bluuebunny/crossref_metadata_2025 huggingface dataset:
Scaling properties of critical bubble of homogeneous nucleation in stretched fluid of square-gradient density-functional model with triple-parabolic free energy
Authors: Iwamatsu Masao
Published: September 2008

The square-gradient density-functional model with triple-parabolic free energy is used to study the homogeneous bubble nucleation in a stretched liquid to check the scaling rule for the work of formation of the critical bubble as a function of scaled undersaturation Δμ∕Δμspin, the difference in chemical potential Δμ between the bulk undersaturated and saturated liquid divided by Δμspin between the liquid spinodal and saturated liquid. In contrast to our study, a similar density-functional study for a Lennard-Jones liquid by Shen and Debenedetti [J. Chem. Phys. 114, 4149 (2001)] found that not only the work of formation but also other various quantities related to the critical bubble show the scaling rule; however, we found virtually no scaling relationships in our model near the coexistence. Although some quantities show almost perfect scaling relations near the spinodal, the work of formation divided by the value deduced from the classical nucleation theory shows no scaling in this model even though it correctly vanishes at the spinodal. Furthermore, the critical bubble does not show any anomaly near the spinodal as predicted many years ago. In particular, our model does not show diverging interfacial width at the spinodal, which is due to the fact that compressibility remains finite until the spinodal is reached in our parabolic models.
A crystalline-orientation self-selected linearly polarized Yb:Y3Al5O12 microchip laser
Authors: Dong Jun , Shirakawa Akira , Ueda Ken-ichi
Published: September 2008

Crystalline-orientation and pump dependent polarization states of Yb:Y3Al5O12 microchip lasers were observed experimentally. Linear polarization was observed at six crystalline orientations in the (111) plane relative to the beam propagation direction along the [111] crystalline axis of Yb:Y3Al5O12 crystal. The extinction ratio of the linear polarization decreases and the laser tends to oscillate at random polarization state at high pump power levels. Linear polarization states of Yb:Y3Al5O12 microchip laser was selected by the anisotropic spectroscopic properties of the Yb3+-ion in cubic Y3Al5O12 crystal. The random polarization oscillation at high pump power was caused by the strong thermal-induced birefringence and depolarization.
Direct responses in breeding values to selection of ostriches for liveweight and reproduction
Authors: Cloete S. W. P. , Brand Z. , Bunter K. L. , Malecki I. A.
Published: September 2008

Estimates of genetic parameters and genetic trends for reproductive traits and for liveweight at the commencement of breeding were obtained using data from a pair-mated ostrich flock located at Oudtshoorn in South Africa. Heritability estimates were 0.17–0.18 for egg production, 0.15–0.17 for chick production and 0.35–0.37 for liveweight. Female permanent environmental effects amounted to 0.11–0.17 for egg production, 0.14–0.19 for chick production and 0.30–0.31 for liveweight. Service sire exerted significant effects only on egg production (0.03–0.08) and chick production (0.05–0.10). Genetic correlations of reproductive traits with liveweight were not different from zero. Initial selection in the flock was based on reproduction, in the sense that replacements were descended from the females with the highest uncorrected number of chicks produced during their season of hatch (Chick Production line). Animals that were hatched during the period from 1996 to 2006 were used to establish two more populations. The heaviest birds at ~16 months of age were used as replacements in the line selected for liveweight (Liveweight line). Birds selected for the Control line were of average uncorrected liveweight at ~16 months, and were descended from females that produced an average number of chicks in their season of hatch. Overall, the Liveweight line had higher breeding values than the Control line for the period from 1996 to 2006. The response seemed to be associated with screening from the larger population on breeding values for liveweight, as no cumulative genetic gains were evident since 1996. Breeding values for chick production in the Chick Production line were increased by 3.1% per year from 1990 to 2006. Regressions of individual breeding values in the Control line on the year of hatch indicated no genetic change in either liveweight or chick production. Genetic change in particularly reproduction thus seems feasible in commercial ostriches.
Artificial insemination technology for ratites: a review
Authors: Malecki I. A. , Rybnik P. K. , Martin G. B.
Published: September 2008

In ratite farming, the low male to female ratio in the mating system restricts genetic improvement and prevents reduction of the number of males kept on-farm for fertilisation of the female flock. These issues can be overcome and the industry can better realise its potential by using artificial insemination (AI) technology. It is the only practical method for intensive genetic improvement of reproduction and the production of eggs, chicks, oil, meat and leather. For AI to be feasible, we need reliable methods for semen collection, artificial insemination, prolonged storage of spermatozoa in the female tract, high rates of lay, efficient protocols for semen storage, and a panel of quantitative methods for measuring true fertility and hatchability, sperm supply rates in vivo and sperm viability in vitro. For both emus and ostriches, prolonged sperm storage in females has already been demonstrated. Methods for semen collection and artificial insemination, using animal-friendly techniques, have also been developed. Semen storage and cryopreservation protocols are yet to be optimised and we still need to overcome the male-dependent rate of lay, but adoption of AI technology by the ratite industries is now feasible. It also seems likely that these technologies will be relevant to wild ratites that need intensive conservation efforts, such as cassowaries, rheas and ostrich subspecies.
The relevance of captive breeding to conservation of native ratites in Argentina: an overview
Authors: Navarro J. L. , Martella M. B.
Published: September 2008

