
, with a high correlation between quantification by allele-specific oligonucleotide PCR and IGH-HTS (
r
= 0.85). From the same dataset used to quantify MRD, IGH-HTS also allowed us to profile IGH repertoire reconstitution after HCT—information not provided by the other MRD methods. IGH-HTS using consensus primers will broaden the availability of MRD quantification in CLL and other B cell malignancies, and this approach has potential for quantitative evaluation of immune diversification following transplant and nontransplant therapies.
Control of glucose homeostasis and insulin sensitivity by the
Let-7
family of microRNAs
Authors: Frost Robert J. A. , Olson Eric N.
Published: December 2011

Diabetes mellitus is the most common metabolic disorder worldwide and a major risk factor for cardiovascular disease. MicroRNAs are negative regulators of gene expression that have been implicated in many biological processes, including metabolism. Here we show that the
Let-7
family of microRNAs regulates glucose metabolism in multiple organs. Global and pancreas-specific overexpression of
Let-7
in mice resulted in impaired glucose tolerance and reduced glucose-induced pancreatic insulin secretion. Mice overexpressing
Let-7
also had decreased fat mass and body weight, as well as reduced body size. Global knockdown of the
Let-7
family with an antimiR was sufficient to prevent and treat impaired glucose tolerance in mice with diet-induced obesity, at least in part by improving insulin sensitivity in liver and muscle. AntimiR treatment of mice on a high-fat diet also resulted in increased lean and muscle mass, but not increased fat mass, and prevented ectopic fat deposition in the liver. These findings demonstrate that
Let-7
regulates multiple aspects of glucose metabolism and suggest antimiR-induced
Let-7
knockdown as a potential treatment for type 2 diabetes mellitus. Furthermore, our
Cre
-inducible
Let-7
-transgenic mice provide a unique model for studying tissue-specific aspects of body growth and type 2 diabetes.
Revisiting Mode 2 at Noors Slott
Authors: Gibbons Michael , Limoges Camille , Scott Peter
Published: December 2011

In November 2009, at Noors Slott in Sweden, a small group of distinguished individuals from academia and government met to reflect on the ideas developed in the New Production of Knowledge (Gibbons et al., 1994) and Re-thinking Science (Nowotny et al., 2001). The aim was less to determine the impact of these works on science and policy than to identify what, if anything, the authors had overlooked or, indeed, what developments had occurred during the past 25 years that might alter the conclusions reached in these two books. The purpose of this introduction is not to provide a summary of each paper, but rather to present some of the key elements that emerged in the discussion, configured to point to future questions which science policy researchers might address. Five areas have been identified within the overall Mode 2 theme: bibliometrics; regime change; the role of laboratory spaces; open innovation; and the politics of innovation.
Autophagy in antigen-presenting cells results in presentation of citrullinated peptides to CD4 T cells
Authors: Ireland Jamie M. , Unanue Emil R.
Published: December 2011

Antibody responses to citrullinated self-proteins are found in autoimmunities, particularly in rheumatoid arthritis, where they serve as a diagnostic indicator. We show here that processing of the protein hen egg-white lysozyme (HEL) resulted in citrullination of peptides presented on class II MHC molecules by antigen-presenting cells. The presentation of the citrullinated peptides but not of the unmodified peptides was associated with autophagy. Dendritic cells (DCs), macrophages, and thymic DCs presented citrullinated peptides constitutively. Their treatment with 3-methyladenine (3MA) blocked presentation of citrullinated HEL peptides, but presentation of unmodified peptides was not affected. Presentation of citrullinated peptides was not detected on B cells or B lymphoma cells under normal culture conditions. In B cells, engagement of the B cell antigen receptor was required for presentation of the citrullinated peptides, also inhibited by 3MA. B lymphoma–expressing HEL cells presented citrullinated peptides only after brief serum starvation. This presentation was reduced by 3MA or by reduction in Atg5 expression. Presentation of the unmodified peptides was not changed. The findings indicate a linkage between autophagy and autoreactivity through the generation of this neo-epitope.
ETV6 mutations in early immature human T cell leukemias
Authors: Van Vlierberghe Pieter , Ambesi-Impiombato Alberto , Perez-Garcia Arianne , Haydu J. Erika , Rigo Isaura , Hadler Michael , Tosello Valeria , Della Gatta Giusy , Paietta Elisabeth , Racevskis Janis , Wiernik Peter H. , Luger Selina M. , Rowe Jacob M. , Rue Montserrat , Ferrando Adolfo A.
Published: December 2011

