bluuebunny/crossref_metadata_2025 huggingface dataset:
Slow down of the light-induced-degradation in compensated solar-grade multicrystalline silicon
Authors: Dubois S. , Enjalbert N. , Garandet J. P.
Published: September 2008

This letter focuses on the kinetics of the light-induced-degradation in multicrystalline silicon, comparing electronic grade and strongly compensated solar-grade materials. In electronic grade material, the results fit well with the models developed for Czochralski grown single-crystals. In contrast, in solar grade material, the light-induced-degradation kinetics are much slower and cannot be described by the existing models. We discuss how the formation of boron-oxygen complexes may be altered by the effects of compensation.
Dystrophic skeletal muscle fibers display alterations at the level of calcium microdomains
Authors: DiFranco Marino , Woods Christopher E. , Capote Joana , Vergara Julio L.
Published: September 2008

The spatiotemporal properties of the Ca2+-release process in skeletal muscle fibers from normal andmdxfibers were determined using the confocal-spot detection technique. The Ca2+indicator OGB-5N was used to record action potential-evoked fluorescence signals at consecutive locations separated by 200 nm along multiple sarcomeres ofFDBfibers loaded with 10- and 30-mM EGTA. Three-dimensional reconstructions of fluorescence transients demonstrated the existence of microdomains of increased fluorescence around the Ca2+-release sites in both mouse strains. The Ca2+microdomains inmdxfibers were regularly spaced along the fiber axis, displaying a distribution similar to that seen in normal fibers. Nevertheless, both preparations differed in that in 10-mM EGTA Ca2+microdomains had smaller amplitudes and were wider inmdxfibers than in controls. In addition, Ca2+-dependent fluorescence transients recorded at selected locations within the sarcomere ofmdxmuscle fibers were not only smaller, but also slower than their counterparts in normal fibers. Notably, differences in the spatial features of the Ca2+microdomains recorded inmdxand normal fibers, but not in the amplitude and kinetics of the Ca2+transients, were eliminated in 30-mM EGTA. Our results consistently demonstrate that Ca2+-release flux calculated from release sites inmdxfibers is uniformly impaired with respect to those normal fibers. The Ca2+-release reduction is consistent with that previously measured using global detection techniques.
Rifamycins do not function by allosteric modulation of binding of Mg
2+
to the RNA polymerase active center
Authors: Feklistov Andrey , Mekler Vladimir , Jiang Qiaorong , Westblade Lars F. , Irschik Herbert , Jansen Rolf , Mustaev Arkady , Darst Seth A. , Ebright Richard H.
Published: September 2008

Rifamycin antibacterial agents inhibit bacterial RNA polymerase (RNAP) by binding to a site adjacent to the RNAP active center and preventing synthesis of RNA products >2–3 nt in length. Recently, Artsimovitch
et al.
[(2005)
Cell
122:351–363] proposed that rifamycins function by allosteric modulation of binding of Mg
2+
to the RNAP active center and presented three lines of biochemical evidence consistent with this proposal. Here, we show that rifamycins do not affect the affinity of binding of Mg
2+
to the RNAP active center, and we reassess the three lines of biochemical evidence, obtaining results not supportive of the proposal. We conclude that rifamycins do not function by allosteric modulation of binding of Mg
2+
to the RNAP active center.
Visual long-term memory has a massive storage capacity for object details
Authors: Brady Timothy F. , Konkle Talia , Alvarez George A. , Oliva Aude
Published: September 2008

One of the major lessons of memory research has been that human memory is fallible, imprecise, and subject to interference. Thus, although observers can remember thousands of images, it is widely assumed that these memories lack detail. Contrary to this assumption, here we show that long-term memory is capable of storing a massive number of objects with details from the image. Participants viewed pictures of 2,500 objects over the course of 5.5 h. Afterward, they were shown pairs of images and indicated which of the two they had seen. The previously viewed item could be paired with either an object from a novel category, an object of the same basic-level category, or the same object in a different state or pose. Performance in each of these conditions was remarkably high (92%, 88%, and 87%, respectively), suggesting that participants successfully maintained detailed representations of thousands of images. These results have implications for cognitive models, in which capacity limitations impose a primary computational constraint (e.g., models of object recognition), and pose a challenge to neural models of memory storage and retrieval, which must be able to account for such a large and detailed storage capacity.
Quantitative visualization of passive transport across bilayer lipid membranes
Authors: Grime John M. A. , Edwards Martin A. , Rudd Nicola C. , Unwin Patrick R.
Published: September 2008

The ability to predict and interpret membrane permeation coefficients is of critical importance, particularly because passive transport is crucial for the effective delivery of many pharmaceutical agents to intracellular targets. We present a method for the quantitative measurement of the permeation coefficients of protonophores by using laser confocal scanning microscopy coupled to microelectrochemistry, which is amenable to precise modeling with the finite element method. The technique delivers well defined and high mass transport rates and allows rapid visualization of the entire pH distribution on both the
cis
and
trans
side of model bilayer lipid membranes (BLMs). A homologous series of carboxylic acids was investigated as probe molecules for BLMs composed of soybean phosphatidylcholine. Significantly, the permeation coefficient decreased with acyl tail length contrary to previous work and to Overton's rule. The reasons for this difference are considered, and we suggest that the applicability of Overton's rule requires re-evaluation.
Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase
Authors: Li Lenong , Chang Zhenzhan , Pan Zhiqiang , Fu Zheng-Qing , Wang Xiaoqiang
Published: September 2008