The two South American ratites (Lesser Rhea, Pterocnemia pennata and Greater Rhea, Rhea americana) are categorised as ‘Near Threatened’ in the Red List of Threatened Species of the International Union for Conservation of Nature and Natural Resources, and are included in Appendices 1 and II of Convention on International Trade in Endangered Species of Wild Fauna and Flora. The wild populations of rheas are affected by human activities, such as illegal hunting and egg harvesting, and conversion of natural habitats into croplands. On the other hand, commercial farming of rheas has been expanding in the last two decades. Studies on farms have led to improved production, not only for commercialisation, but also for the release of individuals to the wild. Effectiveness of this latter strategy was confirmed by fieldwork and radio-telemetry. Molecular studies revealed that genetic variability of captive populations of Greater Rhea were similar to those of wild ones, and they do not show signs of inbreeding depression or differences in allele frequencies. Consequently, as natural populations of rheas continue to decline, farms will arguably serve as genetic reservoirs and provide a source of individuals for repopulation. Therefore captive breeding should be regarded as having high value as a conservation tool for native ratites.
Pim-1 kinase antagonizes aspects of myocardial hypertrophy and compensation to pathological pressure overload
Authors: Muraski John A. , Fischer Kimberlee M. , Wu Weitao , Cottage Christopher T. , Quijada Pearl , Mason Matt , Din Shabana , Gude Natalie , Alvarez Roberto , Rota Marcello , Kajstura Jan , Wang Zeping , Schaefer Erik , Chen Xiongen , MacDonnel Scott , Magnuson Nancy , Houser Stephen R. , Anversa Piero , Sussman Mark A.
Published: September 2008

Pim-1 kinase exerts potent cardioprotective effects in the myocardium downstream of AKT, but the participation of Pim-1 in cardiac hypertrophy requires investigation. Cardiac-specific expression of Pim-1 (Pim-WT) or the dominant-negative mutant of Pim-1 (Pim-DN) in transgenic mice together with adenoviral-mediated overexpression of these Pim-1 constructs was used to delineate the role of Pim-1 in hypertrophy. Transgenic overexpression of Pim-1 protects mice from pressure-overload-induced hypertrophy relative to wild-type controls as evidenced by improved hemodynamic function, decreased apoptosis, increases in antihypertrophic proteins, smaller myocyte size, and inhibition of hypertrophic signaling after challenge. Similarly, Pim-1 overexpression in neonatal rat cardiomyocyte cultures inhibits hypertrophy induced by endothelin-1. On the cellular level, hearts of Pim-WT mice show enhanced incorporation of BrdU into myocytes and a hypercellular phenotype compared to wild-type controls after hypertrophic challenge. In comparison, transgenic overexpression of Pim-DN leads to dilated cardiomyopathy characterized by increased apoptosis, fibrosis, and severely depressed cardiac function. Furthermore, overexpression of Pim-DN leads to reduced contractility as evidenced by reduced Ca
2+
transient amplitude and decreased percentage of cell shortening in isolated myocytes. These data support a pivotal role for Pim-1 in modulation of hypertrophy by impacting responses on molecular, cellular, and organ levels.
Cell wall peptidoglycan architecture in
Bacillus subtilis
Authors: Hayhurst Emma J. , Kailas Lekshmi , Hobbs Jamie K. , Foster Simon J.
Published: September 2008

The bacterial cell wall is essential for viability and shape determination. Cell wall structural dynamics allowing growth and division, while maintaining integrity is a basic problem governing the life of bacteria. The polymer peptidoglycan is the main structural component for most bacteria and is made up of glycan strands that are cross-linked by peptide side chains. Despite study and speculation over many years, peptidoglycan architecture has remained largely elusive. Here, we show that the model rod-shaped bacterium
Bacillus subtilis
has glycan strands up to 5 μm, longer than the cell itself and 50 times longer than previously proposed. Atomic force microscopy revealed the glycan strands to be part of a peptidoglycan architecture allowing cell growth and division. The inner surface of the cell wall has a regular macrostructure with ≈50 nm-wide peptidoglycan cables [average 53 ± 12 nm (
n
= 91)] running basically across the short axis of the cell. Cross striations with an average periodicity of 25 ± 9 nm (
n
= 96) along each cable are also present. The fundamental cabling architecture is also maintained during septal development as part of cell division. We propose a coiled-coil model for peptidoglycan architecture encompassing our data and recent evidence concerning the biosynthetic machinery for this essential polymer.
Effects of local mRNA structure on posttranscriptional gene silencing
Authors: Rudnick Stephen I. , Swaminathan Jyothishmathi , Sumaroka Marina , Liebhaber Stephen , Gewirtz Alan M.
Published: September 2008

Antisense oligodeoxynucleotides (AONs) and short interfering RNAs (siRNAs) effect posttranscriptional gene silencing (PTGS) by hybridizing to an mRNA and then directing its cleavage. To understand the constraints that mRNA structure imposes on AON- vs. siRNA-mediated PTGS, AON- and siRNA-mediated cleavage of defined mRNA structures was monitored in
Drosophila
embryo whole-cell lysates. We observed that AON-directed cleavage was ≈3-fold faster than cleavage with a siRNA directed to the same target site. Furthermore, and unexpectedly, AON-mediated cleavage was found to be much less fastidious with respect to target sequence accessibility, as measured by the presence of unpaired nucleotides, than a corresponding siRNA. Nonetheless,
in vivo
, siRNAs silenced their mRNA target at least 2-fold more efficiently than the corresponding AON. These seemingly contradictory results suggested that additional, as yet undefined factors play an important role in regulating PTGS efficiency
in vivo
. We used a well defined RNA-binding protein, αCP, and its corresponding high-affinity RNA-binding site to explore this hypothesis. We found that prebound αCP effectively blocked AON-mediated cleavage of the RNA-binding site compared with cleavage of the site in the absence of αCP. We conclude that higher-order structures formed by RNA and bound proteins play an important role in determining the efficiency of AON-directed PTGS. We hypothesize that strategies aimed at removing RNA-binding proteins might significantly improve AON-mediated PTGS
in vivo
.
Burst analysis spectroscopy: A versatile single-particle approach for studying distributions of protein aggregates and fluorescent assemblies
Authors: Puchalla Jason , Krantz Kelly , Austin Robert , Rye Hays
Published: September 2008