Early immature T cell acute lymphoblastic leukemias (T-ALLs) account for ∼5–10% of pediatric T-ALLs and are associated with poor prognosis. However, the genetic defects that drive the biology of these tumors remain largely unknown. In this study, analysis of microarray gene expression signatures in adult T-ALL demonstrated a high prevalence of early immature leukemias and revealed a close relationship between these tumors and myeloid leukemias. Many adult immature T-ALLs harbored mutations in myeloid-specific oncogenes and tumor suppressors including IDH1, IDH2, DNMT3A, FLT3, and NRAS. Moreover, we identified ETV6 mutations as a novel genetic lesion uniquely present in immature adult T-ALL. Our results demonstrate that early immature adult T-ALL represents a heterogeneous category of leukemias characterized by the presence of overlapping myeloid and T-ALL characteristics, and highlight the potential role of ETV6 mutations in these tumors.
Coder Reliability and Misclassification in the Human Coding of Party Manifestos
Authors: Mikhaylov Slava , Laver Michael , Benoit Kenneth R.
Published: December 2011

The Comparative Manifesto Project (CMP) provides the only time series of estimated party policy positions in political science and has been extensively used in a wide variety of applications. Recent work (e.g., Benoit, Laver, and Mikhaylov 2009; Klingemann et al. 2006) focuses on nonsystematic sources of error in these estimates that arise from the text generation process. Our concern here, by contrast, is with error that arises during the text coding process since nearly all manifestos are coded only once by a single coder. First, we discuss reliability and misclassification in the context of hand-coded content analysis methods. Second, we report results of a coding experiment that used trained human coders to code sample manifestos provided by the CMP, allowing us to estimate the reliability of both coders and coding categories. Third, we compare our test codings to the published CMP “gold standard” codings of the test documents to assess accuracy and produce empirical estimates of a misclassification matrix for each coding category. Finally, we demonstrate the effect of coding misclassification on the CMP's most widely used index, its left-right scale. Our findings indicate that misclassification is a serious and systemic problem with the current CMP data set and coding process, suggesting the CMP scheme should be significantly simplified to address reliability issues.
Development and Evaluation of Two Pecan Scab Prediction Models
Authors: Payne A. F. , Smith D. L.
Published: December 2011

Fusicladium effusum (syn. Cladosporium caryigenum), causal agent of pecan scab, is the most economically important pathogen of pecan (Carya illinoinensis). A weather-based advisory is currently used in Oklahoma to assess the need for fungicide application and requires the accumulation of scab hours. A scab hour is defined as an hour of average temperature and relative humidity ≥ 21.1°C and 90%, respectively. To assess the validity of the thresholds in the advisory, repeated ratings of disease severity were taken on fruit each year during the 1994–96 and 2009–10 growing seasons. Hourly weather variables were also examined, including temperature, relative humidity, dew point, dew point depression, total solar radiation, and total rainfall. Rain and disease severity were converted to binomial variables where a rain event (≥2.5mm) and disease severity (≥25%) were coded as 1 and all other events as 0. Logistic regression models adjusted for correlated data were developed using generalized estimating equations. Two models were developed: a temperature/relative humidity model and a dew point/dew point depression model. For the temperature/relative humidity model, the best fitting model included all main effects. Using this model, validation exercises assuming no rain and total solar radiation of 22.5 MJ m–2 resulted in a 0.62 probability of pecan scab development when the temperature was 21°C and relative humidity was 90%. Findings of this model were further validated during field studies that evaluated different combinations of temperature and relative humidity thresholds for scheduling fungicide applications. These analyses indicated that the current thresholds of temperature and relative humidity are viable but a modification of the relative humidity component should be considered. For the dew point/dew point depression model, a reduced model, including dew point, dew point depression, and the binomial rain variable, was considered adequate for explaining scab events, which suggests that future model building to describe pecan scab epidemics should include dew point, dew point depression, rain, and total solar radiation as independent variables.
Epiphytic Survival of Erwinia tracheiphila on Muskmelon (Cucumis melo L.)
Authors: Rojas E. Saalau , Gleason M. L.
Published: December 2011