Cytochrome P450s exist ubiquitously in all organisms and are involved in many biological processes. Allene oxide synthase (AOS) is a P450 enzyme that plays a key role in the biosynthesis of oxylipin jasmonates, which are involved in signal and defense reactions in higher plants. The crystal structures of guayule (
Parthenium argentatum
) AOS (CYP74A2) and its complex with the substrate analog 13(
S
)-hydroxyoctadeca-9
Z
,11
E
-dienoic acid have been determined. The structures exhibit a classic P450 fold but possess a heme-binding mode with an unusually long heme binding loop and a unique I-helix. The structures also reveal two channels through which substrate and product may access and leave the active site. The entrances are defined by a loop between β3–2 and β3–3. Asn-276 in the substrate binding site may interact with the substrate's hydroperoxy group and play an important role in catalysis, and Lys-282 at the entrance may control substrate access and binding. These studies provide both structural insights into AOS and related P450s and a structural basis to understand the distinct reaction mechanism.
Surface-controlled dislocation multiplication in metal micropillars
Authors: Weinberger Christopher R. , Cai Wei
Published: September 2008

Understanding the plasticity and strength of crystalline materials in terms of the dynamics of microscopic defects has been a goal of materials research in the last 70 years. The size-dependent yield stress observed in recent experiments of submicrometer metallic pillars provides a unique opportunity to test our theoretical models, allowing the predictions from defect dynamics simulations to be directly compared with mechanical strength measurements. Although depletion of dislocations from submicrometer face-centered-cubic (FCC) pillars provides a plausible explanation of the observed size-effect, we predict multiplication of dislocations in body-centered-cubic (BCC) pillars through a series of molecular dynamics and dislocation dynamics simulations. Under the combined effects from the image stress and dislocation core structure, a dislocation nucleated from the surface of a BCC pillar generates one or more dislocations moving in the opposite direction before it exits from the surface. The process is repeatable so that a single nucleation event is able to produce a much larger amount of plastic deformation than that in FCC pillars. This self-multiplication mechanism suggests a need for a different explanation of the size dependence of yield stress in FCC and BCC pillars.
Large-scale reconstruction and phylogenetic analysis of metabolic environments
Authors: Borenstein Elhanan , Kupiec Martin , Feldman Marcus W. , Ruppin Eytan
Published: September 2008

The topology of metabolic networks may provide important insights not only into the metabolic capacity of species, but also into the habitats in which they evolved. Here we introduce the concept of a metabolic network's “seed set”—the set of compounds that, based on the network topology, are exogenously acquired—and provide a methodological framework to computationally infer the seed set of a given network. Such seed sets form ecological “interfaces” between metabolic networks and their surroundings, approximating the effective biochemical environment of each species. Analyzing the metabolic networks of 478 species and identifying the seed set of each species, we present a comprehensive large-scale reconstruction of such predicted metabolic environments. The seed sets' composition significantly correlates with several basic properties characterizing the species' environments and agrees with biological observations concerning major adaptations. Species whose environments are highly predictable (e.g., obligate parasites) tend to have smaller seed sets than species living in variable environments. Phylogenetic analysis of the seed sets reveals the complex dynamics governing gain and loss of seeds across the phylogenetic tree and the process of transition between seed and non-seed compounds. Our findings suggest that the seed state is transient and that seeds tend either to be dropped completely from the network or to become non-seed compounds relatively fast. The seed sets also permit a successful reconstruction of a phylogenetic tree of life. The “reverse ecology” approach presented lays the foundations for studying the evolutionary interplay between organisms and their habitats on a large scale.
Atypical E2F activity restrains APC/C
CCS52A2
function obligatory for endocycle onset
Authors: Lammens Tim , Boudolf Véronique , Kheibarshekan Leila , Panagiotis Zalmas L. , Gaamouche Tarik , Maes Sara , Vanstraelen Marleen , Kondorosi Eva , La Thangue Nicholas B. , Govaerts Willy , Inzé Dirk , De Veylder Lieven
Published: September 2008

The endocycle represents an alternative cell cycle that is activated in various developmental processes, including placental formation,
Drosophila
oogenesis, and leaf development. In endocycling cells, mitotic cell cycle exit is followed by successive doublings of the DNA content, resulting in polyploidy. The timing of endocycle onset is crucial for correct development, because polyploidization is linked with cessation of cell division and initiation of terminal differentiation. The anaphase-promoting complex/cyclosome (APC/C) activator genes
CDH1
,
FZR
, and
CCS52
are known to promote endocycle onset in human,
Drosophila
, and
Medicago
species cells, respectively; however, the genetic pathways governing development-dependent APC/C
CDH1/FZR/CCS52
activity remain unknown. We report that the atypical E2F transcription factor E2Fe/DEL1 controls the expression of the
CDH1
/
FZR
orthologous
CCS52A2
gene from
Arabidopsis thaliana
. E2Fe/DEL1 misregulation resulted in untimely
CCS52A2
transcription, affecting the timing of endocycle onset. Correspondingly, ectopic
CCS52A2
expression drove cells into the endocycle prematurely. Dynamic simulation illustrated that E2Fe/DEL1 accounted for the onset of the endocycle by regulating the temporal expression of
CCS52A2
during the cell cycle in a development-dependent manner. Analogously, the atypical mammalian E2F7 protein was associated with the promoter of the APC/C-activating
CDH1
gene, indicating that the transcriptional control of APC/C activator genes by atypical E2Fs might be evolutionarily conserved.
Recombination between inverted
loxP
sites is cytotoxic for proliferating cells and provides a simple tool for conditional cell ablation
Authors: Grégoire Damien , Kmita Marie
Published: September 2008