Many essential cellular functions depend on the assembly and disassembly of macromolecular complexes. The size, form, and distribution of these assemblies can be heterogeneous and complex, rendering their detailed characterization difficult. Here we describe a simple non-correlation-based method capable of directly measuring population distributions at very low sample concentrations. Specifically, we exploit the highest signal-to-noise light bursts from single fluorescent particles transiting a confocal excitation spot to recursively determine the brightness and size distribution of complex mixtures of fluorescent objects. We refer to this method as burst analysis spectroscopy (BAS) and demonstrate the sensitivity of this technique by examining the free-solution, time-resolved distribution of assembled protein aggregates by using two fluorescently labeled proteins: the aggregation-prone, chaperonin-dependent, folding model protein ribulose-bisphosphate carboxylase/oxygenase (RuBisCO), and an amyloidogenic fragment of the yeast prion protein Sup35. We find that the assembly kinetics of both proteins display complex multimodal behavior not readily quantifiable with other methods.
The combination of huperzine A and imidazenil is an effective strategy to prevent diisopropyl fluorophosphate toxicity in mice
Authors: Pibiri Fabio , Kozikowski Alan P. , Pinna Graziano , Auta James , Kadriu Bashkim , Costa Erminio , Guidotti Alessandro
Published: September 2008

Diisopropyl fluorophosphate (DFP) causes neurotoxicity related to an irreversible inhibition of acetylcholinesterase (AChE). Management of this intoxication includes: (i) pretreatment with reversible blockers of AChE, (ii) blockade of muscarinic receptors with atropine, and (iii) facilitation of GABAAreceptor signal transduction by benzodiazepines. The major disadvantage associated with this treatment combination is that it must to be repeated frequently and, in some cases, protractedly. Also, the use of diazepam (DZP) and congeners includes unwanted side effects, including sedation, amnesia, cardiorespiratory depression, and anticonvulsive tolerance. To avoid these treatment complications but safely protect against DFP-induced seizures and other CNS toxicity, we adopted the strategy of administering mice with (i) small doses of huperzine A (HUP), a reversible and long-lasting (half-life ≈5 h) inhibitor of AChE, and (ii) imidazenil (IMI), a potent positive allosteric modulator of GABA action selective for α5-containing GABAAreceptors. Coadministration of HUP (50 μg/kg s.c., 15 min before DFP) with IMI (2 mg/kg s.c., 30 min before DFP) prevents DFP-induced convulsions and the associated neuronal damage and mortality, allowing complete recovery within 18–24 h. In HUP-pretreated mice, the ED50of IMI to block DFP-induced mortality is ≈10 times lower than that of DZP and is devoid of sedation. Our data show that a combination of HUP with IMI is a prophylactic, potent, and safe therapeutic strategy to overcome DFP toxicity.
Mammographic features and histopathological findings of interval breast cancers
Authors: Hofvind S. , Geller B. , Skaane P.
Published: September 2008

Background: Interval cancers are considered a shortcoming in screening mammography due to less favorable prognostic tumor characteristics compared to screening-detected cancers and consequently a lower chance of survival from the disease.

Purpose: To describe the mammographic features and prognostic histopathological tumor characteristics of interval breast cancers.

Material and Methods: A total of 231 interval breast cancer cases diagnosed in prevalently screened women aged 50–69 years old were examined. Thirty-five percent of the cases were retrospectively classified as missed cancers, 23% as minimal sign, and 42% as true negative (including occult cancers) in a definitive classification performed by six experienced breast radiologists. The retrospective classification described the mammographic features of the baseline screening mammograms in missed and minimal-sign interval cancers, while histopathological reports were used to describe the tumor characteristics in all the subgroups of interval cancers.

Results: Fifty percent of the missed and minimal-sign interval cancers combined presented poorly defined mass or asymmetric density, and 26% calcifications with or without associated density or mass at baseline screening. Twenty-seven percent of invasive tumors were <15 mm for missed and 47% for true interval cancers ( P<0.001). Lymph node involvement was more common in missed (49%) compared with the true cases (33%, P<0.05).