Erwinia tracheiphila, the causal agent of bacterial wilt of cucurbits, is transmitted by striped (Acalymma vittatum) and spotted (Diabrotica undecimpunctata howardi) cucumber beetles. Transmission occurs when infested frass with E. tracheiphila is deposited on plant surfaces with fresh feeding wounds. However, it is unclear whether the pathogen can survive as an epiphyte on leaves. Experiments were conducted in controlled environments to monitor E. tracheiphila survival on muskmelon (Cucumis melo) leaves under various temperature and moisture conditions. In the first experiment, muskmelon seedlings that had been spray inoculated with a rifampicin-resistant strain of E. tracheiphila were incubated at 10, 15, 20, 25, 30, or 35°C (±2°C) at ≥95% relative humidity, and E. tracheiphila populations were monitored for 72 h. In the second experiment, E. tracheiphila was monitored during alternating 12-h wet and dry periods, or continuous wet or dry conditions for 48 h at 20°C. Survival of E. tracheiphila on wet muskmelon leaves depended on temperature (P < 0.01), with the greatest survival at 10 and 15°C and least at 30 and 35°C. Leaf wetness also impacted survival; an initial 12-h dry period resulted in a 1,000- to 10,000-fold reduction in population size, followed by stabilization of the surviving population. These results demonstrate that E. tracheiphila can survive on muskmelon leaves under a wide range of environmental conditions, suggesting that epiphytic populations might serve as a reservoir of inoculum for infections.
Is the Emergence of Dothistroma Needle Blight of Pine in France Caused by the Cryptic Species Dothistroma pini?
Authors: Fabre B. , Ioos R. , Piou D. , Marçais B.
Published: December 2011

Dothistroma needle blight (DNB) emerged in France in the past 15 years. This disease is induced by two closely related species: Dothistroma septosporum and D. pini. Although both species are currently present in France, only D. septosporum was reported in the past. We investigated whether a recent arrival of D. pini in France could be a cause of the DNB emergence. We analyzed herbarium specimens of pine needles with DNB symptoms using polymerase chain reaction techniques to study the past frequency of D. pini in France. We also determined the present distribution within the country of D. septosporum and D. pini and compared it with the spatial pattern of DNB reported in the Département de la Santé des Forêts (DSF; French forest health monitoring agency) database. Although D. pini was detected on herbarium specimens from 1907 and 1965, it was not frequent in France in the past. Today, it is frequent, although not present throughout the country, being absent from the north and the east. There is no relationship between the D. pini distribution in France and the spatial pattern of DNB reported in the DSF database. Thus, the emergence of DNB in France cannot be explained by a recent arrival of D. pini.
A Single Ancient Origin for Prototypical Serine/Arginine-Rich Splicing Factors
Authors: Califice Sophie , Baurain Denis , Hanikenne Marc , Motte Patrick
Published: December 2011

Eukaryotic precursor mRNA splicing is a process involving a very complex RNA-protein edifice. Serine/arginine-rich (SR) proteins play essential roles in precursor mRNA constitutive and alternative splicing and have been suggested to be crucial in plant-specific forms of developmental regulation and environmental adaptation. Despite their functional importance, little is known about their origin and evolutionary history. SR splicing factors have a modular organization featuring at least one RNA recognition motif (RRM) domain and a carboxyl-terminal region enriched in serine/arginine dipeptides. To investigate the evolution of SR proteins, we infer phylogenies for more than 12,000 RRM domains representing more than 200 broadly sampled organisms. Our analyses reveal that the RRM domain is not restricted to eukaryotes and that all prototypical SR proteins share a single ancient origin, including the plant-specific SR45 protein. Based on these findings, we propose a scenario for their diversification into four natural families, each corresponding to a main SR architecture, and a dozen subfamilies, of which we profile both sequence conservation and composition. Finally, using operational criteria for computational discovery and classification, we catalog SR proteins in 20 model organisms, with a focus on green algae and land plants. Altogether, our study confirms the homogeneity and antiquity of SR splicing factors while establishing robust phylogenetic relationships between animal and plant proteins, which should enable functional analyses of lesser characterized SR family members, especially in green plants.
Expression profile of heat shock proteins in acute myeloid leukaemia patients reveals a distinct signature strongly associated with FLT3 mutation status – consequences and potentials for pharmacological intervention
Authors: Reikvam Håkon , Hatfield Kimberley J. , Ersvær Elisabeth , Hovland Randi , Skavland Jørn , Gjertsen Bjørn T. , Petersen Kjell , Bruserud Øystein
Published: December 2011