The
loxP
/
Cre
recombination system is a widely used tool for mouse functional genomics, in particular for
in vivo
conditional mutagenesis. Depending on the relative orientation and position of
loxP
sites, Cre-mediated recombination can result in a variety of targeted genomic rearrangements. It was previously reported that loss of the
loxP
-carrying chromosome can occur when
loxP
sites are arranged in inverse orientation. By using a chromosome 2 carrying inverted
loxP
sites, we found that Cre-mediated recombination not only causes chromosomal loss but also triggers apoptosis. We show that targeted recombination between inverted
loxP
sites (TRIP) triggers cell death specifically in proliferating
Cre
-expressing cells, and we provide evidence that TRIP is an efficient tool to ablate proliferating cells within genetically defined cell populations. Furthermore, the procedure requires only a simple, one-step intercross but neither the use of toxins nor the additional step of prodrug injection. With the large repertoire of tissue-specific or inducible
Cre
-expressing transgenes available, TRIP-mediated cell ablation is valuable to investigate the function of a large variety of cell populations in the context of a whole organism, which includes mechanisms underlying organ development and tissue homeostasis.
Science andMithāl: Demonstrations in Arabic and Persian Scientific Traditions
Authors: Kheirandish Elaheh
Published: September 2008

Addressing the Arabic and Persian scientific traditions in eastern Islamic lands, this study focuses on the nature and place of demonstrations in optics and mechanics, sub-disciplines of geometry. A focus on the comparative context of demonstrations facilitates clearer understanding of local coordinates that affected the development of these fields, which are shown to have had distinct, and sometimes opposite, cases of transmission and application in Islamic and European lands. Sample demonstrations are presented in an appendix to highlight the concept and terminology of “mithāl” to identify shifts from geometrical to experimental methods in the case of optics, and from physical productions to model duplications in the case of mechanics.
Habitat use and the effect of shrimp trawling on fish and invertebrate communities over the northern Gulf of Mexico continental shelf
Authors: Wells R. J. David , Cowan James H. , Patterson William F.
Published: September 2008

Wells, R. J. D., James H. Cowan Jr, and William F. Patterson III. 2008. Habitat use and the effect of shrimp trawling on fish and invertebrate communities over the northern Gulf of Mexico continental shelf. – ICES Journal of Marine Science, 65: 1610–1619. The goals of this study were to characterize habitat-specific fish and invertebrate community structure over sand, shell-rubble, and natural reef substrata, and to assess the effects of trawling on the sand and shell-rubble habitats and their associated communities during quarterly trawl surveys over a 2-year period. Fish and invertebrate communities differed significantly among habitat types [analysis of similarities (ANOSIM); Global R = 0.436, p < 0.001), and with respect to trawling exposure (ANOSIM; Global R = 0.128, p < 0.001). Habitat characteristics were quantified from video transects sampled with a remotely operated vehicle, and included percentage coverage of tubeworms, bryozoans, anemones, corals, and algae, significantly affecting fish community structure. Diversity indices differed among habitats, with the highest Shannon diversity (H′) and Pielou's evenness (J′) over shell-rubble, specifically non-trawled shell-rubble. In addition, higher values of H′ and J′ were found over trawled sand relative to non-trawled sand habitats. Length frequency distributions of several abundant fish species showed truncated size distributions over trawled and non-trawled habitats and were both habitat- and species-specific. The study describes habitat-specific differences in community structure, highlighting the differences between trawled and non-trawled areas on the northern Gulf of Mexico continental shelf.
Systematics of Plant Pathogenic Fungi: Why It Matters
Authors: Rossman Amy Y. , Palm-Hernández Mary E.
Published: September 2008

Systematics is the study of biological diversity; it is the science that discovers, describes, and classifies all organisms and includes taxonomy, nomenclature, and phylogeny. Scientific names accurately define a set of organisms and are used to communicate about them. As systematic scientists learn more about species, scientific names change to reflect this increased knowledge. Accurately named and precisely defined species reflect what is known about their biology, host range, and geographic distribution. Online resources are available to help users determine the accepted scientific name of fungal plant pathogens. Recent advances in the systematics of fungi are discussed, including the knowledge that: (i) true Fungi are more closely related to animals than to plants; and (ii) the Oomycetes are not true Fungi; rather they are closely related to the yellow-brown algae, known as stramenopiles or Kingdom Chromista. Using molecular data, the higher level classification of true Fungi is more precisely defined, as are fungal genera and species. In addition, the asexually reproducing fungi that constitute a majority of plant-associated fungi are being integrated into the phylogeny of the Ascomycota. The importance of documenting research on plant pathogens by depositing cultures in culture collections and voucher specimens in herbaria is emphasized.
Detached-Leaf Method for Propagating Puccinia coronata and Assessing Crown Rust Resistance in Oat
Authors: Jackson E. W. , Obert D. E. , Chong J. , Avant J. B. , Bonman J. M.
Published: September 2008