Conclusion: Missed interval cancers have less prognostically favorable histopathological tumor characteristics compared with true interval cancers. Improving the radiologist's perception and interpretation by establishing systematic collection of features and implementation of organized reviews may decrease the number of interval cancers in a screening program.
Memories as Assets: Strategic Memory Protection in Choice over Time
Authors: Zauberman Gal , Ratner Rebecca K. , Kim B. Kyu
Published: September 2008

We present five studies supporting our strategic memory protection theory. When people make decisions about experiences to consume over time, they treat their memories of previous experiences as assets to be protected. The first two studies demonstrate that people tend to avoid situations that they believe will threaten their ability to retrieve special (rather than merely pleasant) memories. The next three studies demonstrate that people seek to obtain memory pointers to help them cue special memories at a later time when they anticipate interference from subsequent events. These preferences are driven by people's lay theories about the importance and difficulty of obtaining and retrieving special memories.
Yeast Golgi-localized, γ-Ear–containing, ADP-Ribosylation Factor-binding Proteins Are but Adaptor Protein-1 Is Not Required for Cell-free Transport of Membrane Proteins from theTrans-Golgi Network to the Prevacuolar Compartment
Authors: Abazeed Mohamed E. , Fuller Robert S.
Published: September 2008

Golgi-localized, γ-Ear–containing, ADP-ribosylation factor-binding proteins (GGAs) and adaptor protein-1 (AP-1) mediate clathrin-dependent trafficking of transmembrane proteins between the trans-Golgi network (TGN) and endosomes. In yeast, the vacuolar sorting receptor Vps10p follows a direct pathway from the TGN to the late endosome/prevacuolar compartment (PVC), whereas, the processing protease Kex2p partitions between the direct pathway and an indirect pathway through the early endosome. To examine the roles of the Ggas and AP-1 in TGN–PVC transport, we used a cell-free assay that measures delivery to the PVC of either Kex2p or a chimeric protein (K-V), in which the Vps10p cytosolic tail replaces the Kex2p tail. Either antibody inhibition or dominant-negative Gga2p completely blocked K-V transport but only partially blocked Kex2p transport. Deletion of APL2, encoding the β subunit of AP-1, did not affect K-V transport but partially blocked Kex2p transport. Residual Kex2p transport seen with apl2Δ membranes was insensitive to dominant-negative Gga2p, suggesting that the apl2Δ mutation causes Kex2p to localize to a compartment that precludes Gga-dependent trafficking. These results suggest that yeast Ggas facilitate the specific and direct delivery of Vps10p and Kex2p from the TGN to the PVC and that AP-1 modulates Kex2p trafficking through a distinct pathway, presumably involving the early endosome.
Novel Cross-Talk between Three Cardiovascular Regulators: Thrombin Cleavage Fragment of Jagged1 Induces Fibroblast Growth Factor 1 Expression and Release
Authors: Duarte Maria , Kolev Vihren , Kacer Doreen , Mouta-Bellum Carla , Soldi Raffaella , Graziani Irene , Kirov Aleksandr , Friesel Robert , Liaw Lucy , Small Deena , Verdi Joseph , Maciag Thomas , Prudovsky Igor
Published: September 2008

Angiogenesis is controlled by several regulatory mechanisms, including the Notch and fibroblast growth factor (FGF) signaling pathways. FGF1, a prototype member of FGF family, lacks a signal peptide and is released through an endoplasmic reticulum–Golgi-independent mechanism. A soluble extracellular domain of the Notch ligand Jagged1 (sJ1) inhibits Notch signaling and induces FGF1 release. Thrombin, a key protease of the blood coagulation cascade and a potent inducer of angiogenesis, stimulates rapid FGF1 release through a mechanism dependent on the major thrombin receptor protease-activated receptor (PAR) 1. This study demonstrates that thrombin cleaves Jagged1 in its extracellular domain. The sJ1 form produced as a result of thrombin cleavage inhibits Notch-mediated CBF1/Suppressor of Hairless [(Su(H)]/Lag-1–dependent transcription and induces FGF1 expression and release. The overexpression of Jagged1 in PAR1 null cells results in a rapid thrombin-induced export of FGF1. These data demonstrate the existence of novel cross-talk between thrombin, FGF, and Notch signaling pathways, which play important roles in vascular formation and remodeling.
Integrin-mediated Protein Kinase A Activation at the Leading Edge of Migrating Cells
Authors: Lim Chinten J. , Kain Kristin H. , Tkachenko Eugene , Goldfinger Lawrence E. , Gutierrez Edgar , Allen Michael D. , Groisman Alex , Zhang Jin , Ginsberg Mark H.
Published: September 2008

cAMP-dependent protein kinase A (PKA) is important in processes requiring localized cell protrusion, such as cell migration and axonal path finding. Here, we used a membrane-targeted PKA biosensor to reveal activation of PKA at the leading edge of migrating cells. Previous studies show that PKA activity promotes protrusion and efficient cell migration. In live migrating cells, membrane-associated PKA activity was highest at the leading edge and required ligation of integrins such as α4β1 or α5β1 and an intact actin cytoskeleton. α4 integrins are type I PKA-specific A-kinase anchoring proteins, and we now find that type I PKA is important for localization of α4β1 integrin-mediated PKA activation at the leading edge. Accumulation of 3′ phosphorylated phosphoinositides [PtdIns(3,4,5)P3] products of phosphatidylinositol 3-kinase (PI3-kinase) is an early event in establishing the directionality of migration; however, polarized PKA activation did not require PI3-kinase activity. Conversely, inhibition of PKA blocked accumulation of a PtdIns(3,4,5)P3-binding protein, the AKT-pleckstrin homology (PH) domain, at the leading edge; hence, PKA is involved in maintaining cell polarity during migration. In sum, we have visualized compartment-specific PKA activation in migrating cells and used it to reveal that adhesion-mediated localized activation of PKA is an early step in directional cell migration.
JAMP Optimizes ERAD to Protect Cells from Unfolded Proteins
Authors: Tcherpakov Marianna , Broday Limor , Delaunay Agnes , Kadoya Takayuki , Khurana Ashwani , Erdjument-Bromage Hediye , Tempst Paul , Qiu Xiao-Bo , DeMartino George N. , Ronai Ze'ev
Published: September 2008