Heat shock proteins (HSPs) are molecular chaperones that assist proteins in their folding to native structures. HSPs are regarded as possible therapeutic targets in acute myeloid leukaemia (AML). We used bioinformatical approaches to characterize the HSP profile in AML cells from 75 consecutive patients, in addition to the effect of the HSP90 inhibitor 17‐DMAG. Patients harbouring a FLT3‐internal tandem duplication (FLT3‐ITD) were extensively overrepresented in the cluster with high HSP levels, indicating a strong dependence of HSPs in stabilizing FLT3‐ITD encoded oncoproteins. FLT3 ligation further increased the levels of HSP90 and its co‐chaperone HSP70. HSP90 inhibition had a stronger pro‐apoptotic effect for AML cells with FLT3‐ITD than for cells with wild‐type FLT3, whereas the anti‐proliferative effect of HSP90 inhibition was similar for the two patient subsets. HSP90 inhibition altered the constitutive cytokine release profile in an anti‐angiogenic direction independent of FLT3 mutational status: (i) pro‐angiogenic CXCL8, MMP‐2 and MMP‐9 showed a stronger decrease than anti‐angiogenic CXCL9–11, (ii) the Tie‐2 agonist Ang‐1 showed a stronger decrease than the potentially antagonistic Ang‐2, and (iii) VEGF and HGF levels were decreased. Finally, HSP90 inhibition counteracted the leukaemia‐stimulating effect of endothelial cells. Our studies demonstrate that HSP90 inhibition mediates anti‐leukaemic effects through both direct and indirect activity.
Low serum high‐density lipoprotein cholesterol in childhood is associated with adolescent asthma
Authors: Yiallouros P. K. , Savva S. C. , Kolokotroni O. , Behbod B. , Zeniou M. , Economou M. , Chadjigeorgiou C. , Kourides Y. A. , Tornaritis M. J. , Lamnisos D. , Middleton N. , Milton D. K.
Published: December 2011

Background

Whilst emerging evidence from animal and cell experiments has shown high‐density lipoprotein cholesterol to have anti‐inflammatory effects consistent with a protective role in asthma, human studies investigating the relationship of high‐density lipoprotein cholesterol with asthma have produced conflicting results.

Objective

To examine the association between serum lipids among Cypriot children aged 11–12 years and prevalence of asthma at age 15–17 years.

Methods

In 3982 children, we assessed serum lipids, body mass index and maximal oxygen consumption at baseline (2001–2003) and explored associations with respiratory health at follow‐up (2007) using multiple logistic regression models.

Results

Lower levels of high‐density lipoprotein cholesterol at age 11–12 years were found in subjects who reported ever asthma (58.2 vs. 60.0 mg/dL, P = 0.005) and active asthma (57.5 vs. 59.9 mg/dL, P = 0.010) in adolescence, in comparison with their respective reference groups. Total cholesterol, low‐density lipoprotein and triglycerides had no association with any of the asthma outcomes. In contrast, with estimated odds ratios of 1.89 (95% CI 1.19–3.00) and 1.89 (95% CI 1.02–3.53), ever asthma and active asthma respectively appeared particularly pronounced among those who at baseline had high‐density lipoprotein cholesterol <40 mg/dL, even after adjusting for potential confounders including body mass index and maximal oxygen consumption.