The crown rust pathogen Puccinia coronata is an obligate biotroph with wind-disseminated propagules and numerous races. These characteristics make propagation of single-race cultures difficult. Genetic studies using single races in field and greenhouse environments are also problematic because pure cultures can easily become contaminated. In this study, we developed an isolated propagation system for P. coronata and tested its ability to assess host resistance. Oat (Avena sativa) leaf sections (10 cm each) were harvested, disinfested, and suspended in sterile plastic boxes by enclosing 3.5-cm linear sections of each leaf end between 4% agar blocks amended with various chemical constituents. The exposed sections (approximately 3 cm) were inoculated with P. coronata urediniospores suspended in water. Boxes were sealed and incubated in a lighted growth cabinet until the pathogen sporulated. Viable spores were produced on leaves in all treatments, whereas 6-benzylaminopurine (BAP) and kinetin treatments sustained the leaves longer and yielded the most viable spores. Based on these data, the BAP treatment was adopted and used for additional studies. Detached leaves of differential oat cultivars produced the same reactions as whole plants screened under standard conditions in a growth chamber. The proposed detached-leaf system should be useful for the propagation of numerous single-race cultures of P. coronata as well as evaluation of host resistance under highly controlled conditions.
Influence of Fruit Maturity, Cultivar Susceptibility, and Inoculation Method on Infection of Olive Fruit byColletotrichum acutatum
Authors: Moral J. , Bouhmidi K. , Trapero A.
Published: September 2008

Detached olive (Olea europaea) fruit inoculated with isolates of Colletotrichum acutatum, causal agent of olive anthracnose, were used to study host–pathogen interactions. Fruit susceptibility increased with increasing fruit maturity. Wounded fruit were more severely affected than nonwounded fruit; however, the wound effect depended on cultivar and inoculation method. Severity of fruit infection increased with inoculum density, although this effect also depended on fruit maturity and cultivar susceptibility. The susceptibility of selected olive cultivars to anthracnose under field conditions correlated well with the response of immature fruit under controlled conditions. As fruit matured, there were fewer differences among cultivars. Based on these results, an inoculation method using immature green fruit and high inoculum densities (105to 106conidia/ml) sprayed on the fruit has been proposed to evaluate olive cultivars for anthracnose resistance under controlled conditions.
Fitness of Isolates ofPhytophthora capsiciResistant to Mefenoxam from Squash and Pepper Fields in North Carolina
Authors: Café-Filho Adalberto C. , Ristaino Jean Beagle
Published: September 2008

Despite the wide adoption of mefenoxam (Ridomil Gold EC) for vegetables in North Carolina, the incidence of Phytophthora blight on pepper (Capsicum annuum) and squash (Cucurbita pepo) is high. Seventy-five isolates of Phytophthora capsici were collected in five pepper and one squash field in order to assess mefenoxam sensitivity. The relative fitness of resistant and sensitive isolates was contrasted in vitro by their respective rates of colony growth and their ability to produce sporangia in unamended V8 juice agar medium. In in vivo experiments, the aggressiveness of isolates on pepper was evaluated. The frequency of resistant isolates in North Carolina populations was 63%, considerably higher than resistance levels in areas where mefenoxam is not widely adopted. Resistant isolates grew on amended media at rates >80 to 90% and >100% of the nonamended control at 100 μg ml-1and 5 μg ml-1, respectively. Sensitive isolates did not growth at 5 or 100 μg ml-1. All isolates from three fields, including two pepper and a squash field, were resistant to mefenoxam. Populations from other fields were composed of either mixes of sensitive and resistant isolates or only sensitive isolates. Response to mefenoxam remained stable during the course of in vitro and in planta experiments. Occurrence of a mefenoxam-resistant population of P. capsici on squash is reported here for the first time in North Carolina. When measured by rate of colony growth, sporulation in vitro, or aggressiveness in planta, fitness of resistant isolates was not reduced. Mefenoxam-resistant isolates from squash were as aggressive on pepper as sensitive or resistant pepper isolates. These results suggest that mefenoxam-resistant populations of P. capsici are as virulent and fit as sensitive populations.
Distribution of Baseline Sensitivities to Natural Product Physcion Among Isolates of Sphaerotheca fuliginea and Pseudoperonospora cubensis
Authors: Yang X. J. , Yang L. J. , Zeng F. S. , Xiang L. B. , Wang S. N. , Yu D. Z. , Ni H.
Published: September 2008

The ethanol extract from rhubarb was commercialized in China (Veguard, Physcion, 5 g/liter AS) for control of cucumber powdery mildew (Sphaerotheca fuliginea) and cucumber downy mildew (Pseudoperonospora cubensis). To provide the basic data for the risk assessment of resistance to this product, physcion was selected to represent the active ingredients to establish baseline sensitivity of powdery mildew and downy mildew populations. For powdery mildew, 262 isolates of S. fuliginea from nine regions and, for downy mildew populations, 116 isolates of P. cubensis from six regions were collected in China during 2004 and 2005 and tested for sensitivity. In addition, the sensitivity of a powdery mildew isolate was monitored for 15 asexual generations under selection pressure with physcion. The results showed that there was no significant difference among regions in the frequency distribution of baseline sensitivity to this ingredient for either cucumber powdery mildew isolates or cucumber downy mildew isolates. Baseline sensitivity was distributed as a normal unimodal curve with a mean median (50%) effective concentration (EC50) of 0.304 μg/ml for powdery mildew population and mean EC50 of 0.501 μg/ml for downy mildew population. The variation of sensitivity to physcion was low because the range factor (maximum EC50/minimum EC50 of isolates within population) varied from 1.63 to 3.42 among powdery mildew populations and from 1.70 to 2.38 among downy mildew populations. The powdery mildew isolate XZ4 did not decrease sensitivity under the selection pressure of physcion at the dose of EC70 for 15 generations.
Actigard Increases Fungicide Efficacy Against Tobacco Blue Mold
Authors: LaMondia J. A.
Published: September 2008