Clearance of misfolded proteins from the ER is central for maintenance of cellular homeostasis. This process requires coordinated recognition, ER-cytosol translocation, and finally ubiquitination-dependent proteasomal degradation. Here, we identify an ER resident seven-transmembrane protein (JAMP) that links ER chaperones, channel proteins, ubiquitin ligases, and 26S proteasome subunits, thereby optimizing degradation of misfolded proteins. Elevated JAMP expression promotes localization of proteasomes at the ER, with a concomitant effect on degradation of specific ER-resident misfolded proteins, whereas inhibiting JAMP promotes the opposite response. Correspondingly, a jamp-1 deleted Caenorhabditis elegans strain exhibits hypersensitivity to ER stress and increased UPR. Using biochemical and genetic approaches, we identify JAMP as important component for coordinated clearance of misfolded proteins from the ER.
Chemical substructures that enrich for biological activity
Authors: Klekota Justin , Roth Frederick P.
Published: September 2008

Motivation: Certain chemical substructures are present in many drugs. This has led to the claim of ‘privileged’ substructures which are predisposed to bioactivity. Because bias in screening library construction could explain this phenomenon, the existence of privilege has been controversial.

Results: Using diverse phenotypic assays, we defined bioactivity for multiple compound libraries. Many substructures were associated with bioactivity even after accounting for substructure prevalence in the library, thus validating the privileged substructure concept. Determinations of privilege were confirmed in independent assays and libraries. Our analysis also revealed ‘underprivileged’ substructures and ‘conditional privilege’—rules relating combinations of substructure to bioactivity. Most previously reported substructures have been flat aromatic ring systems. Although we validated such substructures, we also identified three-dimensional privileged substructures. Most privileged substructures display a wide variety of substituents suggesting an entropic mechanism of privilege. Compounds containing privileged substructures had a doubled rate of bioactivity, suggesting practical consequences for pharmaceutical discovery.

Contact:  fritz_roth@hms.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks
Authors: Reverter Antonio , Chan Eva K. F.
Published: September 2008

Motivation: We present PCIT, an algorithm for the reconstruction of gene co-expression networks (GCN) that combines the concept partial correlation coefficient with information theory to identify significant gene to gene associations defining edges in the reconstruction of GCN. The properties of PCIT are examined in the context of the topology of the reconstructed network including connectivity structure, clustering coefficient and sensitivity.

Results: We apply PCIT to a series of simulated datasets with varying levels of complexity in terms of number of genes and experimental conditions, as well as to three real datasets. Results show that, as opposed to the constant cutoff approach commonly used in the literature, the PCIT algorithm can identify and allow for more moderate, yet not less significant, estimates of correlation (r) to still establish a connection in the GCN. We show that PCIT is more sensitive than established methods and capable of detecting functionally validated gene–gene interactions coming from absolute r values as low as 0.3. These bona fide associations, which often relate to genes with low variation in expression patterns, are beyond the detection limits of conventional fixed-threshold methods, and would be overlooked by studies relying on those methods.

Availability: FORTRAN 90 source code to perform the PCIT algorithm is available as Supplementary File 1.

Contact:  tony.reverter-gomez@csiro.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cell-to-Cell Signaling inXylella fastidiosaSuppresses Movement and Xylem Vessel Colonization in Grape
Authors: Chatterjee Subhadeep , Newman Karyn L. , Lindow Steven E.
Published: September 2008

Cell-to-cell signaling mediated by a fatty acid diffusible signaling factor (DSF) is central to the regulation of the virulence of Xylella fastidiosa. DSF production by X. fastidiosa is dependent on rpfF and, although required for insect colonization, appears to reduce its virulence to grape. To understand what aspects of colonization of grape are controlled by DSF in X. fastidiosa and, thus, those factors that contribute to virulence, we assessed the colonization of grape by a green fluorescent protein–marked rpfF-deficient mutant. The rpfF-deficient mutant was detected at a greater distance from the point of inoculation than the wild-type strain at a given sampling time, and also attained a population size that was up to 100-fold larger than that of the wild-type strain at a given distance from the point of inoculation. Confocal laser-scanning microscopy revealed that approximately 10-fold more vessels in petioles of symptomatic leaves harbored at least some cells of either the wild type or rpfF mutant when compared with asymptomatic leaves and, thus, that disease symptoms were associated with the extent of vessel colonization. Importantly, the rpfF mutant colonized approximately threefold more vessels than the wild-type strain. Although a wide range of colony sizes were observed in vessels colonized by both the wild type and rpfF mutant, the proportion of colonized vessels harboring large numbers of cells was significantly higher in plants inoculated with the rpfF mutant than with the wild-type strain. These studies indicated that the hypervirulence phenotype of the rpfF mutant is due to both a more extensive spread of the pathogen to xylem vessels and unrestrained multiplication within vessels leading to blockage. These results suggest that movement and multiplication of X. fastidiosa in plants are linked, perhaps because cell wall degradation products are a major source of nutrients. Thus, DSF-mediated cell-to-cell signaling, which restricts movement and colonization of X. fastidiosa, may be an adaptation to endophytic growth of the pathogen that prevents the excessive growth of cells in vessels.
2,4-Diacetylphloroglucinol Alters Plant Root Development
Authors: Brazelton Jessica N. , Pfeufer Emily E. , Sweat Teresa A. , Gardener Brian B. McSpadden , Coenen Catharina
Published: September 2008