Conclusions & Clinical Relevance

Low‐serum high‐density lipoprotein cholesterol in childhood is associated with an increased risk for asthma in adolescence, suggesting a potential role of this lipoprotein in the pathogenesis of paediatric asthma.
Probiotic effects on T‐cell maturation in infants during weaning
Authors: West C. E. , Hernell O. , Andersson Y. , Sjöstedt M. , Hammarström M.‐L.
Published: December 2011

Background

We previously reported that feeding the probiotic Lactobacillus paracasei ssp. paracasei F19 (LF19) during weaning reduced the cumulative incidence of eczema.

Objective

To investigate the impact of feeding LF19 on T‐cell maturation.

Methods

One hundred and seventy‐nine healthy, term infants with no prior allergic manifestations were randomized to daily intake of cereals with (n = 89) or without (n = 90) the addition of LF19 108 colony forming units per serving from 4 to 13 months of age. Venous blood was drawn at 5.5 and 13 months of age. We used the cytokine response to polyclonal T‐cell stimulation by anti‐CD3 plus anti‐CD28 monoclonal antibodies, and in vitro stimulation with the vaccine tetanus toxoid (TT) as measures of global adaptive immunity and capacity to raise a specific T‐cell response, respectively. Expression levels of IL‐2, IFN‐γ, IL‐4, IL‐17A and IL‐10 messenger RNAs (mRNAs) were used as proxies for general T‐cell stimulation and naive Th0 cells, Th1‐, Th2‐, Th17‐ and T regulatory lineages.

Results

There was no difference between the two groups at 5.5 months of age. At 13 months, the polyclonal IL‐2 response was higher in the placebo group (P < 0.05), whereas the IFN‐γ/IL‐2 (P < 0.01) and IL‐17A/IL‐2 (P < 0.05) ratios after polyclonal stimulation were higher in the probiotic group, as was the TT‐specific IL17‐A response (P < 0.001). In both groups, the IFN‐γ and IL‐4 responses increased from 5.5 to 13 months upon both polyclonal and specific stimulation (P < 0.01), whereas the IL‐10 response remained low (P > 0.05).

Conclusion and Clinical Relevance

Our findings suggest modest effects by probiotics on T‐cell maturation following 9 months of probiotic intake. Future studies should address if specific probiotics may drive immune development with possible preventive effects on the development of allergic disease.
Effects of long‐term repeated mineral and organic fertilizer applications on soil nitrogen transformations
Authors: Zhang J. B. , Zhu T. B. , Cai Z. C. , Qin S. W. , Müller C.
Published: December 2011

Repeated applications of mineral and/or organic fertilizer will probably affect gross nitrogen (N) dynamics in soils in the long term but only a limited number of observations are available. Here we present results of a 15N tracing study with soil from the various fertilizer treatments of the Huang‐Huai‐Hai Plain experiment that has been in operation for more than 17 years. Mineral fertilizer in various combinations of N, phosphorus (P) and potassium (K), organic manure (OM) or a mixture of mineral fertilizer and manure had been repeatedly applied for 17 years. The gross N transformation rates were quantified with a 15N tracing model, which uses a parameter optimization routine based on Bayesian principles. Mineralization of soil organic matter was at least 2.7 times greater in all fertilizer treatments compared with the untreated control (0.67 µg N g−1 day−1). While application of mineral N enhanced mineralization from recalcitrant organic N, the application of organic fertilizers stimulated the mineralization of labile organic N. Gross nitrate (NO3−) production solely resulted from ammonium (NH4+) oxidation. Compared with the gross NO3− production in the control treatment (2.22 µg N g−1 day−1), long‐term N applications stimulated gross nitrification by more than 5.3 times. The largest gaseous N emissions were associated with the organic manure treatments. The ratio of gross NO3− production to total mineral N consumption, a ratio proposed previously to determine potential NO3− loss, was a good indicator except for the treatment without N application. This ratio increased from 0.8 in the control to 2.7 in the mixture of mineral fertilizer and manure treatment. The largest gaseous N emissions (N2O + NO) (P < 0.05) were generally found at greater ratios. Results clearly showed that various fertilizers have a differential effect on N dynamics and potential gaseous N losses in the long term.
The Goldilocks effect: intermittent streams sustain more plant species than those with perennial or ephemeral flow
Authors: KATZ GABRIELLE L. , DENSLOW MICHAEL W. , STROMBERG JULIET C.
Published: December 2011

1. Drylands worldwide are typified by extreme variability in hydrologic processes, which structures riparian communities at various temporal and spatial scales. One key question is how underlying differences in hydrology over the length of interrupted perennial rivers influence spatial and temporal patterns in species richness and species composition.