Blue mold, caused by Peronospora tabacina, can be economically damaging to cigar wrapper tobacco (Nicotiana tabacum). We evaluated acibenzolar-S-methyl (ASM) as Actigard 50WG alone and in combination with a standard fungicide program for efficacy against blue mold on shade-grown cigar wrapper tobacco in Windsor, CT. The standard fungicide program consisted of dimethomorph (Acrobat MZ or Forum) plus mancozeb (Dithane), alternated with azoxystrobin (Quadris), and applied at label rates on six occasions at 14-day intervals. Treated and untreated 5-by-5-m plots were replicated four times in 2003, 2004, 2005, 2006, and 2007. ASM treatments were applied alone or in combination with fungicides at the third, fourth, and fifth spray dates at rates ranging from 1.1 to 17.5 g a.i./ha. Disease was greatest in nontreated plots and reduced in all fungicide, Actigard, or combination treatments. The combination of three ASM applications at rates of 17.5 g a.i./ha down to 4.4 g a.i./ha with the standard fungicide program was more efficacious than either fungicides or ASM alone (P < 0.001) in reducing the number of blue mold lesions per plot or number of diseased leaves harvested. The combination of fungicides and low rates of ASM (2.2 or 1.1 g a.i./ha) was similar to either fungicides or ASM (17.5 g a.i./ha) applied alone. Combining low rates of ASM with fungicide applications greatly increased efficacy and marketable yield.
First Report of Fire Blight Caused by Erwinia amylovora on Cotoneaster dammeri cv. Skogholm in Croatia
Authors: Križanac I. , Vukadin A. , Ðermić E. , Cvjetković B.
Published: September 2008

In July of 2007, fire blight symptoms were observed on Cotoneaster dammeri cv. Skogholm in a nursery near Županja, Vukovarsko-Srijemska County, in eastern Croatia. In this region, the first outbreak of fire blight was noted on apple in 1995 (2). Symptoms on cotoneaster were necrotic shoots and petioles. Immunofluorescence assay (IFA) with polyclonal antibodies (Loewe Biochemica GmbH, Sauerlach, Germany) was performed on extracts from blighted C. dammeri cv. Skogholm shoots and were found to be positive for Erwinia amylovora. Round, mucoid, whitish colonies were isolated from extracts of plant tissues with symptoms of fire blight spread on King's medium B and incubated for 2 days at 28°C. Bacterial ooze and necrosis of the inoculation site were observed on immature pear fruits inoculated with a 106 CFU/ml suspension of the isolate. Bacteria were reisolated and the species identity was confirmed by PCR and primers targeting pEA29 DNA (1). E. amylovora was previously reported only on native Cotoneaster spp. (3). To our knowledge, this is the first report of fire blight on C. dammeri cv. Skogholm from a commercial ornamental nursery in Croatia.

References: (1) S. Bereswill et al. Appl. Environ. Microbiol. 58:3522, 1992. (2) B. Cvjetković et al. Glas. zaštite bilja 1:13, 1996. (3) E. Halupecki et al. Eur. J. Plant Pathol. 114:435, 2006.
First Report from Syria of Citrus tristeza virus in Citrus spp.
Authors: Kubaa R. Abou , Djelouah K. , D'Onghia A. M. , Addante R. , Jamal M.
Published: September 2008

During the spring of 2006, the main Syrian citrus-growing areas of Lattakia (Jableh, Aledyye, Eseelya, Siano, and Hresoon provinces) and Tartous (Almintar, Aljammase, Karto, Majdaloonelbahr, Yahmour, Amreet, Althawra, and Safita provinces) were surveyed to assess the presence of Citrus tristeza virus (CTV). Eight nurseries (approximately 130 plants per nursery), two budwood source fields (approximately 230 trees per field), and 19 groves (approximately 60 trees per grove) containing the main citrus varieties were visually inspected and sampled for serological assays. The hierarchical sampling method was carried out in each selected grove (2). Infected samples were collected from two nurseries, two budwood source fields, and six groves. Stems and leaf petioles from nursery trees and flower explants from the groves were collected and analyzed for CTV by direct tissue blot immunoassay (DTBIA) with the commercial kit from Plantprint (Valencia, Spain). Of 2,653 samples tested, 89 (4%) CTV-infected plants were detected. Five citrus varieties were found to be infected and Meyer lemon (Citrus limon ‘Meyer’) had the highest incidence at 16%. Numerous sweet orange varieties (Citrus sinensis L.) were found to be highly infected in the field, but only the Washington navel sweet orange was found to be infected in the nurseries. No clear CTV symptoms were observed during the survey. Samples that were positive for CTV by DTBIA were also positive by biological indexing on Mexican lime (C. aurantifolia) and immunocapture-reverse transcription-PCR as described by Nolasco et al. (3). Coat protein gene sequences obtained from five selected clones of a Syrian CTV isolate (GenBank Accession No. EU626555) showed more than 99 and 98% nucleotide sequence identity to a Jordanian CTV isolate (GenBank Accession No. AY550252) and the VT isolate (GenBank Accession No. U56902), respectively. Almost all infected samples induced moderate vein clearing symptoms when grafted to Mexican lime. Symptoms of vein clearing, leaf cupping, stunting, and stem pitting on Mexican lime were induced by graft transmission of CTV from one Valencia sample from the Tartous area. The viral inoculum is widely and randomly distributed in commercial groves, especially in the southern Tartous area and in some nurseries. To our knowledge, this is the first report of CTV in Syria. However, CTV was reported from the neighboring citrus-growing countries of Lebanon, Turkey, and Jordan (1), and the severe seedling yellows strain is present in this area, which poses a potential threat to Syrian citriculture.