Pseudomonas fluorescens isolates containing the phlD gene can protect crops from root pathogens, at least in part through production of the antibiotic 2,4-diacetylphloroglucinol (DAPG). However, the action mechanisms of DAPG are not fully understood, and effects of this antibiotic on host root systems have not been characterized in detail. DAPG inhibited primary root growth and stimulated lateral root production in tomato seedlings. Roots of the auxin-resistant diageotropica mutant of tomato demonstrated reduced DAPG sensitivity with regards to inhibition of primary root growth and induction of root branching. Additionally, applications of exogenous DAPG, at concentrations previously found in the rhizosphere of plants inoculated with DAPG-producing pseudomonads, inhibited the activation of an auxin-inducible GH3 promoter∷luciferase reporter gene construct in transgenic tobacco hypocotyls. In this model system, supernatants of 17 phlD+ P. fluorescens isolates had inhibitory effects on luciferase activity similar to synthetic DAPG. In addition, a phlD– mutant strain, unable to produce DAPG, demonstrated delayed inhibitory effects compared with the parent wild-type strain. These results indicate that DAPG can alter crop root architecture by interacting with an auxin-dependent signaling pathway.
Pantoea stewartii subsp. stewartii Exhibits Surface Motility, Which is a Critical Aspect of Stewart's Wilt Disease Development on Maize
Authors: Herrera Carmen M. , Koutsoudis Maria D. , Wang Xiaolei , von Bodman Susanne B.
Published: September 2008

Pantoea stewartii subsp. stewartii is a plant-pathogenic bacterium that causes Stewart's vascular wilt in maize. The organism is taxonomically described as aflagellated and nonmotile. We recently showed that P. stewartii colonizes the xylem of maize as sessile, cell-wall-adherent biofilms. Biofilm formation is a developmental process that generally involves some form of surface motility. For that reason, we reexamined the motility properties of P. stewartii DC283 based on the assumption that the organism requires some form of surface motility for biofilm development. Here, we show that the organism is highly motile on agar surfaces. This motility is flagella dependent, shown by the fact that a fliC mutant, impaired in flagellin subunit synthesis, is nonmotile. Motility also requires the production of stewartan exopolysaccharide. Moreover, surface motility plays a significant role in the colonization of the plant host.
A Predictive Model for Spotted Wilt Epidemics in Peanut Based on Local Weather Conditions and the Tomato spotted wilt virus Risk Index
Authors: Olatinwo R. O. , Paz J. O. , Brown S. L. , Kemerait R. C. , Culbreath A. K. , Beasley J. P. , Hoogenboom G.
Published: September 2008

Tomato spotted wilt virus (TSWV), a member of the genus Tospovirus (family Bunyaviridae), is an important plant virus that causes severe damage to peanut (Arachis hypogaea) in the southeastern United States. Disease severity has been extremely variable in individual fields in Georgia, due to several factors including variability in weather patterns. A TSWV risk index has been developed by the University of Georgia to aid peanut growers with the assessment and avoidance of high risk situations. This study was conducted to examine the relationship between weather parameters and spotted wilt severity in peanut, and to develop a predictive model that integrates localized weather information into the risk index. On-farm survey data collected during 1999, 2002, 2004, and 2005 growing seasons, and derived weather variables during the same years were analyzed using nonlinear and multiple regression analyses. Meteorological data were obtained from the Georgia Automated Environmental Monitoring Network. The best model explained 61% of the variation in spotted wilt severity (square root transformed) as a function of the interactions between the TSWV risk index, the average daily temperature in April (TavA), the average daily minimum temperature between March and April (TminMA), the accumulated rainfall in March (RainfallM), the accumulated rainfall in April (RainfallA), the number of rain days in April (RainDayA), evapotranspiration in April (EVTA), and the number of days from 1 January to the planting date (JulianDay). Integrating this weather-based model with the TSWV risk index may help peanut growers more effectively manage tomato spotted wilt disease.
Spatial and Temporal Stability of the Estimated Parameters of the Binary Power Law
Authors: Gent D. H. , Turechek W. W. , Mahaffee W. F.
Published: September 2008

The incidence of hop powdery mildew on leaves, caused by Podosphaera macularis, collected from 1,606 transects in 77 commercial hop yards in Oregon and Washington over 9 years was used to assess variability in heterogeneity of disease and the estimated binary power law parameters. Spatial analyses of data sets were conducted at the level of individual rows (row level) and multiple rows within a yard (yard level). The binary power law provided a good fit to all data sets, with R2values ranging from 0.933 to 0.993. At the row level, the intercept parameter ln(Ax) was >0 for 8 years, but was not significantly greater than 0 in 2006. The parameter b was greater than 1 for all row-level data sets collected from 1999 to 2005, but was <1 in 2006 and not significantly different from 1 in 2007. Covariance analysis indicated the factor ‘region’ affected ln(Ax) in 3 years, and b in 2 years. ‘Cultivar’ had an effect on ln(Ax) in 3 years and b in year. At the yard level, ln(Ax) was greater than 0 for 6 years, but in 2006 and 2007, ln(Ax) was not significantly different from 0. The slope parameter b was greater than 1 in 6 years, but was not significantly different from 1 in 2006 and 2007. Differences in b among years were large enough to have practical implications for sample sizes and precision of fixed and sequential sampling. Although the binary power law parameter tended to be relatively stable, variability of the estimated parameters may have practical consequences for sampling precision and costs.
XA27 Depends on an Amino-Terminal Signal-Anchor-Like Sequence to Localize to the Apoplast for Resistance to Xanthomonas oryzae pv oryzae
Authors: Wu Lifang , Goh Mei Ling , Sreekala Chellamma , Yin Zhongchao
Published: September 2008