2. We examined effects of differences in dry season hydrology on species richness, composition and cover of herbaceous plant communities in the streamside zone (the zone influenced directly by low flows in the channel). Data were collected at ephemeral, intermittent and perennial flow reaches on three rivers of the desert Southwest (Arizona, U.S.A.): Lower Cienega Creek, Hassayampa River and Lower San Pedro River.

3. Patterns of species richness varied with temporal scale of analysis, that is between single‐year and multi‐year time frames. At the annual timescale, quadrat species richness (m−2) and herbaceous cover were higher at sites with perennial flow than at either intermittent or ephemeral sites. In contrast to this single‐year pattern, the highest long‐term richness occurred at intermittent sites.

4. Quadrat species richness, total species richness at a site (per 18 1‐m2 plots) and cover were more variable year to year at non‐perennial sites than at perennial flow sites. On two of the three rivers, ephemeral sites had the highest inter‐annual compositional variance, while the perennial sites had the lowest.

5. Compositional differences between the hydrologic site types were dominated by species turnover, not nestedness. The perennial sites had more wetland and perennial species than the other two site types. The intermittent sites had more annual species than did the other two types.

6. High long‐term species richness and distinct species composition of intermittent sites are probably sustained by pronounced temporal variability in environmental conditions (i.e. frequent and persistent flow events, and dry periods). Plants at these sites take advantage of greater moisture than those at ephemeral sites and also experience less competition from resident species than those at perennial sites.

7. Conservation of desert riparian diversity depends upon the protection of consistently wet conditions at perennial flow sites, as well as the maintenance of the processes that cause fluctuations in environmental conditions at non‐perennial sites.
Temperature affects the limitation of Daphnia magna by eicosapentaenoic acid, and the fatty acid composition of body tissue and eggs
Authors: SPERFELD ERIK , WACKER ALEXANDER
Published: December 2011

1. Poikilothermic animals incorporate more polyunsaturated fatty acids (PUFAs) into their cellular membranes as temperature declines, suggesting an increased sensitivity to PUFA limitation in cool conditions. To test this we raised Daphnia magna at different temperatures and investigated the effect of varying dietary PUFA on life history parameters (i.e. growth, reproduction) and the PUFA composition of body tissue and eggs.

2. Upon a PUFA‐rich diet (Cryptomonas sp.) females showed higher concentrations of several ω3 PUFAs in their body tissue at 15 °C than at 20 °C and 25 °C, indicating a greater structural requirement for ω3 PUFAs at low temperature. Their eggs had an equal but higher concentration of ω3 PUFAs than their body tissue.

3. In a life history experiment at 15 and 20 °C we supplemented a diet of a PUFA‐free cyanobacterium with the ω3 PUFA eicosapentaenoic acid (EPA). The growth of D. magna was more strongly EPA limited at low temperature. A greater requirement for structural EPA at 15 °C was indicated by a steeper increase in somatic EPA content with dietary EPA compared to 20 °C.

4. At 20 °C the development of eggs to successful hatching was high when EPA was supplied to the mothers. At 15 °C the hatching success was generally poor, despite of a higher maternal provision of EPA to eggs, compared to that at 20 °C, suggesting that EPA alone was insufficient for proper neonatal development at the low temperature. The growth of offspring from mothers raised at 20 °C without EPA supplementation was very low, indicating that the negative effects of EPA deficiency can be carried on to the next generation.

5. The fatty acid composition of Daphnia sp. in published field studies shows increasing proportions of saturated fatty acids with increasing environmental temperature, whereas ω3 PUFAs and EPA show no clear pattern, suggesting that variations in dietary PUFA may mask temperature‐dependent adjustments in ω3 PUFA concentrations of cladocerans in nature.