References: (1) G. H. Anfoka et al. Phytopathol. Mediterr. 44:17, 2005. (2) G. Hughes and T. R. Gottwald, Phytopathology 88:715, 1998. (3) G. Nolasco et al. Eur. J. Plant Pathol. 108:293, 2002.
Capsicum chlorosis virus (Genus Tospovirus) Infecting Chili Pepper (Capsicum annuum) in India
Authors: Krishnareddy M. , Rani R. Usha , Kumar K. S. Anil , Reddy K. Madhavi , Pappu H. R.
Published: September 2008

Chili pepper (Capsicum annuum L.) is one of the most important spice crops in India. In October of 2006, symptoms indicative of tospovirus infection were noticed in several commercial fields of chili pepper near Bangalore in Karnataka State. Chlorotic and necrotic spots and rings on leaves, apical necrosis, and leaf distortion were observed. Disease incidence was more than 20%. Mechanical inoculation with sap extracts from these symptomatic plants showed that the host range and symptomatology of the virus was similar to those described for Capsicum chlorosis virus (CaCV) (1,3). The virus reacted with antisera specific to Groundnut bud necrosis virus (GBNV) and Watermelon silver mottle virus of serogroup IV tospoviruses in antigen-coated plate ELISA. It did not react with antisera specific to Tomato spotted wilt virus, Impatiens necrotic spot virus, or Iris yellow spot virus in double-antibody sandwich-ELISA. Immunosorbent electron microscopy of infected sap using GBNV antiserum revealed the presence of strongly decorated quasi-spherical virus particles. Reverse transcription (RT)-PCR was conducted to further identify the virus. No amplification was observed from extracts of symptomatic plants (n = 10) by RT-PCR using GBNV-specific primers (4), indicating that the diseased chili was not infected with GBNV. However, a DNA fragment of approximately 850 bp was amplified by using primers specific to the nucleocapsid (N) gene of CaCV (CaCF 5′-CTATAGAWGTACTAGGCTTTGAGC-3′ and CaCR 5′-CATGTCTAACGTCAGGCAACTTAC-3′). Direct sequencing of the amplicon (GenBank Accession No. EF625227) revealed a nucleotide sequence identity ranging from 85.5% with isolates from Thailand (GenBank Accession Nos. AY846366, AY647437, and AF134400) and China (GenBank Accession No. DQ355974) to 98.1% with isolates from Australia (GenBank Accession Nos. AY036057 and AY036058). Phylogenetic analysis of the N protein sequences showed that the chili pepper isolate from India formed a cluster with those from Australia. This cluster was distinct from the one formed by the peanut isolates from Thailand and a tomato isolate from India (2). To our knowledge, this is the first report of CaCV infection of chili pepper in India. The potential impact of CaCV on tomato and chili pepper production in India remains to be seen.

References: (1) D. Knierim et al. Arch. Virol. 90:377, 2006. (2) S. Kunkalikar et al. Online publication. doi:10.1094/PHP-2007-1204-01-BR. Plant Health Progress, 2007. (3) L. A. Mc Michael et al. Aust. Plant Pathol. 31:231, 2002. (4) K. Umamaheswaran et al. Indian Phytopathol. 56:168, 2003.
First Report of Anthracnose of Lycium barbarum Caused by Colletotrichum acutatum in China
Authors: Sun G. Y. , Cui J. Q. , Wang S. F. , Zhang R. , Gleason M. L.
Published: September 2008

Barbary wolfberry (Lycium barbarum, Solanaceae) is an important Chinese traditional medicine that is widely planted in northwestern China (6.7 × 104 ha under cultivation, including Ningxia Hui Autonomous Region). After a recent, large increase in the planting area and density, anthracnose has become more damaging. In China, Colletotrichum gloeosporioides was assumed to be the sole causal agent of anthracnose on L. chinense (wolfberry) (3), whereas in Korea, C. dematium was reported to cause anthracnose on wolfberry (4). During the summer and autumn of 2007, 29 barbary wolfberry fruit samples were collected from three orchards in Zhongning County, Ningxia Hui Autonomous Region. Conidia were 8.5 to 16.5 × 2.5 to 4 μm and fusiform or pointed at one or both ends. Slow-growing colonies on potato dextrose agar were white to orange or pink; sclerotia and setae were absent. The morphological traits were identical to those of C. acutatum and clearly distinct from those of C. gloeosporioides (conidia cylindrical with both ends rounded, gray colony color) or C. dematium (conidia falcate, sclerotia and setae abundant) (2–4). Koch's postulates were performed to verify that the isolates were capable of causing anthracnose on wolfberry. Six wolfberry fruits were surface sterilized with 70% alcohol, allowed to dry 1 min, then wounded with a sterile needle, and dipped in 6 ml of spore suspension (1 × 105 conidia/ml). Anthracnose symptoms were observed on inoculated fruit after 3 days, whereas control fruits inoculated with sterile water did not develop symptoms. The pathogenicity test was performed three times; in each trial, fungi reisolated from symptomatic tissue were morphologically identical to those that had been used as inoculum. Amplification of the internal transcribed spacer (ITS) region of rDNA with primers ITS1 and ITS4 resulted in bands of approximately 600 bp. The sequences of both isolates were compared with sequences deposited in the GenBank database and demonstrated 99% similarity to C. acutatum isolate DQ286123. PCR amplification of the ITS region was also carried out using species-specific primer CaInt2 in conjunction with the universal primer ITS4 (1). A DNA fragment of approximately 500 bp was amplified from all isolates, whereas no amplification products were obtained from reference cultures of C. gloeosporioides and C. dematium. To our knowledge, this is the first report of C. acutatum causing anthracnose on L. barbarum.