The rice (Oryza sativa) gene Xa27 confers resistance to Xanthomonas oryzae pv oryzae, the causal agent of bacterial blight disease in rice. Sequence analysis of the deduced XA27 protein provides little or no clue to its mode of action, except that a signal-anchor-like sequence is predicted at the amino (N)-terminal region of XA27. As part of an effort to characterize the biochemical function of XA27, we decided to determine its subcellular localization. Initial studies showed that a functional XA27-green fluorescent protein fusion protein accumulated in vascular elements, the host sites where the bacterial blight pathogens multiply. The localization of XA27-green fluorescent protein to the apoplast was verified by detection of the protein on cell walls of leaf sheath and root cells after plasmolysis. Similarly, XA27-FLAG localizes to xylem vessels and cell walls of xylem parenchyma cells, revealed by immunogold electron microscopy. XA27-FLAG could be secreted from electron-dense vesicles in cytoplasm to the apoplast via exocytosis. The signal-anchor-like sequence has an N-terminal positively charged region including a triple arginine motif followed by a hydrophobic region. Deletion of the hydrophobic region or substitution of the triple arginine motif with glycine or lysine residues abolished the localization of the mutated proteins to the cell wall and impaired the plant's resistance to X. oryzae pv oryzae. These results indicate that XA27 depends on the N-terminal signal-anchor-like sequence to localize to the apoplast and that this localization is important for resistance to X. oryzae pv oryzae.
Cell Wall-Bound Invertase Limits Sucrose Export and Is Involved in Symptom Development and Inhibition of Photosynthesis during Compatible Interaction between Tomato andXanthomonas campestrispvvesicatoria
Authors: Kocal Nurcan , Sonnewald Uwe , Sonnewald Sophia
Published: September 2008

Cell wall-bound invertase (cw-Inv) plays an important role in carbohydrate partitioning and regulation of sink-source interaction. There is increasing evidence that pathogens interfere with sink-source interaction, and induction of cw-Inv activity has frequently been shown in response to pathogen infection. To investigate the role of cw-Inv, transgenic tomato (Solanum lycopersicum) plants silenced for the major leaf cw-Inv isoforms were generated and analyzed during normal growth and during the compatible interaction with Xanthomonas campestris pv vesicatoria. Under normal growth conditions, activities of sucrolytic enzymes as well as photosynthesis and respiration were unaltered in the transgenic plants compared with wild-type plants. However, starch levels of source leaves were strongly reduced, which was most likely caused by an enhanced sucrose exudation rate. Following X. campestris pv vesicatoria infection, cw-Inv-silenced plants showed an increased sucrose to hexose ratio in the apoplast of leaves. Symptom development, inhibition of photosynthesis, and expression of photosynthetic genes were clearly delayed in transgenic plants compared with wild-type plants. In addition, induction of senescence-associated and pathogenesis-related genes observed in infected wild-type plants was abolished in cw-Inv-silenced tomato lines. These changes were not associated with decreased bacterial growth. In conclusion, cw-Inv restricts carbon export from source leaves and regulates the sucrose to hexose ratio in the apoplast. Furthermore, an increased apoplastic hexose to sucrose ratio can be linked to inhibition of photosynthesis and induction of pathogenesis-related gene expression but does not significantly influence bacterial growth. Indirectly, bacteria may benefit from low invertase activity, since the longevity of host cells is raised and basal defense might be dampened.
What is Dasya ocellata indeed (Dasyaceae, Rhodophyta)?
Authors: Pena‐Martín Carolina , Gómez‐Garreta Amelia , Crespo Manuel B.
Published: September 2008

A delailed study of the original material of Dasya ocellata and related taxa revealed that the current concept of the species is not fully coincident with that of its basionym, Ceramium ocellatum. The original material is conserved at LD, and consist of two specimens affixed on the same voucher and these do in fact belong to two different species. One of them, which was selected as the lectotype, fits the current concept of D. ocellata whilst the other corresponds to D. hutchinsiae. Although the former specimen is not apparently the best to fit the protologue, it is not in serious conflict with it, and that choice ensures the traditional usage of the name. Several nomenclatural and historical features related to the name are also discussed.
Noninvasive radiographic analysis of an Egyptian falcon mummy from the late period 664–332 BC
Authors: Morgan Lee W. , McGovern‐Hoffman Susan
Published: September 2008

The practice of mummification by the ancient Egyptians is well known. However, it is less widely known that the ancient Egyptians also mummified animals, including birds, for religious and ceremonial reasons. Few radiographic descriptions of avian mummies are published in the scientific literature. This paper describes the radiographic findings from a falcon mummy from the ancient Egyptian Late Period (664–332 BC). The mummy is believed to be a kestrel Falco tinnunculus, based on anatomical comparisons made with type skeleton specimens held at the Smithsonian National Museum of Natural History located in Washington D.C. Photographs of the mummy and radiographs of the mummy's contents are presented.
Evidence for two transferrin loci in the Salmo trutta genome
Authors: Rozman T. , Dovc P. , Marić S. , Kokalj‐Vokač N. , Erjavec‐Škerget A. , Rab P. , Snoj A.
Published: September 2008