References: (1) S. Sreenivasaprasad et al. Plant Pathol. 45:650, 1996. (2) B. C. Sutton. Page 523 in: The Coelomycetes. Commonwealth Mycological Institute, Kew, Surrey, England, 1980. (3) X. M. Wang and J. Y. Li. Acta Mycol. Sinica 6:211, 1987. (4) S. H. Yu. Korean J. Plant Pathol. 2:31, 1986.
First Detection of Grapevine leafroll-associated virus 4 in Chilean Grapevines
Authors: Escobar P. F. , Fiore N. , Valenzuela P. D. T. , Engel E. A.
Published: September 2008

Grapevine leafroll is one of the most widespread and economically relevant viral diseases of grapevines. At least nine distinct Grapevine leafroll-associated viruses (GLRaVs), all members of the Closteroviridae family, have been associated with this disease in grapevine. Grapevine leafroll-associated virus 4 (GLRaV-4), currently classified as a Closteroviridae member under the Ampelovirus genus, was initially described in California. To determine if GLRaV-4 was present in Chilean grapevines, in addition to the previously reported GLRaV-1, -2, -3, -7, and -9 (1,2), 35 dormant cane samples from 12 different cultivars were collected from different regions of Chile and screened by reverse transcription-PCR. Two of the 35 samples (both cv. Thompson Seedless) collected from the III and VI regions of Chile were found to be infected with GLRaV-4 using two different pairs of GLRaV-4 specific primers. The first pair of primers, HSPV-F: 5′- ACA TTC TCC ACC TTG TGC TTT T -3′ and HSPC-R: 5′- CAT ACA AGC GAG TGC AAT TAC -3′ (3), was used to amplify a 321-bp fragment corresponding to a partial region of the HSP70h gene. The sequence (GenBank Accession Nos. EU746618 and EU746619) from both positive samples shared 98.4% nucleotide identity and approximately 99% identity with the corresponding fragment of a Californian GLRaV-4 isolate (GenBank Accession No. AF039553). Since there are no commercial antibodies available for GLRaV-4 detection, a second pair of primers, LR4CPINT-F: 5′- GAG AGT GAC AAG CAC CAG GTG C -3′ and LR4CPFIN-R: 5′- TCA CCT CCT GTT GCC CA -3′ (4), that amplified a 492-bp fragment of the coat protein gene was also used. The sequences of the 492-bp fragment from both Chilean samples (GenBank Accession Nos. EU746620 and EU746621) shared 99.6% nucleotide identity with one another and had 96.5% identity with an Israeli GLRaV-4 isolate (GenBank Accession No. AM176759). To our knowledge, this is the first report of GLRaV-4 in Chile. Further studies will help to establish the effects and incidence of this virus in Chilean grapevines.

References: (1) E. Engel et al. Plant Dis. 92:1252, 2008 (2) N. Fiore et al. J. Plant Pathol. 90:125, 2008. (3) F. Osman et al. J. Virol. Methods 141:22, 2007. (4) P. Saldarelli et al. J. Plant Pathol. 88:203, 2006.
Analysis of a Distribution of Point Events Using the Network‐Based Quadrat Method
Authors: Shiode Shino
Published: September 2008

This study proposes a new quadrat method that can be applied to the study of point distributions in a network space. While the conventional planar quadrat method remains one of the most fundamental spatial analytical methods on a two‐dimensional plane, its quadrats are usually identified by regular, square grids. However, assuming that they are observed along a network, points in a single quadrat are not necessarily close to each other in terms of their network distance. Using planar quadrats in such cases may distort the representation of the distribution pattern of points on a network. The network‐based units used in this article, on the other hand, consist of subsets of the actual network, providing more accurate aggregation of the data points along the network. The performance of the network‐based quadrat method is compared with that of the conventional quadrat method through a case study on a point distribution on a network. The χ2 statistic and Moran's I statistic of the two quadrat types indicate that (1) the conventional planar quadrat method tends to overestimate the overall degree of dispersion and (2) the network‐based quadrat method derives a more accurate estimate on the local similarity. The article also performs sensitivity analysis on network and planar quadrats across different scales and with different spatial arrangements, in which the abovementioned statistical tendencies are also confirmed.
Interferon‐γ‐mediated activation of enterocytes in immunological control of Encephalitozoon intestinalis infection
Authors: CHOUDHRY N. , KORBEL D. S. , ZAALOUK T. K. , BLANSHARD C. , BAJAJ‐ELLIOTT M. , MCDONALD V.
Published: September 2008

The microsporidian Encephalitozoon intestinalis develops within intestinal epithelial cells (enterocytes) and is an important opportunistic diarrhoeal pathogen associated with AIDS. Little is known about the protective immune response against the parasite although in mice IFN‐γ is involved and is required to prevent dissemination of the infection to other organs. The present study was designed to establish a suitable short‐term in vitro culture technique for E. intestinalis that would enable studies of the role of cytokines such as IFN‐γ in the effector phase of immunity. Encephalitozoon intestinalis reproduced considerably better in the murine enterocyte cell line CMT‐93 than in the three human enterocyte cell lines Caco‐2, HT29 and HCT‐8. Treatment of CMT‐93 cells with IFN‐γ significantly reduced parasite reproduction in a dose‐ and time‐dependent manner. IFN‐γ also inhibited development of the parasite in Caco‐2 cells. Neither production of NO nor Fe deprivation appeared to be involved in IFN‐γ‐mediated parasite killing. However studies suggested that tryptophan catabolism by indoleamine 2,3‐dioxygenase played an important part in inactivation of E. intestinalis.
The Mhc class II DRB genotype of Macaca fascicularis does not influence infection by simian retrovirus type 2
Authors: Mee E. T. , Murrell C. K. , Sauermann U. , Wilkinson R. C. , Cutler K. , North D. , Heath A. , Ladhani K. , Almond N. , Rose N. J.
Published: September 2008

Simian retrovirus type 2 (SRV‐2) is a natural pathogen of Macaca fascicularis. Although SRV‐2 may be endemic in macaque colonies, it is not necessarily detected in all individuals suggesting differential susceptibility to SRV‐2; factors contributing to this susceptibility are not fully understood. We have investigated the role of host genetic origin on virus susceptibility. We have shown that high levels of anti‐SRV‐2 antibodies correlate with failure to establish persistent virus infection, thus we targeted our genetic analysis of virus susceptibility with an investigation of the role of the polymorphic macaque major histocompatibility complex (MHC) class II locus. DRB genotypes, both novel and previously characterised, were identified in individuals and family groups. A discordance with SRV‐2 infection status suggests that an Mhc II DRB genotype is not overtly associated with the outcome of viral infection.
Intradermal CD30‐positive mononuclear cells in superficial fungal infections of the skin
Authors: Murphy Michael
Published: September 2008

CD30 protein expression was initially considered a reliable marker for the identification of CD30‐positive cutaneous lymphoproliferative disorders. Subsequently, CD30 expression has also been found in cutaneous pseudolymphoma and increasing numbers of cutaneous non‐neoplastic inflammatory disorders. This paper describes two cases of superficial fungal infection of the skin that demonstrate prominent expression of CD30 within the dermal inflammatory infiltrates. This is the first report of CD30 expression associated with superficial cutaneous fungal infections.
Differential expression of Aspergillus fumigatus protein in response to treatment with a novel antifungal compound, diethyl 4‐(4‐methoxyphenyl)‐2,6‐dimethyl‐1,4‐dihydropyridin‐3,5‐dicarboxylate
Authors: Chhillar A. K. , Yadav V , Kumar A , Kumar M , Parmar V. S. , Prasad A , Sharma G. L.
Published: September 2008

A dihydropyridine derivative, diethyl 4‐(4‐methoxyphenyl)‐2,6‐dimethyl‐1,4‐dihydropyridin‐3,5‐dicarboxylate (2e), having potent antifungal activity against pathogenic species of Aspergillus was investigated for its possible molecular mechanism of action. The SDS‐PAGE coupled with nano‐high‐performance liquid chromatography–tandem mass spectrometry was used directly to assess both absolute abundance and differential expression of proteins in the secretory phases of Aspergillus fumigatus under the influence of 2e. It was observed that the compound inhibited the expression of two proteins of 60.99 and 79.77 kDa. Both of these secretory proteins that were inhibited by 2e, were analysed further by matrix assisted laser desorption ionization time‐of‐flight mass spectrometry. The 60.99‐ and 79.77‐kDa proteins were identified as probable retroelement pol polyprotein and elongation factor G respectively. These targeted proteins could be the products of potentially virulence‐related genes of A. fumigatus which may unravel the mode of action of 2e and pathobiology of A. fumigatus.
Diversity of deep‐water cetaceans in relation to temperature: implications for ocean warming
Authors: Whitehead Hal , McGill Brian , Worm Boris
Published: September 2008

Understanding the effects of natural environmental variation on biodiversity can help predict response to future anthropogenic change. Here we analyse a large, long‐term data set of sightings of deep‐water cetaceans from the Atlantic, Pacific and Indian Oceans. Seasonal and geographic changes in the diversity of these genera are well predicted by a convex function of sea‐surface temperature peaking at c. 21 °C. Thus, diversity is highest at intermediate latitudes – an emerging general pattern for the pelagic ocean. When applied to a range of Intergovernmental Panel on Climate Change global change scenarios, the predicted response is a decline of cetacean diversity across the tropics and increases at higher latitudes. This suggests that deep‐water oceanic communities that dominate > 60% of the planet’s surface may reorganize in response to ocean warming, with low‐latitude losses of diversity and resilience.
Phylogenetic diversity of cyanobacterial narB genes from various marine habitats
Authors: Paerl Ryan W. , Foster Rachel A. , Jenkins Bethany D. , Montoya Joseph P. , Zehr Jonathan P.
Published: September 2008

Nitrate, the most abundant combined, dissolved form of inorganic nitrogen in global oceans, is a common source of nitrogen (N) for phytoplankton including cyanobacteria. Using a nested polymerase chain reaction (PCR) method, the diversity of the cyanobacterial nitrate reductase gene, narB, was examined in plankton samples from a variety of marine habitats. A total of 480 narB gene fragment sequences were obtained from a coastal coral reef (Heron Island, Australia), open‐ocean tropical and subtropical oceanic waters (Atlantic and Pacific Oceans) and a temperate N. Pacific Ocean site (34°N, 129°W). Phylogenetic analyses distinguished eight picocyanobacterial narB clades comprised of DNA sequences derived from the nutrient‐replete coastal, nutrient‐deplete pelagic and tidally influenced coral reef habitats. The phylogeny of recovered narB gene sequences was consistent with 16S rRNA and ITS sequence phylogenies, suggesting minimal horizontal gene transfer of the narB gene. Depending on sampled habitat, environmental narB sequence types segregated into three divisions: non‐picocyanobacterial, coastal picocyanobacterial and open‐ocean picocyanobacterial sequences. Using a reverse transcription PCR method, narB mRNA sequences were amplified from Heron Island samples, indicating that narB expression can be detected in environmental samples.