To determine the organization of transferrin (TF) locus in the Salmo trutta genome, partial DNA and cDNA sequencing, fluorescent in situ hybridization (FISH) and Salmo salar BAC analysis were performed. TF expression levels and copy number prediction were assessed using real‐time PCR. In addition to two previously reported DNA TF variant sequences of S. trutta and Salmo marmoratus (TF1), two novel variant sequences (TF2) were revealed in both species. Variant‐specific sequence tags, characterizing two variants for each TF type (TF1 and TF2), were identified in genomic clones from each of the F1 hybrids between S. trutta and S. marmoratus. These clearly documented double heterozygote status at the TF loci. The real‐time PCR data showed that each of the two TF types (TF1 and TF2) existed in one copy only and that the transcription of TF2 was considerably lower compared with TF1. Using FISH, hybridization signals were observed on two medium‐sized acrocentric chromosomes of S. trutta karyotype. A TF type‐specific PCR followed by a restriction analysis revealed the presence of two TF loci in the majority of analysed BAC clones. It was concluded that the TF gene is duplicated in the genome of S. trutta, and that the two TF loci are located adjacent to one another on the same chromosome. The differing transcription levels of TF1 and TF2 appear to depend on the corresponding promoter activity, which at least for TF2 seems to vary between different Salmo congeners.
A potential role of connexin 43 in epidermal growth factor‐induced proliferation of mouse embryonic stem cells: Involvement of Ca2+/PKC, p44/42 and p38 MAPKs pathways
Authors: Park J. H. , Lee M. Y. , Heo J. S. , Han H. J.
Published: September 2008

Abstract.  Objectives: The gap junction protein, connexin (Cx), plays an important role in maintaining cellular homeostasis and cell proliferation by allowing communication between adjacent cells. Therefore, this study has examined the effect of epidermal growth factor (EGF) on Cx43 and its relationship to proliferation of mouse embryonic stem cells. Materials and methods: Expressions of Cx43, mitogen‐activated protein kinases (MAPKs) and cell cycle regulatory proteins were assessed by Western blot analysis. Cell proliferation was assayed with [3H]thymidine incorporation. Intercellular communication level was measured by a scrape loading/dye transfer method. Results: The results showed that EGF increased the level of Cx43 phosphorylation in a time‐ (≥5 min) and dose‐ (≥10 ng/mL) dependent manner. Indeed, EGF‐induced increase in phospho‐Cx43 level was significantly blocked by either AG 1478 or herbimycin A (tyrosine kinase inhibitors). EGF increased Ca2+ influx and protein kinase C (PKC) translocation from the cytosolic compartment to the membrane compartment. Moreover, pre‐treatment with BAPTA‐AM (an intracellular Ca2+ chelator), EGTA (an extracellular Ca2+ chelator), bisindolylmaleimide I or staurosporine (PKC inhibitors) inhibited the EGF‐induced phosphorylation of Cx43. EGF induced phosphorylation of p38 and p44/42 MAPKs, and this was blocked by SB 203580 (a p38 MAPK inhibitor) and PD 98059 (a p44/42 MAPK inhibitor), respectively. EGF or 18α‐glycyrrhetinic acid (GA; a gap junction inhibitor) increased expression levels of the protooncogenes (c‐fos, c‐jun and c‐myc), cell cycle regulatory proteins [cyclin D1, cyclin E, cyclin‐dependent kinase 2 (CDK2), CDK4 and p‐Rb], [3H]thymidine incorporation and cell number, but decreased expression levels of the p21WAF1/Cip1 and p27Kip1, CDK inhibitory proteins. Transfection of Cx43 siRNA also increased the level of [3H]thymidine incorporation and cell number. EGF, 18α‐GA or transfection of Cx43 siRNA increased 2‐DG uptake and GLUT‐1 protein expression. Conclusions: EGF‐induced phosphorylation of Cx43, which was mediated by the Ca2+/PKC, p44/42 and p38 MAPKs pathways, partially contributed to regulation of mouse embryonic stem cell proliferation.
Stem cell antigen 2: a new gene involved in the self‐renewal of erythroid progenitors
Authors: Bresson‐Mazet C. , Gandrillon O. , Gonin‐Giraud S.
Published: September 2008

Abstract.  Objectives: Stem cell antigen 2 (SCA2), also known as TSA1 and LY6E, is a glycosylphosphatidylinositol‐anchored molecule that belongs to the Ly‐6 family and whose function remains largely unknown. We have previously shown that SCA2 is overexpressed in self‐renewing avian erythroid progenitors (T2ECs) as opposed to differentiating T2ECs. The aim of this study was to define the role of SCA2 in the switch between self‐renewal and differentiation of erythroid progenitors. Materials and methods: We have investigated the cellular processes controlled by SCA2 in T2ECs by RNA interference and overexpression approaches. Moreover, we have used a SAGE Querying and analysis tools developed in our laboratory, to investigate the expression level of SCA2 gene in different human cell types. Results: We demonstrate the regulation of SCA2 expression by TGF‐β, a growth factor essential for self‐renewal of T2ECs. We establish that SCA2 knockdown by RNA interference reduced the proliferation and promoted the differentiation of T2ECs. In contrast, SCA2 overexpression inhibited differentiation of T2ECs only. Furthermore, by using a bioinformatic approach, we found that SCA2 is highly expressed in a variety of human cancer cells. We confirmed this result by quantitative PCR on human colon and kidney tissues. Conclusions: Altogether, these findings imply that SCA2 may function in a dose‐dependent manner to support the self‐renewal state and that its deregulation might contribute to the development of some human cancers.